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Weyand CA, Piller KR. Assessing phylogeographic variation in the Rosyside Dace (Teleostei, Leuciscidae), a widespread morphologically variable taxon. ZOOL SCR 2020. [DOI: 10.1111/zsc.12439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Courtney A. Weyand
- Department of Biological Sciences; Southeastern Louisiana University; Hammond LA USA
- Department of Biological Sciences; Auburn University; Auburn AL USA
| | - Kyle R. Piller
- Department of Biological Sciences; Southeastern Louisiana University; Hammond LA USA
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Schönhuth S, Vukić J, Šanda R, Yang L, Mayden RL. Phylogenetic relationships and classification of the Holarctic family Leuciscidae (Cypriniformes: Cyprinoidei). Mol Phylogenet Evol 2018; 127:781-799. [PMID: 29913311 DOI: 10.1016/j.ympev.2018.06.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 06/12/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022]
Abstract
The phylogenetic relationships and classification of the freshwater fish order Cypriniformes, like many other species-rich groups of vertebrates, has evolved over time with some consistency and inconsistencies of relationships across various studies. Within Cypriniformes, the Holarctic family Leuciscidae is one of the most widely distributed and highly diverse monophyletic groups of cyprinoids. Despite several studies conducted on this group, alternative hypotheses exist as to the composition and relationships within Leuciscidae. Here we assess the extent, composition, phylogenetic relationships, and taxonomy of this highly diverse group of fishes, using multiple mitochondrial and nuclear loci and a comprehensive and dense taxonomic sampling. Analyses of 418 specimens (410 species) resolve a well-supported Leuciscidae including 362 specimens (358 taxa) in six well-supported subfamilies/major clades: Pseudaspininae/Far East Asian clade (FEA); Laviniinae/North American Western clade (WC); Plagopterinae/North American Creek Chub-Plagopterin clade (CC-P); Leuciscinae/Eurasian Old World clade (OW) (minus Phoxinus) plus North American Notemigonus; Phoxininae/Eurasian Phoxinus clade (PHX); and Pogonichthyinae/North American clade (NA) including all remaining leuciscids. Within Leuciscidae, neither the traditional phoxinins (Phoxinus, FEA, Nearctic genera) nor all Nearctic genera (minus Notemigonus) are resolved as monophyletic; whereas the WC and CC-P form two independent lineages from remaining North American cyprinoids. A close relationship exists between Eurasian Phoxinus, NA, and OW clades, while FEA is the sister group to all remaining Leuciscidae. Major lineages resolved within these six subfamilies are mostly congruent with some previous studies. Our results suggests a complex evolutionary history of this diverse and widespread group of fishes.
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Affiliation(s)
- Susana Schönhuth
- Biology Department, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103, USA.
| | - Jasna Vukić
- Department of Ecology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic
| | - Radek Šanda
- Department of Zoology, National Museum, Vaclavske namesti 68, 115 79 Prague, Czech Republic
| | - Lei Yang
- Florida Museum of Natural History, University of Florida, 1659 Museum Rd., Gainesville, FL 32611, USA
| | - Richard L Mayden
- Biology Department, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103, USA
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Stout CC, Tan M, Lemmon AR, Lemmon EM, Armbruster JW. Resolving Cypriniformes relationships using an anchored enrichment approach. BMC Evol Biol 2016; 16:244. [PMID: 27829363 PMCID: PMC5103605 DOI: 10.1186/s12862-016-0819-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/28/2016] [Indexed: 11/10/2022] Open
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.
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Affiliation(s)
- Carla C. Stout
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
| | - Milton Tan
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306 USA
| | - Emily Moriarty Lemmon
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306 USA
| | - Jonathan W. Armbruster
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
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Morphometric and meristic characterization of the endemic Desert chub Gila eremica (Teleostei: Cyprinidae), and its related congeners in Sonora, Mexico. REV MEX BIODIVERS 2016. [DOI: 10.1016/j.rmb.2016.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Kartavtsev YP, Batischeva NM, Bogutskaya NG, Katugina AO, Hanzawa N. Molecular systematics and DNA barcoding of Altai osmans, oreoleuciscus (pisces, cyprinidae, and leuciscinae), and their nearest relatives, inferred from sequences of cytochrome b (Cyt-b), cytochrome oxidase c (Co-1), and complete mitochondrial genome. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:502-517. [PMID: 27159700 DOI: 10.3109/24701394.2016.1149822] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mitochondrial DNA (mtDNA) at the protein-coding Cyt-b gene along with data retrieved from GenBank for Co-1 gene fragments and complete mitochondrial genome (mitogenome) of Altai osmans and the nearest relatives of Leuciscinae fish species were compared for the estimation of variability and phylogenetic tree building. Phylogenetic trees were built by four techniques: Bayesian (BA), maximum likelihood (ML), maximum parsimony (MP), and neighbor-joining (NJ). Resolution of Cyt-b trees for species of two genera (Oreoleuciscus and Phoxinus) was quite distinct at all the approaches. For Tribolodon, the single gene trees were not well resolved; however, the mitogenome tree was resolved. Species identification on per individual basis (DNA barcoding) was high for both Cyt-b and Co-1 genes. The trees built using the data for 13 protein mitochondrial genes revealed a complicated phylogenetic pattern within the subfamily Leuciscinae. Scores of the average p-distances at three taxonomic levels were considerably different: (1) 1.16 ± 0.96, (2) 8.21 ± 1.01, and (3) 16.41 ± 0.85 for Cyt-b and (1) 1.04 ± 0.78, (2) 8.30 ± 0.92, and (3) 10.74 ± 0.79 for 13 protein genes of mitogenome, where (1) is intraspecies, (2) is intragenus, and (3) is intrasubfamily levels. Data on mitogenome distances were summarized for the taxonomic hierarchy for the first time. A concordant increase in distance score with growth of the rank of taxa (having the minimum score at the intraspecies level), both for a single gene and the whole mitogenome, substantiates the concept that speciation in the subfamily Leuciscinae in most cases follows the geographic mode. The distinct clustering of Altai osmans, Oreoleuciscus potanini and O. humilis, in the Cyt-b and Co-1 gene trees with small overall genetic distances, obtained for both genes, allows us to consider these taxa as separate but genetically sister species.
