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施鹏  研究员
进化与功能基因组学学科组
职  务: 副所长
学  历: 博士
电  话: +86 871 68125408
传  真: +86 871 68125408
电子邮件: ship@mail.kiz.ac.cn
通讯地址: 云南省昆明市教场东路32号 中国科学院昆明动物研究所    650223
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  简  历

施鹏,男,1973年出生,理学博士,研究员,现任中国科学院昆明动物研究所副所长,遗传资源与进化国家重点实验室主任,进化与功能基因组学科组负责人。

1996年毕业于厦门大学生物系生化专业,获理学学士学位;2004年毕业于中国科学院昆明动物研究所,动物学与进化生物学专业,获理学博士学位;2004-2006年在美国密歇根大学生态与进化生物学系做博士后研究;2007-2008年在德国人类营养研究所分子遗传系任Research Scientist 2008年入选中科院“百人计划”引进回国,2014年获国家杰出青年基金,同年 “动物适应性进化的分子机制”获云南省自然科学奖一等奖(第二获奖人),2015年获科技部“中青年科技创新领军人才”,中科院“王宽诚西部学者突出贡献奖”,2017年入选第二批国家“万人计划”领军人才。2018年入选人社部“国家百千万人才”。

主要从事进化基因组学和功能基因组学研究,建立应用适应性进化的理论来解析动物复杂性状遗传基础新的研究范式。这一范式的建立不仅解决了长期以来悬而未决的进化可预测性难题,而且为遗传学表型与基因型的研究提供了一条崭新的思路。利用这个研究范式,解决了哺乳动物回声定位、高原适应等复杂性状,并为生物多样性资源挖掘和可持续利用提供了新的研究驱动力。

曾任中科院先导B类项目“动物复杂性状的进化解析与调控”共同首席科学家。迄今,在Nature GeneticsGenome Research, Cell Research, PNAS, Molecular Biology and Evolution, Current Biology等国际著名期刊发表SCI论文40余篇,总影响因子350,其中以(共同)第一作者、通讯作者发表IF9以上论文10篇,完成2部国际著作中的特邀章节,发表的文章多次被 Science NowCurrent BiologyFaculty of 1000 Biology等评注。论文共被引用2000余次,相关内容写入50多部国外著作。

现任中国遗传学会动物专业委员会主任,中国遗传学会进化遗传专业委员会主任,云南省遗传学会副理事长,《遗传》杂志编委会编委。曾应邀为Trends in Genetics, PNAS, Genome Research, PLoS Genetics, Molecular Biology and Evolution21 个国际和国内知名期刊审稿。

  研究方向

运用自然选择理论在基因组范围内探讨基因型和表型的关系;结合生物信息学和功能实验的方法来研究:

1. 动物适应极端环境的基因组机制,并从新的视角理解人类长寿、心血管疾病和肿瘤发生的机制机理及进化;

2.  回声定位及高频听力保护的进化基础,结合功能基因组分析,探索解决生物体再生与保护问题;

3. 珊瑚礁生物颜色多样性的基因组机制。

  承担科研项目

1. 回声定位蝙蝠高频听力适应性进化的遗传发育机制,31930011,国家自然科学基金重点项目,2020.01-2024.12,303万元,主持

2. 第二次青藏高原综合科学考察研究高原动物多样性保护和可持续利用专题,2019QZKK0501,国家科技重大专项下属动物专题,2019.11-2024.10,8442万元,主持

3. 凸颅鼢鼠属快速物种形成及种间基因交流的基因组机制研究,91731313,国家自然科学基金重大研究计划集成项目,2018.01-2019.12,150万元

4. 长寿人群基因组大数据综合分析平台及健康老龄促进的适宜技术整合、推广和策略,SQ2018YFC200162-05,国家重点研发计划《主动健康和老龄化科技应对》 专项- 《中国健康长寿达人群多队列的系统研究》 项目,2018.12-2022.1257.76万元,参与

  专家类别
研究员
  社会任职
  获奖及荣誉

《动物适应性进化的分子机制》,云南省自然科学奖一等奖(第二获奖人),2013年。

中科院“王宽诚西部学者突出贡献奖”,2015年。

  代表论著

论文:

