title: Phylogeny and polyploidy: resolving the classification of cyprinine fishes (Teleostei: Cypriniformes).
abstract: Cyprininae is the largest subfamily (>1300 species) of the family Cyprinidae and contains more polyploid species (∼400) than any other group of fishes. We examined the phylogenetic relationships of the Cyprininae based on extensive taxon, geographical, and genomic sampling of the taxa, using both mitochondrial and nuclear genes to address the phylogenetic challenges posed by polyploidy. Four datasets were analyzed in this study: two mitochondrial gene datasets (465 and 791 taxa, 5604bp), a mitogenome dataset (85 taxa, 14,771bp), and a cloned nuclear RAG1 dataset (97 taxa, 1497bp). Based on resulting trees, the subfamily Cyprininae was subdivided into 11 tribes: Probarbini (new; Probarbus+Catlocarpio), Labeonini Bleeker, 1859 (Labeo & allies), Torini Karaman, 1971 (Tor, Labeobarbus & allies), Smiliogastrini Bleeker, 1863 (Puntius, Enteromius & allies), Poropuntiini (Poropuntius & allies), Cyprinini Rafinesque, 1815 (Cyprinus & allies), Acrossocheilini (new; Acrossocheilus & allies), Spinibarbini (new; Spinibarbus), Schizothoracini McClelland, 1842 (Schizothorax & allies), Schizopygopsini Mirza, 1991 (Schizopygopsis & allies), and Barbini Bleeker, 1859 (Barbus & allies). Phylogenetic relationships within each tribe were discussed. Two or three distinct RAG1 lineages were identified for each of the following tribes Torini, Cyprinini, Spinibarbini, and Barbini, indicating their hybrid origin. The hexaploid African Labeobarbus & allies and Western Asian Capoeta are likely derived from two independent hybridization events between their respective maternal tetraploid ancestors and Cyprinion.
authors.affiliation: Department of Biology, Saint Louis University, St. Louis, MO 63103, USA. Electronic address: leiyangslu@gmail.com.
authors.forename: Lei
authors.initials: L
authors.lastname: Yang
authors.affiliation: Department of Zoology, Natural History Museum and Institute, Chiba, 955-2 Aoba-cho, Chuo-ku, Chiba 260-8682, Japan.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Sado
authors.affiliation: Graduate Program in Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA.
authors.forename: M
authors.initials: M
authors.lastname: Vincent Hirt
authors.affiliation: Evo-devo of Vertebrate Dentition, and Molecular Zoology, Institut de Ge ́nomique Fonctionnelle de Lyon (IGFL), UMR CNRS 5242, Universite ́ de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supe ́rieure de Lyon, Lyon 69007, France.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Pasco-Viel
authors.affiliation: Sri Paramakalyani Centre for Environmental Sciences, Manonmaniam Sundaranar University, Alwarkurichi 627 412, Tamil Nadu, India.
authors.forename: M
authors.initials: M
authors.lastname: Arunachalam
authors.affiliation: Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
authors.forename: Junbing
authors.initials: J
authors.lastname: Li
authors.affiliation: Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
authors.forename: Xuzhen
authors.initials: X
authors.lastname: Wang
authors.affiliation: German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Freyhof
authors.affiliation: National Research Institute of Fisheries Science, Aquatic Genomics Research Center, Fukuura, Kanazawa, Yokohama 236-8648, Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Saitoh
authors.affiliation: Department of Fisheries, Wildlife, and Conservation Biology and Bell Museum of Natural History, University of Minnesota, St. Paul, MN 55108, USA.
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Simons
authors.affiliation: Department of Zoology, Natural History Museum and Institute, Chiba, 955-2 Aoba-cho, Chuo-ku, Chiba 260-8682, Japan.
authors.forename: Masaki
authors.initials: M
authors.lastname: Miya
authors.affiliation: Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
authors.forename: Shunping
authors.initials: S
authors.lastname: He
authors.affiliation: Department of Biology, Saint Louis University, St. Louis, MO 63103, USA. Electronic address: cypriniformes@gmail.com.
authors.forename: Richard L
authors.initials: RL
authors.lastname: Mayden
mesh_terms: D000818:Animals; D003531:Cypriniformes / Q000145:classification*; D019143:Evolution, Molecular; D050259:Genes, Mitochondrial; D016654:Genes, RAG-1; D005843:Geography; D016013:Likelihood Functions; D010802:Phylogeny; D011123:Polyploidy; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
keywords: Biogeography; Cyprinidae; Evolution; Hexaploids; Taxonomy; Tetraploids