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, 5604. bp), a mitogenome dataset (85 taxa, 14,771. bp), and a cloned nuclear RAG1 dataset (97 taxa, 1497. bp). 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), Schiz. othoracini 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.
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This study was developed from the Ph.D. Dissertation of LY (Saint Louis University, 2010; Advisor: RLM). LY would like to express his gratitude to Larry Page, Jonathan Armbruster, Milton Tan, Jarungjit Grudpan, and Chaiwut Grudpan and his students for either organizing or participating in the fieldwork in Thailand. Preserved specimens in Saint Louis University, University of Kansas, and Auburn University and some type materials stored at Institute of Hydrobiology (Wuhan), Kunming Institute of Zoology, Institute of Zoology (Beijing) were examined for this study. We thank Wei-Jen Chen, Mary Agnew and Qiu Ren for help with data collection. Kevin Tang, Lanping Zheng, and Leyang Yuan are thanked for helpful discussion. David Neely is thanked for providing samples. We are grateful to Hsin-Hui Wu and Joe Besser for help using the Cluster computing system. Maurice Kottelat and Carl Ferraris are thanked for discussion on the availability of several family-group names. Maurice Kottelat kindly commented on the discussion part of this paper. LY sincerely appreciates the enormous support from Gavin Naylor. We are very grateful to the associate editor and two anonymous reviewers for their valuable comments and suggestions that helped improve this paper. This research was supported in part by personal funds of RLM, by the USA National Science Foundation grants including The Cypriniformes Tree of Life initiative (CToL) ( EF 0431326 to RLM; EF 0431132 to AMS) and the Collaborative PBI All Cypriniformes Species – Phase II of An Inventory of the Otophysi (ACSI-II) ( DEB1021840 to RLM), by the Japan Society for the Promotion of Science ( 17207007 and 22370035 ) and by Saint Louis University , St. Louis, Missouri.
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