1.     Zhao SL#, Zhang T#, Liu Q, Wu H, Su B, Shi P ,Chen H*,Identifying Lineage-Specific Targets of Natural Selection by a Bayesian Analysis of Genomic Polymorphisms and Divergence from Multiple Species. Molecular Biology and Evolution,2019, 36(6): 1302-1315

2.     Liu Z#, Qi FY#, Xu DM#, Zhou X, Shi P*, Genomic and functional evidence reveals molecular insights into the origin of echolocation in whales, Science Advances ,2018, 4:eaat8821

3.     Tu Q#, Hao JJ#, zhou X#, Yan LZ, Dai HJ, Sun B, Yang D, An SQ, Lv LB, Jiao BW, Chen CS Lai R, Shi P*, Zhao XD*, CDKN2B deletion is essential for pancreatic cancer development instead of unmeaningful co-deletion due to juxtaposition to CDKN2A, Oncogene, 2018, 37(1): 128-138

4.     Li YY#  , Liu Z#*  , Qi FY , Zhou X , Shi P*,Functional effects of a retained ancestral polymorphism in prestin , Molecular Biology and Evolution , 2017 ,34(1):88-92

5.     Zhang ZG# , Xu DM#   , Wang L#  , Hao JJ , Wang JF , Zhou X , Wang WW , Qiu Q , Huang Xi D , Zhou JW , Long RJ * , Zhao FQ * ,  Shi P*Convergent Evolution of Rumen Microbiomes in High-Altitude Mammals , Current Biology ,  2016 , 26(14):1873-9

6.     Liu Z#  , Qi FY , Zhou X , Ren HQ ,  Shi P*,Parallel Sites Implicate Functional Convergence of the Hearing Gene Prestin among Echolocating Mammals , Molecular Biology and Evolution , 2014 , 31(9):2415-2424

7.     Zhang ZG# , Geng JW # , Tang XD , Fan H , Xu JC , Wen XJ , Ma ZS *,Shi P* , Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota , ISME Journal , 2014 , 8(4):881-893

8.      Mu D #, Yang H# , Zhu JW , Liu FL , Tian RR , Zheng HY , Han JB ,  Shi P* , Zheng YT*  ,  Independent Birth of a Novel TRIMCyp in Tupaia belangeri with a Divergent Function from Its Paralog TRIM5 , Molecular Biology and Evolution , 2014,  31(11):2985-2997

9.     Wu T #, Zhang ZG #  , Liu B , Hou DZ , Liang Y , Zhang J*,  Shi P*,Gut microbiota dysbiosis and bacterial community assembly associated withcholesterol gallstones in large-scale study , BMC Genomics , 2013 , 14:669

10. Zhang ZG #* , Zhai HQ#, Geng JW# , Yu R , Ren HQ, Fan H*, Shi P*,Large scale survey of gut microbiota associated with MHE Via 16S rRNA-based pyrosequen , American Journal of Gastroenterology ,  2013, 108(10):1601-1611

11. Gao TX#  , Li N , Zhang YP , Shi P*,The complete mitochondrial genome of Japanese sandeel Ammodytes personatus (Perciformes ,  Ammodytidae): Rare structure in control region compared , Mitochondrial DNA , 2013,24(4):320-322

12.  Liu Z#, Wang W#, Zhang TZ# , Li GH , He K , Huang JF , Jiang XL , Murphy RW , Shi P *,Repeated functional convergent effects of NaV1.7 on acid insensitivity in hibernating mammals , Proceedings of the Royal Society B:Biological Sciences ,  2013 , 281(1776), e20132950

13.  Hu LL# , Shi P*,Smallest bitter taste receptor (T2Rs) gene repertoire in carnivores , Zoological Research,2013, 34(3):75-81 

