Tackling Evolutionary Questions in Fishes with Genome-Wide Data from Recent Speciation to Ancient Divergences
by Lily Claire Hughes
B.A. in Biology, May 2011, Clark University M.A. in Biology, October 2012, Clark University
A Dissertation submitted to
The Faculty of The Columbian College of Arts and Sciences of The George Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy
January 19, 2018
Dissertation directed by
Guillermo Ortí Louis Weintraub Professor of Biology
The Columbian College of Arts and Sciences of The George Washington University certifies that Lily Claire Hughes has passed the Final Examination for the degree of
Doctor of Philosophy as of August 30, 2017. This is the final and approved form of the dissertation.
Tackling Evolutionary Questions in Fishes with Genome-Wide Data from Recent Speciation to Ancient Divergences
Lily Claire Hughes
Dissertation Research Committee:
Guillermo Ortí, Louis Weintraub Professor of Biology, Dissertation Director
Robert Alexander Pyron, Robert F. Griggs Assistant Professor of Biology, Committee Member
Vanessa Liz González, Computational Genomics Scientist, Global Genome Initiative, Smithsonian Institution, National Museum of National History, Committee Member
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© Copyright 2018 by Lily Claire Hughes All rights reserved
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Acknowledgements
The author wishes to thank her advisor, Guillermo Ortí, and her wonderful committee, Alex Pyron, Vanessa González, Keith Crandall, and Liz Alter, for their comments and valuable insights on this dissertation. Additionally, I would like to acknowledge the support from the Biological Sciences department I received, and funding from the Weintraub and Harlan families that supported me over the course of my studies at the George Washington University.
I want to thank the many collaborators I worked with during the course of my research, from all over the world. These individuals include: Gustavo M. Somoza and
Yamila Cardoso (Instituto de Investigaciones Biotecnológicas- Instituto Tecnológico de
Chascomús (CONICET-UNSAM), Chascomús, Argentina), Bryan B. Nguyen and James
P. Bernot (Computational Biology Institute, George Washington University), Mariano
González-Castro and Juan Martín Díaz de Astarloa (Grupo de Biotaxonomía Morfológica y molecular de peces, IIMyC- CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina), Julie Sommer (School of Biological Sciences, University of
Nebraska-Lincoln), Roberto Cifuentes and Evelyn Habit (Departmento de Sistemas
Acuáticos, Facultad de Ciencias Ambientales y Centro EULA, Universidade Concepción y Centro de Ivestigaciones en Ecosistemas Patagónicos, Concepción, Chile), Mariela
Cuello (Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata,
Buenos Aires, Argentina), Victor Cussac (Instituto de Investigaciones en Biodiversidad y
Medioambiente (INIBIOMA), Universidad Nacional del Comahue, Consejo Nacional de
Investigaciones Cieníficas y Técnicas (CONICET), Bariloche, Rio Negro, Argentina),
Luiz Malabarba (Departamento de Zoologia, Intituto de Biociências, Universidade
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Federal do Rio Grande do Sul, Porto Alegre, Brazil), Yu Huang, Ying Sun, Xiaomeng
Zhao, Xiafeng Li, Min Wang, Chao Fang, Bing Xie, Qiong Shi (BGI-Shenzhen,
Shenzhen, China), Zhuocheng Zhou (China Fisheries Association, Beijing, China),
Soling Chen (Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery
Sciences, Quingdao, China), Carole Baldwin (Smithsonian Institution, National Museum of Natural History), Chenhong Li (Key Laboratory of Exploration and Utilization of
Aquatic Genetic Resources, Shanghai Ocean University, China), Leandro Becker and
Nicolás Bellora (Universidad Nacional de Comahue (CONICET), Laboratorio de
Ictiología y Acuicultura Experimental (IPATEC), Bariloche, Argentina.
I especially want to thank all the members of the GO Lab who supported and inspired me along the way: Andrew W. Thompson, Daniela Campanella, Dahiana Arcila and Ricardo Betancur-R (now at University of Puerto Rico- Rio Piedras). My fellow graduate students in Biological Sciences including Robert Kallal, Jesus Ballesteros,
Mariana Abarca, Joao Tonini, Andrew Moore, Thiago Moreira, Amy Milo, David Stern,
Meredith Fontana, Karen Poole, and Joshua Storch were an invaluable source of knowledge and support. Hartmut Doebel and Catriona Hendry made me a better teacher during my time as a T.A. The incredible faculty of the department also supported me, including Gustavo Hormiga, Jim Clark, Diana Lipscomb, Kathy Forester, Leon Grayfer,
Keryn Gedan, Arnaud Martin, and Amy Zanne. I would also like to thank my Master’s advisors Susan Foster and John Baker at Clark University, for encouraging me to pursue my PhD in the first place.
Finally, on a personal note, I want to thank my mom, Linda Ziemer, and Mary
Peterson, for all the love, support, and care packages a woman could ask for. I want to
v thank Pepper, for reminding me to take breaks when I was writing this dissertation by standing on my keyboard. Last, but never least, I thank Joey Stiegler, who told me I could do it, every step of the way.
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Abstract of Dissertation
Tackling Evolutionary Questions in Fishes with Genome-Wide Data from Recent Speciation to Ancient Divergences
Ray-finned fishes (Actinopterygii) form the largest clade of vertebrates with more than 34,000 valid species currently described. Here, I use a variety of sequencing approaches to tackle evolutionary questions in fishes, from recent habitat transitions in a group of silverside fishes, to disentangling over 400 million years of evolutionary change to infer the phylogeny of all ray-finned fishes. Chapter two of my dissertation focuses on silverside fishes in the genus Odontesthes (Atherinopsidae), which have recently and rapidly transitioned from marine to freshwater. Two closely related species, marine O. argentinensis and freshwater O. bonariensis, span this ecological divide, and yet show little genetic divergence in mitochondrial markers. We sequenced gill transcriptomes from wild-caught O. argentinensis and O. bonariensis to look for candidate genes that might be of ecological importance in the adaptation of these fish to freshwater habitats.
Chapter three focues on resolving relationships in the genus Odontesthes using a large ddRADseq dataset with more than 150 samples, and cytochrome b haplotype dataset with more than 400 individuals, spanning the geographic range of Odontesthes. This chapter addresses the evolutionary relationships and some species boundaries in this group, which have been difficult to disentangle. Marine O. argentinensis and freshwater O. argentinensis, (discussed in chapter 2), despite having no differentiation in cytochrome b, clearly separate into distinct clades with ddRAD data. Chapter four produced the largest phylogenomic matrix (in basepairs, and backbone taxonomic sampling) to date for
Actinopterygiians, using a database of 305 genomes and transcriptomes to address paralogy for an exon-capture set for fish phylogenomics. We developed a heuristic using
vii topology tests to detect paralogs in our marker set based on known genome duplications affecting fishes, and inferred a phylogenetic tree to test our marker set of 1105 exons. We also addressed topological conflict in the literature using the ‘gene genealogy interrogation’ technique.
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Table of Contents
Acknowledgments ...... iv
Abstract of Dissertation ...... vi
List of Figures ...... x
List of Tables ...... xii
Chapter 1: Introduction ...... 1
Chapter 2: Transcriptomic differentiation underlying marine-to-freshwater transitions in South American silversides Odontesthes argentinensis and O. bonariensis (Atheriniformes) ...... 6
Chapter 3: Broad survey of mitochondrial DNA and genomic RAD data: species boundaries, introgression, and phylogeny of Odontesthes silverside fishes (Teleostei: Atheriniformes) ...... 32
Chapter 4: Comprehensive phylogeny of ray-finned fishes (Actinopterygii) enhanced by transcriptomic and genomic data ...... 62
References ...... 91
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List of Figures
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List of Tables
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Chapter 1: Introduction
Ray-finned fishes (Actinopterygii) form the largest clade of vertebrates with more than 34,000 valid species currently described (Eschmeyer and Fong 2017). They inhabit diverse aquatic environments across the globe, offering a huge variety systems to explore ecology and evolution. Here, I use several DNA sequencing approaches to tackle evolutionary questions in fishes, from recent habitat transitions in a group of silverside fishes (genus Odontesthes, Atherinopsidae), to disentangling over 400 million years of evolutionary change to infer the phylogeny of all ray-finned fishes. First I employed transcriptomics to look at a recent habitat transition in a pair of silverside species, then double-digest RADseq (ddRADseq) (Peterson et al. 2012) to look at evolutionary relationships and genomic changes related to habitat transitions across the entire genus
Odontesthes, and finally I study over 300 fish genomes and transcriptomes to extract single-copy exons necessary to resolve the relationships among all bony fishes, and designed for future synthesis of sequence capture probes.
The ability to generate and analyze genome-scale data for non-model species has greatly transformed approaches in ecological and evolutionary genetics in recent years.
This revolution has been fueled by development of new DNA sequencing technologies, decreasing prices to collect data, and increasingly powerful bioinformatics resources. In
2012, the year I started my PhD at the George Washington University, fewer than ten bony fish genomes (model organisms) had been fully sequenced and described in publications, but more than 100 already were in progress in various laboratories
(Bernardi et al. 2012). Nevertheless, most studies in ecology and evolution still were based on few molecular markers (mitochondrial and nuclear genes, microsatellite loci)
1 under the traditional PCR and Sanger sequencing methodologies to try to disentangle phylogenetic relationships, or discover ecologically important genes that might be implicated in speciation. But the field is being rapidly transformed with new genomic techniques such as target capture (Faircloth et al. 2012; Lemmon et al. 2012) and
RADseq (Baird et al. 2008) that provide hundreds or thousands of genetic loci for population or phylogenetic studies. With more than sixty fish genomes recently published in a single study (Malmstrøm et al. 2016), the field of fish genomics also is moving rapidly, and researchers are no longer confined to investigating a handful of genome- enabled model organisms.
Reduced-representation genomic techniques allow the sequencing of multiple individuals from many populations or species for comparative approaches at a relatively low cost, producing different types of data appropriate to answer questions at several evolutionary time scales. These techniques target only specific parts of a genome for sequencing, significantly reducing complexity to assemble and analyze datasets.
Transcriptomics or RNAseq methods target expressed genes, which can be used to assess expression differences if replicates are sequenced, or may be a useful way to sequence expressed genes from a variety of organisms for broader comparisons (Sun et al. 2016).
Restriction enzyme associated DNA (RAD) techniques alternatively target regions across the genome, sequencing DNA adjacent to restriction enzyme cut sites (Baird et al. 2008;
Peterson et al. 2012). These techniques have been used to bring previously unattainable phylogenetic resolution to a rapid radiation of cichlids (Wagner et al. 2013), but have also been used to look at genomic islands of divergence between populations and species occupying different ecological niches (Hohenlohe et al. 2010; Gaither et al. 2015).
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Sequence capture is another way of reducing genomic complexity, using single-stranded probes to hybridize with pre-selected genomic DNA (Faircloth et al. 2012; Lemmon et al.
2012), and is popular in phylogenomics because it can be applied to relatively deep evolutionary divergences and markers can be selected for desirable properties before sequencing (Lemmon and Lemmon 2013). Though unlike the previous approaches, sequence capture requires reference genomes for probe design.
Chapter two of my dissertation focuses on silverside fishes in the genus
Odontesthes, which have recently and rapidly transitioned from marine to freshwater, crossing an ecological barrier. Two closely related species, marine O. argentinensis and freshwater O. bonariensis, span this ecological divide, and yet show little genetic divergence using traditional phylogeographic mitochondrial markers (García et al. 2014).
We sequenced gill transcriptomes from wild-caught O. argentinensis and O. bonariensis to look for candidate genes that might be of ecological importance in the adaptation of these fish to freshwater habitats, and further evaluate whether there is plasticity in O. bonariensis in response to salinity changes in the laboratory that resembles O. argentinensis in mRNA expression. We find more than three thousand transcripts differentially expressed, with osmoregulatory/ion transport genes and immune genes showing very different expression patterns across species. Additionally, we characterize the gill bacterial microbiome from our transcriptomic reads. We also identified more than one thousand transcripts with non-synonymous SNPs in the coding sequences, most of which were not differentially expressed. The diversity of functions associated with both the differentially expressed set of transcripts and those with sequence divergence suggest that multiple abiotic and biotic differences in marine and freshwater habitats are
3 influencing genomic changes in these species.
Chapter three of my dissertation is focused on the interrelationships in the genus
Odontesthes using a large ddRADseq dataset with more than 150 samples, and cytochrome b haplotype dataset with more than 500 individuals, spanning the geographic range of Odontesthes. This chapter addresses the evolutionary relationships and some species boundaries in this group, which have been difficult to disentangle (García et al.
2014; Campanella et al. 2015). Marine O. argentinensis and freshwater O. argentinensis,
(discussed in chapter 2), despite having no differentiation in cytochrome b, clearly separate into distinct clades with ddRAD data. However, our results do not support the differentiation of all nominal species and independently evolving lineages (De Quieroz
2007), and suggest that O. regia and O. gracilis, a species described only from the Juan
Fernandez Islands, are in fact a single lineage. Additionally, O. mauleanum and O. brevianalis, the freshwater species that inhabit the Valvidian lakes region of Chile, also appear to be a single lineage. Interestingly, cytochrome b haplotypes suggest that there has been introgression across a marine-freshwater gradient in southern Chile between the marine O. regia and freshwater O. mauleanum in some populations, and a weak signal remains of nuclear introgression for individuals in these populations. Additionally, we were able to determine that there were at least two, possibly three, separate invasions into freshwater, which rejects a previous hypothesis that Odontesthes are primary freshwater fishes.
In chapter four I assemble and analyze the largest phylogenomic matrix (in basepairs, and backbone taxonomic sampling) to date for Actinopterygiians, using a database of 305 genomes and transcriptomes to address paralogy for an exon-capture set
4 for fish phylogenomics. It is widely accepted that two rounds of whole genome duplication occurred during the early stages of vertebrate evolution, with a third round of whole genome duplication taking place at the base of teleost fishes (Meyer and Van De
Peer 2005), complicating the search for orthologous markers. Moreover, the search for single-copy orthologs for fishes has generally been based on just a handful of model reference genomes (Li et al. 2007; Faircloth et al. 2013). We developed a heuristic using topology tests to detect paralogs in our marker set based on known genome duplications affecting fishes, and inferred a phylogenetic tree to test our marker set of 1105 exons. We also addressed topological conflict in the literature at the base of Teleost fishes,
Ostariophysans, Protacanthopterygii, the base of Acanthoptergii, and the base of
Percomorphaceae using the ‘gene genealogy interrogation’ technique (Arcila et al. 2017).
Employing these different sequencing techniques allowed me to examine different evolutionary questions at different time scales. In chapter 2, I used transcriptome sequencing to try to examine the specific genes involved in ecological adaptation to divergent marine and freshwater environments between a pair of Odontesthes species. In my next chapter, I used ddRADseq to focus more on the patterns of divergence and speciation among the Odontesthes species, which sheds light on their biogeographic patterns. Finally, I used a combination of genomes and transcriptomes to try to filter for the best genes to infer the deep phylogeny of all Actinopterygiian fishes, looking for conserved genes that were not impacted by the history of whole genome duplications in vertebrates.
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Chapter 2: Transcriptomic differentiation underlying marine-to-freshwater transitions in South American silversides Odontesthes argentinensis and O. bonariensis (Atheriniformes)
Abstract
Salinity gradients are critical habitat determinants for freshwater organisms.
Silverside fishes in the genus Odontesthes have recently and repeatedly transitioned from marine to freshwater habitats, overcoming a strong ecological barrier. Genomic and transcriptomic changes involved in this kind of transition are only known for a few model species. We present new data and analyses of gene expression and microbiome composition in the gills of two closely related silverside species, marine O. argentinensis and freshwater O. bonariensis and find more than three thousand transcripts differentially expressed, with osmoregulatory/ion transport genes and immune genes showing very different expression patterns across species. Inter-specific differences also involve more than one thousand transcripts with non-synonymous SNPs in the coding sequences, most of which were not differentially expressed. In addition to characterizing gill transcriptomes from wild-caught marine and freshwater fishes, we test experimentally the response to salinity increases by O. bonariensis collected from freshwater habitats.
Patterns of expression in gill transcriptomes of O. bonariensis exposed to high salinity do not resemble O. argentinensis mRNA expression, suggesting lack of plasticity for adaptation to marine conditions in this species. The diversity of functions associated with both the differentially expressed set of transcripts and those with sequence divergence plus marked microbiome differences suggest that multiple abiotic and biotic factors in marine and freshwater habitats are driving transcriptomic differences between these species.
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Introduction
The marine-freshwater boundary is a strong ecological gradient for aquatic organisms across the tree of life. Ray-finned fish lineages have transitioned from marine to fresh water multiple times in their evolutionary history, more frequently than in the opposite direction (Betancur-R et al. 2015), repeatedly adapting to meet this ecological challenge. There are many obstacles for the successful colonization of freshwater habitats by marine fishes, and the most physiologically demanding is the salt concentration in the water. Most fishes are stenohaline (have narrow salinity tolerance), and just 2% of all fishes are euryhaline, occupying both marine and freshwater environments (Betancur-R et al. 2015).
Maintaining osmotic homeostasis is a major challenge for organisms that move between marine and freshwater habitats. Osmoregulation in fresh water is energetically expensive for marine fish, whereas sea water is closer to the internal solute concentration of fishes, requiring less energy to maintain this homeostasis (Lee and Bell 1999). Coping with the salinity concentration gradient, however, may not be the main or only challenge.
Other abiotic impacts include the relative lack of calcium available in fresh water, critical because teleosts absorb calcium for bone formation directly from the surrounding waters
(Simmons 1971; Bell et al. 1993). Temperature fluctuations are greater in freshwater habitats, presenting less opportunity to escape inhospitable temperatures (Lee and Bell
1999). Biotic factors also are likely to be important, given that microbial communities are strongly structured by salinity (Lozupone and Knight 2007; Logares et al. 2009), and fish must tolerate drastic challenges to their immune system as they experience complete
7 turnover of their microbiomes (Schmidt et al. 2015; Lokesh and Kiron 2016) or interactions with novel parasites. These ecological differences often drive genetic divergence between closely related marine and freshwater organisms.
Genomes are shaped by an organism’s ecology (Ungerer et al. 2008), and fish species and populations that transition from marine to fresh water offer important insight into how this occurs. For example, significant divergence of SNPs associated with freshwater adaptation has been detected in or near genes related to osmoregulation, stress, and immune function by comparing marine and freshwater populations of sticklebacks and killifishes (Hohenlohe et al. 2010; Jones et al. 2012; Kozak et al. 2013). Since many of these habitat transitions may lead to speciation, detecting and characterizing transcriptomic divergences may be of importance to better understand this process, as patterns of gene expression can evolve rapidly (Wolf et al. 2010). Osmoregulatory genes have population and species-specific expression patters in fundulid killifishes inhabiting different salinities (Whitehead et al. 2011, 2012; Kozak et al. 2013), and transcriptional responses to temperature are more variable in freshwater than marine stickleback (Morris et al. 2014). Furthermore, marked and predictable differences in microbiome composition have been reported to follow acclimation of the Black Molly (Poecilia sphenops) to different water salinity, suggesting a key role of the immune system in habitat transitions (Schmidt et al. 2015)
Here we investigate adaptation in gill function following marine to fresh water invasions by presenting new data and analyses of transcriptomes and microbiomes obtained from gills of silverside fishes of the genus Odontesthes. If ecology is driving speciation between marine and freshwater silversides, we would expect fixed genetic
8 differences and diverging patterns of gene expression between fishes occupying these two habitats, notably for genes related to salinity tolerance, calcium intake, temperature fluctuation, and the immune system. The combined challenges presented by abiotic
(salinity, temperature) and biotic (microbiome composition) factors may lead to complex interactions driving genomic and transcriptomic differentiation between habitats.
Alternatively, if expression differences are plastic responses to habitat transitions, common garden experiments would reveal similar expression patterns for marine and freshwater species under the same conditions.
We study Odontesthes silversides that comprise 19 marine and freshwater species, commonly known as pejerreyes (Dyer 2006), which have recently and frequently transitioned from marine to fresh water in southern South America. (Bloom et al. 2013;
Campanella et al. 2015). They are members of the order Atheriniformes, whose members inhabit coastal marine and freshwater environments worldwide, having successfully and independently colonized freshwater habitats on multiple continents (Campanella et al.
2015). Plastic responses to the environment observed in some estuarine atherinid species are hypothesized to be a pre-adaptation for successfully undertaking transitions to fresh water (Bamber and Henderson 1988), and species or species complexes that inhabit different salinity gradients often show genetic structuring and evidence for incipient speciation (Beheregaray and Sunnucks 2001; Kraitsek et al. 2008; Fluker et al. 2011).
We focus on a pair of species, one marine and one freshwater: O. bonariensis, native to lakes and rivers of the Pampas region of Argentina, the Rio de la Plata and Lower Paraná and Uruguay basins, up to the Tramandaí coastal lagoon system in Brazil (Liotta 2005;
Dyer 2006; Somoza et al. 2008); and O. argentinensis, is its marine (putative) sister
9 species that ranges along the South Atlantic coast of Buenos Aires Province (Argentina) to Southern Brazil (Dyer 2006; Campanella et al. 2015). Up to eight, sometimes sympatric, freshwater Odontesthes species have been described in this region, associated with rapid divergence in freshwater habitats as a result of recent changes in sea level
(Beheregaray et al. 2002). All these freshwater species are closely related to O. argentinensis and O. bonariensis.
Whether due to rapid speciation in freshwater habitats or ongoing gene flow among incipient freshwater species and marine fishes, there is little genetic differentiation among species in the argentinensis-bonariensis species complex (García et al. 2014;
Campanella et al. 2015; Díaz et al. 2016; González-Castro et al. 2016). Odontesthes argentinensis and O. bonariensis show patterns of genetic divergence that fall well within the range of intraspecific variation (Heras and Roldán 2011), but they differ in some meristic counts of morphological characters and their body shape (Dyer 2006; González-
Castro et al. 2016), and their mechanism of sex-determination appears to be different
(Strussmann et al. 1997; Fernandino et al. 2013; Yamamoto et al. 2014). One of the most conspicuous differences between the two species is the different habitats they occupy.
Considering the substantial ecological boundary that the marine-to-fresh water transition poses for fishes but lack of known genetic divergence between these two species, we investigate underlying changes at the genomic level associated with freshwater adaptation in these species by comparing gill transcriptomes from wild caught
O. argentinensis (marine) and O. bonariensis (freshwater). We also test for phenotypic plasticity in gene expression by comparing gill transcriptomes from laboratory-housed O. bonariensis, which is still relatively euryhaline (Vigliano et al. 2006; Tsuzuki et al.
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2008), in freshwater and brackish salinities. Adaptive genetic divergence can take place by mutations in the coding sequences or by changes to cis-regulatory elements that affect expression, though often changes are the result of both (Hoekstra and Coyne 2007). The teleost gill is of critical physiological importance through its direct interaction with the environment, fulfilling respiratory, osmoregulatory and immune functions (Evans 2005;
Díaz et al. 2009), and genes of adaptive significance in marine or fresh water are likely to be expressed in this tissue, which could be implicated in speciation between O. argentinensis and O. bonariensis. We provide new data to characterize diverging patterns of gene expression and genetic differences associated with functions related to freshwater adaptation, including ion transport, calcium uptake, temperature acclimation and the immune system. We also experimentally test whether the pattern of gene expression is a plastic response to the environment. Finally, we characterize the gill microbiomes of O. bonariensis and O. argentinensis, which are predicted to diverge along the water salinity gradient, hence providing a baseline for understanding putative changes in immune- response transcripts in the gills.
Methods
Sampling and experimental design
We obtained gill tissue from three individuals of O. argentinensis collected by beach seining along the Atlantic coast near Mar del Plata (38˚ 2’ S, 57˚ 31’ W) on March
3, 2014, and three O. bonariensis fished by trawl from Lake Chascomús (35˚ 34’ S, 58˚
01’ W) on March 10, 2014, in Buenos Aires Province, Argentina (Figure 1). Natural salinity in this lake is about 2 g/L. Gills were immediately preserved in RNAlater® in the field, kept at ambient temperature, and promptly transferred to -80˚ C in the lab until
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RNA extraction. An experiment to test the effect of increasing salinity was set up with an additional six adult O. bonariensis collected from Lake Chascomús. These fish were transferred to nearby freshwater tanks at IIB-INTECH (Chascomús) with recirculating water at 18˚ C and kept under natural photoperiod. There, three silversides were placed in a second tank where salinity was increased over two days to 15 g/L salinity. This is not beyond the salinity tolerance for this relatively euryhaline species, which is in fact known to have reduced cortisol levels at 20 g/L salinity compared to 0 g/L waters (Tsuzuki et al.
2001). Fish were allowed to acclimate for five days, before they were sacrificed with an
MS-222 overdose and gill tissue was collected. All procedures followed the UFAW
Handbook on the care and management of laboratory animals (http://www.ufaw.org.uk) and internal IIB-INTECH institutional regulations. Tissues were stored in RNAlater® at
-80 °C until RNA was extracted using a Qiagen RNeasy kit, following manufacturer’s instructions.
RNA sequencing
Messenger RNA (mRNA) was isolated from total RNA using a Dynabeads® mRNA purification kit (Ambion). We prepared paired-end Illumina sequencing libraries for each gill sample with a SMARTer Stranded RNA-seq kit (Clontech). Resulting cDNA libraries were quantified via qPCR with the KAPA Library Quantification kit (KapaBiosystems).
We sequenced 92-bp paired-end reads on four lanes of an Illumina HiScan, with two separate runs at Children’s National Medical Center in Washington, DC. Samples were multiplexed and sequenced together across all lanes. Raw sequences for all samples in this project are accessible at NCBI (BioProject PRJNA311227).
Transcriptome Assembly
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Bioinformatics analyses were performed on the Colonial One high performance computing system at George Washington University. Raw Illumina base calls were converted to fastq-formatted files and demultiplexed with CASAVA v1.8.2 (Illumina).
These reads were deposited in the SRA database with accession numbers noted in Table
1. We used Trimmomatic v0.33 (Bolger et al. 2014) to quality control our sequences and remove adapter contamination using ILLUMINACLIP:2:30:7 HEADCROP:13
SLIDINGWINDOW:7:15 MINLEN:20 as trimming parameters. Contaminating ribosomal RNA (rRNA) sequences were removed with SortMeRNA v2.0 (Kopylova et al. 2012). Paired-end reads from all samples were mapped against the O. bonariensis genome (Campanella 2014) using STAR v2.5 (Dobin et al. 2013), and assembled using
Trinity v2.1.1 in genome-guided mode. Open reading frames (ORFs) were predicted using Transdecoder v2.0.1 (Grabherr et al. 2011; Haas et al. 2013). We collapsed identical transcripts with ORFs using the program CD-HIT v4.6, retaining the longest transcripts (Li and Godzik 2006; Fu et al. 2012). We functionally annotated transcripts by blasting protein sequences against NCBI’s Non-Redundant (nr) protein database, accessed June 1st, 2016, and mapping gene ontology terms using Blast2GO Basic v3.2 software.
Differential Expression and Gene Set Enrichment Analyses
We used assembled transcripts with ORFs to test for differential expression among gill transcriptomes of wild specimens obtained from marine and freshwater habitats, as well as the two experimental lots (freshwater and brackish water tanks).
Sequence reads were mapped for each individual sample back to the reference sequences with Bowtie2 (Langmead and Salzberg 2012). Transcript abundance was estimated using
13 the Trinity wrapper for RSEM (Li and Dewey 2011). We quantified expression patterns using the R package EBSeq, which allows for testing different expression patterns when the experimental design has more than two treatments (Leng et al. 2013). We tested all 15 possible expression patterns for four treatments (wild-marine, wild-lake, freshwater-lab, brackish-lab; Figure 2), and ran EBSeq with 50 iterations. We considered transcripts with a posterior probability >0.95 for a particular expression to be differentially expressed, which corresponds to an FDR of 0.05.
Gene ontology (GO) terms were mapped using Blast2GO Basic software. We used Fisher’s Exact Test to determine which biological processes (GO terms) were enriched among differentially expressed genes from O. argentinensis from any O. bonariensis treatment, as well as those transcripts that were similarly differentially expressed in O. argentinensis and O. bonariensis at brackish salinity.
SNP Calling
We followed the protocol for SNP detection on transcriptome assemblies described by De Wit et al. (De Wit et al. 2012). We used Picard-tools v1.129 to coordinate sort, add read group names, and mark suspected duplicate reads in our SAM files obtained from Bowtie2 for each of our separate individuals, and to index and merge these into a single BAM file for SNP discovery. We used the recommendations of De Wit et al. (2012) to run the Genome Analysis Toolkit v3.4-46 for SNP calling (McKenna et al. 2010). We used only those SNPs that were completely differentiated between marine and freshwater samples and fell in ORFs for further analysis, and had been genotyped for all individuals. We then examined whether these SNPs resulted in synonymous or non- synonymous changes in the coding sequence of these transcripts, and pulled annotation
14 information from our blastp output.
Microbiome Characterization
For each individual gill sequenced we characterized the associated microbiome using the following steps. Filtered reads greater than 36 bp were error-corrected with
BLESS v0.22 using default settings (Heo et al. 2014). Reads matching conserved, informative loci were taxonomically assigned with PhyloSift (Darling et al. 2014) using the default settings and core marker set (version 1413946442), but excluding the 18S_rep marker. The matching reads were phylogenetically placed using Pplacer (Matsen et al.
2010). The 16S marker analysis was further used to quantify phylogenetic differences between samples with the Kantorovich-Rubinstein distance function in Pplacer, which is functionally similar to the weighted UniFrac metric (Evans and Matsen 2012), and further explored using a phylogenetic edge PCA (Matsen and Evans 2013) generated with the guppy package in Pplacer. Taxonomic diversity plots based on 16S identifications were generated in R using the ‘phyloseq’ package (McMurdie and Holmes 2013; Team
2014).
Results
Sequencing and Transcriptome Assembly
Sequences generated for each of our biological replicates are reported in Table 1, along with SRA accession numbers. Trinity, using the genome-guided mode, assembled
100,845,415 bases into 168,570 transcripts, with an N50 of 838. Only 40,384 non- redundant transcripts contained open reading frames detected using Transdecoder, which was the set of transcripts we used to map reads from our replicates to assess differential expression. One replicate from our laboratory-brackish water treatment had significantly
15 fewer reads, and this replicate was not included in differential expression analysis, though these reads were included in the assembly. There is no difference in mapping O. argentinensis RNA-seq reads back to the O. bonariensis reference genome, thus any transcript expressed by O. argentinensis and not O. bonariensis still exists in the O. bonariensis genome.
Differential Expression, SNP Detection, and Gene Ontology Enrichment
A total of 3,271 transcripts were differentially expressed between O. argentinensis and any O. bonariensis treatment (Pattern 8, Figure 2). These transcripts were enriched for Gene Ontology biological process categories that included several functions related to ion transport including ion transmembrane transport, chloride transmembrane transport, and hydrogen transmembrane transport (Table 2). The GO term
‘immune system process’ was also enriched for this differentially expressed set. Far fewer transcripts (96) in O. bonariensis show a plastic response to salinity that is similar to wild marine O. argentinensis (Pattern 6, Figure 2). This set of transcripts was not enriched for any biological process, although it did contain transcripts that have osmosensing functions, including NEDD4 ubiquitin ligase (Fiol and Kültz 2007).
A total of 1417 transcripts have non-synonymous SNPs putatively fixed between the marine and freshwater samples. A minority (201) of these transcripts are also differentially expressed between O. argentinensis and all O. bonariensis treatments. The set of transcripts with non-synonymous SNPs were not enriched for any biological process GO terms.
Microbiome Characterization
There was substantial variation in the composition of bacterial gill microbiota
16 among wild-caught individuals but far less among laboratory treatments (Figure 3).
Though there is some differentiation between wild-caught freshwater and marine gill microbiomes, laboratory-housed fish displayed the most distinct microbiome. This characteristic laboratory microbiome was not substantially changed by increasing water salinity to 15 g/L. Laboratory individuals were caught in the wild along with those individuals from Lake Chascomús, and so changes in their microbiome likely occurred during the week-long period while they were housed at IIB-INTECH. Phylogenetic edge
PCA results suggest that a substantial amount of variation between samples is explained by comparing wild specimens with fish being housed in the laboratory (see supplemental files on Figshare). While all bacterial communities were dominated by Proteobacteria, gills collected from laboratory individuals had a large proportion of bacterial reads assigned to taxa from the family Alteromonadaceae, which was uncommon in wild individuals of either O. argentinensis or O. bonariensis (Figure 4).
Discussion
Divergence between marine and freshwater fishes
The genetic data (mitochondrial DNA and few nuclear gene sequences) available to compare O. argentinensis and O. bonariensis prior to our transcriptome analysis suggested very little genetic divergence, within the typical boundaries of intraspecific variation (Heras and Roldán 2011; García et al. 2014; Díaz et al. 2016; González-Castro et al. 2016). The transcriptomic differences reported here likely reflect rapid speciation and adaptation to different environmental conditions, while still failing to accumulate the level of genetic differentiation in mitochondrial markers that are sometimes used to distinguish species.
17
The most significant pattern of differentially expressed genes separates O. argentinensis from all O. bonariensis samples. This suggests that habitat differences are potentially driving divergent patterns of expression between these two species. Our study detected differential expression of many candidate genes known to be involved in osmoregulation and ion permeability in fish gills, putatively ecologically important for the transition from marine to fresh water. As predicted, many transcripts that were differentially expressed between the two species were enriched for gene ontology terms related to ion transport (Table 2), as major physiological changes need to occur in order to maintain internal solute concentrations in these different environments. Although our sample sizes are relatively small to consider these differences at face value to represent fixed species-level differences (Conesa et al. 2016), our results reveal consistent changes predicted on the basis of gill function adapting to different habitats.
Also based on a limited number of individuals (3 marine, 8 freshwater), we discovered 1417 transcripts carrying non-synonymous differences in coding sequences that are putatively fixed between O. argentinensis and O. bonariensis. With deeper sampling of individuals, however, many of these differences may turn out to be shared between these species. Furthermore, many of these differences are likely neutral or may have no significant adaptive advantages for these environments. In any case, we consider this list of candidate genes worth investigating, as it contains some well-known osmoregulatory genes in fishes that likely are under selection to adapt to different habitats, including Na/K transporting ATPase subunit alpha 1. This ion transporter—one of the most well-known osmoregulatory genes in fish— is both differentially expressed between O. argentinensis and all O. bonariensis treatments, and contains a non-
18 synonymous SNP. Variants of this gene have been linked to freshwater transitions in the stickleback system (Jones et al. 2012). Aquaporin 3 also contained non-synonymous
SNPs, a gene thought to be adaptive for osmoregulation in sticklebacks, tilapia, and killifishes (Shimada et al. 2011; Whitehead et al. 2012; Yan et al. 2013). An additional eight transcripts belonging to the Claudin family of tight-junction proteins also have non- synonymous SNPs. The expansion of this gene family in the European sea bass is suggested to have allowed it to adapt to variable salinities (Tine et al. 2014), and this is also one of the largest gene families in the pejerrey genome (Campanella 2014).
The transition from marine to freshwater involves ecological changes beyond the salinity gradient. Calcium concentrations are higher in marine water than fresh water, which has been implicated in bony plate (armor) loss in sticklebacks that have transitioned to fresh water (Bell et al. 1993; Spence et al. 2012). Odontesthes species have no bony armor, but all teleosts absorb environmental calcium for bone formation
(Simmons 1971). Bone morphogenic protein 3 (BMP3) was expressed at least 5 times higher in in O. argentinensis than any O. bonariensis treatment, suggesting that pejerrey fish also experience differences in bone growth in these different environments. Heat shock protein 90-beta also was both differentially expressed and contained a non- synonymous SNP that distinguished the two species. While in the gill, this gene is probably responsible for mediating responses to changes in temperature and other stressors. Otherwise, over expression of this gene has been reported in ovary during the thermo-labile sex-differentiation period in larval O. bonariensis (Fernandino et al. 2011).
Plasticity in O. bonariensis
The transcriptomic response measured through gene expression of O. bonariensis
19 individuals from Lake Chascomús acclimated to brackish water does not approach the natural state of an O. argentinensis marine fish, suggesting that the expression differences we see between the two species are not due to plasticity. While marine salinity (30 ppt) can be lethal to O. bonariensis, this species is more comfortable at brackish salinities
(Tsuzuki et al. 2000, 2001), and is reported to have a relatively euryhaline gill structure
(Vigliano et al. 2006). Given this, we might expect some plasticity in response of the gills of O. bonariensis to changes in salinity, but they have evidently lost the ability to move completely between salinities, and due to this we are unable to evaluate the changes in expression for this freshwater fish in a marine environment. We are able to determine that when exposed over several days to a higher salinity (15 ppt), relatively few transcripts of
O. bonariensis show a similar expression pattern to O. argentinensis. In contrast, the expression profiles of O. argentinensis and O. bonariensis are largely different, and have more than 3,000 differentially expressed transcripts that distinguish them.
However, a few transcripts show a plastic response in salinity in O. bonariensis that is similar in expression to a marine O. argentinensis. Notably, several NEDD4 ubiquitin ligases are expressed more highly in O. argentinensis, which interact with epithelial sodium channels, and may be a response to changes in osmolality (Fiol and
Kültz 2007), and one isoform was also expressed by O. bonariensis when exposed to brackish water. The higher proportion of these NEDD4 ubiquitin ligases expressed in O. argentinensis may be due to these fish often entering estuaries, including the Mar
Chiquita estuary, which is near Mar del Plata, where these individuals were collected, even though they were collected in seawater (González-Castro et al. 2016). Although production of O. argentinensis larvae for aquaculture is well established (Sampaio 2006),
20 no success has been achieved to transfer to the laboratory adult O. argentinensis captured at sea to test its ability to tolerate fresh water conditions (Gonzalez-Castro pers. com.), precluding common garden experiments involving this species.
Candidate Genes in Immune Response
The marine-freshwater boundary strongly structures microorganism communities
(Logares et al. 2009) and, while teleost microbiomes have not been extensively characterized, salinity has been shown to influence microbiota in fishes (Schmidt et al.
2015; Lokesh and Kiron 2016). We found differentially expressed genes between O. argentinensis and all O. bonariensis to be enriched for the immune response GO term, suggesting that the marine-to-fresh water transition may also require changes to the immune system. Within this differentially expressed set we annotated six pathogen- detecting MHC I and two MHC II transcripts, and additionally six MHC II transcripts contain non-synonymous SNPs differentiated between marine and freshwater in our dataset. These genes have been linked to habitat diversity and speciation in fishes
(Malmstrøm et al. 2016), and differences between marine and freshwater pathogens and parasites are likely being reflected in our Odontesthes system, though these genes also play a role in mate selection in the wild (Bernatchez and Landry 2003).
In addition to the MHC transcripts, nine lectin transcripts were differentially expressed between these two species. Lectins are pathogen-recognition molecules important in the innate immune system, which is thought to be the primary defense against pathogens in fish (Vasta et al. 2011), and of which the C-type lectin is known to be differentially expressed between anadromous and resident populations of trout (Boulet et al. 2012). Four different C-type lectin isoforms are expressed differently between these
21 species of silversides, which is one strategy for lectins to increase the repertoire of pathogens to which they bind (Bianchet et al. 2002; Suzuki et al. 2003). Thus, the different repertoires of lectins expressed by marine and freshwater fish suggest a possible plastic response to different pathogen regimes between environments.
Some genes related to immune function also are involved in cell signaling, including interleukin 2 and 12 receptors that were differentially expressed here.
Interleukin 12 receptors act as a cytokine that is released by antigen-presenting cells to stimulate many immune-related cells in response (Wang and Secombes 2013). However, genes involved in cell signaling can also act in stress responses to other environmental factors like salinity. Interleukin-8, also differentially expressed between species, may play a role in immune function as well as osmotic signaling (Kültz 2012). Whether these genes play a primarily osmotic-sensing role or immunological role in the wild is difficult to difficult to disentangle here, but their complex role in stress responses make them all the more relevant to overcoming the challenge of adapting to a new environment.
Microbiome Differentiation
There was substantial individual variation in the gill bacterial communities of wild O. argentinensis and O. bonariensis, which were somewhat differentiated between marine and freshwater for wild-collected individuals (Figure 3), further highlighting the different microbial regimes. However, the microbiome of laboratory individuals showed a very different composition that did not appear to be impacted by changing the tank salinity. Fewer than thirty taxa identified by PhyloSift were shared across all individuals, which suggests that there is not a consistent core Odontesthes gill microbiome across the natural and experimental environments.
22
Marine and freshwater microbial taxa are often from phylogenetically distinct lineages, and have made relatively few transitions between these environments (Logares et al. 2009). This is a challenge that marine fish will have to overcome as they adapt to fresh water. Studies have documented substantial overturn of the microbiome in different fish tissues as the salinity is increased (Schmidt et al. 2015; Lokesh and Kiron 2016), though this is frequently accomplished in the laboratory. Our data show that the microbial community observed in the lab are likely to be very different from the microbes that inhabit fish the in the wild, although amplicon-based sequencing would reveal a more complete picture of the microbial communities as a whole. This may hinder future inferences about host-microbe interactions conducted in the laboratory.
Conclusions
Mitochondrial markers have previously suggested very little divergence between
O. argentinensis and O. bonariensis, despite their occupation of highly divergent habitats. This preliminary analysis identified more than 3000 transcripts that are differentially expressed between these species, and additionally transcripts with non- synonymous coding SNPs that we propose as candidate genes for this habitat transition and as the basis for divergent ecological adaptation in these species. The broad range of physiological functions associated with these genes suggests that salinity is only one of many abiotic and biotic factors that are driving this divergence. Laboratory experiments focusing on qPCR validation of a few candidate genes have certainly shed light on some of the physiological requirements to make a shift between salt and freshwater, but relatively few studies look at gene expression in natural populations of fishes. Our results suggest that there are both gene expression and sequence divergence differences in these
23 sister species that are driven by the different environments that they inhabit, and that their speciation may be driven by adaptation to different local conditions.
Figure 1: Sampling localities for O. argentinensis at Mar del Plata, and O. bonariensis at Lake Chascomús, Argentina, with abiotic factors that are typically different between marine and freshwater environments.
24
Pattern 15 Pattern 14 Pattern 13 Pattern 12 Pattern 11 Pattern 10 Pattern 9 Pattern 8 Pattern 7 Pattern 6 Pattern 5 Pattern 4 Pattern 3 Pattern 2 Pattern 1 Brackish Marine Laboratory Laboratory Freshwater Freshwater Mar del Plata Lake Chascomús O. bonariensis O. bonariensis O. bonariensis O. argentinensis
Figure 2: Expression condition comparisons for four treatments in Ebseq. Patterns discussed in the text are highlighted with black boxes, including the pattern that differentiates the different species (pattern 8), and the pattern that differentiates higher from lower salinity treatments (pattern 6). Pattern 8, which differentiates marine O. argentinensis treatment, was detected for 3,271 transcripts, while only 96 were detected for pattern 6. For 230 transcripts, pattern 4 was the best fit, suggesting some stress in laboratory conditions.
25
16S Kantorovich−Rubinstein distance PCoA
0.2
0.1 BW lab O. bonariensis FW lab O. bonariensis
PCoA 2 Wild O. argentinensis Wild O. bonariensis 0.0
−0.1
−0.2 0.0 0.2 0.4 PCoA 1
Figure 3: Principal coordinate analysis using Kantorovich-Rubenstein distance comparing bacterial gill communities. Identification of microbial taxa was based on the 16S marker, using the Phylosift pipeline.
26
Phylosift Proteobacteria Diversity by Family
Family Alteromonadaceae 0.4 Enterobacteriaceae
undance Oxalobacteraceae b Pseudomonadaceae e a v 0.2 Shewanellaceae Thiotrichaceae Relati Vibrionaceae
0.0
O. bonariensis 1 O. bonariensis 1 O. bonariensis 1 O. bonariensis 3 O. bonariensis 2 O. bonariensis 2 O. bonariensis 3 O. bonariensis 2 O. argentinensis 1 O. argentinensis 2 O. argentinensis 3 Laboratory Laboratory Marine Lake Chascomús Brackish Freshwater Mar del Plata Freshwater
Figure 4: Relative abundance of Proteobacteria families detected from gill samples, identified via Phylosift. Because samples are RNA, relative abundance represents the confounded variables of microbe presence and microbial gene expression.
27
Table 1: Gill Transcriptomes of Odontesthes argentinensis and O. bonariensis and their associated NCBI database accession numbers
Species Treatment Filtered Reads SRA (PE) Accessions O. argentinensis Wild, Mar del Plata 4,457,408 SRX1671790 O. argentinensis Wild, Mar del Plata 5,198,031 SRX1681012 O. argentinensis Wild, Mar del Plata 3,364,197 SRX1681017 O. bonariensis Wild, Lake 2,371,170 SRX1681471 Chascomús O. bonariensis Wild, Lake 7,908,074 SRX1681473 Chascomús O. bonariensis Wild, Lake 1,930,665 SRX1681474 Chascomús O. bonariensis Laboratory, 0 g/L 2,028,758 SRX1681475 salinity O. bonariensis Laboratory, 0 g/L 6,504,388 SRX1681516 salinity O. bonariensis Laboratory, 0 g/L 2,093,475 SRX1681556 salinity O. bonariensis Laboratory, 15 g/L 118,799 SRX1681557 salinity O. bonariensis Laboratory, 15 g/L 6,099,175 SRX1681558 salinity O. bonariensis Laboratory, 15 g/L 4,324,427 SRX1681559 salinity
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Table 2: Over-represented biological process gene ontology terms for differentially expressed transcripts between O. argentinensis and all O. bonariensis treatments
GO Term Description FDR P-Value GO:0015031 protein transport 1.65E-05 4.37E-09 GO:0045184 establishment of protein localization 1.65E-05 4.96E-09 GO:0071702 organic substance transport 2.03E-05 9.15E-09 GO:0033036 macromolecule localization 9.93E-05 5.98E-08 GO:0008104 protein localization 1.34E-04 1.01E-07 GO:0006886 intracellular protein transport 2.53E-04 2.29E-07 inorganic ion transmembrane GO:0098660 transport 7.12E-04 7.50E-07 GO:0044283 small molecule biosynthetic process 2.21E-03 2.66E-06 GO:0034613 cellular protein localization 2.24E-03 3.37E-06 GO:0070727 cellular macromolecule localization 2.24E-03 3.37E-06 glycosyl compound metabolic GO:1901657 process 2.45E-03 4.05E-06 GO:0046034 ATP metabolic process 3.41E-03 6.16E-06 GO:0006810 transport 4.22E-03 9.33E-06 GO:0046907 intracellular transport 4.22E-03 9.34E-06 ribonucleoside triphosphate GO:0009199 metabolic process 4.22E-03 9.52E-06 GO:0009119 ribonucleoside metabolic process 4.48E-03 1.08E-05 GO:0051649 establishment of localization in cell 5.28E-03 1.35E-05 GO:0009116 nucleoside metabolic process 5.42E-03 1.59E-05 monovalent inorganic cation GO:0015672 transport 5.42E-03 1.64E-05 glycosyl compound biosynthetic GO:1901659 process 5.42E-03 1.66E-05 nucleoside triphosphate metabolic GO:0009141 process 5.42E-03 1.71E-05 ribonucleoside monophosphate GO:0009161 metabolic process 6.15E-03 2.04E-05 GO:0051234 establishment of localization 6.29E-03 2.18E-05 GO:0006364 rRNA processing 6.33E-03 2.29E-05 nucleoside monophosphate GO:0009123 metabolic process 6.70E-03 2.52E-05 purine ribonucleoside triphosphate GO:0009205 metabolic process 6.85E-03 2.69E-05 GO:0006818 hydrogen transport 6.85E-03 2.89E-05 GO:0015992 proton transport 6.85E-03 2.89E-05 purine nucleoside triphosphate GO:0009144 metabolic process 6.92E-03 3.02E-05 GO:0016072 rRNA metabolic process 7.62E-03 3.44E-05
29
GO:0044711 single-organism biosynthetic process 8.15E-03 3.93E-05 purine nucleoside monophosphate GO:0009126 metabolic process 8.15E-03 4.05E-05 purine ribonucleoside GO:0009167 monophosphate metabolic process 8.15E-03 4.05E-05 GO:0042278 purine nucleoside metabolic process 1.07E-02 5.69E-05 purine ribonucleoside metabolic GO:0046128 process 1.07E-02 5.69E-05 GO:0002376 immune system process 1.07E-02 5.91E-05 negative regulation of mRNA GO:0050686 processing 1.07E-02 6.27E-05 GO:0033119 negative regulation of RNA splicing 1.07E-02 6.27E-05 negative regulation of mRNA GO:0048025 splicing, via spliceosome 1.07E-02 6.27E-05 GO:0051641 cellular localization 1.20E-02 7.20E-05 GO:0034220 ion transmembrane transport 1.53E-02 9.44E-05 GO:1902476 chloride transmembrane transport 1.62E-02 1.03E-04 inorganic cation transmembrane GO:0098662 transport 1.96E-02 1.27E-04 GO:0051179 localization 1.98E-02 1.33E-04 GO:0098655 cation transmembrane transport 1.98E-02 1.34E-04 GO:0009117 nucleotide metabolic process 2.17E-02 1.50E-04 hydrogen ion transmembrane GO:1902600 transport 2.34E-02 1.66E-04 nucleoside phosphate metabolic GO:0006753 process 2.86E-02 2.07E-04 retrograde transport, endosome to GO:0042147 Golgi 3.51E-02 2.66E-04 ATP hydrolysis coupled proton GO:0015991 transport 3.51E-02 2.70E-04 energy coupled proton transmembrane transport, against GO:0015988 electrochemical gradient 3.51E-02 2.70E-04 regulation of guanyl-nucleotide GO:1905097 exchange factor activity 3.63E-02 2.91E-04 regulation of Rho guanyl-nucleotide GO:2001106 exchange factor activity 3.63E-02 2.91E-04 carbohydrate derivative metabolic GO:1901135 process 3.63E-02 2.95E-04 GO:0042254 ribosome biogenesis 3.73E-02 3.09E-04 generation of precursor metabolites GO:0006091 and energy 4.64E-02 3.92E-04 ATP hydrolysis coupled GO:0090662 transmembrane transport 4.99E-02 4.28E-04
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Chapter 3: Broad survey of mitochondrial DNA and genomic RAD data: species boundaries, introgression, and phylogeny of Odontesthes silverside fishes (Teleostei: Atheriniformes)
Abstract
Odontesthes silversides (pejerreyes) inhabit coastal marine and freshwater habitats in temperate South America. With patterns of rapid speciation and gene flow, their relationships have been difficult to disentangle. We collected a large survey of mitochondrial cytochrome b haplotypes spanning the range of this genus. Mitochondrial
DNA does not distinguish species in the O. argentinensis species group, between O. mauleanum and O. brevianalis, nor between marine species O. regia and O. gracilis.
