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深海鱼类物种与基因组多样性研究组
研究方向

1深海鱼类比较基因组学和环境适应机理

对深渊生物开展大规模的资源调查、分类学研究和科学数据库建立;使用DNA条形码对深渊生物开展生物多样性的评估。系统发育和生物地理学分析探索海沟生物之间以及与浅海生物的演化关系;通过稳定同位素示踪研究深渊食物链和食物网的结构和功能;首次使用二代、三代、nanopore和Hi-C基因组测序和分析技术对深渊的特有物种开展极端环境适应的分子机理的分析;首次使用同步辐射和CT扫描技术对深渊狮子鱼和沟虾开展形态学研究,探索形态变化与深渊适应的关系;

2 深海生物多样性及形成机制的研究

从深渊生物多样性的格局、形成过程和机理三个层次开展研究。基于比较基因组学方法探讨深渊生物起源与演化的过程、揭示影响深渊生物群体遗传结构和分布模式的内外因子;通过功能基因组分析及研究,寻找更多宏观生物包括狮子鱼、端足类沟虾等对深渊环境适应的分子机理以及深渊宏生物和共生微生物建立和维持共生关系的分子机制;通过追踪马里亚纳海沟大型生物中富集沉积物及生物体的碳源,了解深海海沟生物的生活环境特性;获得大量全面的深海宏观生物的标本,构建特定基因品系的模式动物

 

研究团队

何舜平,博士、研究员、博士导师, 深海鱼类物种与基因组多样性研究组学科带头人(clad@idsse.ac.cn)

主要从事鱼类系统发育、分子进化和生物地理学研究工作。对青藏高原和东亚特有鱼类的起源、系统发育和适应性演化及生物多样性历史重建开展了大量和深入的研究。研究确立了基于自然分类的鲤科系统,澄清了传统人为分类对鲤科亚科的划分以及对亚科间关系的解释;发现了青藏高原及其东部区域分布的单系的鰋鮡鱼类生物地理学过程与青藏高原东部的水系变迁相一致,其主要类群的分化时间与青藏高原阶段隆升的假说相一致;还发现了青藏高原冰川湖泊中两种裸鲤的同域物种分化现象,为验证同域物种形成理论找到了新的分子证据。通过对东亚淡水鱼类重要类群系统发育关系的重建及其生物地理学格局和物种形成分子生态学机制的揭示,为理解东亚地区复杂的环境条件与淡水鱼类物种分化之间的相互关系提供了重要分子证据,也为认识东亚淡水鱼类生物多样性历史提供了新的观点。近年来,结合我国深渊科学考察,对深渊特有的狮子鱼进行了深入的研究,从分子、细胞和整体结构上发现了狮子鱼适应环境的分子机理;对其基因组的高精度的分析表明了其进化和适应的过程.

    在鱼类系统发育、分子进化和生物地理学研究方面有重要贡献。在Nature Ecology and Evolution, Molecular Ecology, Molecular Ecology Resource, Genome Biology and Evolution, Molecular Phylogenetic and  Evolution, Plos One, BMC Evolutionary Biology, BMC Genomics, JEZ, DCI等领域前沿的刊物上发表论文200余篇。担任中国动物志、生物多样性杂志、四川动物杂志以及Scientific Reports杂志编委。

代表性论文(不超过10篇)

1. Kang J, Ma X, He S. 2017. Evidence of high-altitude adaptation in the glyptosternoid fish, Creteuchiloglanis macropterus from the Nujiang River obtained through transcriptome analysis. Bmc Evolutionary Biology 17:229.

2. Wang Y, Yang L, Zhou K, Zhang Y, Song Z, He S. 2015. Evidence for Adaptation to the Tibetan Plateau Inferred from Tibetan Loach Transcriptomes. Genome Biol Evol 7:2970-2982.

3. Fang C, Guan L, Zhong Z, Gan X, He S. 2015. Analysis of the nicotinamide phosphoribosyltransferase family provides insight into vertebrate adaptation to different oxygen levels during the water-to-land transition. FEBS Journal 282:2858-2878.

4. Yang L, Wang Y, Zhang Z, He S. 2015. Comprehensive transcriptome analysis reveals accelerated genic evolution in a Tibet fish, Gymnodiptychus pachycheilus. Genome Biol Evol 7:251-261.

