The Initial Response of Females Towards Congeneric Males Matches the Propensity to Hybridize
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Spatial Models of Speciation 1.0Cm Modelos Espaciais De Especiação
UNIVERSIDADE ESTADUAL DE CAMPINAS INSTITUTO DE BIOLOGIA CAROLINA LEMES NASCIMENTO COSTA SPATIAL MODELS OF SPECIATION MODELOS ESPACIAIS DE ESPECIAÇÃO CAMPINAS 2019 CAROLINA LEMES NASCIMENTO COSTA SPATIAL MODELS OF SPECIATION MODELOS ESPACIAIS DE ESPECIAÇÃO Thesis presented to the Institute of Biology of the University of Campinas in partial fulfill- ment of the requirements for the degree of Doc- tor in Ecology Tese apresentada ao Instituto de Biologia da Universidade Estadual de Campinas como parte dos requisitos exigidos para a obtenção do título de Doutora em Ecologia Orientador: Marcus Aloizio Martinez de Aguiar ESTE ARQUIVO DIGITAL CORRESPONDE À VERSÃO FINAL DA TESE DEFENDIDA PELA ALUNA CAROLINA LEMES NASCIMENTO COSTA, E ORIENTADA PELO PROF DR. MAR- CUS ALOIZIO MARTINEZ DE AGUIAR. CAMPINAS 2019 Ficha catalográfica Universidade Estadual de Campinas Biblioteca do Instituto de Biologia Mara Janaina de Oliveira - CRB 8/6972 Costa, Carolina Lemes Nascimento, 1989- C823s CosSpatial models of speciation / Carolina Lemes Nascimento Costa. – Campinas, SP : [s.n.], 2019. CosOrientador: Marcus Aloizio Martinez de Aguiar. CosTese (doutorado) – Universidade Estadual de Campinas, Instituto de Biologia. Cos1. Especiação. 2. Radiação adaptativa (Evolução). 3. Modelos biológicos. 4. Padrão espacial. 5. Macroevolução. I. Aguiar, Marcus Aloizio Martinez de, 1960-. II. Universidade Estadual de Campinas. Instituto de Biologia. III. Título. Informações para Biblioteca Digital Título em outro idioma: Modelos espaciais de especiação Palavras-chave em inglês: Speciation Adaptive radiation (Evolution) Biological models Spatial pattern Macroevolution Área de concentração: Ecologia Titulação: Doutora em Ecologia Banca examinadora: Marcus Aloizio Martinez de Aguiar [Orientador] Mathias Mistretta Pires Sabrina Borges Lino Araujo Rodrigo André Caetano Gustavo Burin Ferreira Data de defesa: 25-02-2019 Programa de Pós-Graduação: Ecologia Powered by TCPDF (www.tcpdf.org) Comissão Examinadora: Prof. -
Comparative Phylogenetic Analyses of the Adaptive Radiation of Lake
J Mol Evol (2005) 61:666–681 DOI: 10.1007/s00239-004-0217-2 Comparative Phylogenetic Analyses of the Adaptive Radiation of Lake Tanganyika Cichlid Fish: Nuclear Sequences Are Less Homoplasious But Also Less Informative Than Mitochondrial DNA Ce´ line Clabaut,1 Walter Salzburger,1,2 Axel Meyer1 1 Lehrstuhl fu¨ r Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany 2 Center for Junior Research Fellows, University of Konstanz, 78457 Konstanz, Germany Received: 15 July 2004 / Accepted: 5 May 2005 [Reviewing Editor: Dr. Rafael Zardoya] Abstract. Over 200 described endemic species make much phylogenetic information as we expected, we up the adaptive radiation of cichlids in Lake Tanga- suggest that this marker might be useful in the reso- nyika. This species assemblage has been viewed as lution of the phylogeny of older groups. both an evolutionary reservoir of old cichlid lineages and an evolutionary hotspot from which the modern Key words: Adaptive radiation — Cichlid species cichlid lineages arose, seeding the adaptive radiations flocks — Explosive speciation — Nuclear DNA in Lakes Victoria and Malawi. Here we report on a phylogeny — NADH Dehydrogenase Subunit II — phylogenetic analysis of Lake Tanganyika cichlids RAG1 — C-lineage combining the previously determined sequences of the mitochondrial ND2 gene (1047 bp) with newly derived sequences of the nuclear RAG1 gene (700 bp of intron 2 and 1100 bp of exon 3). The nuclear data—in agreement with mitochondrial DNA—sug- Introduction gest that Lake Tanganyika harbors several ancient lineages that did not undergo rampant speciation The Great Lakes of East Africa are among the worldÕs (e.g., Bathybatini, Trematocarini). -
The Initial Response of Females Towards Congeneric Males Matches the Propensity to Hybridize
