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Resolving Cypriniformes Relationships Using an Anchored Enrichment Approach Carla C
Stout et al. BMC Evolutionary Biology (2016) 16:244 DOI 10.1186/s12862-016-0819-5 RESEARCH ARTICLE Open Access Resolving Cypriniformes relationships using an anchored enrichment approach Carla C. Stout1*†, Milton Tan1†, Alan R. Lemmon2, Emily Moriarty Lemmon3 and Jonathan W. Armbruster1 Abstract Background: Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average locus length of 1011 bp). Results: Concatenation analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap support. Species tree analysis was highly congruent with the concatenation analysis with only two major differences: monophyly of Cobitoidei and placement of Danionidae. Conclusions: Most major clades obtained in prior molecular studies were validated as monophyletic, and we provide robust resolution for the relationships among these clades for the first time. These relationships can be used as a framework for addressing a variety of evolutionary questions (e.g. phylogeography, polyploidization, diversification, trait evolution, comparative genomics) for which Cypriniformes is ideally suited. Keywords: Fish, High-throughput -
Adding Nuclear Rhodopsin Data Where Mitochondrial COI Indicates Discrepancies – Can This Marker Help to Explain Conflicts in Cyprinids?
DNA Barcodes 2015; 3: 187–199 Research Article Open Access S. Behrens-Chapuis*, F. Herder, H. R. Esmaeili, J. Freyhof, N. A. Hamidan, M. Özuluğ, R. Šanda, M. F. Geiger Adding nuclear rhodopsin data where mitochondrial COI indicates discrepancies – can this marker help to explain conflicts in cyprinids? DOI 10.1515/dna-2015-0020 or haplotype sharing (12 species pairs) with presumed Received February 27, 2015; accepted October 1, 2015 introgression based on mtCOI data. We aimed to test Abstract: DNA barcoding is a fast and reliable tool for the utility of the nuclear rhodopsin marker to uncover species identification, and has been successfully applied reasons for the high similarity and haplotype sharing in to a wide range of freshwater fishes. The limitations these different groups. The included labeonine species reported were mainly attributed to effects of geographic belonging to Crossocheilus, Hemigrammocapoeta, scale, taxon-sampling, incomplete lineage sorting, or Tylognathus and Typhlogarra were found to be nested mitochondrial introgression. However, the metrics for within the genus Garra based on mtCOI. This specific the success of assigning unknown samples to species or taxonomic uncertainty was also addressed by the use genera also depend on a suited taxonomic framework. of the additional nuclear marker. As a measure of the A simultaneous use of the mitochondrial COI and the delineation success we computed barcode gaps, which nuclear RHO gene turned out to be advantageous for were present in 75% of the species based on mtCOI, but the barcode efficiency in a few previous studies. Here, in only 39% based on nuclear rhodopsin sequences. -
