Research interests of the Research Group of Fish Phylogenetics and Biogeography encompass phylogenetics, molecular and genome evolution, speciation, and phenotypic evolution of fishes. Researchers from this group use a diverse set of technologies and approaches to explore several fundamental issues in the phylogenetic relationships and biodiversity of fishes over evolution time, study their gene/genome evolution and morphological change as well as their evolutionary interconnections, with special focuses on Cypriniformes, Siluriformes, Tetraodontiform, and ancient fishes.  

Current Research Interests:  

* Fish phylogenetics/phylogenomics, speciation, and biogeography 

* Fish adaptive genomics 

* Short interspersed repetitive elements (SINEs) and their evolutionary pattern in fish 

* Gene and gene family evolution in fish (e.g., retrogene, Hox gene) 

* Fish morphological differentiation and its developmental basis within a phylogenetic framework (e.g., pharyngeal genesis) 

　　 He, S.P., Cao, W.X., Chen, Y.Y., 2001. The uplift of Qinghai-Xizang (Tibet) Plateau and the vicariance speciation of glyptosternoid fishes (Siluriformes : Sisoridae). Sci China Ser C Life Sci 44, 644-651. 

　　 He, S.P., Chen, Y.Y., Tsuneo, N., 2001. Sequences of cytochrome b gene for primitive cyprinid fishes in East Asia and their phylogenetic concerning. Chin Sci Bull 46, 661-665. 

　　 Wang, W., He, S.P., Chen, Y.Y., 2002. Mitochondrial d-loop sequence variation and phylogeny of gobiobotine fishes. Progr Nat Sci 12, 866-868. 

　　 Wang, X.Z., He, S.P., Chen, Y.Y., 2002. Sequence variations of the S7 ribosomal protein gene in primitive cyprinid fishes: Implication on phylogenetic analysis. Chin Sci Bull 47, 1638-1643. 

　　 Zhang, E., He, S.P., Chen, Y.Y., 2002. Revision of the cyprinid genus Placocheilus Wu, 1977 in China, with description of a new species from Yunnan. Hydrobiologia 487, 207-217. 

　　 Chen, Y., Wang, Y., He, S., Zhu, Z., 2004. Cloning and sequencing of the growth hormone gene of large yellow croaker and its phylogenetic significance. Biochem Genet 42, 365-375. 

　　 He, S., Liu, H., Chen, Y., Kuwahara, M., Nakajima, T., Zhong, Y., 2004. Molecular phylogenetic relationships of Eastern Asian Cyprinidae (Pisces: Cypriniformes) inferred from cytochrome b sequences. Sci China Ser C Life Sci 47, 130-138. 

　　 Peng, Z., He, S., Zhang, Y., 2004. Phylogenetic relationships of glyptosternoid fishes (Siluriformes: Sisoridae) inferred from mitochondrial cytochrome b gene sequences. Mol Phylogenet Evol 31, 979-987. 

　　 Sun, Y., Liu, S.Y., Zhao, G., He, S.P., Wu, Q.J., Taniguchi, N., Yu, Q.X., 2004. Genetic structure of Chinese sucker population Myxocyprinus asiaticus in the Yangtze River based on mitochondrial DNA marker. Fisheries Science 70, 412-420. 

　　 Wang, X., Liu, H., He, S., Chen, Y., 2004. Sequence analysis of cytochrome b gene indicates that East Asian group of cyprinid subfamily Leuciscinae (Teleostei : Cyprinidae) evolved independently. Progr Nat Sci 14, 132-137. 

　　 Zhang, E., Chen, Y.Y., 2004. Qianlabeo striatus, a new genus and species of Labeoninae from Guizhou Province, China (Teleostei : Cyprinidae). Hydrobiologia 527, 25-33. 

　　 Guo, X., He, S., Zhang, Y., 2005. Phylogeny and biogeography of Chinese sisorid catfishes re-examined using mitochondrial cytochrome b and 16S rRNA gene sequences. Mol Phylogenet Evol 35, 344-362. 