Interestingly, this dataset suggests mitochondrial capture of a marine haplotype by some populations of O. mauleanum and O. brevianalis. We further explored relationships and species boundaries in this genus with a large ddRAD dataset. Genome-wide data clearly distinguishes among O. argentinensis, O. humensis, and O. bonariensis, though does not fully separate O. perugiae and O. ledae into monophyletic groups. It also places the
Patagonian pejerrey O. hatcheri sister to the O. argentinensis species group, contrary to previous findings. This ddRAD data, like the mitochondrial dataset, does not separate O. regia or O. gracilis into clearly monophyletic groups, suggesting that they are the same species. Despite mitochondrial capture of a marine haplotype, populations of freshwater
Odontesthes in Chile have a very low signal of nuclear introgression. Over all, genome- wide RAD data clearly resolve relationships and distinguish species where classical mitochondrial markers have failed to provide resolution.
Introduction
Genomic data produced by high throughput sequencing have vastly improved our
31 ability to understand evolutionary patterns and processes in rapidly speciating groups, questions that were often intractable with PCR-based molecular markers. Restriction- enzyme associated DNA markers (RADseq) are genome-wide markers with demonstrated utility for resolving phylogenetic relationships in recently diverged species
(Wagner et al. 2013), and delimiting species boundaries (Pante et al. 2014). They are also very useful for detecting gene flow and introgression among populations and species, processes that can confound phylogenetic inferences and species delimitation (Eaton and
Ree 2013; Eaton et al. 2015).
Speciation can occur in the face of potentially homogenizing gene flow if there is sufficient disruptive selection, often in response to divergent ecological conditions (Feder et al. 2012). The marine-freshwater interface has yielded several examples in fishes where parapatric marine and freshwater populations have strongly different selection regimes (Seehausen and Wagner 2014). Gene flow from marine populations into freshwater ones may be strongly selected against in freshwater environments, leaving little signal of marine introgression in the nuclear genomes of freshwater individuals.
Conversely, if the ability to adapt to freshwater environments is derived from standing genetic variation in marine populations (Schluter and Conte 2009), gene flow from freshwater individuals into marine populations will have little effect, thus gene flow from freshwater populations into marine populations should be difficult to detect.
Even as genomic data have revolutionized phylogenetics, mitochondrial DNA
(mtDNA) markers, traditionally popular in the field of phylogeography (Avise et al.
1987), still have utility in understanding evolutionary patterns. Unlike nuclear markers, mtDNA does not readily recombine, and in cases of introgression it may be retained
32 intact. There are numerous cases of mtDNA crossing species boundaries, highlighting ancient introgression events that may have a weak nuclear signal (Bryson et al. 2014;
Willis et al. 2014; Good et al. 2015).
Odontesthes Evermann and Kendall 1906 is a genus of New World silverside fishes in the family Atherinopsidae (subfamily Atherinopsinae, tribe Sorgentinini), distributed in temperate marine habitats and in rivers and lakes in Chile, Argentina,
Uruguay, and Brazil (Figure 5). Their sister genus Basilichthys contains just four freshwater species, while Odontesthes contains 19 currently valid species (Eschmeyer and Fong 2017), seven marine and twelve freshwater, often only distinguishable by one or two known morphological characters (Dyer 2006). Phylogenetic studies of
Odontesthes were pioneered by Dyer (1997, 1998, 2006) based on morphology and electrophoretic characters (Figure 6A). Based on this evidence, all marine species in the genus except O. argentinensis (O. regia, O. gracilis, O. smitti, O. platensis, O. nigricans, and O. incisa) are placed in a nested phylogenetic position, while early speciation events gave rise to exclusively freshwater species. This hypothesis implies that freshwater habitats are the ancestral state for Odontesthes (plus its sister genus Basilichthys) and that a freshwater-to-marine transition is necessary to explain the distribution of marine species. A recent molecular phylogeny of Atheriniformes based on DNA sequences from seven nuclear genes and the mitochondrial cytochrome b gene (Campanella et al. 2015) reached the opposite conclusion (Figure 6B), instead implying several instances of marine dispersal and subsequent freshwater colonization by silversides. This pattern of frequent marine dispersal followed by freshwater colonization also was documented for other genera of atherinopsids, suggesting that it is a widespread feature of these fishes, an
33 interesting system in which to study the processes of speciation and diversification along the marine to fresh-water barrier (Bloom et al. 2013).
One group of Odontesthes defined on the basis of molecular characters contains marine O. argentinensis and several other freshwater species in northern Argentina,
Uruguay, and southern Brazil, that presumably diversified just in the last one million years (Beheregaray et al. 2002; Campanella et al. 2015). Speciation in the O. argentinensis species group has been rapid (Beheregaray et al. 2002), and gene flow among incipient species rampant (García et al. 2014), making their phylogenetic relationships and species boundaries difficult to disentangle. This is in contrast with long- isolated O. hatcheri, the only Odontesthes species endemic to Patagonian lakes and rivers, which has only recently hybridized with introduced O. bonariensis in the northern part of its range (Rueda et al. 2017). No studies to date have examined patterns of speciation and gene flow among the species distributed in southern Chile, including the freshwater O. mauleanum and O. brevianalis, and the marine O. regia and O. gracilis in the southern Pacific Ocean, which are closely related to O. smitti, occupying the southwestern Atlantic along the coast of Argentina. Interestingly, a previously described species no longer considered valid, O. weibrichi (de Buen 1953), is thought to have been a hybrid between O. regia and O. brevianalis (Dyer 2006), suggesting that this group may also have ongoing gene flow.
Here we use a broad survey of the mitochondrial cytochrome b (cytb) gene for twelve Odontesthes species to generate hypotheses about species boundaries and introgression that we then test with genome-wide RAD markers. We employ RAD markers to bring new resolution to the Odontesthes phylogeny, and test whether species
34 boundaries between morphologically described species that are indistinguishable in the mtDNA phylogeny can be separated with genomic data. We use BPP to test the enforced monophyly of different morphospecies using the topology obtained from the ddRADseq concatenated phylogeny, to see whether each node is supported as a speciation event.
Finally, we explore with nuclear data a pattern of marine introgression detected by mtDNA analysis in some freshwater Chilean populations. The combination of mtDNA and nuclear RAD markers provides a powerful tool to disentangle species limits and phylogenetic relationships among species in the face of past or ongoing gene flow across species boundaries.
Methods
Sample Collection and DNA Extraction
Silversides were collected via seine or gill nets between 2006 and 2014, and immediately euthanized by an MS-222 overdose, with fin clips preserved in 95% ethanol for later DNA extraction. Sampling localities in Argentina, Uruguay, Brazil, and Chile span the range of Odontesthes (Figure 6). Genomic DNA for cytochrome b (cytb) sequencing was extracted with a DNeasy Blood & Tissue Kit (Qiagen). Samples for RAD sequencing were extracted in 96-plate format via Autogen automated DNA extraction.
Odontesthes brevianalis and O. mauleanum were difficult to distinguish in the field, and are named here based on typical habitat, which is estuarine/riverine for O. brevianalis, and primarily lacustrine for O. mauleanum; these two species are separated by only one morphological character (Dyer 2006).
Cytochrome b Sequencing and Analysis
We used the forward primer GLU31 (Unmack et al. 2009) and the Odontesthes-
35 specific reverse primer Pej15929 (Conte-Grand et al. 2015) to amplify the target fragment of the cytb mitochondrial gene. The 12 µL PCR reaction contained 25 ng of
DNA, 0.25 mM of both the forward and reverse primers, 0.625 µL Taq DNA polymerase,
0.1 mM dNTPs, 1.25 µL of 25 mM MgCl2, and 1.25 µL of 10X reaction buffer.
Thermocycler conditions were as follows: 2 minutes at 94˚C; then 35 cycles of 94˚C for
30 seconds, 50.7˚C for 45 seconds, 72˚C for 1 minute; finally, 10 minutes at 72˚C. PCR products were purified on 96-well Excelapure plates (Edge Biosystems), and cycle sequenced using the same forward and reverse primers as the PCR reaction at the
Brigham Young University DNA sequencing center. Contigs were assembled from raw chromatograms in Sequencher v. 4.8 (Gene Codes Corp.), and then aligned in MAFFT v1.30b (Katoh and Standley 2013). Identical sequences were collapsed into single haplotypes with duplicate sequences removed before phylogenetic analysis.
Sequences were partitioned by codon and 100 maximum likelihood tree searches were conducted in RAxML v. 8.2 (Stamatakis 2014) under the GTRGAMMA model, with support values from 100 bootstrap replicates written to the best scoring tree. ddRAD-seq Sequencing and Assembly
We followed the protocol developed by Peterson et al. (Peterson et al. 2012), modified to use the enzymes MseI and PstI and a 350-550 bp size selection. Genomic libraries for 154 Odontesthes samples (Table 3) were prepared at the University of Puerto
Rico Sequencing and Genomics Facility. Pooled samples were sequenced on two lanes of a HiSeq 4000 at the University of Chicago Genomics Facility.
Sequences were demultiplexed, filtered, and assembled into RAD loci using ipyrad v. 0.7.2 (Eaton 2014). We used the default parameters for filtering, and the
36
‘reference’ assembly method, using the Odontesthes bonariensis genome (Campanella
2014) as the reference. We used two different thresholds, 30 and 50, for the minimum number of individuals to keep a particular locus, and discarded 11 individuals that had very few (<100) loci in either dataset. Additionally, because the O. bonariensis genome is still relatively fragmented, we assembled a dataset using the reference plus de novo method in ipyrad, which does an additional de novo assembly of reads that do not map to the genome. We enforced a minimum of 30 individuals for this assembly.
Phylogenetic Analysis and Species Delimitation
We used both concatenation and multi-species coalescent approaches to analyze ddRAD-seq data. Two matrices of concatenated ddRAD loci (with a minimum of 30 or
50 individuals per locus) were analyzed in ExaML (Kozlov et al. 2015) under the
GTRCAT model, with 100 bootstrap replicates. Unlinked SNPs (.u.snps output of ipyrad) were analyzed under the multispecies coalescent model implemented in SVDQuartets
(Chifman and Kubatko 2014) using PAUP* Version 4.0a (build 156) for Macintosh
(X86) (Swofford 2017).
We used the A10 algorithm of the program BBP (Yang and Rannala 2010) to test species boundaries on a reduced dataset of 1875 ddRAD loci and 42 taxa, representing all nominal species in our dataset. The topology inferred in ExaML was used as a guide tree
(Figure 2), with morphological species enforced as monophyletic lineages when necessary. Thus, O. regia and O. gracilis were considered sister species, to the exclusion of O. smitti; O. brevianalis (river populations RMAU and REL, see Figure 1) was sister to O. mauleanum (lake populations LLA and LCAL); O. ledae and O. perugiae were also considered sister species. The rjMCMC chain was run for 50,000 generations with a
37
5,000 generation burn-in, with four separate runs subsampling 500 loci per run. We also ran the program without sequence data to determine the effect of prior choices.
We tested for nuclear introgression after observing a discordant pattern in the mitochondrial DNA tree where some populations of O. mauleanum/brevianalis in southern Chile carried a cytb haplotype more closely related to O. regia/gracilis and O. smitti than to other O. mauleanum/brevianalis haplotypes. We used Patterson’s D statistic
(also known as the ABBA-BABA test) (Durand et al. 2011) to test whether there was a pattern of genomic introgression between the populations with the discordant haplotype for which we had ddRADseq data (Lago Llanquihue, Río Maullín), and the populations of O. regia, with O. smitti as the putatively ‘non-introgressing’ sister lineage. We calculated Patterson’s D statistic with the R package evobiR (Blackmon 2013), both including and excluding ambiguous sites, and assessed significance with 1000 bootstrap replicates. Because we tested all possible combinations of individuals, we used an alpha
= 0.00004 to determine significance to correct for multiple testing, using a Bonferroni correction. We also excluded tests with fewer than 20 ABBA-BABA biallelic sites.
Results
Mitochondrial DNA Survey
Our dataset for cytb sequences included 486 individuals representing 13 nominal species of Odontesthes and also included 23 sequences from its sister genus Basilichthys, and 5 from Atherinops, and Leuresthes belonging to Atherinopsini, the sister tribe to
Sorgentinini (Dyer and Chernoff 1996). Variation among DNA sequences was collapsed into 265 unique haplotypes for phylogenetic analysis. Odontesthes cytb sequences form a monophyletic group in the maximum likelihood tree separated into six well-supported
38 clades (99-100% bootstrap support; Figure 7). Marine Odontesthes incisa and O. nigricans are grouped together with strong support and form the sister-group to all other species in the genus Odontesthes. Relationships among all other haplotype clades are poorly supported (<70% bootstrap values), resulting in poor resolution for the species phylogeny. Most haplotypes from freshwater O. brevianalis or O. mauleanum were contained in a single well-supported haplogroup that showed no segregation of haplotypes according to species. However, individuals from a few populations of these nominal species in southern Chile, namely Lago Llanquihue (LLA) and Rio Pescado
(Figure 6, Figure 8) carried divergent mtDNA haplotypes that are more closely related to the marine species O. regia, O. smitti, and O. gracilis (Figure 7). Odontesthes regia and
O. gracilis individual haplotypes also fail to group according to morphospecies concepts, but O. smitti samples collected from geographically distant localities in the Atlantic basin
(Puerto Madryn (MADR) and Mar del Plata (MDP); Figure 6), form a monophyletic group (Figure 7).
Sequences obtained from Patagonian silversides (O. hatcheri) clustered into a distinct and well supported haplogroup, with the exception of some hybrid individuals that carried O. bonariensis haplotypes, most likely the consequence of recent introductions of the latter species into Patagonia (Rueda et al. 2017). Another well- supported clade includes haplotypes from six species associated with the Atlantic basin in eastern South America (marine O. argentinensis, and freshwater O. bonariensis, O. ledae, O. perugiae, O. humensis, and O. piquava). These species did not carry distinct mtDNA haplotypes and therefore their separation and phylogenetic relationships are not resolved in the cytb genealogy (Figure 7). Most of these freshwater species are sympatric
39 for at least part of their ranges (Figure 6). ddRADseq species phylogeny
Genomic libraries of RAD loci were obtained and sequenced for 154 individuals.
Using the ‘reference’ assembly pipeline in ipyrad, we assembled two matrices from the raw ddRAD reads. The first was compiled with a minimum of 30 individuals per locus, resulting in 33,191 loci (Figure 9). A second matrix was compiled to minimize missing data by increasing the constraint to a minimum of 50 individuals per locus, resulting in
4,956 loci meeting this condition (Figure 10). Additionally, a third matrix was assembled that also enforced a minimum of 30 individuals, but employed the reference plus de novo assembly method in ipyrad, which resulted in 35,536 ddRAD loci (Figure 11). In all cases, loci were concatenated for phylogenetic analyses under ML. Resulting phylogenies based on the three matrices produced almost identical results, resolving with confidence relationships for all major groups (Figure 7), although some relationships among individuals within these groups were different. Phylogenies obtained via SVDQuartets also were largely congruent with ML topologies, with some differences discussed below.
The phylogeny resolved by RAD data differs significantly from the topology obtained with mtDNA by clearly separating most nominal species into their own clades
(with some exceptions discussed below) and by resolving their phylogenetic relationships with confidence. Support values for the relationships among mtDNA haplotype clades were generally low (< 70%). In agreement with the mtDNA genealogy, the RAD phylogenies resolve O. incisa as the sister group of all other species in the genus (no ddRAD data were obtained for O. nigricans). The remaining Odontesthes species split into two groups, mostly corresponding to geography, both by concatenation (Figure 7),
40 and under the multispecies coalescent model implemented in SVDQuartets
(Supplemental Figures 5,6). A mostly Pacific basin clade (from localities west of the
Andes) contains the two freshwater Chilean species O. brevianalis and O. mauleanum and the marine O. regia and O. gracilis, plus O. smitti from Atlantic localities (MADR and SUR). The nominal species O. mauleanum and O. brevianalis do not form separate clades in either concatenation or multispecies coalescent trees, but some structure grouping individuals from the same collection localities was observed in trees obtained by concatenation. Individuals from Lago Llanquihue that carried the marine O. regia/gracilis mtDNA haplotype, were grouped by the RAD data with other freshwater populations of O. mauleanum and O. brevianalis with high support. Individuals of O. smitti from the marine Atlantic localities form a clade that is sister to a clade containing interspersed O. regia and O. gracilis individuals (no separation of these two species is resolved in any of our analyses). In the SVDQuartet analysis of 33,191 SNPs (from loci assembled against the reference genome), O. smitti is nested within a larger O. regia/gracilis clade (Figure 12), although reducing the amount of missing data to a set of
4,956 SNPs achieves the same result as concatenation (Figure 13).
An Atlantic basin clade (excluding O. smitti) contains O. hatcheri sister to the O. argentinensis species group, a finding also obtained with ExaML and SVDQuartets analyses. In stark contrast to the cytb genealogy that does not differentiate morphological species, analyses of genome-wide ddRADseq data clearly delineate O. argentinensis and
O. bonariensis into reciprocally monophyletic groups, although O. perugiae and O. ledae do not come out entirely monophyletic and only one individual of O. humensis was available (Figure 7).
41
Species Delimitation under the Multispecies Coalescent
BPP did not support a model where all morphological species were independent lineages. With >0.99 posterior probability, in two of four runs the highest support was found for a model that collapsed the node separating O. regia and O. gracilis; the node separating O. mauleanum and O. brevianalis; and the node separating O. perugiae and O. ledae. Collapsing these nodes is consistent with the finding that these taxa were not monophyletic in concatenation or multispecies coalescent analyses. Another run converged on a model that also collapsed the node separating O. smitti from O. regia/gracilis, and the other did not collapse the node between O. ledae and O. perugiae.
Still, O. regia/gracilis, and O. brevianalis/mauleanum were not supported as separate lineages in any analysis. Running BPP on prior information only (without sequence data) did not converge on any model, suggesting that the prior choices were not significantly affecting the results.
Introgression between freshwater (O. brevianalis/mauleanum) and marine species
The mitochondrial haplotypes of individuals collected in Lago Llanquihue did not cluster with other O. brevianalis/mauleanum haplotypes, but with haplotypes of the marine species O. regia in a haplogroup that also contains O. gracilis and O. smitti
(Figure 7). Using Patterson’s D statistic, we tested whether these individuals O. brevianalis/mauleanum that carry the “marine haplotype” also carried an excess of nuclear RAD alleles shared with O. regia individuals (here we included O. gracilis individuals from the Juan Fernandez Islands, which do not appear to be a separate lineage from O. regia, Figure 7). These tests did not result in any significant signal of introgression, given the large number of tests and conservative Bonferroni correction.
42
However, several individuals from Lago Llanquihue and one individual from Rio Maullín had near significant tests. These localities are close to marine environments, and the individuals from Lago Llanquihue have the more ‘marine’ cytochrome b haplotype.
Discussion
Phylogenetic Resolution with Genome-Wide Data
Odontesthes silversides seem to have speciated rapidly since the end of the
Miocene (Campanella et al. 2015), resulting in a dearth of morphological characters to distinguish species and challenging the resolution of phylogenetic relationships. For cases like this, high throughput sequencing technology may provide unprecedented resolution, as shown by a study of previously intractable species flocks in Lake Victoria cichlids
(Wagner et al. 2013). It has been suggested that O. argentinensis and O. bonariensis exhibit genetic diversity in PCR-based markers more typical of intraspecific variation than interspecific variation (Heras and Roldán 2011), and that gene flow may be rampant among freshwater and marine species in the O. argentinensis species group (García et al.
2014). Intermediate morphological phenotypes between O. argentinensis and O. bonariensis have been documented in coastal Argentina at Mar Chiquita (González-
Castro et al. 2016), but most of the evidence to support these views was based on indistinguishable mtDNA haplotypes among species (as shown in Figure 7). However, comparison of gill transcriptomes of O. argentinensis and O. bonariensis revealed significant gene expression differences and many non-synonymous substitutions that clearly differentiate the two species (Hughes et al. 2017). Many, though certainly not all, morphological characters that differentiate species are related to tooth and gill raker differences. Differences in gill raker morphology and meristic counts have been tied to
43 differences in feeding ecology in other fish species (Wund et al. 2008; Kahilainen et al.
2011)
Mitochondrial markers and genome-wide transcriptomic or nuclear ddRAD data provide different (complementary) kinds of information on the relationships among
Odontesthes species. In contrast to the mtDNA phylogeny, ddRAD data provide significantly more resolution to separate species and infer their relationships (Figure 7).
Double-digest RAD data are able to distinguish different lineages in the O. argentinensis species group (O. argentinensis, O. humensis, O. bonariensis, O. ledae/perugiae) that display no differentiation in their mitochondrial haplotypes (Figure 6), and whose relationships have long been difficult to determine with genetic data (García et al. 2014;
Campanella et al. 2015; Díaz et al. 2016). These results are somewhat similar to a phylogeny (Figure 5B) obtained with seven conserved nuclear markers and cytb that included many of the same lineages but sampled only one individual per species
(Campanella et al. 2015). The tree with genome-wide RAD data presented here, however, differs significantly in the relationships of O. hatcheri, the Patagonian silverside. The ddRADseq tree places this species as the sister group to the O. argentinensis species group, while other studies (and the mtDNA genealogy) suggested greater affinity between
O. hatcheri and O. smitti and related taxa occupying western South America (Heras and
Roldán 2011; Campanella et al. 2015), though that grouping was always poorly supported. There is almost no congruence between molecular studies and the relationships obtained with morphology (Figure 5B) (Dyer 2006).
Biogeographic Implications
Unlike their strictly freshwater sister genus Basilichthys, Odontesthes species
44 inhabit both marine and freshwater habitats. Many species in Odontesthes appear to be relatively euryhaline (Tsuzuki et al. 2001; Vigliano et al. 2006; Hughes et al. 2017), and some marine species show genetic structure along salinity gradients in estuaries
(Beheregaray and Sunnucks 2001). The oldest Odontesthes fossil dates to the early
Miocene at 20 million years old (Cione and Báez 2007), but the crown Odontesthes clade started to diverge approximately five million years ago (Campanella et al. 2015). This date is considerably younger than the last major marine incursions in the late Miocene inundating areas now occupied by freshwater Odontesthes populations. Based on the morphological phylogeny of this genus, it was hypothesized that Odontesthes were primary freshwater fish, having invaded marine habitats only secondarily (Dyer 2006).
But transitions from freshwater to marine environments are quite rare events in the fish tree of life (Betancur-R et al. 2015), and ancestral area reconstruction under the DEC model (Ree and Smith 2008) for Atheriniformes based on a molecular phylogeny did not support a primary freshwater origin (Campanella et al. 2015). Excluding the two marine species O. nigricans and O. incisa, our ddRAD phylogeny would imply three invasions of freshwater by marine ancestors: (i) when O. mauleanum/brevianalis occupied southern
Chile, (ii) when O. hatcheri invaded Patagonia, and (iii) when freshwater members of the
O. argentinensis species group colonized the Paraná-Uruguay watershed, the Pampas region and coastal drainages along Uruguay and southern Brazil. While it has been suggested that the marine species O. argentinensis spawned a localized species radiation in the coastal freshwater lagoons of southern Brazil that includes O. perugiae, O. ledae, and several other species (Beheregaray et al. 2002), our results from ddRADseq suggest that these freshwater populations are more closely related to the freshwater species that
45 occupy the Paraná/Rio de a Plata basin and drainages in the Pampas region to the south
(O. bonariensis, O. perugiae from the Paraná basin), than to O. argentinensis directly.
This suggests a single invasion into fresh water by O. argentinensis that radiated into many species in northern Argentina, Uruguay, and southern Brazil--unlike the freshwater invasions in southern Chile and Patagonia that only produced a single freshwater species.
In addition to salinity, temperature also appears to be correlated with biogeographic patterns in Odontesthes. The subfamily Atherinopsinae to which
Odontesthes belongs has an anti-tropical distribution (White 1986), with Basilichthys and
Odontesthes living in temperate South American waters as far south as Tierra del Fuego, and the tribe Atherinopsini inhabiting temperate Pacific waters in North America.
Odontesthes regia has the farthest extending northward range, reaching southern Peru
(Figure 2), but upwelling makes these marine waters reasonably cool. On the Atlantic coast, few marine species except O. argentinensis range further north than the Rio de la
Plata estuary. The Brazil Current runs just north of this estuary, bringing warmer tropical waters with it. Only O. argentinensis occupies these warmer waters, and the freshwater species that branch after this lineage invaded freshwater habitats (O. humensis, O. bonariensis, O. perugiae, O. ledae; and others not included in this study) also occupy the warmest freshwater habitats, in contrast to their cold-water adapted relative O. hatcheri in
Patagonia. Odontesthes bonariensis has a notable relationship with temperature as it has temperature-dependent sex determination (TSD) (Strussmann et al. 1996; Fernandino et al. 2013), which O. hatcheri lacks. Whether the other closely related species in the O. argentinensis species group have TSD is currently unknown.
Species boundaries and taxonomic implications
46
Mitochondrial DNA does not clarify species boundaries among Odontesthes, and several haplogroups contain multiple morphologically described species (Figure 7). In some cases, ddRAD data also fails to distinguish these species as monophyletic.
Odontesthes regia and O. gracilis form a monophyletic group, but O. gracilis individuals from the Juan Fernandez Islands are interspersed among O. regia individuals collected along the coast of Chile. While BPP seems to find support for different models of species delimitation in Odontesthes, these two species are never supported as independent lineages. Taken together, the evidence does not seem to support these as ‘independently evolving metapopulations’ under the generalized lineage species concept (De Quieroz
2007), and therefore we consider O. gracilis as a junior synonym of Odontesthes regia
(Humboldt and Valenciennes 1821). Likewise, BPP never supports the separation of O. mauleanum and O. brevianalis into separate lineages, even though these taxa do show some structure by locality in the concatenated ddRAD phylogeny, and BPP may be prone to delimiting population structure (Sukumaran and Knowles 2017). Therefore we also consider O. mauleanum as a junior synonym of Odontesthes brevianalis (Günther 1880).
Regarding the status of O. smitti, it is not possible to reach a conclusion with the data analyzed in this study, since O. smitti specimens were sampled from the Atlantic basin in geographically distant localities from southern Chile, where the O. regia samples were collected. The genetic distinctiveness and monophyly of the O. smitti individuals in the
RAD and mtDNA genealogies could reflect a true species boundary or a signature of population structure due to isolation by distance among populations of the same species.
Additional sampling towards the southern reaches of both species’ geographical ranges is necessary to determine their taxonomic status.
47
In contrast to these cases, ddRAD data bring resolution to the O. argentinensis species group, where mitochondrial haplotypes fail to differentiate morphological species. Odontesthes argentinensis, O. humensis (though we were limited to just one individual), and O. bonariensis all separate into independent lineages. Odontesthes perugiae and O. ledae present a more complex case, as many more species are thought to occupy the coastal lakes and lagoons of Brazil that are not represented here. One sample of O. perugiae from the Paraná basin branches more deeply from the samples of O. perugiae and O. ledae from the Laguna dos Patos and Tramandaí systems in Brazil.
Dense sampling of the species that occupy this range is necessary to fully determine whether they represent independently evolving lineages, where speciation is thought to have occurred multiple times in the last 120,000 years (Beheregaray et al. 2002).
Utility of mtDNA for detecting introgression
Mitochondrial DNA is notorious for crossing species boundaries and is generally expected to be less prone to incomplete lineage sorting (ILS) because the reduced effective population size should cause polymorphisms to sort out more quickly than in nuclear DNA (Sloan et al. 2017). The topology obtained with cytb sequences differs significantly from the relationships obtained with genome-wide nuclear DNA. This difference may be explained by ILS, ancient introgression, or by gene tree estimation error likely to affect the relatively small cytb dataset (1116 bp). The RAD topology obtained with SVDquartet analysis is similar to that obtained by ML on the concatenated data, suggesting that ILS is not biasing the species tree inference and that gene-tree estimation error on the cytb data is a more likely explanation.
Our broad survey of cytb sequences for some species, however, uncovered an
48 interesting pattern of genealogical discordance (Figure 7) involving freshwater populations of O. brevianalis in southern Chile. We hypothesize that this pattern is most likely caused by mitochondrial capture of the marine haplotype following a marine incursion or the invasion of marine O. regia into freshwater habitats. This “marine haplotype” is most common in Lago Llanquihue (LLA) and associated drainages, which was the site of one of the last glaciations in the Pleistocene in this region (Rabassa and
Clapperton 1990), and the recession of this glacier might have caused a temporary link with the ocean before post-glacial rebound. The signal for nuclear introgression in some
Lago Llanquihue individuals is weak in contrast to the strong signal in mitochondrial data. This is the expected pattern, however, since mitochondrial DNA does not easily recombine.
Furthermore, our tests had relatively low power to detect nuclear introgression, given the high amount of missing data in RADseq and the large number of tests necessary to incorporate multiple individuals (Eaton and Ree 2013). While these tests were not statistically significant, a few individuals had near-significant nuclear introgression (Table 4). One Rio Maullín (RMAU) individual that did not carry the marine haplotype in our survey was one of the individuals that had near-significant nuclear introgression, though a second individual appears to belong to O. regia, rather than O. brevianalis, clearly clustering with O. regia in all of our ddRAD phylogenies.
The other individuals that had near-significant tests were from Lago Llanquihue, where many individuals have the more marine mitochondrial haplotype. Taken together, these results suggest that patterns of gene flow and introgression may be complex in freshwater habitats close to the sea, and that the Odontesthes model may provide an interesting
49 system to further explore cases of divergence with gene flow.
Acknowledgements
Collection of materials for this project was possible only due to the effort of numerous colleagues and students who participated in field trips, including J. Johnson
(BYU), B. Dyer, and D. Ruzzante (Dalhousie). Funding for this project was supported in part by NSF grants (OISE-0530267 and DEB-1457426) to G.O. and an award (Programa
RAICES, PICT #35241) from the Agencia Nacional de Investigación Científica y
Tecnológica (Argentina) to G.O.,V.C., and Daniel Ruzzante, and start-up funds from the
UPR to R. Betancur-R.
50
A (Dyer 1997, 2006)
B (Campanella et al 2015)
Figure 5 – Phylogenetic hypotheses based on analysis of (A) 123 morphological characters and (B) seven nuclear markers and cytochrome b (6,432 bp).
51
Figure 6: Sampling localities for ddRAD samples and approximate geographic distribution ranges of Odontesthes species. Population codes are explained in Table 3. Range of O. nigricans is included, though this species only had cytochrome b.
52
Figure 7: Comparison of cytochrome b genealogy and ddRAD concatenated phylogeny. The tree on the left is the ML phylogeny obtained with RAxML for 265 unique cytb haplotypes (1,116 bp). The complete tree with labeled tips is shown in Supplementary Figure 1. The tree on the right is the species tree based on ML analysis of concatenated RADseq data assembled with the O. bonariensis reference genome (33,191 concatenated ddRAD loci, 6,395,288 bp). The complete RAD tree with labeled tips is shown in Supplementary Figure 2.
53
Leuresthes_tenuisJQ282032 Atherinopsini Leuresthes_KLM04 Atherinopsis_califJQ282018 Atherinops_affKM400705 Atherinops_SIO07n157 BsemotilusANSP4404 AVM4407 BsemotilusANSP4406 B. semotilus MAI54 Basilichthys RAP35 MAT01 ILL13 RITA800 BIO800 BIO801 ULE04 RBUE505 CHOL01 B. microlepidotus/ CRU19 LPAN91 B. australis Complete ML tree for 293 cytochrome b haplotypes IMP01 RTOL07 inferred in RAxML, with tip labels ELQ01 ILL04 (shown without tip labels in Figure 3) ALI023 NIL02 ILL14 ULE35 MAR_24 MAR12 O. incisa SCZ03 SCZ04 TF04 TF05 SCZ06 SCZ07 SCZ01O. nigricans SCZ02 SCZ09 Odsp001 TOP51 LCAL05 CALA01 CHOL28 CRUE40 BUD03 Sorgentinini CRU31 RITA532 H326_3 TEN31 COB05 H323_3 BTA11 COS04 HUI501 REL34 QUE273 BUD07 BUD04 H244_Omauleanum15 BUD08 RMAU345 RMAU327 IMP502 NIL74 H318_RAQ2 LAR08 TOP53 H316_Obrevianalis3 RMAU337 RMAU330 O. mauleaum/ IMP501 RMAU334 O. brevianalis RMAU349 RMAU339 COS03 H333_RAQ2 H331_LAR2 BTA07 H330_COB2 COB08 TOP55 COS02 Odontesthes NIL73 RMAU348 LOA01 RMAU344 RMAU329 RMAU325 RMAU323 HUI500 RMAU343 RMAU336 H182_Omauleanum2 PESC017 H125_omauleanum5 PESC04 H180_Omauleanum2 PESC028 PESC006 RLPU03 BOCA06 BUCEO341 TEC832B TEC833S RLD12 TEC833I TEC837 RLPU04 RLD11 RLTA06 RLPA05 H213_3 RLPA07 H214_Obona2 RLPU09 RLD20 BUCEO342 RLD4M BUCEO339 RLD2 ELCOND08 BOCA09 RLTA08 TEC915A TEC915B TEC913C TEC913D TEC913B O. argentinensis/ BOCA08 RLD01 O. bonariensis/ TEC833A O. perugiae/ TEC832A BOCA01 O. ledae/ BUCEO33 ELCOND01 O. piquava RLPA06 H230_Obona3 BOCA03 RLD2M H8_Ohatcheri2 NIHL028 RL03 RLPU01 RLC02 RV05 TEC358 AND26 H219_Obona2 NIHL025 PELE16 CDP02 PELE07 H7_Obona19 TEC420C D6 ULLM01 TEC420A Obonaerensis RLPA08 RLPA02 CHU15 H266_Ohatcheri2 RL14 ROS04 EPU06 H93_Ohatcheri8 EPU001 EPU08 MUS06 ESM33 H11_Ohatcheri63 MIT003 MUS002 MUS15 AME13 MUS14 PMON001 URRE06 H165_Ohatcheri2 MUS09 CHU002 PLOTT03 CARI03 H9_Ohatcheri2 ESM37 ESM36 LGCBJ03 LBA12 H6_Ohatcheri3 H164_Ohatcheri2 MIT002 PELE05 VREG03 H5_Ohatcheri10 URRE04 MUS11 H148_Ohatcheri2 MUS001 H144_Ohatcheri2 ANT01 O. hatcheri PUY001 RIV001 RIV002 PELE14 CHOEL05 H37_Ohatcheri5 PELE24 CHOEL01 VREG04 CEAN06 CEAN02 H161_Ohatcheri13 PELE12 CEAN03 CARI02 H212_Ohatcheri3 H71_Ohatcheri3 H168_Ohatcheri2 CEAN01 CDP17 CDP35 CDP013 CDP01 CDP16 MAR_08 MADR009 MADR006 MADR004 MADR002 O. smitti MAR_02 MADR005 PMON02 CHAI027 PMON10 H334_2 QUI06 PMON03 PESC012 PESC016 LLA507 LLA152 H120_Omauleanum6 H127_Omauleanum2 PESC024 LLA506 O. regia/ LLA509 PESC022 O. mauleaum/ LLA150 PESC010 O. brevianalis LLA157 H121_Omauleanum4 PESC025 LLA500 H116_Omauleanum2 LLA505 BTA09 CHAI023 H54_Oregia2 CHAI008 CHAI009 TOP54 CHAI001 JUAN05 CHAI05 GONZ15 CHAI04 RMAU346 PMON07 CHAI007 CHAI016 CHAI010 CHAI029 PMON01 O. regia/ CHAI015 H61_Oregia2 O. gracilis/ CHAI03 CHAI006 O. brevianalis? RLIN285 CHAI021 H49_Oregia2 H107_Oregia3 GONZ16 CHAI019 CHAI014 RMAU331 PMON05 PMON09 RMAU351 RLIN284 H59_Oregia4 H57_Oregia4 CHAI018 0.03
Figure 8: Complete ML tree for 293 cytochrome b haplotypes inferred in RAxML.
54
MAS_660_ 100 MAS_661_ 5 6 MAS_662_ O. incisa PUY_11_ O. hatcheri PUY_16_ 10PUY_190 _ 2PUY_71 _ 3 5 6PUY_202 _ PUY_3_ 1PUY_139 _ Complete ML tree for 33,191 concatenated ddRAD loci (6,395,288 bp), 3 3 2PUY_188 _ PUY_4_ all assembled against the reference O. bonariensis genome, with at 2 0 PUY_1_ least 30 individuals sequenced per locus, inferred in ExaML 1PUY_147 _ PUY_15_ 5416 PUY_10_ 3 3 PUY_8_ 1 5 PUY_12_ ELC_2_ 100 ELC_9_ 9 83 3 ELC_14_ 5 4 ELC_13_ 4 8 ELC_4_ 4 1 100 ELC_3_ MDP_1434_ 1 9 MIR_9_ 5 6 MDP_1440_ O. argentinensis 4 7 MIR_4_ 1 2 MIR_6_ 1 8 MDP_1436_ 2 4 MDP1443_ 1 1 MIR_5_ 5 100 MDP_1439_ 1 6 MIR_2_ 1 4 PQ_2216_ 2 2 MIR_11_ RPP_1395 O. humensis RPAR_240_ 7 0 RPAR_239_ 10RPAR_2410 _ 5 1CHAS_332_ CHAS_215_ 100 3 8 6 9 CHAS_214_ CHAS_324_ 2296 O. bonariensis CHAS_318_ CHAS_319_ 1200 CHAS_323_ 100 1 6 CHAS_201_ 3 7 CHAS_325_ 8 CHAS_216_ 7 4CHAS_331_ 3 8 CHAS_322_ RPLP_1298_ LRO_2553_ 100 LDP_H_ LDP_L_ 6 8 LDP_J_ 100 574 LDP_E_ 1 9 LDP_D_ 5 2 LDP_A_ O. perugiae/ 100 5 7 LDP_M_ 9 8 1 5 O. ledae LDP_C_ 4 7 LDP_S_ LRO_2552_ LFA_4_ 1 1 2 9 LRO_2557_ LDP_I_ 3 4 6 LRO_2556_ 0 LRO_2555_ 3 2 8 LRO_2558_ LFA_1_ 0 LRO_2551_ 5 LRO_2559_ 8 LFA_2_ 2 2 LRO_2550_ MADR_6_ 100 MADR_2_ MADR9_ 6 45 5 SUR_679_ O. smitti 4 5 SUR_676_ 7 0 100 MADR_5_ CHAI10_ CHAI20_ 5 JUAN_10_ 0 100 CHAI02_ 4 5 CHAI03_ CHAI13_ 7 5 CHAI15_ 4 CHAI01_ CHAI12_ 0 1 0 TOP_54_ 2 2 RMAU_351_ PMON_05_ O. regia/ 6 CHAI16_ 0 O. gracilis 2 CHAI04_ 1 4 PMON_08_ 3 1 CHAI05_ 0 JUAN_12_ 1 1 CHAI17_ 6 CHAI11_ 7 100 CHAI09_ 0 PMON_07_ 2 5 CHAI19_ 3 CHAI06_ 1 JUAN_13_ 2 0 CHAI14_ 1 9 PMON_10_ HUI_501_ 2 4 HUI_504_ HUI_505_ 4 0 5 4TOP_55_ REL_32_ 3 14 6REL_35_ 2 8REL_34_ 3 5 TOP_60_ 1 5 RMAU_336_ 2 3RMAU_339_ 2 7 6 3RMAU_344_ RMAU_345_ 2 6RMAU_334_ 1003HUI_5022 _ 4 5 RMAU_329_ LCAL_08_ LCAL_27_ 102 70 LCAL_03_ O. brevianalis/ 6LC4 AL_17_ O. mauleanum 1LC1 AL_29_ 5LCAL_05_ 3LCAL_30_ 1LC6 AL_20_ 8 7 9LCAL_22_ 4LCAL_11_ 9LCAL_06_ 2 2 LCAL_14_ LLA_152_ LLA_505_ 100 LLA_157_ 3LLA_500_ 82 1 LLA_513_ LLA_155_ 4 7 LLA_509_ 1 4 LLA_154_ 1 LLA_150_ 6LLA_151_ 2 1 4LLA_156_ LLA_502_ 4LLA_504_ 1 4LLA_518_ 1 1 LLA_507_ 0.003
Figure 9: Complete ML tree for 33,191 concatenated ddRAD loci (6,395,288 bp), all assembled against the reference O. bonariensis genome, with at least 30 individuals sequenced per locus, inferred in ExaML. For tip label in formation see Table 3.
55
MAS_662_ MAS_661_ O. incisa MAS_660_ PUY_19_ O. hatcheri PUY_7_ PUY_20_ Complete ML tree for 4,956 concatenated ddRAD loci (964,810 bp), PUY_16_ all assembled against the reference O. bonariensis genome, with at PUY_3_ least 50 individuals sequenced per locus, inferred in ExaML PUY_11_ PUY_13_ PUY_1_ PUY_18_ PUY_4_ PUY_8_ PUY_12_ PUY_15_ PUY_14_ PUY_10_ MDP_1439_ MIR_6_ MDP1443_ MIR_2_ MDP_1434_ ELC_2_ ELC_13_ ELC_14_ O. argentinensis ELC_9_ ELC_3_ MIR_5_ MIR_4_ MIR_9_ PQ_2216_ MIR_11_ ELC_4_ MDP_1436_ RPP_1395 O. humensis RPAR_241_ RPAR_239_ RPAR_240_ CHAS_324_ CHAS_319_ CHAS_201_ CHAS_323_ CHAS_332_ CHAS_214_ CHAS_215_ O. bonariensis CHAS_331_ CHAS_216_ CHAS_325_ CHAS_322_ CHAS_318_ RPLP_1298_ LRO_2553_ LDP_D_ LDP_H_ LDP_J_ LDP_L_ LDP_E_ LDP_S_ LDP_C_ O. perugiae/ LDP_A_ O. ledae LDP_M_ LRO_2552_ LRO_2551_ LFA_4_ LDP_I_ LRO_2557_ LRO_2555_ LRO_2556_ LRO_2558_ LFA_2_ LRO_2550_ LRO_2559_ LFA_1_ MADR_2_ SUR_679_ MADR_5_ O. smitti MADR9_ SUR_676_ CHAI16_ CHAI15_ PMON_08_ CHAI04_ JUAN_13_ CHAI01_ PMON_05_ CHAI02_ CHAI03_ PMON_10_ CHAI14_ CHAI10_ CHAI09_ CHAI05_ O. regia/ TOP_54_ O. gracilis CHAI12_ CHAI13_ CHAI20_ RMAU_351_ CHAI11_ JUAN_12_ JUAN_10_ CHAI06_ CHAI19_ LCAL_29_ LCAL_05_ LCAL_27_ LCAL_06_ LCAL_08_ LCAL_11_ LCAL_20_ LCAL_30_ LCAL_17_ LCAL_14_ LCAL_03_ LCAL_22_ HUI_504_ TOP_55_ REL_35_ TOP_60_ REL_34_ REL_32_ HUI_505_ RMAU_334_ O. brevianalis/ RMAU_336_ O. mauleanum RMAU_344_ RMAU_345_ RMAU_329_ RMAU_339_ LLA_150_ LLA_504_ LLA_507_ LLA_509_ LLA_155_ LLA_157_ LLA_500_ LLA_156_ LLA_518_ LLA_505_ LLA_513_ LLA_502_ LLA_152_ LLA_151_ LLA_154_ 0.002
Figure 10: Complete ML tree for 4,956 concatenated ddRAD loci (964,810 bp), all assembled against the reference O. bonariensis genome, with at least 50 individuals sequenced per locus, inferred in ExaML. For tip label information see Table 3.
56
MAS_660_ MAS_662_ MAS_661_ O. incisa PUY_1_ PUY_6_ O. hatcheri PUY_11_ PUY_13_ PUY_7_ PUY_20_ Complete ML tree for 35,536 concatenated ddRAD loci (6,804,759 bp), which included PUY_3_ both reference and de novo assembled sequences, with a minimum of 30 individuals s PUY_18_ PUY_16_ equenced per locus, inferred in ExaML PUY_4_ PUY_19_ PUY_14_ PUY_12_ PUY_15_ PUY_8_ PUY_10_ MDP_1434_ MIR_6_ ELC_4_ ELC_2_ ELC_9_ ELC_14_ ELC_13_ ELC_3_ MDP_1436_ O. argentinensis MIR_9_ MIR_2_ PQ_2216_ MDP_1440_ MIR_4_ MIR_5_ MDP1443_ MDP_1439_ MIR_11_ RPP_1395 O. humensis RPAR_239_ RPAR_240_ RPAR_241_ CHAS_216_ CHAS_331_ CHAS_325_ CHAS_323_ CHAS_318_ O. bonariensis CHAS_319_ CHAS_322_ CHAS_324_ CHAS_214_ CHAS_215_ CHAS_201_ CHAS_332_ RPLP_1298_ LRO_2553_ LDP_L_ LDP_A_ LDP_C_ LDP_S_ LDP_E_ LDP_M_ LDP_H_ LDP_D_ O. perugiae/ LDP_J_ LDP_I_ O. ledae LFA_4_ LFA_2_ LRO_2557_ LRO_2559_ LRO_2550_ LRO_2556_ LRO_2552_ LFA_1_ LRO_2551_ LRO_2558_ LRO_2554_ LRO_2555_ MADR_4_ MADR_6_ SUR_679_ MADR9_ MADR_5_ O. smitti SUR_676_ MADR_2_ RMAU_351_ PMON_10_ JUAN_12_ JUAN_10_ CHAI14_ PMON_08_ CHAI15_ CHAI20_ TOP_54_ TOP_58_ CHAI02_ CHAI01_ PMON_07_ CHAI19_ CHAI10_ CHAI11_ CHAI09_ O. regia/ CHAI17_ O. gracilis CHAI06_ CHAI05_ CHAI12_ CHAI03_ CHAI13_ CHAI16_ PMON_05_ CHAI04_ JUAN_13_ LCAL_17_ LCAL_29_ LCAL_11_ LCAL_14_ LCAL_20_ LCAL_30_ LCAL_22_ LCAL_05_ LCAL_08_ LCAL_03_ LCAL_27_ LCAL_06_ HUI_505_ HUI_504_ TOP_55_ TOP_60_ REL_32_ REL_34_ HUI_501_ REL_35_ RMAU_339_ RMAU_336_ O. brevianalis/ RMAU_344_ O. mauleanum RMAU_345_ RMAU_329_ RMAU_334_ HUI_502_ HUI_503_ LLA_155_ LLA_154_ LLA_151_ LLA_509_ LLA_152_ LLA_156_ LLA_504_ LLA_518_ LLA_505_ LLA_150_ LLA_157_ LLA_500_ LLA_513_ LLA_507_ LLA_502_ 0.003
Figure 11: Complete ML tree for 35,536 concatenated ddRAD loci (6,804,759 bp), which included both reference and de novo assembled sequences, with a minimum of 30 individuals sequenced per locus, inferred in ExaML. For tip label information see Table 3.
57
MAS_661 MAS_660 MAS_662 O. incisa PUY_18 SVDQuartets tree based on 33,191 unlinked SNPs PUY_1 PUY_3 PUY_4 PUY_19 PUY_13 PUY_16 PUY_7 PUY_11 O. hatcheri PUY_15 PUY_12 PUY_20 PUY_10 PUY_14 PUY_8 MDP_1439 MIR_2 MIR_4 PQ_2216 MIR_11 MIR_6 MDP_1434 MIR_5 MDP1443 O. argentinensis MDP_1436 MDP_1440 MIR_9 ELC_4 ELC_2 ELC_13 ELC_9 ELC_14 ELC_3 RPP_1395 O. humensis CHAS_216 CHAS_332 CHAS_319 RPAR_239 CHAS_201 CHAS_215 CHAS_214 O. bonariensis CHAS_324 CHAS_331 CHAS_323 CHAS_322 RPAR_240 RPAR_241 CHAS_318 CHAS_325 RPLP_1298 LFA_4 LDP_J LDP_C LDP_H LDP_D LDP_E LDP_S LDP_L O. perugiae/ LDP_A LDP_I LDP_M O. ledae LRO_2557 LRO_2550 LFA_2 LRO_2552 LRO_2559 LRO_2556 LFA_1 LRO_2553 LRO_2551 LRO_2555 LRO_2558 CHAI17 PMON_10 JUAN_13 PMON_05 JUAN_12 O. regia/ PMON_07 RMAU_351 O. gracilis JUAN_10 MADR_6 MADR_2 MADR9 SUR_679 MADR_5 O. smitti SUR_676 CHAI15 CHAI02 CHAI19 CHAI14 CHAI05 CHAI16 CHAI10 CHAI20 TOP_54 CHAI13 O. regia CHAI12 CHAI06 CHAI09 PMON_08 CHAI04 CHAI03 CHAI11 CHAI01 LCAL_14 LCAL_03 LCAL_05 LCAL_06 LCAL_11 LCAL_17 HUI_501 LCAL_08 REL_35 HUI_504 HUI_502 RMAU_334 REL_32 REL_34 HUI_505 RMAU_345 RMAU_336 RMAU_329 O. brevianalis/ RMAU_339 RMAU_344 O. mauleanum TOP_55 TOP_60 LCAL_20 LCAL_29 LCAL_30 LCAL_22 LCAL_27 LLA_509 LLA_155 LLA_518 LLA_502 LLA_504 LLA_505 LLA_507 LLA_152 LLA_500 LLA_154 LLA_513 LLA_157 LLA_151 LLA_150 LLA_156
200.0
Figure 12: SVDQuartets tree based on 33,191 unlinked SNPs. For tip label information see Table 3.
