遗传资源与进化国家重点实验室2013年年报.pdf

目录 // CONTENTS 主任致辞 1 Director’s Report 2 实验室概况 Laboratory Overview 3 课题组年度工作进展 Annual Progress by Groups 5 支撑平台 Infrastructure 39 重要基金项目 Key Projects and Fundings 45 发表论文 Publications 49 获 奖 Awards 55 研究生优秀论文奖 Outstanding Paper Awards for Graduate Students 56 大事记 Major Events 57 开放课题 Open Projects 60 专家学术报告 Invited Lectures 61 人员名单 64 Personnel 66 遗传资源与进化国家重点实验室 2013 年 度 报 告 主任致辞 2013 年，遗传资源与进化国家重点实验室积极学习贯彻党的十八大精神和中科院“创新 2020”跨越发展 体系精神，在各级主管部门的领导与支持下，面向国家和地区的战略需求和学科领域的国际前沿，凝心聚力， 全面扎实推进各方面工作，在任务承担、创新研究、人才队伍建设、开放交流等各方面工作均取得了可喜进展。 2013 年，实验室在承担重大科技任务方面成绩显著，主持的 1 个 973 项目开始启动，新争取其它科研项 目 73 项。年度到位科研经费达到 6723 万元，增幅 38%。另有 64 项课题圆满结题。目前在研省部级项目 170 项， 国际合作项目 8 项、横向协作项目 24 项。在致力于基础研究的同时，实验室也积极推进科技成果的应用转化， 例如与企业合作挖掘动植物重要经济性状功能基因。 2013 年，在科研项目的支持下，实验室围绕三大研究方向，在遗传资源收集保护、家养动物的起源与驯化、 动植物重要经济性状功能基因挖掘、动物适应性进化机制等方面取得了显著进展。发表论文 120 篇，其中 SCI 收录 97 篇，EI 收录 1 篇，以第一作者或通讯作者（含并列）发表 SCI 和 EI 收录论文 79 篇，包括发表在 Nat Biotechnol, Science，Ecol Lett, Am J Psychiatry，Nat Commun，Mol Biol Evol 等 IF5-year>9 的国际著名期 刊论文 12 篇，授权专利 4 项。相关成果也获得了云南省自然科学特等奖 1 项，1 等奖 2 项。 2013 年，实验室“培养 + 引进”的人才队伍建设模式也取得了明显成效。实验室荣获国家基金委创新群 体 1 个， 1 人入选国家“万人计划”（王文），2 人获得“国家杰出青年科学基金”资助（施鹏、王瑞武）， 1 人获得国家基金委优秀青年科学基金支持（孔庆鹏），另有 2 名青年博士入选“中科院青年创新促进会会员” （吴东东、彭旻晟）。新引进“青年千人计划”1 名（焦保卫），成立“发育的印记调控与进化研究组”；室 内培养研究员 1 名（王瑞武），成立“实验与理论生态学研究组”，实验室研究组扩大至 17 个。新引进青年 博士 10 名。研究生培养方面，为国家输送硕士 12 名，博士 15 名，博士后 3 名，多名研究生获得中科院各类 奖学金；成功举办 2013 年“进化生物学”暑期班， 吸引更多有志青年加入实验室。 在对外学术交流与合作共享方面，2013 年，实验室通过组织和参加高水平的国际学术会议以及与世界各 地的知名学者互访开展短期学术交流。10 月，参与承办了“第五届国际生命条形码大会”，期间达成多项合 作协议。此外，外出参加国内外学术会议 80 余人次，其中特邀报告 13 人次；邀请国内外专家来室讲学 29 人次。 另外，实验室继续本着“取长补短、强强联合”的宗旨，积极发挥实验室在国内相关研究领域的辐射和带动作 用，对外设立开放课题 13 项。在国际合作方面，除继续推动国际条形码中国计划外、还开辟了与非洲、东南 亚一些单位的合作研究计划。 旧岁已展千重锦，新年再进百尺竿！ 2014 年，面对百舸争流的新形势，实验室将继续遵循“开放、流动、 联合、竞争”的运行机制，在学术委员会指导下，发挥自己的学科与资源优势，凝练目标，深化战略规划，强 化团队交叉协作，提高自主创新和承担重大项目的能力，力争取得更多系统性、原创性成果，为我国遗传资源 的进化与发育研究领域做出重要贡献。 实验室的发展离不开各级领导及各位朋友的关心与帮助，在此，我谨代表实验室向大家致以最诚挚的感谢， 并希望能得到大家一如既往的关心和支持！ 张亚平 1 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Director's Report The “State Key Laboratory of Genetic Resources and Evolution” has made considerable progress in 2013, with regards to grant awards, scientific research output, talent recruitment and scientific exchange. Grant awards. –One key project from the National Basic Research Program (‘973’ grants) hosted by the key lab was started, other 73 new grants were awarded. In 2013, the grant funds to the key lab summed 67.23 million RMB, an increase of 38% over 2012. Sixty four grants were successfully completed. Currently the key lab holds 170 provincial and ministerial projects, 8 international cooperation projects and 24 horizontal collaboration projects. In addition to basic research, the key lab promoted applied researches including the mining of important phenotypic genes of economical plants and animals in cooperation with companies. Publications and Awards. – The key lab made systematic progress in genetic resources collection, adaptive evolution, the mining of important phenotypic genes of economical plants and animals , and mechanisms of animal adaptive evolution in 2013. The key lab published in total 96 papers in SCI journals, 1 paper in EI journals, including 12 papers in top journals such as Nat Biotechnol, Science, Ecol Lett, Am J Psychiatry, Nat Commun, Mol Biol Evol (IF5year>9). The key lab was also granted four patents. Relevant outcomes won one Special award and two First prizes for Natural Science of Yunnan province. Talent recruitment. - In 2013, 4 groups of the lab won the “Innovation Team Grant” from NSFC. Prof. Wen Wang was selected into the “National High-Level Talent Special Support Plan”, Drs. Peng Shi and Ruiwu Wang were awarded the Distinguished Young Scholar Grant of the NSFC., Dr. Qingpeng Kong was awarded the Excellent Young Scholar Grant of the NSFC, Drs. Dongdong Wu and Minsheng Peng were selected as members of the " Youth Innovation Promotion Association,CAS ". Dr. Baowei Jiao, who was enrolled by the “National Youth Thousand Talents Program”, joined the lab and established his group on "Imprinting in Development and Evolution ". Dr. Ruiwu Wang established his group on "Experimental and Theoretical Ecology " in the lab. The groups of the key lab increased to 17. Ten young doctors were also recruited. Fifteen Ph.D. and 12 M.Sc. students graduated and 3 postdoctoral researchers completed their work in the key lab in 2013. Several students were awarded various types of scholarships from CAS. The Summer School on "Evolutionary Biology" was successfully held in August, which attracted 47 young students interested in the key lab. Scientific exchange. –As one of the organizers, the key lab hosted the "Fifth International Barcode of Life Conference" in Kunming in October, and established some cooperation agreements during the conference. Members of the key lab attended scientific meetings both at home and abroad for more than 80 times, including 13 times as invited speakers. Twenty- nine scholars were invited to the lab and gave lectures this year. In 2013, the key lab funded 13 “open projects”. For international cooperation, the key lab continued to promote the “International Barcode of Life Project (iBOL) in China”, and established new cooperative projects with some institutes in Africa and Southeast Asia. In the future, the key lab hopes to make more systematic and original achievements in the field of adaptive evolution as well as collection of genetic resources, and exploitation of domesticated animal resources. The goal of the key lab is to make major contribution on the researches on genetic resources and evolution in China, and to promote the key lab to become an internationally renowned research center in the field. Finally, I would like to thank all organizations and friends who have provided supports and assistance to our lab and hope to have your continued help in the future! Yaping Zhang 2 遗传资源与进化国家重点实验室 2013 年 度 报 告 实验室概况 Laboratory Overview 一、第二届学术委员会 (The Second Academic Committee) 主 任 (Director): 朱作言 院 士，北京大学 Academician Zuoyan Zhu, Peking University 副主任 (Deputy Director): 王 文 研究员，中国科学院昆明动物研究所 Prof. Wen Wang, Kunming Institute of Zoology, Chinese Academy of Sciences 委 员 （Members，按姓氏笔画排序 ）： 文建凡 研究员，中国科学院昆明动物研究所 Prof. Jianfan Wen, Kunming Institute of Zoology, Chinese Academy of Sciences 朱有勇 院 士，云南农业大学 Academician Youyong Zhu, Yunnan Agricultural University 李德铢 研究员，中国科学院昆明植物研究所 Prof. Dezhu Li, Kunming Institute of Botany, Chinese Academy of Sciences 张亚平 院 士，中国科学院 Academician Yaping Zhang, Kunming Institute of Zoology, Chinese Academy of Sciences 张克勤 教 授，云南大学 Prof. Keqin Zhang, Yunnan University 汪小全 研究员，中国科学院植物研究所 Prof. Xiaoquan Wang, Institute of Botany, Chinese Academy of Sciences 金 力 院 士，复旦大学 Academician Li Jin, Fudan University 康 乐 院 士，中国科学院动物研究所 Academician Le Kang, Institute of Zoology, Chinese Academy of Sciences 宿 兵 研究员，中国科学院昆明动物研究所 Prof. Bing Su, Kunming Institute of Zoology, Chinese Academy of Sciences 黄路生 院 士，江西农业大学 Academician Lusheng Huang, Jiangxi Agricultural University 黄京飞 研究员，中国科学院昆明动物研究所 Prof. Jingfei Huang, Kunming Institute of Zoology, Chinese Academy of Sciences 二、现任实验室领导 (Leaders of the Lab.) 主任 (Director): 张亚平 院 士 Academician Yaping Zhang 副主任 (Deputy Directors): 文建凡 研究员 Prof. Jianfan Wen 毛炳宇 研究员 Prof. Bingyu Mao 3 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT 三、研究方向 （Research Direction） 遗传资源多样性的演化与保护 Evolution and conservation of the diverse genetic resources 基因与基因组的进化 Evolution of genes and genomes 遗传发育与进化 Genetics, development and evolution 四、研究团队与组织结构 （Groups and Organization ） 实验室有研究组 17 个，支撑部门 3 个，现有固定人员 110 人，其中博士 61 人，平均年龄 35 岁。拥有中 科院院士 1 人，国家杰出青年基金获得者 5 人，中科院“百人计划”7 人，云南省“高端人才”3 人。 There are 17 research groups and 3 facility centers in the lab. Among the 110 staff members, 61 of them hold Ph.D. degrees. The average age of the team is 35 years old. The research team includes one academician of CAS, 5 winners of the "National Science Fund for Distinguished Young Scholars", 7 holders of the "Hundred Talents Program"of CAS and 3 holders of "Top talent" project of Yunnan Province. 4 遗传资源与进化国家重点实验室 2013 年 度 报 告 系统进化与生物地理学 杨君兴，博士，研究员，博士生导师 , 昆明分院党组副书记、副院长。研 究方向包括：生物多样的考察监测、系统分类、系统发育与生物地理学；珍稀特 有物种的生态学研究和保育；湿地生态系统的恢复研究。本年度共有在研课题 31 项，其中新申请批准的项目 12 项。出版专著 1 章；发表 SCI 论文 11 篇，获 授权国家发明专利 4 项。 重要成果（Highlights） 论著（Publications） 1.Shu-Sen Shu, Wan-Sheng Jiang, Tony Whitten, Jun-Xing Yang*, Xiao-Yong Chen*. 2013. Drought and China’s Cave Species, Science, 340: 272 2.Mo Wang, Jun-Xing Yang*, Xiao-Yong Chen*. 2013. Molecular phylogeny and biogeography of Percocypris (Cyprinidae, Teleostei), PloS One, 8(6): e61827 3.Jiang W. S., Zhao Y. P., Wang W. Y., Yang J.X., Chen X. Y.*. 2013. Lengthweight relationship and biological data of a threatened fish, Ptychobarbus chungtienensis (Tsao, 1964) in Bita Lake of Shangri-La, Yunnan, China, Journal of Applied Ichthyology, 28(4): 1-4 4.Rui Min, Jun-Xing Yang*, XiaoYo n g C h e n * . 2 0 1 3 . H o m a t u l a disparizona, a new species of loach from the Red River drainage in China ( Te l e o s t e i : N e m a c h e i l i d a e ) f r o m China, Ichthyological Exploration of Freshwaters , 23 (4): 351-355. 1. 干旱对洞穴生物影响 2009 年起，我国西南地区遭受到了连续多年的干旱，而干旱发生地区正是喀 斯特洞穴分布最密集的地区。长期的干旱导致洞穴补水减少，加之干旱区群众存 在大量抽取地下水的迫切需求，将导致洞穴地下河水位迅速下降，甚至干涸；进 而使原有生境不复存在；依赖其生存的洞穴生物也将面临大量死亡的威胁。更加 严重的是，上述威胁并不仅限于某一个洞穴，而是整个干旱地区的多数洞穴都面 临同样的威胁。由此可见，目前发生的连续大规模干旱对我国西南喀斯特地区洞 穴生物区系的破坏性将不可估量。希望全世界的科学工作者共同关注中国西南地 区持续干旱对洞穴生物的影响，共同探讨应对干旱和洞穴生物保护之间的难题。 2. 鲈鲤属（Percocypris）的系统发育与生物地理学研究 以线粒体基因和核基因作为分子标记，首次对鲈鲤属的系统发育关系进行研 究。该属的单系性得到证实，其姐妹群为裂腹鱼属，属内各类群之间的系统发育 关系得以阐明，填补了该类群的系统发育研究空白。另外，通过多变量形态度量 学分析和骨骼特征分析对鲈鲤属鱼类各主要支系的形态特征进行了比较。结合分 子系统学和形态学分析结果，认为鲈鲤属的分类体系应该进行重新修订，应包括 六个种（之前正式命名的有 2 种 3 亚种）。并且，基于新的分类框架，该属每个 物种的保护等级应被重新评估。通过分化时间估计和祖先水系推断，对鲈鲤属的 起源和演化提出如下假说：鲈鲤属起源于中新世的一个青藏高原东部的古水系。 由青藏高原隆起造成的水系格局变化的隔离作用可能在其物种分化过程中起着重 5. 陈小勇 , 王剑 伟 , 杨 剑 , 高欣 . 2013. 第 8 章 鱼 类 监 测 . 169-199. 见 徐海根，孙红英，陈小勇，曹铭昌， 崔鹏，房丽君 . 生物物种资源监测概论 . 科学出版社 . 304pp. 6. 杨君兴 , 潘晓赋 , 李再云 , 陈小勇 . 201210111579.X. 一种暗色唇鱼的人工 繁殖方法 (2013.10.12 授权） 7. 王晓爱，杨君兴，潘晓赋，陈小勇 . ZL 2012 1 0277940.6. 一种鱇浪白鱼 鳍细胞系的构建方法 （2013.5.29 授权） 要作用。此外，探讨了该属鱼类不同生态型的形态分歧与其环境的相关性。 3. 重要湿地物种资源监测 中甸叶须鱼 Ptychobarbus chungtienensis 为中国云南高原特有的裂腹鱼类。 该种被《中国物种红色名录》认定为濒危（EN）物种。自 2008 年起，对中甸地 区原中甸叶须鱼的分布区域进行了水生生物监测。监测结果表明，中甸叶须鱼现 在仅在碧塔海中还残存在一定的种群，物种地位更加濒危。通过多年的监测和数 据的收集，首次明确了中甸叶须鱼的体长与体重关系、年龄与生长曲线、繁殖时间、 周期等基础生物学和生态学资料。 监测期间，针对高原湿地的特殊性，研究人员综合采用了各种不同的方法， 并对各种方法的有效性进行了探讨，制定了高原湿地水生生物监测规范，该规范 将由环保部发布。并参编专著《生物物种资源监测概论》。 5 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Phylogenetics and Biogeography Dr. Junxing Yang , Professor, Deputy Secretary of the Party Committee and Vice Director of the Kunming Branch, Chinese Academy of Science. The research team is mainly interested in biodiversity monitoring survey, fauna taxonomic, phylogenetic and biogeographic; ecology and conservation research to rare and native species; especially focuses on the restoration of wetland ecosystem and application. In 2013, total 31 research programs have been implementing with 12 programs newly applied. Published 1 monograph and 11 SCI papers. 4 national invention patent licensing. Email: yangjx@mail.kiz.ac.cn 1. Drought and China’s Cave Species The impact of severe drought in southwestern China since 2009 appears to be an example of how climate change and poor environmental management can combine to create a biodiversity disaster. The impact on cave biodiversity has been overlooked. Water resources in caves will decrease during drought seasons, especially when people are searching for and exstracting water. This will cause the endemic aquatic biodiversity to decline dramatically, or even disappear. This part of China and other karst regions in Asia and beyond have exceptionally range-restricted and acutely poorly known faunas, which are under threat from a range of climate change and human actions. We do not want to see a newly revealed global biodiversity hotspot lost before it is known. 2. Molecular phylogeny and biogeography of Percocypris The molecular phylogenetic relationships of Percocypris were investigated based on three mitochondrial genes (16S; COI; Cyt b) and one nuclear marker (Rag2). The results show that Percocypris is a strongly supported monophyletic group. Combined with analyses of morphological characters, it suggests that Percocypris needs to be reclassified to six species. Based on the results of the estimation of divergence times and ancestral drainages, we hypothesize that Percocypris likely originated in the early Miocene from a paleo-connected drainage system containing the contemporary main drainages of the Southeastern Tibetan Plateau. This study suggests that vicariance has played an important role in the speciation of the genus. Furthermore, external morphological characters and an internal trait appear to be correlated with different habitats in rivers and the lake. 3. Monitoring of key species Ptychobarbus chungtienensis is a schizothoracin fish endemic to high plateau region of Yunnan, and was evaluated as an endangered species by China red data book of endangered animals. Since 2008, a biological monitoring has been carried on in the distribution area of Ptychobarbus chungtienensis. The result shows there is a relic population left only in Lake Bita. Based on years of monitoring and data collected, some basic biological information were firstly clarified, such as relationship between body length and body weight, age and grow function, breeding season etc. During monitoring, different methods were applied and tested in practice considering specialty of wetland in high plateau, and based on which, a Technical Guidelines for Species Monitoring (Fish Resources) was prepared and will be released by the national ministry of environment protection, and a monograph on biological monitoring published. 6 员工简介（Lab Staff） 工作人员（Staff） 陈小勇 副研究员 Chen Xiaoyong, Associate Professor 李再云 高级工程师 Li Zaiyun, Associate Professor 贾 黎 高级实验师 Jia Li, Senior Technician 郑兰平 副研究员 Zheng Lanping, Associate Professor 潘晓赋 副研究员 Pan Xiaofu， Associate Professor 刘 倩 秘书 Liu Qian, Secretary 余国华 助理研究员 Yu Guohua, Assistant Professor 杜丽娜 助理研究员 Du Lina, Assistant Professor 蒋万胜 助理研究员 Jiang Wansheng, Assistant Professor 舒树森 助理研究员 Shu Shusen, Assistant Professor 闵 锐 助理研究员 Min Rui , Assistant Professor 刘淑伟 助理研究员 Liu Shuwei , Assistant Professor 彭 云 研究实习员 Peng Yun, Research assistant 研究生（Graduate Students） 王 茉 Wang Mo 2008 王晓爱 Wang Xiaoai 2009 赵亚鹏 Zhao Yapeng 2010 赵婷怡 Zhao Tingyi 2011 杨坤凤 Yang Kunfeng 2012 程 城 Cheng Cheng 2012 秦 涛 Qin Tao 2012 张源伟 Zhang YuanWei 2013 遗传资源与进化国家重点实验室 2013 年 度 报 告 兽类生态与进化 蒋学龙，博士，研究员。博士，研究员。立足于东喜马拉雅 - 横断山地区开展 哺乳动物生态与进化研究，主要研究内容包括哺乳动物分类、系统演化与生物地理， 灵长类动物的生态行为，兽类资源与保护，以揭示横断山地区哺乳动物多样性的形 成机制及在特殊生态条件下的适应性进化与保护。近年来，主要以东喜马拉雅 - 横 断山地区特有与常见小型哺乳动物、灵长类及偶蹄类动物为研究对象，重点探讨横 断山区哺乳动物多样性形成、西黑冠长臂猿的生态行为与适应性、麝类及其他偶蹄 类动物资源与保护现状及其致危因素分析。 重要成果（Highlights） 论著（Publications） 1.Wan T, He K, Jiang XL*. 2013. Multilocus phylogeny and cryptic diversity in Asian shrewlike moles (Uropsilus, Talpidae): implications for taxonomy and conservation. BMC Evolutionary Biology, 13:232. 2.Li XY, Buzzard P, Chen YC, Jiang XL*, 2013. Patterns of Livestock Predation by Carnivores: Human–Wildlife Conflict in Northwest Yunnan, China. Environmental Management, 52:1334– 1340. 3.Huang B, Guan ZH, Ni QY, Orkin J, Fan PF, Jiang XL*. 2013. Observation of intra- and extragroup copulation and reproductive characters 1. 鼩鼹亚科系统发育研究新进展 现生 鼩 鼹（shrew-like moles）栖息在中国西南的横断山系及周边地 区，是鼹科中最原始的一支。本研究第一次通过 分子系统发育方法解决了 鼩 鼹亚科现生类群长期遗留的问题。构建了采自不同地区的 鼩 鼹样 品的系 统发育关系，并基于化石和分子校正点估算了 物种分歧时间。结果显示，现生鼩鼹的物种分 化 时 间（6.32-0.82Ma） 与 中 新 世 以 来 的 气 候变化和造山运动有强烈的对应关系 , 而目前 主要的“pre-Pleistocene speciation”假说和 “Pleistocene speciation pump”假说都不能 较好地解释这一物种分化模式。与基因树的结 果基本一致，基于溯祖理论模型（Coalescent model）构建的物种树认为目前认可的 5 个物 种代表了 10 个进化上独立的支系，且大都分布狭域，提示该类群的生物多样 性被严重地低估并且保护等级亟待提高。 2. 白马雪山保护区人与野生动物冲突研究 在中国，特别是偏远山区，由于人口增长、耕种和放牧面积扩张、猎物 in free ranging groups of western black crested gibbon (Nomascus concolor jingdongensis). 种类和数量减少，人与野生动物冲突也在增加，不仅给当地居民带来人身和 Integrative Zoology, 8:427-440. 财产损失，也给保护区的管理工作带来困难。为了掌握白马雪山自然保护区 4.Guan ZH, Huang B, Ning WH, Ni QY, 周边居民与食肉动物的冲突及对野生动物保护的态度，在该保护区北段系统 Sun GZ, Jiang XL*. 2013. Significance of grooming behavior in two polygynous groups of western black crested gibbons: 收集了野生动物危害的类型、时空格局、造成的经济损失、损失赔付以及受 implications for understanding social relationships among immigrant and resident group members. American Journal of Primatology,75:1165–1173. 5.Yuan SL, Jiang XL, Li ZJ, He K, Harada M, Oshida1 T, Lin Lk, 2013. A Mitochondrial Phylogeny and Biogeographical Scenario for Asiatic Water Shrews of the Genus Chimarrogale: Implications for Taxonomy and Low-Latitude Migration Routes. PLoS ONE, 8(10): e77156. 损牧民对野生动物保护的态度等数据。研究结果显示：狼（Canis lupus）是 该保护区奔子栏片区为最主要肇事动物；犏牛为主要的危害对象 ( 占所有损 失的 40.3%)；年均牲畜损失数量占牲畜存栏总量的 2.1%，约占牧民户均年 收入的 17%。然而保护区周边居民因要从保护区采集松茸获到更大益处，而 对保护区的存在持积极态度。因此，适度、可持续、有规划的利用保护区内 林下非木材林产产品资源，有利于保护区与社区协调和共管，缓解保护区周 边居民对保护区和肇事动物的矛盾。 3. 红外照相技术在野生动物种群生态研究中的应用 采用红外相机技术和粪堆计数法研究了 4 种同域分布高山林栖偶蹄类动物的相对丰富度 6. 何锴，王文智，李权，罗培鹏，孙悦华，蒋 学龙 *，2013. DNA 条形码技术在小型兽类鉴 和生境利用特征。二者之间具有不随样线、物 定中的探索：以甘肃莲花山为例。生物多样性 , 21:19-205 动物监测和管理中具有应用价值，可快速、准 种而改变的显著相关关系，说明拍摄率在野生 确的评估某个地区的物种丰富度或比较不同生 境、地区的物种丰富度。 7 图 1. 红外感应相机拍摄的高 山麝照片 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Mammal Ecology and Evolution Dr. Jiang Xuelong, Professor, The laboratory is mainly interested in specimen-based investigations of biodiversity inventory, taxonomy and systematics, phylogenetics and phylogeography of small mammals with a special focus in the Henduanshan region, and also in endangered species-based investigations of ecology, behavior and conservation of black crested gibbon, musk deer and other large mammals. E-mail: jiangxl@mail.kiz.ac.cn 1. Multilocus phylogeny reveal cryptic diversity in shrew like moles (Uropsilus, Talpidae, Mammalia) The genus Uropsilus comprises the most primitive living talpids (Talpidae, Mammalia). The taxonomy, phylogeny and evolutionary histories of these animals were poorly understood. To provide insight into the systematics of this group, we estimated a multi-locus phylogeny, including fine taxon sampling throughout their distribution ranges. We sequenced ~ 6 kbp sequences of 10 genes, recovered 10 distinct lineages and 8 putative species within the 3 recognized species. Our results highlight the existence of cryptic and hence potentially new species. Taxonomic revision based on comprehensive morphological and morphometric approaches is war r anted. The conservation status of Uropsilus spp. should also be re-evaluated as most of the species/potential species Fig. 1.Nuclear gene network trees and distribution of each have very limited distribution. 2.Copulation and reproductive characters in free ranging groups of western black crested gibbon (Nomascus concolor jingdongensis) Based on population monitoring over 7 years and direct observation for 26 months of the study groups in Wuliang Mountain, central Yunnan, we describe for the first time the copulation behavior and breeding pattern of free-ranging western black crested gibbons. We observed 2 intra-group copulations and 5 extra-group copulations. Copulations were initiated when a female gave a ‘solicitation’ gesture. When a male made any mating attempt, the female might refuse it. These results demonstrate direct female mate choice. The average breeding interval is 3.5 years, and infant independents at approximately 2.5 years. Both male and female gibbons dispersed from their natal groups and sometimes replaced paired adults in other groups. Our result indicate a flexible social organization and complex mating system in this species. . 8 员工简介（Lab Staff） 工作人员（Staff） 饶定齐 副研究员 Rao Dingqi, Associate Professor 黄 蓓 助理研究员 Huang Bei, Assistant Professor 何 锴 助理研究员 He Kai, Assistant Professor 张栋儒 助理研究员 Zhang Dongru, Assistant Professor 林 苏 助理实验师 Lin Su, Assistant Engineer 李学友 助理研究员 Li Xueyou, Assistant Professor 宁文鹤 研究实习员 Ning Wenhe, Research Assistant 研究生（Graduate Students） 胡遒清 Hu Naiqing, 2009 万 韬 刘 熙 张 斌 陈中正 戴 然 李 权 赵启龙 黄 程 Wan Tao, 2010 Liu Xi, 2011 Zhang Bin, 2012 Chen Zhongzheng, 2012 Dai Ran, 2012 Li Quan, 2012 Zhao Qilong, 2012 Huang Cheng, 2013 遗传资源与进化国家重点实验室 2013 年 度 报 告 鸟类学 杨晓君，研究员，从事中国西南地区鸟类分类区系、系统演化、生物 地理、群落生态学及珍稀鸟类的行为生态学和保护生物学研究。近年来 更关注青藏高原旗舰物种 -- 黑颈鹤的保护及鸟类系统演化研究。目前 已出版执行主编和副主编专著 8 部，发表论文 100 余篇。 重要成果（Highlights） 论著（Publications） 1. Dong F, Li SH, Zou FS, Lei FM, Liang W, Yang JX, Yang XJ*. 2013. Molecular systematics and plumage coloration evolution of an enigmatic babbler (Pomatorhinus ruficollis) in East Asia. Molecular Phylogenetics and Evolution. DOI: 10.1016/ j.ympev.2013.09.008. 2. 舒树森，陈非洲，杨君兴， 杨晓君 * ，陈小勇 *. 2013. 普 达措国家公园淡水甲壳动物多 样性及区系的初步分 . 动物学 研究 , 34(3): 204−208. 1. 棕颈钩嘴鹛的分子系统学研究 棕颈钩嘴鹛隶属于雀形目画眉科，是东洋区特有鸟类。具有复杂的分类历史， 主要体现在其与灰头钩嘴鹛的分类关系及其台湾亚种的分类地位上。为探讨棕颈钩 嘴鹛的分类地位，本研究共采集或收集了所有 15 个中的 14 个亚种的两个线粒体基 因（总计 2184bp），并对中国分布的 10 个亚种进行了 5 个核基因（总计 2657bp） 的测定。基于线粒体数据集的系统发育分析揭示棕颈钩嘴鹛是并系群，来自灰头钩 嘴鹛的 olivaceus 支系聚合于其内部；传统棕颈钩嘴鹛共分化为 4 个地理支系 , 即 东部支系，台湾支系，中部支系和西部支系。结合棕颈钩嘴鹛与 olivaceus 支系在东 南亚北部存在杂交的现象，建议将这一支系合并进入棕颈钩嘴鹛。基于多核基因的 网络图和物种树分析皆显示台湾亚种独立于大陆所有亚种的支系，而后者内部无显 著分化。这一结果支持近期基于形态分析将台湾亚种提升到种（台湾钩嘴鹛）的分 类处理。研究中揭示了基于形态特征的传统分类学与分子系统学的显著不一致性， 暗示多基因数据在分类学研究中的优势。 3. Wang WJ, McKay, Bailey D.; Dai CY, Zhao N, Zhang RY, Qu YH, Song G, Li SH, Liang W, Yang XJ, Pasquet Eric, Lei FM. 2013. Glacial expansion and diversification of an East Asian montane bird, the green-backed tit (Parus monticolus). Journal of Biogeography, 40 (6):1156-1169. 4. Chu JH, Daniel Wegmann, Yeh CF, Lin RC, Yang XJ, Lei FM, Yao CT, Zou FS, Li SH. 2013 Inferring the geographic mode of speciation by contrasting autosomal and sex-linked genetic diversity. Molecular Biology and Evolution, 30(11):2519-2530. 2. 第二次陆生野生动物资源调查 受云南省林业厅委托开展云南省第二次野生动物资源调查，该工作 2012 年 12 月 31 日得到云南省人民政府办公厅的正式批复，项目汇集了云南全省 8 家从事动物 资源多样性研究的科研院所，并建立了全省统一的资源调查方法和技术规范，目前 已经开展了怒江州、保山市等 5 个州市的调查，项目完成后将有望了解云南省动物 资源的现状及其资源变化情况，为生态文明建设以及制定动物多样性的保护和利用 政策提供科学依据。 