　　 He, S., Wang, D., Wang, W., Chen, D., Zhao, Q., Gong, W., 2005. Genetic diversity in the Yangtze finless porpoise by RAPD analysis. High Technology Letters 11, 207-210. 

　　 Li, J.B., Wang, X.Z., He, S.P., Chen, Y.Y., 2005. Phylogenetic studies of Chinese labeonine fishes (Teleostei: Cyprinidae) based on the mitochondrial 16S rRNA gene. Progr Nat Sci 15, 213-219. 

　　 Peng, Z.G., Zhang, Y.G., He, S.P., Chen, Y.Y., 2005. Phylogeny of chinese catfishes inferred from mitochondrial cytochrome b sequences. Acta Genet Sin 32, 145-154. 

　　 Son, Y.-M., He, S.-P., 2005. Cobitis zhejiangensis, a new species from the Ling River, China (Teleostei: Cobitidae) Korean Journal of Ichthyology 17, 236-240. 

　　 Wang, X., Liu, H., 2005. Phylogenetic relationships of the Chinese cyprinid genus Rhinogobio Bleeker (Teleostei: Cyprinidae) based on sequences of the mitochondrial DNA control region, with comments on character adaptations. Hydrobiologia 532, 215-220. 

　　 Zhao, K., Li, J.B., Yang, G.S., Duan, Z.Y., He, S.P., Chen, Y.Y., 2005. Molecular phylogenetics of Gymnocypris (Teleostei: Cyprinidae) in Lake Qinghai and adjacent drainages. Chin Sci Bull 50, 1325-1333. 

　　 Chen, J., Xie, Z., He, S., 2006. A taxonomic study of Oconnorella (Enchytraeidae, Oligochaeta) from Changbaishan Mountain, China. Zoological Science 23, 917-922. 

　　 Peng, Z., He, S., Wang, J., Wang, W., Diogo, R., 2006. Mitochondrial molecular clocks and the origin of the major Otocephalan clades (Pisces: Teleostei): A new insight. Gene 370, 113-124. 

　　 Peng, Z., Ho, S.Y.W., Zhang, Y., He, S., 2006. Uplift of the Tibetan plateau: Evidence from divergence times of glyptosternoid catfishes. Mol Phylogenet Evol 39, 568-572. 

　　 Peng, Z., Wang, J., He, S., 2006. The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes. Gene 376, 290-297. 

　　 Xu, H.G., Ding, H., Li, M.Y., Qiang, S., Guo, J.Y., Han, Z.M., Huang, Z.G., Sun, H.Y., He, S.P., Wu, H.R., Wan, F.H., 2006. The distribution and economic losses of alien species invasion to China. Biol Invasions 8, 1495-1500. 

　　 Xu, H.G., Qiang, S., Han, Z.M., Guo, J.Y., Huang, Z.G., Sun, H.Y., He, S.P., Ding, H., Wu, H.R., Wan, F., 2006. The status and causes of alien species invasion in China. Biodivers Conserv 15, 2893-2904. 

　　 Yang, J., He, S., Freyhof, J., Witte, K., Liu, H., 2006. The Phylogenetic Relationships of the Gobioninae (Teleostei: Cyprinidae) Inferred from Mitochondrial Cytochrome b Gene Sequences. Hydrobiologia 553, 255-266. 

　　 Guo, X., He, S., Zhang, Y., 2007. Phylogenetic relationships of the Chinese sisorid catfishes: a nuclear intron versus mitochondrial gene approach. Hydrobiologia 579, 55-68. 

　　 Han, Y., He, S., Chen, Y., 2007. Identification of novel SINEs from Cyprinidae and their evolutionary significance. Progr Nat Sci 17, 270-279. 