58
MAS_662 MAS_660 O. incisa MAS_661 SVDQuartets tree based on 4,956 unlinked SNPs PUY_18 PUY_11 PUY_3 PUY_1 PUY_8 PUY_20 PUY_4 O. hatcheri PUY_10 PUY_7 PUY_13 PUY_16 PUY_12 PUY_19 PUY_14 PUY_15 MDP_1439 ELC_3 MDP1443 ELC_9 PQ_2216 MDP_1436 MIR_11 MIR_5 MIR_4 O. argentinensis MIR_6 MIR_9 ELC_4 MDP_1434 ELC_13 ELC_2 ELC_14 MIR_2 RPP_1395 O. humensis CHAS_215 CHAS_214 CHAS_332 CHAS_331 RPAR_239 RPAR_240 RPAR_241 CHAS_323 O. bonariensis CHAS_201 CHAS_324 CHAS_216 CHAS_318 CHAS_319 CHAS_322 CHAS_325 RPLP_1298 LFA_1 LRO_2551 LRO_2558 LRO_2553 LRO_2555 LRO_2550 LRO_2552 LDP_M O. perugiae/ LRO_2559 LFA_2 O. ledae LRO_2556 LRO_2557 LDP_J LDP_C LDP_H LDP_S LDP_I LFA_4 LDP_A LDP_L LDP_D LDP_E MADR_5 SUR_676 O. smitti MADR9 MADR_2 SUR_679 JUAN_10 JUAN_13 RMAU_351 JUAN_12 PMON_05 PMON_10 CHAI20 PMON_08 CHAI02 CHAI13 CHAI03 CHAI06 CHAI15 O. regia/ CHAI19 CHAI01 O. gracilis CHAI04 CHAI05 CHAI16 CHAI09 TOP_54 CHAI10 CHAI11 CHAI12 CHAI14 LCAL_05 LCAL_14 LCAL_03 LCAL_06 LCAL_11 TOP_55 LCAL_17 RMAU_334 RMAU_345 REL_32 REL_34 REL_35 TOP_60 RMAU_336 RMAU_344 HUI_505 RMAU_329 RMAU_339 LLA_509 HUI_504 O. brevianalis/ LCAL_08 O. mauleanum LCAL_29 LCAL_30 LCAL_22 LCAL_27 LCAL_20 LLA_152 LLA_500 LLA_150 LLA_155 LLA_151 LLA_154 LLA_157 LLA_518 LLA_156 LLA_513 LLA_502 LLA_507 LLA_504 LLA_505 90.0
Figure 13: SVDQuartets tree based on 4,956 unlinked SNPs. For tip label information see Table 3.
59
Table 3: Odontesthes samples for ddRAD sequencing (localities are indicated in the map shown in Figure 2)
Species Locality Code N Lat Lon O. regia Chaiten, Chile CHAI 17 -42.91 -72.72 O. regia Puerto Montt, Chile PMON 4 -41.47 -72.94 O. regia Rio Maullín, Chile RMAU 1 -41.6 -73.6 O. regia Topacalma, Chile TOP 2 -34.12 -71.99 O. argentinensis El Condor, Argentina ELC 6 -41.02 -62.79 O. argentinensis Mar del Plata, MDP 5 -38.01 -57.53 Argentina O. argentinensis Miramar, Argentina MIR 6 -38.26 -57.81 O. argentinensis Praia de Quintao, Brazil PQ 1 -30.40 -50.29 O. perugiae Rio Paraná de las RPLP 1 -34.28 -58.66 Palmas, Argentina O. perugiae Laguna dos Patos, LDP 10 Brazil O. humensis Rio de la Plata, Canal RPP 1 -34.44 -58.51 San Antonio, Argentina O. gracilis Islas Juan Fernandez, JUAN 3 Chile O. ledae Lagoa Rondinha, Brazil LRO 10 -30.52 -50.83 O. ledae Lagoa Fortaleza, Brazil LFA 3 -30.39 -50.29 O. mauleanum Lago Llanquihue, Chile LLA 15 -41.24 -73.00 O. mauleanum Lago Calafquen, Chile LCAL 12 -39.55 -72.27 O. brevianalis Lago Huillinco, Chile HUI 5 -42.68 -73.91 O. brevianalis Rio Maullín, Chile RMAU 6 -41.6 -73.6 O. brevianalis Rio Reloca, Chile REL 4 -35.62 -72.66 O. bonariensis Laguna de Chascomús, CHAS 12 -35.56 -58.03 Argentina O. bonariensis Rio Paraná, Argentina RPAR 3 -33.47 -59.96 O. smitti Puerto Madryn, MADR 5 -42.78 -65.02 Argentina O. smitti Mar Atlantico Sur, SUR 2 -38.04 -58.52 Argentina O. incisa Mar Atlantico Sur, MAS 3 -36.54 -56.69 Argentina
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Table 4: Results of Patterson’s D statistics for different populations of O. brevianalis/mauleanum in southern Chile P1 P2 P3 Outgroup Range Significant Z Tests/Total Tests O. O. RMAU O. argentinensis/O. 0,4.8 0/273 regia smitti perugiae/ O. ledae
O. O. REL O. argentinensis/O. 0,2.49 0/236 regia smitti perugiae/ O. ledae
O. O. LLA O. argentinensis/O. 0,3.23 0/563 regia smitti perugiae/ O. ledae
O. O. LCAL O. argentinensis/O. 0,2.87 0/49 regia smitti perugiae/ O. ledae
61
Chapter 4: Comprehensive phylogeny of ray-finned fishes (Actinopterygii) enhanced by transcriptomic and genomic data
Abstract
Our understanding of phylogenetic relationships among bony fishes and their classification --about one-half of all living vertebrates-- has been transformed in recent years with the influx of molecular genetic data. Many novel groups have been defined on evidence from a handful of genes, but critical nodes of the fish phylogeny still remain controversial. Phylogenomics is a powerful yet challenging resource to improve this knowledge based on genome-wide evidence. Here we leverage 132 newly sequenced transcriptomes combined with genomic databases (5 new genomes) to investigate the evolution of fishes with an unparalleled scale of data: >500,000 bases of exon sequences from each of 305 species, representing all major bony fish lineages (66 out of 72 orders).
Selection of genetic loci from genomic and transcriptomic data was based on stringent criteria to address potential systematic errors arising from whole genome duplications and base composition biases, establishing a novel set of 1,105 exon markers for general application in fish phylogenomics. Maximum likelihood analyses supported a well- resolved phylogeny that mostly agrees with previous hypotheses and gene genealogy interrogation resolved some long-standing uncertainties, such as the early divergence of elopomorphs at the base of the teleosts, the branching order among early euteleosts, and the sister group of percomorphs, the largest radiation of living ray-finned fishes. The set of 1,105 molecular markers tested in this study, applied via hybrid enrichment and high- throughput sequencing, is a promising resource to increase taxonomic sampling to resolve remaining uncertainties in percomorph evolution and to consolidate the tree of
62 life for fishes.
Introduction
Establishing phylogenetic relationships among organisms is a fundamental step towards interpreting and explaining biodiversity and the key natural processes that gave rise to all forms of life. Much progress has been achieved in recent years in elucidating the phylogeny of major groups of fishes, especially among the vast diversity of percomorphs, through analysis of 20-23 gene fragments (Betancur-R et al. 2013; Near et al. 2013). The first large-scale comparative analyses and a new classification of living forms have been conducted on these comprehensive molecular phylogenies (Near et al.
2013; Betancur-R et al. 2017) and a consensus is emerging among ichthyologists about relationships among the main groups of fishes (Nelson et al. 2016). New phylogenomic approaches based on analyses of hundreds or thousands of genes are powerful alternatives to advance this knowledge further and resolve the phylogeny of recalcitrant groups with analyses of ever-larger datasets (Faircloth et al. 2013; Stout et al. 2016;
Arcila et al. 2017). The sheer number of genetic loci available and the size of phylogenomic datasets, in turn, present new methodological challenges for analysis that are currently actively debated in search for new best practices (Jeffroy et al. 2006; Chen et al. 2015; Brown and Thomson 2017). While new bioinformatics pipelines are frequently proposed (Irisarri et al. 2017), standards have yet to emerge for selecting suitable loci (orthologous genes), assembling and curating data, and tree-inference methods for phylogenomic datasets. New studies based on genome-wide datasets obtained by high-throughput sequencing are necessary to test, corroborate, and advance our phylogenetic knowledge. Identification of orthologous genes from genomic and
63 transcriptomic datasets and designing robust analyses for phylogenetic inference are major challenges for such studies.
The set of legacy markers successfully used in fish phylogenetic studies under the
PCR-Sanger-sequencing paradigm (Chen et al. 2003, 2008, Li et al. 2007, 2009;
Betancur-R et al. 2013) have not been explicitly tested for orthology. Distinguishing orthologous genes, whose sequence divergence follows speciation, from paralogous genes that also include duplication events in their history, is a crucial task for resolving the tree of life (Fitch 1970). Molecular phylogenetic analyses designed to infer species trees may be flawed when the assumption of orthology among aligned sequences fails to be met (Maddison 1997; Delsuc et al. 2005; Boussau et al. 2013). However, the effect of including paralogous genes in phylogenetic datasets is not routinely evaluated. Although undetected paralogy is a pervasive problem for phylogenetic inference across the tree of life (Philippe et al. 2005), it is of particular concern for resolving the phylogeny of ray- finned fishes (Actinopterygii)—half of all vertebrate diversity—due to their complex history of whole-genome duplications. There is strong evidence showing that the ancient vertebrate ancestors underwent two rounds of whole-genome duplication (VGD1 and
VGD2 events) (Dehal and Boore 2005), while the teleost ancestor experienced a third genome duplication event (TGD) (Taylor et al. 2003; Meyer and Van De Peer 2005)
(Figure 14 A, B). The TGD has been associated with higher rates of evolution and phenotypic innovation in the radiation of teleosts, the largest and most diverse clade of extant fishes (Wittbrodt et al. 1998; Hoegg et al. 2004; Glasauer and Neuhauss 2014), but recent analyses drawing heavily on the paleontological record has not supported this view
(Clarke et al. 2016). Regardless of their effect on fish diversification, duplicated genes
64 pose a significant challenge for phylogenomic inference in fishes. While many duplicate gene copies were rapidly lost soon after the TGD (Inoue et al. 2015), nearly a quarter of genes present in teleost genomes are duplicated as a consequence of this event (Braasch et al. 2015).
Ongoing efforts by the Fish T1K project (Sun et al. 2016) to sequence transcriptomes from across the diversity of fishes, combined with increasing availability of genomic data (Braasch et al. 2015; Malmstrøm et al. 2016), open up an unprecedented opportunity for testing current phylogenetic hypotheses and for establishing a genome- wide set of orthologous markers for phylogenomic analysis of fishes. Explicit criteria for choosing molecular markers for phylogenetic studies have been discussed at length (Li et al. 2007; Lemmon and Lemmon 2013; Inoue et al. 2015; Malmstrøm et al. 2016), but this issue remains particularly relevant in the genomic era when data availability is the least concern. Increases in size and complexity of phylogenomic datasets have the desirable property of augmenting phylogenetic signal (Dunn et al. 2008) while also increasing the potential sources of phylogenetic error (Philippe et al. 2011). Thus, reduced- representation approaches that target a sufficient number of carefully selected genetic loci
(rather than whole-genome or transcriptome comparisons) hold promise to minimize estimation error while maximizing taxonomic sampling to provide strong phylogenetic signal to accurately resolve phylogeny (Lemmon and Lemmon 2013). However, the definition of an optimal set of markers remains contingent upon the taxonomic group and the phylogenetic scope of the problem.
Here, we explicitly address the issue of orthology in exon markers suitable for fish phylogenomics in the context of vertebrate whole-genome duplications by leveraging
65 the largest database of transcriptomes—newly generated for this study—and recently available genomes for fishes. Using explicit topology tests on gene trees to predict gene duplication events, we identify 1105 orthologous exon markers free of paralogy from the
VGD1/2 and TGD events. We target exon markers because their protein translations can be used for phylogenetic analysis, rather than raw DNA sequences, to reduce the confounding effects of strong base-composition heterogeneity among taxa (non- stationarity) (Saccone et al. 1989; Weisburg et al. 1989). Base compositional heterogeneity has been shown to be extensive among fishes, with strong effects on phylogenetic results (Betancur-R. et al. 2013; Dornburg et al. 2017), which may be further exacerbated due to increased sensitivity to model misspecification in large genomic datasets (Jeffroy et al. 2006). Furthermore, a rich collection of DNA sequences already has been compiled for thousands of fish species for the legacy set of exon markers. For this study, we assembled the largest phylogenomic data matrix for fishes
(1105 exon markers, >0.5 million bp, for 305 taxa) for tree inference (Figure 15). The maximum-likelihood phylogeny based on these data (Figure 14 C) is fully resolved and provides a highly supported backbone topology that agrees with previous hypotheses
(Near et al. 2012; Betancur-R et al. 2013, 2017), with a few exceptions that are addressed below.
Increasing the length or number of loci usually improves estimates of phylogeny by providing representative evidence from across the genome for many species (Lemmon and Lemmon 2013), but often some nodes are recalcitrant or hard to resolve with standard analytical approaches (Salichos and Rokas 2013; Gatesy and Springer 2014;
Song et al. 2015). We address conflict among gene tree topologies and test specific
66 hypotheses still considered controversial in the fish tree of life using Gene Genealogy
Interrogation (GGI) (Arcila et al. 2017). These hypotheses include the branching order at the base of the teleost and percomorph clades, relationships among ostariophysan orders, and among atherinomorph orders (Fink and Fink 1981; Rosen and Parenti 1981; Arratia
1997; Setiamarga et al. 2008; Betancur-R et al. 2013; Bian et al. 2016; Arcila et al. 2017;
Dornburg et al. 2017). We also test a suite of hypotheses from the literature regarding membership in the protacanthopterygian and paracanthopterygian clades, which have proven difficult to resolve (Johnson and Patterson 1993; Miya et al. 2003b; Li et al. 2008,
2009; Burridge et al. 2012; Near et al. 2012; Betancur-R et al. 2013; Campbell et al.
2013; Grande et al. 2013; Nelson et al. 2016; Davesne et al. 2016; Malmstrøm et al.
2016).
Materials and Methods
Taxonomic sampling
A total of 131 new transcriptomes included in this study are newly sequenced as a part of the Fish 1000 Transcriptome project (Fish T1K) (Sun et al. 2016). Specimens representative of all major lineages of ray-finned fishes (Actinopterygii) were collected in the field by numerous colleagues around the world (see Supplemental Table 1 for source of materials used in this study). Fish were euthanized immediately after capture and samples of gills were taken and placed in RNAlater, and shipped to the laboratory for
RNA extraction (LAB-NMNH, Washington DC, or BGI-Shenzhen, China).
RNA Sequencing
Gill tissues were homogenized in a CryoMill, and total RNA was extracted using
Trizol reagent (Invitrogen), following manufacturer’s instructions. RNAs extracted at the
67
NMNH (Smithsonian, Washington DC) were placed in GenTegra-RNA 0.5 ml screw cap tubes and dried with a vacu-fuge at room temperature for two hours to stabilize the RNA.
Dried RNAs were shipped to BGI-Shenzhen, where RNA was rehydrated and prepared for sequencing. Raw reads were quality-controlled and assembled to transcriptomes using
SOAP de novo-Trans (Xie et al. 2014).
The newly obtained transcriptomes database was expanded using published data to include an additional 32 transcriptomes and 142 genomes from public repositories.
These sources are documented in Supplementary Table 1.
Marker Selection
A set of 17,817 single-copy conserved nuclear coding markers identified by Song et al. (Song et al. 2017) was filtered for size (keeping loci that were at least 200 bp in length) and similarity (at least 60% identity) across the alignment of eight well-annotated fish genomes: Lepisosteus oculatus, Anguilla anguilla, Danio rerio, Gadus morhua,
Oryzias latipes, Oreochromis niloticus, Gasterosteus aculeatus, and Tetraodon nigroviridis, hereafter referred to as ‘model genomes.’ After size and similarity filtering, analysis with CD-HIT-EST at 100% identity (Fu et al. 2012), revealed ten loci to be completely identical to one of the other model loci in the set, and were excluded in favor of the longer locus for all subsequent analyses. This procedure reduced the original set of
Song et al (2017) to 1721 exon markers. Sequences for all markers from each of the model genomes were aligned to each other in Mafft v7.130b (Katoh and Standley 2013).
To search for these loci in the new transcriptomic and genomic data sets ('non-model data') we used the hidden Markov procedure available in Hmmer 3.1 (Wheeler and Eddy
2013). For each of the 1721 eight-model-species alignments, we created a profile model
68 and executed an nHmmer search on each of our non-model genomes and transcriptomes
(Supplementary Table 1), using default settings. Hits were retained if they had at least a bit score of 100 and covered at least 70% of the shortest model fragment. Zero, one, or more hits were obtained for each marker for each of the non-model species for subsequent analyses, and extracted from genomes and transcriptomes with custom python scripts. Identical hits were removed using CD-HIT, with 100% similarity (Li and Godzik
2006; Fu et al. 2012). We aligned all DNA sequences passing this filter to the markers from the original model genomes using Mafft v7.130b, and removed regions of the alignment only containing undetermined sites using RAxML v8.2.9, although retaining identical sequences across taxa using the –keep-identical-sequences flag. Maximum likelihood (ML) analysis was performed in RAxML v8.2.9 (Stamatakis 2014) for each
DNA alignment, executing ten separate searches with different starting trees under the
GTRGAMMA model. This procedure yielded 1,721 unconstrained ML gene trees, one for each exon marker.
Paralogy Filtering
Two sets of topological constraints were generated and analyzed to test hypotheses of paralogy originating from inferred whole genome duplications (WGD) in ancestral vertebrates or teleosts (Figure 14 A). The first constrained tree enforced all teleost sequences in a given gene alignment to a monophyletic group. Topology tests were subsequently performed comparing the constrained tree with the unconstrained ML topology with the expectation that teleost monophyly would be rejected for duplicated loci originating from the ancestral vertebrate WGD events (VGD1/2, Figure 14). Ten separate ML tree searches for constrained trees for each locus were conducted in RAxML
69 under the GTRGAMMA model. A second set of constraint trees was inferred by enforcing monophyly of Ostariophysi (Figure 14), a large and well-supported clade within teleosts (Betancur-R et al. 2013; Arcila et al. 2017), to identify paralogs originating from the TGD. For the topology tests, we obtained site likelihoods using
RAxML, then executed the Approximately Unbiased (AU) test in Consel (Shimodaira and Hasegawa 2001; Shimodaira 2002) to evaluate whether constrained topologies could be rejected for each gene tree. Rejection of teleost monophyly (AU test, P<0.05) was used to flag the marker as a potential paralog originating from the VGD1/2 events. Loci that passed this step were tested for the potential effects of the TGD, this time comparing
Ostariophysan-monophyly-constrained trees against the unconstrained tree for each locus. As a second diagnostic test for paralogy arising from TGD we also tested the monophyly of a third group, the euteleosts (Figure 14), for which taxon sampling was more complete than for ostariophysans. When monophyly of any of these groups was significantly rejected by the AU-test, the locus alignment was considered to contain paralogs and was removed from future phylogenetic analysis.
Paralogy of Legacy Markers
Seven exon markers commonly used for PCR-based studies of fish phylogenetics
(Li et al. 2007) were included in the filtered set of 1721 markers: TBR1, FICD, RAG1,
RAG2, GLYT, KIAA1239, and MYH6. These 'legacy' markers also were tested for paralogy as described above and flagged loci were analyzed further to test whether the published data (sequences obtained by PCR-Sanger sequencing methods) may contain paralogous sequences. For this analysis, we included sequences from a previous study that included 1,410 bony fish (Betancur-R et al. 2013) and added them to their respective
70 loci alignments using Mafft --add. Alignments were trimmed to the length of the PCR products and gene trees were inferred for each locus using RAxML (as described above), to test whether the PCR products are placed on a single clade (orthologous) or in one or more paralogous clades as defined by the topology tests described above. This test was performed by visual inspection of the distribution of PCR fragments in the resulting phylogenies.
Phylogenomic Analyses and Gene Genealogy Interrogation
Each alignment that passed the paralogy filter was inspected by eye to verify the presence of a continuous open reading frame. If particular species had lineage-specific duplications (inparalogs), only one sequence was retained. Curated alignments were used to infer species trees using concatenated data or summary coalescent approaches. A species tree was inferred from individual RAxML-generated gene trees using ASTRAL-
II (Mirarab et al. 2014), with each locus alignment partitioned by codon and optimized under the GTRGAMMA model. Gene alignments were concatenated using PhyloUtensils
(https://github.com/ballesterus/PhyloUtensils), and a concatenated analysis was conducted in ExaML 3.0 (Kozlov et al. 2015) under the GTRCAT model. The concatenated nucleotide alignment was partitioned by codon (GTRCAT model) while the protein alignment was not partitioned, but both used the GTRCAT model to account for among-site rate heterogeneity. Each ExaML run was replicated with 10 different parsimony-starting trees generated in RAxML. We generated a time-calibrated tree based on the topology found with proteins, using penalized likelihood in TreePL (Sanderson
2002; Smith and O’Meara 2012), and age estimates for major nodes from Betancur et al.
(2013) for the following clades: Osteichthys, Sarcopterygii, Actinopterygii, Acintopteri,
71
Neopterygii, Holostei, Teleostei, Elopomorpha, Osteoglossomorpha, Otophysa,
Euteleostei, Neoteleostei, Acanthomorphata, and Percomorphaceae.
Individual gene trees are extremely useful for reconstructing the species tree while taking into account coalescent variation that might mislead a concatenated analysis.
However, since individual gene alignment can be short and often contain little information, trees inferred from these genes are prone to error. Gene Genealogy
Interrogation (GGI) has been proposed to test specific hypotheses in a phylogenomic framework while taking into account gene tree error (Arcila et al. 2017). We used GGI to test long-standing areas of conflict in the ray-finned fish tree of life: (i) the first branch at the base of the Teleosts (Elopomorpha, Osteoglossomorpha, and Clupeocephala) (e.g.
Patterson and Rosen 1977; Le 1993; Arratia 1997; Austin et al. 2015; Bian et al. 2016);
(ii) relationships among Otophysan orders (Characiformes- possibly not monophyletic,
Cypriniformes, Gymnotiformes, and Siluriformes) (e.g. Fink and Fink 1981; Arcila et al.
2017; Chakrabarty et al. 2017); (iii) relationships and membership of Protacanthopterygii
(Salmoniformes, Esociformes, Argentiniformes, Galaxiiformes, Osmeriformes, and
Stomatiiformes, and Neoteleostei) (e.g. Li et al. 2009; Burridge et al. 2012; Grande et al.
2013); (iv) relationships at the base of Acanthopterygii (Polymixiformes, Percopsiformes,
Zeiformes, Gadiformes, Stylephoriformes, Lampriformes, Acanthopterygii) (e.g.
Patterson and Rosen 1977; Miya et al. 2003b; Eytan et al. 2015; Harrington et al. 2016);
(v) relationships at the base of Percomorphaceae (Trachyicthyformes, Beryciformes,
Holocentriformes, Percomorphs) (e.g. Betancur-R et al. 2017; Dornburg et al. 2017); and
(vi) relationships among orders in Atherinomorpha (Beloniformes, Cyprinodontiformes, and Atheriniformes) (Rosen and Parenti 1981; Setiamarga et al. 2008). Because of the
72 wealth of possible hypotheses for the membership of Protacanthopterygii and at the base
Acanthopterygii, we selected a set of the main hypotheses proposed in the literature, as opposed to all possible topologies. The details of this method are described by Arcila et al. 2017, but briefly we generated constraint trees for each hypothesis we tested (see
Supplemental File 13), then conducted gene tree searches for each of those constraints
(using the DNA and protein alignments). We calculated site likelihoods in RAxML and used the AU test in Consel to rank the best-supported topology.
Results
Defining Orthologs for Fish Phylogenomics
An initial set of 1,721 exon markers used in this study was identified using an established pipeline to search for single-copy genes (Li et al. 2012; Song et al. 2017) among eight well-annotated actinopterygian genomes evenly distributed across the tree of life of fishes (spotted gar, Japanese eel, zebrafish, cod, tilapia, medaka, stickleback, and green pufferfish; Figure 14 C, taxa with asterisks). This set included seven exon markers frequently used in fish phylogenetics: TBR1, MYH6, KIAA1239, RAG1, RAG2, FICD,
GLYT (Li et al. 2007, 2012; Near et al. 2012; Betancur-R et al. 2017). For each of the
1,721 eight-model-species alignments, we used nHmmer (Wheeler and Eddy 2013) to create a profile model and to search and extract these loci from each of 297 additional genomes and transcriptomes (Supplementary table 1). Significant hits (ranging from zero to several gene copies per species) were added to each original alignment to create a database of 305 species to search for orthologous exon markers. Individual gene trees were inferred with RAxML for all 1,721 exons and analyzed to detect gene duplications at the base of the vertebrate tree (VGD1/2) and at the base of the teleosts (TGD). A total
73 of 470 paralogous genes explained by the VGD1/2 events were identified with topology tests enforcing the monophyly of Teleosts (Figure 14). These tests were based on the detection of two or more significantly supported clades of teleosts in each gene tree
(Figure 14). We further identified 110 paralogous loci originating from the TGD event after constraining for euteleost monophyly, and 34 additional loci after constraining for ostariophysan monophyly. Altogether, by explicitly accounting for whole-genome duplication events in our assessment of orthology and greatly expanding our taxonomic sampling, we reduced our marker set to 1,105 paralogy-free exons.
Among the seven legacy PCR markers included in the initial set of 1,721 loci, three (TBR1, MYH6, KIAA1239) were flagged as having paralogous sequences, while the others (RAG1, RAG2, FICD, GLYT) were not. In order to test for confounding effects of paralogy on published phylogenies using TBR1, MYH6, and KIAA1239
(Betancur-R et al. 2013), we compiled alignments for these loci obtained from published sequences of PCR-amplified products and added them to our in silico-captured dataset for additional phylogenetic analyses. All sequences from PCR-sequenced loci clustered in a single orthogroup (Figures 17-18), confirming that the nested-PCR technique used in that study was selective enough to amplify only orthologous copies for these loci, and that previous results based on these markers were not compromised by undetected paralogy.
However, sequence capture methods using shotgun approaches may be more sensitive to the presence of paralogs, and the quality of the assembled data may be highly dependent on which loci are chosen for analysis.
Resolution in the Fish Tree of Life
After filtering for paralogs, we assembled a data matrix with 555,288 base pairs
74
(bp) (185,096 amino acids) from 1,105 exons, the largest phylogenomic alignment assembled thus far for fishes with taxonomic sampling that includes 66 out of the 72 orders of bony fishes (Betancur-R et al. 2017). We resolve the backbone of ray-finned fishes with confidence, from the early-branching ray-finned lineages to the most derived and diverse percomorph groups (Figure 14 C). Methods of phylogenetic inference based on concatenated nucleotide (Figure 20) and protein sequences (Supplementary Figure 5), or on a multi-species coalescent approach implemented in ASTRAL (Figure 22) converge on virtually the same topology, with some exceptions discussed below. Our phylogenetic results corroborate the recently proposed classification of percomorphs into nine series (Betancur-R et al. 2013) with 99-100% bootstrap support for both protein
(Figure 14 C) and nucleotide analyses. This includes strong support for a clade containing
Pelagiaria (tunas, jacks) and Syngnatharia (seahorses, pipefishes), previously obtained with lower support in other studies (Near et al. 2012; Betancur-R et al. 2013; Small et al.
2016).
We tested alternative topologies based on the GGI approach using gene trees
(Arcila et al. 2017) to address six areas of the phylogeny for which there is little consensus in the literature (Figure 14 C, brown ovals labeled 1-6; Figure 16), some of which we were able to test exhaustively with all possible topological hypotheses. Our concatenated and multi-species coalescent analyses support Elopomorpha (eels and tarpons) and Osteoglossomorpha (bony tongues and mooneyes) as sister taxa (Figure 14
C.1), however GGI tests reject this topology in favor of placing elopomorphs alone as the sister-group to all remaining Teleosts (Figure 16.1). For the Otophysan orders (Figure 14
C.2; Figure 16.2), GGI supports a traditional morphological hypothesis (Fink and Fink
75
1981), also obtained by Arcila et al. (Arcila et al. 2017) with a partially overlapping phylogenomic dataset. This result was obtained by the concatenated protein analysis
(Figure 14 C), although not supported in other analyses. Regarding the sister-group of percomorphs (Figure 14 C; Figure 16.5), GGI tests overwhelmingly support
Holocentriformes (squirrelfishes, soldierfishes) as the sister to Percomorphs, rejecting the topology obtained by protein (Figure 14 C) and DNA analysis. Similarly, GGI resolves the relationship among the three orders of Atherinomorpha (Figure 14 C; Figure 16.6) with Beloniformes (ricefishes, flying fishes) as the first branch sister to a group composed by Cyprinodontiformes (killifishes, mollies, guppies) and Atheriniformes
(silversides, rainbowfishes).
GGI provides less power to resolve nodes where there are too many alternative hypotheses to run exhaustive tests. Composition of the Protacanthopterygii clade is ambiguous (Figure 14 C; Figure 16.3): a group that sometimes includes four orders
(Salmoniformes, Esociformes, Galaxiiformes, Argentiniformes), but alternatively defined as only two (Salmoniformes and Esociformes). GGI supports the latter and a clade composed by Argentiniformes, Galaxiiformes, Osmeriformes and Stomiatiiformes
(superorder Osmeromorpha, recently proposed by Nelson et al 2016) as the sister group to the neoteleosteans. Lack of strong preference for a single hypothesis also is obtained at the base of the acanthomorphs (Figure 14 C; Figure 16.4, Figures 20-21), in particular regarding the placement of deep sea orders Polymixiiformes (beardfishes) and
Lampriformes (oarfishes).
Discussion
Improving Orthology Assessment with Hypothesis Testing
76
The history of these genome duplications generates testable hypotheses for potential duplications in gene trees for vertebrate groups (Figure 14 A, B), but this is rarely taken into account when determining orthology for phylogenetic analysis (but see
(Boussau et al. 2013)). We find that limiting orthology assessment to only a few model genomes and ignoring the history of these genome duplications significantly underestimates the number of potentially paralogous genes. Using eight model genomes, we identified 1721 ‘single-copy’ exon markers, but a broader search of 305 transcriptomes and genomes across bony fish diversity reduced this to 1105 orthologs.
While synteny analysis may be a reasonable criterion to identify orthologs after genome duplications (Braasch et al. 2015), we are still far from having chromosome-level whole genome assemblies for many taxa. The new transcriptomes sequenced here, and the many draft genomes generated recently for fishes provide a rich database for orthology assessment using explicit hypothesis testing on gene trees, without relying on high- quality genomic assemblies or even annotated genomes. Using exon markers also allows us to integrate transcriptomes, genomes, and many ‘legacy’ exon markers from PCR- based sequencing studies into future studies.
Many widely-used exon markers for fish phylogenetics, originally developed by screening just two model genomes available a decade ago (Li et al. 2007), were not found to map to single-copy genes, a result also found in a previous study that focused on cichlids (Ilves and López-Fernández 2014). However, four exons, RAG1, RAG2, GLYT, and FICD, for which many sequences are already available were deemed paralogy-free.
With more than 17,000 fish sequences for RAG1 available on GenBank (as of May 17,
2017), this is a potentially rich source of data that can be integrated with newly generated
77 sequences from current sequencing technology. Our results also show that the specificity of PCR primers used in those studies avoided the amplification of paralogous genes
(Figures 17-19), therefore previous results using these markers were unlikely to be biased due to hidden paralogy. But current target-capture technology, now in wide use in phylogenomics, does not rely on PCR primers but rather on single-stranded RNA probes that hybridize with genomic DNA, producing many short reads from targeted areas of the genome (Lemmon and Lemmon 2013). Assembling these short reads under the assumption that they come from a single ortholog is potentially problematic, as even a few stray reads from a paralogous locus could be introduced to create a chimeric assembly, violating phylogenetic assumptions and introducing error into the analysis. By filtering loci for known paralogs, we have provided a set of markers that can easily be obtained in sequence-capture experiments for phylogenomics, but that also connect with older datasets and new genomic resources, unlike other recently developed markers based on ultraconserved elements (UCEs) or anchored enrichment (Faircloth et al. 2012;
Lemmon et al. 2012; Eytan et al. 2015; Harrington et al. 2016). Due to significantly lower costs per specimen compared to transcriptomic or whole genome sequencing, target-capture methods and high-throughput sequencing using the set of orthologous exons proposed here will encourage large-scale phylogenomic studies with dense sampling of fish taxa.
Resolving difficult nodes in the fish tree of life
Phylogenetic resolution of relationships among groups of fishes has lagged behind other vertebrate groups, partly due to the fact that until recently, there was a paucity of genomic resources for this group. By generating 131 novel transcriptomes we have
78 expanded the genomic resources available for this group significantly. Molecular phylogenetic analyses of fishes overturned many previously hypothesized groups proposed on morphological evidence (Near et al. 2012; Betancur-R et al. 2013), but groups in the rapidly radiated percomorph lineages were often found with only weak support. We validate these groups with high bootstrap support in our protein tree, as the nine series following a recent phylogenetic classification of bony fishes (Betancur-R et al. 2017): Ophidiaria (100%), Batrachoidaria (100%), Gobiaria (100%), Syngnatharia
(99%), Pelagiaria (99%), Anabantaria (100%), Carangaria (100%), Ovalentaria (100%), and Eupercaria (100%). With one exception (Lutjaniformes), our protein analysis (Figure
1) supports the monophyly of all orders proposed by Betancur et al. (2017) where we have more than one representative taxon, including Perciformes. However, far more work is necessary to resolve relationships within this large group of fishes, some of them containing thousands of species.
We addressed some contentious areas of the tree (Figure 14) with the GGI approach (Arcila et al. 2017), designed to address gene tree discordance and estimation error. The branching order at the base of the teleosts has received much attention and has been alternatively proposed that (i) the Elopomorphs constitute the first branch on morphological and later molecular evidence (Arratia 1997; Near et al. 2012; Betancur-R et al. 2013), (ii) Osteoglossomorphs branch first on morphological, mitogenomic, and genomic evidence (Patterson and Rosen 1977; Miya et al. 2003a; Austin et al. 2015), or
(iii) these two lineages are sister to all other Teleosts (Clupeocephalans) (Le 1993; Bian et al. 2016; Shen et al. 2017) on 28S rRNA and genomic evidence. GGI supports the
Elopomorph-sister hypothesis (Figure 16.1), although other analyses support the
79
Osteoglossomorphs and Elopomorphs as sister taxa (Figure 14 C). While our study has better taxon sampling for Elopomorphs and Osteoglossomorphs (7 and 6 taxa, respectively) than previous genome-scale analyses (Austin et al. 2015; Bian et al. 2016), our analyses fall short of representing the diversity of these groups, as Elopomorphs contain more than 900 species and Osteoglossomorphs more than 200. Still, we conclude that the majority of gene trees support an Elopomorph-sister hypothesis. We also obtain the same result as Arcila et al. (2017) for the canonical morphological relationships among Otophysan (Fink and Fink 1981) orders using this approach on a different dataset, with poorer taxonomic sampling. We find that GGI supports the same topology as
Betancur et al. (2013) for the sister group of Percomorphs, though the topology we obtain in our concatenated and multispecies coalescent analyses more closely resembles a recent phylogenomic hypothesis (Dornburg et al. 2017). GGI also supports Beloniformes as the sister to Atheriniformes and Cyprinodontiformes, though we only have three Beloniform taxa in our analysis.
Other areas of the backbone remain enigmatic. The placement of
Argentiniformes, for which we only have one representative, varies in our analyses, forming a clade with Salmoniformes and Esociformes in our protein analysis, as in (Near et al. 2012), but breaking away from this group in nucleotide analyses. Likewise, the placement of Lampriformes and Polymixiiformes is variable, though both concatenation and multispecies coalescent approaches suggest that Lampriformes are the sister to
Acanthamorphs. Both of these areas of the tree would benefit from more taxon sampling to break up long branches. With a well-curated set of exons, fully resolving the backbone of ray-finned fish phylogeny with more taxa is well within our reach.
80
Acknowledgements:
We thank all Fish-T1K members and partners who have made Fish-T1K possible. Special thanks go to our colleagues who provided valuable samples: Yong Zhang (School of Life
Sciences, Sun Yat-Sen University, Guangzhou 510275, China), Hai Huang (Sanya
Science and Technology Academy for Crop Winter Multiplication, Sanya 572000,
China), Junxing Yang (Kunming Institute of Zoology, Chinese Academy of Sciences,
Kunming 650223, China), Jun Zhao (College of Life Sciences, South China Normal
University, Guangzhou 510631, China), Jose V. Lopez and Kirk Kilfoyle (Oceanographic
Center, Nova Southeastern University, Fort Lauderdale, FL 33004, USA), Brad Pusey and Stephen Beatty (TropWATER, James Cook University, Townsville 4811, Australia),
Peter Rask Møller and Mads Reinholdt (Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark), Luiz Rocha (Dept. of Ichthyology,
California Academy of Sciences, San Francisco CA, USA), Donald J. Stewart (Dept. of
Environmental and Forest Biology, SUNY College of Environmental Science and
Forestry, Syracuse, NY 13210, USA), Carol A. Stepien, (Ocean Environment Research
Division (OERD), NOAA-PMEL, Seattle, WA 98115, USA). Many thanks to Yong
Zhang, Zhixiang Yan, Shanshan Liu, Yamin Huo, Jing Zhang, Nanxi Liu (China National
GeneBank, BGI-Shenzhen, Shenzhen 518120, China) for their great efforts in sample processing and data management. Yadira Ortiz-Ruiz (Univ. of Puerto Rico, San Juan,
Puerto Rico) and Jesus Ballesteros (George Washington University, USA) helped with data analysis. Thanks to Colonial One HPC cluster personnel (CCAS, George
Washington University, USA) for help with data processing.
81
Figure 14: (A) Gene genealogies expected as a result of the VGD1/2 and (B) TGD events shown on a model gene tree, providing a testable hypothesis to identify paralogs as a result of these events. (C) ML likelihood tree inferred from 185,096 amino acid sites for 302 Actinopterygiians and three Sarcopterygiian outgroups. Major fish radiations are highlighted: ostariophysans with ‘O’ (red), and percomorphs with ‘P’ (blue). The basal node of teleosts is denoted with ‘T’, and euteleosts with ‘E’. Naming reflects the recent classification of Betancur et al. (2017). Asterisks next to names represent the distribution of the eight model species used for marker selection. Areas of the tree with uncertain relationships tested in this study are highlighted in brown ovals and indicated with numbers: (1) base of the teleosts, (2) orders of otophysans, (3) protacanthopterygians and base of the euteleosts, (4) paracanthopterygians and sister group to acanthomorphs, (5) sister group to percomorphs, (6) orders of atherinomophs.
82
Number of Taxa x Alignment Length
180,000,000 1105 160,000,000
140,000,000
120,000,000
100,000,000
80,000,000 1051 60,000,000 219
40,000,000 21 973 20,000,000 996 132 107 491 988 177 10 567 567 177 0
Zou et al 2012 Near et al 2013 Stout et al 2016 Eytan et al 2015Gilbert et al 2015 Austin et al 2015Longo et al 2017 Arcila et al 2017 Dornburg et al 2017Faircloth et al 2013 Betancur et al 2013 Malmstrom et alHarrington 2016 et al 2017 Chakrabarty et al 2017 Hughes et al (this study)
Figure 15: Comparison of data size among recent phylogenetic studies of fishes showing the total alignment length by the number of taxa, compared to the current study. Numbers on top of the bars refer to the number of loci used in each study.
83
Figure 16: GGI results based on protein alignments. For each specific hypothesis tested (1-6), the distribution of all gene trees supporting each alternative hypotheses (left panels) or only the significantly supported hypotheses (right panels) are shown. The top topologies favored by these tests are shown on the right-most panel.