bioRxiv preprint doi: https://doi.org/10.1101/2021.08.07.455508; this version posted August 8, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 The initial response of females towards congeneric males matches the propensity to hybridize 2 in Ophthalmotilapia. 3 4 Maarten Van Steenberge1,2, Noémie Jublier3,4, Loïc Kéver3, Sophie Gresham1,5, Sofie 5 Derycke1,6, Jos Snoeks2,7, Eric Parmentier3, Pascal Poncin4, Erik Verheyen1,5 6 7 1. Operational Directorate Taxonomy and phylogeny, Royal Belgian Institute of Natural 8 Sciences, 1000 Brussels, Belgium 9 2. Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles 10 Deberiotstraat 32, 3000 Leuven, Belgium 11 3. Laboratory of Functional and Evolutionary Biology, FOCUS, Liège University, 4000 12 Liège, Belgium 13 4. Laboratory of Fish and Amphibian Ethology, Behavioural Biology Unit, FOCUS, 14 Liège University, 4000 Liège, Belgium 15 5. Department Biology, Evolutionary Ecology, University of Antwerp, 2610 Antwerp, 16 Belgium 17 6. Flanders research institute for agriculture, fisheries and food, Animal Sciences Unit – 18 Aquatic Environment and Quality, Ankerstraat 1, 8400 Oostende, Belgium. 19 7. Section Vertebrates, Ichthyology, Royal Museum for Central Africa, 3080 Tervuren, 20 Belgium 21 22 Corresponding author: Maarten Van Steenberge ([email protected]) 23 24 Key words: 25 Species recognition, mate choice, behaviour, Lake Tanganyika, Africa 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.08.07.455508; this version posted August 8, 2021. -
Testing the Potential of Environmental DNA Methods for Surveying Lake Tanganyika's Highly Diverse Fish Communities Christopher J
Testing the potential of environmental DNA methods for surveying Lake Tanganyika's highly diverse fish communities Christopher James Doble A thesis submitted for the degree of Doctor of Philosophy Department of Genetics, Evolution and Environment University College London April 2020 1 Declaration I, Christopher James Doble, confirm the work presented in this thesis is my own. Where information has been derived from other sources, I confirm this has been indicated in the thesis. Christopher James Doble Date: 27/04/2020 2 Statement of authorship I planned and undertook fieldwork to the Kigoma region of Lake Tanganyika, Tanzania in 2016 and 2017. This included obtaining research permits, collecting environmental DNA samples and undertaking fish community visual survey data used in Chapters three and four. For Chapter two, cichlid reference database sequences were sequenced by Walter Salzburger’s research group at the University of Basel. I extracted required regions from mitochondrial genome alignments during a visit to Walter’s research group. Other reference sequences were obtained by Sanger sequencing. I undertook the DNA extractions and PCR amplifications for all samples, with the clean-up and sequencing undertaken by the UCL Sequencing facility. I undertook the method development, DNA extractions, PCR amplifications and library preparations for each of the next generation sequencing runs in Chapters three and four at the NERC Biomolecular Analysis Facility Sheffield. Following training by Helen Hipperson at the NERC Biomolecular Analysis Facility in Sheffield, I undertook the bioinformatic analysis of sequence data in Chapters three and four. I also carried out all the data analysis within each chapter. Chapters two, three and parts of four have formed a manuscript recently published in Environmental DNA (Doble et al. -
Masaryk University Faculty of Science
MASARYK UNIVERSITY FACULTY OF SCIENCE The parasite fauna of economically important pelagic fishes in Lake Tanganyika Ph.D. Thesis NIKOL KMENTOVÁ Supervisor: Maarten Vanhove, Ph.D. Department of Botany and Zoology Brno 2019 Bibliographic Entry Author Mgr. Nikol Kmentová Faculty of Science, Masaryk University Department of Botany and Zoology Title of Thesis: The parasite fauna of economically important pelagic fishes in Lake Tanganyika Degree programme: Ecological and Evolutionary Biology Specialization: Parasitology Supervisor: Maarten Vanhove, Ph.D. Academic Year: 2019/2020 Number of Pages: 350 + 72 Keywords: Kapentagyrus, Dolicirrolectanum, Cryptogonimidae, Clupeidae, Latidae, Bathybatini Bibliografický záznam Autor: Mgr. Nikol Kmentová Přírodovědecká fakulta, Masarykova univerzita Ústav botaniky a zoologie Název práce: Parazité ekonomicky významných ryb pelagické zóny jezera Tanganika Studijní program: Ekologická a evoluční biologie Specializace: Parazitologie Vedoucí práce: Maarten Vanhove, Ph.D. Akademický rok: 2019/2020 Počet stran: 350 + 72 Klíčová slova: Kapentagyrus, Dolicirrolectanum, Cryptogonimidae, Clupeidae, Latidae, Bathybatini ABSTRACT Biodiversity is a well-known term characterising the variety and variability of life on Earth. It consists of many different levels with species richness as the most frequently used measure. Despite its generally lower species richness compared to littoral zones, the global importance of the pelagic realm in marine and freshwater ecosystems lies in the high level of productivity supporting fisheries worldwide. In terms of endemicity, Lake Tanganyika is one of the most exceptional freshwater study areas in the world. While dozens of studies focus on this lake’s cichlids as model organisms, our knowledge about the economically important fish species is still poor. Despite their important role in speciation processes, parasite taxa have been vastly ignored in the African Great Lakes including Lake Tanganyika for many years. -
