导师队伍
| 职 称： | 研究员 |
|---|---|
| 学 历： | 博士研究生 |
| 联系方式： | 86-27-68780430 |
| 电子邮件： | clad#ihb.ac.cn(请改#为@) |
| 办 公 室： | 标本馆308 |
| 个人网页： |
简历介绍：
1962年12月2日出生，法国国家自然历史博物馆理学博士，中国科学院水生生物标本馆馆长、中国科学院水生生物多样性与保护重点实验室主任、鱼类系统发育与生物地理学学科组责任研究员。中国动物学会理事，湖北省暨武汉动物学会理事长。湖北省科协第六届委员；任《中国动物志》编委，以及《生物多样性》，《动物学研究》，《应用与环境生物学报》和《水生生物学报》编委。先后主持和承担欧盟项目、国家自然科学重点基金、国家自然科学青年基金、国家863项目和973专题。 得到美国NSF有关生命之树项目的资助开展鲤形目系统发育研究。研究工作运用了生物技术、网络和数字化技术相结合的手段，使鱼类系统学和生物地理学这一进化生物学的前沿学科达到了较高的水平。使用多个基因序列数据重建鲤科和鲇形目鱼类的系统(Zhao, Duan et al. 2009; Fu, Chen et al. 2010; Chen, Zou et al. 2011; Fu and He 2012; Zou, Guo et al. 2012; Yang, Zou et al. 2013; Yang and He 2014)发育过程、提出了鲤科鱼类系统发育新的模式，保持了对鲤形目鱼类系统学研究在世界上的主导地位。最近，更得到中国科学院战略性先导科技专项项目的资助，这对了解青藏高原和深海，这两个极端环境的鱼类的基因组及其适应进化，有重要意义。所在学科组在选题、使用的理论和方法上都达到国际先进水平并直接参与国际竞争。尤其是在辐鳍鱼类的转录组、基因组、蛋白质组等组学水平的研究，达到国际先进水平。目前，已完成的有鲢鱼、鳙鱼的全基因组，正在进行中的有塞内加尔多鳍鱼、似鲶高原鳅、小眼高原鳅和黑斑原鮡全基因组。成功组装、注释了鲢、鳙鱼的转录组和全基因组，找到鲢鱼的鲢鱼可以在水体中大量滤食有毒蓝藻而不被MC所毒害的原因，可能与鲢鱼体内的 GSH 合成通路中某些基因在进化过程中受到了正向选择有关，使其适应这种有毒的环境。塞内加尔多鳍鱼，是淡水硬骨鱼类的原始类型，是比较古老的辐鳍鱼类。多鳍鱼的全基因组测序工作对了解整个辐鳍鱼类，甚至是四足类的进化有重要意义。而高原鳅和黑斑原鮡，这三种高原鱼类的基因组，有助于对高原这一低氧、低温、高海拔的极端环境的鱼类适应性状的解析。
主要创新表现在：鱼类生物多样性和标本信息的数字化管理，创建了ChinaFishBase鱼类生物信息数据库；运用分子系统学方法在鲤科鱼类系统发育研究方面取得重要成果，发现了鲤科鱼类系统发育新格局；运用生物地理学方法研究了鱼类物种分化与青藏高原隆升的关系；在国际上率先使用分子系统学方法对亚洲鲇类及相关类群开展系统发育研究，率先对青藏高原这一高原极端环境鱼类的转录组和基因组进行研究。研究成果为分子系统学与生物地理学学科的后续发展开拓了新的领域。
研究方向：
鱼类生物地理学；鱼类比较基因组学；生物信息学；鱼类系统发育
代表论著：
[1] Yang, L. and S. He (2014). "A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)." Gene 533(1): 261-269.
[2] Yang, L., M. Zou, et al. (2013). "Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish." Bmc Genomics 14.
[3] Tao, W., R. L. Mayden, et al. (2013). "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." Molecular Phylogenetics and Evolution 66(3): 603-616.
[4] Tao, W., J. Yuan, et al. (2013). "Characterization of Gonadal Transcriptomes from Nile Tilapia (Oreochromis niloticus) Reveals Differentially Expressed Genes." Plos One 8(5).
[5] Zou, M., B. Guo, et al. (2012). "Integrating multi-origin expression data improves the resolution of deep phylogeny of ray-finned fish (Actinopterygii)." Sci Rep 2.
[6] Fu, B. and S. He (2012). "Transcriptome Analysis of Silver Carp (Hypophthalmichthys molitrix) by Paired-End RNA Sequencing." DNA Research 19(2): 131-142.
[7] Chen, M., M. Zou, et al. (2011). "Evolutionary Patterns of RNA-Based Duplication in Non-Mammalian Chordates." Plos One 6(7).
[8] Fu, B., M. Chen, et al. (2010). "The rapid generation of chimerical genes expanding protein diversity in zebrafish." Bmc Genomics 11.
[9] Zhao, K., Z. Y. Duan, et al. (2009). "The youngest split in sympatric schizothoracine fish (Cyprinidae) is shaped by ecological adaptations in a Tibetan Plateau glacier lake." Mol Ecol 18(17): 3616-3628.
[10] 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.
[11] Li, Z., He, S., 2009. Relaxed purifying selection of rhodopsin gene within a Chinese endemic cavefish genus Sinocyclocheilus (Pisces: Cypriniformes). Hydrobiologia 624, 139-149.
[12] 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, -.
[13] 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.
[14] 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.
[15] 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.
[16] 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.
[17] 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.
[18] 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.
[19] 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.
[20] 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.
[21] 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.
[22] 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.
[23] 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.
[24] Han, Y., He, S., Chen, Y., 2007. Identification of novel SINEs from Cyprinidae and their evolutionary significance. Progr Nat Sci 17, 270-279.
[25] 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.
[26] 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.
[27] 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.
[28] 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.
[29] 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.
[30] 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.
[31] 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.
[32] 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.
[33] 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.
[34] 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.
[35] 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.
[36] Chen, J., Xie, Z., He, S., 2006. A taxonomic study of Oconnorella (Enchytraeidae, Oligochaeta) from Changbaishan Mountain, China. Zoological Science 23, 917-922.
[37] 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.
[38] 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.
[39] 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.
[40] 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.
[41] 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.
[42] 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.
[43] 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.
[44] 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.
[45] 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.
[46] 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.
[47] 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.
[48] 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.
[49] 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.
[50] 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.
[51] 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.
[52] 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.
[53] 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.
[54] 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.
[55] 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.
[56] 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.
[57] 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.
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