84
Amia_calva_gill|E1541|scaffold7594|1296|575 Anguilla_rostrata|E1541|LTYT01010275.1|10579|11307 Anguilla_japonica|E1541|KI304844.1|35159|34431 Umbra_pygmae|E1541|YUP_EOMES.1.1|1144|408 Supplemental Figure 1: TBR1 gene tree with PCR products Stylephorus_chordatus|E1541|utg7180004454456|3155|2416 Gadiculus_argenteus|E1541|utg7180000137338|4011|4759 Pollachius_virens|E1541|utg7180000127513|955|207 Gadus_morhua|E1541|GeneScaffold_948|468520|469268 Sequences of the TBR1 gene and paralogs found via Lampris_guttatus|E1541|utg7180001325948|868|126 Monocentris_japonica|E1541|utg7180000067812|10079|9343 nHmmer searches in our 305 taxa, with the addition of PCR Holocentrus_rufus|E1541|utg7180000427352|2226|1487 Myripristis_jacobus|E1541|utg7180000857479|25178|24440 products from Betancur et al. 2013 (2) highlighted in red. Pampus_argenteus|E1541|JHEK01072017.1|3741|3002 Thunnus_orientalis|E1541|BADN01032909.1|1268|529 Syngnathoides_biaculeatus|E1541|scaffold36099|1001|262 Tree was inferred with RAxML under the GTRGAMMA model. Hippocampus_erectus|E1541|scaffold75|1277251|1276512 Cynoglossus_semilaevis|E1541|NC_024324.1|8924301|8925038 Boleophthalmus_pectinirostris|E1541|KN524664.1|10991394|10992130 Periophthalmus_magnuspinnatus|E1541|KN466139.1|226772|227508 Periophthalmodon_schlosseri|E1541|KN485050.1|35767|36503 Lepidonotothen_nudifrons|E1541|gi|1066955195|emb|HACN01042381.1||1383|2119 Notothenia_coriiceps|E1541|NW_011369945.1|16974624|16973888 Chaenocephalus_aceratus|E1541|utg7180000167185|539|1275 Gymnodraco_acuticeps|E1541|comp89226_c0_seq2|1313|577 Gasterosteus_aculeatus|E1541|groupX|4249619|4250355 Dendrochirus_zebra|E1541|scaffold17768|914|175 Sebastes_nigrocinctus|E1541|AUPR01057908.1|3075|3803 Sebastes_rubrivinctus|E1541|KI458079.1|7984|8712 Acanthurus_tractus|E1541|scaffold13934|1033|294 Dicentrarchus_labrax|E1541|HG916849.1|17552668|17551929 Morone_saxatilis|E1541|JTCL01001937.1|24457|25196 Oplegnathus_punctatus|E1541|scaffold12585|601|1340 Acanthopagrus_schlegelii|E1541|scaffold16|6883518|6882779 Chaetodon_auriga|E1541|scaffold27115|862|123 Equetus_punctatus|E1541|scaffold17031|667|1381 Larimichthys_crocea|E1541|NW_011322922.1|80509|79770 Miichthys_miiuy|E1541|JXSJ01000033.1|228552|227813 Eucinostomus_sp|E1541|scaffold27771|1025|286 Labrus_bergylta|E1541|FKLU01000144.1|576832|576090 Symphodus_melops|E1541|utg7180000173682|3954|4697 Diodon_holocanthus|E1541|scaffold16934|695|1428 Mola_mola|E1541|KV751318.1|5119515|5120242 Tetraodon_nigroviridis|E1541|21_random|2658442|2657706 Perca_fluviatilis|E1541|utg7180000052911|4602|5342 Monopterus_albus|E1541|TRINITY_DN47885_c0_g1_i2|2036|2750 Sinibotia_superciliaris|E1541|scaffold20930|1103|364 Helostoma_temminckii|E1541|utg7180000006383|15311|16049 Channa_argus|E1541|scaffold205|392438|393174 Channa_micropeltes|E1541|scaffold11314|1017|284 Lates_calcarifer|E1541|LBLR01012606.1|193629|192890 Trachinotus_ovatus|E1541|scaffold29099|862|123 Coryphaena_hippurus|E1541|TRINITY_DN34515_c0_g1_i2|1131|392 Selene_dorsalis|E1541|utg7180000940017|1741|1002 Paralichthys_olivaceus|E1541|CHR20|5388706|5389445 Pseudopleuronectes_yokohamae|E1541|BBOV01120231.1|988|250 Toxotes_jaculatrix|E1541|scaffold25616|890|181 Toxotes_jaculatrix|E1541|scaffold25617|995|281 Lamprogrammus_exutus|E1541|utg7180000161845|1349|2088 Brotula_barbata|E1541|utg7180000629282|3895|4633 Acanthemblemaria_sp|E1541|scaffold12306|1067|352 Parablennius_parvicornis|E1541|utg7180000245547|238|976 Oryzias_mekongensis|E1541|scaffold36224|868|126 Amphiprion_melanopus|E1541|scaffold17969|1129|390 Stegastes_partitus|E1541|NW_007577737.1|541086|540347 Chromis_chromis|E1541|utg7180000140197|7225|6486 Amphilophus_citrinellus|E1541|CCOE01000820.1|77629|76890 Oreochromis_niloticus|E1541|GL831250.1|802078|802817 Neolamprologus_brichardi|E1541|NW_006272013.1|9673558|9672819 Pundamilia_nyererei|E1541|NW_005187503.1|1751233|1750494 Haplochromis_burtoni|E1541|NW_005179488.1|1415404|1414665 Maylandia_zebra|E1541|NW_014447427.1|2901817|2902556 Pseudomugil_paskai|E1541|TRINITY_DN32365_c1_g1_i1|1140|403 Odontesthes_bonariensis|E1541|Odontesthes_bonariensis_98|149791|150518 Menidia_menidia|E1541|gb|GEVY01010903.1||986|258 Aplocheilus_lineatus|E1541|TR81865|c1_g1_i2|971|232 Kryptolebias_marmoratus|E1541|LHSH01002597.1|11419|12158 Austrofundulus_limnaeus|E1541|NW_013952500.1|1072543|1073282 Nothobranchius_furzeri|E1541|NC_029667.1|9747471|9748198 Ameca_splendens|E1541|TRINITY_DN29550_c0_g1_i1|121|860 Fundulus_heteroclitus|E1541|NW_012224609.1|70939|70201 Cyprinodon_nevadensis_pectoralis|E1541|JSUU01015777.1|30637|29876 Cyprinodon_varigatus|E1541|KL653272.1|206375|205636 Poecilia_reticulata|E1541|NC_024341.1|20535419|20536155 Poecilia_formosa|E1541|NW_006800066.1|770863|771602 Xiphophorus_hellerii|E1541|KQ556860.1|9100103|9099364 Xiphophorus_couchianus|E1541|KQ557205.1|9084013|9083274 Xiphophorus_maculatus|E1541|NW_005373761.1|2281|1542 PCR_G1347_Latimeria_chalumnae Latimeria_chalumnae|E1541|NW_005821339.1|102449|101616 Xenopus_tropicalis|E1541|CM004451.1|67218310|67217476 PCR_G1511_Xenopus_tropicalis PCR_G1378_Monodelphis_domestica PCR_G1328_Homo_sapiens PCR_G1382_Mus_musculus PCR_G1446_Polypterus_senegalus Acipenser_sinensis|E1541|scaffold348915|1|233 Acipenser_sinensis|E1541|C35615755|160|0 Acipenser_sinensis|E1541|scaffold328084|3283|2995 Acipenser_sinensis|E1541|C40653304|1|194 Acipenser_sinensis|E1541|C43776177|1|230 Acipenser_sinensis|E1541|scaffold246690|524|890 Acipenser_sinensis|E1541|C43814921|229|0 PCR_E0461_Amia_calva PCR_G1214_Atractosteus_spatula PCR_G1215_Atractosteus_tropicus PCR_E0993_Lepisosteus_osseus PCR_G1354_Lepisosteus_oculatus PCR_G1353_Lepisosteus_platostomus Lepisosteus_oculatus|E1541|LG12|18547371|18546530 Lepisosteus_oculatus|E1541|model|0 PCR_G1325_Hiodon_tergisus PCR_E0990_Hiodon_alosoides Scleropages_formosus|E1541|JARO02000048.1|5329|4526 Osteoglossum_bicirrhosum|E1541|COB_TBR1B.1.1|1092|1932 PCR_E0084_Osteoglossum_bicirrhosum PCR_G1510_Xenomystus_nigri PCR_G1253_Chitala_ornata PCR_G1301_Gnathonemus_petersii PCR_G1307_Gymnarchus_niloticus PCR_E0769_Elops_saurus PCR_E0501_Albula_vulpes PCR_G1193_Aldrovandia_affinis Megalops_cyprinoides|E1541|brain_C1308269|293|1 Megalops_cyprinoides|E1541|brain_C1315335|25|306 PCR_G1372_Megalops_atlanticus PCR_E0788_Halosauropsis_macrochir PCR_G1192_Albula_glossodonta Anguilla_rostrata|E1541|LTYT01008461.1|10450|11288 Anguilla_anguilla|E1541|AZBK01S001138.1|130310|131148 Anguilla_anguilla|E1541|model|0|0 Anguilla_japonica|E1541|KI304699.1|338153|338991 Lepidogalaxias_salamandroides|E1541|C475303|377|1 Borostomias_antarcticus|E1541|utg7180003293916|4509|3855 Osmerus_eperlanus|E1541|utg7180000089284|1223|603 Plecoglossus_altivelis|E1541|ZPA_TBR1.1.1|1295|1906 Protosalanx_hyalocranius|E1541|scaffold491|136503|135894 Umbra_pygmae|E1541|YUP_TBR1.1.1|1007|1614 Esox_lucius|E1541|NC_025989.2|15854196|15854837 Oncorhynchus_mykiss|E1541|ENA|CCAF010059715|CCAF010059715.1|13511|12905 Salmo_salar|E1541|NC_027315.1|70008589|70009195 Oncorhynchus_mykiss|E1541|ENA|CCAF010022383|CCAF010022383.1|13267|12652 Salmo_salar|E1541|NC_027316.1|11983129|11983744 Lepidogalaxias_salamandroides|E1541|C395054|1|198 Clupea_harengus|E1541|NW_012223947.1|960074|959265 Coilia_nasus|E1541|TRINITY_DN60066_c0_g1_i1|1239|1694 Ictalurus_punctatus|E1541|CM004423.1|23908171|23907460 Pangasianodon_hypophthalamus|E1541|GPH_TBR1.1.1|1173|1884 Electrophorus_electricus|E1541|scaffold5750|114015|113261 Apteronotus_albifrons|E1541|A2AA_TBR1.1.1|1433|612 Danio_rerio|E1541|NC_007122.6|10829991|10829346 Leuciscus_waleckii|E1541|FLSR01004882.1|5100330|5099646 Pimephales_promelas|E1541|JNCD01004818.1|18928|19613 Cyprinus_carpio|E1541|LHQP01013548.1|12271|12887 Sinocyclocheilus_anshuiensis|E1541|LAVE01S019323.1|1169782|1169091 Sinocyclocheilus_grahami|E1541|LCYQ01S000025.1|553011|553701 Sinocyclocheilus_rhinoceros|E1541|LAVF01S032661.1|538678|539369 Cyprinus_carpio|E1541|LHQP01017954.1|119546|120193 Sinocyclocheilus_rhinoceros|E1541|LAVF01S017964.1|1911979|1911255 Sinocyclocheilus_anshuiensis|E1541|LAVE01S011841.1|4876955|4876231 Sinocyclocheilus_grahami|E1541|LCYQ01S000165.1|807851|808576 Coilia_nasus|E1541|TRINITY_DN103713_c0_g1_i1|106|954 Clupea_harengus|E1541|NW_012222919.1|4465625|4464780 PCR_E0359_Talismania_bifurcata PCR_G1223_Bathylaco_nigricans PCR_E0779_Xenodermichthys_copei PCR_E0977_Rouleina_attrita PCR_E0358_Alepocephalus_tenebrosus PCR_G1194_Alepocephalus_agassizii PCR_E0971_Normichthys_operosus PCR_E0978_Maulisia_microlepis PCR_E0366_Sagamichthys_abei PCR_G1481_Searsia_koefoedi PCR_G1306_Gonorynchus_greyi Lepidogalaxias_salamandroides|E1541|C458424|1|162 PCR_E0345_Chanos_chanos PCR_G1269_Cromeria_nilotica PCR_G1419_Parakneria_sp PCR_G1495_Sternopygus_macrurus PCR_G1310_Gymnotus_sp PCR_G1204_Apteronotus_albifrons PCR_G1282_Eigenmannia_macrops PCR_G1466_Rhamphichthys_sp PCR_G1285_Electrophorus_electricus Electrophorus_electricus|E1541|scaffold21619|198536|199382 PCR_G1280_Distichodus_maculatus PCR_G1257_Citharinus_congicus Pygocentrus_nattereri|E1541|KV575308.1|1392459|1391545 Astyanax_mexicanus|E1541|NW_006738821.1|509195|510109 Thayeria_boehlkei|E1541|C1093336|13|285 Hemigrammus_bleheri|E1541|C943736|372|130 PCR_G1392_Nematogenys_inermis PCR_G1360_Loricaria_simillima PCR_G1505_Trichomycterus_sp PCR_G1277_Diplomystes_nahuelbutaensis PCR_E0991_Ictalurus_punctatus Ictalurus_punctatus|E1541|CM004419.1|7873556|7872708 PCR_G1468_Rheoglanis_dendrophorus PCR_G1314_Helogenes_marmoratus PCR_G1241_Cetopsis_coecutiens PCR_G1200_Amphilius_jacksonii PCR_G1358_Liobagrus_aequilabris PCR_G1208_Ariopsis_felis_seemanni PCR_G1415_Pangasianodon_hypophthalmus Pangasianodon_hypophthalamus|E1541|GPH_TBR1B.1.1|1417|2265 PCR_G1317_Hemisilurus_moolenburghi PCR_G1219_Bagrus_ubangensis PCR_G1201_Anduzedoras_oxyrhynchus PCR_G1221_Barbatula_barbatula PCR_G1337_Ictiobus_bubalus PCR_E1015_Carpiodes_carpio PCR_G1332_Hypentelium_nigricans PCR_G1406_Opsariichthys_uncirostris_bidens PCR_G1361_Luciobrama_macrocephalus PCR_G1509_Xenocypris_argentea PCR_G1334_Hypophthalmichthys_molitrix PCR_G1493_Squaliobarbus_curriculus Cyprinus_carpio|E1541|LHQP01022080.1|37721|38570 Sinocyclocheilus_rhinoceros|E1541|LAVF01S041935.1|1377549|1378398 Sinocyclocheilus_anshuiensis|E1541|LAVE01S019689.1|54455|55301 Sinocyclocheilus_grahami|E1541|LCYQ01S000780.1|411927|412776 PCR_G1273_Danio_rerio Danio_rerio|E1541|model|0 Danio_rerio|E1541|NC_007120.6|51972641|51971792 Tinca_tinca|E1541|C523934|136|1 Cyprinus_carpio|E1541|LHQP01015701.1|25428|26104 Sinocyclocheilus_anshuiensis|E1541|LAVE01S019328.1|1517484|1516638 Sinocyclocheilus_anshuiensis|E1541|LAVE01S073491.1|645|0 Sinocyclocheilus_grahami|E1541|LCYQ01S000891.1|265576|264730 Tinca_tinca|E1541|C574515|174|0 Sinocyclocheilus_rhinoceros|E1541|LAVF01S035698.1|207576|208413 PCR_G1485_Semotilus_atromaculatus Leuciscus_waleckii|E1541|FLSR01004877.1|14726651|14727498 PCR_G1400_Notemigonus_crysoleucas PCR_G1439_Pimephales_promelas_notatus Pimephales_promelas|E1541|JNCD01051637.1|8586|9435 PCR_G1363_Luxilus_coccogenis PCR_G1434_Phenacobius_uranops PCR_G1236_Campostoma_oligolepis PCR_G1470_Rhinichthys_cataractae Lepidogalaxias_salamandroides|E1541|C385592|1|187 Lepidogalaxias_salamandroides|E1541|C446378|0|286 Guentherus_altivela|E1541|utg7180004961478|6|367 PCR_G1263_Coregonus_clupeaformis Oncorhynchus_mykiss|E1541|ENA|CCAF010004166|CCAF010004166.1|71935|72771 Salmo_salar|E1541|NC_027320.1|14880385|14881222 Umbra_pygmae|E1541|YUP_LOC100706824.1.1|2369|1529 PCR_G1289_Esox_americanus Esox_lucius|E1541|NC_025983.2|12379113|12378273 PCR_E0688_Esox_lucius PCR_G1502_Thymallus_brevirostris PCR_G1522_Salmo_salar Salmo_salar|E1541|NC_027324.1|12815022|12815855 PCR_G1418_Parahucho_perryi PCR_G1473_Salvelinus_alpinus PCR_E0437_Oncorhynchus_nerka_mykiss Oncorhynchus_mykiss|E1541|ENA|CCAF010003223|CCAF010003223.1|11006|10173 PCR_G1368_Macropinna_microstoma PCR_E0814_Nansenia_longicauda_ardesiaca PCR_G1224_Bathylagus_euryops PCR_E0352_Argentina_sialis_silus PCR_E1031_Argentina_striata PCR_G1496_Stokellia_anisodon Protosalanx_hyalocranius|E1541|scaffold74|1260502|1259646 Plecoglossus_altivelis|E1541|ZPA_LOC100706824.1.1|1582|743 PCR_G1333_Hypomesus_pretiosus PCR_E0095_Thaleichthys_pacificus PCR_G1409_Osmerus_mordax Osmerus_eperlanus|E1541|utg7180000982932|3782|4621 PCR_E0492_Diplophos_taenia PCR_E0036_Polymetme_corythaeola_sp PCR_G1207_Argyropelecus_gigas PCR_G1272_Cyclothone_microdon PCR_E0037_Stomias_boa Borostomias_antarcticus|E1541|utg7180003263852|4764|5604 PCR_E0812_Rhadinesthes_decimus PCR_E0483_Leptostomias_longibarba PCR_E0439_Tactostoma_macropus PCR_E0782_Melanostomias_margaritifer PCR_E0778_Eustomias_polyaster PCR_E0783_Malacosteus_niger PCR_E1000_Chirostomias_pliopterus PCR_G1517_Aplochiton_taeniatus Galaxiella_nigrostriata|E1541|scaffold17802|881|48 PCR_G1394_Neochanna_burrowsius PCR_G1230_Brachygalaxias_bullocki PCR_G1294_Galaxias_maculatus PCR_E0785_Bathysaurus_ferox PCR_E0440_Benthalbella_dentata PCR_E0493_Scopelarchus_sp Parasudis_fraserbrunneri|E1541|utg7180000174331|3348|2517 PCR_E0965_Alepisaurus_ferox PCR_E0479_Scopelosaurus_lepidus PCR_G1225_Bathypterois_atricolor PCR_E0757_Synodus_foetens PCR_G1479_Scopelengys_tristis PCR_E0451_Neoscopelus_macrolepidotus PCR_G1397_Neoscopelus_microchir PCR_E0781_Lampadena_speculigera PCR_E0061_Symbolophorus_californiensis Benthosema_glaciale|E1541|utg7180001409712|1075|1358 PCR_G1340_Krefftichthys_anderssoni Benthosema_glaciale|E1541|utg7180006869044|529|93 Percopsis_transmontana|E1541|utg7180000014452|18489|19317 PCR_G1433_Percopsis_omiscomaycus Percopsis_omiscomaycus|E1541|C420714|1|163 Percopsis_omiscomaycus|E1541|C449903|0|185 PCR_E0151_Aphredoderus_sayanus Typhlichthys_subterraneus|E1541|utg7180001099331|1246|2072 PCR_G1490_Speoplatyrhinus_poulsoni PCR_G1254_Chologaster_cornuta PCR_G1198_Amblyopsis_rosae Stylephorus_chordatus|E1541|utg7180000640164|974|148 Melanonus_zugmayeri|E1541|utg7180002075733|576|78 Macrourus_berglax|E1541|utg7180000456781|122|372 Malacocephalus_occidentalis|E1541|utg7180000050435|740|298 Merluccius_capensis|E1541|utg7180003223093|316|8 Muraenolepis_marmoratus|E1541|utg7180003106583|401|51 Merluccius_merluccius|E1541|utg7180001140149|339|105 Merluccius_polli|E1541|utg7180001802120|3|327 Bathygadus_melanocrachus|E1541|utg7180002253558|710|1554 Mora_moro|E1541|utg7180000010118|4147|4991 Laemonema_laureysi|E1541|utg7180001520747|900|56 Phycis_blennoides|E1541|utg7180004340399|945|107 Phycis_phycis|E1541|utg7180001597927|861|83 Molva_molva|E1541|utg7180000140666|4366|5207 Brosme_brosme|E1541|utg7180001862683|2712|3556 Lota_lota|E1541|utg7180000117431|2703|3544 Trisopterus_minutus|E1541|utg7180000414497|2|253 Pollachius_virens|E1541|utg7180001452070|542|139 Boreogadus_saida|E1541|utg7180000989807|442|29 Theragra_chalcogramma|E1541|utg7180001035902|356|28 Melanogrammus_aeglefinus|E1541|utg7180001918770|536|87 Merlangius_merlangus|E1541|utg7180000382927|1926|1417 Merlangius_merlangus|E1541|utg7180000404238|431|0 Merluccius_capensis|E1541|utg7180003767587|324|1 Merluccius_merluccius|E1541|utg7180000198820|2035|2240 Merluccius_polli|E1541|utg7180001900872|242|11 Muraenolepis_marmoratus|E1541|utg7180003835049|306|1 Trachyrincus_scabrus|E1541|utg7180000247770|1886|1054 Trachyrincus_murrayi|E1541|utg7180002968609|3884|4716 Malacocephalus_occidentalis|E1541|utg7180000102653|4276|4654 Gadus_morhua|E1541|model|0 Gadus_morhua|E1541|GeneScaffold_1311|710299|710134 Melanogrammus_aeglefinus|E1541|utg7180000626128|201|356 Theragra_chalcogramma|E1541|utg7180000591901|1658|1815 Merlangius_merlangus|E1541|utg7180000980483|213|352 Boreogadus_saida|E1541|utg7180000814941|355|491 Trisopterus_minutus|E1541|utg7180002151859|89|248 PCR_E0019_Polymixia_japonica Polymixia_japonica|E1541|utg7180001115555|859|29 PCR_E1025_Polymixia_lowei Lampris_guttatus|E1541|utg7180007755483|502|75 Regalecus_glesne|E1541|utg7180000375723|1395|2223 Lampris_guttatus|E1541|utg7180007502017|328|0 Guentherus_altivela|E1541|utg7180001591291|191|10 Guentherus_altivela|E1541|utg7180004965636|342|1 Guentherus_altivela|E1541|utg7180004769922|432|2 Guentherus_altivela|E1541|utg7180006113317|7|228 PCR_G1421_Paratrachichthys_sajademalensis PCR_G1376_Monocentris_japonicus Monocentris_japonica|E1541|utg7180000227083|0|561 PCR_E1018_Hoplostethus_occidentalis_atlanticus PCR_E0649_Gephyroberyx_darwinii Beryx_splendens|E1541|utg7180005712452|0|442 PCR_E0159_Beryx_decadactylus PCR_G1238_Centroberyx_druzhinini Beryx_splendens|E1541|utg7180004471566|146|1 Beryx_splendens|E1541|utg7180004505639|148|0 Acanthochaenus_luetkenii|E1541|utg7180000942833|1|250 PCR_G1222_Barbourisia_rufa Tomicodon_sp|E1541|scaffold12094|187|1 Rondeletia_loricata|E1541|utg7180000358197|302|0 PCR_E1058_Rondeletia_loricata Rondeletia_loricata|E1541|utg7180003935440|0|494 PCR_G1386_Myripristis_violacea Myripristis_jacobus|E1541|utg7180000830844|956|117 PCR_E0720_Plectrypops_lima PCR_E1072_Neoniphon_sammara PCR_E0504_Plectrypops_retrospinis Neoniphon_sammara|E1541|utg7180001053428|1718|1195 PCR_E0101_Sargocentron_vexillarium Beryx_splendens|E1541|utg7180004499978|148|1 PCR_E0105_Sargocentron_coruscum Beryx_splendens|E1541|utg7180001655915|358|0 Monocentris_japonica|E1541|utg7180000293436|247|1 Neoniphon_sammara|E1541|utg7180001247556|1472|1792 Holocentrus_rufus|E1541|utg7180001219700|886|47 PCR_G1474_Sargocentron_cornutum PCR_E1042_Neoniphon_opercularis PCR_E0236_Diancistrus_sp PCR_E0794_Bidenichthys_capensis PCR_E0261_Cataetyx_rubrirostris_lepidogenys PCR_E0883_Brotula_multibarbata Brotula_barbata|E1541|utg7180000068269|3139|2300 PCR_E0629_Brotula_barbata Lamprogrammus_exutus|E1541|utg7180001605449|137|1 Carapus_acus|E1541|utg7180000149867|4657|5500 PCR_E1033_Ophidion_holbrookii PCR_E1007_Ophidion_robinsi PCR_E0659_Brotulotaenia_crassa PCR_E0817_Brotulotaenia_nigra Lamprogrammus_exutus|E1541|utg7180003071484|4|178 Lamprogrammus_exutus|E1541|utg7180004546015|965|126 Lamprogrammus_exutus|E1541|utg7180000141012|0|147 Lamprogrammus_exutus|E1541|utg7180002976980|145|1 PCR_G1336_Icosteus_aenigmaticus PCR_E0693_Gempylus_serpens PCR_E0976_Scombrolabrax_heterolepis PCR_E0518_Neoepinnula_orientalis PCR_E0810_Caristius_sp PCR_E0226_Ruvettus_pretiosus PCR_E0387_Icichthys_lockingtoni PCR_E0274_Aphanopus_carbo PCR_G1210_Assurger_anzac PCR_E0996_Pterycombus_brama PCR_E0684_Taractichthys_longipinnis PCR_E0970_Brama_brama PCR_G1271_Cubiceps_baxteri Pampus_argenteus|E1541|JHEK01292137.1|1|518 Nomeus_gronovii|E1541|C479658|193|1 PCR_E0626_Scomber_scombrus PCR_E0247_Scomber_japonicus PCR_E0927_Acanthocybium_solandri PCR_E0694_Scomberomorus_regalis_commerson PCR_E0631_Scomberomorus_maculatus_sp PCR_E0243_Sarda_sarda PCR_E0832_Gymnosarda_unicolor PCR_E0673_Auxis_rochei PCR_E0747_Katsuwonus_pelamis PCR_E0830_Euthynnus_affinis PCR_E0696_Euthynnus_alletteratus Thunnus_albacares|E1541|utg7180001926178|749|1026 Thunnus_orientalis|E1541|BADN01048017.1|2090|1251 PCR_E0831_Thunnus_albacares Thunnus_albacares|E1541|utg7180002155467|505|26 PCR_E0188_Kurtus_gulliveri PCR_E0546_Cercamia_eremia PCR_E0506_Phaeoptyx_pigmentaria PCR_G1247_Cheilodipterus_quinquelineatus PCR_G1203_Apogon_lateralis PCR_E0109_Astrapogon_puncticulatus PCR_E0702_Apogon_exostigma PCR_G1367_Macrognathus_siamensis PCR_E1134_Monopterus_albus PCR_E1151_Xiphias_gladius PCR_E1028_Astroscopus_y_graecum PCR_G1239_Centrogenys_vaigiensis PCR_E0324_Kathetostoma_averruncus PCR_E1022_Kathetostoma_albigutta PCR_E0293_Aulostomus_maculatus PCR_E1144_Gadopsis_marmoratus PCR_G1291_Eugerres_plumieri PCR_G1507_Ulaema_lefroyi Channa_argus|E1541|scaffold834|520006|519175 PCR_E1133_Channa_striata PCR_G1226_Betta_splendens PCR_G1315_Helostoma_temminkii Helostoma_temminckii|E1541|utg7180000674826|6948|6106 PCR_E1141_Ctenopoma_acutirostre_kingsleyae PCR_G1373_Microctenopoma_nanum PCR_E0923_Parapriacanthus_ransonneti PCR_E0886_Pempheris_vanicolensis PCR_E0718_Pempheris_oualensis PCR_E0652_Epigonus_telescopus PCR_E1019_Epigonus_pandionis PCR_E0227_Stereolepis_gigas PCR_E0242_Polyprion_americanus PCR_E0392_Ambloplites_rupestris PCR_E0132_Lepomis_cyanellus PCR_E1113_Lepomis_macrochirus PCR_E1110_Micropterus_salmoides PCR_G1284_Elassoma_zonatum PCR_E0146_Elassoma_evergladei PCR_G1365_Maccullochella_peelii PCR_E0712_Kuhlia_mugil PCR_G1341_Kuhlia_marginata PCR_E0202_Kyphosus_incisor PCR_G1342_Kyphosus_elegans PCR_E0775_Kyphosus_sectator PCR_E0585_Chirodactylus_jessicalenorum PCR_E0796_Chirodactylus_brachydactylus PCR_E0797_Cheilodactylus_pixi PCR_E0795_Cheilodactylus_fasciatus PCR_E0924_Paracirrhites_forsteri_arcatus PCR_E0578_Lophius_americanus PCR_E0686_Cryptopsaras_couesii PCR_E1119_Lophius_gastrophysus PCR_E0827_Monodactylus_argenteus Morone_saxatilis|E1541|JTCL01003779.1|8820|8225 PCR_E0992_Morone_chrysops PCR_E0017_Morone_americana PCR_E0087_Morone_mississippiensis Dicentrarchus_labrax|E1541|HG916832.1|12116594|12117436 Takifugu_flavidus|E1541|KE121716.1|331842|331659 Morone_saxatilis|E1541|JTCL01014724.1|32380|32713 Hyporhamphus_intermedius|E1541|C806721|189|0 PCR_E0898_Platax_orbicularis PCR_E0858_Platax_teira PCR_E0894_Zanclus_cornutus PCR_E0608_Stellifer_lanceolatus PCR_E0165_Bairdiella_chrysoura PCR_E0127_Menticirrhus_undulatus_littoralis PCR_G1349_Leiostomus_xanthurus PCR_E0123_Seriphus_politus PCR_E0699_Pogonias_cromis PCR_E0511_Cynoscion_arenarius PCR_E1108_Aplodinotus_grunniens Miichthys_miiuy|E1541|JXSJ01000069.1|414706|415548 Larimichthys_crocea|E1541|NW_011322542.1|58918|58076 PCR_E0632_Prognathodes_aya_aculeatus PCR_E0719_Chaetodon_reticulatus PCR_G1243_Chaetodon_ornatissimus PCR_E0753_Chaetodon_striatus PCR_E0921_Chaetodon_auriga PCR_G1248_Chelmon_rostratus PCR_E0547_Heniochus_varius PCR_E0240_Hemitaurichthys_polylepis PCR_E0562_Forcipiger_flavissimus PCR_E0748_Heniochus_chrysostomus PCR_G1488_Siganus_stellatus PCR_E0090_Siganus_vulpinus PCR_E0051_Scatophagus_argus PCR_G1483_Selenotoca_multifasciata PCR_E1117_Chaunax_suttkusi PCR_E0177_Gigantactis_vanhoeffeni PCR_E0655_Oneirodes_macrosteus PCR_E0657_Melanocetus_johnsonii PCR_E0656_Himantolophus_albinares_sagamius PCR_E0610_Ogcocephalus_parvus_nasutus PCR_E0975_Dibranchus_tremendus PCR_G1326_Histiophryne_cryptacanthus PCR_E0643_Histrio_histrio PCR_E1092_Antennarius_coccineus Antennarius_striatus|E1541|utg7180002567101|2541|3383 PCR_E1024_Antigonia_capros PCR_G1205_Aracana_aurita PCR_E0588_Ostracion_cubicus PCR_G1469_Rhinesomus_triqueter PCR_G1531_Triacanthus_biaculeatus PCR_E0382_Triacanthodes_anomalus PCR_E0312_Diodon_holocanthus PCR_E0517_Chilomycterus_schoepfii PCR_G1513_Tetraodon_nigroviridis Tetraodon_nigroviridis|E1541|2|14334502|14333660 Tetraodon_nigroviridis|E1541|model|0 Takifugu_flavidus|E1541|KE121716.1|331375|331000 Takifugu_flavidus|E1541|KE121716.1|331661|331513 Takifugu_rubripes|E1541|NC_018890.1|15951536|15950693 PCR_E0460_Takifugu_rubripes PCR_E0509_Luvarus_imperialis PCR_E0859_Zebrasoma_scopas PCR_E0002_Paracanthurus_hepatus PCR_E0029_Zebrasoma_veliferum PCR_E0005_Acanthurus_bahianus PCR_E0050_Ctenochaetus_strigosus PCR_E0854_Ctenochaetus_truncatus PCR_E0880_Acanthurus_leucosternon PCR_E0889_Acanthurus_lineatus PCR_E0954_Erythrocles_schlegelii PCR_E0570_Heteropriacanthus_cruentatus PCR_G1514_Naso_lituratus PCR_E0824_Sillago_sihama PCR_E0857_Plectorhinchus_chaetodonoides PCR_E0607_Orthopristis_chrysoptera PCR_E0635_Haemulon_aurolineatum PCR_E0218_Haemulon_vittatum PCR_E0199_Haemulon_sciurus PCR_E0279_Haemulon_plumierii PCR_E0770_Apsilus_dentatus PCR_E0746_Pristipomoides_auricilla PCR_E0563_Aphareus_furca PCR_E0592_Lutjanus_campechanus PCR_E0920_Caesio_caerulaurea_lunaris PCR_E0951_Caesio_teres PCR_E0950_Caesio_xanthonota PCR_E0949_Caesio_varilineata PCR_E0961_Pterocaesio_tile PCR_E0939_Macolor_niger PCR_E0569_Lutjanus_biguttatus PCR_G1362_Lutjanus_mahogoni PCR_E0593_Rhomboplites_aurorubens PCR_E0283_Ocyurus_chrysurus PCR_G1379_Monotaxis_grandoculis PCR_E0751_Lethrinus_olivaceus PCR_E0905_Lethrinus_harak PCR_E0910_Lethrinus_obsoletus PCR_E0750_Lethrinus_atkinsoni PCR_E0774_Malacanthus_plumieri PCR_E0595_Caulolatilus_intermedius PCR_E0028_Scolopsis_bilineata PCR_G1427_Pentapodus_caninus PCR_G1478_Scolopsis_margaritifer PCR_E0802_Argyrozona_argyrozona PCR_E0514_Pagrus_pagrus PCR_E0762_Calamus_penna PCR_E0249_Archosargus_probatocephalus PCR_G1346_Lagodon_rhomboides PCR_E0807_Diplodus_capensis PCR_E0806_Sarpa_salpa Spondyliosoma_cantharus|E1541|utg7180001159502|894|52 Acanthopagrus_schlegelii|E1541|scaffold120|1748548|1749390 PCR_E0953_Acanthopagrus_catenula PCR_E0246_Stenotomus_chrysops PCR_E0651_Masturus_lanceolatus PCR_E0683_Mola_mola Mola_mola|E1541|KV751321.1|14481058|14480213 PCR_E0919_Melichthys_indicus PCR_E0591_Balistes_capriscus PCR_E0922_Melichthys_niger PCR_E0935_Sufflamen_fraenatum PCR_E0936_Abalistes_stellatus Gambusia_affinis_whole|E1541|C758079|23|206 Anoplopoma_fimbria|E1541|AWGY01034555.1|863|21 PCR_E0423_Anoplopoma_fimbria PCR_E0191_Bathymaster_caeruleofasciatus PCR_E0420_Bathymaster_signatus PCR_G1437_Pholis_crassispina PCR_E0675_Lycodes_terraenovae PCR_E0370_Zoarces_americanus_viviparus PCR_E0791_Apeltes_quadracus PCR_G1217_Aulorhynchus_flavidus PCR_G1335_Hypoptychus_dybowskii PCR_G1460_Pungitius_pungitius PCR_G1491_Spinachia_spinachia PCR_E0368_Culaea_inconstans PCR_E1012_Gasterosteus_aculeatus Gasterosteus_aculeatus|E1541|model|0 Gasterosteus_aculeatus|E1541|groupXVI|10903516|10902674 Enneanectes_sp|E1541|scaffold23799|186|1 PCR_E0363_Hexagrammos_lagocephalus_otakii PCR_E0220_Cyclopterus_lumpus PCR_E0224_Liparis_gibbus PCR_E0225_Liparis_pulchellus PCR_E0454_Paraliparis_hystrix PCR_E0262_Rhinoliparis_barbulifer PCR_E0453_Paraliparis_copei Cottus_rhenanus|E1541|LKTN01151845.1|5817|6083 Cottus_rhenanus|E1541|LKTN01151845.1|5058|5597 PCR_E0281_Cottus_carolinae Myoxocephalus_scorpius|E1541|utg7180002613134|10119|10331 PCR_E0264_Sarritor_frenatus PCR_E0277_Icelinus_filamentosus Myoxocephalus_scorpius|E1541|utg7180000032447|0|475 PCR_E0916_Enneapterygius_gruschkai PCR_E0801_Coccotropsis_gymnoderma PCR_E1026_Bellator_militaris Peristedion_sp|E1541|C561041|0|203 Peristedion_sp|E1541|C467184|133|0 PCR_E1029_Peristedion_gracile PCR_E0417_Sebastolobus_alascanus PCR_E0897_Dendrochirus_zebra PCR_E1010_Pontinus_longispinis PCR_E1035_Setarches_guentheri PCR_E0903_Scorpaenopsis_longispina PCR_G1482_Sebastes_fasciatus Sebastes_norvegicus|E1541|utg7180001736939|794|1 Sebastes_norvegicus|E1541|utg7180001736936|342|203 Sebastes_nigrocinctus|E1541|AUPR01131608.1|2043|1177 Sebastes_rubrivinctus|E1541|KI446608.1|33089|32223 PCR_E0311_Mycteroperca_bonaci_microlepis PCR_E0868_Cephalopholis_argus PCR_E0391_Perca_flavescens PCR_E1054_Percina_caprodes PCR_E0168_Etheostoma_juliae PCR_E0147_Etheostoma_vitreum PCR_E1111_Etheostoma_zonale PCR_E0152_Etheostoma_simoterum PCR_E0143_Romanichthys_valsanicola PCR_E0144_Zingel_streber Perca_fluviatilis|E1541|utg7180002628967|0|519 PCR_G1428_Perca_fluviatilis PCR_E0140_Gymnocephalus_cernuus PCR_E0141_Gymnocephalus_schraetser PCR_G1229_Bovichtus_diacanthus PCR_G1267_Cottoperca_gobio PCR_G1453_Pseudaphritis_urvillii PCR_G1286_Eleginops_maclovinus PCR_G1528_Aethotaxis_mitopteryx PCR_E0157_Parachaenichthys_charcoti PCR_E0158_Pogonophryne_barsukovi PCR_G1525_Artedidraco_orianae PCR_E0156_Chionodraco_rastrospinosus PCR_G1250_Chionobathyscus_dewitti Chaenocephalus_aceratus|E1541|utg7180000014676|7027|6185 PCR_G1529_Gobionotothen_gibberifrons Notothenia_coriiceps|E1541|NW_011357368.1|4634442|4633600 PCR_G1526_Notothenia_coriiceps PCR_E0155_Gymnodraco_acuticeps PCR_G1530_Patagonotothen_tessellata PCR_G1524_Harpagifer_antarcticus PCR_G1279_Dissostichus_eleginoides Perca_fluviatilis|E1541|utg7180000389135|2213|2574 PCR_E0900_Grammistes_sexlineatus PCR_E0764_Rypticus_saponaceus PCR_E0745_Pseudoplesiops_revellei PCR_E1120_Bembrops_anatirostris PCR_E1128_Bembrops_gobioides PCR_G1452_Pseudanthias_pascalus PCR_E0860_Pseudanthias_squamipinnis PCR_E0163_Centropristis_striata PCR_G1486_Serranus_tigrinus PCR_E0325_Paralabrax_nebulifer PCR_E0505_Hypoplectrus_puella PCR_E1002_Diplectrum_formosum PCR_E1008_Diplectrum_bivittatum PCR_E0836_Sphyraena_barracuda PCR_E0707_Parapercis_clathrata Cynoglossus_semilaevis|E1541|NC_024322.1|12023176|12022334 PCR_E0826_Terapon_jarbua PCR_E0849_Pomacanthus_semicirculatus PCR_E0839_Apolemichthys_trimaculatus PCR_E0550_Centropyge_bicolor PCR_E0448_Poecilopsetta_beanii PCR_E0446_Citharichthys_sordidus Enneanectes_sp|E1541|C768313|1|401 Bregmaceros_cantori|E1541|utg7180005401264|49|886 Hippocampus_erectus|E1541|scaffold13|3928474|3927656 Cyttopsis_roseus|E1541|utg7180001763123|336|70 Zeus_faber|E1541|utg7180001813030|54|875 Paralichthys_olivaceus|E1541|CHR22|17441807|17440965 PCR_E0444_Eopsetta_jordani PCR_E0035_Pseudopleuronectes_americanus Pseudopleuronectes_yokohamae|E1541|BBOV01008569.1|1100|1942 PCR_E0416_Glyptocephalus_zachirus PCR_E0053_Pleuronectes_platessa PCR_E0424_Hippoglossoides_elassodon PCR_E0445_Parophrys_vetulus PCR_E0438_Lepidopsetta_bilineata PCR_E0014_Lachnolaimus_maximus PCR_G1312_Haletta_semifasciata PCR_E0015_Clepticus_parrae PCR_E0948_Wetmorella_nigropinnata PCR_E0560_Bodianus_mesothorax PCR_E0877_Leptoscarus_vaigiensis PCR_E0566_Cetoscarus_bicolor PCR_E0878_Scarus_ghobban PCR_E0875_Scarus_niger PCR_E0013_Scarus_croicensis PCR_E0837_Chlorurus_sordidus PCR_E0874_Scarus_rubroviolaceus PCR_E0872_Scarus_quoyi PCR_G1457_Pteragogus_enneacanthus PCR_E0945_Pseudocheilinus_hexataenia PCR_G1500_Tautogolabrus_adspersus Symphodus_melops|E1541|utg7180000009329|18702|17860 PCR_G1499_Tautoga_onitis Labrus_bergylta|E1541|FKLU01000214.1|612443|611601 PCR_E0901_Cheilinus_oxycephalus PCR_E0908_Stethojulis_strigiventer PCR_E0879_Epibulus_insidiator PCR_E0876_Cheilinus_fasciatus PCR_G1412_Oxycheilinus_celebicus PCR_E0873_Oxycheilinus_digramma Coryphopterus_lipernes|E1541|scaffold36316|1247|2052 PCR_E0852_Pseudogramma_polyacantha Lesueurigobius_cf_sanzoi|E1541|utg7180004106835|908|103 Boleophthalmus_pectinirostris|E1541|KN524065.1|4740587|4739785 Scartelaos_histophorus|E1541|JACN01158175.1|6754|7556 Periophthalmodon_schlosseri|E1541|KN478048.1|60051|59249 Periophthalmus_magnuspinnatus|E1541|KN465473.1|214799|213997 PCR_E0907_Cheilinus_chlorourus PCR_E0016_Xyrichtys_novacula_martinicensis PCR_E0928_Halichoeres_iridis PCR_E0895_Macropharyngodon_bipartitus PCR_E0637_Halichoeres_bathyphilus_bivittatus PCR_E0932_Anampses_lineatus PCR_G1344_Labrichthys_unilineatus PCR_E0848_Labroides_dimidiatus PCR_G1345_Labropsis_australis PCR_E0091_Coris_gaimard PCR_E0861_Coris_caudimacula PCR_E0891_Thalassoma_amblycephalum PCR_E0085_Gomphosus_varius PCR_E0092_Thalassoma_quinquevittatum PCR_E0902_Thalassoma_lunare Coryphaena_hippurus|E1541|TRINITY_DN31122_c0_g1_i1|140|0 Pseudochromis_fuscus|E1541|utg7180000155139|332|0 PCR_E1155_Toxotes_jaculatrix PCR_E0766_Centropomus_ensiferus PCR_E0194_Centropomus_undecimalis PCR_E0842_Leptomelanosoma_indicum PCR_E0217_Polydactylus_virginicus PCR_E1131_Mene_maculata PCR_E0468_Rachycentron_canadum Coryphaena_hippurus|E1541|TRINITY_DN31122_c0_g2_i1|776|52 PCR_E0615_Echeneis_naucrates Chatrabus_melanurus|E1541|utg7180006714008|790|1631 PCR_E0058_Porichthys_notatus PCR_E0590_Porichthys_plectrodon PCR_E0009_Sanopus_sp PCR_E0513_Opsanus_pardus PCR_E0040_Opsanus_tau Lates_calcarifer|E1541|LBLR01001322.1|46422|47264 PCR_E0738_Scomberoides_lysan PCR_G1504_Trachinotus_carolinus PCR_E0623_Seriola_dumerili PCR_E0841_Elagatis_bipinnulata PCR_E0598_Trachurus_lathami PCR_E0833_Selar_crumenophthalmus PCR_E0616_Hemicaranx_amblyrhynchus PCR_E0938_Gnathanodon_speciosus PCR_E0510_Caranx_crysos_ruber Nomeus_gronovii|E1541|C439384|163|0 PCR_E0917_Carangoides_plagiotaenia PCR_E0942_Atule_mate PCR_E0869_Carangoides_ferdau Selene_dorsalis|E1541|utg7180001236449|683|1525 PCR_E0574_Caranx_ignobilis PCR_G1444_Polycentrus_schomburgki PCR_G1377_Monocirrhus_polyacanthus PCR_G1262_Congrogadus_subducens PCR_E0589_Natalichthys_sam PCR_E0793_Halidesmus_scapularis PCR_E0135_Zalembius_rosaceus PCR_E0134_Hyperprosopon_anale_argenteum PCR_E0122_Phanerodon_furcatus PCR_E0124_Rhacochilus_vacca PCR_E0120_Embiotoca_jacksoni PCR_E0139_Cymatogaster_aggregata Odontesthes_bonariensis|E1541|Odontesthes_bonariensis_207|105348|106191 PCR_E1112_Labidesthes_sicculus PCR_E0174_Menidia_beryllina Menidia_menidia|E1541|gb|GEVY01008433.1||1392|2235 PCR_E0167_Menidia_menidia PCR_E0145_Iso_sp Glossolepis_incisus|E1541|C770867|1|287 Pseudomugil_paskai|E1541|TRINITY_DN22116_c0_g1_i1|390|1 PCR_E0182_Pseudomugil_gertrudae Pseudomugil_paskai|E1541|TRINITY_DN22116_c1_g1_i1|313|0 PCR_G1467_Rheocles_wrightae PCR_E0180_Craterocephalus_honoriae PCR_E0115_Atherinomorus_stipes PCR_E0548_Atherinomorus_lacunosus PCR_E0181_Atherinomorus_vaigiensis PCR_G1197_Ambassis_urotaenia Mugil_cephalus|E1541|C796426|320|0 PCR_E0031_Mugil_curema Mugil_cephalus|E1541|scaffold13191|1|287 PCR_E0049_Mugil_cephalus PCR_E0847_Valamugil_buchanani PCR_E0846_Crenimugil_crenilabis PCR_E0809_Myxus_capensis PCR_E0845_Chelon_macrolepis Liza_haematocheila|E1541|C925444|798|1 PCR_E0808_Liza_richardsonii PCR_E0133_Etroplus_maculatus PCR_G1423_Paretroplus_maculatus PCR_G1256_Cichla_temensis Amphilophus_citrinellus|E1541|CCOE01001704.1|569341|568499 PCR_G1319_Herichthys_cyanoguttatus PCR_G1320_Heros_efasciatus_appendiculatus PCR_G1459_Ptychochromis_grandidieri PCR_G1420_Paratilapia_polleni PCR_G1321_Heterochromis_multidens PCR_G1407_Oreochromis_niloticus Oreochromis_niloticus|E1541|GL831187.1|2373528|2372686 Oreochromis_niloticus|E1541|model|0 PCR_G1520_Neolamprologus_brichardi Neolamprologus_brichardi|E1541|NW_006272014.1|8625496|8624654 Melanochromis_auratus|E1541|ABPL01020477.1|235|1075 PCR_G1518_Astatotilapia_burtoni PCR_G1521_Pundamilia_nyererei Pundamilia_nyererei|E1541|NW_005187410.1|3376144|3376986 Haplochromis_burtoni|E1541|NW_005179423.1|997384|996542 PCR_G1519_Metriaclima_zebra Maylandia_zebra|E1541|NW_014444809.1|3861727|3860885 PCR_E0211_Lipogramma_anabantoides PCR_E0280_Gramma_loreto PCR_G1209_Arrhamphus_sclerolepis Hyporhamphus_intermedius|E1541|C790828|1|245 PCR_E0624_Cheilopogon_dorsomacula PCR_E0400_Prognichthys_brevipinnis PCR_E0401_Hirundichthys_marginatus PCR_G1275_Dermogenys_collettei PCR_G1508_Xenentodon_cancila PCR_E0110_Strongylura_notata PCR_E0114_Platybelone_argalus PCR_G1276_Diademichthys_lineatus Tomicodon_sp|E1541|C612712|189|1 Tomicodon_sp|E1541|scaffold11302|403|32 PCR_G1408_Oryzias_latipes Oryzias_latipes|E1541|21|23073383|23074226 Oryzias_latipes|E1541|model|0 Kryptolebias_marmoratus|E1541|LHSH01000092.1|710799|711641 Aplocheilus_lineatus|E1541|TR119035|c0_g1_i1|1|290 Austrofundulus_limnaeus|E1541|NW_013952554.1|6699|5858 Aplocheilus_lineatus|E1541|TR62664|c0_g1_i1|1241|2080 Nothobranchius_furzeri|E1541|NC_029662.1|30488942|30488099 Cyprinodon_varigatus|E1541|JPKM01108812.1|937|94 Cyprinodon_nevadensis_pectoralis|E1541|JSUU01007439.1|105548|106398 Ameca_splendens|E1541|TRINITY_DN13584_c0_g1_i1|885|42 PCR_E1064_Lucania_parva_goodei PCR_E0389_Fundulus_parvipinnis PCR_G1293_Fundulus_heteroclitus Fundulus_heteroclitus|E1541|NW_012234395.1|422128|421285 PCR_E0186_Fundulus_chrysotus PCR_E0173_Adinia_xenica Poecilia_reticulata|E1541|NC_024332.1|32267519|32266676 PCR_E0185_Heterandria_formosa Poecilia_formosa|E1541|NW_006799955.1|4210852|4210009 PCR_G1296_Gambusia_affinis Xiphophorus_couchianus|E1541|KQ557222.1|15512854|15512011 Xiphophorus_hellerii|E1541|KQ556855.1|15544036|15543193 Xiphophorus_maculatus|E1541|NW_005372315.1|823422|824265 PCR_E0855_Plesiops_coeruleolineatus PCR_G1442_Plesiops_melas PCR_E0300_Labrisomus_guppyi_multiporosus PCR_G1299_Gillellus_semicinctus Acanthemblemaria_sp|E1541|scaffold26794|1000|608 PCR_E0313_Chaenopsis_sp_alepidota Acanthemblemaria_sp|E1541|C511649|142|1 Parablennius_parvicornis|E1541|utg7180000064352|205|1047 PCR_E0296_Ophioblennius_atlanticus PCR_E0980_Entomacrodus_niuafoouensis PCR_E0987_Entomacrodus_striatus PCR_E0989_Alticus_arnoldorum PCR_E0986_Blenniella_chrysospilos_paula PCR_E0984_Ecsenius_bicolor PCR_E0979_Blenniella_paula PCR_E0988_Salarias_fasciatus PCR_E0526_Meiacanthus_oualanensis_grammistes PCR_E0909_Petroscirtes_mitratus PCR_G1436_Pholidochromis_cerasina PCR_G1343_Labracinus_cyclophthalmus PCR_G1403_Ogilbyina_novaehollandiae Pseudochromis_fuscus|E1541|utg7180001223182|1|468 PCR_E0535_Pseudochromis_jamesi PCR_E0706_Pseudochromis_cyanotaenia PCR_E0851_Chromis_dimidiata PCR_E0201_Chromis_cyanea Chromis_chromis|E1541|utg7180001194933|14623|13781 PCR_E0820_Abudefduf_saxatilis PCR_E0881_Abudefduf_sexfasciatus PCR_E0559_Pomachromis_richardsoni PCR_E0564_Chrysiptera_taupou Amphiprion_melanopus|E1541|C949548|211|1 PCR_E0557_Pomacentrus_spilotoceps PCR_E0465_Neoglyphidodon_melas PCR_E0464_Dischistodus_perspicillatus PCR_E0193_Amphiprion_ocellaris Stegastes_partitus|E1541|NW_007578288.1|154897|155739 PCR_E0219_Stegastes_diencaeus PCR_E0203_Stegastes_fuscus PCR_E0204_Stegastes_partitus PCR_E0929_Lepidozygus_tapeinosoma PCR_E0713_Stegastes_albifasciatus PCR_E0580_Azurina_hirundo PCR_E0572_Plectroglyphidodon_dickii PCR_E0722_Plectroglyphidodon_johnstonianus PCR_E0724_Dascyllus_reticulatus Caranx_ignobilis|E1541|C472372|0|146 PCR_E0459_Hypsypops_rubicundus PCR_G1375_Microspathodon_bairdii PCR_E0772_Microspathodon_chrysurus 0.4
Figure 17: TBR1 gene tree with PCR products. Sequences of the TBR1 gene and paralogs found via nHmmer searches in our 305 taxa are in black, with the addition of PCR products from Betancur et al. (2013) highlighted in red. Tree was inferred with RAxML under the GTRGAMMA model.