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15 3 NOTES ON GEOGRAPHIC DISTRIBUTION Check List 15 (3): 369–374 https://doi.org/10.15560/15.3.369 Expanding the geographical distribution of Rhynchocypris czekanowskii (Dybowski, 1869) (Cypriniformes, Cyprinidae) in the basin of the Yenisei River, Eastern Siberia, Russia Ivan Vladimirovich Zuev,1 Sergey Mikhailovich Chuprov,1 Anastasiya Vyacheslavovna Zueva2 1 Siberian Federal University, Svobodny av. 79, Krasnoyarsk, 660041, Russia. 2 Institute of Biophysics of Federal Research Center, “Krasnoyarsk Science Center” of Siberian Branch of Russian Academy of Sciences, Akademgorodok, Krasnoyarsk, 660036, Russia. Corresponding author: Ivan Zuev, [email protected] Abstract The currently known geographical distribution of Chekanovskii’s Minnow, Rhynchocypris czekanowskii (Dybowski, 1869), is limited only by the lower reaches of the arctic river basins in which this species lives. We report R. cze- kanowskii from the small water bodies of middle part of Yenisei river basin, expanding its distribution to the south of the river basin to 55°51ʹ41ʺ N latitude, more than 100 km south from previously known occurrences of this species. Key words Arctic river basins, Chekanovskii’s Minnow, Krasnoyarsk region, Leuciscinae, Northern Asia. Academic editor: Sarah Steele | Received 18 January 2019 | Accepted 9 April 2019 | Published 10 May 2019 Citation: Zuev IV, Chuprov SM, Zueva AV (2019) Expanding the geographical distribution of Rhynchocypris czekanowskii (Dybowski, 1869) (Cypriniformes, Cyprinidae) in the basin of the Yenisei River, Eastern Siberia, Russia. Check List 15 (3): 369–374. https://doi.org/10.15560/15.3.369 Introduction this species inhabits only the lower reaches (Reshetnikov 2002, Freyhof and Kottelat 2008; Fig. 1). Our previous Chekanovskii’s Minnow, Rhynchocypris czekanowskii studies confirmed the presence of R. -
Eurasian Minnow (Phoxinus Phoxinus) ERSS
Eurasian Minnow (Phoxinus phoxinus) Ecological Risk Screening Summary U.S. Fish & Wildlife Service, August 2012 Revised, February 2019 Web Version, 8/28/2019 Photo: J. Renoult. Licensed under CC BY-SA 4.0 International. Available: https://api.gbif.org/v1/image/unsafe/https%3A%2F%2Fstatic.inaturalist.org%2Fphotos%2F1624 9424%2Foriginal.jpeg%3F1524597277. (March 2019) 1 Native Range and Status in the United States Native Range From Froese and Pauly (2019): “Eurasia: basins of Atlantic, North and Baltic Seas, Arctic and northern Pacific Ocean, from Garonne (France) eastward to Anadyr and Amur drainages and Korea; Ireland (possibly introduced), Great Britain northward to 58°N. Scandinavia and Russia northernmost extremity, Rhône drainage. Recorded from upper and middle Volga and Ural drainages, Lake Balkhash 1 (Kazakhstan) and upper Syr-Darya drainage (Aral basin), but else identifications need verification.” From GISD (2019): “Albania, Armenia, Azerbaijan, Belarus, Belgium, Bosnia And Herzegovina, Bulgaria, China, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Hungary, Italy, Kazakhstan, Korea, Democratic People's Republic Of Korea, Republic Of Latvia, Liechtenstein, Lithuania, Luxembourg, Macedonia, The Former Yugoslav Republic Of Moldova, Republic Of Mongolia, Montenegro, Netherlands, Norway, Poland, Romania, Russian Federation, Serbia, Slovakia, Slovenia, Spain, Sweden, Switzerland, Turkey, Ukraine, and the United Kingdom.” In addition to the above locations, Freyhof and Kottelat (2008) lists Andorra and Austria as locations where Phoxinus phoxinus is native. CABI (2019) lists Phoxinus phoxinus as localized in Egypt. Status in the United States No records of introductions of Phoxinus phoxinus in the United States were found. Phoxinus phoxinus was officially listed as an injurious wildlife species in 2016 under the Lacey Act (18.U.S.C.42(a)(1)) by the U.S. -
Adding Nuclear Rhodopsin Data Where Mitochondrial COI Indicates Discrepancies – Can This Marker Help to Explain Conflicts in Cyprinids?