Functional Coupling Constrains Craniofacial Diversification in Lake
Downloaded from http://rsbl.royalsocietypublishing.org/ on July 3, 2017 Evolutionary biology Functional coupling constrains craniofacial rsbl.royalsocietypublishing.org diversification in Lake Tanganyika cichlids Masahito Tsuboi1, Alejandro Gonzalez-Voyer2,3 and Niclas Kolm3 1Evolutionary Biology Centre, Department of Ecology and Genetics/Animal Ecology, Uppsala University, Research Norbyva¨gen 18D, 75236 Uppsala, Sweden 2Laboratorio de Conducta Animal, Instituto de Ecologı´a, Universidad Nacional Auto´noma de Me´xico, Cite this article: Tsuboi M, Gonzalez-Voyer A, Circuito Exterior S/N, Ciudad Universitaria, UNAM, D.F. 04510, Me´xico 3 Kolm N. 2015 Functional coupling constrains Department of Zoology/Ethology, Stockholm University, Svante Arrhenius va¨g 18B, 10691 Stockholm, Sweden craniofacial diversification in Lake Tanganyika MT, 0000-0002-0144-2893 cichlids. Biol. Lett. 11: 20141053. http://dx.doi.org/10.1098/rsbl.2014.1053 Functional coupling, where a single morphological trait performs multiple func- tions, is a universal feature of organismal design. Theory suggests that functional coupling may constrain the rate of phenotypic evolution, yet empirical tests of this hypothesis are rare. In fish, the evolutionary transition from guarding the Received: 11 December 2014 eggs on a sandy/rocky substrate (i.e. substrate guarding) to mouthbrood- ing introduces a novel function to the craniofacial system and offers an ideal Accepted: 9 April 2015 opportunity to test the functional coupling hypothesis. Using a combination of geometric morphometrics and a recently developed phylogenetic compara- tive method, we found that head morphology evolution was 43% faster in substrate guarding species than in mouthbrooding species. Furthermore, for Subject Areas: species in which females were solely responsible for mouthbrooding the evolution, ecology, behaviour males had a higher rate of head morphology evolution than in those with bi- parental mouthbrooding. -
The Molecular Evolution of Rhodopsin in Marine-Derived
THE MOLECULAR EVOLUTION OF RHODOPSIN IN MARINE-DERIVED AND OTHER FRESHWATER FISHES by Alexander Van Nynatten A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Cell and Systems Biology University of Toronto © Copyright by Alexander Van Nynatten (2019) THE MOLECULAR EVOLUTION OF RHODOPSIN IN MARINE-DERIVED AND OTHER FRESHWATER FISHES A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Cell and Systems Biology University of Toronto © Copyright by Alexander Van Nynatten (2019) ABSTRACT Visual system evolution can be influenced by the spectral properties of light available in the environment. Variation in the dim-light specialized visual pigment rhodopsin is thought to result in functional shifts that optimize its sensitivity in relation to ambient spectral environments. Marine and freshwater environments have been shown to be characterized by different spectral properties and might be expected to place the spectral sensitivity of rhodopsin under different selection pressures. In Chapter two, I show that the rate ratio of non- synonymous to synonymous substitutions is significantly elevated in the rhodopsin gene of a South American clade of freshwater anchovies with marine ancestry. This signature of positive selection is not observed in the rhodopsin gene of the marine sister clade or in non-visual genes. ii In Chapter three I functionally characterize the effects of positively selected substitutions occurring on another independent invasion of freshwater made by ancestrally marine croakers. In vitro spectroscopic assays on ancestrally resurrected rhodopsin pigments reveal a red-shift in peak spectral sensitivity along the transitional branch, consistent with the wavelengths of light illuminating freshwater environments. -
Supporting Information CONTENTS