85
Coregonus_clupeaformis|E1730|UCC_MYSS.4.10|85|5863 Coryphaena_hippurus|E1730|TRINITY_DN37547_c2_g3_i1|5896|125 Alosa_alosa|E1730|EAA_LOC101481490.2.2|5357|546 Menidia_menidia|E1730|gb|GEVY01002758.1||7955|2190 Thymallus_thymallus|E1730|ITT_MYSS.1.5|1|4971 Alosa_alosa|E1730|EAA_MYHZ2.1.3|5994|212 Engraulis_encrasicolus|E1730|muscle_ID.302496|5952|169 Thymallus_thymallus|E1730|ITT_MYHZ2.1.1|66|5785 Plecoglossus_altivelis|E1730|ZPA_MYSS.6.8|3|4734 Umbra_pygmae|E1730|YUP_MYSS.3.8|11329|5561 Thymallus_thymallus|E1730|ITT_WU_FD14A01.1.1|60|5833 Supplemental Figure 2: MYH6 gene tree with PCR products Thymallus_thymallus|E1730|ITT_MYHA.1.1|5423|3 Apteronotus_albifrons|E1730|A2AA_MYSS.1.4|65|5841 Coregonus_clupeaformis|E1730|UCC_MYSS.1.10|5756|1 Salvelinus_fontinalis|E1730|QSF_MMYHL2.1.1|1058|5912 Alosa_alosa|E1730|EAA_MYSS.3.17|5875|102 Sequences of the MYH6 gene and paralogs found Salvelinus_fontinalis|E1730|QSF_MYSS.2.11|5892|132 Thymallus_thymallus|E1730|ITT_MYHZ1.1.1.1|6260|481 Alosa_alosa|E1730|EAA_MYSS.2.17|11192|16975 via nHmmer searches, with PCR products from Betancur Alosa_alosa|E1730|EAA_MYSS.6.17|96|5891 Engraulis_encrasicolus|E1730|muscle_ID.177886|86|5876 et al. 2013 (2) added and highlighted in red. The alignment Alosa_alosa|E1730|EAA_MYSS.1.17|83|5858 Osteoglossum_bicirrhosum|E1730|COB_MYSS.1.9|140|5910 was trimmed to the length of the PCR-based locus, as Gnathonemus_petersii|E1730|B2GP_MYSS.1.6|264|6043 Apteronotus_albifrons|E1730|A2AA_MYSS.4.4|78|5854 Pangasianodon_hypophthalamus|E1730|GPH_MYSS.1.7|67|5844 MYH6 is considerably longer. Tree was inferred with Thymallus_thymallus|E1730|ITT_MYSS.5.5|5978|201 Pangasianodon_hypophthalamus|E1730|GPH_LOC101163414.1.1|5033|364 RAxML under the GTRGAMMA model. Plecoglossus_altivelis|E1730|ZPA_MYSS.3.8|97|5878 Umbra_pygmae|E1730|YUP_MYSS.2.8|5963|175 Thymallus_thymallus|E1730|ITT_VMHC.2.2|6054|255 Thymallus_thymallus|E1730|ITT_MYSS.4.5|83|5871 Haemulon_flavolineatum|E1730|scaffold4146|98|5893 Solea_ovata|E1730|scaffold561|86|5711 Liza_haematocheila|E1730|scaffold4589|79|5341 Erythrinus_erythrinus|E1730|scaffold5327|91|5859 Gyrinocheilus_aymonieri|E1730|scaffold4738|5402|114 Rhamphichthys_rostratus|E1730|scaffold2896|5848|611 Liobagrus_styani|E1730|scaffold579|108|5872 Hemibagrus_guttatus|E1730|scaffold802|5137|37 Sargocentron_vexillarium|E1730|scaffold226|73|5411 Sargocentron_vexillarium|E1730|scaffold229|73|4817 Bythidae_sp|E1730|scaffold899|76|5796 Bythidae_sp|E1730|scaffold898|76|5837 Bythidae_sp|E1730|scaffold895|76|5536 Lutjanus_sebae|E1730|C782113|5916|138 Caranx_ignobilis|E1730|scaffold26162|70|5848 Pseudobalistes_fuscus|E1730|scaffold690|1|4756 Pseudobalistes_fuscus|E1730|scaffold687|1|4817 Pseudobalistes_fuscus|E1730|scaffold689|1|4755 Scarus_ghobban|E1730|scaffold2812|86|5868 Scarus_ghobban|E1730|scaffold2813|87|5896 Haemulon_flavolineatum|E1730|scaffold4149|81|5247 Haemulon_flavolineatum|E1730|scaffold4147|97|5263 Ostracion_rhinorhynchos|E1730|scaffold5240|79|5738 Ostracion_rhinorhynchos|E1730|scaffold5239|79|4788 Diodon_holocanthus|E1730|scaffold10835|5575|1 Diodon_holocanthus|E1730|scaffold10838|5547|1 Diodon_holocanthus|E1730|scaffold10834|5872|118 Osphronemus_goramy|E1730|scaffold113|80|5827 Gerres_filamentosus|E1730|scaffold1911|5938|157 Gerres_filamentosus|E1730|scaffold1913|4748|2 Parapercis_xanthozona|E1730|scaffold351|5115|137 Parapercis_xanthozona|E1730|scaffold348|5115|137 Parapercis_xanthozona|E1730|scaffold347|5134|137 Parapercis_xanthozona|E1730|scaffold349|5115|137 Parapercis_xanthozona|E1730|scaffold350|5115|137 Polypterus_endlicheri|E1730|scaffold46677|137|5912 Osteoglossum_bicirrhosum|E1730|COB_LOC100462944.4.5|4965|10114 Alosa_alosa|E1730|EAA_MYH7BB.1.1|790|5921 Engraulis_encrasicolus|E1730|muscle_ID.269280|6682|1546 Apteronotus_albifrons|E1730|A2AA_MYH7BB.1.2|676|5818 Hepsetus_odoe|E1730|scaffold35627|1|4945 Erythrinus_erythrinus|E1730|scaffold19257|5585|318 Umbra_pygmae|E1730|YUP_MYH7BB.1.1|912|6051 Coregonus_clupeaformis|E1730|UCC_LOC100701355.2.2|582|5721 Salvelinus_fontinalis|E1730|QSF_LOC100462944.1.1|6184|1045 Plecoglossus_altivelis|E1730|ZPA_LOC100701355.1.1|5336|188 Coryphopterus_lipernes|E1730|scaffold23007|117|5906 Oxyeleotris_marmorata|E1730|scaffold17311|146|5868 Oxyeleotris_marmorata|E1730|scaffold17310|684|5818 Gymnodraco_acuticeps|E1730|comp109043_c0_seq1|5255|128 Channa_gachua|E1730|scaffold18002|5894|110 Tomicodon_sp|E1730|scaffold13361|4825|113 Amblycirrhitus_pinos|E1730|scaffold5812|652|5806 Polypterus_endlicheri|E1730|scaffold46712|6149|394 Atractosteus_spatula|E1730|scaffold41548|6140|426 Lepisosteus_platyrhincus|E1730|scaffold39528|3|4768 Osteoglossum_bicirrhosum|E1730|COB_LOC100015891.1.1|152|5857 Polynemus_dubius|E1730|scaffold36070|6282|575 Apteronotus_albifrons|E1730|A2AA_LOC100015891.1.1|5178|421 Hemigrammus_bleheri|E1730|scaffold1229|3|4634 Alosa_alosa|E1730|EAA_LOC100015891.1.1|142|5854 Hyporhamphus_intermedius|E1730|scaffold1663|160|5821 Alosa_alosa|E1730|EAA_BM1_40715.1.1|6052|324 Alosa_alosa|E1730|EAA_MYO4.1.1|6398|660 Gymnodraco_acuticeps|E1730|comp101546_c0_seq1|98|5733 Lepidonotothen_nudifrons|E1730|gi|1066858842|emb|HACN01078682.1||1739|7045 Lepidonotothen_nudifrons|E1730|gi|1066858838|emb|HACN01078686.1||1739|7081 Lepidonotothen_nudifrons|E1730|gi|1066858843|emb|HACN01078681.1||320|5758 Lepidonotothen_nudifrons|E1730|gi|1066858839|emb|HACN01078685.1||320|5723 Lepidonotothen_nudifrons|E1730|gi|1066858837|emb|HACN01078687.1||1004|6396 Lepidonotothen_nudifrons|E1730|gi|1066858847|emb|HACN01078677.1||320|5712 Gnathonemus_petersii|E1730|B2GP_MYH11.4.4|231|5306 Polypterus_endlicheri|E1730|scaffold8342|7375|1758 Alosa_alosa|E1730|EAA_MYH14.2.3|7738|2089 Alosa_alosa|E1730|EAA_MYH14.3.3|398|5945 Apteronotus_albifrons|E1730|A2AA_MYH14.2.2|9355|3665 Pangasianodon_hypophthalamus|E1730|GPH_MYH14.2.2|417|6100 Pangasianodon_hypophthalamus|E1730|GPH_MYH14.1.2|9026|3415 Osteoglossum_bicirrhosum|E1730|COB_MYH14.2.3|10359|16026 Osteoglossum_bicirrhosum|E1730|COB_MYH14.3.3|616|6214 Plecoglossus_altivelis|E1730|ZPA_MYH10.1.3|404|5961 Umbra_pygmae|E1730|YUP_MYH14.2.2|412|5973 Umbra_pygmae|E1730|YUP_MYH10.1.5|735|6255 Umbra_pygmae|E1730|YUP_MYH14.1.2|454|6098 Thymallus_thymallus|E1730|ITT_MYH14.3.3|552|6194 Salvelinus_fontinalis|E1730|QSF_LOC101164562.2.3|14139|8558 Salvelinus_fontinalis|E1730|QSF_MYH10.3.7|476|6022 Salvelinus_fontinalis|E1730|QSF_MYH9.4.5|237|5801 Apogonichthyoides_cathetogramma|E1730|scaffold19968|8959|3417 Tomicodon_sp|E1730|scaffold5133|8404|2900 Scarus_ghobban|E1730|scaffold10038|412|5942 Parambassis_pulcinella|E1730|scaffold1886|6398|932 Liza_haematocheila|E1730|scaffold31227|6562|1069 Channa_gachua|E1730|scaffold27972|406|5926 Foetorepus_agassizii|E1730|scaffold502|423|5966 Lactoria_cornuta|E1730|scaffold18659|413|5404 Dendrochirus_zebra|E1730|scaffold20265|346|5930 Thayeria_boehlkei|E1730|scaffold7173|17|5407 Apteronotus_albifrons|E1730|A2AA_MYH10.1.1|6551|977 Apteronotus_albifrons|E1730|A2AA_LOC100707073.3.3|7273|1660 Alosa_alosa|E1730|EAA_MYH10.1.5|592|6183 Alosa_alosa|E1730|EAA_LOC100690099.1.1|350|5950 Osteoglossum_bicirrhosum|E1730|COB_MYH10.1.3|375|5978 Osteoglossum_bicirrhosum|E1730|COB_MYH10.2.3|364|6030 Gnathonemus_petersii|E1730|B2GP_MYH10.3.5|7134|1584 Gnathonemus_petersii|E1730|B2GP_MYH10.2.5|7097|1484 Plecoglossus_altivelis|E1730|ZPA_LOC100707073.1.2|337|5934 Plecoglossus_altivelis|E1730|ZPA_LOC100707073.2.2|6863|1273 Menidia_menidia|E1730|gb|GEVY01005976.1||6610|1015 Syngnathoides_biaculeatus|E1730|scaffold5232|5434|637 Umbra_pygmae|E1730|YUP_LOC100690099.1.1|395|5939 Salvelinus_fontinalis|E1730|QSF_LOC101164959.1.1|289|5883 Salvelinus_fontinalis|E1730|QSF_MYH10.6.7|7933|2439 Coregonus_clupeaformis|E1730|UCC_LOC101165692.1.1|578|6172 Thymallus_thymallus|E1730|ITT_MYH10.1.6|8336|2748 Megalops_cyprinoides|E1730|brain_scaffold5037|24|5120 Lepisosteus_platyrhincus|E1730|scaffold11219|6131|1020 Syngnathoides_biaculeatus|E1730|scaffold5234|6219|637 Polypterus_bichir|E1730|scaffold13277|5990|1270 Alosa_alosa|E1730|EAA_MYH10.4.5|7545|1941 Plecoglossus_altivelis|E1730|ZPA_MYH10.2.3|370|5979 Coregonus_clupeaformis|E1730|UCC_LOC101164562.1.1|7394|1754 Coregonus_clupeaformis|E1730|UCC_MYH10.1.3|312|5942 Thymallus_thymallus|E1730|ITT_MYH10.3.6|168|5794 Salvelinus_fontinalis|E1730|QSF_MYH10.1.7|7350|1651 Salvelinus_fontinalis|E1730|QSF_MYH10.5.7|301|5926 Salvelinus_fontinalis|E1730|QSF_MYH10.4.7|4|5537 Protopterus_aethiopicus|E1730|scaffold1870|6216|610 Lepisosteus_platyrhincus|E1730|scaffold11218|6588|1020 Polypterus_endlicheri|E1730|scaffold40667|6853|1309 Polypterus_bichir|E1730|scaffold13276|6840|1277 Polypterus_bichir|E1730|scaffold13275|6896|1355 Hepsetus_odoe|E1730|scaffold16546|217|5823 Thayeria_boehlkei|E1730|scaffold7174|139|4844 Plecoglossus_altivelis|E1730|ZPA_LOC777990.1.1|2171|7707 Coregonus_clupeaformis|E1730|UCC_LOC777990.1.1|267|5829 Hyporhamphus_intermedius|E1730|scaffold12020|6172|616 Gerres_filamentosus|E1730|scaffold278|429|6048 Terapon_jarbua|E1730|scaffold4901|6444|865 Lutjanus_sebae|E1730|scaffold12614|469|6051 Siganus_guttatus|E1730|scaffold23290|304|5890 Osteoglossum_bicirrhosum|E1730|COB_LOC100691292.1.1|6859|1316 Gnathonemus_petersii|E1730|B2GP_MYH11.2.4|5888|400 Alosa_alosa|E1730|EAA_LOC100707073.1.2|7250|1645 Alosa_alosa|E1730|EAA_MYH11A.2.2|7004|1431 Misgurnus_anguillicaudatus|E1730|scaffold10920|18|5329 Gyrinocheilus_aymonieri|E1730|scaffold4353|8196|2628 Distichodus_sexfasciatus|E1730|scaffold7089|10033|4540 Hemigrammus_bleheri|E1730|scaffold6384|202|5812 Gasteropelecus_sp|E1730|scaffold11976|287|5854 Gasteropelecus_sp|E1730|scaffold11978|287|5731 Apteronotus_albifrons|E1730|A2AA_MYH11A.1.2|316|5919 Pangasianodon_hypophthalamus|E1730|GPH_LOC101164562.2.4|2516|7633 Pangasianodon_hypophthalamus|E1730|GPH_MYH10.1.4|5841|254 Pangasianodon_hypophthalamus|E1730|GPH_MYH11A.1.1|6768|1199 Megalops_cyprinoides|E1730|gill_scaffold2386|255|5740 Osteoglossum_bicirrhosum|E1730|COB_MYH11A.1.1|6771|1215 Mormyrus_tapirus|E1730|scaffold36111|7239|1690 Gnathonemus_petersii|E1730|B2GP_LOC101487875.1.1|7297|1705 Papyrocranus_afer|E1730|scaffold23586|854|5953 Papyrocranus_afer|E1730|scaffold23587|250|5772 Plecoglossus_altivelis|E1730|ZPA_LOC101487875.1.2|2529|8088 Argentina_sp|E1730|scaffold3302|7368|1922 Umbra_pygmae|E1730|YUP_LOC100707073.2.2|8001|2456 Umbra_pygmae|E1730|YUP_MYH10.4.5|7992|2456 Umbra_pygmae|E1730|YUP_MYH10.5.5|6853|1317 Umbra_pygmae|E1730|YUP_LOC100690391.1.1|359|5902 Salvelinus_fontinalis|E1730|QSF_LOC101164562.2.3|202|5747 Salvelinus_fontinalis|E1730|QSF_MYH9.3.5|6811|1260 Coregonus_clupeaformis|E1730|UCC_LOC101164959.1.2|7376|1756 Coregonus_clupeaformis|E1730|UCC_LOC101487875.1.1|6740|1179 Thymallus_thymallus|E1730|ITT_LOC100707073.1.4|435|5985 Thymallus_thymallus|E1730|ITT_LOC101164562.2.3|6956|1395 Thymallus_thymallus|E1730|ITT_LOC100691292.2.2|4369|9931 Synodus_sp|E1730|scaffold6101|6928|1384 Myripristis_berndti|E1730|scaffold2277|294|5821 Sargocentron_rubrum|E1730|scaffold20696|281|5845 Sargocentron_rubrum|E1730|scaffold20698|281|5775 Caranx_ignobilis|E1730|scaffold7571|375|5939 Polynemus_dubius|E1730|scaffold24630|7479|2460 Polynemus_dubius|E1730|scaffold24631|8784|3331 Polynemus_dubius|E1730|scaffold24629|8105|2539 Hippoglossus_hippoglossus|E1730|contig00096|4941|5 Solea_ovata|E1730|scaffold1976|6645|1080 Gambusia_affinis_whole|E1730|scaffold16391|7206|1545 Dascyllus_trimaculatus|E1730|scaffold746|403|5956 Mugil_cephalus|E1730|scaffold23831|0|4992 Liza_haematocheila|E1730|scaffold11065|5692|809 Liza_haematocheila|E1730|scaffold11064|6566|1037 Sinibotia_superciliaris|E1730|scaffold13403|6665|1093 Channa_micropeltes|E1730|scaffold3266|199|5633 Channa_gachua|E1730|scaffold26895|283|5851 Channa_gachua|E1730|scaffold26896|283|5776 Nomeus_gronovii|E1730|scaffold16712|5121|19 Apogonichthyoides_cathetogramma|E1730|scaffold8499|307|5840 Apogonichthyoides_cathetogramma|E1730|scaffold8500|307|5794 Oxyeleotris_marmorata|E1730|scaffold20404|353|5887 Hyporhamphus_intermedius|E1730|scaffold5591|6545|950 Scarus_iseri|E1730|scaffold8657|6601|1031 Scarus_iseri|E1730|scaffold8659|5948|472 Thalassoma_bifasciatum|E1730|scaffold5203|787|5726 Thalassoma_bifasciatum|E1730|scaffold5201|331|5726 Siniperca_scherzeri|E1730|scaffold4742|369|5903 Siniperca_scherzeri|E1730|scaffold4745|245|5760 Dendrochirus_zebra|E1730|scaffold20264|283|5831 Peristedion_sp|E1730|scaffold2041|6427|952 Priacanthus_tayenus|E1730|scaffold1841|6616|1096 Equetus_punctatus|E1730|scaffold15057|332|5898 Drepane_punctata|E1730|scaffold4835|6728|1164 Foetorepus_agassizii|E1730|scaffold19995|265|5764 Chaunax_pictus|E1730|scaffold12280|6635|1658 Pseudobalistes_fuscus|E1730|scaffold10032|320|5886 Diodon_holocanthus|E1730|scaffold16167|6569|1011 Lactoria_cornuta|E1730|scaffold31262|10917|5356 Ostracion_rhinorhynchos|E1730|scaffold1953|310|5866 Eucinostomus_sp|E1730|scaffold14927|229|5795 Photopectoralis_bindus|E1730|scaffold14401|262|5682 Photopectoralis_bindus|E1730|scaffold14400|262|5527 Chaetodon_auriga|E1730|scaffold4171|6657|1093 Datnioides_microlepis|E1730|scaffold1188|463|5835 Datnioides_microlepis|E1730|scaffold1187|375|5942 Protopterus_aethiopicus|E1730|scaffold1869|6992|1423 Polypterus_bichir|E1730|scaffold26496|7195|1642 Polypterus_endlicheri|E1730|scaffold21622|1186|6269 Polypterus_endlicheri|E1730|scaffold21621|397|5950 Lepisosteus_platyrhincus|E1730|scaffold11216|6554|1020 Lepisosteus_platyrhincus|E1730|scaffold11220|7050|1721 Lepisosteus_platyrhincus|E1730|scaffold11217|7133|1758 Osteoglossum_bicirrhosum|E1730|COB_LOC100707073.3.3|283|5880 Gnathonemus_petersii|E1730|B2GP_LOC100707073.4.4|366|5945 Osteoglossum_bicirrhosum|E1730|COB_LOC100707073.2.3|12516|7369 Osteoglossum_bicirrhosum|E1730|COB_LOC100707073.1.3|322|5916 Gnathonemus_petersii|E1730|B2GP_MYH9.7.7|360|5904 Gnathonemus_petersii|E1730|B2GP_MYH10.4.5|352|5902 Gnathonemus_petersii|E1730|B2GP_LOC100707073.2.4|356|5906 Plecoglossus_altivelis|E1730|ZPA_LOC101164562.1.1|424|5993 Plecoglossus_altivelis|E1730|ZPA_contig_003250|420|5987 Plecoglossus_altivelis|E1730|ZPA_MYH10.3.3|3493|9088 Plecoglossus_altivelis|E1730|ZPA_LOC100691292.3.3|360|5915 Plecoglossus_altivelis|E1730|ZPA_LOC101478531.3.4|376|5930 Plecoglossus_altivelis|E1730|ZPA_LOC100705764.1.1|6520|947 Umbra_pygmae|E1730|YUP_LOC100705764.1.1|442|6011 Umbra_pygmae|E1730|YUP_LOC100691292.2.2|6814|1249 Coregonus_clupeaformis|E1730|UCC_LOC100705764.1.1|7019|1427 Thymallus_thymallus|E1730|ITT_LOC101164562.3.3|0|5477 Salvelinus_fontinalis|E1730|QSF_MYH9.2.5|6404|838 Salvelinus_fontinalis|E1730|QSF_LOC101164562.1.3|6939|1374 Salvelinus_fontinalis|E1730|QSF_LOC101154782.1.1|338|5881 Gyrinocheilus_aymonieri|E1730|scaffold4352|6695|1151 Pangasianodon_hypophthalamus|E1730|GPH_LOC101164562.1.4|12769|7660 Apteronotus_albifrons|E1730|A2AA_MYH9A.1.1|394|5959 Alosa_alosa|E1730|EAA_MYH9A.1.1|585|6149 Alosa_alosa|E1730|EAA_MYH10.2.5|381|5950 Synodus_sp|E1730|scaffold10784|398|5960 Syngnathoides_biaculeatus|E1730|scaffold5230|6155|597 Sargocentron_vexillarium|E1730|scaffold2704|7035|1495 Foetorepus_agassizii|E1730|scaffold500|411|6022 Foetorepus_agassizii|E1730|scaffold501|414|6022 Phaeoptyx_sp|E1730|scaffold4302|6442|1131 Exyrias_puntang|E1730|scaffold27311|6193|652 Priacanthus_tayenus|E1730|scaffold1839|6664|1096 Hippoglossus_hippoglossus|E1730|contig00019|293|5876 Tomicodon_sp|E1730|scaffold9392|6469|810 Parupeneus_indicus|E1730|scaffold1556|9195|3665 Parupeneus_indicus|E1730|scaffold1558|9960|4451 Scomberomorus_regalis|E1730|scaffold4676|336|5975 Channa_gachua|E1730|scaffold19128|5124|46 Micropterus_floridanus|E1730|scaffold2532|333|5937 Equetus_punctatus|E1730|scaffold7422|7042|1547 Pseudobalistes_fuscus|E1730|scaffold593|321|5817 Coryphaena_hippurus|E1730|TRINITY_DN37708_c0_g2_i4|428|6040 Coryphaena_hippurus|E1730|TRINITY_DN37708_c0_g2_i3|428|6037 Menidia_menidia|E1730|gb|GEVY01016075.1||374|5994 Dascyllus_trimaculatus|E1730|scaffold748|364|5901 Aulostomus_maculatus|E1730|scaffold14233|298|5817 Aulostomus_maculatus|E1730|scaffold14234|298|5871 Aulostomus_maculatus|E1730|scaffold14236|298|5227 Tinca_tinca|E1730|scaffold9437|313|5897 Gyrinocheilus_aymonieri|E1730|scaffold15199|6635|1499 Misgurnus_anguillicaudatus|E1730|scaffold16341|6816|1236 Misgurnus_anguillicaudatus|E1730|scaffold16342|6874|1317 Alosa_alosa|E1730|EAA_MYH9.1.3|6199|1073 Alosa_alosa|E1730|EAA_MYH9.3.3|284|5901 Apteronotus_albifrons|E1730|A2AA_LOC101164562.1.2|11290|16516 Apteronotus_albifrons|E1730|A2AA_LOC100691292.1.1|2518|7650 Apteronotus_albifrons|E1730|A2AA_MYH14.1.2|2445|7562 Apteronotus_albifrons|E1730|A2AA_LOC100707073.2.3|3610|8732 Apteronotus_albifrons|E1730|A2AA_LOC100707073.1.3|2345|7468 Corydoras_julii|E1730|scaffold4370|6730|1123 Thayeria_boehlkei|E1730|scaffold7171|284|5841 Plotosus_lineatus|E1730|scaffold28945|358|5891 Pangasianodon_hypophthalamus|E1730|GPH_MYH9B.1.1|2069|7549 Pangasianodon_hypophthalamus|E1730|GPH_LOC101478531.2.2|417|5919 Pangasianodon_hypophthalamus|E1730|GPH_LOC100707073.1.1|6580|1092 Umbra_pygmae|E1730|YUP_LOC100707073.1.2|272|5849 Salvelinus_fontinalis|E1730|QSF_LOC100691292.1.2|331|5931 Salvelinus_fontinalis|E1730|QSF_LOC100707073.1.3|349|5918 Salvelinus_fontinalis|E1730|QSF_contig_031007|6950|1366 Salvelinus_fontinalis|E1730|QSF_MYH11.2.2|412|5994 Thymallus_thymallus|E1730|ITT_LOC100707073.4.4|7|5092 Thymallus_thymallus|E1730|ITT_contig_038045|0|5393 Thymallus_thymallus|E1730|ITT_MYH14.2.3|552|6110 Thymallus_thymallus|E1730|ITT_LOC100707073.2.4|6935|1324 Thymallus_thymallus|E1730|ITT_contig_038045|14146|8539 Coregonus_clupeaformis|E1730|UCC_MYH11.1.1|366|5965 Coregonus_clupeaformis|E1730|UCC_SMYHC2.1.1|284|5895 Coregonus_clupeaformis|E1730|UCC_MYH10.2.3|8258|2655 Coregonus_clupeaformis|E1730|UCC_LOC101478531.1.1|483|6050 Coregonus_clupeaformis|E1730|UCC_LOC100707073.1.1|476|6027 Coregonus_clupeaformis|E1730|UCC_MYH10.3.3|7058|1460 Coregonus_clupeaformis|E1730|UCC_LOC101164959.2.2|6275|671 Galaxiella_nigrostriata|E1730|scaffold12343|364|5952 Sargocentron_vexillarium|E1730|scaffold2706|6922|1424 Sargocentron_vexillarium|E1730|scaffold2707|6470|1424 Exyrias_puntang|E1730|scaffold24050|426|6026 Coryphopterus_lipernes|E1730|scaffold21647|6886|1287 Oxyeleotris_marmorata|E1730|scaffold1679|5670|615 Oxyeleotris_marmorata|E1730|scaffold1677|6190|615 Gymnodraco_acuticeps|E1730|comp106909_c0_seq5|7182|1626 Gymnodraco_acuticeps|E1730|comp106909_c0_seq3|8073|2525 Tomicodon_sp|E1730|scaffold6722|7905|2432 Foetorepus_agassizii|E1730|scaffold499|412|5793 Channa_gachua|E1730|scaffold10702|425|5908 Channa_gachua|E1730|scaffold10703|425|5858 Scarus_ghobban|E1730|scaffold29298|0|4934 Scarus_iseri|E1730|scaffold8656|7037|1499 Hippoglossus_hippoglossus|E1730|contig00023|6699|1559 Polynemus_dubius|E1730|scaffold6801|343|5908 Basilichthys_microlepidotus|E1730|gb|GEVG01000291.1||343|5883 Menidia_menidia|E1730|gb|GEVY01000498.1||494|6027 Scophthalmus_maximus|E1730|scaffold10091|9148|3683 Scophthalmus_maximus|E1730|scaffold10089|7144|1635 Scophthalmus_maximus|E1730|scaffold10090|6490|991 Amblycirrhitus_pinos|E1730|scaffold4872|422|5955 Amblycirrhitus_pinos|E1730|scaffold4875|422|5960 Micropterus_floridanus|E1730|scaffold2533|388|5938 Equetus_punctatus|E1730|scaffold7425|5315|39 Equetus_punctatus|E1730|scaffold7421|7027|1551 Oplegnathus_punctatus|E1730|scaffold16|417|5843 Terapon_jarbua|E1730|scaffold11231|6832|1682 Terapon_jarbua|E1730|scaffold11232|6593|1572 Lateolabrax_maculatus|E1730|gb|GBZV01030575.1||367|5926 Lutjanus_fulviflamma|E1730|scaffold6849|883|5780 Acanthurus_tractus|E1730|scaffold2334|7091|1577 Chaunax_pictus|E1730|scaffold19057|431|5850 Pseudobalistes_fuscus|E1730|scaffold21333|6683|1577 Diodon_holocanthus|E1730|scaffold1278|407|5910 Diodon_holocanthus|E1730|scaffold1277|289|5853 PCR_G1511_Xenopus_tropicalis PCR_G1378_Monodelphis_domestica PCR_G1328_Homo_sapiens PCR_G1382_Mus_musculus Atractosteus_spatula|E1730|scaffold21051|1|5064 Lepisosteus_platyrhincus|E1730|scaffold24947|67|5840 Atractosteus_spatula|E1730|scaffold21049|68|5855 Scarus_iseri|E1730|scaffold1387|77|4902 Scarus_iseri|E1730|scaffold1386|77|4973 Terapon_jarbua|E1730|scaffold1379|4884|0 Ostracion_rhinorhynchos|E1730|scaffold296|6100|708 Lipogramma_evides|E1730|scaffold7064|5907|119 Alosa_alosa|E1730|EAA_VMHCL.1.1|5347|0 Umbra_pygmae|E1730|YUP_LOC101483728.1.1|5103|402 Plecoglossus_altivelis|E1730|ZPA_LOC100690099.1.2|6295|1273 Lepidogalaxias_salamandroides|E1730|scaffold1349|249|5615 Homatula_potanini|E1730|scaffold12004|5930|145 Apteronotus_albifrons|E1730|A2AA_VMHCL.1.4|3341|8488 Pangasianodon_hypophthalamus|E1730|GPH_VMHCL.1.2|198|5968 Osteoglossum_bicirrhosum|E1730|COB_SMYHC2.3.3|52|5845 Gnathonemus_petersii|E1730|B2GP_LOC100329670.1.1|1|5795 Umbra_pygmae|E1730|YUP_SMYHC3.1.1|10562|5627 Umbra_pygmae|E1730|YUP_VMHC.1.1|1639|7418 Salvelinus_fontinalis|E1730|QSF_LOC101483728.1.2|3257|9046 Thymallus_thymallus|E1730|ITT_LOC100329748.1.1|6852|1136 Coregonus_clupeaformis|E1730|UCC_LOC101483728.1.1|6692|902 Plecoglossus_altivelis|E1730|ZPA_SMYHC2.1.2|5914|134 Plecoglossus_altivelis|E1730|ZPA_SMYHC1.1.1|6942|1166 Umbra_pygmae|E1730|YUP_SMYHC2.1.1|62|5848 Thymallus_thymallus|E1730|ITT_SMYHC2.1.1|245|6036 Salvelinus_fontinalis|E1730|QSF_SMYHC1.1.1|5965|173 Coregonus_clupeaformis|E1730|UCC_SMYHC1.1.1|5970|179 Pangasianodon_hypophthalamus|E1730|GPH_SMYHC2.1.1|65|5862 Apteronotus_albifrons|E1730|A2AA_LOC100329670.2.3|428|6226 Alosa_alosa|E1730|EAA_LOC100329670.1.3|5915|121 Hemibagrus_guttatus|E1730|scaffold4609|0|5267 Hemibagrus_guttatus|E1730|scaffold4610|0|4968 Hemibagrus_guttatus|E1730|scaffold4611|0|5194 PCR_E0896_Enneapterygius_abeli PCR_E0885_Helcogramma_fuscopinna PCR_E0331_Helcogramma_ellioti_sp PCR_E0102_Arcos_sp PCR_G1276_Diademichthys_lineatus PCR_E1080_Lepadichthys_lineatus PCR_E0151_Aphredoderus_sayanus PCR_G1433_Percopsis_omiscomaycus PCR_E0189_Percopsis_transmontana Percopsis_transmontana|E1730|utg7180000583269|1211|6996 PCR_G1198_Amblyopsis_rosae PCR_G1254_Chologaster_cornuta Typhlichthys_subterraneus|E1730|utg7180001025138|1780|7564 PCR_G1490_Speoplatyrhinus_poulsoni PCR_E1083_Parapercis_hexophtalma PCR_E1091_Parapercis_punctulata PCR_E0707_Parapercis_clathrata PCR_G1348_Leiognathus_equulus PCR_G1298_Gazza_minuta PCR_E1126_Ariomma_bondi PCR_E0181_Atherinomorus_vaigiensis PCR_E1086_Hyporhamphus_dussumieri PCR_G1209_Arrhamphus_sclerolepis PCR_E0414_Ammodytes_hexapterus PCR_E0508_Lophogobius_cyprinoides PCR_E0736_Amblygobius_phalaena PCR_E0733_Fusigobius_neophytus PCR_E0617_Bollmannia_communis PCR_E1117_Chaunax_suttkusi PCR_E1121_Chaunax_stigmaeus PCR_E1120_Bembrops_anatirostris PCR_E1043_Amblyeleotris_guttata PCR_E0537_Periophthalmus_kalolo PCR_E1044_Eviota_prasites PCR_E1073_Amblyeleotris_wheeleri PCR_E1094_Valenciennea_strigata PCR_E1097_Ctenogobiops_crocineus PCR_E1084_Trimma_haima PCR_E1088_Vanderhorstia_ornatissima PCR_E1057_Caffrogobius_saldanha PCR_E1056_Caffrogobius_caffer PCR_E1089_Asterropteryx_semipunctatus PCR_E1077_Priolepis_cincta PCR_E1078_Istigobius_decoratus PCR_E1076_Fusigobius_inframaculatus PCR_E1075_Gnatholepis_anjerensis PCR_E0863_Fusigobius_duospilus PCR_E0667_Cubiceps_pauciradiatus PCR_E1052_Belonesox_belizanus PCR_G1465_Retropinna_semoni PCR_G1296_Gambusia_affinis Poecilia_reticulata|E1730|NC_024351.1|795038|789251 Poecilia_formosa|E1730|NW_006800299.1|109967|104180 Xiphophorus_hellerii|E1730|KQ556862.1|4326103|4320316 Xiphophorus_maculatus|E1730|NW_005372411.1|218602|224389 Xiphophorus_couchianus|E1730|KQ557207.1|4316385|4310598 PCR_E0926_Novaculichthys_taeniourus PCR_E0016_Xyrichtys_novacula_martinicensis PCR_E1092_Antennarius_coccineus PCR_E0587_Antennarius_nummifer Antennarius_striatus|E1730|utg7180000002640|0|5367 PCR_E0906_Cheilio_inermis PCR_E0014_Lachnolaimus_maximus PCR_E0015_Clepticus_parrae PCR_E0620_Decodon_puellaris PCR_E0560_Bodianus_mesothorax PCR_E0947_Bodianus_axillaris PCR_E0553_Cirrhilabrus_punctatus PCR_E0728_Cirrhilabrus_katherinae PCR_E0091_Coris_gaimard PCR_E0092_Thalassoma_quinquevittatum PCR_E0902_Thalassoma_lunare PCR_E0891_Thalassoma_amblycephalum PCR_E0895_Macropharyngodon_bipartitus PCR_E0637_Halichoeres_bathyphilus_bivittatus PCR_G1345_Labropsis_australis PCR_E0848_Labroides_dimidiatus PCR_G1344_Labrichthys_unilineatus PCR_E0908_Stethojulis_strigiventer PCR_E0567_Hologymnosus_doliatus PCR_E0912_Coris_formosa PCR_E0861_Coris_caudimacula PCR_G1499_Tautoga_onitis Symphodus_melops|E1730|utg7180000783567|6620|839 Labrus_bergylta|E1730|FKLU01001110.1|35033|29252 PCR_E0907_Cheilinus_chlorourus PCR_G1412_Oxycheilinus_celebicus PCR_E0948_Wetmorella_nigropinnata PCR_E0879_Epibulus_insidiator PCR_E0877_Leptoscarus_vaigiensis PCR_E0004_Sparisoma_viride PCR_E0566_Cetoscarus_bicolor PCR_E0872_Scarus_quoyi PCR_E0013_Scarus_croicensis PCR_E0874_Scarus_rubroviolaceus PCR_E0837_Chlorurus_sordidus PCR_E0875_Scarus_niger PCR_E0561_Chlorurus_gibbus PCR_E0878_Scarus_ghobban PCR_E0074_Plagiopsetta_glossa PCR_E0044_Helicolenus_dactylopterus Sebastes_norvegicus|E1730|utg7180001555773|5982|198 Sebastes_nigrocinctus|E1730|KI489908.1|5946|162 Sebastes_rubrivinctus|E1730|KI466896.1|7475|13259 PCR_E0349_Sebastes_aurora PCR_E0350_Sebastes_jordani PCR_E0354_Sebastes_paucispinis PCR_E0456_Peristedion_ecuadorense PCR_E0340_Prionotus_carolinus PCR_E0328_Prionotus_stephanophrys PCR_E0291_Scorpaena_guttata PCR_E0512_Scorpaena_dispar PCR_E0583_Iracundus_signifer PCR_E0581_Scorpaenopsis_oxycephala PCR_E0619_Neomerinthe_hemingwayi PCR_E0463_Pontinus_rathbuni PCR_E1010_Pontinus_longispinis PCR_E0532_Scorpaenodes_albaiensis PCR_E0870_Scorpaenodes_guamensis PCR_E0897_Dendrochirus_zebra PCR_E0705_Pterois_antennata PCR_G1229_Bovichtus_diacanthus PCR_G1267_Cottoperca_gobio PCR_G1327_Holanthias_chrysostictus PCR_G1452_Pseudanthias_pascalus PCR_E0338_Hemanthias_vivanus PCR_E0142_Zingel_zingel PCR_E0144_Zingel_streber PCR_E0391_Perca_flavescens PCR_G1428_Perca_fluviatilis PCR_G1453_Pseudaphritis_urvillii PCR_G1286_Eleginops_maclovinus PCR_G1527_Trematomus_borchgrevinki PCR_E0155_Gymnodraco_acuticeps PCR_G1524_Harpagifer_antarcticus PCR_G1525_Artedidraco_orianae PCR_E0158_Pogonophryne_barsukovi PCR_G1526_Notothenia_coriiceps PCR_E0157_Parachaenichthys_charcoti PCR_G1529_Gobionotothen_gibberifrons PCR_G1250_Chionobathyscus_dewitti Chaenocephalus_aceratus|E1730|utg7180003029502|6037|259 PCR_G1530_Patagonotothen_tessellata PCR_G1528_Aethotaxis_mitopteryx PCR_E0801_Coccotropsis_gymnoderma PCR_E0867_Synanceia_verrucosa PCR_E0423_Anoplopoma_fimbria Anoplopoma_fimbria|E1730|AWGY01111945.1|4047|9831 PCR_E0353_Zaniolepis_frenata PCR_G1335_Hypoptychus_dybowskii PCR_G1217_Aulorhynchus_flavidus PCR_G1216_Aulichthys_japonicus PCR_E0368_Culaea_inconstans PCR_G1491_Spinachia_spinachia PCR_G1460_Pungitius_pungitius Gasterosteus_aculeatus|E1730|model|0 PCR_E1012_Gasterosteus_aculeatus PCR_E0191_Bathymaster_caeruleofasciatus PCR_E0442_Bryozoichthys_marjorius PCR_G1437_Pholis_crassispina PCR_E0362_Zaprora_silenus PCR_E0371_Lumpenus_lampretaeformis PCR_E0361_Lumpenus_fabricii PCR_E0117_Anarhichas_orientalis_lupus PCR_E0370_Zoarces_americanus_viviparus PCR_G1364_Lycodes_diapterus PCR_E0365_Melanostigma_pammelas PCR_E0675_Lycodes_terraenovae PCR_E0327_Eucryphycus_californicus PCR_E0355_Lycodapus_mandibularis PCR_E0357_Bothrocara_brunneum PCR_E0367_Pleurogrammus_monopterygius PCR_E0348_Hexagrammos_decagrammus PCR_E0363_Hexagrammos_lagocephalus_otakii PCR_E0270_Eumicrotremus_orbis PCR_E0220_Cyclopterus_lumpus PCR_E0225_Liparis_pulchellus PCR_E0224_Liparis_gibbus PCR_E0262_Rhinoliparis_barbulifer PCR_E0255_Careproctus_rastrinus PCR_E0422_Careproctus_melanurus PCR_E0453_Paraliparis_copei PCR_E0454_Paraliparis_hystrix PCR_E0281_Cottus_carolinae Cottus_rhenanus|E1730|LKTN01055293.1|372|6156 Myoxocephalus_scorpius|E1730|utg7180000068923|6|5590 PCR_E0266_Leptocottus_armatus PCR_E0276_Psychrolutes_phrictus PCR_E0253_Malacocottus_zonurus PCR_E0429_Radulinus_asprellus PCR_E0256_Rastrinus_scutiger PCR_E0233_Chitonotus_pugetensis PCR_E0277_Icelinus_filamentosus PCR_E0228_Icelinus_quadriseriatus PCR_E0254_Sarritor_leptorhynchus PCR_E0278_Xeneretmus_latifrons PCR_E0268_Bathyagonus_alascanus PCR_E0430_Bathyagonus_pentacanthus PCR_E0626_Scomber_scombrus PCR_E0693_Gempylus_serpens PCR_E0516_Pomatomus_saltatrix PCR_E0243_Sarda_sarda Thunnus_orientalis|E1730|BADN01087780.1|3532|9316 Thunnus_albacares|E1730|utg7180001602982|4|5261 PCR_E0976_Scombrolabrax_heterolepis PCR_E0665_Ariomma_melanum PCR_E0226_Ruvettus_pretiosus PCR_E1106_Kali_indica PCR_E0475_Benthodesmus_simonyi PCR_E0650_Evoxymetopon_taeniatus PCR_E0596_Trichiurus_lepturus PCR_G1210_Assurger_anzac PCR_E0474_Lepidopus_altifrons PCR_E0820_Abudefduf_saxatilis PCR_G1427_Pentapodus_caninus PCR_E0911_Scolopsis_frenatus PCR_E0028_Scolopsis_bilineata PCR_E0124_Rhacochilus_vacca PCR_E0122_Phanerodon_furcatus PCR_E0139_Cymatogaster_aggregata PCR_E0120_Embiotoca_jacksoni PCR_E0134_Hyperprosopon_anale_argenteum PCR_E0129_Amphistichus_argenteus PCR_E0855_Plesiops_coeruleolineatus PCR_G1442_Plesiops_melas PCR_E0589_Natalichthys_sam PCR_G1403_Ogilbyina_novaehollandiae PCR_G1343_Labracinus_cyclophthalmus Pseudochromis_fuscus|E1730|utg7180000061529|10271|4484 PCR_E0706_Pseudochromis_cyanotaenia PCR_E0535_Pseudochromis_jamesi PCR_E0211_Lipogramma_anabantoides PCR_E0210_Lipogramma_trilineata PCR_G1196_Ambassis_agrammus PCR_E0115_Atherinomorus_stipes PCR_E0548_Atherinomorus_lacunosus PCR_E0178_Melanotaenia_trifasciata PCR_G1467_Rheocles_wrightae PCR_E0182_Pseudomugil_gertrudae PCR_E0184_Pseudomugil_signifer PCR_E0406_Marosatherina_ladigesi PCR_G1283_Elassoma_okefenokee PCR_E0146_Elassoma_evergladei PCR_E0945_Pseudocheilinus_hexataenia PCR_E0944_Pseudocheilinus_evanidus PCR_E0163_Centropristis_striata PCR_E1002_Diplectrum_formosum PCR_E0336_Serranus_phoebe PCR_E0337_Serranus_notospilus PCR_E0322_Serranus_baldwini PCR_G1486_Serranus_tigrinus PCR_E0505_Hypoplectrus_puella PCR_E0325_Paralabrax_nebulifer PCR_E0031_Mugil_curema PCR_E0049_Mugil_cephalus PCR_E0765_Mugil_trichodon PCR_E0808_Liza_richardsonii PCR_E0809_Myxus_capensis PCR_E0742_Neomyxus_leuciscus PCR_E0847_Valamugil_buchanani PCR_E0846_Crenimugil_crenilabis PCR_G1388_Nandus_nandus PCR_E0170_Membras_martinica PCR_E1167_Rhombosolea_plebeia PCR_E1168_Rhombosolea_tapirina PCR_E1170_Neoachiropsetta_milfordi PCR_E1169_Mancopsetta_maculata PCR_E0090_Siganus_vulpinus PCR_E1112_Labidesthes_sicculus Hippocampus_erectus|E1730|scaffold298|355625|361372 PCR_E0792_Syngnathus_fuscus PCR_E0397_Oxyporhamphus_micropterus PCR_E0399_Cheilopogon_pinnatibarbatus PCR_E0401_Hirundichthys_marginatus PCR_E0400_Prognichthys_brevipinnis PCR_E0402_Cypselurus_callopterus PCR_E0403_Exocoetus_monocirrhus PCR_G1309_Gymnoscopelus_nicholsi PCR_E0664_Hygophum_hygomii PCR_E0500_Myctophum_punctatum PCR_E0741_Eleotris_acanthopoma_pisonis PCR_E1137_Odontobutis_potamophila PCR_G1429_Perccottus_glenii PCR_E1093_Cabillus_lacertops PCR_E0099_Gnatholepis_cauerensis PCR_E1098_Paragobiodon_modestus PCR_E1085_Gobiodon_quinquestrigatus PCR_E0409_Amblyeleotris_gymnocephala PCR_E0533_Amblygobius_decussatus PCR_E0740_Psammogobius_biocellatus PCR_G1351_Lepidogobius_lepidus PCR_E0207_Opistognathus_maxillosus PCR_E0216_Opistognathus_aurifrons PCR_E0603_Lonchopisthus_micrognathus PCR_E0305_Enneanectes_boehlkei PCR_E0315_Enneanectes_altivelis PCR_E0317_Stathmonotus_stahli PCR_E0301_Labrisomus_bucciferus PCR_E0303_Starksia_fasciata PCR_E0304_Starksia_atlantica PCR_E0295_Acanthemblemaria_paula PCR_E0320_Acanthemblemaria_aspera PCR_E0313_Chaenopsis_sp_alepidota PCR_E0310_Emblemaria_pandionis PCR_E0302_Labrisomus_nigricinctus PCR_E0326_Neoclinus_blanchardi PCR_E0319_Platygillellus_rubrocinctus PCR_G1299_Gillellus_semicinctus PCR_E0946_Callionymus_sp_bairdi PCR_E0887_Cantherhines_pardalis_pullus PCR_E0536_Amanses_scopas PCR_E0316_Aluterus_scriptus PCR_E0646_Stephanolepis_hispidus PCR_E0913_Paraluteres_prionurus PCR_E0297_Entomacrodus_nigricans PCR_E0980_Entomacrodus_niuafoouensis PCR_E0715_Blenniella_cyanostigma PCR_E0984_Ecsenius_bicolor PCR_E0979_Blenniella_paula PCR_E0330_Cirripectes_quagga PCR_E0296_Ophioblennius_atlanticus PCR_E0520_Cirripectes_stigmaticus PCR_E0934_Ecsenius_midas PCR_E0909_Petroscirtes_mitratus PCR_E0526_Meiacanthus_oualanensis_grammistes PCR_E0586_Plagiotremus_rhinorhynchos PCR_E0540_Plagiotremus_tapeinosoma PCR_E0307_Liopropoma_mowbrayi PCR_E0306_Liopropoma_rubre PCR_E0531_Aporops_bilinearis PCR_E0900_Grammistes_sexlineatus PCR_E0764_Rypticus_saponaceus PCR_E0347_Rypticus_subbifrenatus PCR_E1130_Lateolabrax_japonicus PCR_E0242_Polyprion_americanus PCR_E0227_Stereolepis_gigas PCR_E0910_Lethrinus_obsoletus PCR_G1188_Acropoma_japonicum PCR_E1125_Synagrops_bellus PCR_E1123_Synagrops_spinosus PCR_E0311_Mycteroperca_bonaci_microlepis PCR_E0552_Epinephelus_merra PCR_E0549_Epinephelus_maculatus PCR_E0231_Caulolatilus_princeps PCR_E0595_Caulolatilus_intermedius Miichthys_miiuy|E1730|JXSJ01000091.1|1149722|1155506 Larimichthys_crocea|E1730|NW_011323351.1|362573|356789 PCR_E0166_Menticirrhus_saxatilis PCR_E0127_Menticirrhus_undulatus_littoralis PCR_E0125_Atractoscion_nobilis PCR_E0511_Cynoscion_arenarius PCR_E0164_Cynoscion_regalis PCR_E1055_Sciaenops_ocellatus PCR_G1349_Leiostomus_xanthurus PCR_E1108_Aplodinotus_grunniens PCR_E0123_Seriphus_politus PCR_E1048_Larimus_breviceps PCR_E0628_Umbrina_coroides PCR_E0165_Bairdiella_chrysoura PCR_E0608_Stellifer_lanceolatus PCR_G1405_Oplegnathus_punctatus PCR_E0795_Cheilodactylus_fasciatus PCR_E0202_Kyphosus_incisor PCR_G1318_Hephaestus_fuliginosus PCR_G1480_Scortum_barcoo PCR_G1341_Kuhlia_marginata PCR_E0712_Kuhlia_mugil PCR_G1239_Centrogenys_vaigiensis PCR_E0884_Cirrhitichthys_oxycephalus PCR_E0314_Amblycirrhitus_pinos PCR_E0725_Neocirrhites_armatus PCR_E0924_Paracirrhites_forsteri_arcatus PCR_G1291_Eugerres_plumieri PCR_E0292_Gerres_cinereus PCR_G1507_Ulaema_lefroyi Eucinostomus_sp|E1730|scaffold404|6247|965 PCR_E0575_Eucinostomus_argenteus PCR_E0756_Eucinostomus_gula PCR_G1287_Enoplosus_armatus PCR_E0802_Argyrozona_argyrozona PCR_E0806_Sarpa_salpa PCR_G1430_Percichthys_trucha PCR_G1365_Maccullochella_peelii PCR_G1366_Macquaria_ambigua PCR_E1144_Gadopsis_marmoratus PCR_G1389_Nannoperca_australis PCR_G1264_Coreoperca_whiteheadi PCR_E1136_Siniperca_chuatsi PCR_E0131_Pomoxis_nigromaculatus PCR_E0392_Ambloplites_rupestris PCR_G1185_Acantharchus_pomotis PCR_E1110_Micropterus_salmoides PCR_E1113_Lepomis_macrochirus PCR_E0132_Lepomis_cyanellus PCR_E1132_Dicentrarchus_labrax Dicentrarchus_labrax|E1730|HG916851.1|22803348|22797567 PCR_E0087_Morone_mississippiensis Morone_saxatilis|E1730|JTCL01025335.1|5427|1 PCR_E0992_Morone_chrysops PCR_E0607_Orthopristis_chrysoptera PCR_E0613_Conodon_nobilis PCR_E0229_Xenistius_californiensis PCR_E0279_Haemulon_plumierii PCR_E0635_Haemulon_aurolineatum PCR_E0632_Prognathodes_aya_aculeatus PCR_E0205_Chaetodon_capistratus PCR_G1248_Chelmon_rostratus PCR_E0562_Forcipiger_flavissimus PCR_E0748_Heniochus_chrysostomus PCR_E0547_Heniochus_varius PCR_E0240_Hemitaurichthys_polylepis PCR_E0701_Naso_unicornis PCR_E0002_Paracanthurus_hepatus PCR_E0859_Zebrasoma_scopas PCR_E0730_Zebrasoma_flavescens PCR_E0029_Zebrasoma_veliferum PCR_E0774_Malacanthus_plumieri PCR_E0954_Erythrocles_schlegelii PCR_E0569_Lutjanus_biguttatus PCR_E0283_Ocyurus_chrysurus PCR_E0592_Lutjanus_campechanus PCR_E0593_Rhomboplites_aurorubens PCR_E0594_Pristipomoides_aquilonaris PCR_E0894_Zanclus_cornutus PCR_E0563_Aphareus_furca PCR_E0250_Drepane_punctata PCR_G1469_Rhinesomus_triqueter PCR_E0588_Ostracion_cubicus PCR_G1533_Anoplocapros_lenticularis PCR_G1205_Aracana_aurita PCR_E0827_Monodactylus_argenteus PCR_E0550_Centropyge_bicolor PCR_E0542_Centropyge_nox PCR_E0284_Centropyge_loricula PCR_E0198_Holacanthus_tricolor PCR_E0282_Holacanthus_passer PCR_E0209_Holacanthus_ciliaris PCR_E0534_Pygoplites_diacanthus PCR_E0710_Pomacanthus_imperator PCR_E0849_Pomacanthus_semicirculatus PCR_E0618_Priacanthus_arenatus PCR_E0252_Pristigenys_alta PCR_E1024_Antigonia_capros PCR_G1532_Triacanthodes_ethiops PCR_E0382_Triacanthodes_anomalus PCR_E0051_Scatophagus_argus PCR_G1483_Selenotoca_multifasciata PCR_G1531_Triacanthus_biaculeatus PCR_E0625_Lophiodes_reticulatus PCR_E1119_Lophius_gastrophysus PCR_E0578_Lophius_americanus PCR_E0610_Ogcocephalus_parvus_nasutus PCR_E0975_Dibranchus_tremendus PCR_G1326_Histiophryne_cryptacanthus PCR_E0386_Bertella_idiomorpha PCR_E0656_Himantolophus_albinares_sagamius PCR_E0655_Oneirodes_macrosteus PCR_E1053_Gigantactis_ios PCR_E0177_Gigantactis_vanhoeffeni PCR_E0175_Ceratias_holboelli PCR_E0657_Melanocetus_johnsonii PCR_E0477_Melanocetus_murrayi PCR_E0509_Luvarus_imperialis PCR_E0050_Ctenochaetus_strigosus PCR_E0854_Ctenochaetus_truncatus PCR_E0711_Acanthurus_triostegus PCR_E0005_Acanthurus_bahianus PCR_E0955_Sphyraena_putnamae PCR_E0957_Kuhlia_rupestris Spondyliosoma_cantharus|E1730|utg7180000177514|3999|9773 PCR_E0246_Stenotomus_chrysops PCR_G1346_Lagodon_rhomboides PCR_E0249_Archosargus_probatocephalus PCR_E0614_Chaetodipterus_faber PCR_E0898_Platax_orbicularis PCR_E0858_Platax_teira PCR_G1463_Ranzania_laevis Mola_mola|E1730|KV751387.1|1605655|1611445 