遗传资源与进化国家重点实验室2012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 35 重要基金项目 Key Projects and Fundings 41 发表论文 Publications 44 获 奖 Awards 50 研究生优秀论文奖 Outstanding Paper Awards for Graduate Students 51 大事记 Major Events 52 开放课题 Open Projects 55 专家学术报告 Invited Lectures 56 人员名单 58 Personnel 60 遗传资源与进化国家重点实验室 2012 年 度 报 告 主任致辞 2012 年，在全国十八大创新精神及中科院“创新 2020”跨越发展体系精神的指导下，遗传资源与进化国 家重点实验室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，同时结合 自己的资源优势，进一步全面推进各方面工作，在任务承担、创新研究、人才队伍建设、开放交流、平台建设 等各方面均取得了显著进展。 2012 年，实验室在争取重大科技任务方面成绩斐然，新争取科研项目 57 项，其中包括主持 973 项目 1 项， 国家自然科学基金委重大研究计划重点项目 2 项、优秀国家重点实验室项目 1 项。年度到位科研经费突破性达 到 4872 万元。另有 29 项课题顺利结题。在基础研究的同时，实验室也积极推进科技成果的应用转化，例如 与企事业单位合作挖掘动植物重要经济性状功能基因。在国际合作方面，实验室继续推动国际条形码中国计划、 国际山羊基因组计划，并在本年度取得重要进展。 在科研进展方面，2012 年实验室继续围绕三大研究方向，在遗传资源收集保护、家养动物的起源与驯化、 新基因起源机制、基因组进化、动物适应性进化机制等方面取得了丰硕的成果。共发表 SCI 收录论文 111 篇， 包 括 发 表 在 Nat Biotechnol, Nat Genet, Ecol Lett, Mol Biol Evol, PLos Genet 等 IF5-year>9 的 国 际 著 名 期 刊 论 文 11 篇，授权专利 1 项。尤其值得庆贺的是王文研究员带领的团队在“年轻新基因起源和遗传进化的机制研究” 方面取得的成果荣获 2012 年度国家自然科学二等奖。 2012 年，实验室人才培养措施也取得了显著成果。车静博士提升为研究员，新成立“两栖爬行类多样性 与进化研究组”加入实验室；新引进 8 名青年博士。研究生培养方面，为夯实研究生相关研究领域的理论知 识，实验室与所研究生部合作，继续推进极具特色的研究生学位课程，邀请了 2 名国内外学者为研究生授课。 2012 年，毕业硕士 9 人，博士 15 人，出站博士后 4 人。1 篇博士论文入选中科院百篇优博，2 名研究生获得 院长奖学金优秀奖，另有多名研究生获得中科院各类奖学金。 在对外学术交流与合作共享方面，2012 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。8 月，举办了“遗传发育与进化国际研讨会暨学科发展战略研讨会”； 10 月，参与主办了“中国灵长类专家组 2012 年会暨中国长臂猿保护国际研讨会”。此外，实验室人员外出参 加国内外学术会议 60 余人次，其中在国内外学术会议上做特邀报告 8 人次；邀请国内外专家来室讲学 17 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，投入经费 150 万元。 在平台建设方面，国家重点实验室设备专项获批 38 台（套）大型设备，目前已陆续投入运行。这批设备 极大地提升了实验室科研硬件实力，为实验室达成“成为本领域国际知名的研究中心”的目标提供了强有力地 支撑。在满足室内需求的同时，实验室也积极通过中科院昆明大型仪器共享管理网络系统将大型设备对外开放 共享。 2013 年是全面深入贯彻落实党的十八大精神的开局之年，是“创新 2020”深入实施的关键落实年。实验 室将在新一届学术委员会的指导下，进一步发挥资源与学科优势，凝练目标，强化团队交叉协作，提高自主创 新能力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。 在此，我谨向给予实验室关心与帮助的各级领导、各位朋友致以最诚挚的感谢，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》 》 》 》 》 ■■■ 2012 ANNUAL REPORT Director's Report The “State Key Laboratory of Genetic Resources and Evolution” has made considerable progress in 2012, with regards to genetic resource collections, scientific research output, talent recruitment, scientific exchange and instruments share. Grant awards. – Fifty seven new grants were awarded to the lab in 2012, including 1 key project from the National Basic Research Program (‘973’ grants), two key projects from the Major Program of the National Natural Science Foundation of China and 1 grant for outstanding State Key Laboratories from NSFC. In 2012, the funds to the lab reached a new high of 48.72 million RMB. In addition to basic researches, the lab promoted applied researches including the mining of important phenotypic genes of economical plants and animals in cooperation with companies. The lab also continued to promote the “International Barcode of Life Project (iBOL) in China” and the “International Goat Genome Project” and made important progresses this year. Publications and Awards. – The lab made systematic progresses in adaptive evolution, gene and genomic evolution in 2012. The lab published in total 111 papers in SCI journals, including 11 papers in top journals such as Nat Biotechnol, Nat Genet, Ecol Lett, Mol Biol Evol, PLos Genetics (IF5-year>9). The lab was also granted one patent. Especially, the team lead by Prof. Wen Wang won the second prize for State Natural Science Award due to their outstanding works on “Mechanism of origin and genetic evolution of newly evolved genes”. Talent recruitment. - In 2012, Dr. Jing Che of the lab was promoted to full professor and established her research group on “Herpetological Diversity and Evolution”. The lab has also recruited 8 young research assistants with Ph.D. degrees. Fifteen Ph.D. and 9 M.Sc. students graduated and 4 postdoctoral researchers completed their work in the lab in 2012. One Doctoral thesis was selected as one of the “100 excellent Ph.D. thesis” of CAS. Two graduate students were awarded “CAS Presidential Scholarship (Excellence Award)” and several other students were awarded various types of scholarships from CAS. In cooperation with the Graduate Student Department of the institute, the lab invited two wellknown professors to give courses on “molecular evolution” and “population genetics” this year. Scientific exchange and Instruments share. – In August, the International Symposium on “Genetics, Development and Evolution”was held by the lab in Kunming. As one of the organizers, the lab hosted the “2012 Annual Meeting of the China Primate Specilist Group (CPSG) and the International Symposium on the Black Crested Gibbon Protection” in Jingdong in September. Members of the lab attended scientific meetings both at home and abroad for more than 60 times including 8 times as invites speakers. Seventeen scholars were invited to visit the lab and to give lectures this year for scientific exchange and co-operation. In 2012, the lab funded 13“open projects” (1.5 million RMB total). This year, 38 large instruments were approved to the lab which are now coming into operation. This batch of instruments greatly improved the facilities of the lab which will also be open to researchers from outside. In the future, the 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 lab is to make major contribution on the researches on genetic resources and evolution in China, and to promote the 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 2012 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 教 授， 复旦大学 Prof. 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》 》 》 》 》 ■■■ 2012 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 15 个，支撑部门 3 个，现有固定人员 95 人，其中博士 48 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 4 人，中科院“百人计划”7 人，云南省“高端人才”2 人。 There are 15 research groups and 3 facility centers in the lab. Among the 95 staff members, 48 of them hold Ph.D. degrees. The average age of the team is 35 years old. The research team includes one academician of CAS, 4 winners of the "National Science Fund for Distinguished Young Scholars", 7 holders of the "Hundred Talents Program"of CAS and 2 holders of "Top talent" project of Yunnan Province. 4 遗传资源与进化国家重点实验室 2012 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：中国－喜马拉雅地区生物多样性的考察监测、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 22 项，其中新申请批准的项目 4 项。出版专著 1 章；发表 SCI 论文 18 篇，获授权国家发明专利 1 项。 重要成果（Highlights） 论著（Publications） 1. Yang Jian, Jun Xing Yang*, Xiao Yong Chen*. 2012. A re-examination of the molecular phylogeny and biogeography of the genus Schizothorax (Teleostei: Cyprinidae) through enhanced sampling, with emphasis on the species in the Yu n n a n – G u i z h o u P l a t e a u , C h i n a . Journal of Zoological Systematics and Evolutionary Research 50(3): 184-191 2. Min Rui, Jun-Xing Yang﹡, Xiao-Yong Chen﹡, Richard Winterbottom, Richard Mayden. 2012. Phylogenetic Relationships of the Genus Homatula (Cypriniformes: Nemacheilidae), with Special Reference to the Biogeographic History around the Yunnan-Guizhou Plateau. Zootaxa 3586: 78–94 3. Du Li-Na, Yang Jun-Xing, Thomas von Rintelen, Chen Xiao-Yong, David Aldridge. 2012. Molecular Phylogenetic Evidence that the Chinese Viviparid Genus Margarya (Gastropoda: Viviparidae) is Polyphyletic. Chinese Science Bulletin 57(1): 1-9 4. Jiang Wan-Sheng, Heok Hee Ng, Jun-Xing Yang*, Xiao-Yong Chen*. 2012. A taxonomic review of the catfish identified as Glyptothorax zanaensis (Teleostei: Siluriformes: Sisoridae), with the descriptions of two new species. Zoological Journal of the Linnean Society 165: 363–389 5. 杨 君 兴 , 李 再 云 , 潘 晓 赋 , 陈 小 勇 , 崔 桂 华 . 2012. 一 种 抚 仙 金线鲃的人工受精方法 . ( 专利号 ZL201010114389.4，2012.3.2 授权） 1. 裂腹鱼属（Schizothorax）系统发育及其在云贵高原的演化过程 重点加强了云南贵高原地区该属鱼样本的收集，构建了这一地区较为完整的 裂腹鱼属鱼类的系统进化树。研究结果表明：系统树不支持裂腹鱼属鱼类亚属的 划分；不同种类 Cyt b 基因序列的最大遗传距离为 11.2%；怒江和澜沧江的个体 以较高的支持率聚成一单系；伊洛瓦底江水系与雅鲁藏布江的个体以较高的支持 率聚成一单系；识别了一新地理单元群体——泛金沙江群体 ( 金沙江、元江、南盘江、 北盘江 )；不支持长江第一湾为袭夺湾的观点，古金沙江入古红河可能不经剑川 洱海一线；起源于 3.6Ma 的青藏运动是横断山区各大水系发育的主要力量，也是 该地区裂腹鱼属鱼类成种的主要时期。 2. 副鳅属（Homatula）的系统发育和谱系地理学研究 通过线粒体 cytb 基因和核基因 RAG1 基因的扩增，构建副鳅属的系统发育 关系。研究结果显示副鳅属是一个单系群，主要分成五支：无量副鳅是最先分化 的一支，其次是澜沧江 - 怒江组与金沙江 - 南盘江组的分化，再次是长江分布的 短体副鳅从金沙江 - 南盘江组中分化出来，然后是嵩明牧羊河的待定种从金沙江 南盘江组中分化。物种分化事件的时间分别与青藏运动的三次隆升相对应，青藏 高原的隆升所导致的水系的变迁可能是导致副鳅属鱼类进化的主要原因，通过对 副鳅属的研究验证了青藏运动三次隆升的事件。 3. 中国特有腹足类—螺蛳属 (Margarya) 的系统发育学研究 利用线粒体基因 COI 和 16S rRNA 构建了螺蛳属的系统发育关系，系统发育 结果揭示螺蛳属并非是一个单系，其主要被分为三大支：阳宗海支、抚仙湖 - 星 云湖 - 杞麓湖支、滇池 - 洱海支。另外，滇池 - 洱海支中螺蛳属种类与圆田螺 属种类交错聚在一起。这一结果暗示亚洲田螺科的种类需要进一步详细的整理， 螺蛳属现存种类的分类地位也需要重新确定。另外，螺蛳分布于滇池和洱海，两 湖相隔较远，而软体动物的扩散能力较弱，对于螺蛳分布在两个湖泊的现象可以 再次证明水鸟在螺类扩散过程中所起到的作用。 4. 扎那纹胸鮡复合体的系统分类学整理 通过形态学常规测量性状、骨骼解剖和多变量形态度量值的主成分分析，并 结合扩大取样范围的分子系统发育学结果，重新界定和描述了扎那纹胸 鮡，恢 复和重新描述了长须纹胸鮡；同时还描述了怒江水系的两个新种——粒线纹胸鮡 Glyptothorax granosus 和异色纹胸鮡 Glyptothorax fucatus。 5 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 ANNUAL REPORT Phylogenetics and Biogeography Dr. Junxing Yang, Professor, Deputy Secretary of the Party Committee and Vice Director of the Kunming Branch. The research team is mainly interested in biodiversity monitoring survey, fauna taxonomic, phylogenetic and biogeographic study in the area of China-Himalayan; ecology and conservation research to rare and native species; especially focuses on the restoration of wetland ecosystem and application. In 2012, total 22 research programs have been implementing with 4 programs newly applied. Published 1 monograph and 18 SCI papers. 1 national invention patent licensing. Email：yangjx@mail.kiz.ac.cn 1. A re-examination of the molecular phylogeny and biogeography of the genus Schizothorax with emphasis on the species in the Yunnan–Guizhou Plateau, China 员工简介（Lab Staff） The mitochondrial DNA cytochrome b sequences of 36 Schizothorax species from 51 localities in the Yunnan–Guizhou Plateau (YGP) and its adjacent areas were analysed. Samples from the YGP were tentatively grouped into three geographically distributed clades: the Tsangpo-Irrawaddy, the Mekong-Salween and the Trans-Jinsha River. The phylogenetic history of the species is congruent with events caused by the uplift of the Tibetan Plateau and the YGP. Our phylogenetic trees did not support the hypothesis that the paleo Jinsha River was drained through the Yangtze River-Jianchuan Lake-Erhai Lake to the Red River. 陈小勇 副研究员 2. Phylogenetic Relationships of the Genus Homatula with Special Reference to the Biogeographic History around the Yunnan-Guizhou Plateau Liu Qian, Secretary 李 松 副研究员 Li Song, Associate Professor Herein we provide phylogenetic inferences of species relationships based on complete sequences of cyt b and RAG 1. Both gene trees support the recognition of five clades in the genus. Divergence times of the major clades in Homatula are inferred to be Late Pliocene and the Early Pleistocene, and are correlated with the massive geological events associated with the uplift of the Qinghai-Tibetan Plateau occurring at these times. The reconstruction of drainage histories suggests that the fish faunas of the Nu and Lancang rivers are basal relative to other riverine faunas in the region, and that the Nanpan and the Jinsha rivers share a more recent history than with any other river systems included in our study. 3. Molecular phylogenetic evidence that the Chinese Viviparid genus Margarya (Gastropoda: Viviparidae) is polyphyletic We investigated the phylogeny of the viviparid genus Margarya, endemic to Yunnan, China, using two mitochondrial gene fragments (COI and 16S rRNA). The molecular phylogeny indicates that Margarya is polyphyletic, as two of the three well-supported clades containing species of Margarya also comprise species from other viviparid genera. In one clade, sequences of four species of Margarya even cluster indiscriminately with those of two species of Cipangopaludina, indicating that the current state of Asian viviparid taxonomy needs to be revised. The molecular data also indicate that the species status of the six extant species of Margarya should be re-assessed. 