　　 Huang, S., He, S., Peng, Z., Zhao, K., Zhao, E., 2007. Molecular phylogeography of endangered sharp-snouted pitviper (Deinagkistrodon acutus; Reptilia, Viperidae) in Mainland China. Mol Phylogenet Evol 44, 942-952. 

　　 Kong, X., Wang, X., Gan, X., He, S., 2007. The c-myc coding DNA sequences of cyprinids (Teleostei: Cypriniformes): Implications for phylogeny. Chin Sci Bull 52, 1491-1500. 

　　 Kong, X., Wang, X., Gan, X., Li, J., He, S., 2007. Phylogenetic relationships of Cyprinidae (Teleostei: Cypriniformes) inferred from the partial S6K1 gene sequences and implication of indel sites in intron 1. Sci China C Life Sci 50, 780-788. 

　　 Ku, X., Peng, Z., Diogo, R., He, S., 2007. MtDNA phylogeny provides evidence of generic polyphyleticism for East Asian bagrid catfishes. Hydrobiologia 579, 147-159. 

　　 Luo, J., Stadler, P.F., He, S., Meyer, A., 2007. PCR survey of hox genes in the goldfish Carassius auratus auratus. J Exp Zool Part B Mol Dev Evol 308, 250-258. 

　　 Mayden, R.L., Tang, K.L., Conway, K.W., Freyhof, J., Chamberlain, S., Haskins, M., Schneider, L., Sudkamp, M., Wood, R.M., Agnew, M., Bufalino, A., Sulaiman, Z., Miya, M., Saitoh, K., He, S., 2007. Phylogenetic relationships of Danio within the order Cypriniformes: a framework for comparative and evolutionary studies of a model species. J Exp Zool Part B Mol Dev Evol 308B, 642-654. 

　　 Peng, Z., Ludwig, A., Wang, D., Diogo, R., Wei, Q., He, S., 2007. Age and biogeography of major clades in sturgeons and paddlefishes (Pisces: Acipenseriformes). Mol Phylogenet Evol 42, 854-862. 

　　 Wang, L., He, S., Chen, Y., 2007. Identification of the Angel-related elements in cyprinid fishes and their phylogenetic implications. Progr Nat Sci 17, 168-171. 

　　 Wang, X., Li, J., He, S., 2007. Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences. Mol Phylogenet Evol 42, 157-170. 

　　 Wang, X., Wang, J., He, S., Mayden, R.L., 2007. The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii: Cypriniformes) and an alternative pattern of mitogenomic evolution in vertebrate. Gene 399, 11-19. 

　　 Zhang, J.Q., Chen, J., Xie, Z.C., 2007. Redescription of Nais inflata Liang (Annelida: Oligochaeta) from China. Proc Biol Soc Wash 120, 264-270. 

　　 Zhao, K., Duan, Z.Y., Yang, G.S., Peng, Z., He, S., Chen, Y., 2007. Origin of Gymnocypris przewalskii and phylogenetic history of Gymnocypris eckloni (Teleostei: Cyprinidae). Progr Nat Sci 17, 520-528. 

　　 Chen, J., Xie, Z.C., 2008. Fridericia dianchiensis sp nov (Enchytraeidae, oligochaeta) from Yunnan Province, China. P Biol Soc Wash 121, 283-288. 

　　 Cheng, J.L., Ishihara, H., Zhang, E., 2008. Pseudobagrus brachyrhabdion, a new catfish (Teleostei : Bagridae) from the middle Yangtze River drainage, South China. Ichthyol Res 55, 112-123. 

　　 Guo, B., Li, J., Tong, C., He, S., 2008. Cloning and sequence analysis of Sox genes in a tetraploid cyprinid fish, Tor douronensis. Chin Sci Bull 53, 1988-1995. 

　　 He, C.L., Song, Z.B., Zhang, E., 2008a. Triplophysa lixianensis, a new nemacheiline loach species (Pisces : Balitoridae) from the upper Yangtze River drainage in Sichuan Province, South China. Zootaxa, 41-52. 