9 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Ornithology Yang Xiaojun , Principle Investigator, Kunming Institute of Zoology, Chinese Academy of Sciences. My research interest lies at bird taxonomy and fauna, phylogeny, biogeography, community ecology, as well as behaviour ecology and conservation biology of endangered bird species. Till now, 8 books and more than 100 papers have been published. Email: yangxj@mail.kiz.ac.cn 1. Molecular systematics of the streak-breasted scimitar babbler 员工简介（Lab Staff） The streak-breasted scimitar babbler, Pomatorhinus ruficollis (Passerformes: Timallidae), is a babbler endemic to Oriental Region. This species has long been subject to taxonomic debate, in terms of its relationship with P. schisticeps and the status of the Taiwanese subspecies. To infer the phylogeny of the P. ruficollis, the sequences of two complete mitochondrial genes (2184bp in total) from fourteen of the fifteen known subspecies, and an additional five nuclear genes (2657bp in total) from ten subspecies from China were examined. The mitochondrial phylogeny indicates four major clades (EAST, TAIWAN, CENTRAL and WEST) with large geographical identity in P. ruficollis and paraphyly of the P. ruficollis species complex, with the inclusion of the olivaceus group of congeneric P. schisticeps. Together with their interbreeding in northern Indochina, it was proposed to lump this group into P. ruficollis. Analysis of both multilocus networks and species-tree inference recovered poor phylogenetic structure among mainland subspecies and exclusive groupings of the Taiwanese subspecies, consistent with the recent taxonomic revision of its species status (P. musicus). The analyses also suggest strong incongruence between the morphological-based classification and molecular systematics, implying the strength of multilocus data for taxonomy. 工作人员（Staff） 2. Yunnan second terrestrial wildlife resources survey Commissioned by the Forestry Department of Yunnan Province, the second survey of wildlife resources was formally approved by the Yunnan Provincial People's Government Office on December 31, 2012. This project brings together a collection of eight research institutes on animal resources in Yunnan, and establishes unified resource survey methods and technical specifications. To update, survey work has been launched in five cities (e.g., Baoshan City, Nujiang Prefecture). This project hopes to improve our understanding of the present situation and dynamics of animal resources in Yunnan, and to provide a scientific basis for the construction of ecological civilization and the development of conservation and utilization of animal diversity policy. 10 吴 飞 助理研究员 Fei Wu, Assistant Professor 伍和启 助理研究员 HeQi Wu, Assistant Professor 董 锋 研究实习员 Feng Dong, Research Assistant 岩 道 研究实习员 Dao Yan, Research Assistant 高建云 研究实习员 Jianyun Gao, Research Assistant 研究生（Graduate Students） 董好岩 王荣兴 李欣磊 李 婷 夏 季 卢光义 胡莞钊 HaoYan Dong 2012 RongXing Wang 2011 XinLei Li 2010 Ting Li 2010 Ji Xia 2011 GuangYi Lu 2011 Wanzhao Hu 2013 遗传资源与进化国家重点实验室 2013 年 度 报 告 生态学与环境保护中心 (ECEC) Douglas W. Yu， 博 士， 研 究 员， 博 导。 主 要 关 注 三 个 方 面 的 研 究 内 容： Metabarcoding 技术在快速生物多样性评估中的应用；保护生物学和对热带森林保护 的 方 针、 政 策； 互 利 共 栖 的 演 化。 有 60 余 篇 研 究 成 果 分 别 发 表 于 Nature, Science, PNAS, PLoS Biology, Ecology Letters, Ecological Monographs, Ecology, American Naturalist, Evolution, J. Animal Ecology and Proceedings of the Royal Society of London B. 实验室主页：http://web.mac.com/dougwyu 重要成果（Highlights） 1. 基于高通量条形码进行高效、可靠、可验证的生物多样性监测 论著（Selected Publications） Yinqiu Ji,Louise Ashton, Scott M. Pedley, David P.Edwards,Yong Tang,Akihiro Nakamura, Roger Kitching, Paul M. Dolman, Paul Woodcock, Felicity A. Edwards, Trond H. Larsen, Wayne W. Hsu, Suzan Benedick, Keith C. Hamer, David S. Wilcove, Catharine Bruce, Xiaoyang Wang, Taal Levi, Martin Lott, Brent C. Emerson and Douglas W. Yu 1.Kocher, S., L. Cai, Yang, W., Tan, H., Yi, S.V., Yang, X.Y., Hoekstra, H., Zhang, G.J., H. Pierce, N. E., Yu, D.W. (2013) The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes. Genome Biology. doi:10.1186/gb-2013-14-12-r142. 2.Liu, S.L., Li, Y.Y., Lu, J.L., Su, X., Tang, M., Zhou, L., Zhou, C., Yang, Q., Ji, Y.Q., Yu, D.W., and Zhou, X. (2013) SOA PBa rcode: re vea l ing a rt hropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons. Methods in Ecology & Evolution. 4, 11421150. 3.Ji, Y. Q., Ashton, L., Pedley, S. M., Edwards, D. P., Tang, Y., Nakamura, A., Kitching, R. L., Dolman, P., Woodcock, P., Edwards, F. A., Larsen, T. H., Hsu, W. W., Benedick, S., Hamer, K. C., Wilcove, D. S., Bruce, C., Wang, X. Y., Levi, T., Lott, M., Emerson, B. C. & Yu, D. W. (2013) Reliable, verifiable, and efficient monitoring of biodiversity via metabarcoding. Ecology Letters. 16: 1245-1257. 4 . R a m i r e z - G o n z a l e z R , D W Yu , C Bruce, D Heavens, M Caccamo and BC Emerson (2013) PyroClean: Denoising pyrosequences from protein coding amplicons for the recovery of interspecific and intraspecific genetic variation. PLoS One. 8: 57615e. 5.Beckschäfer P, P Mundhenk, C Kleinn, Y Ji, DW Yu and RD Harrison (2013) Enhanced structural complexity index: an improved index for describing forest structural complexity. Open Journal of Forestry 3: 23-29. 6.Wang H, J Ridley, DW Dunn, RW Wang, JM Cook and DW Yu (2013) Biased oviposition and biased survival together help resolve a fig-wasp conflict. Oikos.122: 533-540. 在生物多样性的管理和保护工作中，工作者必须知道哪个物种正在消失，在哪 儿以及为什么，还应该知道采取哪种补救措施最有效。高通量条形码技术能通过真 核生物或环境 DNA 的大量样本来确定物种组成。此项技术研究中，我们的分类专 家总共花了 2,505 个小时，在马来西亚（热带）、中国（亚热带）和英国（温带） 收集了三个高质量标准数据组，涵盖 55,813 个节肢动物和鸟类物种，来测试并验 证高通量条形码技术。高通量条形码和标准数据组精确地展示了相关的 α- 和 β多样性，两种方法都能对恢复生态和系统保护规划提供政策理论支持。相对于生物 多样性数据组来说，高通量条形码样本在分类学上更全面，获取实验结果所花的时 间成倍缩短，更少的依赖于分类专家，并且是可证伪的，这对于调节纠纷是必不可 少的。 2. 产卵偏好与幸存偏好共同解决榕—榕小蜂的冲突 Hui Wang, Jo Ridley, Derek W. Dunn, Ruiwu Wang, James M. Cook, Douglas W. Yu 对于聚果榕（Ficus racemosa）和传粉榕小蜂（Ceratosolen fusciceps）互利 共生的稳定性，学术界存在两种不同的竞争理论，因而我们对此进行了实验。榕小 蜂在聚果榕的果实中产卵，而一只榕小蜂幼虫的生长需要利用一粒聚果榕的种子。 幼虫成熟后，雌榕小蜂将聚果榕的花粉授到另一株聚果榕上，如此循环。聚果榕的 繁殖依靠种子和雌榕小蜂的数量，而短期内雌榕小蜂的增长则只能依靠榕小蜂数量 的增长，因此导致了利益冲突（产卵利用种子）。我们的实验表明，榕小蜂先进入 聚果榕的果实内层（产卵偏好假说），这符合最佳觅食理论。当产卵数量增多后， 在中间一层的种子就一对一地被榕小蜂卵占据，这也与产卵观点一致。最后，在果 实的外部，大部分种子都不在了，只有少部分种子中有榕小蜂卵，这说明了榕小蜂 死亡率极高（幸存偏好或“打不败种子”假说）。因此我们的结果同时证实了产卵 偏好和幸存偏好两种假说，从而证实了互利共生的稳定性。我们还进一步讨论了产 卵数量多，则能克服聚果榕的防御机制，通过优胜劣汰来选择榕小蜂的特征，维持 幸存榕小蜂的数量。最后，我们证实聚果榕能在自身水平下平衡种子和榕小蜂数量。 因为聚果榕可能具有平均分配雌雄榕小蜂的功能，种子与榕小蜂 1:1 的比例说明聚 果榕是此互利共生关系的主导者。 11 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Ecology, Conservation, & Environment Center (ECEC) Dr. Douglas W. Yu. Yu’s research covers the conservation biology of tropical forests and the evolution and ecology of mutualisms. In the first area, we have developed new methods for estimating and projecting the impact of hunting on large vertebrates in Amazonian forests. In the second, we have been elucidating the mechanisms stabilizing cooperation among species, using in fig-wasp and ant-plant mutualisms as experimental models. Yu has more than 60 publications, including in Nature, Science, PNAS, PLoS Biology, Ecology Letters, Ecological Monographs, Ecology. E-mail: dougwyu@gmail.com 1. Reliable, verifiable and efficient monitoring of biodiversity via Metabarcoding Yinqiu Ji,Louise Ashton, Scott M. Pedley, David P.Edwards,Yong Tang,Akihiro Nakamura, Roger Kitching, Paul M. Dolman, Paul Woodcock, Felicity A. Edwards, Trond H. Larsen, Wayne W. Hsu, Suzan Benedick, Keith C. Hamer, David S. Wilcove, Catharine Bruce, Xiaoyang Wang, Taal Levi, Martin Lott, Brent C. Emerson and Douglas W. Yu To manage and conserve biodiversity, one must know what is being lost, where, and why, as well as which remedies are likely to be most effective. Metabarcoding technology can characterise the species compositions of mass samples of eukaryotes or of environmental DNA. Here, we validate metabarcoding by testing it against three highquality standard data sets that were collected in Malaysia (tropical), China (subtropical) and the United Kingdom (temperate) and that comprised 55,813 arthropod and bird specimens identified to species level with the expenditure of 2,505 person-hours of taxonomic expertise. The metabarcode and standard data sets exhibit statistically correlated alpha- and beta-diversities, and the two data sets produce similar policy conclusions for two conservation applications: restoration ecology and systematic conservation planning. Compared with standard biodiversity data sets, metabarcoded samples are taxonomically more comprehensive, many times quicker to produce, less reliant on taxonomic expertise and auditable by third parties, which is essential for dispute resolution. 2. Biaed oviposition and biased survival together help resolve a fig–wasp conflict Hui Wang, Jo Ridley, Derek W. Dunn, Ruiwu Wang, James M. Cook and Douglas W. Yu We report evidence that helps resolve two competing explanations for stability in the mutualism between Ficus racemosa fig trees and the Ceratosolen fusciceps wasps that pollinate them. The wasps lay eggs in the tree’s ovules, with each wasp larva developing at the expense of a fig seed. Upon maturity, the female wasps collect pollen and disperse to a new tree, continuing the cycle. Fig fitness is increased by producing both seeds and female wasps, whereas short-term wasp fitness increases only with more wasps, thereby resulting in a conflict of interests. We show experimentally that wasps exploit the inner layers of ovules first (the biased oviposition explanation), which is consistent with optimalforaging theory. As oviposition increases, seeds in the middle layer are replaced on a one-to-one basis by pollinator offspring, which is also consistent with biased oviposition. Finally, in the outer layer of ovules, seeds disappear but are only partially replaced by pollinator offspring, which suggests high wasp mortality (the biased survival or ‘unbeatable seeds’ explanation). Our results therefore suggest that both biased oviposition and biased survival ensure seed production, thereby stabilizing the mutualism. We further argue that biased oviposition can maintain biased survival by selecting against wasp traits to overcome fig defenses. Finally, we report evidence suggesting that F. racemosa balances seed and wasp production at the level of the tree. Because figs are probably selected to allocate equally to male and female function, a 1:1 seed:wasp ratio suggests that fig trees are in control of the mutualism. 12 员工简介（Lab Staff） 工作人员（Staff） 朱建国 副研究员 Dr. Zhu Jianguo Associate Researcher zhu@mail.kiz.ac.cn 季吟秋 助理研究员 Dr. Ji Yinqiu Assistant Researcher jiyinqiu@hotmail.com 杨春燕 助理研究员 Dr. Yang Chunyan Assistant Researcher yangyahan@mail.kiz.ac.cn 王 林 研究实习员 Mr. Wang Lin, Research Assistant 汪嘉欣 研究实习员 Ms.Wang Jiaxing, Research Assistant 吴春莹 研究实习员 Ms. Wu Chunying, 研究生 (Graduate Students) 杨晨雪 Yang Chenxue 张 凯 Zhang Kai 王晓阳 Wang Xiaoyang 于龙龙 Yu Longlong Catharine Powell 遗传资源与进化国家重点实验室 2013 年 度 报 告 实验与理论生态学 王瑞武，研究员，实验与理论生态学组 PI，国家杰出青年基 金获得者，中科院优秀青年生命科学家专项资助获得者。现任中 国科学院昆明动物研究所实验与理论生态学学科组负责人，中国 科学院昆明动物所青年科学小组组长。 重要成果（Highlights） 论著（Selected Publications） 1. 植物也会使用胡萝卜加大棒的策略 对于任何一个合作系统而言，总是存在投机的、不合作的行为或个体。这些投机 1.Wang RW*, Dunn DW, Sun BF. 2013. Discriminative host sanction in fig-fig wasp mutualism. Ecology. doi. org/10.1890/13-0749.1(On Line) 行为或投机个体的在合作系统中的扩散将会导致合作系统的解体。然而，是什么机制 能够阻止这种投机行为，从而避免合作系统的解体至今仍是一个争议很大的科学问题。 由于合作双方存在信息、演化路径的不对称性，投机的个体或行为能够得以共存。为 了进一步检验这种理论猜想的可信性，该课题组以著名的榕树 - 榕小蜂这一种间合作 2. He JZ, Zhao Y, Cai HJ, Wang RW*. 2013. Spatial games and the maintenance of cooperation in an asymmetric Hawk–Dove game. Chinese Science Bulletin. doi: 10.1007/s11434013-5810-6 3. Wang RW*, Wang YQ, He JZ, Li YT*. 2013. Resource elasticity of offspring survival and the optimal evolution of sex ratios, PLoS ONE. 8(1): e53904 为模式系统，来验证上述理论猜想。与人类社会合作行为极为相似的是：榕树 - 榕小 蜂这一合作系统中，合作的传粉小蜂中有些个体会采取投机性策略，而不给榕树传粉， 甚至部分个体完全演化出投机行为的适应性特征 ---- 给植物传粉的花粉囊完全退化。 试验发现榕树会通过两种方式惩罚这些投机性小蜂。当投机性小蜂数量比较少时，榕 树通过果实脱落，将这些投机性小蜂的后代全部杀死。反之，榕树则通过抑制这些小 蜂后代发育，降低其种群数量，但又维持其一定的数量，这极可能是由于这些投机性 小蜂将为植物的花粉散布做出一定的贡献有关。把两种惩罚效应结合起来看，投机者 越多，榕树对其惩罚也越大。该结果已于 Ecology 发表。 2. 环境选择压力或影响性别比例 自然界大多数物种的性别比例是 1：1，少数物种在进化过程出现偏雌或偏雄的性 别比例。但传统理论难以解释相同环境下为何有些物种出现偏雌性比，而有些物种偏 雄性，以及同一物种在不同的年龄阶段、环境条件会出现不同性别比例的问题。通过 理论模型发现，生态学著名的”多生少管”和”优生优育”繁殖策略，本质就是资源 变化对幼崽存活率影响大小不同所致。 同时，该模型还发现资源变化对幼崽存活率影响大小与环境选择压力都会影响性 别比例的演化。选择优生优育繁殖策略的个体或物种，如老虎、人类等，环境选择压 力的增大将会导致其后代雌性比例增大。而选择多生少管这样粗放繁殖策略的个体或 物种，如老鼠、蚊子等多数昆虫，环境选择压力的增大将会导致其后代雄性比例增大。 如果资源变化对幼崽存活率影响不大或没影响，环境选择压力的增大，将不会改 变其后代性别比例。性别比例的改变可能是由个体的激素或荷尔蒙水平变化所致。 该理论模型有效解释为何有些物种出现偏雌性，而有些物种却是偏雄性的性别比 例，并解释了包括人类在内的很多物种在局部范围内出现的性别失调现象。该结果已 于 PLoS ONE 发表。 13 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Experimental and Theoretical Ecology Dr. Ruiwu Wang, Professor, Principal Investigator of Experimental and Theoretical Ecology, Kunming Institute of Zoology, Chinese Academy of Sciences.Research interests: (1) evolution and maintenance of cooperative systems, especially in insect-plant mutualisms; (2) mathematical and statistical modeling on the evolution of cooperation and species coexistence; (3) evolution of biodiversity under the influence of climate change; (4) sex ratio evolution under the selective pressure of environment. Study system involves: fig-fig wasps, plant- endofungi, and insect-fungi symbiosis. Email: wangrw@mail.kiz.ac.cn Resource Elasticity of Offspring Survival and the Optimal Evolution of Sex Ratios 员工简介（Lab Staff） The fitness of any organisms includes the survival and reproductive rate of adults and the survival of their offspring. Environmental selection pressures might not affect these two aspects of an organism equally. Assuming that an organism first allocates its limited resources to maintain its survival under environmental selection pressure, our model, based on the evolutionarily stable strategy theory, surprisingly shows that the sex ratio is greatly affected by the environmental pressure intensity and by the reproductive resource elasticity of offspring survival. Moreover, the concept of the resource elasticity of offspring survival intrinsically integrates the ecological concepts of K selection and r selection. The model shows that in a species with reproductive strategy K, increased environmental selection pressure will reduce resource allocation to the male function. By contrast, in a species with reproductive strategy r, harsher environmental selection pressure will increase allocation to the male function. The elasticity of offspring survival might vary not only across species, but also across many other factors affecting the same species (e.g., age structure, spatial heterogeneity), which explains sex ratio differences across species or age structures and spatial heterogeneity in the same species. Derek William Dunn 副研究员 14 工作人员（Staff） Associate Professor 杨 燕 助理研究员 Yang Yan, Assistant Professor 博士后 (Postdoctoral Fellows) 贺军州 He Junzhou Huang Qiang Rafeal Moreno Ripoll 黄 强 Riccardo Pansini 研究生 (Graduate Students) 罗天逊 文晓岚 李肇天 李立立 Luo Tianxun 2013 Wen Xiaolan 2012 Li Zhaotian 2012 Li Lili 2011 遗传资源与进化国家重点实验室 2013 年 度 报 告 分子进化与基因组多样性研究 张亚平， 博士，研究员，中国科学院院士，中国科学院副院长，遗传资源 与进化国家重点实验室主任。主要从事基因组多样性研究，近期的研究重点是人 和野生动物基因组与适应进化的遗传机制，家养动物基因组及人工驯化遗传机制 等。揭示了东亚人群进化的一些规律和我国一些民族的演化历程。系统地研究了 野生动物和家养动物的遗传多样性，对自然选择和人工选择作用下基因组进化的 研究，揭示了一些重要的动物适应进化和畜禽经济性状形成的遗传机制。近 5 年 在 Nature Commun，PNAS，Mol Biol Evol 等国际刊物发表 SCI 文章 100 多篇。 2013 年度获云南省自然科学奖特等奖和一等奖各一项。 重要成果（Highlights） 1. 家犬起源和人工选择的基因组水平研究 1. 2013 年度 纽约时报、国家地理、科学家、亚洲科学家等著名媒体专题报道了本 室家犬起源和人工选择方面的新成果。本研究通过对四只灰狼，三只中国 本地犬和三只品种犬全基因组测序和分析，发现家犬与灰狼的分歧时间大 约为 3 万 2 千年并经历了较弱的瓶颈效应，进而提出了家犬起源的拾荒者 假说。利用群体遗传分析的手段，发现家犬中受选择的基因和人类受选择 的基因存在显著地交集，首次阐明家犬和人类存在显著的平行进化历程。 此外，我们利用全基因组 SNP 数据比较中国土狗群体与灰狼群体间的群体 遗传差异，发现中国土狗与灰狼之间群体分化显著的基因在大脑中偏好表 达，且在控制复杂认知行为的新皮层中偏好最明显，为行为等复杂性状的 研究提供了范例。两项研究分别从基因组层次和表达层次揭示了家犬驯化 后，饮食和行为两大重要性状转变的遗传基础，为研究家犬的起源与进化 提供重要信息，并为我们研究和理解人类的演化和疾病提供了崭新的视角。 【Wang DG et al. 2013 Nat Commun, 5 Year-IF=10.02】 【Li Y et al. 2013 Mol Biol Evol, 5 Year-IF=11.22】 云南省自然科学奖特等奖 “基因组多样性与亚洲人群的演化” 2. 2013 年度 云南省自然科学奖一等奖 “动物适应性进化的分子机制” 论著（Selected Publications） 1. Ge RL*, Cai QL, Shen YY, …, Murphy RW, Wang J, Zhang YP*, Wang J*. Draft genome sequence of the Tibetan antelope. Nature Commun, 2013,4. 2. Li JT*, Li Y, Klaus S, Rao DQ, Hillis DM, Zhang YP*. Diversification of rhacophorid frogs provides evidence for accelerated faunal exchange between India and Eurasia during the Oligocene. PNAS, 2013,110(9):3441-46. 3. Li Y, vonHoldt BM, Reynolds A, Boyko AR, Wayne RK, Wu DD*, Zhang YP*. Artificial selection on brain-expressed genes during the domestication of dog. Mol Biol Evol, 2013,30(8):1867-76. 4. Liang L, Shen YY*, Pan XW, Zhou TC, Yang C, Irwin DM, Zhang YP*. Adaptive evolution of the Hox gene family for development in bats and dolphins. PLoS ONE, 2013,8(6):e65944. 5. Miao YW, Peng MS, ..., Baig M, Chaudhuri TK, Shen YY, Kong QP, Murphy RW, Yao YG, Zhang YP*. Chicken domestication: an updated perspective based on mitochondrial genomes. Heredity, 2013,110(3):277-282. 6. Sun YB, Zhou WP, Liu HQ, Irwin DM, Shen YY*, Zhang YP*. Genome-wide scans for candidate genes involved in the aquatic adaptation of dolphins. Genome Biol Evol, 2013,5(1):130-139. 7. Wang GD, Zhai WW, Yang HC, Fan RX, Cao X, Zhong L, Wang L, Liu F, …, Gao Y, Lv XM, Irwin DM, Savolainen P, Wu CI*, Zhang YP*. The genomics of selection in dogs and the parallel evolution between dogs and humans. Nat Commun, 2013,4:1860. 8. Wang SY, Luo J, Murphy RW, Wu SF, Zhu CL, Gao Y*, Zhang YP*. Origin of chinese goldfish and sequential loss of genetic diversity accompanies new breeds. PLoS ONE, 2013,8(3):e59571. 9. Wu DD*, Zhang YP*. Evolution and function of de novo originated genes. Mol Phylogenet Evol, 2013,67(2):541-545. 图 1. 纽约时报、国家地理、科学家、亚洲科学家等著名媒体专题报道 2. 树蛙研究为板块撞击理论的争论提供新证据 通过对树蛙类物种的生物地理学研究，揭 示了渐新世时期印度板块和欧亚板块之间存在 着快速的物种交流。印度板块和欧亚板块的撞 击事件被认为是目前地球上最大和最积极的造 山运动，但至今对于该碰撞事件的碰撞时间等 模式仍备受争论。通过对树蛙的生物地理学研 究，揭示在早第三纪时期，印度板块和欧亚板 块首次接近碰撞的时候，树蛙类物种由印度板 块扩散至欧亚板块，物种迅速在亚洲大陆，包 括东南亚大陆和岛屿上进行扩散。在始新世中 期，印度板块和欧亚板块之间却无树蛙类物种 交流；此时期，树蛙类物种在东南亚及东亚大 陆和岛屿之间扩散。直至渐新世时期，印度板 块和欧亚板块之间又恢复了树蛙类物种交流。 该研究从生物进化角度支持 Aitchison 和 Ali 的地理模型。【Li JT et al. 2013 PNAS，5 Year-IF=10.58】 15 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Molecular Evolution and Genome Diversity Dr. Ya-Ping Zhang, Academician & Vice-President, Chinese Academy of Sciences. He is an associate editor of Genome Biol Evol, and the editorial board of Anim Genet. This year we focused on genomic evolution and molecular machenism of natural selection in human and wild animals, artificial selection in domesticated animals. Within 2013, we got importance progress and 40 SCI papers have been published and 4 papers have impact factor higher than 10, including PNAS(1), Mol Biol Evol (1), Nat Commun (2). Email: zhangyp@mail.kiz.ac.cn 1. The Origin and Artificial Selection of Domestic Dog at Genomic Level Domesticated dog is the earliest domesticated animals. By perform whole-genome sequencing of four grey wolves, three Chinese indigenous dogs and three breed of dogs, we find that the split between wolves and Chinese indigenous dogs occurred 32,000 years ago and that the subsequent bottlenecks were mild, and further propose the scavengers hypothesis for the origin of domestic dogs. Meanwhile, we discover that the selected genes exist significantly intersection between domestic dogs and human, and firstly illustrate that the process of parallel evolution observably exist between domestic dogs and human. Another study, using genome-wide SNP data, we discovers that populationdifferentiated significant genes between Chinese indigenous dog population and the gray wolf population have expression bias in the brain tissues, particularly in the neocortex, a specific region controlling complex cognitive behavior, and provides an example for studying behavior and other complex traits. Two complementary studies revealed the genetic basis of the transform of two important traits - foods and behaviors in both genic level and expression level during domestication, and offer a new perspective for our studying and comprehending the human evolution and disease. 员工简介（Lab Staff） 研究人员（Researchers） Dr. Robert W. Murphy, Visiting Professor Dr. David Irwin, Visiting Professor 高 云 副研究员 Dr. Yun Gao, Associate Professor 吴东东 副研究员 Dr. DongDong Wu, Associate Professor 彭旻晟 副研究员 Dr. MinSheng Peng, Associate Professor 王国栋 副研究员 Dr. GuoDong Wang, Associate Professor 谢海兵 助理研究员 Dr. HaiBing Xie, Assistant Professor 陈 睿 助理研究员 Dr. Rui Chen, Assistant Professor 何 静 助理研究员 Ms. Jing He, Assistant Professor 马云飞 研究实习员 Mr. YunFei Ma, Resarch Assistant 工程技术人员（Technicians） 吴世芳 朱春玲 杨鹏标 郝伟峰 姚玉萍 Ms. ShiFang Wu Ms. ChunLing Zhu Mr. PengBiao Yang Mr WeiFeng Hao Ms YuPing Yao 博士后（Postdoctoral Fellows） 李家堂 周传江 李 艳 季林丹 倪 刚 Figure 3. Expression pattern between CNs and GSs 2. Tree Frog Study Offers New Insights to India-Asia Collision The accretion of the Indian subcontinent to Eurasia triggered a massive faunal and floral exchange, with Gondwanan taxa entering into Asia and vice versa. The traditional view on the Indian−Asian collision assumes contact of the continental plates during the Early Eocene. However, the exact mode and timing of this geological event is still under debate. The study indicated that rhacophorid tree frogs showed an early dispersal from India to Asia between 46–57 Ma, as reconstructed from the fossil record. During the Middle Eocene, however, faunal exchange ceased, followed by increase of rhacophorid dispersal events between Asia and the Indian subcontinent during the Oligocene that continued until the Middle Miocene. This corroborates recent geological models that argue for a much later final collision between the continental plates. Dr. JiaTang Li，2009 Dr. ChuanJiang Zhou, 2011 Dr. Yan Li, 2012 Dr. LinDan Ji, 2012 Dr. Gang Ni, 2013 研究生（Graduate Students） 王姝妍 Wang, SY 杨贺川 Yang, HC 颜 芳 Yan, F 刘鹤群 Liu, HQ 梁 璐 Liang, L 袁智勇 Yuan, ZY 刘 杰 Liu, J 周中银 Zhou, ZY 曹 雪 Cao, X 王明山 Wang, MS 刘 菲 Liu, F 杨 阳 Yang, Y 韩徐曼 Han, XM 邵 勇 Shao, Y 徐海波 Xu, HB 徐 丹 Xu, D 叶凌群 Ye, LQ 曾 琳 Zeng, L 尹婷婷 Yin, TT 黄翠萍 Huang, CP 史妮妮 Shi, NN 霍永霞 Huo, YX 王运梅 Wang, YM 吕梦蝶 Lu, MD 姚 瑶 Yao, Y Nguyen Ngoc Sang Adeola Adeniyi Charles 16 遗传资源与进化国家重点实验室 2013 年 度 报 告 两栖爬行类多样性与进化 车静， 博士，研究员。