DNA Barcodes 2015; 3: 187–199 Research Article Open Access S. Behrens-Chapuis*, F. Herder, H. R. Esmaeili, J. Freyhof, N. A. Hamidan, M. Özuluğ, R. Šanda, M. F. Geiger Adding nuclear rhodopsin data where mitochondrial COI indicates discrepancies – can this marker help to explain conflicts in cyprinids? DOI 10.1515/dna-2015-0020 or haplotype sharing (12 species pairs) with presumed Received February 27, 2015; accepted October 1, 2015 introgression based on mtCOI data. We aimed to test Abstract: DNA barcoding is a fast and reliable tool for the utility of the nuclear rhodopsin marker to uncover species identification, and has been successfully applied reasons for the high similarity and haplotype sharing in to a wide range of freshwater fishes. The limitations these different groups. The included labeonine species reported were mainly attributed to effects of geographic belonging to Crossocheilus, Hemigrammocapoeta, scale, taxon-sampling, incomplete lineage sorting, or Tylognathus and Typhlogarra were found to be nested mitochondrial introgression. However, the metrics for within the genus Garra based on mtCOI. This specific the success of assigning unknown samples to species or taxonomic uncertainty was also addressed by the use genera also depend on a suited taxonomic framework. of the additional nuclear marker. As a measure of the A simultaneous use of the mitochondrial COI and the delineation success we computed barcode gaps, which nuclear RHO gene turned out to be advantageous for were present in 75% of the species based on mtCOI, but the barcode efficiency in a few previous studies. Here, in only 39% based on nuclear rhodopsin sequences. -
CURRICULUM VITAE Ming Chen
CURRICULUM VITAE Ming Chen School of Genome Sci & Tech University of Tennessee Knoxville, TN37996 Email: [email protected] Education 2015 ~ present Graduate student at GST program, University of Tennessee, Knoxville, TN 2012 ~ 2015.05 M.S. Biology Department of Biology at Baylor University Waco, TX, USA 2009 ~ 2012 M.S. Zoology Institute of Hydrobiology, Chinese Academy of Sciences Wuhan City, Hubei Province, China Thesis Title: "Characteristic Analysis of Behaviors Related to Reproduction of the Rose Bitterling (Rhodeus Ocellatus)" 2005 ~ 2009 B.S. Aquaculture Department of Animal Sciences at Yangtze University Jingzhou City, Hubei Province, China Teaching Experience Teaching Assistants in the following courses: independently teaching laboratories, grading homework and exams, holding office hours for answering students’ questions Bio2106 Genetics Laboratory 2014 Spring, Summer and Fall at Baylor University Bio2106 Genetics Laboratory 2013 Spring, Summer, and Fall at Baylor University Bio1402 Introductory Microbiology 2013 Spring at Baylor University Bio2106 Genetics Laboratory 2012 Fall at Baylor University Research Experience 2015.07 ~ present School of Genome Sci & Tech, University of Tennessee, Knoxville, TN37996 Development of a search module which integrates the Hardwood Genomics Databases (HGD) with elastic search 2013 ~ 2015.05 Department of Biology, Baylor University A test of postzygotic isolation and Haldane’s rule in Lake Malawi cichlids By comparing fitnessrelated traits and sex ratio between hybrids -
Evidence of an Ancient Connectivity and Biogeodispersal of a Bitterling
www.nature.com/scientificreports OPEN Evidence of an ancient connectivity and biogeodispersal of a bitterling species, Rhodeus notatus, across the Korean Peninsula Hari Won1, Hyung-Bae Jeon 1,2 & Ho Young Suk1* The modern-day distribution of freshwater fshes throughout multiple rivers is likely the result of past migration during times when currently separate drainages were once connected. Here, we used mitochondrial and microsatellite analyses for 248 individuals of Rhodeus notatus collected from seven diferent rivers to obtain better understand historical gene fow of freshwater fsh on the Korean Peninsula. Based on our phylogenetic analyses, this Korean species originated through the paleo-Yellow River from China and frst colonized near the west coast. These genetic data also provided evidence of estuary coalescences among the rivers fowing to the west and southwest coast on well-developed continental shelf. In addition, the pattern of population structure revealed the biogeodispersal route from the west coast to the south coast. It could be inferred that massive migration was not involved in the formation of southern populations, since the signature of historical genetic drift was clearly observed. Our study is the frst genetic attempt to confrm hypotheses describing the migration of freshwater species towards the end of East Asia, which have previously been developed using only geological reasoning. Primary freshwater fsh species living in separate river systems are not able to come into contact naturally. Even within a single river system, populations can be isolated by landscape structures1–3. Te high degree of interpop- ulation genetic diferentiation normally found in freshwater fsh species has ofen been attributed to the frag- mented nature of freshwater environments4–7. -