　　 He, S., Gu, X., Mayden, R.L., Chen, W.-J., Conway, K.W., Chen, Y., 2008b. Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): evidence from the mitochondrial genome. Mol Phylogenet Evol 47, 419-425. 

　　 He, S., Mayden, R.L., Wang, X., Wang, W., Tang, K.L., Chen, W.-J., Chen, Y., 2008c. Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: Further evidence from a nuclear gene of the systematic chaos in the family. Mol Phylogenet Evol 46, 818-829. 

　　 Kong, X., Wang, X., Gan, X., Li, J., He, S., 2008. Molecular evolution of connective tissue growth factor in Cyprinidae (Teleostei : Cypriniformes). Progr Nat Sci 18, 155-160. 

　　 Li, J., Wang, X., Kong, X., Zhao, K., He, S., Mayden, R.L., 2008. Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei: Cypriniformes). Mol Phylogenet Evol 47, 472-487. 

　　 Li, Z., Guo, B., Li, J., He, S., Chen, Y., 2008. Bayesian mixed models and divergence time estimation of Chinese cavefishes (Cyprinidae : Sinocyclocheilus). Chin Sci Bull 53, 2342-2352. 

　　 Mayden, R.L., Tang, K.L., Wood, R.M., Chen, W.-J., Agnew, M.K., Conway, K.W., Yang, L., Simons, A.M., Bart, H.L., Harris, P.M., Li, J., Wang, X., Saitoh, K., He, S., Liu, H., Chen, Y., Nishida, M., Miya, M., 2008. Inferring the Tree of Life of the order Cypriniformes, the earth's most diverse clade of freshwater fishes: Implications of varied taxon and character sampling. J Syst Evol 46, 424-438. 

　　 Sullivan, J.P., Peng, Z., Lundberg, J.G., Peng, J., He, S., 2008. Molecular evidence for diphyly of the Asian catfish family Amblycipitidae (Teleostei: Siluriformes) and exclusion of the South American Aspredinidae from Sisoroidea. Proc Acad Nat Sci Phila 157, 51-65. 

　　 Xie, Z.C., Chen, J., 2008. A redescription of Piguetiella denticulata Liang and, Xie (Oligochaeta, Tubificidae, Naidinae) from China, with a key to the genus Piguetiella. Proc Biol Soc Wash 121, 321-325. 

　　 Yang, L., He, S., 2008. Phylogeography of the freshwater catfish Hemibagrus guttatus (Siluriformes, Bagridae): Implications for South China biogeography and influence of sea-level changes. Mol Phylogenet Evol 49, 393-398. 

　　 Yuan, L.Y., Zhang, E., Huang, Y.F., 2008. Revision of the labeonine genus Sinocrossocheilus (Teleostei : Cyprinidae) from South China. Zootaxa, 36-48. 

　　 Zhang, E., Qiang, X., Lan, J.H., 2008. Description of a new genus and two new species of labeonine fishes from South China (Teleostei : Cyprinidae). Zootaxa, 33-44. 

　　 Duan, Z., Zhao, K., Peng, Z., Li, J., Diogo, R., He, S., Zhao, X., 2009. Comparative phylogeography of the Yellow River schizothoracine fishes (Cyprinidae): Vicariance, expansion, and recent coalescence in response to the Quaternary environmental upheaval in the Tibetan Plateau. Mol Phylogenet Evol. 

　　 Guo, B.C., Tong, C.B., He, S.P., 2009. Sox genes evolution in closely related young tetraploid cyprinid fishes and their diploid relative. Gene 439, 102-112. 

　　 Li, Z., He, S., 2009. Relaxed purifying selection of rhodopsin gene within a Chinese endemic cavefish genus Sinocyclocheilus (Pisces: Cypriniformes). Hydrobiologia 624, 139-149. 

　　 Tong, C.B., Guo, B.C., He, S.P., 2009. Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation. BMC Genomics 10, -.