PCR_E0683_Mola_mola PCR_G1513_Tetraodon_nigroviridis Tetraodon_nigroviridis|E1730|14|10149393|10143616 Tetraodon_nigroviridis|E1730|model|0 PCR_E0601_Lagocephalus_laevigatus PCR_E0383_Torquigener_hamiltoni Takifugu_flavidus|E1730|KE120649.1|71393|77172 PCR_E0460_Takifugu_rubripes Takifugu_rubripes|E1730|NW_004072377.1|58551|64332 PCR_E0651_Masturus_lanceolatus PCR_E0378_Canthidermis_maculata PCR_E0735_Rhinecanthus_aculeatus PCR_E0381_Rhinecanthus_assasi PCR_E0743_Balistapus_undulatus PCR_E0373_Balistoides_conspicillum PCR_E0591_Balistes_capriscus PCR_E0935_Sufflamen_fraenatum PCR_E0380_Xanthichthys_auromarginatus PCR_E0922_Melichthys_niger PCR_E0919_Melichthys_indicus PCR_E0844_Mulloidichthys_flavolineatus PCR_E0773_Pseudupeneus_maculatus PCR_E0825_Upeneus_moluccensis PCR_E0634_Mullus_auratus PCR_G1189_Aeoliscus_strigatus PCR_E0237_Dactyloptena_orientalis PCR_E0214_Dactylopterus_volitans PCR_E0473_Macroramphosus_scolopax PCR_E0335_Macroramphosus_gracilis PCR_E0312_Diodon_holocanthus Nothobranchius_furzeri|E1730|NC_029652.1|60923836|60929620 Austrofundulus_limnaeus|E1730|NW_013952796.1|445203|450990 Kryptolebias_marmoratus|E1730|LHSH01003488.1|13122|18909 PCR_E1063_Floridichthys_carpio PCR_E1066_Cyprinodon_variegatus Cyprinodon_varigatus|E1730|KL654119.1|81275|87062 Fundulus_heteroclitus|E1730|NW_012234400.1|1576682|1582466 PCR_G1293_Fundulus_heteroclitus PCR_E0389_Fundulus_parvipinnis PCR_E0130_Fundulus_blairae PCR_E0173_Adinia_xenica PCR_E0590_Porichthys_plectrodon PCR_E0058_Porichthys_notatus Chatrabus_melanurus|E1730|utg7180008690204|1654|7441 PCR_E0513_Opsanus_pardus PCR_E0698_Opsanus_beta PCR_E0793_Halidesmus_scapularis PCR_E0572_Plectroglyphidodon_dickii PCR_G1375_Microspathodon_bairdii PCR_E0459_Hypsypops_rubicundus PCR_E0713_Stegastes_albifasciatus Stegastes_partitus|E1730|NW_007578916.1|160879|155095 PCR_E0219_Stegastes_diencaeus PCR_E0203_Stegastes_fuscus PCR_E0238_Chromis_atripectoralis PCR_E0201_Chromis_cyanea Chromis_chromis|E1730|utg7180000028058|4932|10719 PCR_E0881_Abudefduf_sexfasciatus PCR_E0580_Azurina_hirundo PCR_E0890_Abudefduf_vaigiensis PCR_E0557_Pomacentrus_spilotoceps PCR_E0559_Pomachromis_richardsoni PCR_E0564_Chrysiptera_taupou PCR_E0239_Pomacentrus_brachialis PCR_E0700_Dascyllus_aruanus PCR_E0729_Pomacentrus_pavo PCR_E0251_Pholidichthys_leucotaenia PCR_G1408_Oryzias_latipes Oryzias_latipes|E1730|model|0 Oryzias_latipes|E1730|24|11817408|11811621 PCR_G1508_Xenentodon_cancila PCR_E0110_Strongylura_notata PCR_E0162_Ablennes_hians PCR_E0114_Platybelone_argalus PCR_E0192_Cololabis_saira PCR_E0404_Scomberesox_saurus PCR_G1444_Polycentrus_schomburgki PCR_G1423_Paretroplus_maculatus PCR_E0133_Etroplus_maculatus PCR_G1420_Paratilapia_polleni PCR_G1459_Ptychochromis_grandidieri PCR_G1321_Heterochromis_multidens PCR_G1256_Cichla_temensis PCR_E0390_Symphysodon_discus Amphilophus_citrinellus|E1730|CCOE01000811.1|29211|23424 PCR_G1319_Herichthys_cyanoguttatus PCR_G1407_Oreochromis_niloticus Oreochromis_niloticus|E1730|GL831182.1|3862893|3868680 Oreochromis_niloticus|E1730|model|0 Neolamprologus_brichardi|E1730|NW_006272029.1|837880|832093 PCR_G1520_Neolamprologus_brichardi PCR_G1518_Astatotilapia_burtoni Haplochromis_burtoni|E1730|NW_005180327.1|83961|89748 Pundamilia_nyererei|E1730|NW_005187847.1|221916|216129 PCR_G1521_Pundamilia_nyererei Maylandia_zebra|E1730|NW_014446560.1|294681|288894 PCR_G1519_Metriaclima_zebra PCR_E1134_Monopterus_albus PCR_G1367_Macrognathus_siamensis PCR_E1157_Mastacembelus_erythrotaenia Channa_argus|E1730|scaffold916|397122|402909 PCR_G1373_Microctenopoma_nanum PCR_G1315_Helostoma_temminkii Helostoma_temminckii|E1730|utg7180000540240|7992|2205 PCR_E0745_Pseudoplesiops_revellei PCR_E0503_Remora_osteochir_australis PCR_G1438_Phtheirichthys_lineatus PCR_E0245_Echeneis_neucratoides PCR_E0605_Achirus_lineatus PCR_E0046_Trinectes_maculatus PCR_E0609_Gymnachirus_melas PCR_E0630_Gymnachirus_texae PCR_E1146_Nematistius_pectoralis PCR_E1135_Lates_calcarifer Lates_calcarifer|E1730|LBLR01014977.1|27494|21710 PCR_E0942_Atule_mate PCR_E0217_Polydactylus_virginicus PCR_E0606_Polydactylus_octonemus PCR_E1165_Psettodes_erumei PCR_E0738_Scomberoides_lysan PCR_E0195_Oligoplites_saurus PCR_E1139_Toxotes_chatareus PCR_E1155_Toxotes_jaculatrix PCR_E0515_Uraspis_secunda PCR_E0469_Alectis_ciliaris Selene_dorsalis|E1730|utg7180000147761|6592|811 PCR_E0616_Hemicaranx_amblyrhynchus PCR_E0510_Caranx_crysos_ruber PCR_E0574_Caranx_ignobilis PCR_E1131_Mene_maculata PCR_E1151_Xiphias_gladius PCR_E0692_Makaira_sp PCR_E0681_Tetrapturus_albidus PCR_E0230_Sphyraena_argentea PCR_E0836_Sphyraena_barracuda PCR_E0194_Centropomus_undecimalis PCR_E0467_Seriola_rivoliana PCR_E0623_Seriola_dumerili PCR_E0071_Citharoides_macrolepis PCR_E0080_Lepidoblepharon_ophthalmolepis PCR_E1145_Trachinotus_ovatus PCR_G1504_Trachinotus_carolinus PCR_E0819_Trachinotus_falcatus Trachinotus_ovatus|E1730|scaffold30499|6090|303 PCR_E1148_Psammoperca_waigiensis PCR_E0023_Symphurus_atricaudus PCR_E1164_Symphurus_plagiusa PCR_E0604_Symphurus_civitatium PCR_E1183_Solea_lascaris PCR_E0079_Heteromycteris_japonicus PCR_E0081_Pseudaesopia_japonica PCR_E0943_Soleichthys_heterorhinos PCR_E0039_Scophthalmus_aquosus PCR_E0597_Cyclopsetta_chittendeni PCR_E0633_Syacium_micrurum PCR_E0446_Citharichthys_sordidus PCR_E0043_Citharichthys_arctifrons PCR_E0647_Etropus_crossotus PCR_E0047_Etropus_microstomus PCR_E0082_Laeops_kitaharae PCR_E0038_Bothus_robinsi PCR_E0007_Bothus_lunatus PCR_E0904_Asterorhombus_cocosensis PCR_E0083_Psettina_tosana PCR_E0599_Trichopsetta_ventralis PCR_E0022_Hypsopsetta_guttulata PCR_E0021_Xystreurys_liolepis PCR_E0078_Samariscus_xenicus PCR_E0030_Neosynchiropus_ocellatus PCR_E0026_Platichthys_stellatus PCR_E0690_Limanda_limanda PCR_E0448_Poecilopsetta_beanii PCR_E0077_Pseudorhombus_pentophthalmus PCR_E0640_Gastropsetta_frontalis PCR_E0020_Paralichthys_californicus Paralichthys_olivaceus|E1730|scaffold191.1|73480|67693 PCR_E1171_Paralichthys_albigutta PCR_E0064_Embassichthys_bathybius PCR_E0444_Eopsetta_jordani PCR_E1173_Lyopsetta_exilis PCR_E0433_Microstomus_pacificus PCR_E0416_Glyptocephalus_zachirus PCR_E0424_Hippoglossoides_elassodon PCR_E0035_Pseudopleuronectes_americanus Pseudopleuronectes_yokohamae|E1730|BBOV01000007.1|1558|6963 PCR_E0053_Pleuronectes_platessa PCR_E0445_Parophrys_vetulus PCR_E0438_Lepidopsetta_bilineata PCR_E0025_Psettichthys_melanostictus PCR_E0018_Isopsetta_isolepis PCR_E0145_Iso_sp PCR_E0176_Oneirodes_bulbosus PCR_E0152_Etheostoma_simoterum PCR_E0153_Crystallaria_asprella PCR_E1095_Rhabdamia_cypselura PCR_E1040_Apogon_bandanensis PCR_E0522_Archamia_biguttata PCR_G1247_Cheilodipterus_quinquelineatus PCR_E1087_Apogon_cookii PCR_E0528_Cheilodipterus_isostigmus PCR_E0190_Pterapogon_kauderni PCR_E0702_Apogon_exostigma PCR_E0732_Nectamia_fusca PCR_E1090_Fowleria_aurita PCR_E0546_Cercamia_eremia PCR_E1069_Apogon_campbelli PCR_E0539_Gymnapogon_urospilotus PCR_E0506_Phaeoptyx_pigmentaria PCR_E0148_Ammocrypta_meridiana PCR_E0150_Percina_phoxocephala PCR_E0140_Gymnocephalus_cernuus PCR_E0149_Ammocrypta_pellucida PCR_E0141_Gymnocephalus_schraetser PCR_E0147_Etheostoma_vitreum PCR_E0168_Etheostoma_juliae PCR_E0154_Percina_nigrofasciata PCR_E0970_Brama_brama PCR_E0790_Nannobrachium_lineatum PCR_E0502_Aulopus_filamentosus PCR_E0499_Lepidophanes_guentheri PCR_E0967_Lampanyctus_macdonaldi PCR_E1017_Bathypterois_grallator PCR_E0495_Ceratoscopelus_warmingii PCR_E0010_Lobianchia_gemellarii PCR_E0011_Notolychnus_valdiviae PCR_E0293_Aulostomus_maculatus PCR_E0871_Aulostomus_chinensis PCR_E0188_Kurtus_gulliveri PCR_E0235_Dinematichthys_randalli PCR_E0236_Diancistrus_sp PCR_E0261_Cataetyx_rubrirostris_lepidogenys PCR_E0452_Diplacanthopoma_brachysoma PCR_E0206_Petrotyx_sanguineus Carapus_acus|E1730|utg7180000594768|13661|7874 PCR_E0883_Brotula_multibarbata PCR_E0629_Brotula_barbata Brotula_barbata|E1730|utg7180000516297|6773|989 PCR_E0481_Bassogigas_gillii PCR_E0659_Brotulotaenia_crassa PCR_E0275_Lamprogrammus_niger PCR_E0480_Dicrolene_introniger PCR_E0612_Neobythites_gilli PCR_E0621_Lepophidium_jeannae PCR_E0241_Genypterus_blacodes PCR_E0260_Chilara_taylori PCR_E0648_Ophidion_josephi PCR_E1033_Ophidion_holbrookii PCR_E1082_Sargocentron_diadema PCR_E1046_Holocentrus_rufus PCR_E1071_Sargocentron_caudimaculatum Holocentrus_rufus|E1730|utg7180000099411|9813|4029 PCR_E0105_Sargocentron_coruscum Neoniphon_sammara|E1730|utg7180000872699|7663|1879 PCR_E0101_Sargocentron_vexillarium PCR_G1386_Myripristis_violacea Myripristis_jacobus|E1730|utg7180000946671|6729|945 PCR_E0543_Myripristis_hexagona PCR_E0161_Ostichthys_trachypoma PCR_E0720_Plectrypops_lima PCR_E0504_Plectrypops_retrospinis PCR_G1238_Centroberyx_druzhinini PCR_E0670_Scopelogadus_beanii PCR_E1061_Poromitra_crassiceps PCR_E0482_Gyrinomimus_parri_sp PCR_E1116_Cetomimus_craneae Acanthochaenus_luetkenii|E1730|utg7180001999832|4175|9015 PCR_G1222_Barbourisia_rufa Rondeletia_loricata|E1730|utg7180002562999|8109|2328 PCR_E1058_Rondeletia_loricata PCR_G1376_Monocentris_japonicus Monocentris_japonica|E1730|utg7180000082593|4262|10049 PCR_G1421_Paratrachichthys_sajademalensis PCR_E0649_Gephyroberyx_darwinii PCR_E0472_Diretmichthys_parini PCR_E0662_Anoplogaster_cornuta PCR_G1479_Scopelengys_tristis PCR_G1397_Neoscopelus_microchir PCR_E0822_Lophotus_lacepede Lampris_guttatus|E1730|utg7180007894977|6210|423 PCR_E0811_Regalecus_glesne Regalecus_glesne|E1730|utg7180000139155|292|6079 PCR_E0780_Trachipterus_arcticus PCR_E0974_Desmodema_polystictum PCR_E1014_Zu_cristatus PCR_E0019_Polymixia_japonica Polymixia_japonica|E1730|utg7180001114193|13525|7741 PCR_E1025_Polymixia_lowei PCR_E1032_Cyttopsis_rosea Cyttopsis_roseus|E1730|utg7180001415578|700|6447 PCR_E0449_Zenopsis_conchifer PCR_E1138_Zeus_faber Zeus_faber|E1730|utg7180001875430|1353|7140 PCR_E0997_Stylephorus_chordatus Stylephorus_chordatus|E1730|utg7180003155371|1873|7657 Bregmaceros_cantori|E1730|utg7180004986874|5932|161 Mora_moro|E1730|utg7180001952233|3664|9448 Muraenolepis_marmoratus|E1730|utg7180003809061|2433|8217 PCR_E0412_Laemonema_barbatulum Laemonema_laureysi|E1730|utg7180002856922|14217|8433 PCR_E0334_Lepidion_ensiferus PCR_E0485_Bathygadus_favosus Bathygadus_melanocrachus|E1730|utg7180000108023|14476|8701 Malacocephalus_occidentalis|E1730|utg7180001140021|3211|8984 Macrourus_berglax|E1730|utg7180000045445|8947|3174 Trachyrincus_scabrus|E1730|utg7180001902112|684|6468 Trachyrincus_murrayi|E1730|utg7180001970038|12867|7083 Merluccius_merluccius|E1730|utg7180001902985|6310|526 Merluccius_capensis|E1730|utg7180003762086|2769|8553 Merluccius_polli|E1730|utg7180001428025|1073|6459 Phycis_blennoides|E1730|utg7180003515876|1512|7296 PCR_E0343_Urophycis_chuss PCR_E0369_Enchelyopus_cimbrius Lota_lota|E1730|utg7180001294531|7273|1489 PCR_E0489_Lota_lota Molva_molva|E1730|utg7180001038158|409|6193 Brosme_brosme|E1730|utg7180000010428|13690|7906 Gadiculus_argenteus|E1730|utg7180000011137|8103|2325 PCR_E0491_Micromesistius_poutassou PCR_E0372_Pollachius_virens Pollachius_virens|E1730|utg7180000029628|9178|3400 Melanogrammus_aeglefinus|E1730|utg7180002270504|4081|9859 Merlangius_merlangus|E1730|utg7180002022580|4059|9837 PCR_E0490_Merlangius_merlangus PCR_E0434_Theragra_chalcogramma Theragra_chalcogramma|E1730|utg7180002156917|4193|9971 Boreogadus_saida|E1730|utg7180002133392|9084|3306 Arctogadus_glacialis|E1730|utg7180002006255|9101|3323 Gadus_morhua|E1730|model|0 PCR_E0375_Gadus_morhua PCR_G1213_Ateleopus_japonicus PCR_E0685_Ijimaia_antillarum PCR_E0757_Synodus_foetens PCR_E0703_Saurida_gracilis PCR_E0658_Gigantura_indica PCR_E0818_Gigantura_chuni PCR_E1034_Parasudis_truculenta Parasudis_fraserbrunneri|E1730|utg7180000155815|0|5367 PCR_E0440_Benthalbella_dentata PCR_E0964_Anotopterus_pharao PCR_E0486_Paralepis_coregonoides PCR_E0497_Lestidiops_jayakari PCR_E0973_Stemonosudis_intermedia_macrura PCR_E0661_Ahliesaurus_berryi PCR_E0815_Evermannella_balbo PCR_E0669_Coccorella_atlantica PCR_E0965_Alepisaurus_ferox PCR_E0999_Omosudis_lowei PCR_G1517_Aplochiton_taeniatus PCR_G1394_Neochanna_burrowsius PCR_G1230_Brachygalaxias_bullocki PCR_E0352_Argentina_sialis_silus PCR_G1368_Macropinna_microstoma PCR_E0814_Nansenia_longicauda_ardesiaca PCR_G1224_Bathylagus_euryops PCR_G1402_Novumbra_hubbsi Esox_lucius|E1730|NC_025981.2|28494540|28488760 PCR_E0688_Esox_lucius Umbra_pygmae|E1730|YUP_LOC100700283.1.1|9942|4161 PCR_E0086_Umbra_limi PCR_G1263_Coregonus_clupeaformis PCR_G1502_Thymallus_brevirostris Thymallus_thymallus|E1730|ITT_LOC101463818.1.1|83|5864 Salvelinus_fontinalis|E1730|QSF_LOC101463818.1.1|83|5864 PCR_G1473_Salvelinus_alpinus Oncorhynchus_mykiss|E1730|ENA|CCAF010027868|CCAF010027868.1|8059|2278 Salmo_salar|E1730|NC_027314.1|21012185|21017966 PCR_G1418_Parahucho_perryi PCR_E0496_Bonapartia_pedaliota PCR_E0492_Diplophos_taenia PCR_G1443_Pollichthys_mauli Plecoglossus_altivelis|E1730|ZPA_LOC100700283.1.1|85|5868 Protosalanx_hyalocranius|E1730|scaffold27|2571450|2577233 PCR_E0095_Thaleichthys_pacificus Osmerus_eperlanus|E1730|utg7180000818195|10616|16393 PCR_G1409_Osmerus_mordax PCR_E0679_Gonostoma_elongatum PCR_G1370_Margrethia_obtusirostra PCR_E0036_Polymetme_corythaeola_sp PCR_E0037_Stomias_boa PCR_G1395_Neonesthes_capensis PCR_E0813_Borostomias_antarcticus Borostomias_antarcticus|E1730|utg7180003173752|1028|6806 PCR_E0678_Chauliodus_sloani PCR_E0660_Heterophotus_ophistoma PCR_E0812_Rhadinesthes_decimus PCR_E0966_Photonectes_margarita PCR_E0439_Tactostoma_macropus PCR_E0483_Leptostomias_longibarba PCR_E0782_Melanostomias_margaritifer PCR_E0995_Photostomias_guernei PCR_E0063_Bathophilus_flemingi_pawneei PCR_G1350_Lepidogalaxias_salamandroides PCR_E0461_Amia_calva PCR_G1214_Atractosteus_spatula PCR_G1353_Lepisosteus_platostomus Lepisosteus_oculatus|E1730|model|0 PCR_G1354_Lepisosteus_oculatus PCR_E0990_Hiodon_alosoides PCR_G1253_Chitala_ornata Scleropages_formosus|E1730|JARO02002666.1|22392|16608 Osteoglossum_bicirrhosum|E1730|COB_LOC100700283.1.1|56|5840 PCR_G1307_Gymnarchus_niloticus PCR_G1301_Gnathonemus_petersii PCR_E0769_Elops_saurus PCR_G1372_Megalops_atlanticus PCR_E0501_Albula_vulpes PCR_G1399_Notacanthus_chemnitzii PCR_E0788_Halosauropsis_macrochir PCR_G1193_Aldrovandia_affinis PCR_G1281_Echidna_nebulosa_rhodochilus PCR_G1261_Conger_oceanicus PCR_G1404_Ophichthus_cephalozona PCR_G1385_Myrichthys_maculosus PCR_G1393_Nemichthys_scolopaceus PCR_G1292_Eurypharynx_pelecanoides PCR_G1487_Serrivomer_beanii PCR_E1001_Saccopharynx_ampullaceus Anguilla_japonica|E1730|KI305257.1|88695|82914 Anguilla_anguilla|E1730|model|0|0 Anguilla_rostrata|E1730|LTYT01006321.1|31734|25953 PCR_G1202_Anguilla_rostrata PCR_G1274_Denticeps_clupeoides PCR_G1339_Jenkinsia_lamprotaenia PCR_G1260_Coilia_nasus PCR_G1251_Chirocentrus_dorab PCR_E1016_Dorosoma_cepedianum Clupea_harengus|E1730|NW_012223318.1|38913|44700 PCR_G1195_Alosa_pseudoharengus Alosa_alosa|E1730|EAA_MYH6.1.4|6905|1138 PCR_G1338_Ilisha_elongata PCR_G1425_Pellona_flavipinnis PCR_E0345_Chanos_chanos PCR_G1305_Gonorynchus_forsteri PCR_G1419_Parakneria_sp PCR_G1481_Searsia_koefoedi PCR_E0971_Normichthys_operosus PCR_E0978_Maulisia_microlepis PCR_E0366_Sagamichthys_abei PCR_G1194_Alepocephalus_agassizii PCR_E0358_Alepocephalus_tenebrosus PCR_E0359_Talismania_bifurcata PCR_E0977_Rouleina_attrita PCR_E0779_Xenodermichthys_copei PCR_E0994_Cobitis_lutheri PCR_G1221_Barbatula_barbatula PCR_G1337_Ictiobus_bubalus PCR_E1015_Carpiodes_carpio PCR_G1332_Hypentelium_nigricans Sinocyclocheilus_grahami|E1730|LCYQ01S000587.1|612453|606672 Sinocyclocheilus_anshuiensis|E1730|LAVE01S014582.1|81246|75465 Cyprinus_carpio|E1730|LHQP01045792.1|11108|5327 Sinocyclocheilus_rhinoceros|E1730|LAVF01S039529.1|820475|826256 Danio_rerio|E1730|model|0 PCR_G1498_Tanakia_lanceolata_himantegus Pimephales_promelas|E1730|JNCD01003212.1|19847|25625 PCR_G1439_Pimephales_promelas_notatus PCR_G1485_Semotilus_atromaculatus Leuciscus_waleckii|E1730|FLSR01004875.1|4407427|4413193 PCR_G1400_Notemigonus_crysoleucas PCR_G1512_Zacco_sieboldii_platypus PCR_G1406_Opsariichthys_uncirostris_bidens PCR_G1334_Hypophthalmichthys_molitrix PCR_G1361_Luciobrama_macrocephalus PCR_G1383_Mylopharyngodon_piceus PCR_G1509_Xenocypris_argentea PCR_G1493_Squaliobarbus_curriculus PCR_G1310_Gymnotus_sp Electrophorus_electricus|E1730|scaffold16389|45737|39953 PCR_G1285_Electrophorus_electricus PCR_G1282_Eigenmannia_macrops PCR_G1204_Apteronotus_albifrons Apteronotus_albifrons|E1730|A2AA_MYH6.1.1|6071|289 PCR_G1265_Corydoras_aurofrenatus PCR_G1392_Nematogenys_inermis PCR_G1468_Rheoglanis_dendrophorus PCR_G1268_Cranoglanis_bouderius PCR_G1199_Ameiurus_natalis Ictalurus_punctatus|E1730|CM004438.1|17145526|17139748 PCR_E0991_Ictalurus_punctatus PCR_G1208_Ariopsis_felis_seemanni PCR_G1304_Gogo_arcuatus PCR_G1200_Amphilius_jacksonii PCR_G1201_Anduzedoras_oxyrhynchus PCR_G1190_Ageneiosus_atronasus PCR_G1358_Liobagrus_aequilabris PCR_E0843_Plotosus_lineatus Pangasianodon_hypophthalamus|E1730|GPH_MYH6.2.2|198|6008 PCR_G1415_Pangasianodon_hypophthalmus Alosa_alosa|E1730|EAA_MYH6.2.4|65|5840 Pangasianodon_hypophthalamus|E1730|GPH_MYH6.1.2|72|5847 PCR_G1246_Characidium_pterostictum PCR_G1280_Distichodus_maculatus PCR_G1515_Alestes_baremoze PCR_G1516_Hepsetus_odoe PCR_G1484_Semaprochilodus_insignis PCR_G1449_Prochilodus_magdalenae_lineatus PCR_G1316_Hemiodus_immaculatus PCR_G1424_Parodon_nasus PCR_G1331_Hydrolycus_scomberoides Pygocentrus_nattereri|E1730|KV575297.1|3587869|3593644 PCR_G1461_Pygocentrus_nattereri PCR_G1186_Acestrorhynchus_falcatus PCR_G1233_Bryconamericus_emperador PCR_G1371_Markiana_nigripinnis PCR_G1391_Nematobrycon_palmeri PCR_G1212_Astyanax_mexicanus Astyanax_mexicanus|E1730|NW_006743262.1|6189|11967 PCR_G1506_Triportheus_nematurus PCR_G1462_Pyrrhulina_australis PCR_G1501_Thoracocharax_stellatus PCR_G1228_Boulengerella_maculata PCR_G1297_Gasteropelecus_sternicla PCR_G1249_Chilodus_punctatus 0.5
Figure 18: MYH6 gene tree with PCR products. Sequences of the MYH6 gene and paralogs found via nHmmer searches are in black, with PCR products from Betancur et al. (2013) added and highlighted in red. The alignment was trimmed to the length of the PCR-based locus, as MYH6 is considerably longer. Tree was inferred with RAxML under the GTRGAMMA model.
86
Coryphaena_hippurus|E1728|TRINITY_DN108888_c0_g1_i1|17|317Macrourus_berglax|E1728|utg7180001763609|3221|164 4 Bathygadus_melanocrachus|E1728|utg7180001861700|1110|415Melanonus_zugmayeri|E1728|utg7180001717915|3237|187 5 Trachyrincus_murrayi|E1728|utg7180002318669|3220|626Lota_lota|E1728|utg7180000158406|1232|4283 9 MBrosme_brosmeolva_molva|E1728|E1728|utg7180001144826|utg7180000115707|3923|3163|872|6200 Clupea_harengus|E1728|NW_012220672.1|1479919|148350Trisopterus_minutus|E1728|utg71800016349691 |3780|747 Amblygaster_clupeoides|E1728|TR63946|c1_g1_i4|1477|478Amblygaster_clupeoides|E1728|TR63946|c1_g1_i2|1235|45453 Amblygaster_clupeoides|E1728|TR63946|c1_g1_i3|1561|486Amblygaster_clupeoides|E1728|TR63946|c1_g1_i1|1331|4639 Sinocyclocheilus_anshuiensisPimephales_promelas|E1728|JNCD01044495.1|1238|480|E1728|LAVE01S001481.1|4557563 |459176 Leuciscus_waleckii|E1728|FLSR01004868.1|1853163|185670Osteoglossum_bicirrhosum|E1728|COB_LOC101161570.1.1|6805|3251 7 Lepisosteus_platyrhincus|E1728|scaffoLatimeria_chalumnaeld38874|3963|39|E17281 |NW_005821642.1|188822|192496 PCR_E0108_Elacatinus_oceanops Lepisosteus_oculatus|E1728|LG3|9831601|9835173 PPCR_E0107_Risor_rubeCR_E0171_Evorthodusr_lyricus PCR_E0097_Lesueurigobius_cf_sanzoi|E1728|utg7180003473440|3879|777Gobiosoma_bosc 4 PCR_E1057_Caffrogobius_saldanhPCR_E0736_Amblygobius_phalaenaa PCR_E1056_Caffrogobius_caffePCR_E0126_Lythrypnus_dalli r PCR_E1096_Valenciennea_puellariPCR_E0726_Trimma_okinawae s PCR_E1084_Trimma_haimPCR_E1039_Trimma_caesiua ra Supplemental Figure 3: KIAA gene tree with PCR products PCR_E0565_Ptereleotris_evidePCR_E0388_Microdesmus_longipinnis s PCR_E0554_Ptereleotris_microlepiPCR_E1089_Asterropteryx_semipuns ctatus KIAA1239 and its paralogs found via nHmmer PPCR_E1093_Cabillus_lacertopCR_E1067_Oplopomus_oplopos mus PCR_E0733_1076_Fusigobiuigobius_neoph_inframytacuulas tus searches in our 305 taxa, with the addition of PCR PPCR_E0508_Lophogobius_cyprinoideCR_E0100_Coryphopterus_glaucofraenus m PCR_E1097_CPCR_E0405_Coryphopterus_personatutenogobiops_crocineus s products from Betancur et al. 2013 (2) highlighted in PCR_E1073_Amblyeleotris_wheelerPCR_E0409_Amblyeleotris_gymnocephali a PCR_E1043_Amblyeleotris_guttatPCR_E1041_Eviota_albolineata a red. Tree was inferred with RAxML under the PCR_E0714_1044_EEvvioiotta_a_prasisaipanentes sis PCR_E1085_Gobiodon_quinquestrigatuPCR_E1098_Paragobiodon_modestus s GTRGAMMA model. Boleophthalmus_pectinirostrisScartelaos_histophorus|E1728||E1728KN520824.1|KN522880.1|39937|36044709822 |474877 PerPCR_E0537_Periophthalmus_kaloliophthalmus_magnuspinnatus|E1728|Ko N462097.1|138120|142015 Periophthalmodon_schlosseri|E1728|KN478699.1|35303|3919PCR_E0741_Eleotris_acanthopoma_pisonis 8 PCR_E0188_KurPCR_E1095_Rhabdamia_cypselurtus_gulliveri a PCRCR__E1069_Apogon_campbeE1090_Fowleria_aurita lli PCR_E0732_Nectamia_fuscPCR_E1040_Apogon_bandanena sis PCR_E0528_CheilodipPCR_E0190_Pterapogon_kaudernterus_isostigmui s PCR_E1087_Apogon_cookiPCR_E0702_Apogon_exostigmi a PCR_E0522_Archamia_biguttatPCR_E0506_Phaeoptyx_pigmenataria PPCR_E0546_Cercamia_eremiCR_E0261_Cataetyx_rubrirostra is_lepidogenys PCR_E0452_Diplacanthopoma_brachysomPCR_E0717_Brosmophyciops_pautzkei a PCR_E0794_Bidenichthys_capensiCarapus_acus|E1728|utg7180000912531|2998|689s 3 Brotula_barbata|E1728|utg7180000659434|4445|834PCR_E0883_Brotula_multibarbata 1 PCR_E0817_Brotulotaenia_nigrPCR_E0758_Lepophidium_brevibarba e PPCR_E1007_Ophidion_robinsCR_E0648_Ophidion_josephii PCR_E1033_Ophidion_holbrookiPCR_E0260_Chilara_taylori i PPCR_E0030_Neosynchiropus_ocellatuCR_E1004_Foetorepus_agassizii s Chatrabus_melanurus|E1728|utg7180005868750|5410|151PCR_E0925_Synchiropus_stellatus 4 PCR_E0009_Sanopus_spPCR_E0590_Porichthys_plectrodon PCR_E0040_Opsanus_taPCR_E0513_Opsanus_parduu s PCR_E0662_Anoplogaster_cornutPCR_E1018_Hoplostethus_occidentalis_atlanticua s Monocentris_japonica|E1728|utg7180001093723|1412|530PCR_E1114_Diretmus_argenteus 8 PCR_E0670_Scopelogadus_beaniPCR_E0472_Diretmichthys_parinii PPCR_E1061_Poromitra_crassicepCR_E1062_Melamphaes_suborbsitalis PCR_E1059_Rondeletia_bicoloAcanthochaenus_luetkenii|E1728|utg7180000082542|1847|574r 1 PRondeletia_loricata|E1728|utg7180002564831|682|457CR_E1058_Rondeletia_loricata 6 PCR_E1060_Cetostoma_reganPCR_E1116_Cetomimus_craneai e PCR_E0543_Myripristis_hexagonPCR_E0654_Gyrinomimus_bruunai PCR_E0527_Myripristis_vittatMyripristis_jacobus|E1728|utg7180000915574|5770|187a 5 PCR_E0161_Ostichthys_trachypomPCR_E0720_Plectrypops_lima a PCR_E0504_Plectrypops_retrospiniPCR_E1105_Sargocentron_tiere s HolocenPCR_E1071_Sargocentrus_rufus|E1728tron_caudimacula|utg7180001111828tum |5292|1400 PCR_E0105_Sargocentron_coruscuPCR_E1046_Holocentrus_rufus m PCR_E1042_Neoniphon_operculariPCR_E0101_Sargocentron_vexillarius m Neoniphon_sammara|E1728|utg7180000939899|4678|857PCR_E0731_Neoniphon_argenteus 3 PPCR_E1025_Polymixia_loweCR_E1072_Neoniphon_sammi ara PCR_E0019_Polymixia_japonicPolymixia_japonica|E1728|utg7180001265481|1752|564a 5 Percopsis_transmontana|E1728|utg7180000616228|4535|93Typhlichthys_subterraneus|E1728|utg7180001296436|11216|4992 PCR_E1138_Zeus_fabeZeus_faber|E1728|utg7180000052337|888|478r 2 CPCR_E1032_Cyttopsis_roseyttopsis_roseus|E1728|uatg7180000106577|5138|1244 Stylephorus_chordatus|E1728|utg7180003146389|1264|516Laemonema_laureysi|E1728|utg7180000178531|5054|1158 0 PMora_moro|E1728|utg7180001975944|831|472CR_E0334_Lepidion_ensiferus 7 PCR_E0419_Antimora_microlepiPCR_E1009_Physiculus_fulvus s Trachyrincus_scabrus|E1728|utg7180000037828|2264|615Muraenolepis_marmoratus|E1728|utg7180000279019|5165|1279 0 Trachyrincus_murrayi|E1728|utg7180001974950|1038|493Melanonus_zugmayeri|E1728|utg7180001746916|4998|11042 Bathygadus_melanocrachus|E1728|utg7180001270745|7318|342PCR_E1013_Steindachneria_argentea 2 Macrourus_berglaxPCR_E0428_Coryphaenoides_acrolepi|E1728|utg7180001823540s |1545|5441 PCR_E0969_PCR_E0342_Malacocephalus_laeviTrachonurus_sulcatuss Malacocephalus_occidentalis|E1728|utg7180000045322|1443|533Bregmaceros_cantori|E1728|utg7180000037127|6900|3012 9 Merluccius_polli|E1728|utg7180000071927|7061|316Merluccius_merluccius|E1728|utg7180001934601|64535 |2557 Merluccius_capensis|E1728|utg7180002556805|493|438Molva_molva|E1728|utg7180000070331|849|4745 9 Brosme_brosmePhycis_blennoide|E1728s|E1728|utg7180001886467|utg7180003672464|5016|7078|112|3180 2 PCR_E0489_Lota_lotPhycis_phycis|E1728|utg7180001226438|3303|719a 9 LoGadiculus_argenteus|E1728|utg7180001568021|6331|243ta_lota|E1728|utg7180001969737|1926|5822 5 PCR_E0491_Micromesistius_poutassoTrisopterus_minutus|E1728|utg7180001470315u |916|4812 Pollachius_virensPCR_E0372_Pollachius_viren|E1728|utg7180001618327s |2690|6586 MMelanogrammus_aeglefinus|E1728|utg7180000152898|784|468erlangius_merlangus|E1728|utg7180001512857|148|4044 0 ArctPCR_E0376_Melanogrammus_aeglefinuogadus_glacialis|E1728|utg7180000015699s |7156|3260 Boreogadus_saida|E1728|utg7180000048432|7793|389Theragra_chalcogramma|E1728|utg7180001529193|8387|4734 PCR_E0375_Gadus_morhuGadus_morhua|E1728|GeneScaffold_3970|148353|15224a 9 PCR_E0785_Bathysaurus_feroGadus_morhua|E1728|model|x 0 PCR_E1017_1034_PBarthayspuditesroi_trsu_gculenrallattaor Parasudis_fraserbrunneri|E1728|utg7180003743894|7122|322PCR_E0493_Scopelarchus_sp 6 PCR_E0440_Benthalbella_dentatPCR_E0497_Lestidiops_jayakari a PCR_E0964_Anotopterus_pharaPCR_E0486_Paralepis_coregonoideo s PCR_E0965_Alepisaurus_Lampris_guttatus|E1728|utg7180003865484|2078|597ferox 2 Regalecus_glesne|E1728|utg7180001634427|6575|268PCR_E0822_Lophotus_lacepede 2 PPCR_E1014_Zu_cristatuCR_E0974_Desmodemsa_polystictum PCR_E0500_MycBenthosema_glaciale|E1728|utg7180000937628|1|360tophum_punctatum 9 PCR_E0067_Stenobrachius_leucopsaruPCR_E0494_Benthosema_glaciale s PPCR_E0499_Lepidophanes_guenCR_E0495_Ceratoscopelus_warmtheringii i PCR_E0061_Symbolophorus_californiensiPCR_E0010_Lobianchia_gemellarii s OProtosalanx_hyalocranius|E1728|scaffold12|2651908|265580smerus_eperlanus|E1728|utg7180001830316|12527|8634 4 PCR_E0492_Diplophos_Plecoglossus_altivelis|E1728|ZPA_LOC101483035.1.1|6060|216taenia 6 PCR_E0037_Stomias_boPCR_E0995_Photostomias_guernea i PCR_E0483_LepBorostomias_antarcticus|E1728|utg7180000160695|1359|502tostomias_longibarba 9 PCR_E0966_PhoPCR_E0783_Malatoneccosteutes_margaris_niger ta Umbra_pygmaeEsox_lucius|E1728|NC_025991.2|11071314|1107521|E1728|YUP_LOC100696460.1.1|4818|3919 Salvelinus_fontinalis|E1728|QSF_LOC101483035.1.1|1294|519Salmo_salar|E1728|NC_027306.1|4995426|4999325 3 Thymallus_thymallus|E1728|ITT_LOC100696460.1.1|1|322Salmo_salar|E1728|NC_027317.1|39242438|39246337 8 Oncorhynchus_mykiss|E1728|ENA|CCAF010024252|CCAF010024252.1|32491|3639PCR_E0437_Oncorhynchus_nerka_mykiss 0 PCR_E0352_Argentina_sialis_siluPCR_E0345_Chanos_chanos s PygocenAstyanax_mexicanus|E1728|NW_006740005.1|2434105|243801trus_nattereri|E1728|KV575349.1|2220058|2216154 0 PCR_G1461_Pygocentrus_nattererApteronotus_albifrons|E1728|A2AA_LOC562320.1.1|4459|55i 5 Pangasianodon_hypophthalamus|E1728|GPH_LOC562320.1.1|4190|28Electrophorus_electricus|E1728|scaffold2095|73097|76994 7 PCR_IctaluGru1273_Danio_reris_punctatus|E1728o |CM004420.1|18056353|18060256 Danio_rerio|E1728|NC_007118.6|60858164|6086206Danio_rerio|E1728|model|0 8 Leuciscus_waleckii|E1728|FLSR01004888.1|26704425|2670832Pimephales_promelas|E1728|JNCD01004787.1|9044|12948 3 Cyprinus_carpio|E1728|LHQP01016887.1|128168|12454Sinocyclocheilus_grahami|E1728|LCYQ01S000985.1|193460 |15442 Sinocyclocheilus_anshuiensisSinocyclocheilus_rhinoceros|E1728|LAVF01S020989.1|58081|6198|E1728|LAVE01S014600.1|562187|558285 3 Cyprinus_carpio|E1728|LHQP01001195.1|137739|14164Sinocyclocheilus_grahami|E1728|LCYQ01S000052.1|2534879|2538783 4 Sinocyclocheilus_anshuiensisSinocyclocheilus_rhinoceros|E1728|LAVF01S034904.1|83003|7909|E1728|LAVE01S001478.1|146823|142918 8 PCR_E1016_Dorosoma_cepedianuAlosa_alosa|E1728|EAA_LOC562320.1.1|2283|621m 4 Clupea_harengus|E1728|NW_012222703.1|976510|97259PCR_G1425_Pellona_flavipinnis 3 PCR_G1417_Pantodon_buchholzPCR_E0351_Engraulis_mordax_eurystoli e PPCR_CR_EG0990_Hiodon_alo1510_Xenomystsuoides_nigs ri GPCR_G1307_Gymnarchus_niloticunathonemus_petersii|E1728|B2GPs _LOC562320.1.1|1428|5317 PCR_G1301_Gnathonemus_petersiPCR_G1206_Arapaima_gigas i ScPCR_G1324_Heterotis_niloticuleropages_formosus|E1728|JAs RO02001544.1|9522|5632 OstPCR_eogloE0084_ssum_biOsteogloscirrhosum_bicirrhoum|E1728|CsuOBm _LOC562320.1.1|1526|5416 PCR_E0769_Elops_sauruPCR_G1372_Megalops_astlanticus PPCR_G1399_Notacanthus_chemnitziCR_E0788_Halosauropsis_macrochiri PCR_PCR_G1281_Echidna_nebulosa_rhodochiluG1381_Muraenesox_cinereus s PCR_G1404_Ophichthus_cephalozonPCR_G1393_Nemichthys_scolopaceuas Anguilla_japonica|E1728|KI305668.1|19162|2305PCR_E1001_Saccopharynx_ampullaceus 3 Anguilla_anguilla|E1728|model|0|Anguilla_rostrata|E1728|LTYT010004920 .1|131405|127511 APCR_G1202_Anguilla_rostratnguilla_anguilla|E1728|AZBKa 01S001203.1|95970|99757 PCR_E0501_Albula_vulpePCR_E0461_Amia_calvs a Lepisosteus_oculatusLepisosteus_oculatus||E1728E1728||modelLG4|27833055|0 |27829191 PPCR_G1353_Lepisosteus_platostomuCR_E0993_Lepisosteus_osseus s PCR_G1187_Acipenser_fulvescenPCR_G1445_Polyodon_spathula s PCR_GP1476_CR_GSc1347_Laaphirhytinmcehuria_s_albuchalusmnae Latimeria_chalumnaePCR_G1356_Leu|E1728coraja_erinace|NW_005820000.1a |616057|619929 PCR_G1328_Homo_sapienPCR_G1382_Mus_musculuss PCR_G1511_Xenopus_tropicaliXenopus_tropicalis|E1728|CM004443s .1|24111386|24107523 PCR_E1115_Chiasmodon_nigePCR_E1106_Kali_indica r PPCR_E0385_Kali_kerbertCR_E0631_Scomberomiorus_maculatus_sp PCR_E0927_Acanthocybium_solandrPCR_E0832_Gymnosarda_unicolor i PCR_E0247_Scomber_japonicuPCR_E0626_Scomber_scombrus PPCR_E0747_Katsuwonus_pelamiCR_E0243_Sarda_sarda s TPCR_E0830_Euhunnus_orienttalihynnus_as|E1728ff|BAinis DN01032168.1|6881|2985 PCR_E0831_Thunnus_albacareThunnus_albacares|E1728|utg7180000047926s |7251|3355 PCR_E0672_Cubiceps_graciliPCR_E0667_Cubiceps_pauciradiatus s PCR_E0622_Peprilus_parPCR_E0136_Peprilus_simillimuu s PPCR_E0600_Peprilus_burtCR_E0387_Icichthys_locki ingtoni PCR_E0226_Ruvettus_pretiosuPCR_E0516_Pomatomus_saltatris x PCR_E0810_Caristius_sPCR_E0471_Neoepinnula_americanp a PCR_E0518_Neoepinnula_orientaliPCR_E0287_Nealotus_tripes s PCR_E0976_Scombrolabrax_heterolepiPCR_E0970_Brama_brama s PPCR_E0274_Aphanopus_carbCR_E0996_Pterycombus_braoma PCR_E0475_Benthodesmus_simonyPCR_E0596_Trichiurus_lepturus i PCR_E1126_Ariomma_bondPCR_E0665_Ariomma_melanui m PCR_E0214_Dactylopterus_volitanPCR_E0237_Dactyloptena_orientaliss PCR_E0749_Dactyloptena_petersenPCR_E0335_Macroramphosus_gracilii s PCR_E0871_AulosPCR_E0293_Aulostomus_maculatutomus_chinensiss PCR_E0915_Doryrhamphus_excisuPCR_E0634_Mullus_auratus s Hippocampus_erectus|E1728|scaffold23|1352097|135599PCR_E0829_Corythoichthys_schultzi 3 PCR_E0821_Syngnathus_louisianaPCR_E0346_Syngnathus_scovelli e PCR_E1134_Monopterus_albuPCR_E1157_Mastacembelus_erythrotaenis a PHelostoma_temminckii|E1728|utg7180000581239|6333|244CR_E1141_Ctenopoma_acutirostre_kingsleyae 1 PCR_E1133_Channa_striatChanna_argus|E1728|scaffold369|2079674|208356a 9 PPCR_E1180_Psettodes_belcherCR_E1131_Mene_maculata i PCR_E0623_Seriola_dumerilPCR_E1165_Psettodes_erumei i PPCR_E1145_Trachinotus_ovatuCR_E0819_Trachinotus_falcatuss PCR_E0195_OligoplPCR_E0738_Scomberoides_lysaites_saurus n PPCR_E0503_Remora_osteochir_australiCR_E0841_Elagatis_bipinnulata s PCR_E0468_RachycenPCR_E0615_Echeneis_nautron_canaducrates m PPCR_E0833_Selar_crumenophthalmuCR_E0937_Coryphaena_hippurus s PCR_E0212_Decapterus_macarelluPCR_E0671_Decapterus_punctatuss PCR_E0598_Trachurus_lathamPCR_G1428_Perca_fluviatilis i PCR_E0917_Carangoides_plagiotaeniPCR_E0869_Carangoides_ferdau a PCR_E0469_Alectis_ciliariPCR_E0515_Uraspis_secunds a PCR_E0767_Selene_browniSelene_dorsalis|E1728|utg7180000129869i |3625|7521 PCR_E0510_Caranx_crysos_rubePCR_E0834_Caranx_sexfasciatusr PCR_E0574_Caranx_ignobiliPCR_E0763_Chloroscombrus_chrysurus s PCR_E0938_PCR_E0616_Hemicaranx_amblyrhynchuGnathanodon_speciosus s PCR_E1150_LepPCR_E0942_Atule_mattobrama_muellere i PCR_E0836_Sphyraena_barracudPCR_E0955_Sphyraena_putnamaea PCR_E0230_Sphyraena_argenPCR_E1143_Sphyraena_sphyraentea a Lates_caPCR_E1148_Psammoperca_waigiensilcarifer|E1728|LBLR01011739.1|649153|65304s 9 PCR_E1147_LaPCR_E1135_Lates_japonicues_calcarifers PCR_E1149_Lates_microlepiPCR_E0766_Centropomus_ensiferus s PCR_E1158_Centropomus_mediuPCR_E0194_Centropomus_undecimalis s PCR_E1153_CenPCR_E0681_Tetrtapropomuturus_albidus_viridiss PCR_E0692_Makaira_sPCR_E0695_Istiophorus_platypterup s PCR_E1139_Toxotes_chatareuPCR_E0697_Makaira_nigricanss PPCR_CR_EE0071_Ci1174_Citthaharroideus_linguas_macrtulolepia s PCR_E0217_Polydactylus_virginicuPCR_E0606_Polydactylus_octonemus s PPCR_E0842_Leptomelanosoma_indicuCR_E1154_Eleutheronema_tetradactymlum PCR_E0080_Lepidoblepharon_ophthalmolepiPCR_E0597_Cyclopsetta_chittendeni s PCR_E0633_SPCR_E0647_Etropus_crossotuyacium_micrurums PPCR_E0446_Citharichthys_sordiduCR_E0043_Citharichthys_arctifronss ParaPCR_lichthys_oE0077_Pslivaceus|E1728|eudorhombus_penCHRtoph9|9607689|960379thalmus 6 PPCR_E1171_Paralichthys_albiguttCR_E0020_Paralichthys_californiacus PCR_E0021_Xystreurys_liolepiPCR_E0001_Ancylopsetta_ommas ta PCR_E0022_Hypsopsetta_guttulatPCR_E0640_Gastropsetta_frontalisa PCR_E0055_Atheresthes_evermannPCR_E0444_Eopsetta_jordani i PCR_E0064_Embassichthys_bathybiuPCR_E0433_Microstomus_pacificus s PCR_E0035_Pseudopleuronectes_americanuPCR_E0416_Glyptocephalus_zachirus s PPseudopleuronectes_yokohamae|E1728|BBOV01063222.1|1371|526CR_E0424_Hippoglossoides_elassodon 4 PPCR_E0025_Psettichthys_melanostictuCR_E0053_Pleuronectes_platessa s PCR_E0438_Lepidopsetta_bilineatPCR_E0445_Parophrys_vetulus a PCR_E0462_Lepidorhombus_bosciPCR_E0072_Samariscus_japonicusi PCR_E0078_Samariscus_xenicuPCR_E0074_Plagiopsetta_glossas Cynoglossus_semilaevis|E1728|NC_024307.1|24281333|2427743PCR_E0076_Cynoglossus_interruptus 7 PCR_E0604_Symphurus_civitatiuPCR_E0023_Symphurus_atricaudums PCR_E0073_Poecilopsetta_plinthuPCR_E1164_Symphurus_plagiusas PPCR_CR_EE0448_0582_PAsoeecrilopaggodesetta_beanis_heemstri ai PCR_E0075_Aseraggodes_kobensiPCR_E0079_Heteromycteris_japonicus s PPCR_E1183_Solea_lascarisCR_E0054_Solea_solea PCR_E1182_Brachirus_annulariPCR_E0943_Soleichthys_heterorhinos s PCR_E0630_Gymnachirus_texaPCR_E0081_Pseudaesopia_japonie ca PPCR_E0609_Gymnachirus_melaCR_E0046_Trinectes_maculatuss PCR_E1162_Hypoclinemus_sPCR_E0605_Achirus_lineatusp PPCR_E1169_Mancopsetta_maculatCR_E1184_Oncopterus_darwini a PCR_E1170_Neoachiropsetta_milfordPCR_E1167_Rhombosolea_plebeia i PCR_E0083_PsePCR_E0599_Trictthopina_steosantta_vaentralis PCR_E1160_Arnoglossus_blochePCR_E1163_Arnoglossus_imperialii s PCR_E1181_Chascanopsetta_lugubriPCR_E0082_Laeops_kitaharae s PCR_E0016_Xyrichtys_novacula_martinicensiPCR_E0038_Bothus_robinsi s PCR_E0793_Halidesmus_scapulariPCR_E0015_Clepticus_parrae s PCR_E0589_Natalichthys_saPCR_E0137_Crenicichla_lepidom ta Amphilophus_citrinellus|E1728|CCOE01000600.1|987303|99119PCR_E0390_Symphysodon_discus 9 PCR_G1407_Oreochromis_niloticuOreochromis_niloticus|E1728|GL831208s .1|507303|503407 PCR_G1520_Neolamprologus_brichardOreochromis_niloticus|E1728|model|0i Maylandia_zebraNeolamprologus_brichardi|E1728|NW|E1728_014444863|NW_006272083.1|721305.