昆明动物研究所“青年科学家小组”人才项 目获得者。动物学会两爬分会理事，中科院青年创新促进会理事。2011 年获“中国科学院卢嘉锡青年人才”奖。本课题组长期活跃在中国和东南 亚这一重要区域，以两栖爬行动物为研究对象，系统开展隐存物种发掘， 物种形成与分化，大尺度生物多样性格局形成及演化规律的研究，致力于 生物多样性的可持续保护。目前已在 PNAS、ME、MPE 等国内外本领域 重要杂志刊物发表论文 20 余篇。 重要成果（Highlights） 论著（Selected Publications） 1. Zhou WW, Yan F, Fu J, Wu SF, Murphy RW, Che J*, Zhang YP*. 2013. River islands,refugia, and genetic structuring in the endemic brown frog Rana kukunoris (Anura, Ranidae) of the Qinghai-Tibetan Plateau. Molecular Ecology,22: 130-142. 2. Yan F, Zhou WW, Zhao HT, Yuan ZY, Wang YY, Jiang K, Jin JQ, Murphy RW, Che J*, Zhang YP*. 2013. Geological events play a larger role than Pleistocene climatic fluctuations in the genetic structure of the montane stream-dwelling frog Quasipaa boulengeri (Anura: Dicroglossidae) in southern China. Molecular Ecology, 22(4): 11201133. 3. Murphy RW*, Crawford AJ, Bauer AM, Che J, Donnellan SC, Fritz U, Haddad CFB, Nagy ZT, Poyarkov NA, Vences M, Wang WZ, Zhang YP. 2013. Cold Code: the global initiative to DNA barcode amphibians and nonavian reptiles. Molecular Ecology Resources, 13(2): 161-167. 4 . N g u y e n S N , L e T N T, Tr a n TA D , O r l o v NL,Lathrop A, Macculloch RD, Le TDT, Jin JQ, Nguyen LT, Nguyen TT, Hoang DD, Che J*, Murphy RW*, Zhang YP*. 2013. Phylogeny of the Cyrtodactylus irregularis species complex (Squamata: Gekkonidae) from Vietnam with the description of two new species. Zootaxa, 3737(4): 399-414. 5. Jiang K, Yan F, Suwannapoom C, Chomdej S, Che J*. 2013. A new species of the genus Leptolalax (Anura: Megophryidae) from northern Thailand. Asian Herpetological Research. 4(2) : 100-108. 1. 高原两栖类群体演化历史揭示生物对晚新生代气候环境变化的响应 研究生物多样性格局及其成因是制定生物有效保护策略的前提。以分 布于青藏高原东北缘的高原林蛙群体为研究对象，发现不同与其它类群的 进化模式，高原林蛙在青藏高原东北边缘以及祁连山北部存在多个冰期避 难所；横断山脉分布的种群是末次冰期后由北向南扩张而形成。首次提出 了“river islands”概念，即祁连山北坡群体高度分化，主要围绕内陆河 水系孤立分布。该研究结果是第一个高原面上两栖类物种对气候环境变动 响应的报道，文章也被 FrogLog 收录 (Zhou et al. 2013)。 2. 两栖类研究揭示影响中国南方山区物种遗传结构的主要因素 古地质和古气候变迁是影响生物多样性和群体结构的两个重要因素。 中国南方孕育着复杂的地形，第四纪时并没有发育大规模的冰川，气候波 动对于该地区生物的影响希待探究。以中国南方广泛分布的棘腹蛙为研究 对象，发现地质变动是影响该群体演化的主要因素，而第四纪气候波动并 没有对该物种产生显著作用。这可能是中国南方山区物种较为普遍的模式 （Yan et al. 2013)。 3. 基于 DNA 条形码数据揭示两栖类群隐存多样性 基于 DNA 条形码的研究结果，结合形态数据，发现两栖类群中存在 大量隐存物种。其中 5 个正式发表，包括东南亚三个新种和中国两个新种。 1）分布于泰国北部清迈的掌突蟾属一新种，张氏掌突蟾，Leptolalax zhangyapingi。 这 是 国 内 首 次 独 立 对 国 外 两 爬 物 种 进 行 的 命 名 (Jiang et al. 2013); 2） 分 布 于 越 南 的 裸 趾 虎 属 的 两 个 新 种，Cyrtodactylus phuocbinhensis 和 Cyrtodactylus taynguyenensis(Nguyen et al. 2013) ; 3） 分 布 于 广 东 地 区 的 蝾 螈 属 一 新 种， 蓝 灰 蝾 螈 Cynops glaucus (Yuan et al. 2013); 4）分布于西藏地区的 Protobothrops 属一新种，P. himalayanus (Pan et al. 2013)。 使用生态气候数据模拟末次冰盛期高原 林蛙的适宜分布区域。 6. Yuan ZY, Jiang K, Ding LM, Zhang L, Che J*. 2013. A New Newt of the Genus Cynops (Caudata: Salamandridae) from Guangdong, China. Asian Herpetological Research. 4(2) :116-123. (* corresponding author) 棘腹蛙的群体遗传结构；右上角 为线粒体支系拓扑结构；饼图颜色对 应于线粒体支系。 17 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Herpetological Diversity and Evolution Dr. Jing Che, Principal Investigator. Using amphibian and reptile as model, we often explore the biodiversity issue and evolutionary questions within a phylogenetic framework mostly concentrating on species inhabiting three regions: China’s QinghaiTibetan Plateau and Hengduan Mountain Range, Southeast Asia, and the mainland of East China and nearby islands. Email: chej@mail.kiz.ac.cn 1. River islands, refugia and genetic structuring in the endemic brown frog Rana kukunoris of the Qinghai-Tibetan Plateau Typically, species distributed on the Qinghai-Tibetan plateau have been hypothesized to re-treat to south-eastern refugia. We studied the phylogeography of the wood frog distributed in northeastern margin of plateau, which showed different evolutionary pattern. There are several glacial refuge in the northeast edge of the Tibetan Plateau and the northern Qilian Mountains. “River islands” was first proposed to explain the populations distributed in northern Qilian Mountains. These populations were highly differentiated and isolated by inland rivers. These results were found to have important implications for the habitat conservation in Northwest China. (Zhou et al. 2013). 2. Geological events play a larger role than Pleistocene climatic fluctuations in driving the genetic structure of Quasipaa boulengeri Paleoclimatic and paleogeological events have been identified as being the two main drivers of genetic structuring in extant organisms. We used a montane stream-dwelling frog, Quasipaa boulengeri, to explore the relative roles played by these drivers on species in southern China, a region needing thorough studies. Analyses identified geological events as playing a larger role than climatic fluctuations in driving the population history of Q. boulengeri. The unification of the upper and middle Yangtze River in the Three Gorges mountain region mediated downstream colonization of this frog. (Yan et al. 2013) 3. High cryptic biodiversity in Amphibians was explored based on the DNA barcoding Based on DNA barcoding, a large of cryptic diversity in amphibian was suggested. Five new species here were described.1) Leptolalax zhangyapingi (Jiang et al 2013), distributed in Chiang Mai, northern Thailand; 2) Cyrtodactylus phuocbinhensis and Cyrtodactylus taynguyenensis (Nguyen et al 2013), distributed in Vietnam; 3) Cynops glaucus (Yuan et al 2013), distributed in Guangdong; 4) Protobothrops himalayanus (Pan et al 2013), distributed in Tibet. 员工简介（Lab Staff） 工作人员（Staff） 周炜帏 博士 副研究员 Weiwei Zhou, Associate Professor 孙艳波 博士 副研究员 Yanbo Sun, Associate Professor 颜 芳 博士 助理研究员 Fang Yan, Assistant Professor 金洁琼 学士 实验师 Jieqiong Jin, Technician 陈宏满 硕士 助理工程师 Hongman Chen, Assistant Engineer 研究生（Graduate Students） 袁智勇 Zhiyong Yuan 2010 涂小龙 Xiaolong Tu 2011 高 伟 Wei Gao 2012 付婷婷 Tingting Fu 2013 联合培养 刘 杰 Jie Liu 2009 杨军校 Junxiao 邵 勇 Yong Shao 2011 张宝林 Baolin Zhan 2012 陈进民 Jinmin New species Cyrtodactylus phuocbinhensis New species Cynops glaucus 18 Yang 2010 Chen 2012 遗传资源与进化国家重点实验室 2013 年 度 报 告 基因起源 王 文，博士、研究员，中德马普进化基因组学青年科学家小组组长。 本年度重点完成了水稻中优质等位的新鉴定方法、家蚕丝腺甲基化谱及蜘蛛 转录组的 de novo 测序。2013 年王文研究员入选科技部“万人计划”第一 批科技创新领军人才，获云南省科技厅“云南省科技领军人才培养计划”资助。 实验室主页： http://159.226.149.45/wangw/wangwen2010.htm 重要成果 (Highlights) 论著（Publications） 1. Dong Y, et al., Wang W*. 2013. Sequencing and automated wholegenome optical mapping of the genome of a domestic goat (Capra hircus). Nature Biotechnology. 31(2):135-141. ( IF= 32.438; 32.182). 2. Lyu J, et al., Wang W*. 2013. Analysis of elite variety tag SNPs reveals an important allele in upland rice. Nature Communication. Jul 5:4:2138. (IF= 10.015; 10.02). 3. Xiang H, et al., Wang W*. 2013. Comparative methylomics between domesticated and wild silkworms implies possible epigenetic influences on silkworm domestication. BMC Genomics. Sep 23; 14: 646. (IF= 4.379; 4.615). 4. Zhao YJ, Zeng Y, Chen L, Dong Y, Wa n g W * . 2 0 1 3 . A n a l y s i s o f Transcriptomes of Three Orb-Web Spider Species Reveals Gene Profiles Involved in Silk and Toxin. Insect Sci. Oct 25. doi: 10.1111/1744-7917.12068. ( IF=1.786; 1.59). 5. Song LT, Wang W*. 2013. Genomes and evolutionary genomics of animals. Current Zoology. 59(1): 1674-5507. ( IF= 1.392; 1.392). 6. Zhang Wen-guang. 2013.Development of Genome-Wide Scan for Selection Signature in Farm Animals. Journal of Integrative Agriculture. 12:8 1461-1470. 1. 水稻人工选择研究的新进展：新的比较基因组方法定位改良相关基因 为了高效快速地鉴定优质品系中的优质等位基因，本研究组与国内同行合作提 出一种新的鉴定改良品系中优质等位基因的方法——改良品系标签位点分析（Elite variety tag SNP analysis, ETAS analysis）。该方法基于对特定改良品系高深 度的重测序以及大规模的非改良群体基因组对照数据。使用 ETAS analysis, 该研 究组在著名的水稻改良品种，如高产的桂朝，优质的越光 , 抗旱的 IRAT104 中鉴 定出与这些改良品种对应的标签位点。进一步对陆稻 IRAT104 中的一个标签位点 的深入分析发现此位点在陆稻与水稻中具有很大的频率差异（61% vs 3%），且其 附近具有显著的人工选择信号。功能分析表明，此位点落在脱落酸合成的限速酶 NCED 基因的编码区。在陆稻中高频的基因型引起了一个错义突变，改变了此酶的 底物结合域的空间构象，从而可能影响了陆稻中脱落酸合成的效率。本研究开创性 地提出，通过个体基因组与群体基因组的比较，可以为鉴定改良基因提供重要依据。 同时本研究也指出，进一步的功能验证对于确定功能基因亦是不可或缺的。该研究 发表在 Nature Communication 上 . 2. 家蚕和野蚕丝腺甲基化谱研究新进展 本课题组前期研究证实了昆虫 DNA 甲基化的重要功能意义，在上述研究的基 础上，我们一方面利用 RNAi 技术深入探讨了 DNA 甲基转移酶的生物学功能，发 现 Dnmt1 敲减以后家蚕卵的孵化率显著降低，进而为昆虫甲基转移酶的生物学功 能提供了重要的实验证据。另一方面，我们开展了家蚕和野蚕丝腺甲基化谱的比较。 我们发现家蚕和野蚕的基因区 DNA 甲基化倾向于保守，而 TE 区则倾向于种间变化。 我们筛选到一批甲基化差异区域，并通过 BS-PCR 及 454 高通量测序验证，我们 进一步将鉴定了 5 个甲基化差异相对一致基因。其中一个基因在家蚕中一致的无甲 基化而野蚕中具有一定水平的甲基化，并且家蚕丝腺中表达水平低于野蚕。尤其有 趣的是，该基因是一个候选的驯化基因，经过 SNP 分析，我们推测可能表观遗传 学差异引起该基因的表达差异。我们的研究结果提示，驯化过程中表观遗传学改变 也在发挥作用，这位长期有争议的获得性遗传假说提供一个启示性的例子。该研究 结果发表在 BMC genomics 上。 3. 中国热带三种蜘蛛转录组 de novo 测序 蜘蛛是具有 3.9 亿年历史的古老节肢动物。蜘蛛的蛛丝和毒蛋白在农业、医 学和工程领域有很大的商业应用价值。然而对蜘蛛基因组信息了解的匮乏，阻碍了 对蜘蛛相关生物学知识的探索，同时影响了对相关资源的利用。我们展示了来自 中国西南热带雨林的三种蜘蛛——Gasteracantha arcuata、Nasoonaria sinensis 和 Gasteracantha hasselti 的转录组。通过 Illumina 末端配对的测序方式，对 G. arcuata、N. sinensis 和 G. hasselti 分别预测出 54871、101855 和 75455 条基因， 相应的，在这些预测到的基因中，分别有 9300、10001 和 10494 条基因被注释出 功能信息。同时我们也利用预测出的基因，对蜘蛛中各种蛛丝蛋白和毒蛋白的基因 进行了更深度的分析。我们的研究结果首度提供了上述三种蜘蛛的转录组数据，为 后续利用这些蜘蛛的资源奠定了基础。 19 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Origin and Evolution of New Genes Dr. Wen Wang, Professor, Head of CAS–Max Planck Junior Research Group, KIZ, CAS. This year we mainly focused on elite variety tag SNP analysis allele in upland rice, epigenetic changes and methylomics of silkworm, and transcriptomes of three orb-web spiders. Dr. Wen Wang was elected “Ten Thousand Elite Plan” of MOST, and gained funding from “the science and technology leading talent program of Yunnan”. E-mail: wwang@mail.kiz.ac.cn 1. Analysis of elite variety tag SNPs reveals an important allele in upland rice Elite crop varieties usually fix alleles that occur at low frequencies within non-elite gene pools. Dissecting these alleles for desirable agronomic traits can be accomplished by comparing the genomes of elite varieties with those from non-elite populations. Here we deep-sequence six elite rice varieties and use two large control panels to identify elite variety tag single nucleotide polymorphism alleles (ETASs). Guided by this preliminary analysis, we comprehensively characterize one protein-altering ETAS in the 9-cisepoxycarotenoid dioxygenase gene of the IRAT104 upland rice variety. This allele displays a drastic frequency difference between upland and irrigated rice, and a selective sweep is observed around this allele. Functional analysis indicates that in upland rice, this allele is associated with significantly higher abscisic acid levels and denser lateral roots, suggesting its association with upland rice suitability. This report provides a potential strategy to mine rare, agronomically importantalleles. 2.Comparative methylomics between domesticated and wild silkworms implies possible epigenetic influences on silkworm domestication 员工简介（Lab Staff） 工作人员（Staff） 相 辉 博士 副研究员 Dr. Hui Xiang, Associate Professor xiangh@mail.kiz.ac.cn 李学燕 博士 助理研究员 Dr. Xueyan Li, Assistant Professor lixy@mail.kiz.ac.cn 时晓菲 博士 助理研究员 Dr. Xiaofei Shi, Assistant Professor shixiaofei1@163.com 赵若苹 本科 实验师 Domesticates rapidly gained human-preferred agronomic traits in a relatively short-time frame via artificial selection.By embryonic RNA interference,we reveal that knockdown of silkworm Dnmt1 caused decreased hatchability, providing the first direct experimental evidence of functional significance of insect Dnmt1.We omprehensively compare silk gland methylomes of 3 domesticated (Bombyx mori) and 4 wild (Bombyx mandarina) silkworms to identify differentially methylated genes between the two. We observed 2-fold more differentiated methylated cytosinces (mCs) in domesticated silkworms as compared to their wild counterparts, suggesting a trend of increasing DNA methylation during domestication. We identify a number of differential genes. One such gene showing demethyaltion in domesticates correspondently displays lower gene expression, and more interestingly, has experienced selective sweep. Our results imply epigenetic influences at work during domestication, which gives insight into long time historical controversies regarding acquired inheritance. Ms. Ruoping Zhao, Assistant Professor As an ancient arthropod with a history of 390 million years (Ma), spiders evolved numerous morphological forms resulted from adaptation to different environments. The venom and silk of spiders, which have promising commercial applications in agriculture, medicine and engineering fields, are of special interests to researchers. However, little is known about their genomic components, which hinders not only understanding spider biology but also utilizing their valuable genes. Here we report on deep sequenced and de novo assembled trancriptomes of three orb-web spiders which spread in south China tropical forests, Gasteracantha arcuata, Nasoonaria sinensis and Gasteracantha hasselti. With Illumina paired-end RNA-seq technology, 54,871, 101,855 and 75,455 unigenes for G. arcuata, N. sinensis and G. hasselti were obtained respectively, among which 9,300, 10,001 and 10,494 unique genes are annotated respectively. From these annotated unigenes, we comprehensively analyzed silk and toxin gene components and structures for the three spiders. Our study provides valuable transcriptome data for three spider species which previously lack any genetic/genomic data. The results have laid the first fundamental genomic basis for exploiting gene resources from these spiders. 徐 讯 Xun Xu, 2007 张业胜 Yesheng Zhang, 2010 刘 晖 Hui Liu, 2010 张 田 Tian Zhang, 2011 陈 垒 Lei Chen, 2011 沈文菁 Wenjing Sheng, 2011 苟志恒 Zhiheng Gou, 王 筱 Xiao Wang, 奎 玲 Ling Kui, 任彦栋 Yandong Ren, 2013 赵颖俊 Yingjun Zhao, 2013 张 如 Ru 3. De novo assembly and analysis of transcriptomes of three orb-web spiders 20 zhaorp@mail.kiz.ac.cn 刘贵春 硕士 研究实习员 Ms. Guichun Liu, Assistant Professor liuguichun@mail.kiz.ac.cn 博士后 (Postdoctoral Fellows) 张文广 Wenguang Zhang, 2010 刘 斌 Bin Liu, 苏 蕊 Rui Su，2013 研究生 (Graduate Students) Zhang, 2013 遗传资源与进化国家重点实验室 2013 年 度 报 告 比较基因组学 宿兵 ， 博士、研究员、博士生导师，中国科学院知识创新工程学科带头 人，中科院“百人计划”引进人才、国家基金委杰出青年基金获得者、“新 世纪百千万人才工程”国家级人选，从事灵长类大脑演化的遗传学机制以及 现代人类起源、迁徙与适应性进化的遗传学研究。已在 Science 、Nature 、 Nat Rev Genet 、PNAS 、Am J Hum Genet、Genome Res 、Mol Biol Evol、Hum Mol Genet 等国际核心刊物上发表研究论文 100 余篇。 实验室主页：http://159.226.149.45/compgenegroup/compgenegroup.htm 重要成果（Highlights） 论著（Selected Publications） 1.Zhang X, Qi X, Yang Z, …., Shi H, Su B* 2013. Analysis of mitochondrial genome diversity identifies new and ancient maternal lineages in Cambodian aborigines. Nat Commun. 4: 2599. 2. Qi X, Cui C, Peng Y, Zhang X, Yang Z, ….., Su B* 2013. Genetic evidence of paleolithic colonization and neolithic expansion of modern humans on the tibetan plateau. Mol Biol Evol. 30: 1761-1778. 3. Xiang K, Ouzhuluobu, Peng Y, ….., Qi X*, Su B* 2013. Identification of a Tibetanspecific mutation in the hypoxic gene EGLN1 and its contribution to high-altitude adaptation. Mol Biol Evol. 30: 1889-1898. 4. Li M, Luo XJ, ….., Su B.* 2013. Allelic differences between Europeans and Chinese for CREB1 SNPs and their implications in gene expression regulation, hippocampal structure and function, and bipolar disorder susceptibility. Mol Psychiatry. doi: 10.1038/ mp.2013.73 5. Shi L, Lin Q, Su B* 2013. Human-Specific Hypomethylation of CENPJ, a Key Brain Size Regulator. Mol Biol Evol. 6. Li M, Ge T, Feng J, Su B* 2013. SLC6A15 rs1545843 and depression: implications from brain imaging data. Am J Psychiatry. 170: 805. 7. Li M, Su B* 2013. Up-regulation of NOTCH4 gene expression in bipolar disorder: future studies. Am J Psychiatry. 170: 560-561. 8. Shi L, Li M, Lin Q, Qi X, Su B* 2013. Functional divergence of the brain-size regulating gene MCPH1 during primate evolution and the origin of humans. BMC Biology. 11: 62. 9. Sun Z, Zhang Y, Zhang R, Qi X, Su B* 2013. Functional divergence of the rapidly evolving miR-513 subfamily in primates. BMC Evol Biol 13: 255. 1. 青藏高原史前人类定居与迁徙历史以及藏族人群对高原低氧长期适应的遗传机制 青藏高原是世界上海拔最高的高原地区，是人类居住的最极端环境之一。因此是研究人 类对极端环境适应机制的理想区域。但是人类是何时开始向青藏高原迁徙并实现永久定居、 人类在青藏高原的迁徙过程和群体动态变化历史以及新石器农业在青藏高原地区的扩张模式 及其对现代藏族人群遗传多样性格局形成的影响、藏族人群对高原低氧极端环境适应的遗传 机制等关键科学问题目前还没有清晰的答案。我们首次采用大样本全覆盖的研究策略，对覆 盖西藏全区的 41 个藏族地理群体的 6109 人的 Y- 染色体和线粒体 DNA 进行了系统的谱系 地理学分析。发现藏族人群中的绝大多数的 Y- 染色体（89.80%）和线粒体（90.99%）类 型为中国汉族和东亚大陆人群特有的单倍型类型；除了少数几个相对“年轻”的单倍型类 群外（10,000-7000 年前），大多数的线粒体和 Y- 染色体单倍型类群的共祖年代都在距今 40,000-10,000 年前的末次冰期（22,000-10,000 年前）或旧石器晚期前期（40,000-22,000 年前），表明现代藏族人群的祖先早在 3 万多年前的旧石器晚期可能已经成功定居在青藏高原， 并在距今约 10,000-7,000 年前的新石器早期经历了中国西部农业人口向青藏高原的第二次 迁徙事件。旧石器晚期定居于青藏高原的早期定居者与新石器早期迁入的农业人口经过遗传 融合，形成了现代藏族人群的遗传多样性格局；同时将新石器农业和畜牧业技术带入青藏高 原地区，并成功建立了粟和青稞等农作物种植与牦牛畜牧业经济，导致青藏高原地区在最近 7-8 千年前经历了快速的人口增长。这两次主要的人群迁徙事件对现代藏族人群的遗传多样 性格局的形成具有同等的影响力。同时利用对候选基因全长序列的精细重测序方法，在国内 外高原适应的遗传机制研究中，率先对藏族高原低氧长期适应过程中发挥重要生物学功能的 EPAS1 及其负调控因子 EGLN1 等关键候选基因的功能进行了系统研究，并率先鉴定出这两 个基因的潜在的功能位点，为下一步的体内功能验证实验（转基因小鼠实验）提供了强有力 的基因组学证据。上述研究成果首次从遗传学角度描绘了一幅青藏高原现代人类史前定居与 迁徙的历史画面，从遗传学角度证明现代藏族人群对高原低氧的最佳遗传适应是经过 3 万多 年的长期适应的结果。研究成果发表于国际知名分子进化研究刊物 Molecular Biology and Evolution 2013, 30(8):1761-1778; Molecular Biology and Evolution 2013, 30(8):18891898。 2. 揭示人群进化历史差异对复杂疾病遗传分析的影响 目前，复杂疾病（如双向情感障碍、抑郁症等）的遗传学分析已在世界范围人群中广泛 开展。然而，即使是大样本量和高密度 SNP 的分析，在不同样本尤其是遗传背景差异很大 的人群中往往不能重复出疾病易感基因的相关性。人群生活的环境因素，如气候、饮食和生 活方式等可能是造成这种差异的原因，但更重要的原因可能是由于易感基因在不同种族的人 群中受到不同的自然选择或者遗传漂变等内在因素的影响，从而导致等位基因频率和连锁不 平衡模式的变化，并最终影响不同种族人群遗传相关性分析的结果，但这方面的证据却非常 少。有鉴于此，宿兵研究员的实验室（博士研究生李明）通过与世界数十家科研单位合作， 整合多个欧亚人群的数据，开展人群间复杂疾病遗传相关性分析的比较以检验上述假说。该 研究的前一部分工作主要集中在对欧美人群中一种复杂精神疾病—双向情感障碍的遗传学分 析上。他们通过对欧美人群大样本量（N>60,000）的病例 - 对照研究、大脑结构以及功能 核磁共振分析，鉴定了一个欧洲人群中新的双向情感障碍易感基因 CREB1。他们发现，该 基因区域包含了大量的高度连锁的 , 且与双向情感障碍显著相关的单核苷酸多态位点（SNP）， 并可能影响海马功能从而导致疾病发生。基因表达分析进一步提示，这些 SNP 可以显著影响 CREB1mRNA 的表达。然而，这些 CREB1 易感 SNP 位点在欧洲大陆以外的大部分人群中 （尤其是东亚人群）并不呈现多态性（以 rs6785 为例，下图），其风险等位基因在这些人群 中均不存在。为了解释这种现象产生的可能原因，他们利用千人基因组数据，对 CREB1 及 其邻近基因在欧洲和中国汉族人群中进行了群体遗传学分析。研究结果发现， CREB1 的一 个“邻居”基因—CCNYL1 在欧洲人群中受到强烈的正选择，但在中国汉族人群中并不受选择。 因此，他们推论，在欧洲人群中特有的 CREB1 的双向情感障碍易感 SNP 位点可能是由于 “邻居”基因 CCNYL1 受到选择而发生的遗传搭车效应。换言之，CREB1 在欧洲人群中风 险等位基因频率的增加是 CCNYL1 适应性进化带来的“负效应”，即遗传负荷。该研究进 一步支持了由自然选择造成的群体历史差异可能会影响某些复杂疾病易感性的遗传异质性， 而这也可能是目前在不同种族的人群中相关性分析重复结果很差的重要原因之一。研究结果 发表于国际精神病学著名刊物 Molecular Psychiatry, advance online 9, April 2013，doi: 10.1038/mp.2013.37 21 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Comparative Genomics Dr. Bing Su, principal investigator, The enlarged brain and highly developed cognitive skills are the most significant characteristics that set us apart from our relatives, the non-human primates. This evolutionary expansion is believed to be crucial to the highly developed cognitive abilities in humans, yet its genetic basis remains unsolved. our laboratory focuses on (1) the genetic mechanism underlying the dramatic enlargement of human brain and its highly developed cognitive skills during human evolution; (2) Origins and migration of modern human populations in East Asia and its adaptation to environmental stress. E-mail: sub@mail.kiz.ac.cn 1.Genetic evidence of Paleolithic colonization and Neolithic expansion of modern humans on the Tibetan Plateau Tibetans live on the highest plateau in the world, their current population size is nearly 5 million, and most of them live at an altitude exceeding 3,500 meters. Therefore, the Tibetan Plateau is a remarkable area for cultural and biological studies of human population histories. However, the chronological profile of the Tibetan Plateau’s colonization remains an unsolved question of human prehistory. To reconstruct the prehistoric colonization and demographic history of modern humans on the Tibetan Plateau, we systematically sampled 6,109 Tibetan individuals from 41 geographic populations across the entire region of the Tibetan Plateau and analyzed the phylogeographic patterns of both paternal (n = 2,354) and maternal (n = 6,109) lineages as well as genome-wide SNP markers (n = 50) in Tibetan populations. We found that there have been two distinct, major prehistoric migrations of modern humans into the Tibetan Plateau. The first migration was marked by ancient Tibetan genetic signatures dated to around 30,000 years ago, indicating that the initial peopling of the Tibetan Plateau by modern humans occurred during the Upper Paleolithic rather than Neolithic. We also found evidences for relatively young (only 7-10 thousand years old) shared Y chromosome and mitochondrial DNA haplotypes between Tibetans and Han Chinese, suggesting a second wave of migration during the early Neolithic. Collectively, the genetic data indicate that Tibetans have been adapted to a high altitude environment since initial colonization of the Tibetan Plateau in the early Upper Paleolithic, before the Last Glacial Maximum, followed by a rapid population expansion that coincided with the establishment of farming and yak pastoralism on the Plateau in the early Neolithic. Molecular Biology and Evolution 2013, 30(8):1761-1778; Molecular Biology and Evolution 2013, 30(8):1889-1898. 