Life History Traits of the Chinese Minnow Rhynchocypris
Liang et al. Zoological Studies 2014, 53:36 http://www.zoologicalstudies.com/content/53/1/36 RESEARCH Open Access Life history traits of the Chinese minnow Rhynchocypris oxycephalus in the upper branch of Yangtze River, China Yangyang Liang1,2, Xiaoyun Sui1,3*, Yifeng Chen1, Yintao Jia1 and Dekui He1 Abstract Background: Study of the life history traits of any species plays an essential role for understanding their relationship with the surrounding environment and scientific management. The Chinese minnow Rhynchocypris oxycephalus,an ecologically and economically important species which was widely distributed in East Asia, is currently diminishing. In the present study, we depicted the main life history traits of R. oxycephalus for the first time. Results: A total of 442 individuals were collected from April 2012 to March 2013, with total length (TL) ranging from 32.2 to 158.0 mm. The otolith (lapillus) was proved suitable for age determination. Moreover, the results from marginal increment ratio (MIR) analyses demonstrated its unusual growth pattern: two pairs of opaque and transparent bands were formed each year, which might provide some implications for the age determination of other species. The maximum age for females (4 years) was higher than for males (3 years), while 1- and 2-year-old individuals dominated the population. Both females and males reached maturity at 1 year, and the TL at first maturity was 78.8 mm for females and 60.3 mm for males. Obvious sexual dimorphism was observed as females growing faster and larger than males after maturity. As a multiple spawner, R. oxycephalus releases batches of eggs from April to August. -
Thèse Gaël Denys 2015.Pdf
MUSEUM NATIONAL D’HISTOIRE NATURELLE Ecole Doctorale Sciences de la Nature et de l’Homme – ED 227 Année 2015 N°attribué par la bibliothèque |_|_|_|_|_|_|_|_|_|_|_|_| THESE Pour obtenir le grade de DOCTEUR DU MUSEUM NATIONAL D’HISTOIRE NATURELLE Spécialité : Ecologie et Evolution Présentée et soutenue publiquement par Gaël DENYS Le 16 décembre 2015 Taxonomie intégrative des poissons d’eau douce de France métropolitaine Sous la direction de : Professeur Philippe KEITH et du Docteur Agnès DETTAI JURY : M. Feunteun Eric Professeur, Muséum national d’Histoire naturelle, Dinard Président M. Brito Paulo Professeur, Universidade do Estado do Rio de Janeiro, Brésil Rapporteur M. Laffaille Pascal Professeur des Universités, Institut National Polytechnique de Toulouse Rapporteur M. Persat Henri Chargé de recherche, CNRS, Lyon Examinateur M. Poulet Nicolas Chargé de mission, ONEMA, Toulouse Examinateur M. Keith Philippe Professeur, Muséum national d’Histoire naturelle, Paris Directeur de thèse Mme Dettai Agnès Maître de conférence, Muséum national d’Histoire naturelle, Paris Directrice de thèse 2 Remerciements Je souhaite tout d’abord remercier les membres du jury, Paolo Brito, Pascal Laffaille, Eric Feunteun, Henri Persat et Nicolas Poulet pour le temps et l’attention qu’ils ont consacrés à l’examen de mes travaux. Merci également à Jean Allardi et Georges Carrel, membres de mon comité de thèse, pour m’avoir orienté dans mes recherches et prodigué de nombreux conseils. Je remercie Guy Duhamel de m’avoir accueilli au sein du Département Milieux et Peuplements Aquatiques (DMPA), et Sylvie Dufour de m’avoir accepté à l’UMR Borea pour que je puisse y préparer ma thèse. -
Species Composition of Introduced and Natural Minnow Populations of the Phoxinus Cryptic Complex in the Westernmost Part of the Po River Basin (North Italy)
Biol Invasions (2021) 23:657–668 https://doi.org/10.1007/s10530-020-02406-2 (0123456789().,-volV)( 0123456789().,-volV) INVASION NOTE Species composition of introduced and natural minnow populations of the Phoxinus cryptic complex in the westernmost part of the Po River Basin (north Italy) Vanessa De Santis . Giovanni B. Delmastro . Isabella Vanetti . J. Robert Britton . Serena Zaccara Received: 18 May 2020 / Accepted: 28 October 2020 / Published online: 13 November 2020 Ó The Author(s) 2020 Abstract Invasive alien species are a major driver of via stocking in Alpine lakes vs. natural populations in biodiversity loss, with their impacts potentially more streams). We tested the genetic composition of the intense when complexes of cryptic species are cryptic Phoxinus populations inhabiting these waters, involved. In freshwaters, the anthropogenic manipu- as the species are