|171740|20827079 |2086603 PPCR_G1521_Pundamilia_nyerereCR_G1519_Metriaclima_zebra i PCR_Pundamilia_nyerereiG1518_Astatotilapia_bur|E1728|NW_005187728.1toni |348523|352419 PCR_E0286_Parma_microlepiHaplochromis_burtoni|E1728|NW_005179474.1|254648|25075s 2 PCR_E0772_Microspathodon_chrysuruPCR_E0459_Hypsypops_rubicundus s PCR_E0713_Stegastes_albifasciatuPCR_E0929_Lepidozygus_tapeinosoms a PStegastes_partitus|E1728|NW_007578043.1|97566|9367CR_E0203_Stegastes_fuscus 0 PCR_E0219_Stegastes_diencaeuPCR_E0890_Abudefduf_vaigienssis PCR_E0820_AbudePCR_E0881_Abudefduf_sexfasciatufduf_saxatilis s PCR_E0865_Dascyllus_trimaculatuPCR_E0851_Chromis_dimidiata s PCR_E0862_Dascyllus_carneuPCR_E0580_Azurina_hirundo s Chromis_chromisPCR_E0201_Chromis_cyane|E1728|utg7180001853813a |6073|9969 PCR_E0238_Chromis_atripectoraliPCR_E0559_Pomachromis_richardssoni PCR_E0464_Dischistodus_perspicillatuPCR_E0933_Neopomacentrus_cyanomoss PCR_E0465_Neoglyphidodon_melaPCR_E0564_Chrysiptera_taupou s PCR_E0285_Neoglyphidodon_polyacanthuPCR_E0466_Acanthochromis_polyacanthus PCR_E0239_Pomacentrus_brachialiPCR_E0557_Pomacentrus_spilotoceps s PCR_E1100_Ambassis_interruptPCR_G1196_Ambassis_agrammaus PCR_E0031_Mugil_curemPCR_E0049_Mugil_cephalua s PCR_E0846_Crenimugil_crenilabiPCR_E0847_Valamugil_buchanansi Nothobranchius_furzeriKryptolebias_marmoratus|E1728|LHSH01000967.1|15637|1174|E1728|NC_029652.1|35230736|35234621 8 AusPoetcroilia_fundulus_limnaeusreticulata|E1728||E1728NC_024348|NW_013952593.1|10016399.1||1002029897259|901155 5 PPoecilia_CR_E1065_formosaPoec|ilia_laE1728tipinna_|NW_006799980reticulata .1|1153202|1149306 PCR_E1052_Belonesox_belizanuPCR_E0185_Heterandria_formossa Xiphophorus_couchianus|E1728|KQ557206.1|10696627|1070052Xiphophorus_maculatus|E1728|NW_005372302.1|375868|3797643 PCR_E1063_Floridichthys_carpiCyprinodon_nevadensis_pectoroalis|E1728|JSUU01001874.1|10872|7304 PCR_E1066_Cyprinodon_variegatuCyprinodon_varigatus|E1728|KL652693s .1|143617|147512 Fundulus_heteroclitus|E1728|NW_012224715.1|204645|20074PCR_E0389_Fundulus_parvipinnis 9 PCR_E0173_Adinia_xenicPCR_E1064_Lucania_parva_goodea i PCR_E0186_Fundulus_chrysotuPCR_E0130_Fundulus_blairae s PCR_E1112_Labidesthes_sicculuPCR_E0167_Menidia_menidia s PCR_E0121_AMenidia_menidia|E1728|gb|GEVY01003755.1||1804|569therinopsis_californiensis 8 PCR_E0395_Odontesthes_retropinniOdontesthes_bonariensis|E1728|Odons testhes_bonariensis_3742|64557|68453 PCR_E0393_Odontesthes_argentinensiPCR_E0394_Odontesthes_humensis s PPCR_E0180_CraCR_E0396_Odonterocephalus_honoriatesthes_bonariensise PCR_E0115_Atherinomorus_stipePCR_E0548_Atherinomorus_lacunosus s PCR_E0181_Atherinomorus_vaigiensiPCR_E0182_Pseudomugil_gertrudae s PCR_E0178_Melanotaenia_trifasciatPCR_E0406_Marosatherina_ladigesai PCR_E0179_Melanotaenia_splendidPCR_G1408_Oryzias_latipes a OOryzias_latipesryzias_latipes||E1728E1728||model18|15308397|0 |15304501 PPCR_E1068_Hyporhamphus_aCR_E1086_Hyporhamphus_duffinisssumieri PCR_E0399_Cheilopogon_pinnatibarbatuPCR_E0403_Exocoetus_monocirrhus s PCR_E0624_Cheilopogon_dorsomaculPCR_E0400_Prognichthys_brevipinnis a PCR_E0541_PCR_E0401_Hirundichthys_marginatuZenarchopterus_dispar s PCR_E0110_Strongylura_notatPCR_E0404_Scomberesox_saurua s PPCR_E0192_CololabiCR_E1051_Tylosuruss__scrairoacodilus PCR_E0162_Ablennes_hianPCR_E0114_Platybelone_argalus s PCR_E0210_Lipogramma_trilineatPCR_E0211_Lipogramma_anabantoidea s PCR_E0134_Hyperprosopon_anale_argenteuPCR_E0129_Amphistichus_argenteus m PPCR_E0135_CR_E0120_ZEmalembius_rosaceubiotoca_jacksonsi PCR_E0122_Phanerodon_PCR_E0139_Cymatogaster_aggregatfurcatus a PCR_E0124_Rhacochilus_vaccPCR_E0855_Plesiops_coeruleolineatua s PCR_E0706_Pseudochromis_cyanotaeniPCR_E0102_Arcos_sp a PCR_E0535_Pseudochromis_jamesPseudochromis_fuscus|E1728|utg7180000877380i |17866|13970 PCR_E0280_Gramma_loretPCR_E0603_Lonchopisthus_micrognathuo s PCR_E0315_Enneanectes_altiveliPCR_E0305_Enneanectes_boehlksei PCR_E0916_Enneapterygius_gruschkaPCR_E0896_Enneapterygius_abeli i PPCR_E0885_Helcogramma_fuscopinnCR_E0331_Helcogramma_ellioti_sp a PCR_E0320_Acanthemblemaria_asperPCR_E0295_Acanthemblemaria_paulaa PPCR_E0310_Emblemaria_pandioniCR_E0313_Chaenopsis_sp_alepidos ta PCR_E0800_Blennophis_striatuPCR_E0294_Lucayablennius_zingars o PCR_E0799_Pavoclinus_profunduPCR_E0803_Clinus_superciliosus s PCR_E0805_Muraenoclinus_dorsaliPCR_E0804_Clinus_cottoides s PCR_E0326_Neoclinus_blanchardPCR_E0301_Labrisomus_bucciferui s PCR_E0309_Paraclinus_marmoratuPCR_E0317_Stathmonotus_stahli s PCR_E0319_Platygillellus_rubrocinctuPCR_E0302_Labrisomus_nigricinctus s PCR_E0318_Starksia_ocellatPCR_E0303_Starksia_fasciata PCR_E0289_Hypsoblennius_hentPCR_E0304_Starksia_atlantica z Parablennius_parvicornis|E1728|utg7180000860707|882|477PCR_E0909_Petroscirtes_mitratus 5 PCR_E0934_Ecsenius_midaPCR_E0540_Plagiotremus_stapeinosoma PCR_E0523_Ecsenius_parduPCR_E0723_Ecsenius_opsifrons talis PCR_E0520_Cirripectes_stigmaticuPCR_E0296_Ophioblennius_atlanticus s PCR_E0330_Cirripectes_quaggPCR_E0892_Cirripectes_castaneua s PCR_E0525_APCR_E0893_Cirripectes_filamentosutrosalarias_fuscus s PCR_E0988_Salarias_fasciatuPCR_E0521_Nannosalarias_nativitatis s PCR_E0329_Praealticus_caesiuPCR_E0979_Blenniella_paula s PCR_E0986_Blenniella_chrysospilos_paulPCR_E0556_Istiblennius_dussumieri a PCR_E0297_Entomacrodus_nigricanPCR_E0715_Blenniella_cyanostigmas PCR_E0987_Entomacrodus_striatuPCR_E0984_Ecsenius_bicolor s PPCR_CR_EE1122_Halieu0980_Entomticahcrthoduys_as_niuaculeaftoouenus sis PCR_E0975_Dibranchus_PCR_E0610_Ogcocephalus_parvus_nasututremendus s PCR_E1124_Antennarius_radiosuAntennarius_striatus|E1728|utg7180000210086|1|351s 8 PCR_E1092_Antennarius_coccineuPCR_E0587_Antennarius_nummifesr PCR_E1121_Chaunax_stigmaeuPCR_E1119_Lophius_gastrophsysus PCR_E0477_Melanocetus_murrayPCR_E1053_Gigantactis_ios i PCR_E0657_Melanocetus_johnsoniPCR_E0656_Himantolophus_albinares_sagamiui s PPCR_E0686_Cryptopsaras_couesiCR_E0655_Oneirodes_macrosteuis PCR_E1144_PCR_E0414_GAmmadopsis_marmoraodytes_hexapttuesrus PCR_G1430_Percichthys_truchPCR_E0921_Chaetodon_aurigaa PCR_E0753_Chaetodon_striatuPCR_E0547_Heniochus_varius s PCR_E0509_Luvarus_imperialiPCR_E0748_Heniochus_chrysosstomus PCR_E0918_Naso_brevirostriPCR_E0029_Zebrasoma_veliferus m PCR_E0710_Pomacanthus_imperatoPCR_E0754_Pomacanthus_arcuatus r PCR_E0849_0209_HolaPomaccananthuthuss__csiliaemrisicirculatus PCR_E0839_ApolemichPCR_E0282_Holacanthus_passethys_trimacular tus PCR_E0534_PPCR_E0550_Cenygoplitropyge_bicolotes_diacanthur s PCR_E0542_Centropyge_noPCR_E0914_Oxymonacanthus_x longirostris PCR_E0887_Cantherhines_pardalis_pulluPCR_E0316_Aluterus_scriptus s PCR_E0591_Balistes_capriscuPCR_E0381_Rhinecanthus_asssasi PCR_E0380_Xanthichthys_auromarginatuPCR_E0936_Abalistes_stellatus s PCR_E0382_Triacanthodes_anomaluPCR_E0935_Sufflamen_fraenatum s PCR_E0588_Ostracion_cubicuMola_mola|E1728|KV751366.1|5485504|548161s 1 PCR_E0312_Diodon_holocanthuPCR_E0339_Sphoeroides_maculas tus PCRCR__E0601_LagocephaE0383_Torquigener_hamillus_laevitgatuoni s PCR_E0460_Takifugu_rubripes|E1728|NC_018897.1|12789466|1279335Takifugu_rubripes 1 PCR_E0853_Canthigaster_valentinPCR_E0530_Canthigaster_bennettii PCR_G1513_Tetraodon_nigroviridiPCR_E0374_Tetraodon_fluviatilis s TTetraodon_nigroviridis|E1728|20|847357|84347etraodon_nigroviridis|E1728|model|0 4 PCR_E0823_Gerres_oyenPCR_E0911_Scolopsis_frenaa tus PCR_E0292_Gerres_cinereuPCR_E0835_Gerres_longirostris s PCR_E0756_Eucinostomus_gulPCR_E0575_Eucinostomus_argenteua s PPCR_E0940_Siganus_argenteuCR_E0138_Genyonemus_lineatsus PCR_E1108_Aplodinotus_grunnienPCR_E1055_Sciaenops_ocellatus s PCR_E0166_Menticirrhus_saxatiliPCR_E0127_Menticirrhus_undulatus_littoralis s PCR_E0125_APCR_E0511_Cynoscion_arenariutractoscion_nobiliss PCR_E0164_Cynoscion_regaliLarimichthys_crocea|E1728|Ns W_011323865.1|140023|143916 Miichthys_miiuy|E1728|JXSJ01000623.1|56027|5213PCR_E0123_Seriphus_politus 1 PCR_E0118_Cheilotrema_saturnuPCR_E0628_Umbrina_coroides m PCR_E1048_Larimus_brevicepPCR_E1047_Bairdiella_sanctaelucias e PCR_E0165_Bairdiella_chrysourPCR_E0608_Stellifer_lanceolatuas PCR_E0828_Aprion_virescenPCR_E0563_Aphareus_furcas PCR_E0594_Pristipomoides_aquilonariPCR_E0746_Pristipomoides_auricilla s PCR_E0592_Lutjanus_campechanuPCR_E0926_Novaculichthys_taeniourus s PCR_E0283_Ocyurus_chrysuruPCR_E0593_Rhomboplites_aurorubens s PCR_E0939_Macolor_nigePCR_E0949_Caesio_varilinear ta PCR_E0961_Pterocaesio_tilPCR_E0920_Caesio_caerulaurea_lunarie s PPCR_E0950_Caesio_xanthonotCR_E0951_Caesio_teres a PCR_E0620_Decodon_puellariPCR_E0560_Bodianus_mesothoras x PCR_E0567_Hologymnosus_doliatuPCR_E0912_Coris_formosa s PCR_E0895_Macropharyngodon_biparPCR_E0928_Halichoeres_iridis titus PCR_E0932_Anampses_lineatuPCR_E0908_Stethojulis_strigiventes r Symphodus_melops|E1728|utg7180000100544|5631|173PCR_E0553_Cirrhilabrus_punctatus 5 Labrus_bergylta|E1728|FKLU01000024.1|1048282|104438PCR_E0907_Cheilinus_chlorourus 7 PCR_E0948_Wetmorella_nigropinnatPCR_E0873_Oxycheilinus_digrammaa PCR_E0876_Cheilinus_fasciatuPCR_E0879_Epibulus_insidiatosr PCR_E0566_CePCR_E0877_Leptoscarus_vaigiensitoscarus_bicolor s PPCR_E0561_Chlorurus_gibbuCR_E0013_Scarus_croicensiss PCR_E1024_Antigonia_caproPCR_E0872_Scarus_quoyi s PCR_E0924_Paracirrhites_forsteri_arcatuPCR_E0314_Amblycirrhitus_pinos s PCR_E0725_NeocirrhiPCR_E0884_Cirrhitichttes_armahys_oxycephalutus s PCR_E0131_Pomoxis_nigromaculatuPCR_E0146_Elassoma_evergladei s PCR_E0132_Lepomis_cyanelluPCR_E0392_Ambloplites_rupestris s PCR_E1113_Lepomis_macrochiruPCR_E1110_Micropterus_salmoides s PCR_E0795_CheilodacPCR_E0797_Cheilodactylus_pixtylus_fasciai tus PCR_E0712_Kuhlia_mugiPCR_E0826_Terapon_jarbul a PCR_E1136_Siniperca_chuatsPCR_E0775_Kyphosus_sectatoi r PCR_E1132_DicenDicentrarchus_labrax|E1728|HG916843.1|10812367|1080847trarchus_labrax 1 MPCR_E0992_Morone_chrysoporone_saxatilis|E1728|JTCL01004472s .1|3144|7040 PCR_E0816_Howella_brodiePCR_E0824_Sillago_sihamai PPCR_E1130_Lateolabrax_japonicuCR_G1300_Glaucosoma_hebraicusm PCR_E0923_Parapriacanthus_ransonnetPCR_E1125_Synagrops_bellus i PCR_E0227_SPCR_E0252_Pristereolepis_gigatigenys_alta s PCR_E0570_Heteropriacanthus_cruentatuPCR_E0618_Priacanthus_arenatus s PPCR_E0595_CaulolaCR_E0954_Erythrocletilus_ins_schlegelitermediui s PCR_E0231_Caulolatilus_princepPCR_E0324_Kathetostoma_averruncus s PCR_E0538_Uranoscopus_sulphureuPCR_E1028_Astroscopus_y_graecums PCR_E0250_Drepane_punctatPCR_E0858_Platax_teira a PCR_E0614_Chaetodipterus_fabePCR_E1091_Parapercis_punctulatra PCR_E1083_Parapercis_hexophtalmPCR_E0707_Parapercis_clathrata a PCR_E0856_PlecPCR_E0857_Plecttorhinchus_viorhinchus_chaettatutodonoides s PCR_E0199_Haemulon_sciuruPCR_E0229_Xenistius_californiensis s PCR_E0279_Haemulon_plumieriPCR_E0218_Haemulon_vittatumi PCR_E0635_Haemulon_aurolineatuPCR_E0200_Anisotremus_virginicusm PCR_E0761_Pomadasys_corvinaePCR_E0607_Orthopristis_chrysoptferormia s PCR_E0827_Monodactylus_argenteuPCR_E0613_Conodon_nobilis s PCR_E0905_Lethrinus_haraPCR_E0952_Gymnocranius_grandoculik s PCR_E0750_Lethrinus_atkinsonPCR_E0910_Lethrinus_obsoletuis PCR_E0802_PCR_E0751_Lethrinus_olivaceuArgyrozona_argyrozons a PCR_E0762_Calamus_pennSpondyliosoma_cantharus|Ea 1728|utg7180000705634|7400|3504 PCR_E0807_Diplodus_capensiPCR_E0806_Sarpa_salpa s Acanthopagrus_schlegeliiPCR_E0953_Acanthopagrus_ca|E1728tenul|scaffold154a |1819206|1823102 Perca_PCR_E0143_Rofluviatilism|E1728anichth|uystg7180001854093_valsanicola |7315|3419 PCR_E1109_Sander_vitreuPCR_E0391_Perca_flavescenss PPCR_E0168_Etheostoma_juliaCR_E1111_Etheostoma_zonalee PCR_E0154_Percina_nigroPCR_E0152_Etheostoma_simoterufasciata m PCR_E0150_Percina_phoxocephalPCR_E1054_Percina_caprodes a PPCR_E0187_Ammocrypta_beaniCR_E0141_Gymnocephalus_schraetsei r PPCR_E0153_Crystallaria_asprellCR_E0307_Liopropoma_mowbraa yi PCR_E0306_Liopropoma_rubrPCR_E0531_Aporops_bilinearies PCR_E0900_Grammistes_sexlineatuPCR_E0852_Pseudogramma_polyacanths a PCR_E0347_Rypticus_subbifrenatuPCR_E0571_Grammistops_ocellatus PCR_E0338_Hemanthias_vivanuPCR_E0860_Pseudanthias_squamipinnis s PCR_E0838_Cephalopholis_miniatPCR_G1327_Holanthias_chrysostictua s PPCR_E0552_Epinephelus_merrCR_E0868_Cephalopholis_argua s PPCR_E0549_Epinephelus_maculatuCR_E0627_Hyporthodus_flavolimbas tus PCR_E0311_MycPCR_E0163_Centteroperca_bonaropristis_striataci_microlepis PCR_E0325_Paralabrax_nebulifePCR_E0322_Serranus_baldwini r PCR_E0336_Serranus_phoebPCR_E0337_Serranus_notospilue s PCR_E0505_HypoplecPCR_E1002_Diplectrum_trus_puellformosua m PPCR_E1008_Diplectrum_bivittatuCR_E1120_Bembrops_anatirostrims PCR_E1128_Bembrops_gobioidePCR_E0158_Pogonophryne_barsukovs i Chaenocephalus_aceratus|E1728|utg7180003193006|1426|532Notothenia_coriiceps|E1728|NW_011359314.1|302537|306433 1 PCR_E0867_Synanceia_verrucosPCR_E0888_Sebastapistes_cyanostigma a PCR_E0558_Caracanthus_unipinnPCR_E0583_Iracundus_signifer a PCR_E0581_Scorpaenopsis_oxycephalPCR_E0903_Scorpaenopsis_longispinaa PCR_E0512_Scorpaena_dispaPCR_E0291_Scorpaena_guttatra PCR_CR_E1038_E0759_Scorpaena_agasorpaena_brasiliensiziisis PCR_E1035_Setarches_guentherPCR_E0619_Neomerinthe_hemingwayi i PCR_E1010_Pontinus_longispiniPCR_E0463_Pontinus_rathbuni s PCR_E0882_PPCR_E0870_Scorpaenodes_guamensiterois_miles s PCR_E0850_Pterois_radiatPCR_E0705_Pterois_antennata a Sebastes_norvegicus|E1728|utg7180000022679|6627|1052PCR_E0417_Sebastolobus_alascanus 1 PCR_E0354_Sebastes_paucispiniPCR_E0349_Sebastes_aurora s PSebastes_rubrCR_E0350_Sebaivinctus|E1728|KI445256.1|18551|2244stes_jordani 5 Sebastes_nigrocinctus|E1728|AUPR01138941.1|15942|1204PCR_E0044_Helicolenus_dactylopterus 8 PCR_E0340_Prionotus_carolinuPCR_E1026_Bellator_militaris s PCR_E0450_PerisPCR_E0456_Peristedion_ecuadorenstedion_truncatum e PPCR_E0708_Sunagocia_arenicoluCR_E0864_Thysanophrys_chiltonas e PCR_E0420_BaPCR_E0128_Rathbunella_hypoplectthymaster_signatus a APCR_E0423_Anoplopoma_fimbrinoplopoma_fimbria|E1728|AWGYa 01147910.1|7671|3775 PCR_E0675_Lycodes_terraenovaPCR_E0442_Bryozoichthys_marjoriue s PCR_E0787_Anarhichas_denPCR_E0119_Anarrhichthys_ocellatuticulatuss PCR_E0117_Anarhichas_orientalis_lupuPCR_E0371_Lumpenus_lampretaeformis PCR_E0431_Poroclinus_rothrockPCR_E0362_Zaprora_silenus i PCR_E0116_Cryptacanthodes_maculatuPCR_E0368_Culaea_inconstans s Gasterosteus_aculeatus|E1728|model|Gasterosteus_aculeatus|E1728|groupVII|3942979|3946870 5 PCR_E0353_Zaniolepis_frenatPCR_E1012_Gasterosteus_aculeatua s PCR_E0348_Hexagrammos_decagrammuPCR_E0367_Pleurogrammus_monopterygius s PCR_E0363_Hexagrammos_lagocephalus_otakiPCR_E0269_Hypsagonus_quadricornis i PCR_E0254_Sarritor_leptorhynchuPCR_E0264_Sarritor_frenatus s PCR_E0255_Careproctus_rastrinuPCR_E0272_Hemilepidotus_zapuss PPCR_E0422_CareprocCR_E0454_Paraliparitsus_melanuru_hystrix s PCR_E0453_Paraliparis_copePCR_E0458_Paraliparis_beanii PCR_E0266_Leptocottus_armatuPCR_E0435_Triglops_macellus s Myoxocephalus_scorpiusPCR_E0429_Radulinus_asprellu|E1728s |utg7180000022895|5798|9694 PCR_E0256_Rastrinus_scutigePCR_E0233_Chitonotus_pugetrensis PCR_E0228_Icelinus_quadriseriatuPCR_E0277_Icelinus_filamentosus s 2.0
Figure 19: KIAA gene tree with PCR products. KIAA1239 and its paralogs found via nHmmer searches in our 305 taxa are in blac, with the addition of PCR products from Betancur et al. (2013) highlighted in red. Tree was inferred with RAxML under the GTRGAMMA model.
87
Xenopus_tropicalis 100 Coelacanthiformes_Coelacanthiformes_Latimeriidae_Latimeria_chalumnae 9 9 Ceratodontiformes_Ceratodontiformes_Protopteridae_Protopterus_aethiopicus Polypteriformes_Polypteridae_Erpetoichthys_calabaricus 10Polypteriformes_Polypteriformes_Polypteridae_Polypterus_bichi0 r 10Polyp0 teriformes_Polypteriformes_Polypteridae_Polypterus_endlicheri Acipenseriformes_Polyodontidae_Polyodon_spathula 100 Acipenseriformes_Acipenseridae_Acipenser_naccarii 10Acipenseriformes_Acipenseridae_Acipenser_sinensi0 s 100 Amiiformes_Amiidae_Amia_calva_gill 8 7 Lepisosteiformes_Lepisosteiformes_Lepisosteidae_Atractosteus_spatula 10Lepisos0 teiformes_Lepisosteiformes_Lepisosteidae_Lepisosteus_oculatus 10Lepisosteiformes_Lepisosteiformes_Lepisosteidae_Lepisosteus_platyrhincu0 s Teleost_Osteoglossiformes_Osteoglossiformes_Pantodontidae_Pantodon_buchholzi 100 100 Teleost_Osteoglossiformes_Osteoglossiformes_Osteoglossidae_Osteoglossum_bicirrhosum 100 Teleost_Osteoglossiformes_Osteoglossiformes_Osteoglossidae_Scleropages_formosus 100 Teleost_Osteoglossiformes_Osteoglossiformes_Notopteridae_Papyrocranus_afer 100 100 Teleost_Osteoglossiformes_Osteoglossiformes_Morymridae_Gnathonemus_petersii 100Teleost_Osteoglossiformes_Osteoglossiformes_Mormyridae_Mormyrus_tapirus Teleost_Elopiformes_Elopiformes_Megalopidae_Megalops_cyprinoides 100 Teleost_Anguilliformes_Muraenidae_Gymnothorax_reevesii 100 Teleost_Anguilliformes_Congridae_Conger_cinereus 100 3 1 Teleost_Anguilliformes_Chlopsidae_Kaupichthys_hyporoides 6 9 Teleost_Anguilliformes_Anguillidae_Anguilla_japonica 10Teleos0 t_Anguilliformes_Anguillidae_Anguilla_rostrata 10Teleost_Anguilliformes_Anguillidae_Anguilla_anguill0 a Teleost_Clupeiformes_Clupeiformes_Engraulidae_Coilia_nasus 100 Teleost_Clupeiformes_Clupeiformes_Engraulidae_Engraulis_encrasicolus 100 Teleost_Clupeiformes_Clupeiformes_Clupeidae_Clupea_harengus 100 Teleost_Clupeiformes_Clupeiformes_Clupeidae_Amblygaster_clupeoides 100 Teleost_Clupeiformes_Clupeiformes_Clupeidae_Alosa_alosa Teleost_Otophysa_Gonorynchiformes_Chanidae_Chanos_chanos 100 Teleost_Otophysa_Cypriniformes_Gyrinocheilidae_Gyrinocheilus_aymonieri Teleost_Otophysa_Cypriniformes_Botiidae_Sinibotia_superciliaris 100 100 100 Teleost_Otophysa_Cypriniformes_Nemacheilidae_Homatula_potanini 100 Teleost_Otophysa_Cypriniformes_Cobitidae_Misgurnus_anguillicaudatus 100 100 Teleost_Otophysa_Cypriniformes_Danionidae_Danio_rerio Teleost_Otophysa_Cypriniformes_Tincidae_Tinca_tinca 100100 10T0eleost_Otophysa_Cypriniformes_Leuciscidae_Pimephales_promelas 100 Teleost_Otophysa_Cypriniformes_Leuciscidae_Leuciscus_waleckii Teleost_Otophysa_Cypriniformes_Cyprinidae_Cyprinus_carpio 9 5 10T0eleost_Otophysa_Cypriniformes_Cyprinidae_Sinocyclocheilus_rhinoceros 10Teleost_Otophysa_Cypriniformes_Cyprinidae_Sinocyclocheilus_anshuiensi0 s 10T0eleost_Otophysa_Cypriniformes_Cyprinidae_Sinocyclocheilus_grahami Teleost_Otophysa_Characiformes_Distichodontidae_Distichodus_sexfasciatus Teleost_Otophysa_Gymnotiformes_Apteronotidae_Apteronotus_albifrons 100 Teleost_Otophysa_Gymnotiformes_Gymnotidae_Electrophorus_electricus 100 100 Teleost_Otophysa_Gymnotiformes_Rhamphichthyidae_Rhamphichthys_rostratus Teleost_Otophysa_Characiformes_Serrasalmidae_Pygocentrus_nattereri 100 100 100 Teleost_Otophysa_Characiformes_Erythrinidae_Erythrinus_erythrinus 100 100 Teleost_Otophysa_Characiformes_Hepsetidae_Hepsetus_odoe Teleost_Otophysa_Characiformes_Gasteropelecidae_Gasteropelecus_sp 100 Teleost_Otophysa_Characiformes_Characidae_Hemigrammus_bleheri 100 Teleost_Otophysa_Characiformes_Characidae_Astyanax_mexicanus 100 10Teleost_Otophysa_Characiformes_Characidae_Thayeria_boehlke0 i Teleost_Otophysa_Siluriformes_Callichthyidae_Corydoras_julii 100 Teleost_Otophysa_Siluriformes_Loricariidae_Pterygoplichthys_pardalis 100 Teleost_Otophysa_Siluriformes_Plotosidae_Plotosus_lineatus 6 9 Teleost_Otophysa_Siluriformes_Siluridae_Silurus_asotus 100 Teleost_Otophysa_Siluriformes_Ictaluridae_Ictalurus_punctatus 9 1 Teleost_Otophysa_Siluriformes_Pangasiidae_Pangasianodon_hypophthalamus 5 6 Teleost_Otophysa_Siluriformes_Bagridae_Hemibagrus_guttatus 100 Teleost_Otophysa_Siluriformes_Sisoridae_Glyptothorax_sinensis 100 Teleost_Otophysa_Siluriformes_Amblycipitidae_Liobagrus_styani Teleost_Euteleost_Lepidogalaxiiformes_Lepidogalaxiidae_Lepidogalaxias_salamandroides Teleost_Euteleost_Esociformes_Esocidae_Esox_lucius 100 Teleost_Euteleost_Esociformes_Umbridae_Umbra_pygmae 100 Teleost_Euteleost_Salmoniformes_Salmonidae_Coregonus_clupeaformis 100 5 3 Teleost_Euteleost_Salmoniformes_Salmonidae_Thymallus_thymallus 100 Teleost_Euteleost_Salmoniformes_Salmonidae_Salmo_salar 100Teleost_Euteleost_Salmoniformes_Salmonidae_Oncorhynchus_mykiss 100 10Teleost_Euteleost_Salmoniformes_Salmonidae_Salvelinus_fontinali0 s Teleost_Euteleost_Argentiniformes_Argentinidae_Argentina_sp Teleost_Euteleost_Stomiatiformes_Stomiidae_Borostomias_antarcticus 100 Teleost_Euteleost_Osmeriformes_Osmeridae_Osmerus_eperlanus 7 1 100 Teleost_Euteleost_Osmeriformes_Plecoglossidae_Plecoglossus_altivelis 100 Teleost_Euteleost_Osmeriformes_Salangidae_Protosalanx_hyalocranius 100 Teleost_Euteleost_Galaxiiformes_Galaxiidae_Galaxias_maculatus 100 Teleost_Euteleost_Galaxiiformes_Galaxiidae_Galaxiella_nigrostriata Teleost_Euteleost_Aulopiformes_Synodontidae_Synodus_sp 100 Teleost_Euteleost_Aulopiformes_Chlorophthalmidae_Parasudis_fraserbrunneri 100 100Teleost_Euteleost_Aulopiformes_Chlorophthalmidae_Chlorophthalmus_sp Teleost_Euteleost_Ateleopodiformes_Ateleopodidae_Guentherus_altivela Teleost_Euteleost_Myctophiformes_Myctophidae_Benthosema_glaciale 100 Teleost_Euteleost_Polymixiiformes_Polymixiidae_Polymixia_japonica Teleost_Euteleost_Percopsaria_Percopsiformes_Amblyopsidae_Typhlichthys_subterraneus 4 5 100 Teleost_Euteleost_Percopsaria_Percopsiformes_Percopsidae_Percopsis_transmontana 10Teleost_Euteleost_Percopsaria_Percopsiformes_Percopsidae_Percopsis_omiscomaycu0 s 9 6 Teleost_Euteleost_Zeiogadaria_Zeiformes_Zeidae_Zeus_faber 100 100Teleost_Euteleost_Zeiogadaria_Zeiformes_Parazenidae_Cyttopsis_roseus 10Teleost_Euteleost_Zeiogadaria_Zeiformes_Parazenidae_Cyttopsis_s0 p Teleost_Euteleost_Zeiogadaria_Stylephoriformes_Stylephoridae_Stylephorus_chordatus 100 Teleost_Euteleost_Zeiogadaria_Gadiformes_Bregmacerotidae_Bregmaceros_cantori Teleost_Euteleost_Zeiogadaria_Gadiformes_Moridae_Mora_moro 100 100 100Teleost_Euteleost_Zeiogadaria_Gadiformes_Moridae_Laemonema_laureysi 7 0 Teleost_Euteleost_Zeiogadaria_Gadiformes_Bathygadidae_Bathygadus_melanocrachus 7 0 100 Teleost_Euteleost_Zeiogadaria_Gadiformes_Macrouridae_Macrourus_berglax Examl concatenated nucleotide tree 1006 0 Teleost_Euteleost_Zeiogadaria_Gadiformes_Macrouridae_Malacocephalus_occidentalis Teleost_Euteleost_Zeiogadaria_Gadiformes_Trachyrincidae_Trachyrincus_scabrus 10Teleost_Euteleost_Zeiogadaria_Gadiformes_Trachyrincidae_Trachyrincus_murray0 i Maximum likelihood tree with bootstrap support (based on 100 replicates), 6 0 Teleost_Euteleost_Zeiogadaria_Gadiformes_Melanonidae_Melanorus_zugmayeri partitioned by codon under the GTRCAT model in ExaML. 6 0 Teleost_Euteleost_Zeiogadaria_Gadiformes_Muraenolepididae_Muraenolepis_marmoratus 6 96 0 Teleost_Euteleost_Zeiogadaria_Gadiformes_Merlucciidae_Merluccius_polli 10Teleo0 st_Euteleost_Zeiogadaria_Gadiformes_Merlucciidae_Merluccius_capensis 10Teleost_Euteleost_Zeiogadaria_Gadiformes_Merlucciidae_Merluccius_merlucciu0 s 100 Teleost_Euteleost_Zeiogadaria_Gadiformes_Phycidae_Phycis_phycis 10T0eleost_Euteleost_Zeiogadaria_Gadiformes_Phycidae_Phycis_blennoides 100 Teleost_Euteleost_Zeiogadaria_Gadiformes_Lotidae_Lota_lota 10Teleost_Euteleost_Zeiogadaria_Gadiformes_Lotidae_Molva_molv0 a 7 4Teleost_Euteleost_Zeiogadaria_Gadiformes_Lotidae_Brosme_brosme Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Trisopterus_minutus 7 4 100 Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Gadiculus_argenteus 100Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Pollachius_virens Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Merlangius_merlangus 1010Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Melanogrammus_aeglefinu00 s 10T0eleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Arctogadus_glacialis 10Teleo0 st_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Boreogadus_saida 10Teleos0 t_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Theragra_chalcogramma 10Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Gadus_morhu0 a Teleost_Euteleost_Lampriformes_Regalecidae_Regalecus_glesne 100Teleost_Euteleost_Lampriformes_Lampridae_Lampris_guttatus Teleost_Euteleost_Trachichthyformes_Monocentridae_Monocentris_japonica Teleost_Euteleost_Beryciformes_Berycidae_Beryx_splendens 100 100 Teleost_Euteleost_Beryciformes_Stephanoberycidae_Acanthochaenus_luetkenii 10Teleost_Euteleost_Beryciformes_Rondeletiidae_Rondeletia_loricat0 a 100 Teleost_Euteleost_Holocentriformes_Holocentridae_Myripristis_berndti 10Teleost_Euteleost_Holocentriformes_Holocentridae_Myripristis_jacobu0 s 100 100 Teleost_Euteleost_Holocentriformes_Holocentridae_Sargocentron_rubrum 10Teleost_Euteleost_Holocentriformes_Holocentridae_Holocentrus_rufu0 s 10Teleost_Euteleost_Holocentriformes_Holocentridae_Neoniphon_sammar0 a 10Teleost_Euteleost_Holocentriformes_Holocentridae_Neoniphon_vexillariu0 m Teleost_Euteleost_Ophidiaria_Ophidiiformes_Ophidiidae_Brotula_barbata 100 Teleost_Euteleost_Ophidiaria_Ophidiiformes_Ophidiidae_Carapus_acus 100 100 Teleost_Euteleost_Ophidiaria_Ophidiiformes_Ophidiidae_Lamprogrammus_exutus Teleost_Euteleost_Batrachoidaria_Batrachoidiformes_Batrachoididae_Chatrabus_melanurus 100 Teleost_Euteleost_Batrachoidaria_Batrachoidiformes_Batrachoididae_Batrachomoeus_trispinosus 9 6 Teleost_Euteleost_Batrachoidaria_Batrachoidiformes_Batrachoididae_Porichthys_notatus Teleost_Euteleost_Gobiaria_Kurtiformes_Apogonidae_Apogonichthyoides_cathetogramma 100Teleost_Euteleost_Gobiaria_Kurtiformes_Apogonidae_Phaeoptyx_sp Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Periophthalmodon_schlosseri 100 100 100Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Periophthalmus_magnuspinnatus 100 Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Scartelaos_histophorus 100Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Boleophthalmus_pectinirostris 100 Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Coryphopterus_lipernes 100 Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Lesueurigobius_cf_sanzoi 100 Teleost_Euteleost_Gobiaria_Gobiiformes_Eleotridae_Oxyeleotris_marmorata 100 Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Exyrias_puntang 10T0eleost_Euteleost_Gobiaria_Gobiiformes_Istigobius_decoratus 100 Teleost_Euteleost_Pelagiaria_Scombriformes_Stromateidae_Pampus_argenteus 9 9Teleost_Euteleost_Pelagiaria_Scombrifomres_Nomeidae_Nomeus_gronovii 100 Teleost_Euteleost_Pelagiaria_Scombriformes_Scombridae_Scomber_scombrus 9 3Teleost_Euteleost_Pelagiaria_Scombriformes_Scombridae_Scomberomorus_regalis 7 3Teleost_Euteleost_Pelagiaria_Scombriformes_Scombridae_Thunnus_albacares 100 10Teleos0 t_Euteleost_Pelagiaria_Scombriformes_Scombridae_Thunnus_orientalis Teleost_Euteleost_Syngnatharia_Syngnathiformes_Aulostomidae_Aulostomus_maculatus 10Teleost_Euteleost_Syngnatharia_Syngnathiformes_Aulostomidae_Aulostomus_s0 p 100 Teleost_Euteleost_Syngnatharia_Syngnathiformes_Mullidae_Parupeneus_indicus 100 Teleost_Euteleost_Syngnatharia_Syngnathiformes_Callionymidae_Foetorepus_agassizii 6 Teleost_Euteleost_Syngnatharia_Syngnathiformes_Syngnathidae_Syngnathoides_biaculeatus 100 Teleost_Euteleost_Syngnatharia_Syngnathiformes_Syngnathidae_Syngnathus_scovelli 100 Teleost_Euteleost_Syngnatharia_Syngnathiformes_Syngnathidae_Hippocampus_erectus Teleost_Euteleost_Eupercaria_Perciformes_Percidae_Perca_fluviatilis 100 Teleost_Euteleost_Eupercaria_Perciformes_Percophidae_Chrionema_sp 9 9 Teleost_Euteleost_Eupercaria_Perciformes_Serranidae_Pronotogrammus_martinicensis 100 Teleost_Euteleost_Eupercaria_Perciformes_Nototheniidae_Lepidonotothen_nudifrons 100 10Teleos0 t_Euteleost_Eupercaria_Perciformes_Nototheniidae_Notothenia_coriiceps 100Teleost_Euteleost_Eupercaria_Perciformes_Bathydraconidae_Gymnodraco_acuticeps 10Teleost_Euteleost_Eupercaria_Perciformes_Channichthydae_Chaenocephalus_aceratu0 s 100 Teleost_Euteleost_Eupercaria_Perciformes_Peristediidae_Peristedion_sp 100 Teleost_Euteleost_Eupercaria_Perciformes_Anoplopomatidae_Anoplopoma_fimbria 100 Teleost_Euteleost_Eupercaria_Perciformes_Gasterosteidae_Gasterosteus_aculeatus 100 Teleost_Euteleost_Eupercaria_Perciformes_Cyclopteridae_Cyclopterus_lumpus 100 100Teleost_Euteleost_Eupercaria_Perciformes_Cottidae_Cottus_rhenanus 100Teleost_Euteleost_Eupercaria_Perciformes_Cottidae_Myoxocephalus_scorpius Teleost_Euteleost_Eupercaria_Perciformes_Scorpaenidae_Scorpaenopsis_cirrosa 100 Teleost_Euteleost_Eupercaria_Perciformes_Synanceiidae_Synanceia_verrucosa 100Teleost_Euteleost_Eupercaria_Perciformes_Scorpaenidae_Dendrochirus_zebra 100100Teleost_Euteleost_Eupercaria_Perciformes_Scorpaenidae_Pontinus_castor 100Teleost_Euteleost_Eupercaria_Perciformes_Sebastidae_Sebastes_norvegicus 10Teleo0 st_Euteleost_Eupercaria_Perciformes_Sebastidae_Sebastes_rubrivinctus 10Teleost_Euteleost_Eupercaria_Perciformes_Sebastidae_Sebastes_nigrocinctu0 s Teleost_Euteleost_Eupercaria_Gerreformes_Gerreidae_Gerres_filamentosus 100Teleost_Euteleost_Eupercaria_Gerreformes_Gerreidae_Eucinostomus_sp 100 Teleost_Euteleost_Eupercaria_Uranoscopiformes_Pinguipedidae_Parapercis_xanthozona 100100 Teleost_Euteleost_Eupercaria_Labriformes_Labridae_Thalassoma_bifasciatum 100 Teleost_Euteleost_Eupercaria_Labriformes_Scaridae_Scarus_iseri 10Teleost_Euteleost_Eupercaria_Labriformes_Scaridae_Scarus_ghobba0 n 9 9 Teleost_Euteleost_Eupercaria_Labriformes_Labridae_Symphodus_melops 100Teleost_Euteleost_Eupercaria_Labriformes_Labridae_Labrus_bergylta Teleost_Euteleost_Eupercaria_Pempheriformes_Epigonidae_Epigonus_sp 101000 Teleost_Euteleost_Eupercaria_Pempheriformes_Lateolabracidae_Lateolabrax_maculatus 9 2 Teleost_Euteleost_Eupercaria_Centrarchiformes_Terapontidae_Terapon_jarbua 10Te0 leost_Euteleost_Eupercaria_Centrarchiformes_Oplegnathidae_Oplegnathus_punctatus 100 Teleost_Euteleost_Eupercaria_Centrarchiformes_Cirrhitidae_Amblycirrhitus_pinos 100 Teleost_Euteleost_Eupercaria_Centrarchiformes_Centrarchidae_Micropterus_floridanus 10Teleost_Euteleost_Eupercaria_Centrarchiformes_Percichthyidae_Siniperca_scherzer0 i 9 8100Teleost_Euteleost_Eupercaria_Centrarchiformes_Percichthyidae_Coreoperca_whiteheadi Teleost_Euteleost_Eupercaria_Moronidae_Morone_saxatilis 10Teleos0 t_Euteleost_Eupercaria_Moronidae_Dicentrarchus_labrax Teleost_Euteleost_Eupercaria_Ephippiformes_Ephippidae_Chaetodipterus_faber 100Teleost_Euteleost_Eupercaria_Ephippiformes_Drepaneidae_Drepane_punctata 100 Teleost_Euteleost_Eupercaria_Acanthuriformes_Acanthuridae_Acanthurus_tractus 7 9 Teleost_Euteleost_Eupercaria_Lobotiformes_Datnioididae_Datnioides_microlepis Teleost_Euteleost_Eupercaria_Sciaenidae_Equetus_punctatus 9679 10T0eleost_Euteleost_Eupercaria_Sciaenidae_Larimichthys_crocea 10Teleost_Euteleost_Eupercaria_Sciaenidae_Miichthys_miiu0 y 8 0 Teleost_Euteleost_Eupercaria_Lutjaniformes_Lutjanidae_Lutjanus_sebae 10Teleost_Euteleost_Eupercaria_Lutjaniformes_Lutjanidae_Lutjanus_fulviflamm0 a 8 1 Teleost_Euteleost_Eupercaria_Chaetodontiformes_Leiognathidae_Photopectoralis_bindus 9 7 9 5 Teleost_Euteleost_Eupercaria_Lutjaniformes_Haemulidae_Haemulon_flavolineatum 10Teleost_Euteleost_Eupercaria_Lutjaniformes_Haemulidae_Haemulon_chrysargyreu0 m Teleost_Euteleost_Eupercaria_Chaetodontiformes_Chaetodontidae_Chaetodon_auriga 9 3 Teleost_Euteleost_Eupercaria_Pomacanthidae_Pomacanthus_paru Teleost_Euteleost_Eupercaria_Siganidae_Siganus_guttatus 6690 Teleost_Euteleost_Eupercaria_Spariformes_Sparidae_Evynnis_cardinalis 100 10Teleost_Euteleost_Eupercaria_Spariformes_Sparidae_Spondyliosoma_cantharu0 s 10T0eleost_Euteleost_Eupercaria_Spariformes_Sparidae_Acanthopagrus_latus 7 7 10Teleost_Euteleost_Eupercaria_Spariformes_Sparidae_Acanthopagrus_schlegeli0 i Teleost_Euteleost_Eupercaria_Priacanthiformes_Priacanthidae_Priacanthus_tayenus 7 7 Teleost_Euteleost_Eupercaria_Caproiformes_Caproidae_Antigonia_capros 8 1 Teleost_Euteleost_Eupercaria_Lophiiformes_Chaunacidae_Chaunax_pictus 100 Teleost_Euteleost_Eupercaria_Lophiiformes_Antennariidae_Antennarius_striatus 9 3 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Ostraciidae_Lactoria_cornuta 10T0eleost_Euteleost_Eupercaria_Tetraodontiformes_Ostraciidae_Ostracion_rhinorhynchos 100 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Balistidae_Pseudobalistes_fuscus 8 7 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Molidae_Mola_mola 100 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Diodontidae_Diodon_holocanthus 100 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Tetraodontidae_Tetraodon_nigroviridis 100 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Tetraodontidae_Takifugu_flavidus 10Teleost_Euteleost_Eupercaria_Tetraodontiformes_Tetraodontidae_Takifugu_rubripe0 s Teleost_Euteleost_Anabantaria_Synbranchiformes_Synbranchidae_Monopterus_albus 100 Teleost_Euteleost_Anabantaria_Synbranchiformes_Mastacembelidae_Macrognathus_aculeatus 10Teleost_Euteleost_Anabantaria_Synbranchiformes_Mastacembelidae_Mastacembelus_armatu0 s 100 Teleost_Euteleost_Anabantaria_Anabantiformes_Channidae_Channa_micropeltes 100 100Teleost_Euteleost_Anabantaria_Anabantiformes_Channidae_Channa_argus 100 Teleost_Euteleost_Anabantaria_Anabantiformes_Channidae_Channa_gachua Teleost_Euteleost_Anabantaria_Anabantiformes_Osphronemidae_Osphronemus_goramy 100 Teleost_Euteleost_Anabantaria_Anabantiformes_Anabantidae_Anabas_testudineus 100 8 1 Teleost_Euteleost_Anabantaria_Anabantiformes_Helostomatidae_Helostoma_temminckii Teleost_Euteleost_Carangaria_Toxotidae_Toxotes_jaculatrix 6 5 Teleost_Euteleost_Carangaria_Centropomidae_Centropomus_sp 7 8 Teleost_Euteleost_Carangaria_Centropomidae_Lates_calcarifer Teleost_Euteleost_Carangaria_Carangiformes_Coryphaenidae_Coryphaena_hippurus 10909 Teleost_Euteleost_Carangaria_Carangiformes_Carangidae_Trachinotus_ovatus 100 Teleost_Euteleost_Carangaria_Carangiformes_Carangidae_Seriola_lalandi 100 Teleost_Euteleost_Carangaria_Carangiformes_Carangidae_Selene_dorsalis 6 5 10T0eleost_Euteleost_Carangaria_Carangiformes_Carangidae_Caranx_ignobilis Teleost_Euteleost_Carangaria_Polynemidae_Polynemus_dubius Teleost_Euteleost_Carangaria_Pleuronectiformes_Soleidae_Solea_ovata 9 0 100 Teleost_Euteleost_Carangaria_Pleuronectiformes_Cynoglossidae_Cynoglossus_semilaevis 100 Teleost_Euteleost_Carangaria_Pleuronectiformes_Scophthalmidae_Scophthalmus_maximus 100 Teleost_Euteleost_Carangaria_Pleuronectiformes_Paralichthydae_Paralichthys_olivaceus 100Teleost_Euteleost_Carangaria_Pleuronectiformes_Pleuronectidae_Hippoglossus_hippoglossus 100 100Teleost_Euteleost_Carangaria_Pleuronectiformes_Pleuronectidae_Pseudopleuronectes_yokohamae Teleost_Euteleost_Ovalentaria_Ambassidae_Parambassis_pulcinella 5 3 Teleost_Euteleost_Ovalentaria_Mugiliformes_Mugilidae_Liza_haematocheila 100 Teleost_Euteleost_Ovalentaria_Mugiliformes_Mugilidae_Mugil_cephalus Teleost_Euteleost_Ovalentaria_Pseudochromidae_Pseudochromis_fuscus 5623 Teleost_Euteleost_Ovalentaria_Pomacentridae_Stegastes_partitus 100 Teleost_Euteleost_Ovalentaria_Pomacentridae_Amphiprion_melanopus 100Teleost_Euteleost_Ovalentaria_Pomacentridae_Dascyllus_trimaculatus 5 5 10Teleost_Euteleost_Ovalentaria_Pomacentridae_Chromis_chromi0 s Teleost_Euteleost_Ovalentaria_Grammatidae_Lipogramma_evides 100 Teleost_Euteleost_Ovalentaria_Opistognathidae_Opistognathus_aurifrons 100 Teleost_Euteleost_Ovalentaria_Gobiescociformes_Gobiesocidae_Tomicodon_sp 100 Teleost_Euteleost_Ovalentaria_Gobiescociformes_Gobiesocidae_Acyrtus_sp 100 Teleost_Euteleost_Ovalentaria_Blenniiformes_Tripterygiidae_Enneanectes_sp 100 Teleost_Euteleost_Ovalentaria_Blenniiformes_Blenniidae_Parablennius_parvicornis 100 100 Teleost_Euteleost_Ovalentaria_Blenniiformes_Chaenopsidae_Acanthemblemaria_sp Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Parachromis_managuensis 10Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Amphilophus_citrinellu0 s 100 Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Oreochromis_niloticus 10Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Neolamprologus_brichard0 i 10Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Haplochromis_burton0 i 10Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Pundamilia_nyerere0 i 10Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Maylandia_zebr0 a 10Teleos0 t_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Mchenga_conophoros 4Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Labeotropheus_fuelleborn2 i 7 3Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Rhamphochromis_esox 6 0 5 2Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Melanochromis_auratus Teleost_Euteleost_Ovalentaria_Atheriniformes_Pseudomugilidae_Pseudomugil_paskai 100 10Teleos0 t_Euteleost_Ovalentaria_Atheriniformes_Melanotaeniidae_Glossolepis_incisus 100 Teleost_Euteleost_Ovalentaria_Atheriniformes_Melanotaeniidae_Melanotaenia_praecox Teleost_Euteleost_Ovalentaria_Atheriniformes_Atherinopsidae_Menidia_menidia 100 Teleost_Euteleost_Ovalentaria_Atheriniformes_Atherinopsidae_Basilichthys_microlepidotus 10Teleost_Euteleost_Ovalentaria_Atheriniformes_Atherinopsidae_Odontesthes_bonariensi0 s 100 Teleost_Euteleost_Ovalentaria_Beloniformes_Hemiramphidae_Hyporhamphus_intermedius 100 Teleost_Euteleost_Ovalentaria_Beloniformes_Adrianichthyidae_Oryzias_mekongensis 100Teleost_Euteleost_Ovalentaria_Beloniformes_Adrianichthyidae_Oryzias_latipes Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Aplocheilidae_Pachypanchax_sakaramyi 9 1 100 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Nothobranchiidae_Nothobranchius_furzeri 100 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Aplocheilidae_Aplocheilus_lineatus 100 100 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Rivulidae_Austrofundulus_limnaeus 100 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Rivulidae_Kryptolebias_marmoratus Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Cyprinodontidae_Cyprinodon_varigatus 10Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Cyprinodontidae_Cyprinodon_nevadensis_pectorali0 s 100 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Goodeidae_Ameca_splendens 1 3 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Fundulidae_Fundulus_heteroclitus Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Poecilia_reticulata 100 10Teleos0 t_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Poecilia_formosa 100Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Poeciliopsis_prolifica 10T0eleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Gambusia_affinis_whole 10Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Xiphophorus_helleri0 i 10Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Xiphophorus_maculatu0 s 10Teleos0 t_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Xiphophorus_couchianus 0.2
Figure 20: Examl concatenated nucleotide tree. Maximum likelihood tree with bootstrap support (based on 100 replicates), partitioned by codon under the GTRCAT model in ExaML.