2. Allelic differences between Europeans and Chinese for CREB1 SNPs and their implications in gene expression regulation, hippocampal structure and function, and bipolar disorder susceptibility Bipolar disorder (BD) is a polygenic disorder that shares substantial genetic risk factors with major depressive disorder (MDD). Genetic analyses have reported numerous BD susceptibility genes, while some variants, such as single-nucleotide polymorphisms (SNPs) in CACNA1C have been successfully replicated, many others have not and subsequently their effects on the intermediate phenotypes cannot be verified. Here, we studied the MDD-related gene CREB1 in a set of independent BD sample groups of European ancestry (a total of 64 888 subjects) and identified multiple SNPs significantly associated with BD (the most significant being SNP rs6785[A], P=6.32 × 10−5, odds ratio (OR)=1.090). Risk SNPs were then subjected to further analyses in healthy Europeans for intermediate phenotypes of BD, including hippocampal volume, hippocampal function and cognitive performance. Our results showed that the risk SNPs were significantly associated with hippocampal volume and hippocampal function, with the risk alleles showing a decreased hippocampal volume and diminished activation of the left hippocampus, adding further evidence for their involvement in BD susceptibility. We also found the risk SNPs were strongly associated with CREB1 expression in lymphoblastoid cells (P<0.005) and the prefrontal cortex (P<1.0 × 10−6). Remarkably, population genetic analysis indicated that CREB1 displayed striking differences in allele frequencies between continental populations, and the risk alleles were completely absent in East Asian populations. We demonstrated that the regional prevalence of the CREB1 risk alleles in Europeans is likely caused by genetic hitchhiking due to natural selection acting on a nearby gene. Our results suggest that differential population histories due to natural selection on regional populations may lead to genetic heterogeneity of susceptibility to complex diseases, such as BD, and explain inconsistencies in detecting the genetic markers of these diseases among different ethnic populations. Molecular Psychiatry advance online publication 9 April 2013;doi: 10.1038/mp.2013.37 22 员工简介（Lab Staff） 工作人员（Staff） 石 宏 博士 副研究员 Dr. Hong Shi Associate Professor shihong@mail.kiz.ac.cn 祁学斌 博士 副研究员 Dr. Xuebin Qi, Associate Professor qixuebin@mail.kiz.ac.cn 张 慧 硕士 助理研究员 Ms. Hui Zhang, Research Associate zhanghui@mail.kiz.ac.cn 郭 彦 本科 助理研究员 Ms. Yan Guo, Research Associate Guoyan@mail.kiz.ac.cn 彭 忆 博士 助理研究员 Dr. Yi Peng, PhD. Research Assistant 石 磊 博士 助理研究员 Dr. Lei Shi, PhD. Research Assistant 研究生（Graduate Students） 2005-present 罗雄剑 Xiongjian Luo, 2005 王金凯 Jingkai Wang, 2005 杨若林 Ruolin Yang, 2005 黄 琳 Ling Huang, 2005 韩 冷 Leng Han, 2005 牛傲蕾 Aolei Niu, 2006 孙正华 Zhenghua Sun, 2006 彭 忆 Yi Peng, 2007 石 磊 Lei Shi, 2007 张雁峰 Yanfeng Zhang, 2007 李 明 Ming Li, 2008 杨立新 Lixin Yang, 2008 彭应梅 Yingmei Peng, 2008 杨召辉 Zhaohui Yang, 2009 曹向宇 Xiangyu Cao, 2009 向 坤 Kun Xiang, 2010 王 毅 Yi Wang, 2010 张 煦 Xu Zhang, 2010 林 强 Qiang Lin, 2011 刘杰伟 Jiewei Liu, 2012 杨晏冬 Yandong Yang, 2012 廖世玉 Shiyu Liao，2012 罗 鑫 Xin Luo， 2013 何一博 Yibo He，2013 遗传资源与进化国家重点实验室 2013 年 度 报 告 生物信息学与系统生物学 黄京飞，研究员，博士生导师，中国科学院昆明动物研究所副所长，云南省遗 传学会副理事长，遗传资源与进化国家重点实验室学术委员会委员。主要从事蛋白 质相互作用网络及其功能的演化、基于蛋白质进化的干扰肽的设计、复杂疾病机理 及其潜在药物靶点的发现研究， 先后在 Mol. Biol. Evol.、FEBS Lett.、PLoS ONE、BMC Bioinformatics，BMC Evol Biol, Mol BioSyst, Bioinformatics 等 刊物发表论文 50 余篇。曾获中国科学院自然科学三等奖和云南省自然科学一等奖各 1 项。已培养博士、硕士研究生 20 余名。 实验室主页：http://bsb.kiz.ac.cn/ 重要成果（Highlights） 论著（Publications） 1.Zhang AD, Dai SX, and Huang JF* Reconstruction and Analysis of Human Kidney-Specific Metabolic Network Based on Omics Data. BioMed Research I n t e r n a t i o n a l 2 0 1 3 , Vo l u m e 2 0 1 3 . doi:10.1155/2013/187509. 2. Yu Q, Huang JF*. The DEER database: A bridge connecting drugs, environmental effects, and regulations. Gene. 2013 May 15;520(2):98-105. 3. Wang J, Zhao YQ, Wang Y, Huang JF*. Molecular dynamics simulations and statistical coupling analysis reveal functional coevolution network of oncogenic mutations in the CDKN2ACDK6 complex. FEBS Lett. 2013 Jan 16;587(2):136-141 1. 非酒精性脂肪肝相关蛋白 PNPLA3 的 I148M 突变的分子机制研究 PNPLA3（含类 patatin 磷酸酯酶域蛋白 3）是一种同时具有三酰甘油脂肪酶 和酰基甘油 O- 酰基转移酶活性的多功能酶，最近的全基因组关联分析表面，许多 PNPLA3 的非同义突变与非酒精性脂肪肝密切相关。我们采用分子动力学和柔性对 接方法研究该突变对非酒精性脂肪肝的影响，结果发现突变 I148M 使得底物进入通 道大小显著的减小，限制了棕榈酸进入催化中心。本研究很好的解释了 I148M 突变 对 PNPLA3 酶的影响同时也为非酒精性脂肪肝的药物设计提供新的思路。 （Proteins: Structure, Function, and Bioinformatics） 2. 人类肾脏特异性代谢网络的构建与应用 人体代谢的异常通常会导致一系列的疾病甚至死亡，肾脏的代谢尤其重要。组 织特异的代谢网络有利于理解组织真实的生理与病理状况。我们构建了人类肾脏特 异性代谢网络并进行了详尽的分析和模拟。发现 了在代谢水平上管家基因和肾脏 特异基因在代谢网络中的不同功能特点从代谢水平上阐述了差异表达基因可能是通 过作用于代谢网络而对疾病产生显著影响。（BioMed Research International） 3. 遗传、药物以及环境因素互作网络的构建 药效和药物安全在个体上表现的多样性在目前临床试验中是一个主要的挑战， 个体的药物反应可以由遗传因素和环境因素共同决定，构建一个整合遗传和环境因 4. Wu M, Yu Q, Li X, Zheng J, Huang JF*, Kwoh CK. Benchmarking human protein complexes to investigate drugrelated systems and evaluate predicted protein complexes. PLoS One. 2013;8(2):e53197. 5.Xin YN, Zhao YQ, Lin ZH, Jiang X, Xuan SY, Huang JF*. Molecular dynamics simulation of PNPLA3 I148M polymorphism reveals reduced substrate access to the catalytic cavity. Proteins. 2013 Mar;81(3):406-414. 素与药物反应表型相互关系网络很有必要。我们建立了一个新的化学环境因素影响 药物反应关系的 DEER 数据库，该数据库包含了计算预测的化学环境因素和药物反 应的关系、假定的调节中间体如转录因子、细胞色素 P450（CYPs）、药物靶点、 转运蛋白等，为支持我们的预测我们也提供了化学因素的相似性。我们将该数据库 做成一个易于使用和下载的网页版服务器。 DEER 网址为： http://bsb.kiz.ac.cn:90/DEER/ 4. 人类蛋白质复合物用于评价药物相关系统的研究 蛋白复合体是实现细胞功能的关键实体，建立一个最新的人类蛋白复合体目录 来支持这些领域的研究很有必要，而现有的蛋白复合物数据库存在非常严重的冗余 现象。我们建立了一个强大的蛋白质复合物数据库 CHPC2012，可以用于蛋白相互 作用研究、蛋白功能研究、人类疾病研究、药物开发以及更多的相关领域研究。 23 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Bioinformatics and system biology Prof. Jing-Fei Huang, Principle Investigator, Deputy Director, Kunming Institute of Zoology, Chinese Academy of Sciences. The research is mainly focused on the structure basis of protein functional evolution, the evolutionary mechanism of protein/gene, protein interaction network and functional evolution, disturbing peptide design based on protein evolution, the mechanism of complex disease and potential drug target discovery. More than 50 papers have been published in Mol. Biol. Evol., FEBS Lett., Structure, Acta Crystall., J. Mol. Struct., J. Theor. Biol., J. Mol. Model., Mammalian Genome, PLoS ONE, BMC Bioinformatics, BMC Evol Biol, Mol. BioSyst and Bioinformatics. Email: huangjf@mail.kiz.ac.cn 1. Molecular dynamics simulation of PNPLA3 with mutation I148M reveals reduced substrate access to the catalytic cavity A missense mutation I148M in PNPLA3 is significantly correlated with nonalcoholic fatty liver disease (NAFLD). To glean insights into mutation's effect on enzymatic activity, we performed molecular dynamics simulation and flexible docking studies. Our data show that the size of the substrate-access entry site is significantly reduced in mutants, which limits the access of palmitic acid to the catalytic dyad. Besides, the binding free energy calculations suggest low affinity for substrate to mutant enzyme. The substrate-bound system simulations reveal that the spatial arrangement of palmitic acid is distinct in wild-type from that in mutant. The substrate recognition specificity is lost due to the loop where the I148M mutation was located. Our results provide strong evidence for the mechanism by which I148M affects the enzyme activity. 2.Reconstruction and Analysis of Human Kidney-Specific Metabolic Network Although kidney plays an essential role in the body, the available kidneyspecific model remains incomplete. This paper reports the reconstruction and characterization of the human kidney metabolic network based on transcriptome and proteome data. Importantly, a total of 267 potential metabolic biomarkers for kidneyrelated diseases were successfully explored using this model. Furthermore, we found that the discrepancies in metabolic processes of different tissues are directly corresponding to tissue's functions. Finally, the phenotypes of the differentially expressed genes in diabetic kidney disease were characterized, suggesting that these genes may affect disease development through altering kidney metabolism. 3. The DEER database: a bridge connecting drugs, environmental effects, and regulations Variability in patient drug responses can be caused by genetic factors and environmental factors (ENFs). Frameworks for understanding the association between ENFs and drug responses are lacking. In this study, we constructed a novel database, DEER, for interpretations of chemical ENF effects on drug responses. DEER includes computational predictions of the associations between chemical ENFs and drug responses. DEER currently encompasses 579 drugs, 401 chemical ENFs, and 9247 predicted drug-ENF associations. The entire dataset can be easily queried through a search page. DEER is available at http://bsb.kiz.ac.cn:90/DEER/. 4. Benchmarking Human Protein Complexes to Investigate Drug-Related Systems Human protein complexes are widely used for protein function annotation, inference of human protein interactome, disease gene prediction, and so on. Therefore, it is highly desired to build an up-to-date catalogue of human complexes to support the research in these applications. In this paper, we designed a set of concise operations to compile these redundant human complexes and built a comprehensive catalogue called CHPC2012. CHPC2012 achieves a higher coverage for proteins and protein complexes than those individual databases. It is also verified to be a set of complexes with high quality as its co-complex protein associations have a high overlap with protein-protein interactions (PPI) in various existing PPI databases. We demonstrated two distinct applications of CHPC2012. In particular, CHPC2012 provides more insights into drug development. we believe that the CHPC2012 catalogue is able to enhance the studies for protein interactions, protein functions, human diseases, drugs, and related fields of research. Web site: http://www1.i2r.a-star.edu.sg/xlli/CHPC2012/CHPC2012.htm. 24 员工简介（Lab Staff） 工作人员（Staff） 李功华 博士 助理研究员 Dr Gong-Hua Li, Assistant Professor ligonghua@mail.kiz.ac.cn 赵玉琪 Yu-Qi zhao Dr Yu-Qi zhao, Assistant Professor yookeee@163.com 代绍兴 博士 助理研究员 Dr Shao-Xing Dai, Assistant Professor daishaoxing@mail.kiz.ac.cn 廖爱文 秘书 Ms.Ai-Wen Liao, Secretary awliao@mail.kiz.ac.cn 刘 衡 技术员 Ms. Heng Liu, Technician liuh@mail.kiz.ac.cn 研究生（Graduate Students） 陈舜梅 Sun-Mei Chen 程东强 Dong-Qiang Cheng 张爱娣 Ai-Di zhang 郑俊娟 Jun-juan zheng 韩菲菲 Fei-Fei Han 郭义成 Yi-Cheng Guo 王玉晴 Yu-Qing Wang 张 琳 Lin zhang 廉 婷 Ting Lian 遗传资源与进化国家重点实验室 2013 年 度 报 告 真核细胞进化基因组学 文建凡，博士，研究员，遗传资源与进化国家重点实验室副主任。研究方 向“真核细胞进化基因组学”。以处在真核细胞进化的关键地位的单细胞生物 ( 代 表如贾第虫、衣藻、眼虫、领鞭毛虫等原生生物 ) 为主要研究对象，向下追溯 到原核生物，向上扩展到多细胞生物，开展真核细胞的结构和功能，特别是基因、 基因家族、功能途径基因群和基因组的多样性形成与进化研究，以及从适应性 进化角度开展有害生物 ( 如寄生虫）防治靶标的发掘利用，有益生物 ( 如藻类 ) 的高效、特异代谢途径的进化形成机制与利用等应用基础研究。 重要成果（Highlights） 1. 提出并初步检验了贾第虫为集“极端原始性”和“次生寄生适应性”于 论著（Publications） 一体的“嵌合体”假说 1. Feng JM, Tian HF, Wen JF*. Origin and Evolution of the Eukaryotic SSU Processome Revealed by a Comprehensive Genomic Analysis and Implications for the Origin of the Nucleolus. 2013.Genome Biol Evol.5(12):225567. 2. Zhang YJ, Yang CL, Hao YJ, Li Y, Chen B*, Wen JF*. Macroevolutionary trends of atomic composition and related functional group proportion in eukaryotic and prokaryotic proteins. 2013. Gene. S0378-1119(13)01510-2 . 3. Xiong J, Lu YM, Feng JM, ..., Miao W*. Tetrahymena Functional Genomics Database (TetraFGD): an integrated resource f o r Te t r a h y m e n a f u n c t i o n a l g e n o m i c s . DATABASE-OXFORD. 2013. doi: 10.1093/ database/bat008. （共同一作） 4. Xu J, Cheng YQ, Chen B, …, Wen JF, …. Depression in systemic lupus erythematosus patients is associated with link-polymorphism but not methylation status of the 5HTT promoter region. 2013. Lupus. 22(10):1001-10. 贾第虫究竟是原始的真核细胞还是因寄生而高度退化的细胞，国际上 颇存争议。我们基于长期的研究积累，提出了“贾第虫可能是“集‘极端 原始性’和‘次生寄生适应性’于一体的‘嵌合体’ ”的假说。并首先在 磷脂合成途径上对此进行了初步验证。通过系统的基因组搜索，获得了甘 油磷脂合成途径相关基因在三界生物代表物种中的分布，特别是首次鉴定 出贾第虫中参与该途径的全部 11 个基因。系统发育分析表明，这 11 个基 因中的 8 个位于真核生物的基部分支，而另外 3 个则是起源于原核生物的 水平基因转移。并且，与典型真核生物相比，贾第虫甘油磷脂合成途径中 的 Kennedy 途径和 PA 途径均不完整；对相关基因的进化分布分析结果表 明，贾第虫与原核生物一样，尚未发展出完整的 Kennedy 途径，而 PA 途 径的不完整性则极有可能是由于其寄生于肠道后发生了部分丢失而造成的 （肠道环境中富含溶血磷脂酸等中间产物从而勿需从头合成）。因此，本 研究表明，贾第虫的甘油磷脂合成途径既具有原始真核细胞的特点，又呈 现出寄生退化性的一面。 2. 揭示了蛋白质中有关原子和功能基团在原核生物进化成真核生物过程中 的宏进化规律 在生物的多个“复杂性等级（levels of complexity）”中，真核细胞 是其中重要的一级。从原核细胞（生物）进化出真核细胞（生物）是生物 5. Gao S, Xiong J, …, Wen JF, …, Miao W, and Liu YF. Impaired replication elongation in Tetrahymena mutants deficient in histone H3 Lys 27 monomethylation. 2013.Genes Dev. 27(15):1662-79. 进化史上最重要的跨越之一。在这一宏进化过程中，作为生命活动的最重 6. Sun GL, Yang YF, Xie FL, Wen JF, …. Deep Sequencing Reveals Transcriptome ReProgramming of Taxus × media Cells to the Elicitation with Methyl Jasmonate. 2013. PLoS One. 8(4): e62865. 原核蛋白具有更高比例的的氧、硫、氮原子；而且，功能基团分析结果显 7. 谢钢琴，陈兵，文建凡 *. 血吸虫等寄生扁 虫免疫逃避机制的研究进展 . 寄生虫与医学 昆虫学报 . 2013.22(3):194-198. 变化使得真核蛋白发展出更多的可用于执行复杂多样的生命活动的功能基 要执行者的生物大分子 --- 蛋白质，其原子组成和功能基团发生了怎样的 变化？通过全面地调查并比较了氨基酸的 5 种原子（氧、硫、氮、碳、氢） 及其侧链上功能基团在原核和真核蛋白中的组成情况后发现：真核蛋白较 示出真核蛋白趋向于含有更高比例的巯基、羟基和氨酰基，但甲硫基和羧 基的含量降低。以上结果的综合分析表明，在生物从原核到真核这一宏进 化过程中，氧原子和硫原子含量的明显增加及其所构成的相关功能基团的 团。该研究为原核生物到真核生物的宏进化研究提供了新的视角。 25 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Evolutionary Genomics of Eukaryotic Cells Dr. Jian-Fan Wen, Principal Investigator, Vice Director of the State Key Laboratory of Genetic Resources and Evolution. His group is mainly interested in the origin and evolution of the eukaryotic cell. Taking the protists, which occupy key positions in the eukaryotic cell evolution, as models, and combining with the data of prokaryotes and multicellular organisms, they study the biodiversity and origin and evolution of the structures and functions, especially of genes, gene families, gene groups of functional pathways and genomes, of the eukaryotic cells. Based on these basic studies, they also explore the new ways for the control and treatment of some harmful organisms (e.g. parasitic protozoa and schistosomes) and the applications of the effective and specific metabolic pathways. E-mail: wenjf@mail.kiz.ac.cn 1. Proposition and Verification of the hypothesis that Giardia is the combination of extreme primitiveness and highly parasitic adaptation 员工简介（Lab Staff） It is still controversial whether Giardia is a most primitive eukaryotic cell or a highly evolved parasite. Based on our previous studies, we proposed that this organism might 工作人员（Staff） be a combination of extreme primitiveness and highly parasitic adaptation. To test this hypothesis, we re-identified and confirmed the genes involved in glycerophospholipid biosynthesis pathway in Giardia, and reconstructed the pathway in the organism. We found that, compared with typical eukaryotic, Giardia’s Kennedy pathway and PA pathway are both incomplete. After we investigated the evolutionary history of the whole glycerophospholipid biosynthesis pathway in many representatives of the three domains of life, the following findings were observed: Giardia has not developed a complete Kennedy pathway as prokaryotes; but the PA pathway probably has been partly lost due to the adaption to its parasitic lifestyle. Our phylogenetic analysis of all the genes involvedin the pathway indicated that 8 giardial genes are the earliest-branching ones among eukaryotic homologs, while the other 3 giardial genes are probably acquired through horizontal gene transfer. Therefore Giardia glycerophospholipid biosynthesis pathway itself might be a combination of primitiveness and parasitic adaptation. Thus our results support the hypothesis. 2. Macroevolutionary trends of atomic composition and related functional group proportion in eukaryotic and prokaryotic proteins To fully explore the trends of atomic composition during the macroevolution from prokaryote to eukaryote, five atoms (oxygen, sulfur, nitrogen, carbon, hydrogen) and related functional groups in prokaryotic and eukaryotic proteins were surveyed and compared. Genome-wide analysis showed that eukaryotic proteins have more oxygen, sulfur and nitrogen atoms than prokaryotes do. Clusters of Orthologous Groups (COG) analysis revealed that oxygen, sulfur, carbon and hydrogen frequencies are higher in eukaryotic proteins than in their prokaryotic orthologs. Furthermore, functional group analysis demonstrated that eukaryotic proteins tend to have higher proportions of sulfhydryl, hydroxyl and acylamino, but lower of sulfide and carboxyl. Taken together, an apparent trend of increase was observed for oxygen and sulfur atoms in the macroevolution; the variation of oxygen and sulfur compositions and their related functional groups inmacroevolution made eukaryotic proteins carry more useful functional groups. These results will be helpful for better understanding the functional significances of atomic composition evolution. 26 陈 兵 助理研究员 Bing Chen Research Assistant chenbing@mail.kiz.ac.cn 邵静茹 助理实验师 Jingru Shao Experimentalist shaojr@mail.kiz.ac.cn 研究生（Graduate Students） 叶青青 Qingqing Ye 2010 李毓劲 Yujing Li 2011 谢钢琴 Gangqin Xie 2011 王文敏 Wenmin Wang 2011 姚友旭 Youxu Yao 2012 黄海波 Haibo Huang 2013 薛 敏 Min Xue 2013 遗传资源与进化国家重点实验室 2013 年 度 报 告 进化与功能基因组学研究组 施鹏，博士，研究员。中科院昆明进化与遗传国家重点实验室 PI，进化 和功能基因组学科组负责人。2008 年入选中科院“百人计划”，长期从事进 化基因组学和功能基因组学研究。本研究室的研究兴趣集中在以下两个主要 问题： 1 ）动物如何通过感觉系统的整合来适应它们所处的环境？ 2 ）如何通过自然选择的理论来探讨基因型与表型的关系？ 重要成果（Highlights） 论著（Publications） 1. 肠道微生物紊乱与轻型肝性脑病发生的相关性 肝硬化并发的肝性脑病，是连接消化系统和神经、精神系统的重大疾病， 也是导致肝硬化患者死亡的主要因素之一。其发生与肠道含尿素酶细菌有关。 1. Zhang Z #, Zhai H, Geng J, Yu R, Ren H, Fan H, Shi P#. 2013. Large-scale survey of gut microbiota associated with MHE via 16S rRNA-based pyrosequencing. Am J 以此为出发点，本研究收集了 26 例轻型肝性脑病患者的粪便样品，同时以相 应健康家属以及 25 例非肝性脑病肝硬化患者的粪便样品作为对照，结合细菌 16S rRNA 基因 PCR 扩增和高通量 454-Amplicon 测序 , 我们首先从肠道微 Gastroenterol. 108(10): 1601-1611. 生物多样性和组分、肠道核心微生物共变异网络出发，揭示了三个人群的肠道 2. Wu T, Zhang Z, Liu B, Hou D, Liang Y, Zhang J, Shi P #. 2013. Gut microbiota 微生物组的显著差异；同时，我们也鉴定了一个新的含尿素酶的肠道细菌。该 细菌的鉴定对于未来以降低血氨为目的的肝性脑病的临床治疗提供了重要的靶 dysbiosis and bacterial community assembly associated with cholesterol gallstones in large- 标。相关论文已经在 Am J Gastroenterol （2013）上发表。 scale study. BMC Genomics. 14(1): 669. 2. 肠道微生物失调与胆固醇结石形成相关的细菌群落的组装 3. Gao T, Li N, Zhang Y and Shi P#. 2013. The complete mitochondrial genome of Japanese sandeel Ammodytes personatus (Perciformes, Ammodytidae): rare structure in control region compared. Mitochondrial DNA. 24(4): 320322. 4. Geng J, Fan H, Tang X, Zhai H, Zhang Z#. 2013. Diversified pattern of the human colorectal cancer microbiome. Gut Pathogens. 5(1): 2. 胆囊结石是欧美及我国最为普遍的胃肠道疾病。以往研究提示胆囊结石的 发生一定程度与肠道微生物失调以及胆道细菌感染有关，然而到目前为止仍缺 乏充分的系统论证。为此，我们采用细菌 16S RNA 基因为基础的大规模 454 测序，分析了 29 个胆囊结石患者肠道和胆道（胆汁和胆石）细菌多样性，并 与 38 个正常个体的肠道细菌多样性进行比较。通过以上分析，我们第一次揭 示了胆结石患者肠道微生态失衡以及结石和胆汁相关微生物多样性全貌。在此 基础上，我们进一步探讨了胆道微生物与结石形成的相关性，为进一步理解胆 囊结石细菌学机制具有极其重要的参考价值。相关论文发表在 BMC Genomics （2013）。 27 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Evolutionary and Functional Genomics Dr. Peng Shi, Principal Investigator. There are two major topics in our lab. (1) Exploring the genetic mechanisms of animals adaptation to the extreme environments using large-scale data. (2) Functionally resolving the molecular mechanisms of adaptive evolution for animals using functional platforms. My lab investigates these questions using a combination of empirical and computational approaches to analyze the large-scale data. Email: ship@mail.kiz.ac.cn 1. Large-Scale Survey of Gut Microbiota Associated With MHE Via 16S rRNA-Based Pyrosequencing By using 16S rRNA-based pyrosequencing and multiple comparative analyses, we found the continuous overrepresentation of two bacterial families, Streptococcaceae and Veillonellaceae, in cirrhotic patients with and without MHE, compared with normal individuals. In addition, we also discovered an MHE-unique interplay pattern of gut microbiota largely influenced by the members of those two families. Following these findings, we further revealed that gut urease-containing bacteria Streptococcus salivarius was absent in the normal group but was present in cirrhotic patients with and without MHE. The abundance of S. salivarius was significantly higher in cirrhotic patients with MHE than in those without (P = 0.030), and the change in the amount of this bacteria was positively correlated with ammonia accumulation ( R = 0.58, P = 0.003) in cirrhotic patients with MHE but not in those without. Gut microbiota dysbiosis may be associated with the presence of MHE in cirrhotic patients, in particular with ammonia-increasing phenotype in MHE. Gut ammonia-increasing bacteria S. salivarius might be expected to be a potential biomarker of ammonia-lowering therapies in cirrhotic patients with MHE. 员工简介（Lab Staff） 工作人员（Staff） 刘 振 博士 副研究员 Dr. Zhen Liu, Associate Professor 张志刚 博士 副研究员 Dr. Zhigang Zhang, Associate Professor 杨 晖 博士 助理研究员 Dr. Hui Yang, Assistant Professor 郝军军 博士 助理研究员 Dr. Junjun Hao, Assistant Professor 叶志强 博士 助理研究员 Dr. Zhiqiang Ye, Assistant Professor 胡玲玲 博士 助理研究员 Dr. Lingling Hu, Assistant Professor 余 蕊 实验员 Assistant Experimentalist 任海清 实验员 Assistant Experimentalist 周 鑫 实验员 Assistant Experimentalist 研究生（Graduate Students） 王 维 Wei Wang, 2009 许东明 Dongming Xu, 2010 祁飞燕 Feiyan Qi, 2011 罗 杰 Jie Luo, 2011 Fig. Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study Elucidating gut microbiota in gallstone patients and complex bacterial colonization of cholesterol gallstones may help in predicting and lowering the risk of cholelithiasis. We describe the composition of bacterial communities of gut, bile, and gallstones in 29 gallstone patients and of gut in 38 normal individuals, based upon large-scale 454 sequencing of bacterial 16S rRNA genes of all 120 samples. Conclusively, this study for the first time discovered gut microbiota dysbiosis potentially associated with cholesterol gallstones. This study further showed a first large-scale glimpse of biliary tract microbiota associated with cholesterol gallstones, ultimately which provides potentially biological and medical implications about the role of bacteria in the formation cholesterol gallstones. 28 郑智中 Zhizhong Zheng, 2012 杨松霖 Songlin Yang, 2012 李 芸 Yun Li, 2013 郭雨龙 Yulong Guo, 2013 遗传资源与进化国家重点实验室 2013 年 度 报 告 分子人类学 孔庆鹏，中国科学院昆明动物研究所，研究员、博士生导师。目前已在本领 域著名国际 SCI 期刊 Am J Hum Genet、PNAS、Hum Mol Genet 及 Mol Biol Evol 等上接受发表论文及评论 50 余篇。在国际人类线粒体 DNA 研究领域具有一定 影响。研究组目前的主要研究方向：东亚人群源流历史与人类重大疾病及重要性状 的遗传学基础。 重要成果 (Highlights) 1. 中国人群老年痴呆症的研究 论著（Publications） 老年痴呆症是一种严重的神经系统退行性疾病。2012 年冰岛人群中发现稀有突 变 (A673T) 可以保护正常人群免于老年痴呆症，并降低其认知能力损伤，为老年痴 呆症的研究和治疗提供了新的希望。为了研究该突变在中国长寿人群中是否存在并 发挥作用，我们通过基因测序及高分辨率溶解曲线的方法，在中国长寿人群中对该 基因进行了检测。该研究选取了来自海南和四川两个省的 2641 个健康个体，其中包 括 1,237 个长寿老人平均年龄 96.9 岁 ) 和 1404 个 年 轻 对 照（ 平 均 年 龄 44.2 岁）。研究分析表明，无论是在长寿 人群还是对照人群中，均未发现该突 变的存在。鉴于中国人群的老年痴呆 症发病率远低于欧洲和北美，这提示 中国长寿人群中可能存在其他的保护 机制。 （ * 为通讯作者） 1. Liu Y-W, He Y-H, Zhang Y-X, Cai W-W*, Yang L-Q, Xu L-Y, Kong Q-P* (2013) Absence of A673T variant in APP gene indicates an alternative protective mechanism contributing to longevity in Chinese. Neurobiology of Aging (In press) 2. Cheng Y-T, Liu J, Yang L-Q, Sun C, Kong Q-P* (2013) Mitochondrial DNA content contributes to climate adaptation in Chinese populations. PLoS ONE, 8(11):e79536 3. Li R-L, Wang H-W, Yang L-Q, Zhang B-M, Li Y-J, Hu J-S, Kong Q-P* (2013) The whole mitochondrial genome of the Cynom olgus ma ca que (Mac a ca fascicularis). Mitochondrial DNA (online) 4. He Y-H, Lu X, Cai W-W*, Yang L-Q, Xu L-Y, Sun H-P, Kong Q-P* (2013) Mitochondrial DNA content contributes to healthy aging in Chinese: a study from nonagenarians and centenarians. Neurobiology of Aging (In press) 5. He Y-H, Zhang Y-X, Yang L-Q, Liao X-P, Zhang Q-Y, Cai W-W*, Kong Q-P* (2013) Assessment of the health status of centenarians in the South of China: a cross-sectional study. Journal of the American Geriatrics Society (In press) 6. Liu J, Xu L-Y, Li R-L, Li E-M*, Kong Q-P* (2013) Evaluating the susceptibility of mitochondrial DNA germline mutations in Chinese cancer patients. Current Molecular Medicine (In press) 7. Zhong L, Tang J, Kong Q-P*, Sun C, Zhou W-P, Yang M, Yao Y-G, Zhang Y-P* (2013) Reappraising the relationship between mitochondrial DNA variant m.16189T>C and type 2 diabetes mellitus in East Asian populations. Current Molecular Medicine (In press) 2. 气候适应与 mtDNA 拷贝数的关系研究 为了研究气候适应与 mtDNA 拷贝数之间的关系，我们在全中国范围内收集了 27 个人群样本，并对这些样本进行了 mtDNA 拷贝数测定，研究结果发现北方人群 的 mtDNA 拷贝数水平高于南方群体，此后进一步将所得到的结果与收集到的中国 气候数据进行回归分析发现，线粒体 DNA 拷贝数与气温有较好的拟合关系。根据以 往的功能性研究的推测较高的 mtDNA 含量可增加能量代谢相关酶的表达水平从而 影响生物产热过程。研究工作表明 mtDNA 拷贝数的增加对于寒冷环境下人类机体 的产热有较高的选择优势。 3. 长寿老人线粒体 DNA 含量对健康衰老的影响研究 长寿老人，特别是百岁老人，往往能逃避或延缓老年性疾病的侵扰，提示他们的 线粒体 DNA 含量可能与普通老年人群不同。为了验证这一猜想，我们检测了 426 个 长寿个体（包括 90 岁以上和百岁老人）以及 537 个年轻对照（40-70 岁）外周血白 细胞的线粒体 DNA 含量。结果发现：40 岁到 70 岁个体的线粒体 DNA 含量和年龄 呈负相关关系，即年龄越大，线粒体含量越低。但令人吃惊的是，长寿老人的线粒 体 DNA 含量不但没有下降，反而要显著高于老年组。为了确保结果的真实性，我们 在两个群体（海南和四川 ) 中进行 了验证，并且选择线粒体 DNA 的 不同片段检测线粒体 DNA 含量， 都得到相同的结果。因此，长寿 老人之所以能规避老年性疾病侵 扰的原因很可能是他们拥有相对 较高的线粒体 DNA 含量，使得线 粒体的产能功能得以维护，从而 最终到达健康长寿。 29 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Molecular Anthropology Dr. Qing-Peng Kong, Professor, Kunming Institute of Zoology, Chinese Academy of Sciences. My laboratory is mainly interested in the following fields: (1) mtDNA phylogenomics in Asia (especially Eastern Asia) and reconstructing the prehistory of Asian populations by using multiple genetic markers; (2) understanding the genetic basis of longevity and major disease. E-mail: kongqp@mail.kiz.ac.cn 1. Absence of A673T variant in APP gene in Chinese longevity individuals 员工简介（Lab Staff） Alzheimer’s disease (AD) is a disease characterized by central nervous system degeneration 工作人员（Staff） that produces progressive memory impairment, cognitive dysfunction, personality changes, and linguistic difficulties, and other neuropsychiatric symptoms. Previous studies suggested that 何永捍 助理研究员 mutations in the APP exons 16 and 17, encoding the β-amyloid peptide (Aβ), contributed to occurrence of the disease . However, a recently observed rare mutation A673T in APP exon 16 was suggested to significantly reduce the generation of harmful β-amyloid, thereby decreasing the occurrence of AD and the elderly cognitive decline in Icelander population. To test whether He Yonghan, Assistant Professor 刘 佳 助理研究员 Liu Jia, Assistant Professor 李其刚 研究实习员 the A673T contributes to Chinese population, 1,237 healthy longevity individuals (mean age Li Qigang, Research Assistant 96.9) and 1,404 matched younger controls (mean age 44.2) were collected and genotyped for the variant. Our study failed to observe this variant in either the longevity subjects or the controls. Given the previous observation from Asians, our result suggests that the A673T variant was not 杨利琴 实验师 involved in the longevity in Chinese; some other protective mechanisms may contribute to lower incidence of AD in Chinese centenarians. (Neurobiology of Aging.2014) Chen Xiaoqiong, Assistan Technician 2.Investigation of a relationship between mtDNA content and climate adaption 研究生（Graduate Students） We analyze the distribution of mtDNA content among 27 Chinese ethnic populations residing across China and find a significant association between mtDNA content and climate, with northern populations having significantly higher mtDNA content than southern populations. Functional studies have shown that high mtDNA content Yang Liqin, Technician 陈小琼 助理实验师 程耀霆 Cheng Yaoting 2008 李玉春 Li Yuchun 2009 肖富辉 Xiao Fuhui 2010 王晓雄 Wang Xiaoxiong 2011 correlates with anncrease in the expression of energy metabolism enzymes, which may accelerate thermogenesis. This suggests that the significantly higher mtDNA content observed in northern populations may confer a selective advantage in adapting to colder 李 越 Li Yue 2011 刘耀文 Liu Yaowen 2012 田娇阳 Tian Jiaoyang 2012 吴 焕 Wu Huan 2012 余 琴 northern climates. 3. Effect of mitochondrial DNA content on healthy aging of long lived individuals Mitochondrial DNA (mtDNA) content plays an important role in energy production and sustaining normal physiological function. A decline in the mtDNA content and subsequent dysfunction cause various senile diseases, with decreasing mtDNA content observed in the elderly with age-related diseases. In contrast, the oldest olds, e.g. centenarians, have a delayed or reduced prevalence of these diseases, suggesting centenarians may have a different pattern of the mtDNA content, enabling them to keep normal mitochondrial functions to help delay or escape senile diseases. To test this hypothesis, a total of 961 subjects, consisting of 424 longevity subjects and 537 younger controls from Hainan and Sichuan provinces of China, were recruited for this study. The mtDNA content was found to be inversely associated with age among age group 40-70. Surprisingly, no reduction of mtDNA content was observed in nonagenarians and centenarians; instead, these oldest old showed a significant increase than the elderly people aged between 50 and 70. The results suggest the higher mtDNA content may convey a beneficial effect to the longevity people through assuring sufficient energy supply. 30 Yu Qin 2013 遗传资源与进化国家重点实验室 2013 年 度 报 告 计算生物与医学生态学研究组 马占山 研究员，博导 , 计算生物与医学生态学学科负责人。 2010 年 11 月中科 院“百人计划 ( 杰出技术人才 )”引进。2011 年入选“云南省高端科技人才”和“百名海 外高层次人才”计划。美国 Idaho 大学计算机科学 (2008 年 ) 和昆虫学 (1997 年 ) 双博士、 计算机科学和计算生物学研究科学家。并具有在硅谷等地长达八年多的涵盖电子、网络、 软件、信息安全领域的计算机高级工程师经历。是总部设在英国伦敦的“Faculty 1000 of Biology & Medicine”成员 [ 也是目前该机构在 Microbial Evolution & Genomics 领域的唯一华人 ]，以第一和责任作者在计算机科学、工程数学、仿生计算和通讯、认知 科学、昆虫学、生态学、医学微生物学等领域发表八十余篇论文。 重要成果（Highlights） 论著（Publications） 1. Zhang ZG, Geng JW, Tang XD, Fan H, Xu JC, Wen XJ, Zhanshan(Sam) Ma*,Peng Shi*. 2013. Spatial heterogeneity and cooccurrence patterns of human mucosal associated intestinal microbiota. The ISME Journal, doi:10.1038/ismej.2013.185 2. Zhanshan (Sam) Ma. 2013.Stochastic P o p u l a t i o n s , P o w e r L a w, a n d F i t n e s s Aggregation in Genetic Algorithms. Fundamenta Informaticae,vol. 122, pp173206. 3. Zhanshan (Sam) Ma. 2013.First passage time and first passage percolation models for analyzing network resilience and effective strategies in strategic information warfare research. I.J. Information and Computer Security. 5(4): 334-358. Research Focus: Big-Data Driven, Network-Science Supported 研究领域简介 Computational Biology and Medical Ecology 网络分析作为描述事物间相互关系的科学理论和方法 , 已成为分析复 杂生物学问题的重要手段。其起源可追溯至 18 世纪著名数学家欧拉提 出的“七桥问题”。事实上 , 欧拉创立的图论一直是网络分析最重要的 数学理论基础之一。上世纪 60 年代著名数学家 Erdös & Rényi 的经典论 文奠定了随机图论的理论基础。然而 , 网络分析的广泛应用（即“网络 科学”的崛起）在很大程度归功于物理学家 Watts & Strogatz (1998) 和 Barabasi & Albert (1999) 先后发表于 Nature 和 Science 的两篇论文所 催化。他们的研究发现 , 许多自然、社会、经济等学科中所描述的网络 , 其实很少符合数学家研究多年的 “随机网络”，这些开创性的研究突破 了 Erdos & Renyi 随机图论模型的假设，从而极大的推动了科学界对网 络分析理论和技术的研究。特别是网络科学为生物大数据分析、可视化、 模拟建模提供了理想方法和技术。 本实验室现阶段主要进行“人体宏基因组生态网络”、“癌症基 因调控网络”和“脑神经网络” 三大类生物（生态）网络的研究。例 如通过对人体宏基因组生态网络的研究，我们旨在揭示疾病和健康与 宏基因生态网络稳定性之间的有机关系，从而为医学生态学和个性化医 疗提供理论基础和研究技术。在网络科学理论领域，我们研究旨在建 立网络可靠性、可存活性、稳定性的统一理论，并发展出了一系列数 学模型和计算分析算法（例如：Extended Evolutionary Game Theory, Dynamic Hybrid Fault Models, Three- Layer Survivability Analysis, Byzantine Generals Playing Evolutionary Games)。 这些研究结果汇总 在即将由德国 Springer 出版的一部专著中（Towards a Unified Theory for Reliability, Survivability and Resilience, Springer 2014 in Press)。 其 中 所 讨 论 的“ 进 化 博 弈 网 络”(Extended Evolutionary Games on Networks) 在以上三大类生物网络研究中的应用，应取得一些重要突破。 另外，围绕以上核心研究领域，我们也积极开展高性能 GPU 并行 计算、计算智能、以及面向三代测序技术的基因组装、宏基因组 OTU 分 类、等新算法和软件的研发。这些计算技术的开发研究对于其它基础和 应用研究具有非常关键的支撑作用。 31 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Computational Biology and Medical Ecology Biography of the lab director: Zhanshan (Sam) Ma received his double PhDs in Computer Science, and Entomology in 2008, and 1997, respectively, both from the University of Idaho (UI), USA. In November 2010, he was retained as a Professor and Principal Investigator by Kunming Institute of Zoology (KIZ), the Chinese Academy of Sciences (CAS) through “The Elite 100 Scientists Program” of the CAS. Prior to joining in KIZ, he was a Research Scientist (in Computational Biology & Computer Science) at UI. He was a senior network and software engineer from 1998 to 2006 in the computer industry in Silicon Valley, USA. Dr. Ma has been keeping dual track publishing in both Computer Science and Biology with more than 70 peer-refereed papers in premier platforms such as IEEE Transactions on Reliability, Science Translational Medicine, The ISME Journal. He is a member of London-based “Faculty 1000 of Biology and Medicine”. Email: ma@vandals.uidaho.edu or ma@mail.kiz.ac.cn Monographs 专著 员工简介（Lab Staff） 生物信息学导论 (An Introduction to Bioinformatics) 工作人员（Staff） 科学出版社 (Science Press, Beijing, in Press 2014) 马占山 等编著 Zhanshan (Sam) Ma et al. 第一篇 : 生物信息学的计算科学背景 Part I. Computational Foundations of Bioinformatics 第一章 : 生物信息学的多学科、跨学科框架 1. Multidisciplinary Framework of Bioinformatics 第二章 : 生物信息学的计算科学基础 2. Computational Foundation of Bioinformatics 第三章 : 生物信息学中重要统计计算模型 3. Statistical Bioinformatics 第四章 : 进化计算、进化博弈论、计算智能 4. Applications of Computational Intelligence 第五章 : 生物 ( 生态 ) 网络分析技术和软件 5. Network Biology: Algorithms and Software Tools 叶丹丹 研究实习员 Dandan Ye Research Associate 董 萍 研究实习员 Ping Dong Research Associate 第 二 篇 :Omics 技 术 的 生 物 信 息 学 分 析 Part II. Bioinformatics Supporting-Omics 研究生（Graduate Students） Technologies 第六章 : 基因测序技术和组装软件概述 6. Genome Assembly: Algorithms and Software 第七章 : 基因芯片技术数据分析 7. Bioinformatics Analysis of Microarray Data 第八章 : 宏基因组分析软件平台 8. Bioinformatics Pipeline for Metagenomics Research 第九章 : 转录组组装常用软件 9. Bioinformatics Analysis of Transcriptomics Data 第十章 : 蛋白质组学研究常用软件 10. Bioinformatics Tools for Proteomics Research 第十一章 : 代谢组学研究常用软件 11. Bioinformatics and Mathematical Modeling for Metabolomics 第十二章 : 溯祖树与系统发育树构建常用软件和算法 12. Coalescent and Phylogenetics Trees 关 琼 Qiong Guan，2011 樊萌萌 Mengmeng 李连伟 Lianwei Fan，2012 Li， 2012 王娅丽 Yali Wang, 2013 唐华阳 Huayang Tang， 2013 第三篇 : 生物信息学分析的应用 Part III. Applications 第十三章 : 表观遗传学研究的生物信息学方法 13. Computational Epigenetics 第十四章 : 新药物发现中的生物信息学方法 14. Computational Drug Discovery 第十五章 : 单细胞测序数据生物信息学分析 15. Single-Cell & Single-Molecular Sequencing Techniques 第十六章 : 医学生态学、癌症基因组学、与个性化医疗 16. Medical Ecology, Cancer Genomics and Personalized Medicine Towards a Unified Theory for Reliability, Survivability, and Resilience of Complex Networks by Zhanshan (Sam) Ma, Springer 2014 (in Press) The monograph for the first time presents a unified treatment of three tightly coupled fields: reliability, survivability, and resilience, which underlie many critical problems in diverse scientific and technological fields including engineering reliability, computer networks, biological/ecological systems, critical national infrastructure protection, strategic information warfare, financial stability, as well as emergency response and management. The author identified and/or developed a set of mathematical and computational approaches to the analysis and modeling of the three above-mentioned areas in a coherent manner by integrating survival analysis, dynamic hybrid fault models, and evolutionary game theory. The treatment takes advantages of transdisciplinary approaches by drawing biological/ecological inspirations and integrating computational, mathematical and statistical models, to develop a unified architecture and set of corresponding methods for studying the reliability, survivability and resilience of diverse complex network systems such as wireless sensor networks (WSN), aerospace prognostic and health management (PHM), animal communication networks, financial networks, and human microbiome networks. 32 遗传资源与进化国家重点实验室 2013 年 度 报 告 神经系统的发育机制与演化 毛炳宇，博士，研究员，中德马普青年科学家小组组长，遗传资源与进 化国家重点实验室副主任。先后获得国家自然科学基金委杰出青年基金、重 点项目资助。实验室主要以非洲爪蟾和文昌鱼为动物模型研究神经系统的早 期发育机制及其演化。 实验室主页：http://159.226.149.45/maolab/ 泛素连接酶 RNF220 在 Wnt 信号传导与发育中的功能 重要成果（Highlights） 论著（Publications） 1. Ma P, Xia Y, Ma L, Zhao S, Mao B. (2013) Xenopus Nkx6.1 and Nkx6.2 are required for mid–hindbrain boundary development. Dev Genes Evol. 223:253–259 Wnt/β-catenin 信号在发育与肿瘤发生中具有重要作用。RNF220 是我们鉴定的一个 泛素连接酶。在筛选其可能的蛋白靶点过程中，我们发现 RNF220 可与 β-catenin 结合。 然而，与预期截然相反的是，RNF220 不会促进 β-catenin 的泛素化与降解，反而会引 起其去泛素化而提高其稳定性。进一步的研究发现，这一过程是由一个与 RNF220 相互作 用的去泛素化酶 USP7 介导的。在结肠癌细胞系 HCT116 和 SW480 中，通过 RNAi 敲低 RNF220 的表达，可显著降低细胞中的 Wnt 信号活性， 并降低 Wnt 信号靶基因的表达，表 明 RNF220/USP7 介导的 Wnt 信号调节可能在肿瘤发生中具有一定贡献。 RNF220 敲除小 鼠的中后脑发育出现明显异常，但在这一过程 RNF220 是否是通过调节 Wnt 信号途径活性 而起作用的，这一问题仍有待于进一步的研究。 2. Li X, Pu J, Jiang S, Su J, Kong L, Mao B, Sun H, Li Y. (2013)Henryin, an ent-kaurane diterpenoid, inhibits Wnt signaling through interference with β-catenin/TCF4 interaction in colorectal cancer cells. PLoS ONE, 8:e68525. 图 1. RNF220 特异性结合 β-catenin. A，B, 在 HEK293 细胞系中，RNF220 与 beta-catenin 可相互沉淀下来。C，用于免疫 共沉淀的 RNF220 各种截短形式的示意图。 D，RNF220 的各种截短形式在 HEK293 细胞系 中都可以把 beta-catenin 全长蛋白沉淀下来。 E，用于免疫共沉淀的 beta-catenin 的各种截 短形式的示意图。TAD，transcription activation domain。F，除了缺失 N 端 1-473 氨基酸 的 beta-catenin 的截短形式以外的其它 beta-catenin 的截短形式都可以在 HEK293 细胞系 中把 RNF220 的全长蛋白沉淀下来。 Fig.1. RNF220 interacts with β-catenin. A, B, RNF220 and beta-catenin can pull-down each other in 293 cells. C, The structures of the RNF220 deletion constructs used in D. D, The 3 deletion constructs of RNF220 can all pull-down beta catenin in 293 cells. E,The structures of the beta-catenin deletion constructs used in F. TAD, transcription activation domain. F,The btta-catenin construct lacking the first 1-473 amino acids fails to pull-down RNF220 in 293 cells. 33 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Mechanisms of neural patterning and evolution Dr. Bingyu Mao, Principal Investigator, Ph. D. (1998, Shandong University, China). The molecular mechanisms of neural patterning and how these mechanisms evolved during vertebrate origin are the focuses of our lab. We use the amphibian Xenopus and the cephalochordate amphioxus as our model animals. E-mail: mao@mail.kiz.ac.cn The roles of RNF220 in Wnt signaling and development Wnt/β-catenin signaling plays a central role in development and is also involved in a diverse array of human diseases. RNF220 is an RING finger E3 ubiquitin ligase we identified before. In a screen for potential target of RNF220, we found that RNF220 is able to interact withβ-catenin, the key component of the canonical Wnt signaling pathway. However, instead of promoting its ubquitination and proteasomal degradation, we found that RNF220 in fact de-ubiquitinates and stabilizes β-catenin which is mediated through its interaction with USP7, an ubiquitin specific peptidase. Our studies uncover a new mechanism controlling β-catenin protein level during Wnt/β-catenin signaling transduction. The RNF220 knockout mice showed severe defect in midbrain and hindbrain development. Whether it works through modulating Wnt signaling in this process is under investigation. 员工简介（Lab Staff） 工作人员（Staff） 李朝翠 高级实验师 Chaocui Li, Senior Technician 马鹏程 助理研究员 Pengcheng Ma, Assistant Professor 研究生（Graduate Students） 张祖明 Zuming Zhang, 2008 江世友 Shiyou Jiang， 2009 孙 健 Jian Sun， 2009 图 2，RNF220 促 进 β-catenin 的 去泛素化，而这一过程依赖于去泛素化酶 USP7。 Fig.2. Co-expression of RNF220 d e u b i q u i t i n a te s β - c a t e n i n a n d t h i s process is dependent on ubiquitin specific peptidase 7 (USP7). 杨相彩 Xiangcai Yang, 2010 王晓磊 Xiaolei Wang，2011 刘晓亮 Xiaoliang Liu，2011 谢建新 Jianxin Xie，2012 李永鑫 Yongxin Li，2013 图 3. RNF220 参与调节 Wnt 信号活 性的模型。 Fig.3. A model for the role of RNF220 in Wnt signaling regulation. 34 遗传资源与进化国家重点实验室 2013 年 度 报 告 哺乳动物胚胎发育 郑 萍 , 博士，研究员，课题组长，以灵长类（猕猴）和小鼠为动物模型， 研究哺乳类卵母细胞及着床前胚胎发育调控。2009 年 6 月通过中科院项目“百 人计划”引进昆明动物研究所，加入遗传资源与进化国家重点实验室，并组建 哺乳动物胚胎发育课题组。研究方向为配子发育生物学和早期胚胎发育调控。 重要成果（Highlights） 论著（Publications） 1. 胚胎干细胞维持遗传物质稳定性的分子调控机制 多能干细胞在再生医学中有广阔的应用前景，但多能干细胞的安全性是决 定它们能否成功应用于再生医学的重要前提。理解多能干细胞如何维持遗传物 1. Zheng P, Baibakov B, Wang 质的稳定性是保证多能干细胞安全应用的关键。我们在小鼠胚胎干细胞 (ESC) XH, Dean J. PtdIns(3,4,5)P3 is 中鉴定了一个维持 ESC 遗传物质稳定性的关键多能调控因子 Filia。Filia 在未 constitutively synthesized and 分化 ESC 中特异表达，其缺失使 ESC 的遗传物质迅速发生变异，并产生高致瘤 required for spindle translocation 性。Filia 定位在中心体和线粒体上，调控中心体的功能，也调控 DNA 损伤反 during meiosis in mouse oocytes. J 应的多个环节（包括损伤信号传导、细胞周期检查点功能，DNA 损伤修复以及 Cell Sci, 2013, 126, 715-721 损伤细胞的分化和凋亡）。这些功能的执行受不同的功能结构域和蛋白质磷酸 2. Bo ZHAO, Yi-Xian CUN, XieChao HE, Ping ZHENG. Maternaleffect Floped gene is essential for the derivation of embryonic stem cells in mice. Zoological Research 34 (E3): E82-E86 化修饰调控。 Filia 具有一定的物种保守性。初步分析人类 Filia 的同源蛋白 ECAT1 在人 ESC 中的表达情况及功能，提示 ECAT1 蛋白也可能起着类似功能。人 ESC 中 ECAT1 的具体功能及作用机制正在进一步研究中。 2. 哺乳动物雌性生殖干细胞再生现象的研究 无脊椎动物 ( 如果蝇 ) 和低等脊椎动物 ( 如鸟类和鱼类 ) 卵巢内存在卵巢生 殖干细胞 (Ovarian germ stem cells), 生殖干细胞通过持续更新和分化产生新 的卵细胞。但哺乳动物卵巢内是否也存在生殖干细胞及雌性配子的再生却争议 了近 60 年，目前尚无定论。明确生理条件下哺乳动物卵巢中是否存在生殖干细 胞及其再生活动，并研究其再生活动的规律和调控机制，将使我们重新认识哺 乳动物卵细胞发生的生物学调控，并可能利用卵巢生殖干细胞延缓和治疗生理 及病理情况下女性卵巢功能衰退。我们利用两种转基因工具小鼠，通过体内谱 系示踪技术（in vivo lineage tracing）研究了小鼠卵巢中是否存在生殖干细胞 及卵细胞的再生现象。通过 1 天、3 天、2 月、4 月的细胞示踪研究，我们获得 了确凿的证据证明生理条件下小鼠卵巢中的确存在生殖干细胞及卵细胞的再生 过程，相关结果正在撰写论文。同时，我们也以猕猴为非人灵长类模型，开展 了灵长类是否同样存在卵巢生殖干细胞的研究。 35 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Mammalian Embryonic Development Dr. Ping Zheng, Group leader, joined in Kunming Institute of Zoology, Chinese Academy of Sciences in June 2009.Dr. Zheng’s lab is interested in female germ cell biology and early embryonic development. E-mail: zhengp@mail.kiz.ac.cn 1. Preserving genetic integrity of embryonic stem cells Throughout the development, there is a constant need to ensure the genomic integrity. Early embryos and by extrapolation the pluripotent stem cells (PSCs) are designated to develop into all cell types in the body and therefore equipped with robust mechanisms to preserve their genomic integrity. Furthermore, PSCs have promising implication in cell-based therapy. Investigating the molecular basis governing the genomic integrity of PSCs as well as early embryos is critical to address the tumorigenic challenges and to understand how early embryos sustain their genome stability. We identified Filia as a guardian of genome stability in mouse embryonic stem cells (mESCs). Filia is specifically expressed in early embryos as well as ESCs and localized on centrosome and mitochondria. It functions as a master regulator of genome integrity by regulating centrosome biogenesis and DNA damage response. Depletion of Filia from mESCs led to defective centrosomes, aneuploidy, and impairment of DDR including failure to undergo signaling transduction, cell cycle arrest, DNA damage repair, and ESC differentiation and apoptosis upon DNA damage. As a result, mESCs without Filia display robust genomic instability and undergo malignant transformation. The homologous of Filia was reported in primates. ECAT1, the human homolog of mouse Filia, encode a protein sharing 36% identity of amino acid sequence with mouse Filia. Whether human ECAT1 displays similar critical roles in guarding genomic stability of human ESCs and early embryos are under the investigation. 2. Stem cell-based neo-oogenesis takes place in adult mice ovary under physiological condition Whether neo-oogenesis and follicle replenishment take place post-natally in mammals remain controversial for decades. Although some in vitro studies suggested the existence of germline stem cells in mouse and human ovary, no direct evidence supported the neo-oogenesis under physiological condition. Herein we utilized in vivo lineage tracing strategy to address this question. Oct4expressing cells were labeled with GFP in pubertal mice. Short and long term tracing for up to four months revealed the continuous presence of GFP+Stra8+ or GFP+Sycp3+ germ cell populations in a fraction of GFP-labeled small germ cells. Furthermore, rare GFP-labeled cells were captured in undergoing mitosis to generate two daughter germ cells. These results demonstrated the presence of neo-oogenesis in mice ovary under physiological condition. 36 员工简介（Lab Staff） 工作人员（Staff） 和协超 高级实验师 He, Xiechao: Senior technician 赵 博 助理研究员 Zhao, Bo: Research associate 吕永青 研究实习员 Lu, Yongqing: Research assistant 博士后 （Post-doc) 段莹亮 Duan, Yingliang， 2013 研究生 （Graduate Students） 李朝晖 Li, Chaohui 张锦娟 Zhang, Jinjuan 2011 2011 王鑫轶 Wang, Xinyi 2012 何大健 He, Dajian 2012 郭 琨 Guo, Kun 张伟道 Zhang, Weidao 2013 班文赞 Ban, Wenzan 2013 2012 遗传资源与进化国家重点实验室 2013 年 度 报 告 发育的印迹调控与进化 焦保卫 , 博士，研究员，博士生导师。学科组以小鼠和其它 动物为对象研究发育与进化的遗传印迹调控，主要从事乳腺干细 胞的调控、X 染色体失活机制及进化意义、发育过程印迹基因的 功能等研究。 实验室目前研究方向 重要成果（Highlights） 论著（Publications） 1. XCI 在发育中的作用 activity of RLIM/Rnf12 is regulated a. XCI 对于乳腺发育的表观遗传调控作用 近来愈来愈多的证据表明乳腺的泌乳功能极大程度地被表观遗传机制控制： 如跨代遗传机制影响。我们的结论表明这一隔代现象与表观遗传中的另外一个 重要表观遗传机制 -XCI 有关。该部分将致力于分析 XCI 对于小鼠和其它模式 动物的乳腺及其它营养器官发育的影响。 b. X 耦联基因在乳腺干细胞调控过程中的作用 乳腺干细胞属于成体干细胞的一种，具有自我更新和分化为其他细胞系的 能力。它对于乳腺发育具有至关重要的作用。我们初步数据显示 XCI 对于乳腺 干细胞具有调控作用，并将通过 X 藕联基因的功能研究分析和探讨 XCI 对乳腺 干细胞的影响。 by phosphorylation-dependent 2. XCI 在遗传印迹进化中的角色分析 nucleocytoplasmic shuttling. Mol Biol a. 