Supporting information Non-specific Freshwater Protected Areas conserve cichlid fish taxonomic and trophic diversity in Lake Tanganyika, with particular benefit to herbivores CONTENTS Appendix S1. Study site descriptions. 1 Table S1. Human disturbance factors and relative rank for each site. 5 Table S2. Cichlid species observed across all surveys detailing taxonomy, diet, habitat and brooding- type. 6 Figure S1. Species accumulation curves for all survey sites. 9 Table S3. Mantel tests for survey community dissimilarity vs. distance within each site. 10 Table S4. AIC values for the model fitting to the zeta diversity analyses. 11 Table S5. Relative HD rank and alpha and beta diversity values for tribal and trophic groups at all sites. 12 Figure S2. Pairwise comparisons of alpha diversity values between protected areas (white) and unprotected (grey), 15 Table S6. The correlations between relative HD rank and alpha and beta diversity for cichlids where all sites are standardised to 42 surveys and under 4km shoreline distance. 16 References. 17 1 Appendix S1. Study site descriptions The Tanzania shoreline was selected as it includes several FPAs, although the majority of this coast (as with the rest of the lake) is unprotected regarding both terrestrial and aquatic habitats (Allison 2000) and has been subject to varied anthropogenic impacts (Global Forest Watch 2000). Importantly, this coastline avoids within country political instability (DRC, Burundi, which includes Rusizi NP), and dangerous wildlife (Nsumbu NP, Zambia). Human settlements along the selected shoreline vary in size from isolated fishing communities, small villages, to the large urban area of Kigoma Town, which holds the largest human population on the eastern side of the lake (Worldpop, 2013). -
The Taxonomic Diversity of the Cichlid Fish Fauna of Ancient Lake
JGLR-01482; No. of pages: 12; 4C: Journal of Great Lakes Research xxx (xxxx) xxx Contents lists available at ScienceDirect Journal of Great Lakes Research journal homepage: www.elsevier.com/locate/jglr Review The taxonomic diversity of the cichlid fish fauna of ancient Lake Tanganyika, East Africa Fabrizia Ronco ⁎, Heinz H. Büscher, Adrian Indermaur, Walter Salzburger Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland article info abstract Article history: Ancient Lake Tanganyika in East Africa houses the world's ecologically and morphologically most diverse assem- Received 29 January 2019 blage of cichlid fishes, and the third most species-rich after lakes Malawi and Victoria. Despite long-lasting scien- 10 April 2019 tific interest in the cichlid species flocks of the East African Great Lakes, for example in the context of adaptive Accepted 29 April 2019 radiation and explosive diversification, their taxonomy and systematics are only partially explored; and many Available online xxxx cichlid species still await their formal description. Here, we provide a current inventory of the cichlid fish Communicated by Björn Stelbrink fauna of Lake Tanganyika, providing a complete list of all valid 208 Tanganyikan cichlid species, and discuss the taxonomic status of more than 50 undescribed taxa on the basis of the available literature as well as our Keywords: own observations and collections around the lake. This leads us to conclude that there are at least 241 cichlid spe- Biodiversity cies present in Lake Tanganyika, all but two are endemic to the basin. We finally summarize some of the major Ichthyodiversity taxonomic challenges regarding Lake Tanganyika's cichlid fauna. -
Masaryk University Faculty of Science
MASARYK UNIVERSITY FACULTY OF SCIENCE The parasite fauna of economically important pelagic fishes in Lake Tanganyika Ph.D. Thesis NIKOL KMENTOVÁ Supervisor: Maarten Vanhove, Ph.D. Department of Botany and Zoology Brno 2019 Bibliographic Entry Author Mgr. Nikol Kmentová Faculty of Science, Masaryk University Department of Botany and Zoology Title of Thesis: The parasite fauna of economically important pelagic fishes in Lake Tanganyika Degree programme: Ecological and Evolutionary Biology Specialization: Parasitology Supervisor: Maarten Vanhove, Ph.D. Academic Year: 2019/2020 Number of Pages: 350 + 72 Keywords: Kapentagyrus, Dolicirrolectanum, Cryptogonimidae, Clupeidae, Latidae, Bathybatini Bibliografický záznam Autor: Mgr. Nikol Kmentová Přírodovědecká fakulta, Masarykova univerzita Ústav botaniky a zoologie Název práce: Parazité ekonomicky významných ryb pelagické zóny jezera