4. A taxonomic review of the catfish identified as Glyptothorax zanaensis with the descriptions of two new species Considering of the observation of morphologic differences in different locations in the field surveys and specimens identification, researchers reanalyzed the G. zanaensis complex using the methods that combined the traditional morphologic measurements and truss-based measurements with principal components analysis, as well as molecular methods. The study redescribes G. zanaensis, revalidates and redescribes G. longinema, and describes the two unnamed species from the Nujiang (upper Salween) drainage as Glyptothorax granosus and Glyptothorax fucatus. 6 工作人员（Staff） 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 刘 倩 工程师 郑兰平 副研究员 Zheng Lanping, Associate Professor 潘晓赋 助理研究员 Pan Xiaofu，Assistant Professor 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 刘淑伟 助理研究员 Liu Shuwei, Assistant Professor 舒树森 助理研究员 Shu Shusen, Assistant Professor 闵 锐 研究实习员 Min Rui, Research Assistant 研究生（Graduate Students） 王伟营 Wang Weiying 2006 王 茉 Wang Mo 2008 王晓爱 Wang Xiaoai 2009 赵亚鹏 Zhao Yapeng 2010 赵婷怡 Zhao Tingyi 2011 秦 涛 Qin Tao 2012 杨坤凤 Yang Kunfeng 2012 程 城 Cheng Cheng 2012 遗传资源与进化国家重点实验室 2012 年 度 报 告 兽类生态与进化 蒋学龙， 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。 重要成果（Highlights） 论著（Publications） 1. 西黑冠长臂猿相邻群体理毛社会网络及其与群体构成的关系 通过对无量山大寨子两相邻群体理毛社会网络分析表明：理毛社会网络 1. He K, Chen JH, Gould GC, Yamaguchi N, Ai HS, Wang YX, Zhang YP, Jiang XL, 2012. An Estimation of Erinaceidae Phylogeny: A 可以反映社会构成的变动；形成时间更长、个体间关系更加稳定的群体（G3）， Combined Analysis Approach. PLoS ONE, 7(6): 外）作为自己的首选理毛对象；G3 群中亚成年雄性并没有像一般亚成年雄 e39304. 性个体那样处于群体的边缘位置，而是通过更多的理毛付出使自己处于理毛 2. Liu Q, Chen P, He K, Kilpatrick CW, Liu SY, Yu FH, Jiang XL, 2012. Phylogeographic Study of Apodemus ilex (Rodentia: Muridae) in Southwest China. PLoS ONE 7(2): e31453. 其理毛社会网络明显较为复杂，个体间联系更多（图 1）；G2 群中外来成 年雌性付出更多的理毛努力，并将群体中原有的成年雌性（除其自己的后代 网络的中心位置，2012 年的观察发现其最终替代了 G3 群原有成年雄性。说 明理毛行为虽然在西黑冠长臂猿的时间分配中只占极少比例，但对其社会构 成有重要作用，利用理毛行为构建的社会网络可以预测群体构成的变化。 3. He K, Wang JH, Su WT, Li Q, Nie WH, Jiang XL, 2012. Karyotype of the Gansu mole (Scapanulus oweni): further evidence for karyotypic stability in talpid. Mammal Study, 37: 341–348. 4. He K, Hu NQ, Orkin JO, Nyein DT, Ma C, Xiao W, Fan PF, Jiang XL, 2012. Molecular phylogeny and divergence time of Trachypithecus: with implications for the taxonomy of T. phayrei. Zoological Research, 33(E5-6): 104-110. G2 群 G3 群 图 1. 相邻两西黑冠长臂猿群体理毛社会网络关系图示 2. 甘肃鼹核型研究：鼹科核型稳定性更 多证据 甘肃鼹是中国西南部特有种，形态学 显示该类群应归于 Scalopini 族，但该族 所有其他类群均分布北美洲。前期研究 揭示鼹类染色体相当稳定，然而甘肃鼹 的核型一直未有报道，本研究首次报道 了甘肃鼹的核型，包括 G- 带和 C- 带， 2N=34, FN=64 ( 图 2)，与其他 6 种鼹 类相同，然而现有核型稳定性模型均不 能很好解释这种染色体的保守性。因此， 有必要深入综合探讨染色体重排、系统 发育及生态适应在鼹类染色体进化过程 中的影响。 7 图 2. 甘肃鼹核型 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 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 speciesbased investigations of ecology, behavior and conservation of black crested gibbon, musk deer and other large mammals. E-mail: jiangxl@mail.kiz.ac.cn 1. An Estimation of Erinaceidae Phylogeny: A Combined Analysis Approach Erinaceidae is a family of small mammals that include the spiny hedgehogs (Erinaceinae) and the silky-furred moonrats and gymnures (Galericinae). These animals are widely distributed across Eurasia and Africa, from the tundra to the tropics and the deserts to damp forests. The importance of these animals lies in the fact that they are the oldest known living placental mammals. Although the Family has been well studied, their phylogenetic relationships remain controversial. To test previous phylogenetic hypotheses, we combined molecular and morphological data sets, including representatives of all the genera. The results strongly support the monophyly of both subfamilies (Galericinae and Erinaceinae), the Hylomys group (to include Neotetracus and Neohylomys), and a sister-relationship of Atelerix and Erinaceus. As well, we verified that the extremely long branch lengths within the Galericinae are consistent with their fossil records. Although we discovered new clues to understanding the evolutionary relationships within the Erinaceidae, our results, nonetheless, strongly suggest that more robust analyses employing more complete taxon sampling (to include fossils) and multiple unlinked genes would greatly enhance our understanding of the Erinaceidae. 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 研究生（Graduate Students） Fig. 1. Mitochondrial phylogeny. Result of Bayesian phylogenetic analyses of three mitochondrial genes. Node numbers indicate Bayesian posterior probabilities. 2. Molecular phylogeny and divergence time of Trachypithecus: with implications for the taxonomy of T. phayrei The genus Trachypithecus is the most diverse langur taxon, distributed in southwestern China, south and southeastern Asia. In this study, we include 16 recognized Trachypithecus species to reconstruct the phylogeny with particular concern to the taxonomy of the three subspecies of T. phayrei using multiple genes. Our results support a sister-relationship between T. p. phayrei and T. p. shanicus. However, the mitochondrial CYT B gene supported T. p. crepuscula as a distinct species, but the nuclear PRM1 gene suggested a closer relationship between T. p. crepuscula and T. p. phayrei. The incongruence between nuclear and mitochondrial genes suggests that hybridization may have occurred, a fact that would benefit from re-examination using multiple unlinked nuclear genes. Fig. 2 The median-joining network of the genus Trachypithecus based on partial PRM1 8 胡遒清 倪庆永 李学友 宁文鹤 万 韬 刘 熙 张 斌 陈中正 戴 然 李 权 Hu Naiqing, 2009 Ni Qingyong, 2010 Li Xueyou, 2010 Ning Wenhe, 2010 Wan Tao, 2010 Liu Xi, 2011 Zhang Bin, 2012 Chen Zhongzheng, 2012 Dai Ran, 2012 Li Quan, 2012 遗传资源与进化国家重点实验室 2012 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.Li Q, Li FS, Buzzard P, Qian FW, Zhang F, Zhao JL, Yang JX*, Yang XJ*. Migration Routes and New Breeding Areas of Black-Necked Cranes. The Wilson Journal of Ornithology, 2012, 124(4):704-712. 1. 黑颈鹤的迁徙路线和新繁殖地 2009 年 2 月至 9 月间，我们在纳帕海湿地（海拔 3260m）给 5 只黑颈鹤佩戴了卫 星跟踪器，通过该技术手段调查黑颈鹤繁殖地和越冬地之间的迁徙路线。本研究确定 了四川西南部的沙鲁里山区（平均海拔 4330m），包括稻城、理塘、白玉和新龙县是 新发现的黑颈鹤繁殖地。在 5 只被跟踪的黑颈鹤当中，有 4 只在稻城县度夏。另外一 只仅在稻城县短暂停留，然后继续往北至白玉和新龙县度夏。纳帕海湿地和稻城县间 的这条迁徙路线距离仅有 180km，是鹤类最短的迁徙路线之一，但该条路线却跨越了 1200m 的海拔梯度。第五只鹤的迁徙路线长度约 400km，在 2009 年和 2010 年的春季 迁徙中分别花费了 2 天和 5 天，在 2009 年的秋季迁徙中花费了 19 天。 2.Shu SS, Yang XJ*, Chen XY. Gam marus bitaensis, a new species of am phipod from Yunnan, china (amphipo da, gammaridea). Crustaceana.  2012, 85 (10):1193-1204. 3.Zhang RY, Song G, Qu YH, Alström P, Ramos R, Xing XY, Ericson PGP, Fjeldså J, Wang HT, Yang XJ, Kristin A, Shestopalov AM, Choe JC, Lei FM. Comparative phyloge ography of two widespread magpi es: Importance of habitat preferen ce and breeding behavior on genet ic structure in China. Molecular P hylogenetics and Evolution. 2012, 65(2):562–572. 4.Zhao N, Dai CY, Wang WJ, Zhang RY, Qu YH, Song G, Chen K, Yang X J, Zou FS, Lei FM. Pleistocene climat e changes shaped the divergence and demography of Asian populations of the great tit Parus major: evidence fr om phylogeographic analysis and eco logical niche models. Journal of Avia n Biology. 2012, 43: 001–014. 5. 仇国新 , 杨晓君 主编 . 云南会 泽黑颈鹤国家级保护区 . 云南科技 出版社 , 昆明 . 2012, 1 － 228. 2. 云南会泽黑颈鹤国家级自然保护区 云南会泽黑颈鹤国家级自然保护区 是以保护国家 I 级重点保护野生动物黑 颈鹤 Grus nigricollis 及其越冬栖息地 的生态环境为主的国家级自然保护区。 2003 年至 2011 年课题组先后 3 次对该 地进行考察，并于 2011-2012 年冬季还 开展了黑颈鹤和灰鹤的越冬研究。本书 展现植物、水生生物、两栖动物、爬行 动物、鸟类及兽类以及自然环境、社会 经济状况的调查结果，分析了保护区内 生物资源的多样性，并对保护区规范化 建设和管理现状及其影响因素进行了评 价。 9 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 ANNUAL REPORT Ornithology Yang Xiaojun, Professor. 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 员工简介（Lab Staff） 1. Migration Routes and New Breeding Areas of Black-Necked Cranes 工作人员（Staff） 吴 飞 We equipped five Black-necked Cranes (Grus Fei Wu, Assistant Professor nigricollis) with satellite transmitters between 伍和启 助理研究员 HeQi Wu, Assistant Professor February and November 2009 to investigate their 孔德军 migration routes between breeding areas and China. We identified the Shaluli Mountain region (southwest Sichuan), including Daocheng, Litang, 罗伟雄 研究实习员 WeiXiong Luo，Research Assistant 安萌茵 研究实习员 Baiyu, and Xinlong counties as a new breeding area with a mean elevation of 4,330 m asl. Four of MongYing five tracked cranes spent the summer in Daocheng County. The fifth crane was there briefly and then distance between Napahai Marsh and Daocheng County (180 km) is one of the shortest migration crane was 400 km in length and occurred over 2 or 5 days in spring 2009 and 2010, respectively, and 19 An，Research Assistant 研究生（Graduate Students） moved north to Baiyu and Xinlong counties. The increase of ,1,200 m. The migration route of the fifth 助理研究员 DeJun Kong, Assistant Professor 董 锋 研究实习员 Feng Dong，Research Assistant wintering area at Napahai Marsh (3,260 m asl), routes among crane species, but covered an elevation 助理研究员 F I G . 1 . To p o g r a p h y o f breeding areas, migration paths, and wintering areas of Blacknecked Cranes wintering at Napahai Marsh, China. days in fall 2009 with five stopovers. 2. Yunnan Huize National Nature Reserve of Black-Nacked Crane Huize Black-Nacked Crane National Nature Reserve was established to protect the Black-Nacked Crane, the National Grade I Key Protected Faunal Species, and its overwinter ground. We had conducted three bird surveys to the nature reserve from 2003 to 2011, as well as study about winter of Black-Nacked Crane and Common Crane from 2011 to 2012. The Comprehensive Scientific Investigation Report of Huize BlackNacked Crane National Nature Reserve of Yunnan is compiled based on the investigation of plant, aquatic biota, amphibians, reptiles, birds and mammals, as well as the conditions of its natural and socio-economic environments. We also evaluated the standardized construction and management of the mature reserve based on the investigation. 10 董好岩 王荣兴 李欣磊 李 婷 夏 季 卢光义 廖志鹏 HaoYan Dong 2012 RongXing Wang 2011 XinLei Li 2010 Ting Li 2010 Ji Xia 2011 GuangYi Lu 2011 ZhiPeng Liao 2012 遗传资源与进化国家重点实验室 2012 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） 论著（Selected Publications） 1. Istvan Scheuring and Douglas W.Yu(2012)How to assemble a beneficial microbiome in three easy steps. Ecology Letters 15:1300-1307 2. Hui Wang, Jo Ridley, Derek W. D u n n , R u i w u Wa n g , J a m e s M.Cook and Douglas W.Yu (2012) Biased oviposition and biased survival together help resolve a figwasp conflict. Oikos 000:001-008 3. Chengxi Ye, Zhanshan Sam Ma, Charles H Cannon, Mihai Pop and Douglas W.Yu (2012) Exploiting sparseness in de novo genome assembly. BMC Bioinformatics. 13(Suppl 6):S1 4. Douglas W.Yu, Yinqiu Ji, Brent C . E m e r s o n , X i a o y a n g Wa n g , Chengxi Ye, Chunyan Yang and Zhaoli Ding (2012) Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution. doi:10.1111/j.2041210X.2012.00198.x 1. 生物多样性汤——利用 metabarcoding 方法对节肢动物的多样性进行快速大尺度 的监测及评估 Douglas W.Yu, Yinqiu Ji, Brent C.Emerson, Xiaoyang Wang, Chengxi Ye, Chunyan Yang and Zhaoli Ding 生物多样性测量在解决我国环境问题的工作中收到了越来越多的关注，例如对具 有丰富及特有生物多样性的地区进行调查和监测、病害虫及环境污染的监控、生态保 护项目（如人工橡胶林种植）的管理与监督等。然而，传统的生物多样性测量既耗时 又费钱。我们结合 metabarcoding、生态学、生物信息学和统计学，建立一套环境科 学研究的“生态—信息学 (eco-informatic)”全新模式。我们利用马氏网诱捕节肢动物， 对整个混合样本的 DNA 的 COI 基因进行扩增后进行高通量测序，并结合生物信息学 手段进行分析，整个过程我们称之为“metabarcoding”。我们人为建立了 7 个节肢 动物的群落（主要为昆虫），并证明了 metabarcoding 方法对群落组成成分的还原能 力。我们首次展示了 metabarcoding 方法对成对群落差异度（beta 多样性）以及群落 内系统发育多样性（alpha 多样性）的准确估测能力，尽管在 metabarcoding 过程中 不可避免地发生了分类学信息的丢失。Alpha 和 Beta 多样性数据是生态学及环境科 学研究中的重要材料，它们可以促进我们对环境的深入了解，在更广的尺度更有效地 测量生物多样性。 2. 微生物组共生体系的装配 Istvan Scheuring and Douglas W.Yu 微生物组的互利共生体系是如何装配问题引起了科学家的浓厚兴趣。产生抗生素 的微生物组广泛存在于珊瑚、节肢动物、软体动物、脊椎动物以及植物根际，其作 为互利共生体系中主要组成部分这一观点是一直受到争议的。典型的例子如真菌蚂 蚁（attine ants），这种蚂蚁会培育真菌作为食物，同时又作为一些微生物的寄主， 微生物在蚂蚁的表皮层释放出抗生素以抵御寄生真菌的蔓延。其中一种解释是假诺 卡氏菌（Pseudonocardia）在长期垂直传播的过程中，与其它微生物竞争而形成了新 的装配形式来抵抗寄生真菌。另一种解释是 attines 蚂蚁选择性地从土壤中招募多种 非协同进化的放线菌以产生多种抗生素共同对抗寄生真菌。我们结合了这两个模型， 显示了当寄主对干扰竞争提供剩余资源时，产生抗生素（以及对抗生素有抑制作用） 的微生物在竞争中占有优势。当至少一个放线菌共生体呈垂直传播或是具有较高植 入率时，这种伙伴选择机制更为合适，就和抑病土壤中的情况一样。 11 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 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. Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring Douglas W.Yu, Yinqiu Ji, Brent C.Emerson, Xiaoyang Wang, Chengxi Ye, Chunyan Yang and Zhaoli Ding (1) Traditional biodiversity assessment is costly in time,money and taxonomic expertise.Moreover, data are frequently collected in ways (e.g. visual bird lists) that are unsuitable for auditing by neutral parties, which is necessary for dispute resolution. (2) We present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. The protocols combine mass trapping of arthropods, mass-PCR amplification of the COI barcode gene, pyrosequencing and bioinformatic analysis, which together we call ‘metabarcoding’. (3) We construct seven communities of arthropods (mostly insects) and show that it is possible to recover a substantial proportion of the original taxonomic information. We further demonstrate, for the first time, that metabarcoding allows for the precise estimation of pairwise community dis-similarity (beta diversity) and within-community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information inherent tometabarcoding. (4) Alpha and beta diversity metrics are the raw materials of ecology and the environmental sciences, facilitating assessment of the state of the environment with a broad and ecient measure of biodiversity. 员工简介（Lab Staff） 工作人员（Staff） 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 任国鹏：助理研究员 Dr. Ren Guopeng, Assistant Researcher 王 林：研究实习员 Mr. Wang Lin, Research Assistant 王晓阳：研究实习员 Ms.Wang Xiaoyang, Research Assistant 2. How to assemble a beneficial microbiome in three easy steps Istvan Scheuring and Douglas W.Yu There is great interest in explaining how beneficial microbiomes are assembled. Antibiotic-producing microbiomes are arguably the most abundant class of beneficial microbiome in nature, having been found on corals, arthropods, molluscs, vertebrates and plant rhizospheres. An exemplar is the attine ants, which cultivate a fungus for food and host a cuticular microbiome that releases antibiotics to defend the fungus from parasites. One explanation posits long-term vertical transmission of Pseudonocardia bacteria, which (somehow) evolve new compounds in arms-race fashion against parasites. Alternatively, attines (somehow) selectively recruit multiple, non-coevolved actinobacterial genera from the soil, enabling a ‘multi-drug’ strategy against parasites. We reconcile the models by showing that when hosts fuel interference competition by providing abundant resources, the interference competition favours the recruitment of antibiotic-producing (and -resistant) bacteria. This partner-choice mechanism is more effective when at least one actinobacterial symbiont is vertically transmitted or has a high immigration rate, as in diseasesuppressive soils. 12 研究生 (Graduate Students) 杨晨雪 Yang Chenxue 张 凯 Zhang Kai 刘小虎 Liu Xiaohu 李 娜 Li Na Catharine Powell 遗传资源与进化国家重点实验室 2012 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。主要从分子水平研究生物多样性的演化 及机制，近年来在家养动的起源与人工选择的遗传机制、动物适应进化的 遗传机制、动物分子系统学和系统地理学等方面取得了突出的成果，已 发表两百多篇 SCI 论文。现任国际重要刊物 Genome Biol Evol 副主编、 Anim Genet 编委。2012 年作为项目负责人的国家基金重大项目“动物 DNA 条形码基因和隐存多样性的研究”在基金委组织的项目中期检查中 综合评定为优秀。 重要成果（Highlights） 1. 蝙蝠回声定位通路的进化机制 论著（Selected Publications） 小蝙蝠和某些鲸（包含海豚）各自独立进化出回声定位能力，关于回 声定位分子机制一直是研究热点，回声定位能力的形成，不单单依赖耳蜗 对超声的感知，还依赖大脑对声音信号的处理。通过对完整的回声定位通 路中耳蜗的 Cdh23 基因和它的配体 Pcdh15 基因，以及神经信号传导的 Otof 基因进行分析，发现它们在有回声定位的物种里面都发生了显著的趋 同进化和正选择作用。有回声定位的蝙蝠大脑听皮层中的 Otof 基因表达 丰度远远高于其他皮层以及其它没回声定位蝙蝠的各种皮层。第一次从分 子水平系统揭示了从耳蜗声音感知到大脑神经信号传导完整的回声定位通 路的进化机制。以及基因表达丰度的改变在回声定位起源上的重要作用。 【Shen YY et al. 2012 PLoS Genetics, 5 Year-IF=10.054】 1. Chen R, Irwin DM, Zhang YP*. Differences in selection drive olfactory receptor genes in different directions in dogs and wolf. Molecular Biology and Evolution 2012, 29(11):3475-3484. 2. Gao Y, Wang SY, Luo J, Murphy RW, Du R, Wu SF, Zhu CL, Li Y, Poyarkov AD, Nguyen SN, Luan PT, Zhang YP*. Quaternary palaeoenvironmental oscillations drove the evolution of the Eurasian Carassius auratus complex (Cypriniformes, Cyprinidae). Journal of Biogeography 2012, 02755.x. 3. Ji LD, Qiu YQ, Xu J, Irwin DM, Tam SC, Tang NL, Zhang YP*. Genetic Adaptation of the HypoxiaInducible Factor Pathway to Oxygen Pressure among Eurasian Human Populations. Molecular Biology and Evolution 2012, 29(11):3359-3370. 4. Jin W, Wu DD, Zhang X, Irwin DM, Zhang YP*. Positive Selection on the Gene RNASEL: Correlation between Patterns of Evolution and Function. Molecular Biology and Evolution 2012, 29(10):3161-3168. 5. 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. Molecular Ecology Resources 2012, 6. Shen YY, Liang L, Li GS, Murphy RW, Zhang YP*. Parallel evolution of auditory genes for echolocation in bats and toothed whales. PLoS genetics 2012, 8(6):e1002788. 7. Shen YY, Lim BK, Liu HQ, Liu J, Irwin DM, Zhang YP*. Multiple Episodes of Convergence in Genes of the Dim Light Vision Pathway in Bats. Plos One 2012, 7(4). Fig.1 听觉通路 2. 家犬驯化历史中嗅觉受体基因的不同选择作用研究 家犬一直是研究人工选择和自然选择的重要模式生物。在家犬和人 类的共同历史中，嗅觉发挥了及其重要的作用。通过对分离得到的灰狼、 中国土狗及品种犬嗅觉受体基因家族中的假基因进行分析发现，其在品 种犬中存在着很强的负选择，而狼和中国土狗近乎中性；对非同义位点 的精细分析发现，嗅觉受体基因在狼中积累着无害突变，去除有害突变， 而在中国土狗中近乎中性；随后对这些多态性位点在七次跨膜结构上分 布的分析结果进一步验证了这个结论。研究还发现选择作用在祖先群体 及狼的嗅觉受体基因中精细微妙，而其在品种犬中的就未有这种效果。 该研究结果不仅揭示了家犬的嗅觉受体基因所受的选择作用在其两 次重要的驯化历史阶段发生了两次深刻的变化，而且展示了自然选择和 人工选择的不同作用，为以后的品种培育及改良提供了借鉴意义。 【Chen R, et al. 2012 Mol Biol Evol，5 Year-IF=9.857】。 13 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 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 revealed some molecular machenism of Echolocation pathway in Bats and Toothed Whalesde, Differences in selection olfactory receptor genes in dogs and wolf, Genetic adaptation of the hypoxiainducible factor pathway among Eurasian human populations. Phylogeny and phylogeography of some animal groups are clarified. Within 2012, 40 SCI papers have been published and 4 papers have impact factor higher than 9, including PLoS Genet (1), Mol Biol Evol (3). Email: zhangyp@mail.kiz.ac.cn 1. Parallel evolution of auditory genes for echolocation in bats and toothed whales The ability of bats and toothed whales to echolocate is a hotspot of convergent evolution. Echolocation involves complex mechanisms, including cochlear amplification, nerve transmission, and signal re-coding. Cadherin 23 (Cdh23) and its ligand, protocadherin 15 (Pcdh15), are essential for bundling motility in the sensory hair. Otoferlin (Otof) responds to nerve signal transmission in the auditory inner hair cell. Our synthesis of gene sequence and gene expression analyses reveals that multiple evolution mechanisms, such as positive selection, parallel evolution, and perhaps co-evolution, affect the three hearing genes that play different roles in cochlear amplification, nerve transmission, and brain function. We also show the expression pattern played an important role during echolocation origin. Shen YY et al. 2012 PLoS Genetics, 5 Year-IF=10.054 员工简介（Lab Staff） 研究人员（Researchers） Dr. Robert W. Murphy, Visiting Professor Dr. David Irwin, Visiting Professor 沈永义 副研究员 Dr. YongYi Shen 高 云 副研究员 Dr. Yun Gao 吴东东 副研究员 Dr. DongDong Wu 彭旻晟 副研究员 Dr. MingSheng Peng 谢海兵 助理研究员 Dr. HaiBing Xie 王国栋 助理研究员 Dr. GaoDong Wang 孙艳波 助理研究员 Dr. YanBo Sun 陈 睿 助理研究员 Dr. Rui Chen 何 静 助理研究员 Ms. Jing He 蒋 珂 研究实习员 Mr. Ke Jiang 马云飞 研究实习员 Mr. YunFei Ma 工程技术人员（Technicians） 吴世芳 Ms. ShiFang Wu 朱春玲 Ms. ChunLing Zhu 李桂梅 Ms. GuiMei Li 杨鹏标 Mr. PengBiao Yang 施林明 Mr. LinMing Shi 博士后（Postdoctoral Fellows） 李家堂 Dr. JiaTang Li，2009 周传江 Dr. ChuanJiang Zhou, 2011 Fig.2 Parallel evolution and expression patterns of Otof. (A) gene tree based on amino acid sequence for otof showed the parallel evolution, (B) expression patterns of Otof in different cerebral cortexes of bats. 李 艳 Dr. Yan Li, 2012 季林丹 Dr. LinDan Ji, 2012 研究生（Graduate Students） 2. Different selections drive olfactory receptor genes evolution in dogs and wolf 王姝妍 Wang, SY 杨贺川 Yang, HC 颜 芳 Yan, F Dog is a model organism for studying artificial selections, olfactory receptor (OR) gene family is biggest gene family in mammals, Based on a new subtle discrimination of deleterious mutation and non-deleterious mutation in OR genes, we detect divergences in genes between populations in microscale. After the analysis of polymorphism data, we also found the difference between artificial selections and natural selections, which made a good reference for animal breeding. Chen R, et al. 2012 Mol Biol Evol, 5 Year-IF=9.857 刘鹤群 Liu, HQ 梁 璐 Liang, L 袁志勇 Yuan, ZY 刘 杰 Liu, J 周中银 Zhou, ZY 曹 雪 Cao, X 王明山 Wang, MS 刘 菲 Liu, Fig.3 Distribution of polymorphisms in three domains of olfactory receptor proteins F 涂小龙 Tu, XL 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 Nguyen Ngoc Sang Adeola Adeniyi Charles 14 遗传资源与进化国家重点实验室 2012 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, Wen Y, Fu J, Xu YB, Jin JQ, Ding L, Min MS, Che J*, Zhang YP*. Speciation in the Rana chensinensis complex and its relationship to the uplift of the Qinghai–Tibetan Plateau. Molecular Ecology, 2012, 21: 960–973. 2. Che J, Chen HM, Yang JX, Jin JQ, Jiang K, Yang ZY, Murphy RW, Zhang YP*. Universal COI primers for DNA barcoding amphibians. Molecular Ecology Resources. 2012, 12: 247–258. 3. Jiang K, Chen TB, David P, Vogel G, Hou M, Yuan ZY, Meng YJ, Che J*. On the occurrence of Oligodon joynsoni (Smith, 1917) in China (Squamata: Colubridae). Asian Herpetological Research, 2012, 3(4): 316-321. 4. Poyarkov NA, Che J, Min MS,Kuro-o M, Yan F, Li C, Iizuka K,Vieites DR. Monograph: Review of the systematics, morphology and distribution of Asian Clawed Salamanders, genus Onychodactylus (Amphibia, Caudata: Hynobiidae), with the description of four new species. Zootaxa. 2012, 3465: 1–106. 1. 青藏高原隆升及气候环境变化促进“中国林蛙复合体”物种的形成 物种形成是生物进化的重要标志，是生物学领域重要的科学问题之一。 本研究使用多个独立基因片段，同时结合 GIS 数据进行的生态位分析重建 了中国林蛙复合体物种演化过程。结果支持四大支系的划分包括桓仁林蛙， 中国林蛙秦岭居群（模式标本产地），中国林蛙黄土高原居群以及高原林蛙； 四大支系之间存在明显的生态位分化且与高原隆起造成的气候变化相关； 结合分子钟估计该研究揭示了青藏高原晚新生代以来的隆升以及之后北方 的气候环境变化对于该物种复合体分化的重要作用。此外基于 IM 模型的 基因流分析发现在中国林蛙秦岭居群和高原林蛙之间以及中国林蛙黄土高 原居群和桓仁林蛙之间存在基因流，但是基因流被限制在交界区域，强度 和范围有限，没有影响成种过程。有意思的是，研究也发现中国林蛙秦岭 西部居群存在渐渗杂交现象，线粒体完全被来自高原林蛙的线粒体所替代 （Zhou et al. 2012. ME, 21: 960-973）. 2. DNA 条形码技术为揭示物种隐存多样性提供了快速而有效的手段 优 化 发 展 了 新 的 通 用 两 栖 类 DNA 条 形 码 COI 引 物（Che et al. 2012. MER, 12: 247–258），已得到广泛使用，被评为 DNA 条形码 2012 年度十篇最高引用研究论文之一。通过长期的野外观察并结合条形码 工作，发现原广布于东北亚地区的“爪鲵”居群形态以及遗传差异均很大， 存在大量的隐存支系。通过来自 5 个国家的两爬学者通力合作，此次研究 共发表 4 个新种：韩国爪鲵，日本爪鲵，以及分布在中国的辽宁爪鲵和吉 林爪鲵；而被大家熟知的 “爪鲵”目前仅分布于俄罗斯远东地区。此外 该研究还系统综述了爪鲵属物种目前在形态，生态，分子以及生物学等方 面的最新进展。成果作为专刊发表于 Zootaxa（2012, 3465: 1–106） （106 页）。 吉林爪鲵 O. zhangyapingi Che, Poyarkov & Yan 辽宁爪鲵 O. zhaoermii Che, Poyarkov, Li & Yan 15 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 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 Qinghai-Tibetan Plateau and Hengduan Mountain Range, Southeast Asia, and the mainland of East China and nearby islands. Email: chej@mail.kiz.ac.cn 1. Uplift of the Qinghai-Tibetan Plateau and related climate changes promoted speciation events in Rana chensinensis complex The study of speciation, the evolutionary processes that form new species, has long been one of the central topics of evolutionary biology. Herein, we report an investigation into speciation in the Rana chensinensis species complex using mitochondrial and nuclear genes. A phylogenetic analysis of the data revealed four major clades in the complex, and each of them was found to likely represent a species, including one cryptic species. Ecological divergence were distinctly found based on the ecological niche models generated, which is likely related to the late Cenozoic orogenesis of the Qinghai–Tibetan Plateau. In addition, gene flow between species was detected but only in peripheral portions of the ranges of the four major clades, thus likely had little influence on the speciation processes. Discordances between mitochondrial and nuclear genes were also found; the nominal species, R. chensinensis, contains multiple maternal clades, suggesting potential mitochondrial introgression between R. chensinensis and R. kukunoris. 