乳腺泌乳性状在人工选择下的演化 遗传印迹是进化发育研究中的重要问题，对于其起源及演化目前存在三种 假说：亲本冲突假说（kinship conflict）、共适应假说（coadaptation）和性别 冲突假说（intralocus sexual conflict）。我们在小鼠乳腺中的分析倾向于支持 亲本冲突假说。除了自然选择，人工选择筛选下乳腺性状对于亲本冲突的处理 策略将是一个值得探讨的科学问题。我们将通过各种模式及家养哺乳动物乳腺 和胎盘中 XCI 的状态，分析 XCI 在成体组织和胚胎组织中功能的平衡及其进化 意义。 b. XCI 在性染色体进化中的角色分析 不同的哺乳动物具有不同的 XCI 格局，它们对于 XCI 中的重要分子和现 象都呈现出极大的多样性。即使在小鼠和人这两个相近的物种，人们也已发现 极大的区别。对于这方面进行研究将丰富人们对于包括 X 染色体进化等现象的 理解。 在初步的探讨中，我们将以我所优势动物模型树鼩和猕猴等为切入点， 通过分析对比小鼠 XCI，为揭示 X 染色体进化规律提供支持论据。 Jiao B, Taniguchi-Ishigaki N, Güngör C, Peters MA, Chen YW, Riethdorf S, Drung A, Ahronian LG, Shin J, Pagnis R, Pantel K, Tachibana T, Lewis BC, Johnsen SA, Bach I. Functional Cell. 2013 24(19):3085-96. 3. 印记基因对乳腺发育的影响 印记基因 (imprinted gene) 为父母源等位基因中呈现出单侧表达的等位基 因。研究发现，印记基因不仅在早期胚胎发育过程中扮演重要作用，在哺乳动 物的成体发育、某些遗传疾病及癌症的发生都与印迹基因密切相关。 我们将 以杂交子一代小鼠不同发育时期的乳腺作为研究对象，探讨基因印记在调控乳 腺发育方面的作用及其相关作用机制。 4. lncRNA 对乳腺发育的影响 长链非编码 RNA（lncRNA）是一类转录本长度超过 200 核苷酸的功能性 RNA 分子。它们缺乏编码成蛋白的功能，但能以多种方式调控生命活动。我们 首先通过转录组学等技术筛选得到一些影响乳腺发育的相关 lncRNAs，希望对 这些相关的 lncRNAs 在乳腺发育的作用进行深入全面的探讨。 37 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Imprinting in Development and Evolution Dr. Baowei Jiao, Principal Investigator, joined in Kunming Institute of Zoology, Chinese Academy of Sciencessince July of 2013. The research team is mainly interested in regulation of mammary gland stem cells, mechanism and evolutionary significance of X chromosome inactivation, imprinted genes and long non-coding RNA in development and evolution. E-mail: jiaobaowei@mail.kiz.ac.cn Research Interests: 员工简介（Lab Staff） 1. The role of XCI in development a.The epigenetic regulation of XCI in mammary gland development 工作人员（Staff） Recently, more and more evidence shows that the mammary gland function of lactating is greatly regulated by epigenetic modication, such as inter-generational genetic. Our conclusions demonstrate that the phenomenon of inter-generational epigenetic is closely linked to another important epigenetic mechanism--XCI. We will focus on analyzing the impact of XCI in breast and other nutrients organ development for mice and other animals. 杨 钦 助理实验师 b.The role of X-linked genes on mammary stem cell 研究生 （Graduate Students） As one of adult stem cells, Mammary stem cells are capable of self-renewal and differentiation into other cell lines, which is crucial for breast development. Our preliminary data shows that XCI play an role in regulation of mammary stem cells; next, we will investigate the effects of XCI on mammary stem cells through analyzing the function of X-linked genes locus. 2. The role of XCI in the evolution of genetic imprinting a. Evolution of lactating under artificial selection Evolutionary developmental is an important issue on studying genetic imprinting, which exists three hypotheses: kinship conflict, co-adaptation and intra-locus sexual conflict. Our analysis in mouse mammary gland tends to support the hypothesis of kinship conflict. In addition to natural selection, artificial selection will be a wonderful strategy of exploring kinship conflict in screening breast traits . We will analyze the function of XCI in adult tissues and embryonic tissues development by studying the XCI status of breast and placenta in mouse and other model organism. b. The role of XCI in sex chromosome evolution Different mammals have their own pattern on XCI. Even between mouse and human, it shows a great difference, which will offer more comprehensive understanding on sex chromosome evolution. We will compare pattern of XCI among different animals, such as tree shrews and macaques, in order to reveal the law of the evolution on X chromosome. 3. The impact of imprinted genes on breast development In genomic imprinting, genes within a discrete domain are coordinately regulated and expressed according to parent of origin. Researches show that imprinted genes do not only play an important role in the process of early embryonic development, they are also closely related to the adult mammalian development, certain genetic diseases and cancers. We will investigate the role of breast development and its mechanisms by using mammary tissue at different stages of hybrid F1 mouse. 4. The influence of lncRNA on breast development lncRNA is an RNA molecule that is longer than 200 nucleotides and that is not translated into a protein. lncRNAs of all kinds have been implicated in a range of developmental processes and diseases, but knowledge of the mechanisms by which they act is still surprisingly limited. We will expect to get some lncRNAs related to breast development by transcriptomics technology screening, and then carry out a comprehensive discussion of the role of these related lncRNAs on mammary gland 38 Qin Yang, Research Assistant 胡 佳 助理实验师 Jia Hu, Research Assistant 柯 浩 Ke Hao 2013 博士生 赵丽敏 Zhao Limin 2013 硕士生 遗传资源与进化国家重点实验室 2013 年 度 报 告 昆明野生动物细胞库 昆明野生动物细胞库成立于 1986 年，是以保存动物的遗传资源 和遗传多样性为主要目的的细胞库。现已保存有 317 种动物的细胞系 1689 株 10000 余份。大多数为哺乳动物的细胞系，其中包括 59 种国家 级重点保护动物的细胞系。目前，昆明细胞库是国家实验细胞资源共 享平台、中国科学院野生生物资源库、中国西南野生生物种质库的成 员单位之一，也是遗传资源与进化国家重点实验室的成员单位之一。 2013 年主要工作进展 重要成果（Highlights） 论著（Publications） 2013 年度 , 野生动物细胞库利用从野外采集以及从其他途径获得的动 Ye JJ, Ma L, Yang LJ, Wang JH, Wang YL, Guo H, Gong N, Nie WH, Zhao SH. Partial AZFc duplications not deletions are associated with male infertility in the Yi populication of Yunnan Province, China. J. Zhejiang Univ-Sci B( Biomed &Biotechnol), 2013, 14: 807-815. 物材料，共新建各类动物细胞系 104 株 , 其中包括金线鲃、红原鸡、鸵鸟和 获奖 (Awards) 半野生、半家养的牛种。由于半家养，有的大额牛和黄牛可产生杂种，但仅 滇金丝猴等 4 种野生动物的细胞系 14 株 , 7 种家养动物的细胞系 17 株 ,EBV 转化的人淋巴细胞系 28 株以及人和动物的肿瘤细胞系 45 株；复苏和扩增各 类动物细胞系 266 株；为遗传资源与进化国家重点实验室及全国各地的研究 人员提供细胞服务 256 株次；提供核型分析、支原体检测和荧光检测等技术 服务 23 次。 在今年的对外服务中，我们重点为大额牛的基因组测序提供技术支持。 大额牛，又称为独龙牛，仅分布在云南的独龙江和缅甸北部，是一种珍贵的 从外形上无法区分大额牛及大额牛与黄牛的杂种。2013 年 , 遗传资源与进 ， 杨凤堂，佴文惠，刘瑞清， 王金焕，苏伟婷，陈玉泽。2013 年 度云南省科学技术进步奖三等奖（野 生动物细胞库的创建及其应用） 化国家重点实验室的分子进化与基因多样性研究组要进行大额牛的测序工 作。为了测序结果的准确性，我们首先通过外周血培养的方法，为该课题组 准备做测序的大额牛进行核型分析，结果发现该个体核型为 2n=59，是大额 牛与黄牛的杂种，不能用于测序工作。之后我们从野生动物细胞库中保存的 大额牛细胞系中找到了一株 2n=58 的雄性大额牛的细胞系，为他们进行了 大额牛细胞的复苏扩增，提供了 300 余瓶细胞，满足了课题组的测序需求。 2n=59 的“大额牛”G- 带核型 ( 按黄牛的染色体编号排序 ) 另外，我们还完成了红原鸡不同组织来源的体细胞系的建立工作。红原 鸡是家鸡的野生祖先。我们共建立了来自红原鸡的心、肺、肾、肌肉等不同 组织的各类体细胞系 7 株 , 为后续的基因定位和功能基因研究储备了材料。 39 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Kunming wild animal cell bank In order to conserve genetic resource and genetic diversity of animals, Kunming wild animal cell bank was established in Kunming Institute of Zoology, Chinese Academy of Science in 1986. Up to now 1689 cell lines belonging to 317 species have been preserved in our cell bank. Most cell lines are derived from mammals. Among the species, 59 are national protected wildlife in China. Now it is one branch of National Platform of Experimental Cell Resources for Sci-Tech, Wildlife Resource Bank of CAS, China Germplasm Bank of Wild Species, and State Key Laboratory of Genetic Resources and Evolution. The main work in 2013 In 2013, We have established and frozen 104 cell lines from various wild and domestic animals. Among these cell lines, 14 cell lines are derived from 4 species of wild animals such as Golden-line barbel, Red junglefowl, Ostrich and Black snub-nosed monkey; 17 cell lines are established from 7 species of domestic animals; 28 cell lines are obtained by EBV-transferred human lymphocytes; and 45 cell lines are tumor cell lines from human and other animals. Two hundred and sixty-six of frozen-stored cell lines were also resuscitated and subcultured. In this year, the cell bank provided 256 cell lines and 23 times of technical service such as karyotype analysis, mycoplasma contamination test and Fluorescence detection for the researchers not only at State key laboratory of genetic resources and evolution, but also at other Chinese universities and scientific research institutions. 员工简介（Lab Staff） 工作人员（Staff） 佴文惠 正高级工程师 Wenhui Nie Senior Engineer whnie@mail.kiz.ac.cn 王金焕 高级实验师 Jinhuan Wang Senior Experimentalist wangjing315@163.com 苏伟婷 实验师 Weiting Su, Experimentalist weitingsu@126.com 胡 怡 技术员 Yu Hu Technician 524140624@qq.com The gayal The Red junglefowl In the serve work of this year, an important work that we have done is providing technical supports for the gayal genome sequencing. The gayals, also named as “Dulong” cattles, are mainly distributed in the narrow valley of Dulong river in western Yunnan, China and its adjacent region in northern Burma. Due to half-domesticated, the hybrids of gayal and cattle are possible to be produced. However, it is difficult to distinguish the hybrid of gayal and cattle from the gayals only based on the appearance. The group of molecular evolution and genome diversity in the State Key Laboratory of Genentic Resources and Evolution wanted to do the sequencing of gayal genome and got a gayal individual in 2013. In order to make sure that the sequencing species is right, we analyzed the karyotype of the gayal individual by using the method of peripheral blood lymphocyte culture . The result indicated that the gayal individual has a karyotype of 2n=59. It is a hybrid of gayal and cattle . Therefore, the materials of this individual is not suitable to do the gayal genome sequencing. After then, we found a 2n=58 male gayal cell line in our cell bank. We resuscitated and subcultured this cell line, and provided more than 300 bottles gayal cells to the group, and meet their requirments. Another important work done in 2013 was the establishment of cell lines derived from various tissues of Red junglefowl. The Red junglefowl is thought to be ancestral to the domestic chicken. In total, we have established 7 cell lines derived from the tissues of the Red junglefowl heart, lung, kidney and muscle etc. These cell lines are stored for future use in gene mapping and functional gene research. 40 遗传资源与进化国家重点实验室 2013 年 度 报 告 生命条形码南方中心 生命条形码南方中心是应我国加入国际生命条形码计划 (iBOL) 的 需求，于 2011 年成立的专门从事 DNA 条形码相关的科学研究、技术革 新和应用推广的创新单元，同时也是中国西南野生生物种质资源库动物 分库无脊椎动物遗传资源库和云南濒科委司法鉴定中心分子生物学部的 挂靠部门。主要任务包括：组织和推动我国一系列重大 DNA 条形码计划 的实施；采集和收集野生无脊椎动物资源丰富本室遗传资源；探索分子 生物学技术在经济社会中的应用等。 论著 Publications 1 . L I Z - X , WA N G L - Y, Z HA NG Z - S . , 2 0 1 3 . T h e first record of the wolf spider subfamily Zoicinae from China (Araneae: Lycosidae), with the description of two new species. Zootaxa.3701: 24–34. 2. Pierson T, Yan F, Wang Y-Y, Papenfuss T., 2013. A survey for the Chinese giant salamander (Andrias davidianus Blanchard, 1871) in the Qinghai Province. Amphibian & Reptile Conservation. 8: 1-6 1. 基于 测序技术的混合线粒体基因组测序方法 基于新推出的 Ion Torrent 测序技术，我们开发了一套利用长 PCR 扩增片段混合 测序的线粒体基因组测序方法。该方法已经在两栖纲、哺乳纲、蛛形纲和爬行纲 41 个物种获得了较好的扩增结果，并利用一张 314 芯片获得两栖纲 7 个物种的线粒体全 基因组序列。 Data sheet Data size: 5.6 MB mtDNA data: 94.75% Coverage: 92.68 x N of contig.: 8 N50: 8250 bp N90: 1110 bp Scaffold: 16787 bp Precision rate: 99.7 % 2. 肉制品溯源技术——DNA 条形码方法 食品安全是国家安全战略的一部分，事关全人类的健康福祉，其中食品检测是保 障食品安全的技术基础。我们针对传统食品检测技术无法对肉制品来源和真伪进行检 测的缺点，以 DNA 条码技术为核心，实现了鱼肉和主要畜禽肉类来源快速检测的关 键技术，在工商、食品监督管理等领域取得一批示范性应用成果，获得社会的广泛赞誉。 41 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Southern China DNA Barcoding Center (SCDBC) year of 2013, the SCDBC got several advances in high throughout mtDNA genome sequencing using the In the next generation Ion Torrent technology, highlights on food traceability using DNA barcoding, and co-hosted the fifth international barcode of life conference in Kunming. By widely using the automation and informatics tools, the SCDBC collected over 35K specimens in field, got 11,085 standard DNA barcode, and took over 5000 images from the original pinned specimens. 3. Co-hosted the Fifth International Barcode of Life Conference Follow the voices from the first (2005 London), the second (2007 Taipei), the third (2009, Mexico) and the fourth (2011, Adelaide) international Barcode of Life conference, Kunming ushered the fifth conference. As one of the important partner of this meeting, SCDBC and other departments worked together to host, training, shared knowledge with, and build a social network from over four hundred participants from 43 countries and/or areas in 5 continents. During this conference, the Scientific Steering Committee of the iBOL announced a new declaration, KUNMING Declaration on the Promotion of DNA Barcoding and Biodiversity Science. That is a milestone in the history of barcoding of life project. 员工简介（Lab Staff） 工作人员（Staff） 王文智 助理研究员 Wen-zhi Wang Assistant Research Fellow 王运宇 实验师 Yun-yu Wang Engineer 李宗煦 研究实习员 Zong-xv Lee Fellow 陈 兴 研究实习员 Xing Chen Fellow 王玉水 助理实验师 Yu-shui Wang Technician After the conference, SCDBC co-hosted the international barcoding of life training courses in Kunming and Lijiang. The training course includes three sections: informatics, laboratory techniques, and field work. 20 trainees from 16 countries (mostly from developing countries) spent two weeks in this course. 42 刘 浏 助理实验员 Liu Liu Technician 遗传资源与进化国家重点实验室 2013 年 度 报 告 中心实验室 中心实验室是隶属于遗传资源与进化国家重点实验室的公共技术服务平台，于 2008 年 11 月正式投入使用。 目前，实验室共有基因组学分析平台、蛋白质组学分析平台、高性能计算平台三大技术平台，同时还涵盖一些 中小型仪器设备。每个平台都配有专业技术人员，从实验设计，仪器操作，到数据分析，为仪器设备使用者提 供全方位的技术支持与服务。 实验室主页：http://www.kiz.cas.cn/gre/gre6/gre61/ 三大技术平台 工作人员 （Staff） 许绍斌 工程师 Mr. Shaobin Xu Engineer xushao@mail.kiz.ac.cn 一、基因组学分析平台 2. QuantStudio 12K Flex 实时定量 PCR 1. Ion Torrent 测序系统 仪 QuantStudio 12K Flex 实 时 定 量 Ion Torrent 测序系统（Ion Proton 与 Ion PGM）主要用于基因组测序、转录组 PCR 仪是新一代荧光定量 PCR 仪。在实 测序、外显子组测序、基因测序、ChIP 测序， 现常规定量 PCR 仪功能的基础上，又可 以 满 足 8 连 管、96 孔 板、384 孔 板 以 及 线粒体基因组测序、甲基化分析等等。 OpenArray 芯片等不同通量的实验需求。 李桂梅 实验师 Mrs. Guimei Li Experimentalist liguimei246@mail.kiz.ac.cn 唐 嘉 工程师 Mrs. Jia Tang Engineer tangj@mail.kiz.ac.cn 杨双娟 助理实验师 Ms. Shuangjuan Yang Assistant Experimentalist yangsj@mail.kiz.ac.cn 3. GeXP 多功能遗传分析仪 Beckman GenomeLab 多功能遗传分 析仪是功能基因研究的新平台，可应用于 多基因定量表达谱分析；序列分析；AFLP 分析；STR/SSR 分析；SNP 分析等。 4. 实时定量 PCR 仪 Roche LightCycler 480 实时定量 PCR 仪能够实现 96 个样本实时、在线 的快速循环 PCR 反应。其通过监测核 酸扩增时的荧光，可对产生的结果进行 定量检测或基因分型分析。 二、蛋白质组学分析平台 双向电泳技术是蛋白质组学研究的基础技 术平台，是一种分析细胞、组织或其他生物样 本提取的蛋白质混合物的有力手段。利用该技 术可对一种样本中的许多蛋白质同时进行系统 化的分离、鉴定、定量。另外，该技术还可检 测翻译后和翻译过程中的蛋白质修饰。 三、高性能计算平台 该平台是采用曙光 4000A 为基础的 Linux 高性能计算机群，机群由 39 个曙光 620 机架服务器和 1 个 DELL R910 服务器（512 GB 内存胖节点）组成。机群具有每秒 2.929 万亿次的峰值速度。在线存储采用具有 40GB 缓存 20TB 总容量的 Panasas 8 系列并行 存储，可以支持高吞吐率的并行 IO。系统使用 Torque2.4.8 和 maui3.3 作为机群作业 调度管理软件，可以支持 288 个计算核的并行计算作业。 43 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Core Facility The Core Facility of the State Key Laboratory of Genetic Resources and Evolution is established in November 2008. Currently, the center contains three major technology platforms: Genomic Analysis Platform, Proteomic Analysis Platform, and High Performance Computing Platform. Each platform is supported by professional technicians to assist the users from experimental design, instrument operation, to data analysis. http://www.kiz.cas.cn/gre/gre6/gre61/ The Three Technical Platforms 4. Roche LightCycler 480 The LightCycler 480 System enables you to perform real-time, online PCR combined with rapid cycling of up to 96 samples. After monitoring fluorescence during nucleic acid amplification, results can be analyzed, for example, by quantification or genotyping. The outstanding thermal homogeneity and cycling speed of the LightCycler 480.System provide exact results in a short time. I. Genomic Analysis Platform 1. Ion Torrent Sequencers The Key applications of the Ion Torrent Sequencers ( Ion Proton and Ion PGM ) are genome sequencing, Whole transcriptome sequencing, Exome sequencing, Gene sequencing, ChIP sequencing, Mitochondrial sequencing, Methylation analysis, and so on. II. Proteomic Analysis Platform 2. QuantStudio 12K Flex 实时定量 PCR 仪 III. High Performance Computing Platform QuantStudio 12K Flex Real-Time PCR System is new level for qPCR, designed for maximum throughput, flexibility, and scalability. It contains not only OpenArray®, 384-well, 96-well blocks, but also digital PCR for high accuracy and sensitivity. 3. Beckman GeXP Genetic Analysis System The GenomeLab SNPstream Genotyping System provides an automated scalable system capable of performing from 4,600 to over 3,000,000 SNP genotypes per day. Combined with multiplexing capabilities, experimental layouts and operational flexibility, this enables you to process a wide range of studies. 44 2-D electrophoresis is a powerful and widely used method for the analysis of complex protein mixtures extracted from cells, tissues, or other biological samples. The analysis involves the systematic separation, identification, and quantification of many proteins simultaneously from a single sample. The technique is also unique in its ability to detect postand co-translational modifications. The HPC is a 2.929 TFlops linux cluster consists of 39 servers from dawning (now Sugon) and one huge memory(512GB RAM) R910 server from DELL.A set of 20TB raw volume size high performance PAS8 from Panasas serves as the online storage. Torque and Maui were used to manage the job scheduling system, thus it can support parallel computing jobs scale up to 288 CPU cores.Now we have more than 95 users from KIZ and some other partners such as Yunnan University. The accumulated used walltime is over 1million CPU hours. At the end of 2011 there were more than 60 bioinformatics software such as Qiime ,RaxML installed. 遗传资源与进化国家重点实验室 2013 年 度 报 告 重要基金项目 Key Projects and Fundings 我国重要家养动植物在人工选择下进化的遗传和基因组机制，973 项目；执行年限：2013-2017；项目负责人： 王文；金额：1207 万（2013-2014 年经费）。 The Genetic and Genomic Mechanisms of Important Domesticated Plants and Animals in China during the Evolution of Artificial Selection. National Basic Research Program (973) project, Period: 20132017; Head of project, Wen Wang; Amount: RMB 12.07 million for 2013-2014. 神经网络功能发育中的可塑性机制（抑郁症和阿尔茨海默病的神经发育基础研究子课题），973 课题 ; 执行年限： 2009-2013；项目负责人：黄京飞；金额：200 万元。 Basic Research on Neural Development of Depression and Alzheimer's Disease, ---Neural Plasticity Mechanisms during Neural Network Development. National Basic Research Program (973) project, Period, 2009-2013; Head of project, JingFei Huang; Amount: RMB 2.0 million. 基于自然保护区的 DNA 条形码，科技基础工作专项；执行年限：2012-2017；项目负责人：Douglas W Yu；金额： 808 万元。 DNA Barcoding Based on Nature Conservation Areas; The Special Foundation for Technology Basis Work, Period, 2012-2017; Head of project, Douglas W. Yu; Amount: RMB8.08 million. 基因组中新遗传结构的起源与动物的适应进化 , 国家自然科学基金创新研究群体 , 执行年限：2014-2016；项 目负责人：王文；金额：600 万元。 Evolutionary Origins of New Genetic Structure in Genome and Animals’ Adaptive Evolution. Innovation team project of National Science Foundation of China, Period, 2014-2016; Head of project, Wen Wang; Amount: RMB 6.0 million. 哺乳动物适应性进化的遗传学机制，国家杰出青年基金，执行年限：2014-2017；项目负责人：施鹏；金额： 200 万元。 Genetic mechanisms of adaptive evolution in mammals. National Science Fund for Distinguished Young Scholars, Period, 2014-2017; Head of project, Peng Shi; Amount: RMB2.0 million. 进化生态学与进化博弈论，国家杰出青年基金 , 执行年限：2014-2017；项目负责人：王瑞武；金额：200 万元。 Evolutionary Ecology and Evolutionary Game Theory. National Science Fund for Distinguished Young Scholars, Period, 2014-2017; Head of project, Ruiwu Wang; Amount: RMB2.0 million. 适应性进化的分子机制研究，国家自然科学基金优秀重点实验室项目；执行年限：2012-2015；项目负责人： 黄京飞；金额：300 万 Molecular Mechanisms of Adaptive Evolution, Excellent State Key Laboratory project from the National Science Foundation of China, Period, 2012-2015; Head of project, JingFei Huang; Amount: RMB 3.0 million. 动物 DNA 条形码标准基因及高通量条形码新方法的研究，国家自然科学基金重大项目；执行年限：20112014；项目负责人：张亚平；金额：516 万元（云南省额外匹配 200 万元）。 Standard Gene and High-throughput Methods for Animal DNA Barcoding, Major project of National Science Foundation of China, Period: 2011-2014; Head of project, Yaping Zhang; Amount: RMB 5.16 million（Yunnan Province additionally matched RMB 2 million）. 45 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT 灵长类大脑进化关键基因的功能研究，国家自然科学基金重点项目；执行年限：2012-2016；项目负责人：宿兵； 金额：380 万。 Function of Key Genes in Primate Brain Evolution. Key project of National Science Foundation of China, Period: 2012-2016; Head of project, Bing Su; Amount: RMB 3.8 million. 哺乳动物化学能感觉系统适应性进化的分子机制，国家自然科学基金重点项目；执行年限：2010-2013；项目 负责人：施鹏；金额：179 万元。 Molecular Mechanism of Adaptive Evolution in Mammalian Chemical Sensory System . Key project of National Science Foundation of China, Period, 2010-2013; Head of project, Peng Shi; Amount: RMB1.79 million. 年轻新基因在果蝇发育和进化中的作用，国家自然科学基金重点项目；执行年限：2010-2013；项目负责人：王文； 金额：180 万元。 The Functions of Young New Genes in Drosophila Development and Evolution. Key project of National Science Foundation of China, Period, 2010-2013; Head of project, Wen Wang; Amount: RMB1.80 million. 藏族人群对高原低氧极端环境遗传适应的多基因互作机制研究，国家自然科学基金重大研究计划重点项目；执 行年限：2013-2016；项目负责人：宿兵；金额：320 万。 Genetic Adaptation the Tibetan Population to High Altitude Hypoxia Extreme Environment. Major research plan of National Science Foundation of China, Period, 2013-2016; Head of project, Bing Su; Amount: RMB3.20 million. 荒漠鼠适应荒漠极端生境的分子机制研究，国家自然科学基金重大研究计划重点项目；执行年限：20132016；项目负责人：沈永义；金额：350 万。 Molecular Mechanisms of Desert Rodent to Adapt to the Desert Extreme Habitat. Major Research Plan of National Science Foundation of China, Period, 2013-2016; Head of project, Yongyi Shen; Amount: RMB3.50 million. 家蚕在人工驯化过程中基因组的表观遗传学进化，国家自然科学基金重大研究计划；执行年限：2010-2013； 项目负责人：王文；金额：200 万元。 Epigenetic Evolution of Silkworm Genome during the Domestication Process. Major research plan of National Science Foundation of China, Period, 2010-2013; Head of project, Wen Wang; Amount: RMB2.00 million. 非模式动植物的进化基因组学研究，国家自然科学基金委两岸合作项目；执行年限：2010-2013；项目负责人： 张亚平；金额：120 万元。 Evolutionary Genomic Research on Non-model Plant and Animal. Projects of International Cooperation and Exchanges NSFC, Period, 2010-2013; Head of project, Yaping Zhang; Amount: RMB1.20 million. 中国西南汉族群体中 ZNF804A 基因与精神分裂症的遗传易感性及功能分析，国家自然科学基金 - 云南省联合 基金；执行年限：2013-2016；项目负责人：宿兵；金额：200 万。 Genetic Susceptibility and Functional Analysis of ZNF804A Gene with Schizophrenia in the Han Population of Southwest China. Joint Funds of National Science Foundation of China-Yunnan Province; Period, 2013-2016; Head of project, Bing Su; Amount: RMB 2.0 million. 