5. Ma X, Kang J, Chen W, Zhou C, He S. 2015. Biogeographic history and high-elevation adaptations inferred from the mitochondrial genome of Glyptosternoid fishes (Sisoridae, Siluriformes) from the southeastern Tibetan Plateau. Bmc Evolutionary Biology 15:233.

6. Tao W, Mayden RL, He S. 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 66:603-616.

7. Zhao K, Duan ZY, Peng ZG, Guo SC, Li JB, He SP, Zhao XQ. 2009. The youngest split in sympatric schizothoracine fish (Cyprinidae) is shaped by ecological adaptations in a Tibetan Plateau glacier lake. Molecular Ecology 18:3616-3628.

8. Yang L, Mayden RL, He S. 2009. Population genetic structure and geographical differentiation of the Chinese catfish Hemibagrus macropterus (Siluriformes, Bagridae): evidence for altered drainage patterns. Molecular Phylogenetics and Evolution 51:405-411.

9. Duan Z, Zhao K, Peng Z, Li J, Diogo R, Zhao X, He S. 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. Molecular Phylogenetics and Evolution 53:1025-1031.

10. 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. Molecular Phylogenetics and Evolution 49:393-398.

其他论文(不超过10篇)

1. Chen W, Yue X, He S. 2017. Genetic differentiation of the Schizothorax species complex (Cyprinidae) in the Nujiang River (upper Salween). Sci Rep 7:5944.

2. Chen W, Zhong Z, Dai W, Fan Q, He S. 2017. Phylogeographic structure, cryptic speciation and demographic history of the sharpbelly (Hemiculter leucisculus), a freshwater habitat generalist from southern China. Bmc Evolutionary Biology 17:216.

3. Kang J, Ma X, He S. 2017. Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq. Sci Rep 7:2813.

4. Yang L, Zhang Z, He S. 2016. Both Male-Biased and Female-Biased Genes Evolve Faster in Fish Genomes. Genome Biol Evol 8:3433-3445.

5. Ma X, Dai W, Kang J, Yang L, He S. 2015. Comprehensive Transcriptome Analysis of Six Catfish Species from an Altitude Gradient Reveals Adaptive Evolution in Tibetan Fishes. G3 (Bethesda) 6:141-148.

6. Fu B, He S. 2012. Transcriptome analysis of silver carp (Hypophthalmichthys molitrix) by paired-end RNA sequencing. DNA Research 19:131-142.

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

8. He S, Mayden RL, Wang X, Wang W, Tang KL, Chen WJ, Chen Y. 2008. 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. Molecular Phylogenetics and Evolution 46:818-829.

9. He S, Gu X, Mayden RL, Chen WJ, Conway KW, Chen Y. 2008. Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): evidence from the mitochondrial genome. Molecular Phylogenetics and Evolution 47:419-425.

10. 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. Molecular Phylogenetics and Evolution 42:157-170.

 

客座研究员:王堃

博士生:武宝生,入学时间20189

博士生:徐涵,入学时间20199

硕士生:薄晶,入学时间20189

硕士生:陈洁,入学时间20199

 

承担的科研项目

2018国家自然科学基金面上项目: 深渊鱼类的起源演化及其环境适应的分子机制

2018 国家重点研发计划项目课题: 深渊宏观生物生命过程、环境适应与生命演化过程

 

学科组近年来发表的主要学术论文

Wang K, et al. 2019. Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation. Nat Ecol Evol: 823-833. doi: 10.1038/s41559-019-0864-8

Shen Y, et al. 2017. The first complete mitogenome of the South China deep-sea giant isopod Bathynomus sp. (Crustacea: Isopoda: Cirolanidae) allows insights into the early mitogenomic evolution of isopods. Ecol Evol 7: 1869-1881. doi: 10.1002/ece3.2737.

Shen Y, et al. 2017. Molecular phylogeny and divergence time estimates using the mitochondrial genome for the hadal snailfish from the Mariana trench. Science Bulletin 62: 1106-1108. doi: 10.1016/j.scib.2017.07.010

Jiang H, et al. 2019. Massive Loss of Olfactory Receptors But Not Trace Amine-Associated Receptors in the World's Deepest-Living Fish (Pseudoliparis swirei). Genes 10(11).doi:10.3390/genes10110910. 

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