员工简介（Lab Staff） 工作人员（Staff） 周炜帏 博士 助理研究员 Weiwei Zhou, Assistant Professor 金洁琼 学士 实验师 Jieqiong Jin, Technician 陈宏满 硕士 助理实验师 Hongman Chen, Assist. Technician 研究生（Graduate Students） 袁智勇 Zhiyong Yuan 2010 涂小龙 Xiaolong Tu 2011 联合培养 颜 芳 Fang Yan 2008 刘 杰 Jie Liu 2009 杨军校 Junxiao Yang 2010 丁利民 Limin Ding 2010 张宝林 Baolin Zhang 2012 陈进民 Jinmin Fig. A Bayesian tree and the median–joining network of Cytb haplotypes. Four major clades were recovered. 2. DNA barcoding is a proven tool for the rapid investigation on cryptic biodiversity We report two new pairs of primers that in combination serve to universally amplify and sequence amphibians. These new primers have been widely tested and used by different groups and our work has been reviewed as the “Top 10 DNA Barcoding publications 2012”. Based on morphological and molecular data, we find significant differences among species in the Asian clawed salamanders of the genus Onychodactylus (Caudata: Hynobiidae), which resulted in the recognition and description of four new species in this study. Our analyses comprise all species currently recognized within this genus across its entire distribution range including Japan, Korea, the Russian Far East and northeastern China. We follow an integrative taxonomic approach by combining detailed morphological comparative analyses with molecular phylogenetic analyses. Presently, this work was published as a monograph in ZOOTAXA. 16 Chen 2012 遗传资源与进化国家重点实验室 2012 年 度 报 告 基因起源 王 文，博士、研究员，中科院昆明动物所副所长，中德马普进化基因 组学青年科学家小组组长，遗传资源与进化国家重点实验室学术委员会副主 任。本年度重点完成了山羊全基因组测序、水稻和家蚕驯化过程表观遗传改 变、果蝇性染色体及 B 染色体进化研究。王文研究员受 Annual Review of Ecology, Evolution and Systematics 编委的邀请，撰写了关于新基因起源与 进化机制的综述论文。共在国际知名杂志上发表 SCI 论文 8 篇。“年轻新基 因起源和遗传进化的机制研究”项目获得 2012 年度国家自然科学奖二等奖。 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*. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nature Biotechnology. 2012. doi:10.1038/ nbt.2478 2. Xu X, et al., Wang W*. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology. 2012, 30: 105-111. 3. Ding Y, Zhou Q, Wang W*. Origins of new genes and evolution of their novel functions. Annual Review of Ecology, Evolution, and Systematics. 2012,43:345-363. 4. Li X, et al., Wang W*. Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMC Genomics. 2012,13:300. 5. Zhou Q, et al., Wang W*, Bachtrog D*. Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans. BMC Genomics. 2012, 13: 109. 6. Song LT, Wang W*. Genomes and evolutionary genomics of animals. Current Zoology. 2012, 59(1): 1674-5507. 7. Hou Y, Song LT, et al. Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell. 2012, 148(5): 873-85. 8. Zhan ZB, Ding Y, Zhao RP, Zhang Y, Yu HJ, Zhou Q, Yang S, Xiang H*, Wang W*. Rapid functional divergence of a newly evolved polyubiquitin gene in Drosophila and its role in the trade-off between male fecundity and lifespan. Molecular biology and Evolution. 2012, 29(5): 1407-1416. 1. 山羊基因组图谱解析 本研究组与国内外同行合作，解析了山羊的基因组。该项目整合使用了新一 代测序 (NGS) 技术和最新的 DNA 单分子光学作图 (Whole Genome Mapping) 技 术，克服了 NGS 短读支架 (short read scaffold) 的局限，生成了超长大片段支架， 完成装配达到近染色体水平，成为首个不依赖于遗传图谱而组装到染色体水平的大 型基因组。此外，通过微量 RNA 转录组技术，该研究首次全面揭示了山羊绒囊、 毛囊的在转录层面的差异，鉴定了 50 多个与山羊绒形成密切相关的基因，为提高 绒品质和我国特有资源绒山羊的选育提供了参考基因资源。为了更好地让国内外研 究人员利用基因组数据以进行山羊的育种和研究，研究组还搭建了山羊基因组数据 库 (http://goat.kiz.ac.cn/GGD)。该研究发表在 Nature Biotechnology 上。 2. 受邀撰写的综述文章发表在国际著名杂志 Annual Review of Ecology, Evolution and Systematics 因王文研究团队在年轻新基因起源和遗传进化机制研究方面取得的一些重 要 发 现， 并 引 起 国 际 广 泛 关 注， 国 际 著 名 杂 志 Annual Review of Ecology, Evolution and Systematics 特邀王文研究员撰写了关于新基因起源和进化机制的 综述论文 (2012, 43: 345-363)。在该论文中，王文等系统阐述了新基因及其新 功能起源的分子机制和全基因组模式方面的最新研究进展。尤其是，对于非编码 RNA 基因和从头起源 (de novo) 新基因这个长期以来被忽略直到最近才引起更多 人关注的领域进行了系统论述。该文也介绍了在新基因的功能起源和网络整合方面 的研究进展。 3. 水稻在人工驯化的表观遗传学改变 本研究组与国内外同行合作，解析了栽培和野生稻的甲基化谱。研究结果显 示水稻基因组的甲基化水平是拟南芥的四倍。与拟南芥甲基化格局相一致的是，启 动子区的甲基化抑制基因的表达，而基因内部甲基化通常与基因表达水平呈正相 关。我们发现，甲基化在基因转录终止区 (TTRS) 可以显着抑制基因的表达，而且 效果甚至强于启动子甲基化。此外，我们鉴定到了一批栽培稻与野生稻甲基化差 异的基因。该项研究获得的水稻单碱基分辨率甲基化谱，不仅加深了我们对植物基 因组 DNA 甲基化机制和功能的理解，同时也为今后的水稻表观遗传学研究提供了 宝贵的数据。相关研究成果发表在国际基因组学刊物 BMC Genomics (2012, 13: 300) 上。 4. 果蝇性染色体和 B 染色体的研究 本研究组通过和深圳华大基因研究院和美国加州伯克利大学的合作，对含有 B 染色体和新性染色的银额果蝇进行了全基因组的测定。对基因组的细致研究 发现，尽管新性染色体的起源时间及其晚近，但仅在 12 万年内，该染色体对相 互之间已经积累了大量序列差异。其中和 Y 染色体融合的新 Y 染色体 (neo-Y chromosome) 由于不能重组，已经开始像所有的古老性染色体一样开始逐渐退化： 大约有 80 个基因左右已经完全失去功能，有三分之一的基因表达开始紊乱，积累 了额外的基因重排。而它的 B 染色体的组装序列，同时比对到了古老的性染色体 和 neo-sex 染色体上，提示 B 染色体的起源有可能是在两正常染色体发生融合的 过程中丢失的染色体片段产生的。我们还在 B 染色体的序列上发现了一个有转录 证据的基因片段，提示 B 染色体上有可能有功能序列。该工作在国际基因组学刊 物 BMC Genomics (2012, 13: 109) 上发表以后，很快受到同行关注，两星期内 即成为高度访问“highly access”和杂志首页编辑首选“editor's pick”。 17 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 ANNUAL REPORT Origin and Evolution of New Genes Dr. Wen Wang, Professor, Deputy Director of Kunming Institute of Zoology (KIZ), Chinese Academy of Sciences (CAS); Head of CAS–Max Planck Junior Research Group, KIZ, CAS; Deputy Director of Evolutionary Genomics, State Key Laboratory of Genetic Resources and Evolution. This year we mainly focused on the whole genome sequencing of a domestic goat, epigenetic changes of rice and silkworm genome during domestication and evolution of sex and B chromosomes in Drosophila albomicans. Invited by editor of Annual Review of Ecology, Evolution and Systematics, Dr. Wang wrote a review on origin and evolution of new genes. Totally 7 SCI papers have been published. The project “Mechanism of origin and genetic evolution of newly evolved genes ” won the State Natural Science Award, P.R. China. E-mail: wwang@mail.kiz.ac.cn 1. First Goat Genome Sets a Good Example for Facilitating De Novo Assembly of Large Genomes In this collaborative study published in Nature Biotechnology, we have completed the first genome sequence of domestic goat by a robust approach integrated with next-generation sequencing (NGS) and wholegenome mapping (WGM) technologies. Comparative transcriptomic analyses of the primary and secondary follicles of a cashmere goat reveal that 51 genes are differentially expressed between the two types of hair follicles, which provides candidates for breeding improvement. The goat genome is the first reference genome for small ruminant animals and may help to advance the understanding of distinct ruminants' genomic features from non-ruminant species. This work also yields a valuable experience for facilitating the de novo assemblies of large, complex genomes in the future. In order to share the genome recourse with related researchers, we also built up an goat gnome database (http://goat.kiz.ac.cn/GGD). 员工简介（Lab Staff） 2. An Invited Review Published in Annual Review of Ecology, Evolution and Systematics Thanks to the achievements in origin and evolution of new genes, Dr. Wang was invited by editor of Annual Review of Ecology, Evolution and Systematics to write a review. In this review, we summarize the newest advances in our understanding of the molecular mechanisms and genome-wide patterns of new gene origination and functions. We pay special attention to the origins of noncoding RNA genes and de novo genes, whose processes had been previously overlooked but are gaining increasingly visible importance. We then introduce recent findings that have opened a path to the study of the evolution of novel functions and pathways via novel genes. We also discuss the important issues and potential developments in the field. 李学燕 博士 助理研究员 3. New Light on the Epigenetic Differentiation During Rice Domestication Together with our colleagues we generated single-base resolution DNA methylome maps for Asian cultivated rice Oryza sativa ssp. japonica, indica and their wild relatives, O. rufipogon and O. nivara. Methylation in promoters represses gene expression while gene-body methylation generally appears to be positively associated with gene expression. We discovered that methylation in gene transcriptional termination regions (TTRs) can significantly repress gene expression, and the effect is even stronger than that of promoter methylation. Furthermore, we identified a number of genes with significant difference in methylation level between the wild and cultivated rice. The single-base resolution methylomes of rice have not only broadened our understanding of the mechanism and function of DNA methylation in plant genomes, but also provided valuable data for future studies of rice epigenetics and the epigenetic differentiation between wild and cultivated rice. This work was published on BMC Genomics. Ms. Ruoping Zhao, Assistant Professor 4. Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans Together with our colleagues we sequenced male flies with B chromosomes at 124.5-fold genome coverage using next-generation sequencing. To characterize neo-Y specific changes and B chromosome sequences, we also sequenced inbred female flies derived from the same strain but without B's at 28.5-fold. Despite its very recent origin, the non-recombining neo-Y chromosome shows various signs of degeneration, including a significant enrichment of nonfunctional genes compared to the neo-X, and an excess of tandem duplications relative to other chromosomes. We also characterized a B-chromosome linked scaffold that contains an actively transcribed unit and shows sequence similarity to the subcentromeric regions of both the ancient X and the neo-X chromosome. This work was publishd in BMC Genomics. that of promoter methylation. Furthermore, we identified a number of genes with significant difference in methylation level between the wild and cultivated rice. The single-base resolution methylomes of rice have not only broadened our understanding of the mechanism and function of DNA methylation in plant genomes, but also provided valuable data for future studies of rice epigenetics and the epigenetic differentiation between wild and cultivated rice. This work was published on BMC Genomics. 徐 讯 Xun Xu, 2007 吕 俊 Jun Lv, 2009 张业胜 Yesheng Zhang, 2010 刘 晖 Hui Liu, 2010 张 田 Tian Zhang, 2011 宋卢挺 Luting Song, 2011 陈 垒 Lei Chen, 2011 沈文菁 Wenjing Sheng, 2011 苟志恒 Zhiheng Gou, 2012 王 筱 Xiao Wang, 2012 奎 玲 Ling Kui, 2012 18 工作人员（Staff） 相 辉 博士 副研究员 Dr. Hui Xiang, Associate Professor xiangh@mail.kiz.ac.cn 杨 爽 博士 助理研究员 Dr. Shuang Yang, Assistant Professor yangshuang@mail.kiz.ac.cn Dr. Xueyan Li, Assistant Professor lixy@mail.kiz.ac.cn 董 扬 博士 助理研究员 Dr. Yang Dong, Assistant Professor loyalyang@163.com 赵若苹 本科 实验师 zhaorp@mail.kiz.ac.cn 博士后 (Postdoctoral Fellows) 任立晨 Lichen Ren, 2007 张文广 Wenguang Zhang, 2010 刘 斌 Bin Liu, 2012    研究生 (Graduate Students) 遗传资源与进化国家重点实验室 2012 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. Luo XJ, Li M, …, Su B. The Interleukin 3 gene (IL3) contributes to human brain volume variation by regulating proliferation a nd sur vival of neural pro geni t ors . PLoS One 2012,7: e50375 2. Zhong H, Li XL, Li M, …, Su B. Replicated associations of TNFAIP3, TNIP1 and ETS0 with systemic lupus erythematosus in a southwestern Chinese population. Arthritis Research & Therapy 2012, 13: R186 3 . L i M , S h i C J , S h i Y Y, … , S u B . ZNF804A and schizophrenia susceptibility in Asian populations. American Joural of Medical Genetics part B-Neuropsychiatric Genetics 2012, 159B(7):794-802. 4. Shi L, Li M, Su B. MCPH1/BRIT1 represses transcription of the human telomerase reverse transcriptase gene. Gene 2012, 495:1-9. 5. Shi L, Su B. Identification and functional characterization of a primate-specific E2F1 binding motif regulating MCPH1 expression. FEBS Journal 2012, 279:491503. 6. Wang JK, Cao XY, Zhang YF, Su B. Genome-wide DNA methylation analyses in the brain reveal four differentially methylated regions between humans and non-human primates. BMC Evolutionary Biology 2012, 12:144. 7. Li M, Wang Y, Zheng XB, Ikeda M, …, Su B. Meta-analysis and brain imaging data support the involvement of VRK2 (rs2312147) in schizophrenia susceptibility. Schizophrenia Research 2012, 142(1):200205. 1. 影响人类脑容量变异的白介素 3 基因的遗传学研究 神经系统是人类区别于其他物种最显著的特征之一，相对于其他物种，人类的大脑呈 现出高度的发达，主要包括全脑容量的变化。如人类的大脑容量是旧大陆猴 - 如猕猴脑容 量的 20.6 倍，长臂猿的 14.4 倍，与人类亲缘关系最近的灵长类 - 黑猩猩的 4.3 倍。近年 来基于核磁共振脑影像学研究表明脑容量具有很高的遗传力，并且与智商和记忆等认知能 力高度相关；除此之外，脑容量在多种精神疾病（如精神分裂症）患者中均发生了明显病变， 因此了解脑容量的遗传对于我们理解精神疾病的发病机制以及神经发生的遗传基础可能具 有重要的意义。然而，即便有如此高的遗传力，截止到目前为止，仅仅只有少数几个基因 被发现与脑容量相关。 