基于 Hedgehog 信号通路和纤毛形成的抗肿瘤化合物的发现与机制研究；国家自然科学基金 - 云南省联合基金； 执行年限：2014-2017；项目负责人：毛炳宇；金额：200 万。 Screening and mechanistic study of anticancer drugs targeting Hedgehog signaling pathway and cilogenesis. Joint Funds of National Science Foundation of China-Yunnan Province; Period, 20142017; Head of project, Bingyu Mao; Amount: RMB 2.0 million. 46 遗传资源与进化国家重点实验室 2013 年 度 报 告 榕树 - 榕小蜂合作系统中的非对称性与不确定性选择；国家自然科学基金 - 云南省联合基金；执行年限： 2014-2017；项目负责人：王瑞武；金额：200 万。 The asymmetry and uncertainty choice of fig-fig wasps cooperation system. Joint Funds of National Science Foundation of China-Yunnan Province; Period, 2014-2017; Head of project, Ruiwu Wang; Amount: RMB 2.0 million. 人类进化遗传学；国家自然科学基金委优秀青年科学基金；执行年限：2014-2016；项目负责人：孔庆鹏；金 额：100 万元。 Human Evolutionary Genetics. NSFC Youth Science Foundation; Period, 2014-2016; Head of project, Qingpeng Kong; Amount: RMB 1.0 million. 猪脂肪沉积等优质高产分子模块解析；中科院分子模块设计育种创新体系战略性先导科技专项子课题；执行 年限：2013-2014；项目负责人：张亚平；金额：937 万元。 Molecular Modular Analyses on Pig Fat Deposition and Other High-yield traits. The strategic research program on“Designer Breeding by Molecular Modules”, CAS. Period, 2013-2014; Head of project, Yaping Zhang; Amount: RMB9.37 million. 西南分子育种基地的完善与能力提升；中科院分子模块设计育种创新体系战略性先导科技专项子课题；执行 年限：2013-2014；项目负责人：高云；金额：658 万元。 Improvement of the Molecular Breeding Base in Southwest. The strategic research program on“Designer Breeding by Molecular Modules”, CAS. Period,2013-2014; Head of project, Yun Gao; Amount:RMB6.58million. 猕猴胚胎干细胞向神经终末细胞分化谱系的研究；中科院干细胞先导专项子课题；执行年限：2011-2015；项 目负责人：郑萍；金额：600 万元。 Induced differentiation of Macaque embryonic stem cell into nerve cell, The Pilot Special Project on Stem Cell of Chinese Academy of Sciences, Period, 2011-2015; Head of project, Ping Zheng; Amount:RMB6.0 million. DNA 条形码与类群分子系统进化研究，中科院生物局战略生物资源的保存与可持续利用专项；执行年限： 2011-2013；项目负责人：张亚平；金额：600 万元。 DNA Barcoding and Molecular Phylogenetic studies on some taxonomic groups in animals, plants and fungi, Special Project on the Conservation and Sustainable Use of Strategic Biological Resources from CAS, Period, 2011-2013; Head of project, Yaping Zhang; Amount:RMB6.0 million. 昆虫共生系统的分子生态学研究，中国科学院知识创新工程重要方向项目；执行年限：2010-2013；项目负责 人：Douglas W.Yu；金额：200 万元。 Molecular Ecological Research on Insect Symbiotic Systems. Knowledge Innovation Project of Chinese Academy of Sciences, Period, 2010-2013; Head of project, Douglas W.Yu; Amount: RMB2.00 million. 东非脊椎动物多样性格局及形成机制，中国科学院国际合作课题；执行年限：2013-2015；项目负责人：蒋学 龙；金额：140 万元。 East African vertebrate diversity and formation mechanism, International Cooperation Project of Chinese Academy of Sciences. Period, 2013-2015; Head of project, Xuelong Jiang; Amount: RMB1.40 million. 非洲家禽的分子进化与基因组多样性研究，中国科学院国际合作课题；执行年限：2013-2015；项目负责人： 彭旻晟；金额：120 万元。 Molecular Evolution and Diversity of African Poultry Genome. International Cooperation Project of Chinese Academy of Sciences. Period, 2013-2015; Head of project, Minsheng Peng; Amount: 47 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT RMB1.40 million. 牦牛肠道微生物组高原适应的基因组学机制，云南省高端科技人才引进计划；执行年限：2013-2016；项目负 责人：施鹏；金额：200 万。 Genomics Mechanisms of Gut Microbiome in Yak to Adapt Plateau. Projects for Recruited Top Talent of Sciences and Technology of Yunnan Province, Period: 2013-2016; Head of project, Peng Shi; Amount: RMB 2.0 million. 研发面向“整合计算生物信息学和个性化医学 ( 疗 )”的“GP-GPU 微型超算技术系统”，云南省高端科技人 才引进计划；执行年限：2012-2014；项目负责人：马占山；金额：200 万。 Research on "GP-GPU Micro-Supercomputer Technology System” for “Integration of Computing Bioinformatics and Personalized Medicine (Therapy)”; Projects for Recruited Top Talent of Sciences and Technology of Yunnan Province, Period: 2012-2014; Head of project, Zhanshan Ma; Amount: RMB 2.0 million. 滇池海菜花 - 金线鱼复合生态系统重建及持续利用扩大示范研究，2012 年省级九湖水污染防治专项资金；执 行年限：2012-2014；项目负责人：杨君兴；金额：580 万。 Reconstruction and Continued Usage of the Ottelia - Nemipterus Complex Ecosystem in Dianchi Lake; The Special Funds for Prevention and Control of Nine Lake Water Pollution in Yunnan Province. Period: 2012-2014; Head of project, Junxing Yang; Amount: RMB 5.8 million. 云南珍稀特有优质鱼类滇池金线鲃人工繁殖扩大试验研究 , 云南省环保厅生物多样性保护战略与行动计划； 执行年限：2013-2014；项目负责人：杨君兴；金额：260 万。 Expand Experimental Research on Artificial Propagation of Sinocyclocheilus Grahami; Biodiversity Conservation Strategy and Action Plan of Yunnan Province Environment Department; Period: 20132014; Head of project, Junxing Yang; Amount: RMB 2.6 million. 金沙江中游梨园水电站施工期水生生态监测，企业委托；执行年限：2012-2016；项目负责人：杨君兴；金额： 200 万。 Aquatic Ecological Monitoring of the Jinsha River during the Construction Period of Liyuan Hydropower Station in the Midstream; Company Supported, Period, 2012-2016; Head of project, Junxing Yang; Amount: RMB 2.0 million. 石斛基因组技术开发，企业委托；执行年限：2012-2014；项目负责人：王文；金额：420 万。 Genomic Technology Development of Dendrobium. Company Supported, Period, 2012-2014; Head of project, Wen Wang; Amount: RMB 4.2 million. 三七 RAD 基因组辅助良种选育。企业委托；执行年限：2013-2016；项目负责人：王文；金额：300 万。 RAD Genomic Technology assisted breeding of Panax pseudoginseng. Company Supported, Period, 2013-2016; Head of project, Wen Wang; Amount: RMB 3.0 million. 云南澜沧江糯扎渡水电工程施工期生态监测项目，企业委托项目；执行年限：2009-2014 项目负责人：杨君兴； 金额：135 万元。 Ecological monitoring of Nuozhadu hydro power station in Lancangjiang River, Yunnan, during construction period, Company supported, Period, 2009-2014; Head of project, Junxing Yang; Amount: RMB 1.35 million. 48 遗传资源与进化国家重点实验室 2013 年 度 报 告 发表论文 Publications 1. Baig M, Mitra B, Qu KX, Peng MS, Ahmed I, Miao YW, Zan LS, Zhang YP*. Mitochondrial DNA diversity and origin of Bos frontalis. Curr Sci. 2013, 104(1):115-120. 2. Beckschäfer P, Mundhenk P, Kleinn C, Ji YQ, Yu DW, Harrison RD*. Enhanced structural complexity index: an improved index for describing forest structural complexity. Open J Forest. 2013, 3: 23-29. 3. Blair C, Davy CM, Ngo A, Orlov NL, Shi HT, Lu SQ, Gao L, Rao DQ, Murphy RW*.Genealogy and Demographic History of a Widespread Amphibian throughout Indochina. J Hered.2013, 104(1):72-85. 4. Blair C*, Jiménez Arcos VH, Mendez de la Cruz FR, Murphy RW. Landscape Genetics of Leaf-Toed Geckos in the Tropical Dry Forest of Northern Mexico. PLoS ONE.2013, 8(2):e57433. 5. Cheng YT, Liu J, Yang LQ, Sun C, Kong QP*. Mitochondrial DNA content contributes to climate adaptation in Chinese populations. PLoS ONE, 2013, 8(11): e79536 6. Chen S, Gomes R, Costa V, Santos P, Charneca R, Zhang YP, Liu XH, Wang SQ, Bento P, Nunes JL, Buzgó J, Varga G, Anton I, Zsolnai A, Beja-Pereira A*. How immunogenetically different are domestic pigs from wild boars: a perspective from single-nucleotide polymorphisms of 19 immunity-related candidate genes. Immunogenetics.2013, 65(10):737-748. 7. Debnath M*, Mitra B, Bera NK, Chaudhuri TK, Zhang YP. Lack of association of IL-6 (-174 G > C) and TNF-alpha (-238 G > A) variants with paranoid schizophrenia in Indian Bengalee population. Cytokine.2013, 61(2):455-458. 8. Dong Y#, Xie M#, Jiang Y#, Xiao N#, Du X#, Zhang WG#, Tosser-Klopp G, Wang JH, Yang S, Liang J, Chen WB, Chen J, Zeng P, Hou Y, Bian C, Pan SK, Li YX, Liu X, Wang WL,Servin B, Sayre B, Zhu B, Sweeney D, Moore R, Nie WH, Shen YY, Zhao RP, Zhang GJ, Li JQ, Faraut T, Womack J, Zhang YP, Kijas J, Cockett N, Xu X*, Zhao SH*, Wang J*,Wang W*. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol. 2013. 31(2):135-141. 9. Du LN, Yang JX*, Rintelen TV*, Chen XY, Aldridge D. Molecular phylogenetic evidence that the Chinese viviparid genus Margarya (Gastropoda: Viviparidae) is polyphyletic. Chin Sci Bull. 2013, 58 (18): 2154-2162. 10. Feng JM#, Tian HF#, Wen JF*. Origin and Evolution of the Eukaryotic SSU Processome Revealed by a Comprehensive Genomic Analysis and Implications for the Origin of the Nucleolus. Genome Biol Evol. 2013,5(12):2255-67. 11. Gao S#, Xu J#, Xiong J, Zhang CC, Berquist BR, Yang RD, Zhao M, Molascon AJ, Kwiatkowsky SY, Yuan DX, Qin ZH, Wen JF, Kapler GM, Andrews PC, Miao W*, Liu YF.. Impaired replication elongation in Tetrahymena mutants deficient in histone H3 Lys 27 monomethylation. Genes Dev. 2013,27(15):1662-79. 12. Gao T, 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. 13. Ge RL*, Cai Q, Shen YY, San A, Ma L, Zhang Y, Yi X, Chen Y, Yang L, Huang Y, He R, Hui Y, Hao M, Li Y, Wang B, Ou X, Xu J, Zhang Y, Wu K, Geng C, Zhou W, Zhou T, Irwin DM, Yang Y, Ying L, Bao H, Kim J, Larkin DM, Ma J, Lewin HA, Xing J, Platt RN 2nd, Ray DA, Auvil L, Capitanu B, Zhang X, Zhang G, Murphy RW, Wang J, Zhang YP, Wang J. Draft genome sequence of the Tibetan antelope. Nature Commun. 2013,4,1858. 14. Geng JW#, Fan H#, Tang XD, Zhai HQ, Zhang ZG*.Diversified pattern of the human colorectal cancer microbiome. Gut Pathogens. 2013,5(1): 2. 15. Guan ZH, Huang B, Ning WH, Ni QY, Sun GZ, Jiang XL*. Significance of grooming behavior in two polygynous groups of western black crested gibbons: implications for understanding social relationships among immigrant and resident group members. Am J Primatol.2013,75:1165–1173. 16. Hao XD, Yang Y, Song X, Zhao XK, Wang LD, He JD, Kong QP, Tang NL*, Zhang YP*.Correlation of telomere length shortening with TP53 somatic mutations, polymorphisms and allelic loss in breast tumors and 49 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT esophageal cancer . Oncol Rep. 2013, 29(1):226-236. 17. Hao XD#, Yang YL#, Tang NL, Kong QP, Wu SF, Zhang YP*.Mitochondrial DNA haplogroup Y is associated to Leigh syndrome in Chinese population. Gene. 2013, 512(2):460-463. 18. Huang B, Guan ZH, Ni QY, Orkin J, Fan PF, Jiang XL*. Observation of intra- and extra-group copulation and reproductive characters in free ranging groups of western black crested gibbon (Nomascus concolor jingdongensis). Integr Zool.2013,8:427-440. 19. Hu SJ#, Ning T#, Fu DY, Haack RA, Zhang Z, Chen DD, Ma XY, Ye H*. Dispersal of the Japanese pine sawyer, Monochamus alternatus (Coleoptera: Cerambycidae), in mainland China as inferred from molecular data and associations to indices of human activity. PLoS ONE. 2013, 8(2):e57568. 20. Jiang K, Yan F, Suwannapoom C, Chomdej S, Che J*. A new species of the genus Leptolalax (Anura: Megophryidae) from northern Thailand. Asian Herpetol Res. 2013,4(2) : 100–108. 21. Jiang WS, Zhao YP, Wang W Y, Yang JX, Chen XY*. Length-weight relationship and biological data of a threatened fish, Ptychobarbus chungtienensis (Tsao,1964) in Bita Lake of Shangri-La, Yunnan, China. J Appl Ichthyol. 2013.28(4): 1-4. 22. Ji LD#, Cai XB#, Zhang LN, Fei LJ, Wang L, Su J, Lazar L, Xu J*, ZhangYP*. Association between Polymorphisms in the renin-angiotensin-aldosterone system genes and essential gypertension in the Han Chinese population. PLoS ONE.2013, 8(8):e72701. 23. Ji LD, Chai PF, Zhou BB, Tang NL, Xing WH, Yuan F, Fei LJ, Zhang LN, Xu J*.Lack of association between polymorphisms from genome-wide association studies and tuberculosis in the Chinese population. Scand J Infect Dis. 2013,45(4):310-314 24. Ji YQ#, Ashton L#, Pedley SM#, Edwards DP#, Tang Y, Nakamura A, Kitching RL, Dolman P, Woodcock P, Edwards FA, Larsen TH, Hsu WW, Benedick S, Hamer KC, Wilcove DS, Bruce C, Wang XY, Levi T, Lott M, Emerson BC, Yu DW*. Reliable, verifiable, and efficient monitoring of biodiversity via metabarcoding. Ecol Lett.2013,16: 1245–1257. 25. Li JT*, Li Y, Klaus S, Rao DQ, Hillis DM, Zhang YP*. Diversification of rhacophorid frogs provides evidence for accelerated faunal exchange between India and Eurasia during the Oligocene. PNAS. 2013,110(9):344146. 26. Li Y, vonHoldt BM, Reynolds A, Boyko AR, Wayne RK, Wu DD*, Zhang YP*. Artificial selection on brainexpressed genes during the domestication of dog. Mol Biol Evol. 2013,30(8):1867-76. 27. Liang L#, Shen YY#*, Pan XW, Zhou TC, Yang C, Irwin DM, Zhang YP*. Adaptive evolution of the Hox gene family for development in bats and dolphins. PLoS ONE. 2013,8(6):e65944. 28. Li M, Ge T, Feng J, Su B*. SLC6A15 rs1545843 and depression: implications from brain imaging data. Am J Psychiatry. 2013,170(7): 805. 29. Li M, Su B*. Up-regulation of NOTCH4 gene expression in bipolar disorder: future studies. Am J Psychiatry. 2013,170: 560-561. 30. Li M#, Zhang H#, Luo XJ, Gao L, Qi XB, Gourraud PA, Su B*. Meta-Analysis Indicates That the European GWAS-Identified Risk SNP rs1344706 within ZNF804A Is Not Associated with Schizophrenia in Han Chinese Population. PLoS one.2013, 8: e65780. 31. Li M, Su B*. Impact of the genome-wide schizophrenia risk single nucleotide polymorphism (rs1625579) in miR-137 on brain structures in healthy individuals. Psychiatr Genet. 2013, 23: 267. 32. Li M, Su B*. Meta-analysis supports association of a non-synonymous SNP in ZNF804A with schizophrenia. Schizophr Res. 2013, 149: 188-189. 33. Liu SL, Li YY, Lu JL, Su X, Tang M, Zhou L, Zhou C, Yang Q, Ji YQ, Yu DW, Zhou X. SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons. Methods Ecol Evol. 2013,4, 1142-1150. 34. Luan PT, Ryder OA, Davis H, Zhang YP*, Yu L*. Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora). Mol Phylogenet Evol. 2013, 66(3):748-756. 35. Li XY, Buzzard P, Chen YC, Jiang XL*. Patterns of Livestock Predation by Carnivores: Human–Wildlife Conflict in Northwest Yunnan, China. Environ Manage.2013,2:1334–1340. 50 遗传资源与进化国家重点实验室 2013 年 度 报 告 36. Liu JW, Numata S, Ikeda M, Watanabe Y, Zheng XB, Luo XJ, Kinoshita M, Nunokawa A, Someya T, Ohmori T, Bei JX, Chong SA, Lee J, Li ZQ, Liu JJ, Iwata N, Shi YY, Li M*, Su B*. An Evaluation of Association between a Novel Hippocampal Biology Related SNP (rs7294919) and Schizophrenia. PLoS ONE.2013, 8: e80696. 37. Ma PC, Xia YJ, Ma L, Zhao SH*, Mao BY*. Xenopus N kx6.1 and N kx6.2 are req -uired for mid-hindbrain boundary development. Dev Genes Evol. 2013, 223(4): 253-9. 38. Ma ZS*. Stochastic Populations, Power Law, and Fitness Aggregationn Genetic Algorithms. Fund Inform. 2013,122, 173-206. 39. Ma ZS*. First passage time and first passage percolation models for analyzing network resilience and effective strategies in strategic information warfare research. I. J. Information and Computer Security. 2013, 5(4): 334-358. 40. Miao YW#, Peng MS#, Wu GS, Ouyang YN, Yang ZY, Yu N, Liang JP, Pianchou G, Beja- Pereira A, Mitra B, Palanichamy MG, Baig M, Chaudhuri TK, Shen YY,Kong QP, Murphy RW, Yao YG, Zhang YP*. Chicken domestication: an updated perspective based on mitochondrial genomes. Heredity, 2013,110(3):277-82. 41. Lyu J#, Zhang SL#, Dong Y#, He WM, Zhang J, Deng XN, ZhangYS, Li X, Li BY, Huang WQ, Wan WT, Yu Y, Li Q, Li J, Liu X, Wang B, Tao, DY, Zhang GY, Wang J, Xu X, Hu FY*, Wang W*. Analysis of elite variety tag SNPs reveals an important allele in upland rice. Nat Commun. 2013. 5: 4: 2138. 42. Murphy RW*, Crawford AJ, Bauer AM, Che J, Donnellan SC, Fritz U, Haddad CFB, Nagy ZT, Poyarkov NA, Vences M, Wang WZ, Zhang YP. Cold Code: the global initiative to DNA barcode amphibians and nonavian reptiles. Mol Ecol Res. 2013, 13(2): 161–167. 43. Nguyen SN#, Le TNT#, Tran TAD, Orlov NL, Lathrop A, Macculloch RD, Le TDT, Jin JQ, Nguyen LT, Nguyen TT, Hoang DD, Che J*, Murphy RW*, Zhang YP*. Phylogeny of the Cyrtodactylus irregularis species complex (Squamata: Gekkonidae) from Vietnam with the description of two new species. Zootaxa.2013, 3737(4): 399– 414. 44. Qiu QW, Wu DD, Yu LH, Yan TZ, Zhang W, Li ZT, Liu YH, Zhang YP, Xu XM*. Evidence of recent natural selection on the Southeast Asian deletion (--SEA) causing α-thalassemia in South China. BMC Evol Biol.2013, 13:63. 45. Qi XB#, Cui CY#, Peng Y#, Zhang XM#, Yang ZH#, Zhong H, Zhang H, Xiang K, Cao XY, Wang Y, Ouzhuluobu, Basang, Ciwangsangbu, Bianba, Gonggalanzi, Wu T, Chen H, Shi H*, Su B*. Genetic evidence of paleolithic colonization and neolithic expansion of modern humans on the tibetan plateau. Mol Biol Evol. 2013,30: 1761-1778. 46. Rogers DC, Shu SS*, Yang JX*. The Identity of Branchinella Yunnanensis Shen, 1949, with a brief review of the Subgenus Branchinellites (BRANCHIOPODA: Anostraca: Thamnocephalidae). J Crustacean Biol. 2013, 33(4):576-581. 47. Shen YY*, Chen X, Murphy RW. Assessing DNA barcoding as a tool for species identification and data quality control. PLoS ONE. 2013, 8(2):e57125 48. Shi H#*, Qi XB#, Zhong H#, Peng Y, Zhang XM, Ma RZ, Su B*. Genetic evidence of an East Asian origin and paleolithic northward migration of Y-chromosome haplogroup N. PLoS ONE. 2013, 8: e66102. 49. Shi L, Li M, Lin Q, Qi X, Su B*. Functional divergence of the brain-size regulating gene MCPH1 during primate evolution and the origin of humans. BMC Biology. 2013, 11: 62. 50. Shu SS, Chen FZF, Chen XY*. Redescription and the first record of a rare himalayan species, Arctodiaptomus (Haplodiaptomus) parvispineus Kiefer 1935 from Potatso National Park, Yunnan, China (Copepoda: Calanoida: Diaptomidae). Crustaceana. 2013, 86 (13-14): 1564-1571. 51. Shu SS#, Jiang WS#, Whitten T, YangJX*, ChenXY*. Drought and China’s cave species. Science. 2013,340: 272. 52. Song LT, Wang W*. Genomes and evolutionary genomics of animals. Curr Zool. 2013,59(1): 1674-5507. 53. Sun BF, Xiao JH, He SM, Liu L, Murphy RW, Huang DW*.Multiple ancient horizontal gene transfers and duplications in lepidopteran species. Insect Mol Biol.2013, 22(1):72-87. 54. Sun BF, Xiao JH, He S, Liu L, Murphy RW, Huang DW*. Multiple Interkingdom Horizontal Gene Transfers in Pyrenophora and Closely Related Species and Their Contributions to Phytopathogenic Lifestyles. PLoS ONE.2013, 8(3):e60029. 55. Sun GL#, Yang Y#, Xie F, Wen JF, Wu J, Wilson IW, Tang Q, Liu H, Qiu DY*. Deep Sequencing Reveals 51 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Transcriptome Re-Programming of Taxus × media Cells to the Elicitation with Methyl Jasmonate. PLoS ONE. 2013. 8(4): e62865. 56. Sun YB#, Zhou WP#, Liu HQ, Irwin DM, Shen YY*, Zhang YP*. Genome-wide scans for candidate genes involved in the aquatic adaptation of dolphins. Genome Biol Evol. 2013,5(1):130-139. 57. Sun Z, Zhang YF, Zhang R, Qi XB, Su B*. Functional divergence of the rapidly evolving miR-513 subfamily in primates. BMC Evol Biol. 2013,13: 255. 58. Su YH#,Wu DD#*, ZhouWP, Irwin DM, Zhang YP*. Rapid Evolution of the Mammalian HILS1 Gene and the Nuclear Condensation Process during Mammalian Spermiogenesis. J Genet Genomics. 2013, 40(1):55-59. 59. Wang B, Xiao JH, Bian SN, Niu LM, Murphy RW, Huang DW*. Evolution and expr ession plasticity of opsin genes in a fig pollinator, Ceratosolen solmsi. PLoS ONE. 2013, 8(1):e53907. 60. Wang GD#, Cheng LG#, Fan RX, Irwin DM, Tang SS, Peng JG, Zhang YP*. Signature of balancing selection at the MC1R gene in Kunming dog populations. PLoS ONE. 2013, 8(2):e55469 61. Wang H, Ridley J, Dunn DW, Wang RW, Cook JM, Yu DW*. Biased oviposition and biased survival together help resolve a fig-wasp conflict. Oikos.2013,122: 533-540. 62. Wang J#, Wu XY#, Chen ZM#, Yue ZP, MA W, Chen SY, Xiao H, Murphy RW, Zhang YP, Zan RG* , Luo J. Molecular phylogeny of European and African Barbus and their West Asian relatives in the Cyprininae (Teleostei: Cypriniformes) and orogenesis of the Qinghai-Tibetan Plateau. Chin Sci Bull.2013,58 (31): 37383746. 63. Wang M, Yang JX*, Chen XY*. Molecular phylogeny and biogeography of Percocypris (Cyprinidae, Teleostei). PloS ONE. 2013,8(6): e61827 64. Wang J#, Zhao YQ#, Wang Y#, Huang JF*. Molecular dynamics simulations and statistical coupling analysis reveal functional coevolution network of oncogenic mutations in the CDKN2A-CDK6 complex. FEBS Lett. 2013,16;587(2):136-141 65. Wang GD#, Zhai WW#, Yang HC, Fan RX, Cao X, Zhong L, Wang L, Liu F,Wu H,Cheng LG, Poyarkov AD, Poyarkov NA Jr, Tang SS, Zhao WM, Gao Y, Lv XM, Irwin DM, Savolainen P, Wu CI*, Zhang YP*. The genomics of selection in dogs and the parallel evolution between dogs and humans. Nat Commun. 2013,4:1860. 66. Wang SY, Luo J, Murphy RW, Wu SF, Zhu CL, Gao Y*, Zhang YP*. Origin of chinese goldfish and sequential loss of genetic diversity accompanies new breeds. PLoS ONE. 2013,8(3):e59571. 67. Wang XP, Zhang YP, Yu L*. Summary of phylogeny in subfamily Colobinae (Primate: Cercopithecidae). Chin Sci Bull. 2013, 58(18):2097-2103. 68. Wan T#, He K#, Jiang XL*. Multilocus phylogeny and cryptic diversity in Asian shrew-like moles (Uropsilus, Talpidae): implications for taxonomy and conservation. BMC Evol Biol. 2013,3:232. 69. Wu DD*, Zhang YP*. Evolution and function of de novo originated genes. Mol Phylogenet Evol. 2013,67(2):541-545. 70. Wu M#, Yu Q#, Li X, Zheng J, Huang JF*, Kwoh CK*. Benchmarking human protein complexes to investigate drug-related systems and evaluate predicted protein complexes. PLoS ONE. 2013,8(2):e53197. 71. Wu SJ#, Luo J#, Li QQ, Wang YQ, Murphy RW, Blair C, Wu SF, Yue BS*, Zhang YP*. Ecological genetics of Chinese rhesus macaque in response to mountain building: all things are not equal. PLoS ONE. 2013, 8(2):e55315. 72. Wu XY, Luo J, Huang S, ChenZM, Xiao H*, Zhang YP. Molecular phylogeography and evolutionary history of poropuntius huangchuchieni (Cyprinidae) in southwest China. PLoS ONE. 2013, 8(11):e79975 73. Wu T#, Zhang ZG#, Liu B, Hou DZ, Liang Y, Zhang J*, Shi P *. Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study. BMC Genomics. 2013. 14(1): 669. 74. Xiang H#, Li X#, Dai FY#, Xu X#, Tan AJ#, Chen L, Zhang GJ, Ding Y, Li QY, Lian JM, Willden A, Guo QH, Xia QY, Wang J*, Wang W*. Comparative methylomics between domesticated and wild silkworms implies possible epigenetic influences on silkworm domestication. BMC Genomics. 2013,23(14): 646. 75. Xiang K#, Ouzhuluobu#, Peng Y#, Yang ZH, Zhang XM, Cui CY, Zhang H, Li M, Zhang YF, Bianba, Gonggalanzi, Basang, Ciwangsangbu, Wu T, Chen H, Shi H, Qi XB, Su B*. Identification of a Tibetan-specific mutation in the hypoxic gene EGLN1 and its contribution to high-altitude adaptation. Mol Biol Evol. 2013,30: 18891898. 76. Xin YN, Zhao YQ, Lin ZH, Jiang X, Xuan SY*, Huang JF*. Molecular dynamics simulation of PNPLA3 52 遗传资源与进化国家重点实验室 2013 年 度 报 告 I148M polymorphism reveals reduced substrate access to the catalytic cavity. Proteins. 2013,81(3): 06-414. 