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Affiliation(s)
- Yuri Phedorovich Kartavtsev
- a A.V. Zhirmunsky Institute of Marine Biology FEB RAS , Vladivostok , Russian Federation.,b Far Eastern Federal University, School of Natural Sciences , Vladivostok , Russian Federation
| | - Natalia M Batischeva
- a A.V. Zhirmunsky Institute of Marine Biology FEB RAS , Vladivostok , Russian Federation
| | | | - Anna O Katugina
- a A.V. Zhirmunsky Institute of Marine Biology FEB RAS , Vladivostok , Russian Federation.,b Far Eastern Federal University, School of Natural Sciences , Vladivostok , Russian Federation
| | - Naoto Hanzawa
- d Yamagata University, Graduate school of Science and Engineering , Yamagata , Japan
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6
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Biogeography and divergent patterns of body size disparification in North American minnows. Mol Phylogenet Evol 2015. [DOI: 10.1016/j.ympev.2015.07.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Mayden RL, Allen JS. Molecular Systematics of the Phoxinin Genus Pteronotropis (Otophysi: Cypriniformes). BIOMED RESEARCH INTERNATIONAL 2015; 2015:298658. [PMID: 26114103 PMCID: PMC4465653 DOI: 10.1155/2015/298658] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 12/13/2014] [Accepted: 12/13/2014] [Indexed: 11/21/2022]
Abstract
The genus Pteronotropis is widely distributed along the gulf slope of eastern North America from Louisiana to Florida and rivers in South Carolina along the Atlantic slope. Pteronotropis have very distinctive, flamboyant coloration. The habitats most frequently associated with these species include heavily vegetated backwater bayous to small sluggish or flowing tannin-stained streams. Although Pteronotropis is recognized as a valid genus, no phylogenetic analysis of all the species has corroborated its monophyly. In recent years, four additional species have been either described or elevated from synonymy: P. merlini, P. grandipinnis, P. stonei, and P. metallicus, with the wide-ranging P. hypselopterus complex. To examine relationships within this genus and test its monophyly, phylogenetic analyses were conducted using two nuclear genes, recombination activating gene 1, RAG1, and the first intron of S7 ribosomal protein gene in both maximum parsimony and Bayesian analyses. In no analysis was Pteronotropis, as currently recognized, recovered as monophyletic without the inclusion of the currently recognized Notropis harperi, herein referred to as Pteronotropis. Two major clades are supported: one inclusive of P. hubbsi, P. welaka, and P. harperi and the second inclusive of P. signipinnis, P. grandipinnis, P. hypselopterus plus P. merlini sister to P. euryzonus, and P. metallicus plus P. stonei.
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Affiliation(s)
- Richard L. Mayden
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103, USA
| | - Jason S. Allen
- Department of Biology, Saint Louis Community College, Meramec Campus, 11333 Big Bend Road, St. Louis, MO 63122, USA
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Phylogeography of Pteronotropis signipinnis, P. euryzonus, and the P. hypselopterus Complex (Teleostei: Cypriniformes), with Comments on Diversity and History of the Gulf and Atlantic Coastal Streams. BIOMED RESEARCH INTERNATIONAL 2015; 2015:675260. [PMID: 26114110 PMCID: PMC4465660 DOI: 10.1155/2015/675260] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 11/04/2014] [Accepted: 12/17/2014] [Indexed: 11/18/2022]
Abstract
The cyprinid genus Pteronotropis is endemic to southeastern Gulf of Mexico and Atlantic Ocean of North America. Never before has the genus been demonstrated to be monophyletic. We investigate both the phylogenetic relationships and the phylogeography of some species in the genus using mitochondrial ND2 sequences. In no analysis is the genus resolved as monophyletic if Notropis harperi is not included in the genus. Biogeographic and phylogeographic evaluations are conducted with Pteronotropis, including P. signipinnis, P. euryzonus, and the P. hypselopterus complex. Patterns of relationships and population genetic analyses support divergences within multiple clades both at the species level and within species that are tied to abiotic changes in the region. Replicated patterns across clades are observed, as well as patterns previously found in other taxa. Pteronotropis hypselopterus is likely not a natural grouping as populations from some drainages form clades more closely related to other species of the genus. The general patterns of relationships indicate likely cryptic species not currently recognized. Finally, the patterns of species relationships and clades and population structuring within species serve as another example of replicated divergences in the biodiversity east and west of the Mobile Bay.