为了寻找可能影响脑容量变化的基因，我们选取了 50 个精神分裂症易感基因，并在中 国汉族人群中分析了它们与脑容量的关系，最终发现位于染色体 5q23.2-33.1 区域的 SNP 位点（rs31480 等）与脑容量强烈相关，随后在欧洲人群中也重复出了这一结果。体外功能 实验证明，rs31480 位于白介素 3 基因启动子区并影响转录因子 Sp1 的结合能力，从而上调 白介素 3 基因的转录。小鼠体内分析发现白介素 3 及其受体在发育中的小鼠大脑中持续表达， 并在出生后 1-4 天达到最高，这一时期也是神经发生和增殖的重要时期。进一步的研究发 现白介素 3 受体主要在小鼠的神经前体细胞中表达，并且白介素 3 能够促进神经前体细胞 的增殖和存活能力。这些结果揭示了白介素 3 基因可能是一个真实的影响脑容量变化的基因。 通过体外实验，还发现了白介素 3 基因性别特异性相关的可能机制，白介素 3 的表达并不 受到雌激素的调控，但是它可以活化雌激素受体，并诱导下游的信号通路。相关工作发表 于 PLoS One 2012,7: e50375 。 2. 精神分裂症遗传学研究 精神分裂症是困扰人类的重大精神疾病之一，且具有非常高的遗传力。近年来，随着 全基因组关联性分析（Genome-wide association study, GWAS）的逐步开展，已经报道 了一系列的精神分裂症易感基因。然而，这些研究大多集中在欧洲人群，所报道的易感基 因在亚洲人群中是否也与精神分裂症显著相关并不清楚。 我们通过与新加坡基因组研究所和日本藤田保健衛生大学合作，并结合本实验室已采 集的来自云南玉溪和昆明的样本，对 6565 份亚洲病例 - 对照样本进行了分析，目的基因为 前期欧洲人群中发现的与精神分裂症显著相关的基因（VRK2 rs2312147 等）。分析结果发 现，rs2312147 在亚洲人群中也与精神分裂症强烈相关。随后又增加了来自美国国立精神卫 生研究院等的欧洲人群的病例 - 对照样本，并发现相关性增强。这些证据很好地支持了前 期 GWAS 的发现。同时，发现 VRK2 在精神分裂症患者血液中 mRNA 表达相对正常人明 显升高，进一步支持了相关性分析的结果。利用核磁共振影像学分析，在 286 个汉族健康 个体中，分析了 rs2312147 与脑结构（全脑容量等）的关系，发现 rs2312147 与全脑容量以 及全脑白质体积显著相关，暗示 VRK2 可能在大脑发育中起作用。该研究证实了 VRK2 在 中国人群中也是精神分裂症易感基因，结果发表于 Schizophr Res 2012,142:200-205。 在前期研究的基础上，我们对 ZNF804A 基因在中国人群中对精神分裂症发病的影响 进行了进一步分析，利用来自云南，北京，上海，新加坡等地的汉族样本，对 ZNF804A 全基因进行精细扫描定位，发现在该基因其它区域未发现易感位点，并更进一步的支持了 ZNF804A 的易感位点可能在启动子区域。研究发表于 American Journal of Medical Gene tics Part B: Neuropsychiatric Genetics 2012,159B:794-802。 19 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 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 study on a brain volume related gene IL-3 One of the most significant evolutionary changes underlying the highly developed cognitive abilities of humans is the greatly enlarged brain volume. In addition to being far greater than in most other species, the volume of the human brain exhibits extensive variation and distinct sexual dimorphism in the general population. However, little is known about the genetic mechanisms underlying normal variation as well as the observed sex difference in human brain volume. Here we show that interleukin-3 (IL3) is strongly associated with brain volume variation in four genetically divergent populations. We identified a sequence polymorphism (rs31480) in the IL3 promoter which alters the expression of IL3 by affecting the binding affinity of transcription factor SP1. Further analysis indicated that IL3 and its receptors are continuously expressed in the developing mouse brain, reaching highest levels at postnatal day 1-4. Furthermore, we found IL3 receptor alpha (IL3RA) was mainly expressed in neural progenitors and neurons, and IL3 could promote proliferation and survival of the neural progenitors. The expression level of IL3 thus played pivotal roles in the expansion and maintenance of the neural progenitor pool and the number of surviving neurons. Moreover, we found that IL3 activated both estrogen receptors, but estrogen didn’t directly regulate the expression of IL3. Our results demonstrate that genetic variation in the IL3 promoter regulates human brain volume and reveal novel roles of IL3 in regulating brain development. This study is recently published on PLoS One 2012,7: e50375 . 2. Studies on the schizophrenia susceptibility genes Recent genome-wide association studies have reported a set of schizophrenia susceptibility genes, but many of them await further replications in additional samples. Here we analyzed 5 genome-wide supported variants in a Han Chinese sample, and the variant rs2312147 at VRK2 showed significant association, which was confirmed in the meta-analysis combining multiple Asian and European samples (P=3.17×10-4, N=7 498). Rs2312147 is also associated with brain structure in healthy subjects, including the total brain volume and the white matter volume. Gene expression analyses indicated an up-regulation of VRK2 in schizophrenia patients. Our data provide further evidence for the contribution of VRK2 to schizophrenia. This result is published on Schizophr Res 2012, 142:200-205. In addition, further genotyping and association analysis of a set of SNPs spanning the entire genomic region of ZNF804A (520 kb) identified no association except for SNP rs359895 (P=7.8×10-5, N=5,172), a newly reported risk SNP located in the ZNF804A promoter region with functional implications. This suggests that ZNF804A may also contribute to schizophrenia susceptibility in Chinese although the risk SNP is different from that in Europeans, and it was supported by the detected up-regulation of ZNF804A mRNA expression in the blood cells of Chinese schizophrenia patients compared with normal controls (P=0.004). Additionally, the linkage disequilibrium (LD) structure analyses using data from HapMap indicated distinct LD blocks across ZNF804A between Chinese and Europeans, which may explain the different association patterns between them, and also highlight the compounding difficulty of genetic studies of complex diseases like schizophrenia when studying multiple ethnic populations. This result is published on American Journal of Medical Genetics Part B: Neuropsychiatric Genetics 2012,159B:794-802. 20 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 彭 忆 博士 助理研究员 Dr. Yi Peng Research Associate pypypy2000@163.com 石 磊 博士 助理研究员 Dr. Lei Shi Research Associate yuansishi@gmail.com 王 宏 硕士 助理研究员 Ms. Hong Wang Research Associate wanghong@mail.kiz.ac.cn 陈永昌 博士 助理研究员 Dr. Yongchang Chen Research Associate chengyc@mail.kiz.ac.cn    研究生（Graduate Students） 李 明 Ming Li, 2008 杨立新 Lixin Yang, 2008 杨召辉 Zhaohui Yang, 2009 张晓明 Xiaoming Zhang, 2009 向 坤 Kun Xiang, 2010 王 毅 Yi Wang, 2010 张 煦 Xu Zhang, 2010 林 强 Qiang Zhang, 2011 Bhandari Sushil, 2012 刘杰伟 Jiewei Liu, 2012 杨晏冬 Yandong Yang, 2012 遗传资源与进化国家重点实验室 2012 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。主要从事蛋白质功 能演化的功能基础，蛋白质与基因进化的机制，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.、Structure、Acta Crystall.、J. Mol. Struct.、J. Theor. Biol.、J. Mol. Model.、Mammalian Genome、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. Li GH and Huang JF. CDRUG: a web server for predicting anticancer activity of chemical compounds. Bioinformatics. 2012, 28(24):3334-3335. 2. Zhao YQ, Wang JW, Wang YJ, Huang JF. A comparative analysis of protein targets of withdrawn cardiovascular drugs in human and mouse. J Clin Bioinforma. 2012, 2(1):10 3. Zhang YR, Zhao YQ, Huang JF. Retinoid-Binding Proteins: Similar Protein Architectures Bind Similar Ligands via Completely Different Ways. PLoS ONE. 2012, 7(5):e36772 4. Yu Q, Huang JF. The analysis of the druggable families based on topological features in the protein-protein interaction network. Letters in Drug Design & Discovery. 2012, 9: 426-430 5 . D a i S X , Z h a n g A D , H u a n g J F. Evolution, expansion and expression of the Kunitz/BPTI gene family associated with long-term blood feeding in Ixodes Scapularis. BMC Evol Biol. 2012,12:4 6. Zhao YQ, Sheng ZZ, Huang JF. A systematic analysis of heart transcriptome highlights divergent cardiovascular disease pathways between animal models and humans. Mol. BioSyst. 2012, 8(2):504-10 1. 预测小分子的抗癌活性 癌症是目前世界人口死亡的第一原因。因此，开发新的抗癌药物是科学界和医 学界的热点和难点。但直接采用实验的方法筛选抗癌药物具有花费大、时间长的特 点。为此我们开发了一个新基于药效团的小分子比对算法，并将此算法应用于预测 抗癌小分子的抗癌活性。结果显示我们建立的预测系统其线下面积达到 0.87，显示 该系统能很好的预测小分子的抗癌活性 (Bioinformatics,2012)。 预测小分子抗癌活性的网址： http://bsb.kiz.ac.cn/CDRUG/ 2. 比较转录组学分析揭示分化的心血管疾病通路 动物模型被广泛的应用在心血管疾病的研究中。然而，利用这些动物模型进行 实验，通常会发生实验结果达不到预期目标或者大相径庭。为了深入探讨人类心血 管疾病动物模型与人之间的差异，我们对人类以及四种心血管疾病动物模型（小鼠， 大鼠，猕猴，狗）的转录组进行了全面细致的比较。研究发现，尽管大部分基因受 到强烈的负选择，但是有一些通路在动物模型与人间发生了分化。 并且，不同的 动物模型与人之间发生分化的通路不尽相同。 共表达网络结果还显示，基因的表 达演化并不是单独发生的，而是通过形成模块共同演化的。这项研究为更好的发展 心血管疾病模型以及研究基因表达的演化提供了有力的数据及方法学支持（Mol. BioSyst ，2012）。 3. 揭示了 Kunitz/BPTI 基因家族在硬蜱长时程吸血过程中的作用 蜱是一类在世界范围内广泛分布，专性吸食脊椎动物血液为生的体外寄生虫。 它们是细菌、病毒、蠕虫等病原体的传播者。 Kunitz/BPTI 蛋白大量存在于蜱类 唾液腺中并在吸血过程中发挥着重要作用。我们系统地研究了在肩突硬蜱（Ixodes scapularis）中 Kunitz/BPTI 基因家族的进化，扩张和表达。研究揭示了 Kunitz/ BPTI 基因家族在软蜱和硬蜱中存在的巨大差异。并提示 Kunitz/BPTI 基因家 族在软蜱和硬蜱中存在的巨大差异与硬蜱进化出的长时程吸血行为相关。最后， 我们鉴定出来的六个差异表达基因可以作为控制蜱类的候选靶基因（BMC Evol Biol,2012）。 4. 揭示了视黄醇类物质转运蛋白差异结合的机制 在进化过程中，相似的蛋白结构可以用完全不同的方式结合相同的配体。在 FABP 家族中，CRBPs 和 CRABPs 的配体都是 β 紫罗酮环指向转脂蛋白疏水桶 的内部，而不饱和脂肪酸链指向溶液的方向。而在 RBP 家族 RBP 和 ERABP 蛋白 中配体方向刚好相反。我们运用生物信息学和分子动力学模拟的方法详尽的解释了 这种生物学现象并进一步提出了类维生素 A 物质在生物体内可能的转运模型（PLoS ONE, 2012）。 21 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 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. Prediction of anticancer activity of chemical compounds Cancer causes millions of deaths per year. Screening candidates from natural or synthetic compounds is an efficient way for cancer drug discovery. We developed a novel molecular description method (relative frequency-weighted fingerprint), to implement the compound “fingerprints”. Then, a hybrid score was calculated to measure the similarity between the query and the active compounds. Using this algorithm, a web server, known as CDRUG, was constructed to predict of anticancer activity of chemical compounds. The performance analysis shows that CDRUG has the area under curve (AUC) of 0.878, indicating that CDRUG is effective to distinguish active and inactive compounds. 2. Divergent cardiovascular disease pathways between animal models and humans Animal models have proven useful for studying the genetic basis of cardiovascular disease (CVD), however, animal models fell short of the expected results, or even came out with opposite phenomena in many cases. After compared the expression of orthologous genes in human and four CVD models (rhesus, rat, mouse and dog), we observed that the global expression profiles between animal model and human orthologous genes are highly preserved. Differentially expressed genes (DEGs) between human and each model were identified. Next, we constructed a co-expression network based on intra- and inter-species variation, to elucidate the altered network organization. It indicates that these DEGs evolved as modules rather than independently. 3. The role of Kunitz/BPTI gene family in the long-term blood feeding in hard ticks All ticks are external blood-feeding parasites of mammals, birds and reptiles throughout the world . They can transmit a wide variety of pathogens causing several human and animal diseases. Kunitz/BPTI proteins are abundant in the salivary glands of ticks and perform multiple functions in blood feeding. However, Kunitz/BPTI proteins in soft and hard ticks have different functions and molecular mechanisms. We systematically examined the evolution, expansion and expression of Kunitz/BPTI gene family in Ixodes scapularis. Our study suggests that the differences in the Kunitz/BPTI family between soft and hard ticks may link to the evolution of long-term blood feeding in hard ticks. We proposed that six genes identified in our study may be candidate target genes for tick control. 4. Mechanism of different binding modes in retinoid proteins Similar protein architectures can be used to bind identical ligands via completely different ways. We observed that, although RBP, ERABP, CRBPs and CRABPs have homologous structural motifs and overlapping ligand specificity, they have different binding mechanisms. After analyzed the various retinoid transport mechanisms through bioinformatic and molecular dynamics simulations methods, we proposed a possible transport model for retinoids. 22 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 博士 助理研究员 Dr Yu-Qi zhao, Assistant Professor yookeee@163.com 于 琦 博士 助理研究员 Dr Qi Yu, Assistant Professor yuqi05@mails.gucas.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 代绍兴 Shao-Xing Dai 张爱娣 Ai-Di zhang 王丽丽 Li-Li Wang 韩菲菲 Fei-Fei Han 郭义成 Yi-Cheng Guo 王玉晴 Yu-Qing Wang 遗传资源与进化国家重点实验室 2012 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， 尤其是基因、基因家族和基因组的多样性及其起源进化研究，以及基于这些 基础研究开展有害生物（如寄生原虫和血吸虫）的分子水平防治和高效、特 异代谢途径的利用等应用基础研究。 重要成果（Highlights） 论著（Publications） 1. Jiang Y-H, Wang D-Y, Wen J-F*. 2012. The independent prokaryotic origins of eukaryotic fructose-1,6-bisphosphatase and sedoheptulose-1,7bisphosphatase and the implications of their origins for the evolution of eukaryotic Calvin cycle. BMC Evol. Biol. 12:208 2. Ni T, Yue J-P, Sun G-L, Zou Y, Wen J-F*, Hang J-L*. 