77. Xiong J#, Lu YM#, Feng JM#, Yuan DX, Tian M, Chang Y, Fu CJ, Wang GY, Zeng HH*, Miao W*. Tetrahymena Functional Genomics Database (TetraFGD): an integrated resource for Tetrahymena functional genomics. Database (Oxford). 2013. doi: 10.1093/database/bat008. 78. Xu J#, Cheng YQ#, Chen B, Bai R, Li S, Xu XF, Xu L, Wen JF, Lu ZP, Zeng XF*. Depression in systemic lupus erythematosus patients is associated with link-polymorphism but not methylation status of the 5HTT promoter region. Lupus. 2013, 22(10):1001-1010. 79. Xu J#, Ji LD#, Zhang LN, Dong CZ, Fei LJ, Hua S, Tsai JY, Zhang YP*.Lack of association between STK39 and hypertension in the Chinese population. J Hum Hypertens. 2013, 27(5):294-297 80. Xu P, Lu B, Xiao H, Fu X, Murphy RW, Wu K*. The Evolution and Expression of the Moth Visual Opsin Family. PLoS ONE.2013, 8(10):e78140. 81. Yan F, Zhou WW, Zhao HT, Yuan ZY, Wang YY, Jiang K, Jin JQ, Murphy RW, Che J*, Zhang YP*. Geological events play a larger role than Pleistocene climatic fluctuations in the genetic structure of the montane streamdwelling frog Quasipaa boulengeri (Anura: Dicroglossidae) in southern China. Mol Ecol. 2013,22(4): 1120–1133. 82. Ye JJ, Ma L, Yang LJ, Wang JH, Wang YL, Guo H, Gong N, Nie WH*, Zhao SH*. Partial AZFc duplications not deletions are associated with male infertility in the Yi populication of Yunnan Province, China. J. Zhejiang UnivSci B(Biomed &Biotechnol). 2013, 14: 807-815. 83. Yuan SL, Jiang XL, Li ZJ, He K, Harada M, Oshida1 T, Lin Lk*. A Mitochondrial Phylogeny and Biogeographical Scenario for Asiatic Water Shrews of the Genus Chimarrogale: Implications for Taxonomy and LowLatitude Migration Routes. PLoS ONE. 2013, 8(10): e77156. 84. Yuan ZY, Jiang K, Ding LM, Zhang L, Che J*. A New Newt of the Genus Cynops (Caudata: Salamandridae) from Guangdong. China. Asian Herpetol Res. 2013,4(2) : 116–123. 85. Yu GH, Zhang MW, Rao DQ*, Yang JX*. Effect of Pleistocene Climatic Oscillations on the Phylogeography and Demography of Red Knobby Newt (Tylototriton shanjing) from Southwestern China. PLoS ONE.2013, 8(2): e56066. 86. Yu GH, Zhang MW, Yang JX*. Molecular evidence for taxonomy of Rhacophorus appendiculatus and Kurixalus species from northern Vietnam, with comments on systematics of Kurixalus and Gracixalus (Anura: Rhacophoridae). Biochem Syst Ecol.2013, 47: 31-37. 87. Yu Q, Huang JF*. The DEER database: A bridge connecting drugs, environmental effects, and regulations. Gene. 2013,520(2):98-105. 88. Zeng T, JinW, Sun ZY, Liu Y, Murphy RW, Fu JR,Wang X, Hou QF, Tu FY, Liao R, Liu SY*, Yue BS. Taxonomic position of Eothenomys wardi (Arvicolinae: Cricetidae) based on morphological and molecular analyses with a detailed description of the species. Zootaxa. 2013, 3682(1):85-104 89. Zhang AD, Dai SX, Huang JF*.Reconstruction and Analysis of Human Kidney-Specific Metabolic Network Based on Omics Data. Biomed Res Int. 2013, 2013:187509. 90. Zhang BL, Huang S*. Relationship of old world pseudoxenodon and new world dipsadinae, with comments on underestimation of species diversity of Chinese Pseudoxenodon. Asian Herpetol Res.2013, 4(3):155-165. 91. Zhang LN, Ji LD, Fei LJ, Yuan F, Zhang YM, Xu J*. Association between Polymorphisms of Alpha-Adducin Gene and Essential Hypertension in Chinese Population. Biomed Res Int. 2013,2013:451094. 92. Zhang MW*, Yu GH, Yang MX*, Li Y, Wei J, Xu HL, Yao YF, Wang LJ, Zhang XQ, Rao DQ, Yang JX. Mitochondrial phylogeography of the red-tailed knobby newt (Tylototriton kweichowensis).Biochem Syst Ecol.2013, 51: 195-202. 93. Zhang MW, Yu GH*, Rao DQ*, Li Y, Yang JX*. A Species boundary within the Tylototriton verrucosus group (Urodela: Salamandroidae) based on mitochondrial DNA evidence. J Anim Vet Adv.2013, 13(3): 337-343. 94. Zhang XM#, Qi XB#, Yang ZH#, Serey B, Sovannary T, Bunnath L, Seang Aun H, Samnom H, Zhang H, Lin Q, van Oven M, Shi H*, Su B*. Analysis of mitochondrial genome diversity identifies new and ancient maternal lineages in Cambodian aborigines. Nat Commun.2013,4: 2599. 95. 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 pyrosequencing. Am J Gastroenterol. 2013,108(10): 1601-1611. 96. Zheng P*, Baibakov B, Wang XH, Dean J. PtdIns(3,4,5)P3 is constitutively synthesized and required for 53 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT spindle translocation during meiosis in mouse oocytes. J Cell Sci. 2013, 126, 715–721. 97. Zhou WW, Yan F, Fu J, Wu SF, Murphy RW, Che J*, Zhang YP*. River islands, refugia, and genetic structuring in the endemic brown frog Rana kukunoris (Anura, Ranidae) of the Qinghai-Tibetan Plateau. Mol Ecol.2013, 22: 130-142. 98. Zou G, Zhang YP, Yu L*. Natural selection and adaptive evolution of leptin. Chin Sci Bull. 2013, 58(18):2104-2112. 99. 陈 天 波， 罗 键， 蒙 渊 君， 温 柏 豪， 蒋 珂 *. 广 西 发 现 茂 兰 原 矛 头 蝮 及 分 类 探 讨 . 四 川 动 物 .2013, 32(1),116-118. 100. 陈小勇 . 云南鱼类名录 . 动物学研究 .2013, 34 (4): 281-343 101. 杜丽娜 , 陈小勇 *, 杨君兴 *. 中国科学院昆明动物研究所鱼类模式标本名录 . 动物学研究 .2013, 34 (4): 345-360 102. 杜丽娜 , 杨君兴 *, Rintelen Thomas*, 陈小勇 , Aldridge David. 中国特有腹足类—螺蛳属 (Margarya) 的 系统发育学 . 科学通报 . 2013, 58 (16): 1483-1491 103. 邓 可， 张 利 周， 李 权， 李 学 友， 蒋 学 龙 *. 云 南 天 池 自 然 保 护 区 兽 类 资 源 调 查 . 四 川 动 物 . 2013, 3(3):458-463. 104. He Y*, Chen XY, Xiao TQ, Yang JX*. Three-dimensional morphology of the Sinocyclocheilus hyalinus(Cypriniformes：Cyprinidae) horn based on synchrotron X-ray microtomography. Zool Res.2013, 34 (E4-5): E128-E134 105. 何锴，白明，万韬，李权，王应祥，蒋学龙 *. 白尾鼹 ( 鼹科 : 哺乳纲 ) 下颌骨几何形态测量分析及地 理分化研究 . 兽类学报 . 2013, 33:7 -17. 106. 何锴，王文智，李权，罗培鹏，孙悦华，蒋学龙 *. DNA 条形码技术在小型兽类鉴定中的探索：以甘 肃莲花山为例 . 生物多样性 . 2013, 21:19-205. 107. Guan ZH, Huang B, Ning WH, Ni QY, Jiang XL. Proximity association in polygynous western black crested gibbons (Nomascus concolor jingdongensis): network structure and seasonality. Zool Res.2013, 34 (E1): E1−E8 108. 刘淑伟，杨君兴 *，陈小勇 *. 金沙江中上游中华金沙鳅 (Jinshaia sinensis) 产卵场的发现及意义 . 动物 学研究 .2013,34 (6): 626-630. 109. 潘晓赋，刘倩，王晓爱，杨君兴 * ，陈小勇 *，李再云，李列 . 软鳍新光唇鱼（Neolissochilus benasi） 的人工繁殖与胚胎发育 . 动物学研究 .2013, 34(6): 617-625. 110. 潘晓赋 , 李列 , 杨君兴 *, 陈小勇 *. 云南红河水系金线鲃属鱼类一新种—西畴金线鲃 . 动物学研究 .2013, 34 (4): 368-373 111. 舒树森，陈非洲，杨君兴 , 杨晓君 *，陈小勇 *. 普达措国家公园淡水甲壳动物多样性及区系的初步分析 . 动物学研究 .2013, 34(3): 1-5 112. 谢钢琴，陈兵，文建凡 *. 血吸虫等寄生扁虫免疫逃避机制的研究进展 . 寄生虫与医学昆虫学报 . 2013，22(3):194-198. 113. 许凌，范宇，蒋学龙，姚永刚 . 树鼩进化分类地位的分子证据 . 动物学研究 .2013, 34(2): 70-76. 114. 杨剑 , 郑兰平 , 陈小勇 *, 杨君兴 *. 伊洛瓦底江中国境内江段裂腹鱼属二新种描述及分类整理 . 动物学 研究 .2013, 34 (4): 361-367 115. 杨君兴，舒树森，陈小勇 *. 草鱼引入对滇池湖体海菜花消亡的影响 . 动物学研究 .2013, 34(6):631-635. 116. 杨君兴 *, 潘晓赋 , 陈小勇 , 王晓爱 , 赵亚鹏 , 李建友 , 李再云 . 中国特有淡水鱼类人工增殖放流的研究 现状 . 动物学研究 .2013, 34 (4): 267-280 117. 赵亚鹏 , 潘晓赋 , 杨君兴 *, 陈小勇 *, 王晓爱 , 李再云 . 滇池金线鲃 (Sinocyclocheilus grahami) 耳石的茜 素红及茜素络合物标志 . 动物学研究 .2013, 34 (5): 499-503. 118. 赵亚鹏 , 潘晓赋 , 杨君兴 *, 陈小勇 *, 李再云 , 王晓爱 . 滇池金线鲃（Sinocyclocheilus grahami）与抚仙 金线鲃（S. tingi）肌肉营养成分初步分析 . 动物学研究 .2013, 34(6): 636−639. 119. Zhao B, Cun YX, He XC, Zheng P*. Maternal-effect Floped gene is essential for the derivation of embryonic stem cells in mice. Zool Res. 2013,34 (E3): E82-E86. 120. 郑兰平，陈小勇 *，杨君兴 *. 澜沧江中下游鱼类现状及保护 . 动物学研究 .2013, 34(6): 680-686. 54 遗传资源与进化国家重点实验室 2013 年 度 报 告 获 奖 Awards ２０１３ 张亚平，孔庆鹏， 吴东东， 彭旻晟，孙昌。云南省自然科学奖特等奖（基因组多样性与亚洲人群的演化） 2013 Yaping Zhang, Qingpeng Kong, Dongdong Wu, Mingsheng Peng, Cang Sun. Special Award for Natural Science of Yunnan province.( Genomic diversity and evolution of Asian populations.) ２０１３ 张亚平，施鹏，沈永义，于黎，吴东东。云南省自然科学奖一等奖（动物适应性进化的分子机制） 2013 Yaping Zhang, Peng Shi, Yongyi Shen, Li Yu, Dongdong Wu. First Prize for Natural Science of Yunnan province.( Molecular mechanisms of adaptive evolution of animals). ２０１３ 宿兵，石宏，祁学斌，张慧，卢志祥，张锐。 云南省自然科学奖一等奖（灵长类大脑进化与人类智力 起源的遗传机制） 2013 Bing Su, Hong Shi, Xuebing Qi, Hui Zhang, Zhixiang Lu, Rui Zhang. First Prize for Natural Science of Yunnan province.( Primate brain evolution and genetic mechanism of the origin of human intelligence) ２０１３ 施立明，杨凤堂，佴文惠，刘瑞清，王金焕，苏伟婷，陈玉泽。云南省科技进步奖三等奖（冷冻动物园—— 动物遗传资源库的创建及其应用） 2013 Liming Shi, Fengtang Yang, Wenhui Nie, Rruiqing Liu, Jinhuan Wang, Weiting Shu, Yuze Chen. Third Prize for Science and Technology Progress of Yunnan Province.( Frozen Zoo – The Animal Genetic Resources Library establishing and application) ２０１３ 张亚平研究团队 ． ２０１３ 年云南十大科技进展（亚洲人群进化研究取得新突破） 2013 Research Team of Yaping Zhang. 2013 Top Ten Technology Advances in Yunnan Province . ( Evolution of new breakthroughs in Asian populations) ２０１３ 王文研究员入选“万人计划”第一批科技创新领军人才 2013 Prof. Wen Wang was selected into the first batch of "Ten thousand people plan" ２０１３ 杨召辉获 ２０１３ 年“保罗生物科技优秀学生奖”； 吕俊获吴瑞奖学金并应邀参加第四届吴瑞纪念研讨会； 颜芳获中科院院长奖学金优秀奖；颜芳、余国华获朱李月华优秀博士生奖。 2013 Zhaohui Yang won "Paul biotechnology outstanding student award." Jun LV won Wu-Rui Scholarship and was invited to attend the the fourth seminar to commemorate Wurui; Fang Yan won “the Excellent Award of the President Scholarship of CAS”; Fang Yan and Guohua Yu won “Zhu Li Yuehua Outstanding PhD Graduate Scholarship of CAS”. 55 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT 研究生优秀论文奖 Outstanding Paper Awards for Graduate Students 一等奖 （５ 篇，影响因子≥ ９， 排名按申请时间顺序，影响因子按申请时发布为准 ）： The first prize (5, IF≥9): 李 明 Ming Li(The American Journal of Psychiatry, IF12.679) 李 明 Ming Li(Molecular Psychiatry, IF12.992) 向 坤 Kun Xiang(Molecular Biology and Evolution, IF9.857) 吕 俊 Jun Lv(Nature Communication, IF10.020) 张晓明 Xiaoming Zhang(Nature Communication, IF10.020) 二等奖 （５ 篇，６ ≤影响因子 ＜９）: The second prize (5, 6≤IF<9): 梁 璐 Lu Liang【PloS Genetics, IF9.173（排名第二并列第一作者）】 张晓明 颜 芳 Fang Yan(Molecular Ecology, IF6.347) 刘耀文 林 Xiaoming Zhang【Molecular Biology and Evolution, IF9.857（排名第四并列第一作者）】 Yaowen Liu(Neurobiology of Aging, IF6.098) 强 Qiang Lin 【Molecular Biology and Evolution, IF9.857（排名第二并列第一作者）】 三等奖 （７ 篇，４ ≤影响因子 ＜６）： The third prize (7, 4≤IF<6): 王姝妍 Shuyan Wang(Journal of Biogrograghy, IF4.916) 王姝妍 Shuyan Wang(PloS One, IF4.537) 李 明 Ming Li(PloS One, IF4.537) 梁 璐 Lu Liang(PloS One, IF4.537) 万 韬 Tao Wan(BMC Evolutionary Biolgy, IF4.432) 程耀霆 Yaoting Cheng(PloS One, IF4.244) 刘杰伟 Jiewei Liu(PloS One, IF4.244) 56 遗传资源与进化国家重点实验室 2013 年 度 报 告 大事记 （1）2013 年 4 月 9-11 日，加拿大多伦多大 学著名的分子进化领域专家 David Irwin 教授受邀 来实验室为研究生作了为期 3 天的精彩授课。 On April 9-11,2013, Prof. David Irwin, a wellknown expert on molecular evolution from the University of Toronto, Canada, was invited to the lab and made ​​a series of lectures to graduate students. Major Events （2）2013 年 5 月 18 日，实验室参与举办昆明动物 所第九届“公众科学日”活动。活动中，实验室 3 位科 技人员作了科普报告，部分研究组对外开放参观。 The key lab participated in the ninth “Public Science Day” of Kunming Institute of Zoology on May18,2013. Three staff scientists gave talks and some groups of the lab were open to the public to visit. （3）2013 年 6 月 3 日，实验室第二届学术委员会第二次会议在昆明召开。 The second meeting of the second academic committee of the key lab was held in Kunming on June 3, 2013. （4）2013 年 8 月，由”青年千人计划“入选者焦保 卫研究员负责的“发育的印记调控与进化研究组”以及 由国家杰出青年基金获得者王瑞武研究员负责的“实验 与理论生态学研究组”加入实验室，成为实验室第 16、 17 个研究组。 The 16th research group on “Imprinting in Development and Evolution”, headed by Prof. Baowei Jiao, who was enrolled by the “National Youth Thousand Talents Program”, and the 17th research group on “Experimental and Theoretical Ecology ”, headed by Prof. Ruiwu Wang, who was awarded the “Distinguished Young Scholar Grant” of the National Natural Science Foundation of China, joined the key lab in August, 2013. 焦保卫研究员 Prof. Baowei Jiao 57 王瑞武研究员 Prof. Ruiwu Wang State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT （5）2013 年 8 月 2-7 日，加拿大 Guelph 大学傅金钟教 授来所为研究生讲授了为期 5 天的“现代进化生物学中的 重要课题”课程。 On August 2-7,2013, Prof. Jinzhong Fu, from the University of Guelph, Canada, was invited to the lab and made ​​a series of lectures on several important topics in current evolutionary biology to the graduate students. （6）2013 年 8 月 15 日，实验室举办了 2013 年 研究生墙报比赛。 The 2013 Graduates’ Poster Competition of the key lab was held on August 15, 2013. （7）2013 年 8 月 9-18 日，实验室与所研究生部 合作在昆明主办 “2013 年进化生物学暑期班 ” On August 9-18, 2013, the Evolutionary Biology Summer Course was held in Kunming organized by the key lab and the Office of Postgraduate Affairs of KIZ . （8）2013 年 10 月 27 日 -31 日，实验室参与承办的“第五届国际生命条形码大会” 在昆明召开。 As one of the organizers , the key lab hosted the Fifth International Barcode of Life Conference on October 2731, 2013, in Kunming. 58 遗传资源与进化国家重点实验室 2013 年 度 报 告 （9）2013 年 11 月 16 日，科技部基础司副司长彭以祺携 2013 年全国基础研究工作会的会议代表一行 90 余人实地考察了实验室及 973 计划项目的进展情况。 On Nov.16, 2013, Mr. Yiqi Peng, the Deputy Director of the Department of Basic Research , MOST, inspected the key lab and the progress of the National Basic Research Program (973) projects held by the key lab, together with more than 90 representatives from the National Basic Research Work Conference. （10）2013 年 11 月 15 日，实验室在昆明召开了 2013 年学术交流年会。 The 2013 Annual Meeting of the key lab was held in Kunming, on Nov.15 ,2013. （11）2013 年 12 月 31 日，实验室召开 2013 年 PI 战略研讨会。 The strategic meeting of the key lab was held on Dec. 31, 2013. 59 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT 开放课题 Open Projects 资助经费 课题编号 负责人 职称 负责人单位 课题名称 GREKF13-01 钟 丽 助理研究员 云南大学 高原藏猪的高原低 氧适应性进化研究 11 GREKF13-02 吴江鸿 研究助理 内蒙古农 牧业科学院 绵羊在不同生长环境 中表观遗传学变化研究 11 GREKF13-03 邹晓菊 副教授 昆明学院 GREKF13-04 吴天一 院士 / 教授 GREKF13-05 孙桂玲 副研究员 GREKF13-06 和 友 副研究员 GREKF13-07 陈 鹏 助理研究员 GREKF13-08 张礼标 研究员 GREKF13-09 黄 伟 GREKF13-10 脂肪酸转运蛋白（FABPs）调控脂肪 储存分布的结构和功能研究 青海省高原 青藏高原史前人类 医学科学研究院 迁徙模式的遗传学研究 中国科学院昆明 植物研究所 人贾第虫与蛙贾第 虫的比较基因组学研究 中国科学院上海 基于同步辐射显微 CT 的滇 应用物理研究所 池金线鲃头部三维功能形态研究 成都市大熊猫 （单位：万元） 11 11 11 11 白腹鼠系统发育与生物地理研究 11 广东省昆虫研究所 果蝠味觉与其糖类 和糖浓度选择偏好研究 11 副主任医师 云南省第三人民医院 云南德宏州民族 人群遗传多样性研究 11 黄 松 教授 黄山学院 中国岩蜥属物种多 样性和系统地理学研究 11 GREKF13-11 陈红菊 讲师 红河学院 网络分析和博弈理论在宏基 因组生物信息学研究中的应用 11 GREKF13-12 张立勋 副教授 兰州大学 甘肃盐池湾自然保护区黑颈鹤繁殖生 态、种群迁徙路线卫星跟踪研究 11 GREKF13-13 Thomas Neill Edward Gray Regional Wildlife Biologist World Wildlife Foud Monitoring mammal biodiversity using DNA from leeches in the Annamite mountain range 11 繁育研究基地 60 遗传资源与进化国家重点实验室 2013 年 度 报 告 专家学术报告 Invited Lectures 报告人：Prof. Hans-Jürgen Bandelt 单 位：University of Hamburg, Germany 时 间：2013.1.14\21\25\28 题 目：Four Lectures about Human mtDNA 报告人：Dr. Akihiro Nakamura 单 位：Griffith University,Australia 时 间：2013.1.16 题 目：Forest biodiversity as a key to monitoring responses to climate change and other human disturbance – cross continental collaborations 报告人：Prof. Chris Burwell 单 位：Queensland Museum, Australia 时 间： 2013.1.16 题 目： Ants and altitude -the potential of ants as bio-indicators of climate change 报告人：李代芹教授 单 位：NUS university,Singapore 时 间：2013.1.28 题 目： Ultraviolet (UV) coloration in sexual selection of jumping spiders 报告人：Prof. Mark Robert Band 单 位：University of Illinois at Urbana-Champaign, America 时 间： 2013.5.20 题 目： The Spalax Transcriptome, Insights to Hypoxia Tolerance of an Underground Rodent 报告人：Prof. Aaron Avivi 单 位：University of Haifa,Israel 时 间：2013.5.20 题 目：The Israeli subterranean hypoxia-tolerant mole-rat, Spalax, as a model for cancer resistance 报告人：王彦文教授 单 位：University of Prince Edward Island , Canada 时 间： 2013.5.20 题 目：A new strategy to develop lipid-lowering products 报告人： 许丽艳教授 报告人： 李恩民教授 单 位： 汕头大学 单 位：汕头大学 时 间： 2013.5.31 时 间： 2013.5.31 题 目：fascin 基因在食管癌中的功能、题 目：桥粒糖蛋白 DSC2 负性调控 表达调控及其细胞信号传导通路 食管癌细胞侵袭迁移的分子机制 61 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT 报告人：朱作言院士 单 位：北京大学 时 间：2013.6.3 题 目：从童第周的科研成就回顾我 国现代科学发展历程 报告人： Prof. Yoshihiro Ohmiya 报告人：汪小全研究员 单 位：中科院植物研究所 单 位：National Institute of AIST, Japan 时 间：2013.6.3 题 目：关于植物进化历史研究的几点 时 间： 2013.6.7 题 目：Basic and application of 思考－以裸子植物为例 bioluminescent system 报告人：Prof. Stephen S. Young 单 位：Salem State University, America 时 间：2013.6.25 题 目：Are Mainland China’s National Nature Reserves Protecting Forest Cover Since the Logging-ban? 报告人：万方浩研究员 单 位：中国农业科学院植物保护研 究所 时 间： 2013.7.1 题 目：Omics 时代的生物入侵研究 报告人：丁家桓教授 单 位：昆明理工大学 时 间：2013.7.1 题 目：分子医学在临床中的应用现 状 报告人：Dr. Rugang Zhang 单 位：University of Pennsylvania, America 时 间：2013.7.17 题 目：Cellular Senescence and Cancer: The DNA Damage Response Takes the Center Stage 报告人：温俊宝教授 单 位：北京林业大学 时 间：2013.7.30 题 目：昆虫化学生态学研究的一些 进展 报告人：孙江华研究员 单 位：中科院动物研究所 时 间：2013.8.7 题 目：共生入侵与返入侵 --- 以红 脂大小蠹为例 62 遗传资源与进化国家重点实验室 2013 年 度 报 告 报告人：吴庆龙研究员 单 位：中科院南京地理与湖泊研究 所 时 间：2013.8.28 题 目：内陆水体微生态多样性研究 进展 报告人：Prof. Aaron Ellison 单 位：Harvard University, America 时 间：2013.9.23 题 目：Ants and foundation tree species in the forests of northeastern North America 报告人： 彭凌涛博士 单 位：University of Massachu -setts Medical School, America 时 间： 2013.10.10 题 目：The post-transcriptional regulation of TDP-43 in amyotrophic lateral sclerosis disease 报告人：陈小勇教授 单 位：华东师范大学 时 间： 2013.10.9 题 目：薜荔及其传粉小蜂—物种形 成及比较亲缘地理 报告人：卢欣教授 单 位：武汉大学 时 间：2012.10.24 题 目：晨钟暮鼓：一个西藏鸟类学 者的探索与思考 报告人：Dr. Andrew J. Crawford 单 位：Universidad de Los Andes, Colombia 时 间：2013.11.1 题 目：Evolutionary and conservation applications of DNA barcode data: Lessons from the Amphibians of Panama 报告人：Prof. Wichian Magtoon 单 位：Srinakharinwirot University,Thailand 时 间：2013.11.20 题 目：Taxonomy and Phylogenetic of Ricefish 报告人：Dr. Nguyen Dinh Tao 单 位：Institute of Ecology and Biological Resources of Vietnam 时 间：2013.11.20 题 目：An Overview of Species of Diversity of Freshwater Fish in Vietnam 报告人：Dr. Sheila Ommeh 单 位：Jomo Kenyatta University of Agriculture and Techology 时 间：2013.12.11 题 目：Conservation of Endangered Wildlife and Indigenous Poultry in Kenya 63 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT 人员名单 研究组长 （ 按姓氏笔画排序 ） 马占山 孔庆鹏 文建凡 毛炳宇 王 王瑞武 车 静 张亚平 杨君兴 杨晓君 佴文惠 郑 施 鹏 宿 兵 黄京飞 焦保卫 蒋学龙 Douglas W Yu 萍 文 工作人员 马云飞 马鹏程 牛昱宇 王文智 王华伟 王运宇 王国栋 王 林 王金焕 代绍兴 叶丹丹 叶志强 司 石 宏 石 任国鹏 任海清 刘 维 磊 佳 刘贵春 刘 振 刘淑伟 刘 衡 吕永青 孙艳波 朱春玲 祁学斌 纪少珲 许绍斌 何永捍 何 余国华 余 蕊 吴 飞 吴世芳 吴东东 张志刚 张栋儒 张 慧 时晓菲 李功华 李其刚 李学燕 李宗煦 李桂梅 李朝翠 杨双娟 杨利琴 杨春燕 杨 钦 杨 晖 杨敏敏 杨 爽 苏伟婷 邵静茹 闵 锐 陈小勇 陈小琼 陈永昌 陈 兴 陈 陈宏满 陈 睿 周炜帏 周 鑫 和协超 季吟秋 岩 道 郑兰平 金洁琼 相 辉 胡 胡玲玲 赵玉琪 赵若苹 赵 博 郝军军 饶定齐 唐 高 云 高建云 黄 蓓 彭 忆 彭旻晟 舒树森 董 锋 蒋万胜 谢海兵 韩树标 廖爱文 谭 李 李家堂 苏 蕊 吴江鸿 潘晓赋 颜 芳 刘 斌 佳 静 兵 嘉 韬 博士后 Chatmongkon Suwannapoom 季林丹 艳 贺军州 段莹亮 倪 刚 黄 强 马鹏程 王姝妍 代绍兴 叶志强 刘 振 吕 李学友 李 汪德勇 胡玲玲 赵 博 倪庆永 梁 管振华 ２０１３ 年毕业研究生 博士生 璐 明 颜 芳 64 俊 遗传资源与进化国家重点实验室 2013 年 度 报 告 硕士生 寸益贤 王丽丽 王 毅 宁文鹤 刘 菲 宋卢挺 季 爽 罗 军 范 飞 赵亚鹏 逯 翔 曾燕妮 波 黄 松 周传江 博士后 王 在读研究生 博士生 Adeola Adeniyi Charles Nguyen Ngoc Sang Sushil 万 韬 王明山 王 王晓爱 王晓雄 王晓磊 王 维 王鑫轶 叶青青 刘 杰 刘 晖 刘鹤群 刘耀文 向 坤 孙 健 江世友 许东明 何大健 张业胜 张 田 张 凯 张祖明 张晓明 张 张 煦 李玉春 李朝晖 李毓劲 李肇天 杨召辉 杨立新 杨军校 杨 杨相彩 杨贺川 杨晨雪 杨 森 杨德英 沈文菁 肖富辉 邵 永 陈中正 陈 垒 陈舜梅 周中银 郑俊娟 柯 浩 胡廼清 徐 丹 徐 讯 徐雯雯 袁智勇 郭义成 曹 雪 程东强 程耀霆 韩菲菲 于龙龙 尹婷婷 文晓岚 王文敏 王玉晴 王运梅 王娅丽 王 倩 王晓阳 王 筱 史妮妮 叶凌群 田娇阳 任彦栋 关 琼 刘杰伟 刘晓亮 刘 吕梦蝶 祁飞燕 何一博 余 琴 吴 焕 宋心强 张伟道 张 如 张景娟 张 琳 张源伟 李立立 李 权 李 芸 李连伟 李 越 杨坤凤 杨松霖 杨娅娇 杨晏冬 罗天逊 罗 杰 罗 鑫 苟志恒 虎恩志 郑智中 奎 玲 姚友旭 姚 瑶 赵丽敏 赵启龙（安徽大 学联培） 赵婷怡 赵颖俊 徐海波 涂小龙 郭雨龙 郭 琨 钱立富 高 黄 程 曾 琳 程 斌 茉 阳 硕士生 廉 婷 廖世玉（安徽大 学联培） 城 樊萌萌 65 秦 熙 涛 阎良辰（西南林 学院联培） 黄海波 谢建新 谢钢琴 韩徐曼 薛 霍永霞 戴 伟 敏 然 State Key Laboratory of Genetic Resources and Evolution 2013 ANNUAL REPORT Personnel Principal Investigators Douglas W Yu Zhanshan Ma Qingpeng Kong Jianfan Wen Bingyu Mao Wen Wang Ruiwu Wang Jing Che Yaping Zhang Junxing Yang Xiaojun Yang Wenhui Nie Ping Zheng Peng Shi Bing Su Jingfei Huang Baowei Jiao Xuelong Jiang Yunfei Ma Pengcheng Ma Yuyu Niu Wenzhi Wang Huawei Wang Yunyu Wang Guodong Wang Lin Wang Jinhuan Wang Shaoxing Dai Dandan Ye Zhiqiang Ye Wei Si Hong Shi Lei Shi Guopeng Ren Haiqing Ren Jia Liu Guichun Liu Zhen Liu Suwei Liu Heng Liu Yongqin Lv Yanbo Shun Chunling Zhu Xuebin Qi Saohui Ji Shaobin Xu Yonghan He Jing He Guohua Yu Rui Yu Fei Wu Shifang Wu Dongdong Wu Zhigang Zhang Dongrui Zhang Hui Zhang Xiaofei Shi Gonghua Li Qigang Li Xueyan Li Zongxu Li Guimei Li Chaocui Li Shuangjuan Yang Liqing Yang Chunyan Yang Qing Yang Hui Yang Mingming Yang Shuang Yang Weiting Su Jingru Shao Rui Ming Xiaoyong Chen Xiaoqiong Chen Yongchang Chen Xing Chen Bing Chen Hongman Chen Rui Chen Weiwei Zhou Xing Zhou Xiechao He Yingqiu Ji Dao Yan Lanping Zhen Jieqiong Jin Hui Xiang Jia Hu Lingling Hu Yuqi Zhao Ruoping Zhao Bo Zhao Junjun Hao Dingqi Rao Jia Tang Yun Gao Jianyun Gao Bei Huang Yi Peng Minsheng Peng Shusen Shu Feng Dong Wansheng Jiang Haibing Xie Shubiao Han Aiwen Liao Tao Tan Xiaofu Pan Fang Yan Jianghong Wu Staff Postdoctors Chatmongkon Suwannapoom Bin Liu Yan Li Jiatang Li Rui Shu Lindan Ji Junzhou He Yingliang Duan Gang Ni Qiang Huang Students Graduated in 2013 Dorctors Pengcheng Ma Shuyan Wang Shaoxing Dai Zhiqiang Ye Zhen Liu Jun Lv Xueyou Li Ming Li Deyong Wang Lingling Hu Bo Zhao Qingyong Ni Lu Liang Zhenghua Guan Fang Yan 66 遗传资源与进化国家重点实验室 2013 年 度 报 告 Masters Yixian Cun LiliWang Yi Wang Wenhe Ning FeiLiu Luting Song Shuang Ji Jun Luo Fei Fan Yaping Zhao Xiang Lu Yanni Zeng Song Huang Chuanjiang Zhou Postdoctors Bo Wang Graduate students Doctors Adeola Adeniyi Nguyen Ngoc Sang Sushil Tao Wan Mingshan Wang Mo Wang Xiaoai Wang Xiaoxiong Wang Xiaolei Wang Wei Wang Xinyi Wang Qingqing Ye Jie Liu Hui Liu Hequn Liu Yaowen Liu Kun Xiang Jian Shun Shiyou Jiang Dongming Xu Dajian He Yesheng Zhang Tian Zhang Kai Zhang Zuming Zhang Xiaoming Zhang Bin Zhang Xu Zhang Yuchun Li Zhaohui Li Yujin Li Zhaotian Li Zhaohui Yang Lixin Yang Junxiao Yang Yang Yang Xiangcai Yang Hecuan Yang Chengxue Yang Seng Yang Deying yang Wenjing Shen Fuhui Xiao Yong Shao Zhongzheng Chen Lei Chen Shunmei Chen Zhongyin Zhou Junjuan Zheng Hao Ke Naiqing Hu Dan Xu Xun Xu Wenwen Xu Zhiyong Yuan Yicheng Guo Xue Cao Dongqiang Cheng Yaoting Cheng Feifei Han Longlong Yu Tingting Ying Xiaolan Wen Wenming Wang Yuqing Wang Yunmei Wang Yali Wang Qian Wang Xiaoyang Wang Xiao Wang Nini Shi Lingqun Ye Jiaoyang Tian Yandong Ren Qiong Guan Jiewei Liu Xiaoliang Liu Xi Liu Mengdie Lv Feiyan Qi Yibo He Qing Yu Huan Wu Xinqiang Song Weidao Zhang Ru Zhang Jingjuan Zhang Lin Zhang Yuanwei Zhang Lili Li Quan Li Yun Li Lianwei Li Yue Li Kunfeng Yang Songlin Yang Yajiao Yang Yandong Yang Tianxun Luo Jie Luo Xing Luo Zhiheng Gou Enzhi Hu Zhizhong Zheng Ling Kui Youxu Yao Yao Yao Liming Zhao Qilong Zhao Tingyi Zhao Yingjun Zhao Haibo Xu Xiaolong Tu Tao Qing Yulong Guo Kun Guo Lifu Qian Wei Gao Liangchen Yan Haibo Huang Cheng Huang Lin Zeng Cheng Cheng Jianxin Xie Gangqin Xie Xuman Han Ting Lian Shiyu Liao Mengmeng Fan Ming Xue Yongxia Huo Ran Dai Charles Masters 67