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Britz R, Conway KW, Rüber L. Miniatures, morphology and molecules: Paedocypris and its phylogenetic position (Teleostei, Cypriniformes). Zool J Linn Soc 2014. [DOI: 10.1111/zoj12184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ralf Britz
- Department of Zoology, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Kevin W. Conway
- Department of Wildlife and Fisheries Sciences and Biodiversity Research and Teaching Collections, Texas A&M University, College Station, TX, 77843, USA
| | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005, Bern, Switzerland
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Britz R, Conway KW, Rüber L. Miniatures, morphology and molecules:Paedocyprisand its phylogenetic position (Teleostei, Cypriniformes). Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12184] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ralf Britz
- Department of Zoology; Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Kevin W. Conway
- Department of Wildlife and Fisheries Sciences and Biodiversity Research and Teaching Collections; Texas A&M University; College Station TX 77843 USA
| | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern; Bernastrasse 15 3005 Bern Switzerland
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Unmack PJ, Dowling TE, Laitinen NJ, Secor CL, Mayden RL, Shiozawa DK, Smith GR. Influence of introgression and geological processes on phylogenetic relationships of Western North American mountain suckers (Pantosteus, Catostomidae). PLoS One 2014; 9:e90061. [PMID: 24619087 PMCID: PMC3949674 DOI: 10.1371/journal.pone.0090061] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 01/29/2014] [Indexed: 12/04/2022] Open
Abstract
Intense geological activity caused major topographic changes in Western North America over the past 15 million years. Major rivers here are composites of different ancient rivers, resulting in isolation and mixing episodes between river basins over time. This history influenced the diversification of most of the aquatic fauna. The genus Pantosteus is one of several clades centered in this tectonically active region. The eight recognized Pantosteus species are widespread and common across southwestern Canada, western USA and into northern Mexico. They are typically found in medium gradient, middle-elevation reaches of rivers over rocky substrates. This study (1) compares molecular data with morphological and paleontological data for proposed species of Pantosteus, (2) tests hypotheses of their monophyly, (3) uses these data for phylogenetic inferences of sister-group relationships, and (4) estimates timing of divergence events of identified lineages. Using 8055 base pairs from mitochondrial DNA protein coding genes, Pantosteus and Catostomus are reciprocally monophyletic, in contrast with morphological data. The only exception to a monophyletic Pantosteus is P. columbianus whose mtDNA is closely aligned with C. tahoensis because of introgression. Within Pantosteus, several species have deep genetic divergences among allopatric sister lineages, several of which are diagnosed and elevated to species, bringing the total diversity in the group to 11 species. Conflicting molecular and morphological data may be resolved when patterns of divergence are shown to be correlated with sympatry and evidence of introgression.
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Affiliation(s)
- Peter J. Unmack
- WIDB 401, Department of Biology, Brigham Young University, Provo, Utah, United States of America
- National Evolutionary Synthesis Center, Durham, North Carolina, United States of America
- * E-mail:
| | - Thomas E. Dowling
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Nina J. Laitinen
- WIDB 401, Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Carol L. Secor
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Richard L. Mayden
- Department of Biology, Saint Louis University, St. Louis, Missouri, United States of America
| | - Dennis K. Shiozawa
- WIDB 401, Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Gerald R. Smith
- Museum of Zoology, The University of Michigan, Ann Arbor, Michigan, United States of America
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Tao W, Mayden RL, He S. Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): A proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses. Mol Phylogenet Evol 2013; 66:603-16. [DOI: 10.1016/j.ympev.2012.09.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 09/18/2012] [Accepted: 09/21/2012] [Indexed: 11/16/2022]
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13
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Hollingsworth PR, Darrin Hulsey C. Reconciling gene trees of eastern North American minnows. Mol Phylogenet Evol 2011; 61:149-56. [DOI: 10.1016/j.ympev.2011.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 05/27/2011] [Accepted: 05/30/2011] [Indexed: 11/26/2022]
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Phylogenetic relationships of the North American cyprinid subgenus Hydrophlox. Mol Phylogenet Evol 2011; 59:725-35. [DOI: 10.1016/j.ympev.2011.03.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Revised: 03/15/2011] [Accepted: 03/15/2011] [Indexed: 11/21/2022]
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BUFALINO ANGELOP, MAYDEN RICHARDL. Phylogenetic evaluation of North American Leuciscidae (Actinopterygii: Cypriniformes: Cyprinoidea) as inferred from analyses of mitochondrial and nuclear DNA sequences. SYST BIODIVERS 2010. [DOI: 10.1080/14772000.2010.516029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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