2012. Ancient gene transfer from algae to animals: Mechanisms and evolutionary significance. BMC Evol. Biol. 12:83 3. Feng J-M, Sun J, Xin D-D, Wen J-F*, 2012. Comparative Analysis of the 5S rRNA and Its Associated Proteins Reveals Unique Primitive Rather Than Parasitic Feature in Graidia lamblia. PloS ONE. 7(6):e36978 4. Tian H-F, Feng J-M, Wen J-F*, 2012. The evolution of cardiolipin biosynthesis and maturation pathways and its implications to the evolution for eukaryotes. BMC Evol. Biol. 12:32 5. Lin X-D, …... Tian H-F, Wen J-F, Alexander Plyusnin, Xu J-G, Zhang Y-Z*. 2012. Migration of Norway Rats Resulted in theWorldwide Distribution of Seoul Hantavirus Today. J VIROL. 86(2):972 6. 冯金梅，孙隽，文建凡 *, 2012. 核仁研究 新进展 . 动物学研究 , 33(6):549-556 7. 张玉娟，文建凡 *, 2012. YidC/Oxa/Alb3 蛋白家族 . 生命的化学 , 32(4) 1. 两个重要光合作用酶的起源及其进化机制的揭示 光合作用是地球上最重要的生物化学反应。光合生物吸收太阳光能， 通过卡尔文循环途径将 CO2 固定，转变成化学能，作为地球上几乎所有有 机物和能量的源头。果糖 -1,6- 二磷酸酶 (FBPase) 和景天庚酮糖 -1,7二磷酸酶 (SBPase) 是真核光合生物卡尔文循环途径中受光调节的两个关 键酶。而在原核光合生物中，这两个酶的功能却由一个具有双功能的 F/ SBPase 来承担。那么，光合作用酶 FBPase 和 SBPase 是不是简单地由 F/ SBPase 分化而来呢？我们通过广泛的基因组数据调查分析和比较，发现 原核 F/SBPase 双功能酶具有两种类型的结构域：FBPase domain (I 型， 来源于变形菌 ) 或 FBPase_GlpX domain (II 型，来源于蓝细菌 )，且二者 间进化关系很远。进一步研究还发现，真核生物 FBPase 和 SBPase 并非起 源于原核生物的两类双功能酶 F/SBPase 的任何一类，而是各自具有一个 独立的起源：SBPase 起源于 ε 变形菌的 I 型 FBPase，而 FBPase 来源于 一类目前未知细菌的 I 型 FBPase，且前者的进化是通过“From Specialist to Generalist” 的 机 制 完 成 的。 相 较 于 F/SBPase 双 功 能 酶，FBPase 和 SBPase 各自独立进化出一套完善的光调节系统，使得真核生物的光合作用 较原核生物的光合作用受到了更为精细的光调节 (BMC Evol. Biol. 2012) 。 2. 贾第虫核仁蛋白基因组的鉴定及真核生物 SSU Processome 的起源演 化 我们运用生物信息学方法，在蓝氏贾第虫（Giardia lamblia）基因组中 鉴定出 255 个核仁蛋白基因，从而建立了第一个原生生物的核仁蛋白基因 组。通过与真核生物基本的核仁蛋白基因组（Eukaryotic Basic Nucleolar Protein Genome, EBNPG）的比较分析，并结合定位实验的结果，我们推 测：贾第虫核仁组成具有“原始性”特征，很大程度上代表了真核生物分 化前所共有的祖先状态；核仁在真核生物进化早期的主要功能就是‘与核 糖体相关’，而其它各种功能可能至少是在贾第虫分化后才逐渐发展起来的。 此外，通过基因组数据的系统调查分析，我们还首次描绘出核仁中负责核 糖体小亚基 pre-rRNA 加工的 SSU processome 的起源与进化历史：SSU processome 的雏形在古细菌中就已经出现；然后通过古老的基因重复、从 头合成、招募原核来源的蛋白结构域来形成真核特异的蛋白等机制，在真 核生物共同祖先 (LECA) 中就已形成了复杂的 SSU processome；在 LECA 分化成不同真核生物类群的过程中，通过不同水平的基因重复、丢失，以 及谱系特异性的获得等多种进化方式，SSU processome 在真核生物不同谱 系中发生了进一步的复杂化和分化。 23 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 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 cells. Taking the protists, which occupy key positions in the eukaryotic cell evolution, as materials, 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 and the 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. Evidence to Track Down the Ancestor(s) of FBPase and SBPase Photosynthesis is a process used by plants and other organisms to convert the light energy captured from the sun into chemical energy that can be used to fuel the organism's activities. During this process, the obligation of the Calvin cycle is to fix carbon. Implement this function of two critical light regulated enzymes (FBPase and SBPase) in eukaryotes are performed by a dual-functional enzyme in prokaryotes (F/SBPase). Because of this, we recently have finished their phylogenetic analysis. By comparing the functional domains of prokaryotes’ F/SBPase from different organisms, their results for the first time indicated that prokaryotes bifunctional F/SBPase can be classified into two evolutionarily distant classes: Class I F/SBPase with typical FBPase domain and Class II F/SBPase with FBPase_glpX domain. Whereas, eukaryotic FBPase and SBPase do not diverge from either of the two classes of F/SBPase but have two independent origins. SBPase share a common ancestor with the gluconeogenesis-specific Class I FBPase of epsilon-proteobacteria, while FBPase arise from Class I FBPase of an unknown kind of eubacteria. Moreover, their findings also support that during the evolution of SBPase from eubacterial Class I FBPase, the SBP-dephosphorylation activity was acquired through the transition “from specialist to generalist” (BMC Evol. Biol. 2012) . 2. Identification of the Nucleolar Protein Genome in Giardia lamblia and the Origin and Evolution of Eukaryotic SSU Processome Here, we identified the first nucleolar protein genome in G. lamblia, and established the first nucleolar protein genome in protist; then we compared it with the Eukaryotic Basic Nucleolar Protein Genome (EBNPG) to reveal the real evolutionary position of G. lamblia. All these results indicated the probably primitive feature of nucleolus in G. lamblia and the ‘ribosome related’ is the primary function of nucleolus in the early eukaryotes, and various other nucleolar functions arose at later point after the divergence of G. lamblia from the eukaryotic trunk. Besides, we have charted the picture of the origin and evolutionary history of SSU processome for the first time: a rudimentary SSU processome had likely arisen in archaea; then a complex SSU processome had formed in LECA through ancient gene duplication, de novo eukaryotic protein innovations, and recruiting prokaryote-original protein domains to form novel proteins; finally, during the divergence of various eukaryotic lineages from LECA, lineage-specific and species-specific gene duplications, lineage-specific gene innovations, and lineage-specific and species-specific gene losses, have complicated this complex further in diverse extant eukaryotes. 24 员工简介（Lab Staff） 工作人员（Staff） 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） 汪德勇 Deyong Wang, 2008 程菁菁 Jingjing Cheng, 2009 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 遗传资源与进化国家重点实验室 2012 年 度 报 告 进化与功能基因组学 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. Liu Z, Li GH, Huang JF, Murphy RW, & Shi P . (2012) Hearing aid for vertebrates via multiple episodic adaptive events on prestin genes. Molecular biology and evolution 29(9):2187-2198. 2. Ye Z, Shi P ... et al. (2012) The yak genome and adaptation to life at high altitude. Nature genetics 44(8):946-949. 3. Zhang Z, Liu J, Li M, Yang H, & Zhang C (2012) Evolutionary dynamics of the interferon-induced transmembrane gene family in vertebrates. PloS one 7(11):e49265. 1. 牦牛基因组研究成果揭示高原适应的遗传学机制 牦牛是青藏高原等高海拔地区所特有的牛种。经过长期的自然选择，牦 牛已经获得了能够适应高原环境的解剖学和生理学性状，如心肺发达、没有 肺动脉高压、觅食能力强和能量代谢高等。 我们成功预测出 22,282 个蛋白编码基因，同时在牦牛基因组中检测出 220 万个 SNP 位点。发现了牦牛 3 个与高海拔低氧环境相适应的基因发生了 适应性进化；另有 5 个发生了适应性进化的基因有助于牦牛从高原稀少的食 物中充分获取能量。同时，还发现了一些与嗅觉、防御和免疫相关的基因也 发生了重要选择性变异。这项研究不仅揭示了高海拔地区动物重要生理性状 背后的遗传特征，也将有助于进一步揭示人类所出现的各种高原不适症，促 进对缺氧相关疾病的认识、预防和治疗。此外，还将有助于提高高海拔地区 重要经济动物的产奶、产肉性能。 研究成果于 7 月 1 日在 Nature Genetics 上发表。与此同时，Science 以 “What gets yak high”为题进行了在线评论。 2. prestin 多次适应性进化事件提高了脊椎动物的听觉能力 脊椎动物的听觉能力对其生存和繁衍有着至关重要的作用，但是导致听 觉能力产生适应性进化和多样性的遗传机制却知之甚少。prestin 是一个与耳 蜗放大作用相关的基因，该基因的功能与听觉能力密切相关。我们比较了脊 椎动物不同类群的 prestin 直系同源基因，并分别在四足动物的共同祖先枝， 哺乳动物共同祖先枝，真兽亚纲祖先枝以及胎盘哺乳动物祖先枝检测到了正 选择的信号。我们推断可能正是由于正选择的作用，使 prestin 的功能产生了 变化，从而导致了脊椎动物听力的巨大差异。为了进一步验证该假说，我们 对处于不同进化阶段的哺乳动物代表物种的 prestin 进行了功能分析，结果表 明，这些物种的 prestin 电压依赖非线性电容确实存在着功能分化。这项研究 对听力基因 prestin 的进化和功能分析结果为听觉能力在脊椎动物中的适应性 进化和 prestin 功能分化提供了新的理解。此外，该研究结果还表明直系同 源基因的功能在进化过程中是不断变化的动态过程，提示着在相关研究中这 一点是值得注意的问题。相关论文已经在 Molecular Biology and Evolution （2012）上发表。 25 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 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. The yak genome and adaptation to life at high altitude Domestic yaks (Bos grunniens) provide meat and other necessities for Tibetans living at high altitude on the Qinghai-Tibetan Plateau and in adjacent regions. Comparison between yak and the closely related low-altitude cattle (Bos taurus) is informative in studying animal adaptation to high altitude. Here, we present the draft genome sequence of a female domestic yak generated using Illumina-based technology at 65-fold coverage. Genomic comparisons between yak and cattle identify an expansion in yak of gene families related to sensory perception and energy metabolism, as well as an enrichment of protein domains involved in sensing the extracellular environment and hypoxic stress. Positively selected and rapidly evolving genes in the yak lineage are also found to be significantly enriched in functional categories and pathways related to hypoxia and nutrition metabolism. These findings may have important implications for understanding adaptation to high altitude in other animal species and for hypoxia-related diseases in humans. 员工简介（Lab Staff） 工作人员（Staff） 杨 晖 博士 助理研究员 Dr.Hui Yang, Assistant Professor 张志刚 博士 助理研究员 Dr.Zhigang Zhang, Assistant Professor 郝军军 博士 助理研究员 Dr.Junjun Hao, 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） 胡玲玲 Lingling Hu, 2007 刘 振 Zhen Liu, 2007 2. Hearing Aid for Vertebrates via Multiple Episodic Adaptive Events on Prestin Genes Auditory detection is essential for survival and reproduction of vertebrates, yet the genetic changes underlying the evolution and diversity of hearing are poorly documented. We identify prestin genes from the genomes of 14 vertebrates, including three fishes, one amphibian, one lizard, one bird, and eight mammals. An evolutionary analysis of these sequences and 34 previously known prestin genes reveals for the first time that this hearing gene was under positive selection in the most recent common ancestor (MRCA) of tetrapods. This discovery might document the genetic basis of enhanced high sound sensibility in tetrapods. An investigation of the adaptive gain and evolution of electromotility, an important evolutionary innovation for the highest hearing ability of mammals, detects evidence for positive selections on the MRCA of mammals, therians, and placentals, respectively. It is suggested that electromotility determined by prestin might initially appear in the MRCA of mammals, and its functional improvements might occur in the MRCA of therian and placental mammals. Our patch clamp experiments further support this hypothesis, revealing the functional divergence of voltage-dependent nonlinear capacitance of prestin from platypus, opossum, and gerbil. Moreover, structure-based cdocking analyses detect positively selected amino acids in the MRCA of placental mammals that are key residues in sulfate anion transport. This study provides new insights into the adaptation and functional diversity of hearing sensitivity in vertebrates by evolutionary and functional analysis of the hearing gene prestin, suggesting that orthologous function is a dynamic process during evolution. 26 叶志强 Zhiqiang Ye, 2007 王 维 Wei Wang, 2009 许东明 Dongming Xu, 2010 范 飞 Fei Fan, 2010 祁飞燕 Feiyan Qi, 2011 罗 杰 Jie Luo, 2011 郑智中 Zhizhong Zheng, 2012 杨松霖 Songlin Yang, 2012 遗传资源与进化国家重点实验室 2012 年 度 报 告 分子人类学 孔庆鹏，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 等上发表论文及评论 50 余篇。已发表研究论文被 Nature、Science 等 各类 SCI 刊物累计引用 1800 余次，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) 论著（Publications） 1. Liu J, Wang L-D, Sun Y-B, Li E - M , X u L - Y, Z h a n g Y- P, Ya o Y-G, Kong Q-P#. Deciphering the Signature of Selective Constraints on Cancerous Mitochondrial Genome. Molecular Biology and Evolution, 2012,29(4):1255-1261. 2. Wang H-W, Li Y-C, Sun F, Zhao M, Mitra B, Chaudhuri K-T, Regmi P, Wu S-F, Kong Q-P#, Zhang Y-P. Revisiting the role of the Himalayas in peopling Nepal: insights from mitochondrial genomes. Journal of Human Genetics, 2012,57(4):228-234. 基于大规模的线粒体全基因组探讨早期人类定居欧亚大陆的模式 现代人类近期起源于非洲已得到了大量遗传学及考古学证据支持，但关于人类 走出非洲后如何迁徙定居欧亚大陆等重大史前事件迄今仍存在较大争议。单扩散模 型认为早期人类定居欧亚大陆只经历了一次快速的沿海岸线的迁徙（约 6 万年前）； 而多扩散模型则认为人类走出非洲后通过至少两次迁徙定居欧亚大陆，第一次发生 在 ~7 万年前，第二次则在 ~3 万年前。 由于线粒体 DNA（mitochondrial DNA, mtDNA）具有高突变率以及缺乏重组 等特性，使得该分子能够有效记录并追溯史前人群动态历史事件。鉴于此，我们通 过搜集和分析了覆盖整个欧亚大陆及大洋洲人群的 mtDNA 全基因组序列共 14,000 余条，分析比较各次大陆人群中基部单倍型类群（haplogroup）的分布模式和起源 时间。结果表明：（1）各个次大陆人群中基部类群均源自 M、N 和 R 这三个建群 者世系，且之间几乎不存在重叠（图 1），表明这三个世系在分化前就已经到达不同 大洲，进而演化出各自特有的分支；（2）M、N 和 R 演化出来的不同类群积累的平 均变异（ρ）并未有显著差异，且类群起源时间集中均在 3-7 万年之内，且无明显 时间间隔差异（图 2）；（3）不同次大陆人群的三个建群者的分化时间亦很相似（4-7 万年；图 3）。因此，基于大规模的线粒体基因组数据未发现明显的两次迁移扩散证 据，单扩散伴随着各地区独立分化模型即可解释现今欧亚人群 mtDNA 类群分布模 式及起源时间规律。 图 1. 