14. Qiu Q#, Zhang GJ#, Ma T#, Qian WB#, Wang JY#, Ye ZQ#, Cao CC, Hu QJ, Kim J, Larkin DM, Auvil L, Capitanu B, Ma J, Lewin HA, Qian XJ, Lang YS, Zhou R, Wang LZ, Wang K, Xia JQ, Liao SG, Pan SK, Lu X, Hou HL, Wang Y, Zang XT, Yin Y, Ma H, Zhang J, Wang ZF, Zhang YM, Zhang DW, Yonezawa T, Hasegawa M, Zhong Y, Liu WB, Zhang Y, Huang ZY, Zhang SX, Long RJ, Yang HM, Wang J, Lenstra JA, Cooper DN, Wu Y, Wang J*, Shi P*, Wang J*, Liu JQ*,  The yak genome and adaptation to life at high altitude , Nature Genetics ,   2012 , 44(8) ,  946-949 

15. Liu Z# , Li GH , Huang JF , Murphy RW ,Shi P*,Hearing Aid for Vertebrates via Multiple Episodic Adaptive Events on Prestin Genes , Molecular Biology and Evolution ,   2012, 29(9) : 2187-2197

16. Liu Z#, Li  S#, Wang W, Xu D , Murphy RW, Shi P*, Parallel Evolution of KCNQ4 in Echolocating Bats , PLoS One ,  2011, 6(10) , e26618 

17. Zhang ZG#, Ye  ZQ# , Yu  L*, Shi P*, Phylogenomic reconstruction of lactic acid bacteria: an update , BMC Evolutionary Biology ,   2011 ,11(1) ,  1 

18. Yang H #, Shi P*,Molecular and evolutionary analyses of formyl peptide receptors suggest the absence of VNO-specific FPRs in primates , Journal of Genetics and Genomics , 2010, 37(12):771-778

19. Wang GD#  ,  Shi P* ,Zhu ZH , Zhang YP* ,More Functional V1R Genes Occur in Nest-Living and Nocturnal Terricolous Mammals , Genome Biology and Evolution , 2010 ,2 : 277-283  

20.  Li J# , Yang H , Li JR , Li HP , Ning T , Pan   XR , Shi P * , Zhang YP* , Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication , Heredity ,2010,  105(3):274-81 

21. Wang GD# ,Zhu ZH#, Shi P*, Zhang YP*, Comparative genomic analysisreveals more functional nasal chemoreceptors in nocturnal mammals than in diurnal mammals, Chinese Science Bulletin , 2010,55(34):3901-3910

22. Li Y#, Liu Z#, Shi P, Zhang JZ*, The hearing gene Prestin unites echolocating bats and whales, Current Biology, 2010, 20(2):55-56

23. Shen YY# , Shi P *, Sun YB, Zhang YP* ,Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability , Genome Research ,  2009 , 19(10) : 1760-1765  

24. Smadja C#*, Shi P, Butlin RK, Robertson HM, Large Gene Family Expansions and Adaptive Evolution for Odorant and Gustatory Receptors in the Pea Aphid, Acyrthosiphon pisum, Molecular Biology and Evolution, 2009, 26(9): 2073-2086

25. Shi P#, Zhang JZ*, Comparative genomic analysis identifies an evolutionary shift of vomeronasal receptor gene repertoires in the vertebrate transition from water to land , Genome Research, 2007, 17(2): 166-174

26. Grus WE#, Shi P, Zhang JZ*, Largest vertebrate vomeronasal type 1 receptor gene repertoire in the semiaquatic platypus, Molecular Biology and Evolution, 2007, 24(10): 2153-2157

27. Bakewell MA#, Shi P, Zhang JZ*, More genes underwent positive selection in chimpanzee evolution than in human evolution, Proceedings of the National Academy of Sciences of the United States of America, 2007,104:7489-7494

28. Li G#, Shi P, Wang YQ*, Evolutionary dynamics of the ABCA chromosome 17q24 cluster genes in vertebrates, Genomics, 2007, 89(3): 385-391

29. Shi P#, Bakewell MA#, Zhang JZ*, Did brain-specific genes evolve faster in humans than in chimpanzees? Trends in Genetics, 2006, 22(11): 608-613Shi P#, Yu L#, Fu YX, Huang JF, Zhang KQ, Zhang YP*, Evolutionary implications of avian infectious Bronchitis Virus (AIBV) analysis, Cell Research, 2006, 16(3): 323-327