Tanganika Studijní program: Ekologická a evoluční biologie Specializace: Parazitologie Vedoucí práce: Maarten Vanhove, Ph.D. Akademický rok: 2019/2020 Počet stran: 350 + 72 Klíčová slova: Kapentagyrus, Dolicirrolectanum, Cryptogonimidae, Clupeidae, Latidae, Bathybatini ABSTRACT Biodiversity is a well-known term characterising the variety and variability of life on Earth. It consists of many different levels with species richness as the most frequently used measure. Despite its generally lower species richness compared to littoral zones, the global importance of the pelagic realm in marine and freshwater ecosystems lies in the high level of productivity supporting fisheries worldwide. In terms of endemicity, Lake Tanganyika is one of the most exceptional freshwater study areas in the world. While dozens of studies focus on this lake’s cichlids as model organisms, our knowledge about the economically important fish species is still poor. Despite their important role in speciation processes, parasite taxa have been vastly ignored in the African Great Lakes including Lake Tanganyika for many years. -
Bayesian Node Dating Based on Probabilities of Fossil Sampling Supports Trans-Atlantic Dispersal of Cichlid Fishes
Supporting Information Bayesian Node Dating based on Probabilities of Fossil Sampling Supports Trans-Atlantic Dispersal of Cichlid Fishes Michael Matschiner,1,2y Zuzana Musilov´a,2,3 Julia M. I. Barth,1 Zuzana Starostov´a,3 Walter Salzburger,1,2 Mike Steel,4 and Remco Bouckaert5,6y Addresses: 1Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway 2Zoological Institute, University of Basel, Basel, Switzerland 3Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic 4Department of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand 5Department of Computer Science, University of Auckland, Auckland, New Zealand 6Computational Evolution Group, University of Auckland, Auckland, New Zealand yCorresponding author: E-mail: [email protected], [email protected] 1 Supplementary Text 1 1 Supplementary Text Supplementary Text S1: Sequencing protocols. Mitochondrial genomes of 26 cichlid species were amplified by long-range PCR followed by the 454 pyrosequencing on a GS Roche Junior platform. The primers for long-range PCR were designed specifically in the mitogenomic regions with low interspecific variability. The whole mitogenome of most species was amplified as three fragments using the following primer sets: for the region between position 2 500 bp and 7 300 bp (of mitogenome starting with tRNA-Phe), we used forward primers ZM2500F (5'-ACG ACC TCG ATG TTG GAT CAG GAC ATC C-3'), L2508KAW (Kawaguchi et al. 2001) or S-LA-16SF (Miya & Nishida 2000) and reverse primer ZM7350R (5'-TTA AGG CGT GGT CGT GGA AGT GAA GAA G-3'). The region between 7 300 bp and 12 300 bp was amplified using primers ZM7300F (5'-GCA CAT CCC TCC CAA CTA GGW TTT CAA GAT GC-3') and ZM12300R (5'-TTG CAC CAA GAG TTT TTG GTT CCT AAG ACC-3'). -
The Genetics of Sexual Development in East African Cichlid Fishes
The Genetics of Sexual Development in East African Cichlid Fishes Inauguraldissertation Zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät der Universität Basel von Corina Heule aus Altstätten, Schweiz Basel, 2015 Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Prof. Dr. Walter Salzburger (Universität Basel) und Prof. Judith Mank (University College London) Basel, den 12.11.2013 Prof. Dr. Jörg Schibler (Dekan, Universität Basel) Contents Introduction ..................................................................1 Chapter 1 .................................................................... 11 The ontogenetic development of egg-spots in the haplochromine cichlid fish Astatotilapia burtoni Chapter 2 .................................................................... 21 Genetics of sexual development – an evolutionary playground for fish Chapter 3 .................................................................... 37 Expression and sequence evolution of aromatase cyp19a1 and other sexual development genes in East African cichlid fishes Chapter 4 .................................................................... 59 Genetics and timing of sex determination in the East African cichlid fish Astatotilapia burtoni Perspectives ............................................................... 79 Acknowledgments ...................................................... 85 Introduction The cichlid fishes of East Africa Cichlid fishes occur in tropical