非洲人群 mtDNA 单倍型类群的分布模式 27 图 2. M、N 和 R 基部类群的溯祖时间 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 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 cancer. E-mail: kongqp@mail.kiz.ac.cn Mitochondrial DNA confirms unique human dispersal from Africa into Asia and beyond Agreement on recent origin of modern human in Africa has been widely achieved among the fields of genetics, archaeology and anthropology, however, debates on the routs and times that ancestors of modern humans had adopted out of Africa continue. Hitherto, two models concerning the populating Eurasia were proposed: one argues for a single dispersal that led to the settlement of eastern Eurasia ~60 kya, whereas another proposing that at least two dispersal events had occurred in peopling eastern Eurasia and beyond, with the first exodus at ~70 kya and the second ~30 kya. The specific characters, e.g. rapid mutational rate and non-recombination, of mitochondrial DNA (mtDNA) makes this molecule to be a powerful tool in tracing the prehistoric demographic events. Therefore, to test how many times were the initial modern humans disperse into eastern Eurasia after they migrated out of Africa, we collected and analyzed a total of 14,216 entire mtDNA genome sequences sampled from the Eurasia as well as Oceania. As shown in our results, (1) Virtually all basal haplogroups identified in each sub-continents show non-overlapping distribution pattern in the schematic mtDNA tree worldwide (Fig. 1); (2) no significant differences were found in either the average mutational distance (ρ) or the coalescent ages to the founder types (i.e. M, N or R) among all the basal haplogroups detected (fig. 2); and, moreover, (3) all the three founder types from different sub-continents share similar divergence times (40~70 kya; fig. 3). Our results thus suggest that a single but rapid dispersal model is efficient to explain the contemporarily observed distribution pattern, average mutation accumulated as well as the coalescence ages of the human mtDNA lineages in Eurasia and Oceania. 员工简介（Lab Staff） 工作人员（Staff） 王华伟 Dr. Hua-Wei Wang wanghuawei99@gmail.com 何永捍 Dr. Yong-Han He heyonghan-2008@163.com 刘立娜 Li-Na Liu handyliu@126.com 李其刚 Qi-Gang Li liqigang@gmail.com 杨利琴 Li-Qin Yang miss_de@126.com 陈小琼 Xiao-Qiong Chen chenxiaoduoycc@126.com 研究生（Graduate Students） 刘 佳 Jia Liu, 2010 jane-3223505@163.com 王晓雄 Xiao-Xiong Wang, 2011 yunnanpiao@163.com 程耀霆 Yao-Ting Cheng, 2008 chengx1121@yahoo.com.cn 李玉春 Yu-Chun Li, 2009 liyuchun.123448@163.com 逯 翔 Xiang Lu, 2010 lx.luxiang@gmail.com 肖富辉 Fu-Hui Xiao, 2010 xfhsky1008@yahoo.cn 李 越 Yue Li, 2011 yuelee.stella@gmail.com 刘耀文 Yao-Wen Liu ,2012 dahailyw@yahoo.com.cn 田娇阳 Jiao-Yang Tian ,2012 tianjiaoyang@yeah.net 吴 焕 Huan Wu, 2012 wu2008huan@126.com Fig 3. Differentiation times of the three founder types from different sub-continents. 28 遗传资源与进化国家重点实验室 2012 年 度 报 告 计算生物与医学生态学 研究员，博士生导师 , 计算生物与医学生态学学科负责人。 2010 年 11 月中 马占山 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。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（Publications） 论著（Publications） 1. Zhanshan (Sam) Ma. 2012. Chaotic populations in genetic algorithms. Applied Soft Computing, 12(8):24092424. 2. Zhanshan (Sam) Ma. 2012. A unified definition for reliability, survivability and resilience inspired by the handicap principle and ecological stability. International Journal of Critical Infrastructures, 8:242-272. 3. Zhanshan (Sam) Ma, et al. 2012. A bird's eye view of microbial community dynamics. In “Microbial Ecological Theory: Current Perspectives.” Caister Academic Press, eds. Lesley A. Ogilvie and Penny R. Hirsch, ISBN: 978-1-908230-09-6. 4. Chengxi Ye, Zhanshan (Sam) Ma, Charles H. Cannon, Mihai Pop and Douglas W Yu. 2012. Exploiting sparseness in de novo genome assembly. BMC Bioinformatics, 13(Suppl. 6):S1. 5. Pawel Gajer, Rebecca M. Brotman, Guoyun Bai, Joyce Sakamoto, Ursel M. E. Schütte, Xue Zhong, Sara S. K. Koenig, Li Fu, Zhanshan (Sam) Ma, Xia Zhou, Zaid Abdo, Larry J. Forney and Jacques Ravel. 2012. Temporal dynamics of the human vaginal microbiota. Science Translational Medicine. 4:(132): 132ra52. 6. 叶 丹 丹 , 樊 萌 萌 , 关 琼 , 陈 红 菊 , 马 占 山 . 2012. 宏基因组研究的生物信息学平台现状 . 动物学 研究 .33(6):574-585. 研究兴趣 (Research Interests) Computational Biology & Bioinformatics; Human Microbiome and Medical Ecology; Natural Evolution and Computational Evolution; Bio-Inspired Computing and Communications; Network Science; Game Theory; GPU Computing and Cloud Computing. 学术兼职 (Professional Services) (1) Member of “Faculty 1000 of Biology and Medicine” (www.f1000.com). (2) Editor-in-Chief for “I. J. of Computational Microbiology and Medical Ecology”. (http://www.inderscience.com/ijcmme) (3) Editor-in-Chief for “I. J. of Cyberspace Sciences & Emergency Management”. (http://www.inderscience.com/ijcsem) 现承担科研项目 (Current Funding Grants) (1) 中科院“百人计划”昆明动物所启动基金 (2010 － 2013 年 ) Chinese Academy of Sciences (CAS) startup funding for the “One-hundred Talented PI Program” (PI, Year 2010-2014) (2) 中科院“引进杰出技术人才”基金 (2011 － 2014 年 ) CAS startup funding for the “Exceptional Overseas Technology 2011- 2014) Talents” (PI, (3) 国家自然科学基金 ( 信息科学部 )：“生态“舞台”与进化计算 “演出”(2012 － 2015 年 )。 National Science Foundation of China (NFSC) grant: “Ecological theater and evolutionary computing play” (PI, 2012-2015) (4) 国家自然科学基金 ( 生物科学部 )：基于 metagenetics 技术建立快 速高效的生物多样性检测法（2012 － 2015 年 ) ( 主持人 :Douglas Yu) National Science Foundation of China (NFSC) grant: “Rapid biodiversity measurement with metagenetics.” (2012-2015) (5) 云南省引进高端科技人才项目：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”。 Yunnan Special Funding for High-profile Talents in Science and Technology: “GPGPU Computing for Computational Bioinformatics and Personalized Medicine.” (6）中国科学院昆明动物研究所“计算进化 - 自然进化”协同研究省创新团队 (2012-2014 年 )。 Innovative Research Initiative of the Synergy between Natural Evolution and Computational Evolution” of CAS-Yunan Province (7) 云南省“百名海外高层次人才引进计划”(2012-2015 年 ) 。 The Top Talents (from Overseas) Program of Yunnan Province 29 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 ANNUAL REPORT Computational Biology and Medical Ecology Biography of the lab director: Zhanshan (Sam) Ma received his Ph.Ds 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. Dr. Ma has been keeping dual track publishing in both Computer Science and Biology with more than 80 peer-refereed papers in premier platforms such as “IEEE Transactions on Reliability.” He is a member of London-based “Faculty 1000 of Biology and Medicine”. Email: ma@vandals.uidaho.edu or ma@mail.kiz.ac.cn 1. Chaotic populations in genetic algorithms We set two objectives for this study: one is to emulate chaotic natural populations in GA (Genetic Algorithms) populations by utilizing the Logistic Chaos map model, and the other is to analyze the population fitness distribution by utilizing insect spatial distribution theory. Natural populations are so dynamic that one of the first experimental evidences of Chaos in nature was discovered by a theoretical ecologist, May (1976, Nature, 261,459–467)[30], in his analysis of insect population dynamics. In evolutionary computing, perhaps influenced by the stable or infinite population concepts in population genetics, the status quo of population settings has dominantly been the fixed-size populations. In this paper, we propose to introduce dynamic populations controlled by the Logistic Chaos map model to Genetic Algorithms (GA), and test the hypothesis – whether or not the dynamic populations that emulate chaotic populations in nature will have an advantage over traditional fixed-size populations. The Logistic Chaos map model, arguably the simplest nonlinear dynamics model, has surprisingly rich dynamic behaviors, ranging from exponential, sigmoid growth, periodic oscillations, and aperiodic oscillations, to complete Chaos. What is even more favorable is that, unlike many other population dynamics models, this model can be expressed as a single parameter recursion equation, which makes it very convenient to control the dynamic behaviors and therefore easy to apply to evolutionary computing. The experiments show result values in terms of the fitness evaluations and memory storage requirements. We further conjecture that Chaos may be helpful in breaking neutral space in the fitness landscape, similar to the argument in ecology that Chaos may help the exploration and/or exploitation of environment heterogeneity and therefore enhance a species’ survival or fitness.(published in Applied Soft Computing , 2012). 2. A Bird's Eye View of Microbial Community Dynamics Microbial community dynamics is one of the most important central themes of microbial community ecology, which seems to be experiencing its first golden era thanks to the rapidly expanding datasets derived using metagenomic and other ‘-omic’ methods in microbial biology. For example, much of the ongoing NIH-HMP (Human Microbiome Project) focus has been centred on the dynamics of the human microbiome communities. Microbial ecologists are beginning to actively draw upon ecological theories from macro ecology to study microbial communities. In this article, we present a brief review on several selected topics of ecological theories that are most relevant to community dynamics, including the diversity-stability paradigm, intermediate disturbance hypothesis (IDH), species area/time curves (SAT), species abundance distribution (SAD), and neutral community theory. In perspective, we suggest that the study of microbial community dynamics can not only benefit from applying ecological theories originally developed in macroecology, but also contribute to the development and testing of new ecological theories. These bidirectional interactions are of critical importance to the flourishing of theoretical microbial ecology, and studies of microbial community dynamics offers tremendous opportunities for these intellectual exchanges to occur.(published in “Microbial Ecological Theory” 2012). 30 员工简介（Lab Staff） 工作人员（Staff） 叶丹丹 研究实习员 Dandan Ye Research Associate ydan2010@mail.kiz.ac.cn 研究生（Graduate Students） 关 琼 Guan 向志丹 Zhidan Qiong, 2011 Xiang, 2012 樊萌萌 Mengmeng Fan, 2012 李连伟 Lianwei Li, 2012 遗传资源与进化国家重点实验室 2012 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/ 重要成果（Highlights） 论著（Publications） 1. Xia Y, Zhao S, Mao B*. (2012) Involvement of XZFP36L1, an RNA-binding protein, in Xenopus neural development. Zoological Research, 33 (E5−6): E82− E88. 1. RNA 结合蛋白 ZFP36L1 参与非洲爪蛙神经发育 ZFP36 家族蛋白是一类 RNA 结合蛋白，含有两个或两个以上串联的 CCCH 锌指结构域， 可与 mRNA 的 3’非编码区中的 AU 富集元件相结合并促进靶 mRNA 的降解。本文研究 了非洲爪蛙 ZFP36L1 在神经发育中的表达与功能。发现 ZFP36L1 在非洲爪蛙胚胎神经系统 中特异表达，从神经胚晚期至蝌蚪期，它在脑中的表达逐渐集中于前脑、前 - 中脑边界和中 后脑边界的三个区域。在爪蛙胚胎中过表达 ZFP36L1 可导致严重的神经管缺陷，并伴随着 神经标记基因表达水平的降低。ZFP36L1 蛋白的锌指结构域和 C 末端区域对上述功能都是 必不可少的，免疫组化实验显示，这两个结构域对其细胞内定位有重要影响。上述结果提示 转录后调控在爪蛙神经发育调控中可能起重要作用。 2. Ma P, Xia Y, Ma L, Zhao S, Mao B*. Xenopus Nkx6.1 and Nkx6.2 are required for mid-hindbrain boundary development. Development Genes and Evolution, DOI10.1007/s00427-0130437-9 图 1. 过表达 ZFP36L 及其 ZFC 结构会 引起神经管发育缺陷 Fig.1. Overexpresion of the ZFP36L and the ZFC construct leads to severe neural tube defects. 2. XNkx6.1/6.2 参与爪蛙中后脑边界的发育 XNkx6.1/6.2 在爪蛙胚胎中后脑腹侧表达。通过特异 Morpholino（MO）阻断它们 的内源表达，会抑制中后脑边界标记基因 En2 的表达，到尾芽期，MO 注射侧 MHB 的结构 畸形。进一步的研究表明，Nkx6.1/6.2 可能是通过影响 Wnt1 的表达而调节中后脑发育的。 图 2， XNkx6.2 的表达前沿与 MHB 标记基因 XEn2 重叠 . Fig.2. The overlapping expression of XNkx6.2 and the mid-hind brain boundary marker en2. 31 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 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 1. XZFP36L1, an RNA binding protein, is involved in Xenopus neural development Xenopus ZFP36L1 (zinc finger protein 36, C3H type-like 1) belongs to the ZFP36 family of RNA-binding proteins, which contains two characteristic tandem CCCH-type zinc-finger domains. Here we showed that Xenopus ZFP36L1 was expressed at the dorsal part of the forebrain, forebrain-midbrain boundary and midbrain-hindbrain boundary from late neurula stages to tadpole stages of embryonic development. Over-expression of XZFP36L1 in Xenopus embryos inhibits neural induction and differentiation, leading to severe neural tube defects. The function of XZP36L1 requires both its zinc finger and C terminal domains. These results suggest that XZFP36L1 is likely involved in neural development in Xenopus and might play an important role in the post-transcriptional regulation. 