morphologically indistinct. lation of fish communities has resulted in altered fish Sequences of the mitochondrial cytochrome oxidase communities, and in Europe has increased the com- I (COI) were obtained from 239 specimens, with the plexity of Phoxinus species assemblages. Here, we results indicating that 17 Alpine high-altitude lakes are investigated the Phoxinus communities of the west- now populated by a complex of Phoxinus species, ernmost part of the Po river basin, where adjacent comprising P. septimaniae (native to the Mediter- freshwater ecosystems (Alpine high-altitude lakes and ranean area of France), P. csikii (native to the Central lowland streams) are representative of different man- Balkans) and P. lumaireul (native to the North agement strategies (i.e. manipulated fish communities Adriatic Sea basins). Their introduction resulted from their use as angling live baits. -
Rhynchocypris Oxycephalus) and Amur Minnow (Rhynchocypris Lagowskii): a Review
Mini Review ISSN: 2574 -1241 DOI: 10.26717/BJSTR.2021.34.005600 The Studies of Chinese Minnow (Rhynchocypris oxycephalus) and Amur Minnow (Rhynchocypris lagowskii): A Review In-Seok Park* Division of Convergence on Marine Science, College of Ocean Science and Engineering, Korea Maritime & Ocean University, Republic of Korea *Corresponding author: In-Seok Park, Division of Convergence on Marine Science, College of Ocean Science and Engineering, Korea Maritime & Ocean University, Republic of Korea ARTICLE INFO ABSTRACT Received: March 18, 2021 The Rhynchocypris minnows (Teleostei: Cyprinidae) are typically small cold water Published: March 24, 2021 (Rhynchocypris oxycephalus) and Amur minnow (Rhynchocypris lagowskii) based on thefish, studies mainly collecteddistributed so in far Asia. and This could paper form briefly the basis reviews for thea wide studies category of Chinese of researches minnow including zootaxy, reproduction & development, ecology, starvation, environmental Citation: In-Seok Park. The Studies of Chinese Minnow (Rhynchocypris oxyceph- alus) and Amur Minnow (Rhynchocypris biology, and techniques in order to highlight the recent progress in different fields of Review; lagowskii): A Review. Biomed J Sci & Tech studyKeywords: using these species,Rhynchocypris which were oxycephalus; done over Rhynchocypris a period of 21 lagowskiiyears from 1998 to 2019. Res 34(5)-2021. BJSTR. MS.ID.005600. Introduction and R. lagowskii, which were done over a period of 21 years from The Chinese minniw, Rhynchocypris oxycephalus (Sauvage & Dabry de Thiersant, 1874; synonyms: Lagowskiella czekanowskii suifunensis; Leuciscus costatus; Moroco oxycephalus; Phoxinus Zootaxy1998 to 2019. (Refer to Appendix) czekanowskii suifunensis; Phoxinus lagowskii oxycephalus; Phoxinus Rhynchocypris oxycephalus: oxycephalus; Phoxinus percnurus suifunensis; Pseudophoxinus oxycephalus) is an Asian species of small freshwater cyprinid Two species of Moroco oxycephalus and M. -
Minnows and Molecules: Resolving the Broad and Fine-Scale Evolutionary Patterns of Cypriniformes
Minnows and molecules: resolving the broad and fine-scale evolutionary patterns of Cypriniformes by Carla Cristina Stout A dissertation submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Auburn, Alabama May 7, 2017 Keywords: fish, phylogenomics, population genetics, Leuciscidae, sequence capture Approved by Jonathan W. Armbruster, Chair, Professor of Biological Sciences and Curator of Fishes Jason E. Bond, Professor and Department Chair of Biological Sciences Scott R. Santos, Professor of Biological Sciences Eric Peatman, Associate Professor of Fisheries, Aquaculture, and Aquatic Sciences Abstract Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world. Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. The goal of this dissertation is to provide robust support for relationships at various taxonomic levels within Cypriniformes. For the entire order, an anchored hybrid enrichment approach was used to resolve relationships. This resulted in a phylogeny that is largely congruent with previous multilocus phylogenies, but has much stronger support. For members of Leuciscidae, the relationships established using anchored hybrid enrichment were used to estimate divergence times in an attempt to make inferences about their biogeographic history. The predominant lineage of the leuciscids in North America were determined to have entered North America through Beringia ~37 million years ago while the ancestor of the Golden Shiner (Notemigonus crysoleucas) entered ~20–6 million years ago, likely from Europe. Within Leuciscidae, the shiner clade represents genera with much historical taxonomic turbidity. Targeted sequence capture was used to establish relationships in order to inform taxonomic revisions for the clade.