30. Shi P#, Zhang JZ*, Contrasting modes of evolution between vertebrate sweet/umami receptor genes and bitter receptor genes, Molecular Biology and Evolution, 2006, 23(2): 292-300

31. Yang H#, Shi P#, Zhang YP*, Zhang JZ*, Composition and evolution of the V2r vorneronasal receptor gene repertoire in mice and rats, Genomics, 2005, 86(3):306-315

32. Shi P#, Bielawski JP, Yang H, Zhang YP*, Adaptive diversification of vomeronasal receptor 1 genes in rodents, Journal of Molecular Evolution, 2005, 60(5):566-576.

33. Grus WE#, Shi P#, Zhang YP, Zhang JZ*, Dramatic variation of the vomeronasal pheromone receptor gene repertoire among five orders of placental and marsupial mammals, Proceedings of the National Academy of Sciences of the United States of America, 2005, 102(16):5767-5772

34. Li Y#, Ye C#, Shi P, Zou XJ, Xiao R, Gong YY, Zhang YP*, Independent origin of the growth hormone gene family in New World monkeys and Old World monkeys/hominoids, Journal of Molecular Endocrinology, 2005, 35(2):399-409

35. Ye C#, Li Y#, Shi P, ZhangYP*, Molecular evolution of growth hormone gene family in old world monkeys and hominoids, Gene, 2005, 350(2): 183-192

36. Gu Z#, Zhang Y#, Shi P, Zhang YP, Zhu D*, Li H, Comparison of avian myostatin genes, Animal Genetics, 2004, 35(6):470-472

37.  Shi P#, Zhang JZ, Yang H, Zhang YP*, Adaptive diversification of bitter taste receptor genes in mammalian evolution , Molecular Biology and Evolution, 2003, 20(5): 805-814

38. Chen DY#*, Wen DC#, Zhang YP#, Sun QY, Han ZM, Liu ZH, Shi P, Li JS, Xiangyu JG, Lian L ,Kou ZH, Wu YQ, Chen YC ,Wang PY , Zhang HM, In terspecies implantation and mitochondria fate of panda-rabbit cloned embryos, Biology of Reproduction, 2002, 67(2): 637-642

39. Shi P#, Lu XM, Luo HR, Xiang-Yu JG, Zhang YP*, Melanocortin-1 receptor gene variants in four Chinese ethnic populations, Cell Research, 2001, 11(1): 81-84

40. Ding B#, Shi P, Xiangyu JG, Zhang YP*, Chen DY, Sun QY, Li GP,GP Wang MK, Liu YL, Kang L, Han ZM, Song XF, Li JS, Chen YC, Microsatellite DNA analysis proves nucleus of interspecies reconstructed blastocyst coming from that of donor giant panda, Chinese Science Bulletin, 2000, 45(20) : 1883-1885

 

Invited book chapter:

1.Behrens M , Stahler F , Shi P , Bufe B and Meyerhof W. 2009. Taste: Topics in Chemical Biology. Wiley Encyclopedia of Chemical Biology. Tadhg P. Begley (Eds.), Wiley online library. 

2. Shi P and Zhang J. 2009. Extraordinary diversity of chemosensory receptor gene repertoires among vertebrates. Chemosensory Systems in Mammals , Fishes , and Insects. Meyerhof, Wolfgang, Korsching, Sigrun (Eds.), Springer.

 

  研究团队

Research Assistants:

Dr. Hui Yang (from Emory University , USA)

Dr. Junjun Hao (from Shanghai University , China)

Dr. Jie Luo (from University of Chinese Academy of Sciences)

Technicians:

Xin Zhou

Mengwen Li

Xinran Li

Finance Assistant:

Hongjuan Dai

PhD students:

Zhizhong Zheng , Feiyan Qi, Tao Zhang, Lei Zhu , Qi Liu, Jie Chen, Peng Chen, Yuanting Guo, Menglong Lei

Master students:

Wanzhi Cai, Jing Bai, Rong Hua, Lu Yang, Le Tao, Xioaqing Yao, Yanjie Lv, Qingyang Hua, Yuanshuo Ma, Xuefeng Li

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