88
Coelacanthiformes_Coelacanthiformes_Latimeriidae_Latimeria_chalumnae 100 Xenopus_tropicalis 9 3 Ceratodontiformes_Ceratodontiformes_Protopteridae_Protopterus_aethiopicus Polypteriformes_Polypteridae_Erpetoichthys_calabaricus 10Polypteriformes_Polypteriformes_Polypteridae_Polypterus_bichi0 r 10Polyp0 teriformes_Polypteriformes_Polypteridae_Polypterus_endlicheri Acipenseriformes_Polyodontidae_Polyodon_spathula 100 Acipenseriformes_Acipenseridae_Acipenser_naccarii 10Acipenseriformes_Acipenseridae_Acipenser_sinensi0 s 100 Amiiformes_Amiidae_Amia_calva_gill 100 Lepisosteiformes_Lepisosteiformes_Lepisosteidae_Atractosteus_spatula 10Lepisos0 teiformes_Lepisosteiformes_Lepisosteidae_Lepisosteus_oculatus 10Lepisosteiformes_Lepisosteiformes_Lepisosteidae_Lepisosteus_platyrhincu0 s Teleost_Osteoglossiformes_Osteoglossiformes_Pantodontidae_Pantodon_buchholzi Teleost_Osteoglossiformes_Osteoglossiformes_Osteoglossidae_Osteoglossum_bicirrhosum 100 100 100 Teleost_Osteoglossiformes_Osteoglossiformes_Osteoglossidae_Scleropages_formosus 100 Teleost_Osteoglossiformes_Osteoglossiformes_Notopteridae_Papyrocranus_afer 100 Teleost_Osteoglossiformes_Osteoglossiformes_Morymridae_Gnathonemus_petersii 9 6 100Teleost_Osteoglossiformes_Osteoglossiformes_Mormyridae_Mormyrus_tapirus Teleost_Elopiformes_Elopiformes_Megalopidae_Megalops_cyprinoides Teleost_Anguilliformes_Muraenidae_Gymnothorax_reevesii 100 8 9 Teleost_Anguilliformes_Chlopsidae_Kaupichthys_hyporoides 100 100 Teleost_Anguilliformes_Congridae_Conger_cinereus 5 4 Teleost_Anguilliformes_Anguillidae_Anguilla_japonica 10Teleos0 t_Anguilliformes_Anguillidae_Anguilla_rostrata 10Teleost_Anguilliformes_Anguillidae_Anguilla_anguill0 a Teleost_Clupeiformes_Clupeiformes_Engraulidae_Coilia_nasus 100 Teleost_Clupeiformes_Clupeiformes_Engraulidae_Engraulis_encrasicolus 100 Teleost_Clupeiformes_Clupeiformes_Clupeidae_Clupea_harengus 100 Teleost_Clupeiformes_Clupeiformes_Clupeidae_Amblygaster_clupeoides 100 Teleost_Clupeiformes_Clupeiformes_Clupeidae_Alosa_alosa Teleost_Otophysa_Gonorynchiformes_Chanidae_Chanos_chanos 100 Teleost_Otophysa_Cypriniformes_Gyrinocheilidae_Gyrinocheilus_aymonieri Teleost_Otophysa_Cypriniformes_Botiidae_Sinibotia_superciliaris 100 100 100 Teleost_Otophysa_Cypriniformes_Nemacheilidae_Homatula_potanini 100 Teleost_Otophysa_Cypriniformes_Cobitidae_Misgurnus_anguillicaudatus 100 Teleost_Otophysa_Cypriniformes_Danionidae_Danio_rerio 100 Teleost_Otophysa_Cypriniformes_Tincidae_Tinca_tinca 100100 Teleost_Otophysa_Cypriniformes_Leuciscidae_Pimephales_promelas 100Teleost_Otophysa_Cypriniformes_Leuciscidae_Leuciscus_waleckii 9 5 Teleost_Otophysa_Cypriniformes_Cyprinidae_Cyprinus_carpio 100 Teleost_Otophysa_Cypriniformes_Cyprinidae_Sinocyclocheilus_rhinoceros 100 100Teleost_Otophysa_Cypriniformes_Cyprinidae_Sinocyclocheilus_anshuiensis 100Teleost_Otophysa_Cypriniformes_Cyprinidae_Sinocyclocheilus_grahami Teleost_Otophysa_Characiformes_Distichodontidae_Distichodus_sexfasciatus Teleost_Otophysa_Characiformes_Serrasalmidae_Pygocentrus_nattereri 1 6 100 Teleost_Otophysa_Characiformes_Erythrinidae_Erythrinus_erythrinus 100 Teleost_Otophysa_Characiformes_Hepsetidae_Hepsetus_odoe 100 Teleost_Otophysa_Characiformes_Gasteropelecidae_Gasteropelecus_sp 100 Teleost_Otophysa_Characiformes_Characidae_Astyanax_mexicanus 100 100Teleost_Otophysa_Characiformes_Characidae_Thayeria_boehlkei 100 7 5 Teleost_Otophysa_Characiformes_Characidae_Hemigrammus_bleheri Teleost_Otophysa_Gymnotiformes_Apteronotidae_Apteronotus_albifrons 100 Teleost_Otophysa_Gymnotiformes_Gymnotidae_Electrophorus_electricus 100 Teleost_Otophysa_Gymnotiformes_Rhamphichthyidae_Rhamphichthys_rostratus 3 5 Teleost_Otophysa_Siluriformes_Callichthyidae_Corydoras_julii 100 Teleost_Otophysa_Siluriformes_Loricariidae_Pterygoplichthys_pardalis 100 Teleost_Otophysa_Siluriformes_Plotosidae_Plotosus_lineatus Teleost_Otophysa_Siluriformes_Pangasiidae_Pangasianodon_hypophthalamus 10802 Teleost_Otophysa_Siluriformes_Siluridae_Silurus_asotus 8 2 Teleost_Otophysa_Siluriformes_Ictaluridae_Ictalurus_punctatus 8 6 Teleost_Otophysa_Siluriformes_Bagridae_Hemibagrus_guttatus 100 Teleost_Otophysa_Siluriformes_Sisoridae_Glyptothorax_sinensis 100 Teleost_Otophysa_Siluriformes_Amblycipitidae_Liobagrus_styani Teleost_Euteleost_Lepidogalaxiiformes_Lepidogalaxiidae_Lepidogalaxias_salamandroides Teleost_Euteleost_Argentiniformes_Argentinidae_Argentina_sp Teleost_Euteleost_Esociformes_Esocidae_Esox_lucius 7 2 100 Teleost_Euteleost_Esociformes_Umbridae_Umbra_pygmae 100 100 Teleost_Euteleost_Salmoniformes_Salmonidae_Coregonus_clupeaformis 6 9 Teleost_Euteleost_Salmoniformes_Salmonidae_Thymallus_thymallus 100 Teleost_Euteleost_Salmoniformes_Salmonidae_Salmo_salar 100 Teleost_Euteleost_Salmoniformes_Salmonidae_Oncorhynchus_mykiss 100 9 7 Teleost_Euteleost_Salmoniformes_Salmonidae_Salvelinus_fontinalis Teleost_Euteleost_Stomiatiformes_Stomiidae_Borostomias_antarcticus 100 Teleost_Euteleost_Osmeriformes_Osmeridae_Osmerus_eperlanus 100 Teleost_Euteleost_Osmeriformes_Plecoglossidae_Plecoglossus_altivelis 100 Teleost_Euteleost_Osmeriformes_Salangidae_Protosalanx_hyalocranius Teleost_Euteleost_Galaxiiformes_Galaxiidae_Galaxias_maculatus 100 100 Teleost_Euteleost_Galaxiiformes_Galaxiidae_Galaxiella_nigrostriata Teleost_Euteleost_Aulopiformes_Synodontidae_Synodus_sp 100 Teleost_Euteleost_Aulopiformes_Chlorophthalmidae_Parasudis_fraserbrunneri 100 100 Teleost_Euteleost_Aulopiformes_Chlorophthalmidae_Chlorophthalmus_sp Teleost_Euteleost_Ateleopodiformes_Ateleopodidae_Guentherus_altivela Teleost_Euteleost_Myctophiformes_Myctophidae_Benthosema_glaciale 100 Teleost_Euteleost_Polymixiiformes_Polymixiidae_Polymixia_japonica Teleost_Euteleost_Percopsaria_Percopsiformes_Amblyopsidae_Typhlichthys_subterraneus 100 100 Teleost_Euteleost_Percopsaria_Percopsiformes_Percopsidae_Percopsis_transmontana 10Teleost_Euteleost_Percopsaria_Percopsiformes_Percopsidae_Percopsis_omiscomaycu0 s 9 7 Teleost_Euteleost_Zeiogadaria_Zeiformes_Zeidae_Zeus_faber 7 8 100 Teleost_Euteleost_Zeiogadaria_Zeiformes_Parazenidae_Cyttopsis_roseus 10Teleost_Euteleost_Zeiogadaria_Zeiformes_Parazenidae_Cyttopsis_s0 p 100 Teleost_Euteleost_Zeiogadaria_Stylephoriformes_Stylephoridae_Stylephorus_chordatus Teleost_Euteleost_Zeiogadaria_Gadiformes_Bregmacerotidae_Bregmaceros_cantori 100 Teleost_Euteleost_Zeiogadaria_Gadiformes_Merlucciidae_Merluccius_polli ExaML concatenated protein tree 100 10Teleo0 st_Euteleost_Zeiogadaria_Gadiformes_Merlucciidae_Merluccius_capensis 10Teleost_Euteleost_Zeiogadaria_Gadiformes_Merlucciidae_Merluccius_merlucciu0 s 100 Teleost_Euteleost_Zeiogadaria_Gadiformes_Melanonidae_Melanorus_zugmayeri 9 6 Teleost_Euteleost_Zeiogadaria_Gadiformes_Muraenolepididae_Muraenolepis_marmoratus 8 2 Teleost_Euteleost_Zeiogadaria_Gadiformes_Trachyrincidae_Trachyrincus_scabrus Maximum likelihood tree with bootstrap support (based on 100 replicates), 100 10Teleost_Euteleost_Zeiogadaria_Gadiformes_Trachyrincidae_Trachyrincus_murray0 i 100 Teleost_Euteleost_Zeiogadaria_Gadiformes_Moridae_Mora_moro inferred from 1105 translated genes and 305 taxa, under the GTRCAT 100 Teleost_Euteleost_Zeiogadaria_Gadiformes_Moridae_Laemonema_laureysi 9 9 Teleost_Euteleost_Zeiogadaria_Gadiformes_Bathygadidae_Bathygadus_melanocrachus model in ExaML. 5 2 100 Teleost_Euteleost_Zeiogadaria_Gadiformes_Macrouridae_Macrourus_berglax 100 Teleost_Euteleost_Zeiogadaria_Gadiformes_Macrouridae_Malacocephalus_occidentalis 100 Teleost_Euteleost_Zeiogadaria_Gadiformes_Phycidae_Phycis_phycis 10T0eleost_Euteleost_Zeiogadaria_Gadiformes_Phycidae_Phycis_blennoides 100 Teleost_Euteleost_Zeiogadaria_Gadiformes_Lotidae_Lota_lota 100Teleost_Euteleost_Zeiogadaria_Gadiformes_Lotidae_Molva_molva Teleost_Euteleost_Zeiogadaria_Gadiformes_Lotidae_Brosme_brosme 100 Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Trisopterus_minutus 100 7 4 Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Gadiculus_argenteus 100 Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Pollachius_virens Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Merlangius_merlangus 10100Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Melanogrammus_aeglefinu0 s 10T0eleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Arctogadus_glacialis 10Teleo0 st_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Boreogadus_saida 10Teleos0 t_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Theragra_chalcogramma 10Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Gadus_morhu0 a Teleost_Euteleost_Lampriformes_Regalecidae_Regalecus_glesne 100 Teleost_Euteleost_Lampriformes_Lampridae_Lampris_guttatus Teleost_Euteleost_Trachichthyformes_Monocentridae_Monocentris_japonica Teleost_Euteleost_Beryciformes_Berycidae_Beryx_splendens 5 9 100 Teleost_Euteleost_Beryciformes_Stephanoberycidae_Acanthochaenus_luetkenii 100Teleost_Euteleost_Beryciformes_Rondeletiidae_Rondeletia_loricata 9 5 Teleost_Euteleost_Holocentriformes_Holocentridae_Myripristis_berndti 10Teleost_Euteleost_Holocentriformes_Holocentridae_Myripristis_jacobu0 s 100 100 Teleost_Euteleost_Holocentriformes_Holocentridae_Sargocentron_rubrum 10Teleost_Euteleost_Holocentriformes_Holocentridae_Holocentrus_rufu0 s 10Teleost_Euteleost_Holocentriformes_Holocentridae_Neoniphon_sammar0 a 10Teleost_Euteleost_Holocentriformes_Holocentridae_Neoniphon_vexillariu0 m Teleost_Euteleost_Ophidiaria_Ophidiiformes_Ophidiidae_Brotula_barbata 100 Teleost_Euteleost_Ophidiaria_Ophidiiformes_Ophidiidae_Carapus_acus 100 100 Teleost_Euteleost_Ophidiaria_Ophidiiformes_Ophidiidae_Lamprogrammus_exutus Teleost_Euteleost_Batrachoidaria_Batrachoidiformes_Batrachoididae_Chatrabus_melanurus 100 Teleost_Euteleost_Batrachoidaria_Batrachoidiformes_Batrachoididae_Porichthys_notatus 6 7 Teleost_Euteleost_Batrachoidaria_Batrachoidiformes_Batrachoididae_Batrachomoeus_trispinosus Teleost_Euteleost_Gobiaria_Kurtiformes_Apogonidae_Apogonichthyoides_cathetogramma 100Teleost_Euteleost_Gobiaria_Kurtiformes_Apogonidae_Phaeoptyx_sp Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Periophthalmodon_schlosseri 100 100 100Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Periophthalmus_magnuspinnatus 100 Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Scartelaos_histophorus 100Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Boleophthalmus_pectinirostris 100 Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Coryphopterus_lipernes 9 8 Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Lesueurigobius_cf_sanzoi 100 Teleost_Euteleost_Gobiaria_Gobiiformes_Eleotridae_Oxyeleotris_marmorata 100 Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Exyrias_puntang 10T0eleost_Euteleost_Gobiaria_Gobiiformes_Istigobius_decoratus Teleost_Euteleost_Pelagiaria_Scombrifomres_Nomeidae_Nomeus_gronovii 100 100 Teleost_Euteleost_Pelagiaria_Scombriformes_Stromateidae_Pampus_argenteus 9 9 Teleost_Euteleost_Pelagiaria_Scombriformes_Scombridae_Scomberomorus_regalis 7 4 Teleost_Euteleost_Pelagiaria_Scombriformes_Scombridae_Scomber_scombrus 4 3Teleost_Euteleost_Pelagiaria_Scombriformes_Scombridae_Thunnus_albacares 100 10Teleos0 t_Euteleost_Pelagiaria_Scombriformes_Scombridae_Thunnus_orientalis Teleost_Euteleost_Syngnatharia_Syngnathiformes_Aulostomidae_Aulostomus_maculatus 10Teleost_Euteleost_Syngnatharia_Syngnathiformes_Aulostomidae_Aulostomus_s0 p 9 9 Teleost_Euteleost_Syngnatharia_Syngnathiformes_Mullidae_Parupeneus_indicus 9 8 Teleost_Euteleost_Syngnatharia_Syngnathiformes_Callionymidae_Foetorepus_agassizii 9 8 Teleost_Euteleost_Syngnatharia_Syngnathiformes_Syngnathidae_Syngnathoides_biaculeatus 100 Teleost_Euteleost_Syngnatharia_Syngnathiformes_Syngnathidae_Syngnathus_scovelli 100 Teleost_Euteleost_Syngnatharia_Syngnathiformes_Syngnathidae_Hippocampus_erectus Teleost_Euteleost_Eupercaria_Perciformes_Percidae_Perca_fluviatilis 100 5 2 Teleost_Euteleost_Eupercaria_Perciformes_Percophidae_Chrionema_sp 5 6 Teleost_Euteleost_Eupercaria_Perciformes_Serranidae_Pronotogrammus_martinicensis 8 2 Teleost_Euteleost_Eupercaria_Perciformes_Nototheniidae_Lepidonotothen_nudifrons 10Teleos0 t_Euteleost_Eupercaria_Perciformes_Nototheniidae_Notothenia_coriiceps 100 Teleost_Euteleost_Eupercaria_Perciformes_Bathydraconidae_Gymnodraco_acuticeps 100 10Teleost_Euteleost_Eupercaria_Perciformes_Channichthydae_Chaenocephalus_aceratu0 s Teleost_Euteleost_Eupercaria_Perciformes_Peristediidae_Peristedion_sp 100 Teleost_Euteleost_Eupercaria_Perciformes_Anoplopomatidae_Anoplopoma_fimbria 100 Teleost_Euteleost_Eupercaria_Perciformes_Gasterosteidae_Gasterosteus_aculeatus 100 Teleost_Euteleost_Eupercaria_Perciformes_Cyclopteridae_Cyclopterus_lumpus 100 100 Teleost_Euteleost_Eupercaria_Perciformes_Cottidae_Cottus_rhenanus 100 Teleost_Euteleost_Eupercaria_Perciformes_Cottidae_Myoxocephalus_scorpius Teleost_Euteleost_Eupercaria_Perciformes_Scorpaenidae_Scorpaenopsis_cirrosa 100 Teleost_Euteleost_Eupercaria_Perciformes_Synanceiidae_Synanceia_verrucosa 100Teleost_Euteleost_Eupercaria_Perciformes_Scorpaenidae_Dendrochirus_zebra 100Teleost_Euteleost_Eupercaria_Perciformes_Scorpaenidae_Pontinus_castor 100 Teleost_Euteleost_Eupercaria_Perciformes_Sebastidae_Sebastes_norvegicus 100 10Teleo0 st_Euteleost_Eupercaria_Perciformes_Sebastidae_Sebastes_rubrivinctus 10Teleost_Euteleost_Eupercaria_Perciformes_Sebastidae_Sebastes_nigrocinctu0 s Teleost_Euteleost_Eupercaria_Pempheriformes_Epigonidae_Epigonus_sp 100 Teleost_Euteleost_Eupercaria_Pempheriformes_Lateolabracidae_Lateolabrax_maculatus 6 3 Teleost_Euteleost_Eupercaria_Gerreformes_Gerreidae_Gerres_filamentosus 100 100Teleost_Euteleost_Eupercaria_Gerreformes_Gerreidae_Eucinostomus_sp 100 Teleost_Euteleost_Eupercaria_Uranoscopiformes_Pinguipedidae_Parapercis_xanthozona 100 Teleost_Euteleost_Eupercaria_Labriformes_Labridae_Thalassoma_bifasciatum Teleost_Euteleost_Eupercaria_Labriformes_Scaridae_Scarus_iseri 100 10Teleost_Euteleost_Eupercaria_Labriformes_Scaridae_Scarus_ghobba0 n 9 7 Teleost_Euteleost_Eupercaria_Labriformes_Labridae_Symphodus_melops 100 100Teleost_Euteleost_Eupercaria_Labriformes_Labridae_Labrus_bergylta Teleost_Euteleost_Eupercaria_Centrarchiformes_Terapontidae_Terapon_jarbua 10Te0 leost_Euteleost_Eupercaria_Centrarchiformes_Oplegnathidae_Oplegnathus_punctatus 100 Teleost_Euteleost_Eupercaria_Centrarchiformes_Cirrhitidae_Amblycirrhitus_pinos 100 Teleost_Euteleost_Eupercaria_Centrarchiformes_Centrarchidae_Micropterus_floridanus 100Teleost_Euteleost_Eupercaria_Centrarchiformes_Percichthyidae_Siniperca_scherzeri 100 Teleost_Euteleost_Eupercaria_Centrarchiformes_Percichthyidae_Coreoperca_whiteheadi 3 2 Teleost_Euteleost_Eupercaria_Moronidae_Morone_saxatilis 10T0eleost_Euteleost_Eupercaria_Moronidae_Dicentrarchus_labrax Teleost_Euteleost_Eupercaria_Ephippiformes_Ephippidae_Chaetodipterus_faber 100Teleost_Euteleost_Eupercaria_Ephippiformes_Drepaneidae_Drepane_punctata 100 Teleost_Euteleost_Eupercaria_Lobotiformes_Datnioididae_Datnioides_microlepis 2 7 Teleost_Euteleost_Eupercaria_Lutjaniformes_Lutjanidae_Lutjanus_sebae 10Teleost_Euteleost_Eupercaria_Lutjaniformes_Lutjanidae_Lutjanus_fulviflamm0 a 6445 Teleost_Euteleost_Eupercaria_Lutjaniformes_Haemulidae_Haemulon_flavolineatum 10Teleost_Euteleost_Eupercaria_Lutjaniformes_Haemulidae_Haemulon_chrysargyreu0 m 6 4 Teleost_Euteleost_Eupercaria_Sciaenidae_Equetus_punctatus 10T0eleost_Euteleost_Eupercaria_Sciaenidae_Larimichthys_crocea 10Teleost_Euteleost_Eupercaria_Sciaenidae_Miichthys_miiu0 y 5 7 Teleost_Euteleost_Eupercaria_Acanthuriformes_Acanthuridae_Acanthurus_tractus 6 5 Teleost_Euteleost_Eupercaria_Pomacanthidae_Pomacanthus_paru 6 1 Teleost_Euteleost_Eupercaria_Chaetodontiformes_Leiognathidae_Photopectoralis_bindus 9 0 Teleost_Euteleost_Eupercaria_Chaetodontiformes_Chaetodontidae_Chaetodon_auriga Teleost_Euteleost_Eupercaria_Siganidae_Siganus_guttatus 5530 Teleost_Euteleost_Eupercaria_Spariformes_Sparidae_Evynnis_cardinalis 100Teleost_Euteleost_Eupercaria_Spariformes_Sparidae_Spondyliosoma_cantharus 100 10T0eleost_Euteleost_Eupercaria_Spariformes_Sparidae_Acanthopagrus_latus 6 1 10Teleost_Euteleost_Eupercaria_Spariformes_Sparidae_Acanthopagrus_schlegeli0 i Teleost_Euteleost_Eupercaria_Caproiformes_Caproidae_Antigonia_capros 5 5 Teleost_Euteleost_Eupercaria_Priacanthiformes_Priacanthidae_Priacanthus_tayenus Teleost_Euteleost_Eupercaria_Lophiiformes_Chaunacidae_Chaunax_pictus 9 6 100 Teleost_Euteleost_Eupercaria_Lophiiformes_Antennariidae_Antennarius_striatus 6 3 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Ostraciidae_Lactoria_cornuta 10T0eleost_Euteleost_Eupercaria_Tetraodontiformes_Ostraciidae_Ostracion_rhinorhynchos 100 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Balistidae_Pseudobalistes_fuscus 7 6 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Molidae_Mola_mola 100 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Diodontidae_Diodon_holocanthus 100 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Tetraodontidae_Tetraodon_nigroviridis 100 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Tetraodontidae_Takifugu_flavidus 10Teleost_Euteleost_Eupercaria_Tetraodontiformes_Tetraodontidae_Takifugu_rubripe0 s Teleost_Euteleost_Anabantaria_Synbranchiformes_Synbranchidae_Monopterus_albus 100 Teleost_Euteleost_Anabantaria_Synbranchiformes_Mastacembelidae_Macrognathus_aculeatus 10Teleost_Euteleost_Anabantaria_Synbranchiformes_Mastacembelidae_Mastacembelus_armatu0 s 100 Teleost_Euteleost_Anabantaria_Anabantiformes_Channidae_Channa_micropeltes 100 Teleost_Euteleost_Anabantaria_Anabantiformes_Channidae_Channa_argus 100 Teleost_Euteleost_Anabantaria_Anabantiformes_Channidae_Channa_gachua 100 Teleost_Euteleost_Anabantaria_Anabantiformes_Osphronemidae_Osphronemus_goramy 100 Teleost_Euteleost_Anabantaria_Anabantiformes_Helostomatidae_Helostoma_temminckii 100 9 8 Teleost_Euteleost_Anabantaria_Anabantiformes_Anabantidae_Anabas_testudineus Teleost_Euteleost_Carangaria_Centropomidae_Centropomus_sp 9 0 Teleost_Euteleost_Carangaria_Centropomidae_Lates_calcarifer Teleost_Euteleost_Carangaria_Toxotidae_Toxotes_jaculatrix 100 Teleost_Euteleost_Carangaria_Carangiformes_Coryphaenidae_Coryphaena_hippurus 7 4 Teleost_Euteleost_Carangaria_Carangiformes_Carangidae_Trachinotus_ovatus 7 0100 Teleost_Euteleost_Carangaria_Carangiformes_Carangidae_Seriola_lalandi 100 Teleost_Euteleost_Carangaria_Carangiformes_Carangidae_Selene_dorsalis 5 2 10T0eleost_Euteleost_Carangaria_Carangiformes_Carangidae_Caranx_ignobilis Teleost_Euteleost_Carangaria_Polynemidae_Polynemus_dubius Teleost_Euteleost_Carangaria_Pleuronectiformes_Soleidae_Solea_ovata 7 2 100 Teleost_Euteleost_Carangaria_Pleuronectiformes_Cynoglossidae_Cynoglossus_semilaevis 100 Teleost_Euteleost_Carangaria_Pleuronectiformes_Scophthalmidae_Scophthalmus_maximus 100 Teleost_Euteleost_Carangaria_Pleuronectiformes_Paralichthydae_Paralichthys_olivaceus 100 Teleost_Euteleost_Carangaria_Pleuronectiformes_Pleuronectidae_Hippoglossus_hippoglossus 100 100 Teleost_Euteleost_Carangaria_Pleuronectiformes_Pleuronectidae_Pseudopleuronectes_yokohamae Teleost_Euteleost_Ovalentaria_Ambassidae_Parambassis_pulcinella 100 Teleost_Euteleost_Ovalentaria_Mugiliformes_Mugilidae_Liza_haematocheila 100 Teleost_Euteleost_Ovalentaria_Mugiliformes_Mugilidae_Mugil_cephalus Teleost_Euteleost_Ovalentaria_Pseudochromidae_Pseudochromis_fuscus 8949 Teleost_Euteleost_Ovalentaria_Pomacentridae_Stegastes_partitus 100 Teleost_Euteleost_Ovalentaria_Pomacentridae_Amphiprion_melanopus 100Teleost_Euteleost_Ovalentaria_Pomacentridae_Dascyllus_trimaculatus 9 5 10Teleost_Euteleost_Ovalentaria_Pomacentridae_Chromis_chromi0 s Teleost_Euteleost_Ovalentaria_Grammatidae_Lipogramma_evides 100 Teleost_Euteleost_Ovalentaria_Opistognathidae_Opistognathus_aurifrons Teleost_Euteleost_Ovalentaria_Gobiescociformes_Gobiesocidae_Tomicodon_sp 100 100 Teleost_Euteleost_Ovalentaria_Gobiescociformes_Gobiesocidae_Acyrtus_sp 100 Teleost_Euteleost_Ovalentaria_Blenniiformes_Tripterygiidae_Enneanectes_sp 9 7 Teleost_Euteleost_Ovalentaria_Blenniiformes_Blenniidae_Parablennius_parvicornis 100 100 Teleost_Euteleost_Ovalentaria_Blenniiformes_Chaenopsidae_Acanthemblemaria_sp Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Parachromis_managuensis 10Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Amphilophus_citrinellu0 s 100 Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Oreochromis_niloticus 10Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Neolamprologus_brichard0 i 10Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Haplochromis_burton0 i 10Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Pundamilia_nyerere0 i 8Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Maylandia_zebr4 a 8 4Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Mchenga_conophoros 2 4 Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Labeotropheus_fuelleborni 5 4 Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Rhamphochromis_esox 100 7 0 Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Melanochromis_auratus Teleost_Euteleost_Ovalentaria_Atheriniformes_Pseudomugilidae_Pseudomugil_paskai 100 Teleost_Euteleost_Ovalentaria_Atheriniformes_Melanotaeniidae_Glossolepis_incisus 10Teleost_Euteleost_Ovalentaria_Atheriniformes_Melanotaeniidae_Melanotaenia_praeco0 x 100 Teleost_Euteleost_Ovalentaria_Atheriniformes_Atherinopsidae_Menidia_menidia 100 Teleost_Euteleost_Ovalentaria_Atheriniformes_Atherinopsidae_Basilichthys_microlepidotus 100Teleost_Euteleost_Ovalentaria_Atheriniformes_Atherinopsidae_Odontesthes_bonariensis Teleost_Euteleost_Ovalentaria_Beloniformes_Hemiramphidae_Hyporhamphus_intermedius 10100 0 Teleost_Euteleost_Ovalentaria_Beloniformes_Adrianichthyidae_Oryzias_mekongensis 100 Teleost_Euteleost_Ovalentaria_Beloniformes_Adrianichthyidae_Oryzias_latipes Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Aplocheilidae_Pachypanchax_sakaramyi 100 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Nothobranchiidae_Nothobranchius_furzeri 9 2 100 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Aplocheilidae_Aplocheilus_lineatus 100 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Rivulidae_Austrofundulus_limnaeus 100 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Rivulidae_Kryptolebias_marmoratus 100 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Goodeidae_Ameca_splendens 100 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Fundulidae_Fundulus_heteroclitus 100 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Cyprinodontidae_Cyprinodon_varigatus 10Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Cyprinodontidae_Cyprinodon_nevadensis_pectorali0 s 100 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Poecilia_reticulata 10T0eleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Poecilia_formosa 100 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Poeciliopsis_prolifica 100Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Gambusia_affinis_whole 10Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Xiphophorus_helleri0 i 10Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Xiphophorus_maculatu0 s 10Teleos0 t_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Xiphophorus_couchianus 0.2
Figure 21: ExaML concatenated protein tree. Maximum likelihood tree with bootstrap support (based on 100 replicates), inferred from 1105 translated genes and 305 taxa, under the GTRCAT model in ExaML.
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Xenopus_tropicalis 1 Coelacanthiformes_Coelacanthiformes_Latimeriidae_Latimeria_chalumnae 1 Ceratodontiformes_Ceratodontiformes_Protopteridae_Protopterus_aethiopicus Polypteriformes_Polypteridae_Erpetoichthys_calabaricus 1 Polypteriformes_Polypteriformes_Polypteridae_Polypterus_bichir 1 Polypteriformes_Polypteriformes_Polypteridae_Polypterus_endlicheri Acipenseriformes_Polyodontidae_Polyodon_spathula 1 Acipenseriformes_Acipenseridae_Acipenser_sinensis 1 Acipenseriformes_Acipenseridae_Acipenser_naccarii 1 Amiiformes_Amiidae_Amia_calva_gill 1 Lepisosteiformes_Lepisosteiformes_Lepisosteidae_Atractosteus_spatula 1 Lepisosteiformes_Lepisosteiformes_Lepisosteidae_Lepisosteus_oculatus 1 Lepisosteiformes_Lepisosteiformes_Lepisosteidae_Lepisosteus_platyrhincus Teleost_Osteoglossiformes_Osteoglossiformes_Pantodontidae_Pantodon_buchholzi 1 Teleost_Osteoglossiformes_Osteoglossiformes_Osteoglossidae_Osteoglossum_bicirrhosum 1 1 Teleost_Osteoglossiformes_Osteoglossiformes_Osteoglossidae_Scleropages_formosus 1 Teleost_Osteoglossiformes_Osteoglossiformes_Notopteridae_Papyrocranus_afer 1 1 Teleost_Osteoglossiformes_Osteoglossiformes_Mormyridae_Mormyrus_tapirus 1 Teleost_Osteoglossiformes_Osteoglossiformes_Morymridae_Gnathonemus_petersii Teleost_Elopiformes_Elopiformes_Megalopidae_Megalops_cyprinoides 1 Teleost_Anguilliformes_Muraenidae_Gymnothorax_reevesii 1 Teleost_Anguilliformes_Congridae_Conger_cinereus 1 0.96 Teleost_Anguilliformes_Chlopsidae_Kaupichthys_hyporoides 0.55 Teleost_Anguilliformes_Anguillidae_Anguilla_japonica 1 Teleost_Anguilliformes_Anguillidae_Anguilla_anguilla 1 Teleost_Anguilliformes_Anguillidae_Anguilla_rostrata Teleost_Clupeiformes_Clupeiformes_Engraulidae_Engraulis_encrasicolus 1 Teleost_Clupeiformes_Clupeiformes_Engraulidae_Coilia_nasus 1 Teleost_Clupeiformes_Clupeiformes_Clupeidae_Clupea_harengus 1 Teleost_Clupeiformes_Clupeiformes_Clupeidae_Alosa_alosa 1 Teleost_Clupeiformes_Clupeiformes_Clupeidae_Amblygaster_clupeoides Teleost_Otophysa_Gonorynchiformes_Chanidae_Chanos_chanos 1 Teleost_Otophysa_Cypriniformes_Gyrinocheilidae_Gyrinocheilus_aymonieri Teleost_Otophysa_Cypriniformes_Botiidae_Sinibotia_superciliaris 1 1 1 Teleost_Otophysa_Cypriniformes_Nemacheilidae_Homatula_potanini 1 Teleost_Otophysa_Cypriniformes_Cobitidae_Misgurnus_anguillicaudatus 1 1 Teleost_Otophysa_Cypriniformes_Danionidae_Danio_rerio Teleost_Otophysa_Cypriniformes_Tincidae_Tinca_tinca 1 1 Teleost_Otophysa_Cypriniformes_Leuciscidae_Pimephales_promelas 1 Teleost_Otophysa_Cypriniformes_Leuciscidae_Leuciscus_waleckii 1 Teleost_Otophysa_Cypriniformes_Cyprinidae_Cyprinus_carpio 1 1 Teleost_Otophysa_Cypriniformes_Cyprinidae_Sinocyclocheilus_rhinoceros 1 Teleost_Otophysa_Cypriniformes_Cyprinidae_Sinocyclocheilus_grahami 0.95 Teleost_Otophysa_Cypriniformes_Cyprinidae_Sinocyclocheilus_anshuiensis Teleost_Otophysa_Characiformes_Distichodontidae_Distichodus_sexfasciatus 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Teleost_Otophysa_Siluriformes_Pangasiidae_Pangasianodon_hypophthalamus 0.5 Teleost_Otophysa_Siluriformes_Bagridae_Hemibagrus_guttatus 1 Teleost_Otophysa_Siluriformes_Amblycipitidae_Liobagrus_styani 1 Teleost_Otophysa_Siluriformes_Sisoridae_Glyptothorax_sinensis Teleost_Euteleost_Lepidogalaxiiformes_Lepidogalaxiidae_Lepidogalaxias_salamandroides Teleost_Euteleost_Argentiniformes_Argentinidae_Argentina_sp Teleost_Euteleost_Esociformes_Umbridae_Umbra_pygmae 1 1 Teleost_Euteleost_Esociformes_Esocidae_Esox_lucius 1 1 Teleost_Euteleost_Salmoniformes_Salmonidae_Thymallus_thymallus 0.93 Teleost_Euteleost_Salmoniformes_Salmonidae_Coregonus_clupeaformis 1 Teleost_Euteleost_Salmoniformes_Salmonidae_Salmo_salar 1 Teleost_Euteleost_Salmoniformes_Salmonidae_Salvelinus_fontinalis 1 0.97 Teleost_Euteleost_Salmoniformes_Salmonidae_Oncorhynchus_mykiss Teleost_Euteleost_Stomiatiformes_Stomiidae_Borostomias_antarcticus 1 Teleost_Euteleost_Osmeriformes_Osmeridae_Osmerus_eperlanus 1 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Teleost_Euteleost_Zeiogadaria_Gadiformes_Trachyrincidae_Trachyrincus_murrayi 1 Teleost_Euteleost_Zeiogadaria_Gadiformes_Trachyrincidae_Trachyrincus_scabrus 1 Teleost_Euteleost_Zeiogadaria_Gadiformes_Phycidae_Phycis_phycis 1 Teleost_Euteleost_Zeiogadaria_Gadiformes_Phycidae_Phycis_blennoides Teleost_Euteleost_Zeiogadaria_Gadiformes_Lotidae_Lota_lota 1 1 Teleost_Euteleost_Zeiogadaria_Gadiformes_Lotidae_Molva_molva 1 Teleost_Euteleost_Zeiogadaria_Gadiformes_Lotidae_Brosme_brosme 1 Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Gadiculus_argenteus 1 Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Trisopterus_minutus 1 Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Pollachius_virens Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Merlangius_merlangus 1 1 Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Melanogrammus_aeglefinus 1 Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Gadus_morhua 1 Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Theragra_chalcogramma 1 Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Arctogadus_glacialis 1 Teleost_Euteleost_Zeiogadaria_Gadiformes_Gadidae_Boreogadus_saida Teleost_Euteleost_Polymixiiformes_Polymixiidae_Polymixia_japonica Teleost_Euteleost_Lampriformes_Lampridae_Lampris_guttatus 1 Teleost_Euteleost_Lampriformes_Regalecidae_Regalecus_glesne 1 Teleost_Euteleost_Trachichthyformes_Monocentridae_Monocentris_japonica Teleost_Euteleost_Beryciformes_Berycidae_Beryx_splendens 1 1 Teleost_Euteleost_Beryciformes_Stephanoberycidae_Acanthochaenus_luetkenii 1 Teleost_Euteleost_Beryciformes_Rondeletiidae_Rondeletia_loricata 1 Teleost_Euteleost_Holocentriformes_Holocentridae_Myripristis_jacobus 1 Teleost_Euteleost_Holocentriformes_Holocentridae_Myripristis_berndti 1 1 Teleost_Euteleost_Holocentriformes_Holocentridae_Sargocentron_rubrum 1 Teleost_Euteleost_Holocentriformes_Holocentridae_Holocentrus_rufus 1 Teleost_Euteleost_Holocentriformes_Holocentridae_Neoniphon_sammara 1 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Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Boleophthalmus_pectinirostris 1 Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Coryphopterus_lipernes 1 Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Lesueurigobius_cf_sanzoi 1 Teleost_Euteleost_Gobiaria_Gobiiformes_Eleotridae_Oxyeleotris_marmorata 0.5 Teleost_Euteleost_Gobiaria_Gobiiformes_Gobiidae_Exyrias_puntang 1 Teleost_Euteleost_Gobiaria_Gobiiformes_Istigobius_decoratus 1 Teleost_Euteleost_Pelagiaria_Scombriformes_Scombridae_Scomber_scombrus Teleost_Euteleost_Pelagiaria_Scombriformes_Stromateidae_Pampus_argenteus 10.98 Teleost_Euteleost_Pelagiaria_Scombrifomres_Nomeidae_Nomeus_gronovii 0.4 Teleost_Euteleost_Pelagiaria_Scombriformes_Scombridae_Scomberomorus_regalis 1 1 Teleost_Euteleost_Pelagiaria_Scombriformes_Scombridae_Thunnus_albacares 1 Teleost_Euteleost_Pelagiaria_Scombriformes_Scombridae_Thunnus_orientalis Teleost_Euteleost_Syngnatharia_Syngnathiformes_Callionymidae_Foetorepus_agassizii 1 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Teleost_Euteleost_Eupercaria_Perciformes_Percophidae_Chrionema_sp 1 Teleost_Euteleost_Eupercaria_Perciformes_Serranidae_Pronotogrammus_martinicensis 1 Teleost_Euteleost_Eupercaria_Perciformes_Peristediidae_Peristedion_sp 0.815 Teleost_Euteleost_Eupercaria_Perciformes_Anoplopomatidae_Anoplopoma_fimbria 1 Teleost_Euteleost_Eupercaria_Perciformes_Gasterosteidae_Gasterosteus_aculeatus 1 Teleost_Euteleost_Eupercaria_Perciformes_Cyclopteridae_Cyclopterus_lumpus 1 1 Teleost_Euteleost_Eupercaria_Perciformes_Cottidae_Cottus_rhenanus 1 Teleost_Euteleost_Eupercaria_Perciformes_Cottidae_Myoxocephalus_scorpius Teleost_Euteleost_Eupercaria_Perciformes_Scorpaenidae_Scorpaenopsis_cirrosa 0.88 1 Teleost_Euteleost_Eupercaria_Perciformes_Synanceiidae_Synanceia_verrucosa 1 Teleost_Euteleost_Eupercaria_Perciformes_Scorpaenidae_Dendrochirus_zebra 1 Teleost_Euteleost_Eupercaria_Perciformes_Scorpaenidae_Pontinus_castor 1 Teleost_Euteleost_Eupercaria_Perciformes_Sebastidae_Sebastes_norvegicus 1 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Teleost_Euteleost_Eupercaria_Centrarchiformes_Terapontidae_Terapon_jarbua 0.99 Teleost_Euteleost_Eupercaria_Centrarchiformes_Cirrhitidae_Amblycirrhitus_pinos 1 Teleost_Euteleost_Eupercaria_Centrarchiformes_Centrarchidae_Micropterus_floridanus 1 Teleost_Euteleost_Eupercaria_Centrarchiformes_Percichthyidae_Siniperca_scherzeri 0.96 1 Teleost_Euteleost_Eupercaria_Centrarchiformes_Percichthyidae_Coreoperca_whiteheadi Teleost_Euteleost_Eupercaria_Moronidae_Morone_saxatilis 1 Teleost_Euteleost_Eupercaria_Moronidae_Dicentrarchus_labrax Teleost_Euteleost_Eupercaria_Ephippiformes_Ephippidae_Chaetodipterus_faber 1 Teleost_Euteleost_Eupercaria_Ephippiformes_Drepaneidae_Drepane_punctata 1 Teleost_Euteleost_Eupercaria_Siganidae_Siganus_guttatus 1 Teleost_Euteleost_Eupercaria_Priacanthiformes_Priacanthidae_Priacanthus_tayenus 1 Teleost_Euteleost_Eupercaria_Caproiformes_Caproidae_Antigonia_capros Teleost_Euteleost_Eupercaria_Lophiiformes_Antennariidae_Antennarius_striatus 0.60.88 7 1 Teleost_Euteleost_Eupercaria_Lophiiformes_Chaunacidae_Chaunax_pictus 0.92 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Balistidae_Pseudobalistes_fuscus Teleost_Euteleost_Eupercaria_Tetraodontiformes_Ostraciidae_Ostracion_rhinorhynchos 1 1 1 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Ostraciidae_Lactoria_cornuta 1 0.9 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Molidae_Mola_mola 1 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Diodontidae_Diodon_holocanthus 1 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Tetraodontidae_Tetraodon_nigroviridis 1 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Tetraodontidae_Takifugu_rubripes 1 Teleost_Euteleost_Eupercaria_Tetraodontiformes_Tetraodontidae_Takifugu_flavidus Teleost_Euteleost_Eupercaria_Pomacanthidae_Pomacanthus_paru 0.67 Teleost_Euteleost_Eupercaria_Acanthuriformes_Acanthuridae_Acanthurus_tractus 0.71 Teleost_Euteleost_Eupercaria_Lobotiformes_Datnioididae_Datnioides_microlepis Teleost_Euteleost_Eupercaria_Sciaenidae_Equetus_punctatus 0.54 1 Teleost_Euteleost_Eupercaria_Sciaenidae_Miichthys_miiuy 1 Teleost_Euteleost_Eupercaria_Sciaenidae_Larimichthys_crocea 0.9 Teleost_Euteleost_Eupercaria_Lutjaniformes_Haemulidae_Haemulon_flavolineatum 1 Teleost_Euteleost_Eupercaria_Lutjaniformes_Haemulidae_Haemulon_chrysargyreum 0.64 Teleost_Euteleost_Eupercaria_Lutjaniformes_Lutjanidae_Lutjanus_sebae 1 Teleost_Euteleost_Eupercaria_Lutjaniformes_Lutjanidae_Lutjanus_fulviflamma 0.46 Teleost_Euteleost_Eupercaria_Chaetodontiformes_Chaetodontidae_Chaetodon_auriga 0.83 Teleost_Euteleost_Eupercaria_Spariformes_Sparidae_Evynnis_cardinalis 1 Teleost_Euteleost_Eupercaria_Spariformes_Sparidae_Spondyliosoma_cantharus 1 Teleost_Euteleost_Eupercaria_Spariformes_Sparidae_Acanthopagrus_schlegelii 1 Teleost_Euteleost_Eupercaria_Spariformes_Sparidae_Acanthopagrus_latus Teleost_Euteleost_Anabantaria_Synbranchiformes_Synbranchidae_Monopterus_albus 1 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Teleost_Euteleost_Carangaria_Pleuronectiformes_Paralichthydae_Paralichthys_olivaceus 1 Teleost_Euteleost_Carangaria_Pleuronectiformes_Pleuronectidae_Hippoglossus_hippoglossus 0.57 1 Teleost_Euteleost_Carangaria_Pleuronectiformes_Pleuronectidae_Pseudopleuronectes_yokohamae Teleost_Euteleost_Carangaria_Toxotidae_Toxotes_jaculatrix 0.62 Teleost_Euteleost_Carangaria_Centropomidae_Lates_calcarifer 0.84 Teleost_Euteleost_Carangaria_Centropomidae_Centropomus_sp 1 Teleost_Euteleost_Carangaria_Carangiformes_Coryphaenidae_Coryphaena_hippurus 1 1 Teleost_Euteleost_Carangaria_Carangiformes_Carangidae_Trachinotus_ovatus 0.99 Teleost_Euteleost_Carangaria_Carangiformes_Carangidae_Seriola_lalandi 1 Teleost_Euteleost_Carangaria_Carangiformes_Carangidae_Selene_dorsalis 1 Teleost_Euteleost_Carangaria_Carangiformes_Carangidae_Caranx_ignobilis Teleost_Euteleost_Ovalentaria_Opistognathidae_Opistognathus_aurifrons Teleost_Euteleost_Ovalentaria_Gobiescociformes_Gobiesocidae_Tomicodon_sp 1 1 Teleost_Euteleost_Ovalentaria_Gobiescociformes_Gobiesocidae_Acyrtus_sp 0.75 Teleost_Euteleost_Ovalentaria_Blenniiformes_Tripterygiidae_Enneanectes_sp 1 Teleost_Euteleost_Ovalentaria_Blenniiformes_Blenniidae_Parablennius_parvicornis 1 Teleost_Euteleost_Ovalentaria_Blenniiformes_Chaenopsidae_Acanthemblemaria_sp Teleost_Euteleost_Ovalentaria_Mugiliformes_Mugilidae_Liza_haematocheila 1 Teleost_Euteleost_Ovalentaria_Mugiliformes_Mugilidae_Mugil_cephalus 11 Teleost_Euteleost_Ovalentaria_Pseudochromidae_Pseudochromis_fuscus 0.36 Teleost_Euteleost_Ovalentaria_Grammatidae_Lipogramma_evides 0.96 Teleost_Euteleost_Ovalentaria_Pomacentridae_Stegastes_partitus 1 Teleost_Euteleost_Ovalentaria_Pomacentridae_Amphiprion_melanopus 1 Teleost_Euteleost_Ovalentaria_Pomacentridae_Chromis_chromis ASTRAL species tree based on nucleotide gene trees 1 Teleost_Euteleost_Ovalentaria_Pomacentridae_Dascyllus_trimaculatus 0.96 Teleost_Euteleost_Ovalentaria_Ambassidae_Parambassis_pulcinella Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Amphilophus_citrinellus 1 Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Parachromis_managuensis Topology with local support values inferred via 1 Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Oreochromis_niloticus ASTRAL from nucleotide gene trees from RAxML, 1 Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Neolamprologus_brichardi 0.46 1 Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Haplochromis_burtoni partitioned by codon position under the 1 Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Pundamilia_nyererei Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Labeotropheus_fuelleborni GTRGAMMA model. 1 0.6 Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Rhamphochromis_esox 1 Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Melanochromis_auratus 0.53 0.49 Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Maylandia_zebra 0.39 Teleost_Euteleost_Ovalentaria_Cichliformes_Cichlidae_Mchenga_conophoros Teleost_Euteleost_Ovalentaria_Beloniformes_Hemiramphidae_Hyporhamphus_intermedius 1 Teleost_Euteleost_Ovalentaria_Beloniformes_Adrianichthyidae_Oryzias_mekongensis 1 Teleost_Euteleost_Ovalentaria_Beloniformes_Adrianichthyidae_Oryzias_latipes Teleost_Euteleost_Ovalentaria_Atheriniformes_Atherinopsidae_Menidia_menidia 1 Teleost_Euteleost_Ovalentaria_Atheriniformes_Atherinopsidae_Odontesthes_bonariensis 1 1 Teleost_Euteleost_Ovalentaria_Atheriniformes_Atherinopsidae_Basilichthys_microlepidotus 1 Teleost_Euteleost_Ovalentaria_Atheriniformes_Pseudomugilidae_Pseudomugil_paskai 1 Teleost_Euteleost_Ovalentaria_Atheriniformes_Melanotaeniidae_Melanotaenia_praecox 1 Teleost_Euteleost_Ovalentaria_Atheriniformes_Melanotaeniidae_Glossolepis_incisus Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Rivulidae_Austrofundulus_limnaeus 0.63 1 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Rivulidae_Kryptolebias_marmoratus 1 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Nothobranchiidae_Nothobranchius_furzeri 0.97 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Aplocheilidae_Aplocheilus_lineatus 1 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Aplocheilidae_Pachypanchax_sakaramyi 1 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Goodeidae_Ameca_splendens 1 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Cyprinodontidae_Cyprinodon_varigatus 1 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Cyprinodontidae_Cyprinodon_nevadensis_pectoralis 1 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Fundulidae_Fundulus_heteroclitus Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Poecilia_reticulata 1 1 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Poecilia_formosa 1 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Poeciliopsis_prolifica 1 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Gambusia_affinis_whole 1 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Xiphophorus_hellerii 1 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Xiphophorus_maculatus 1 Teleost_Euteleost_Ovalentaria_Cyprinodontiformes_Poeciliidae_Xiphophorus_couchianus 3.0
Figure 22: ASTRAL species tree based on nucleotide gene trees. Topology with local support values inferred via ASTRAL-II from nucleotide gene trees from RAxML, partitioned by codon position under the GTRGAMMA model.
90
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