2. Xenopus Nkx6.1 /6.2 are required for mid-hindbrain boundary development The mid-hindbrain boundary (MHB) is established by a regulatory network of several transcription factors and signals, including Wnt signaling. In Xenopus embryos, nkx6.1 and nkx6.2 are expressed in the MHB and knockdown of either nkx6.1 or nkx6.2 by specific morpholinos disrupts the MHB expression of en2 as well as wnt1, a key regulator for vertebrate MHB formation. Nkx6.1 and Nkx6.2 activate canonical Wnt signaling in reporter assays in both cultured mammalian cells and Xenopus embryos. An Nkx6.2 deletion construct, which inhibits the ability of wild type Nkx6.2 to activate Wnt signaling, also reduces the MHB expression of en2 in Xenopus embryos. These data suggest that Nkx6.1 and Nkx6.2 are involved in MHB formation in Xenopus embryos likely through regulating wnt1 expression. 图 3， Nkx6.1 和 Nkx6.2 参与爪蛙中后脑边界的发育 Fig. 3. Nkx6.1 and Nkx6.2 are required for MHB formation. 32 员工简介（Lab Staff） 工作人员（Staff） 李朝翠 高级实验师 Mrs. Chaocui Li licc@mail.kiz.ac.cn 研究生（Graduate Students） 张祖明 Zuming Zhang, 2008 马鹏程 Pengcheng Ma, 2008 江世友 Shiyou Jiang， 2009 孙 健 Jian Sun， 2009 杨相彩 Xiangcai Yang, 2010 汤济鑫 Jixin Tang， 2010 王晓磊 Xiaolei Wang，2011 谢建新 Jianxin Xie，2012 遗传资源与进化国家重点实验室 2012 年 度 报 告 哺乳动物胚胎发育 郑萍 , 博士，研究员，哺乳动物胚胎发育课题组组长。以灵长类（猕猴）和 小鼠为动物模型，长期从事哺乳类卵母细胞生物学及着床前胚胎发育的研究。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。研究方向为干细胞及配子发生。 重要成果（Highlights） 论著（Publications） 1. Zheng P#, Baibakov B, Wang XH, Dean J. PtdIns(3,4,5)P3 is constitutively synthesized and required for spindle translocation during meiosis in mouse oocytes. J Cell Sci, in press. 2012 Dec 21.Epub ahead of print. 2. 李朝晖 , 郭琨 , 郑萍 #。哺乳 动物卵巢生殖干细胞研究的现状 与未来 . 动 物 学 研 究 2012， 33(6): 586-590 1. 猕猴胚胎干细胞神经分化的调控研究 神经干细胞在治疗神经系统疾病中有巨大的应用前景，但多能干细胞神经分 化的调控机制仍不是非常清楚。我们通过系统分析猕猴胚胎干细胞神经分化过程 中的基因表达变化及 microRNA 表达变化，从组学水平上鉴定和发现了猕猴胚 胎干细胞神经分化过程中各阶段特异变化的基因和 microRNAs，以及潜在的调 控网络，从而为设计体外灵长类胚胎干细胞的高效神经分化培养系统提供理论依 据。研究结果已整理，正在投稿中。 2. 胚胎干细胞维持遗传物质稳定性的机制研究 多能干细胞具有强大的能力维持其遗传物质的稳定性，这对于个体及其后 代的健康发育至关重要，也是多能干细胞应用于再生医学的重要前提。但是， 多能干细胞维持遗传物质稳定性的调控机制目前尚知之甚少。2012 年我们的工 作发现，小鼠胚胎干细胞特异表达基因 Filia 对维持胚胎干细胞遗传物质稳定 性至关重要，缺失 Filia 导致胚胎干细胞迅速癌变。Filia 蛋白的表达受 DNA 损伤诱导，并全面参与调控胚胎干细胞的 DNA 损伤反应。 我们进一步研究了 Filia 的作用机制，发现它是一个 RNA 结合蛋白，存在于 RNA 及蛋白复合体中 (ribonucleioprotein particle)，其 C- 端和 N- 端的结构域在 DNA 损伤反应中 承担不同功能。对 Filia 作用机制的进一步研究将使我们能更深入理解多能干 细胞维持其遗传物质稳定性的方式。研究论文正在整理和撰写中。 3. 卵细胞减数分裂纺锤体迁移调控机制的研究 卵细胞的减数分裂是极端的不对称分裂，不对称分裂受阻导致卵成熟异常， 而减数分裂过程中纺锤体向皮层部位迁移是实现不对称分裂的先决条件。虽然已 经清楚卵细胞中 actin 的动态聚集对纺锤体的迁移至关重要，但卵细胞中哪些因 子能调控 actin 的动态聚集仍不清楚。我们发现卵细胞中脂类物质 PtdIns(3,4,5) P3 是调控 actin 动态聚集的重要因素，抑制卵细胞中 PtdIns(3,4,5)P3 的产生可 以有效地阻断第一次减数分裂过程中纺锤体的迁移及不对称分裂的发生。并且， 我们寻找到 PtdIns(3,4,5)P3 作用的下游靶基因 Cdc42，也发现卵细胞特异表达 基因 Mater 是 PtdIns(3,4,5)P3 的上游调控因子。这拓宽了我们对卵细胞减数分 裂调控机制的认识。研究结果发表于 Journal of Cell Science 。 33 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 ANNUAL REPORT Mammalian Embryonic Development Dr. Ping Zheng, Group leader, joined in Kunming Institute of Zoology, Chinese Academy of Sciences in June 2009.Research interests: 1) Stem cell biology; 2) Mammalian female germ cell biology. E-mail: zhengp@mail.kiz.ac.cn 1. Rhesus monkey embryonic stem cell neural differentiation Pluripotent stem cells have potential application in treatment of degenerative diseases of nervous system. However, the mechanism regulating neural differentiation of pluripotent stem cells remains elusive. We investigated the dynamics of the mRNA and microRNA expression profiling during the neural differentiation process of rhesus monkey embryonic stem cells and identified a list of candidate genes, microRNAs, and molecular modules implicated in neural differentiation of monkey embryonic stem cells. 员工简介（Lab Staff） 工作人员（Staff） 和协超 高级实验师 HE Xiechao 吕永青 研究实习员 LU Yongqing, Research Assistant 2. How pluripotent stem cells maintain their genomic integrity Preservation of genomic integrity is key to pluripotent stem cells. Although it is known that pluripotent stem cells have much lower mutation rate than somatic cells, little is known regarding the underlying mechanisms. We recently identified an embryonic stem cell (ESC) specific gene Filia which played critical roles in governing ESC genomic integrity. Loss of Filia resulted in transformation of ESCs. Filia maintains ESC genomic stability by governing all aspects of DNA damage response(DDR) in ESCs. Furthermore, we found that Filia functioned as a RNA-binding protein and its C-terminus and N-terminus play distinct roles in DDR. 研究生 （Graduate Students） 桑伟健 SANG Weijian 赵 博 ZHAO Bo 寸益贤 CUN Yixian 季 爽 JI Shuang 3. PtdIns(3,4,5)P3 regulates meiotic spindle translocation to cortex in mouse oocytes 李朝晖 LI Chaohui Prior to ovulation, mammalian oocytes complete their first meiotic division and arrest at metaphase II. During this marked asymmetric cell division, the meiotic spindle moves dramatically from the center of the oocyte to the cortex to facilitate segregation of half of its chromosomal content into the diminutive first polar body. Recent investigations have documented critical roles for filamentous actin (F-actin) in meiotic spindle translocation. However, the identity of the upstream regulators responsible for these carefully orchestrated movements has remained elusive. Utilizing fluorescence-tagged probes and time-lapse confocal microscopy, we document that phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3) is constitutively synthesized with spatial and temporal dynamics similar to that of F-actin and Formin 2 (Fmn2). Blockage of PtdIns(3,4,5)P3 synthesis by LY294002, a specific inhibitor of phosphoinositide 3-kinases (PI3K), disrupts cytoplasmic F-actin organization and meiotic spindle migration to the cortex. F-actin nucleator Fmn2 and Rho GTPase Cdc42 play roles in mediating the effect of PtdIns(3,4,5)P3 on F-actin assembly. Moreover, the spatial and temporal dynamics of PtdIns(3,4,5)P3 is impaired by depletion of MATER or Filia, two oocyte proteins encoded by maternal effect genes. Thus, PtdIns(3,4,5)P3 is synthesized during meiotic maturation and acts upstream of Cdc42 and Fmn2, but downstream of MATER/Filia proteins to regulate the F-actin organization and spindle translocation to the cortex during mouse oocyte meiosis. 王鑫轶 WANG Xinyi 34 张锦娟 ZHANG Jinjuan 何大健 HE Dajian 郭 琨 GUO Kun 遗传资源与进化国家重点实验室 2012 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，现已保存有 315 种动物的细 胞系 1585 株 10000 余份。目前，昆明野生动物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 质资源库的成员单位之一，也是遗传资源与进化国家重点实验的支撑 部门之一。 2012 年主要工作进展 重要成果（Highlights） 论著（Publications） 1. Nie W, Wang J, Su W, Wang D , Ta n o m t o n g A , P e r e l m a n P L , G r a p h o d a t s k y A S , Ya n g F. Chromosomal rearrangements and karyotype evolution in carnivores revealed by chromosome painting. Heredity, 2012,108: 17-27. 新建立和保存了包括针尾鼹、朱鹮、白鹭、三趾心颅跳鼠、长耳跳鼠、 大头鲤和茶花鸡等动物及人的各类细胞系 161 株 1382 份；复苏和扩增各类动 物细胞系 245 株 490 份；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 228 株次；提供核型分析、支原体检测和荧光原位杂交 等技术服务 107 次；发表研究论文五篇。 2.Nie W. Molecular Cytogenetic Studies in Strepsirrhine , Primates, Dermoptera and Scandentia. Cytogenetic and Genome Research, 2012. 137 (2-4): 246-258. 3. 王金焕 , 苏榕 , 苏伟婷 , 成诚 , 魏曙 光 , 丁海华 , 段英 , 李生斌 , 佴文惠 . 朱 鹮细胞系的建立及其生物学特性观 察 . 动 物 学 研 究，2012, 33(6): 591596. 朱鹮 ( 摄影 李生斌 ) 4. He K, Wang J, Su W, Li Q, Nie W, Jiang X. 2012. Karyotype of the Gansu mole (Scapanulus oweni): further evidence for karyotypic stability in talpid. Mammal Study , 37: 341–348. 5. Perelman PL, Beklemisheva VR, Yudkin DV, Petrina TN, Rozhnov VV, Nie W, Graphodatsky AS.2012. Comparative Chromosome Painting in Carnivora and Pholidota. Cytogenetic and Genome Research, 137 (2-4): 174193. 原代培养的朱鹮细胞 其中，我们重点进行了四种沙漠啮齿动物（三趾跳鼠、三趾心颅跳鼠、 长耳跳鼠和地兔）不同组织来源的细胞系的建立工作，共建立各类体细胞 系 27 株。另外，我们再次建立了雌、雄两种个体的朱鹮体细胞系三株，并 完成了朱鹮的细胞遗传学研究。 35 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 ANNUAL REPORT Kunming wild animal cell bank Kunming wild animal cell bank was established in 1986. Now it is a 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. Up to now 1585 cell lines belonging to 315 animal species have been preserved in our cell bank. The main work in 2012 In 2012, We have established and frozen one 161 cell lines from various wild and domestic animals, including long-tailed mole, crested ibis, egret, three-toed pygma jerboa, northern three-toed jerboa, long-eared jerboa, dwarf fat-tailed jerboa, carp, and chicken etc. Two hundred and forty-five of frozen-stored cell lines were also resuscitated and subcultured. In this year, the cell bank provided 228 cell lines and 107 times of technical service such as karyotype analysis, mycoplasma contamination test and Fluorescence in situ hybridization (FISH) for the researchers not only at State key laboratory of genetic resources and evolution, but also at other Chinese universities and scientific research institutions. In addition, five papers have been published in this year. 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 Fig1. Telomere Probe hybridizing onto mouse chromosomes An important work done in 2012 was the establishment of cell lines derived from various tissues of four rodents living in the desert. In total, 27 cell lines from three-toed pygma jerboa, northern three-toed jerboa, long-eared jerboa, dwarf fat-tailed jerboa were established and preserved. In addition, we also reestablished three cell lines from a male and female crested ibis individuals. And we have done the work of crested ibis cytogenetic study. Fig2. Long-eared jerboa (Euchoreutes naso) 36 胡 怡 技术员 Yu Hu Technician 524140624@qq.com 遗传资源与进化国家重点实验室 2012 年 度 报 告 生命条形码南方中心 生命条形码南方中心是应中国加入国际生命条形码计划 (iBOL) 并成为 中心节点的任务和要求，于 2011 年成立的专门从事 DNA 条形码相关的技 术创新和科学研究单元。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；采集和收集野生动物资源丰富本室遗传资源；利用 DNA 条形码技术探索商业应用等。 论著 Publications 1. Murphy R. W, Crawford A. J, Bauer A. M, Che J, Donnellan S. C, Fritz U, Haddad C.F.B, Nacy Z. A. T, Poyarkov N. A., Vences M, Wang WZ and ZhangYP. Cold Code: The Global Initiative to DNA Barcode Amphibians and Nonavian Reptiles . Molecular Ecology Resources 2012, 10.1111/1755-0998.12050 2. Liu D, Liu L, Guo G, Wang W, Sun Q, Parani M. and J. a. BOLD Mirror: a global mirror system of DNA barcode data. Molecular Ecology Resources 2012, 10.1111/17550998.12048 1. 基于自然保护区的 DNA 条形码 科技基础性工作专项“基于自然保护区的 DNA 条形码”于 2012 年正式启动， 该项目将 DNA 条形码工作同自然保护区生物多样性考察结合起来，计划对南方高黎 贡山国家级自然保护区和北方小五台山自然保护区内的生物资源与多样性进行详细 调查，按标准规范采集、保藏、鉴定生物标本，并取材进行 DNA 条形码测序。本中 心与我室 Douglas Yu 课题组共同组织实施高黎贡山动物标本采集和 DNA 条形码实 验。 2012 年 6 月至 7 月，生命条形码南方中心组织了高黎贡山南段的第一次采样，采 得近 15,000 份的昆虫样品。 2. 高通量 DNA 条形码工作平台的建立 2012 年，本中心通过技术创新，建立了生命条形码南方中心标准作业流程 (SOP)， 并搭建了百万级别的二维条形码样品存储和管理平台、可同时进行 15 通量的 PCR 扩 增阵列、超景深三维显微系统。此外，对 DNA 提取和 PCR 产物凑板操作实现了自动化， 并使 PCR 检测的成本大幅度降低。上述工作即将在相关 DNA 条形码实验室进行推广。 37 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 ANNUAL REPORT Southern China DNA Barcoding Center Barcode Counts (SCDBC) Established in 2011, the Center is the first and only facility focus on DNA barcoding in China. The initialization of SCDBC is due to the MOU of China and iBOL project. The mission of this center includes standardization, automation and application of DNA Barcoding; organization and advancement of major DNA barcoding programs in China; collecting, storage and manage the genetic resources for research in the SKL; commercial using DNA barcoding technology and highthroughput barcoding laboratory construction and operation. ● Specimens 15,124 ● DNA 8,309 ● Barcodes 7,439 ● Images 6,917 3. China Signs Memorandum of Understanding with iBOL: Seeks More Prominent Role in Global Barcoding Community Under the coordination of SCDBC and Kunming Institute of Botany, the Memorandum was signed on May 29th, 2012 at the Kunming with representatives of the Chinese Academy of Sciences and the Ministry of Science and Technology in attendance. Prof. Dezhu Li and Prof. Pete Hollingsworth signed on behalf of the Chinese National Node and the international Barcode of Life project. The signing ceremony was chaired by Prof. Wang Wen, who’s the leader of SCDBC. 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 数据分析员 Yun-yu WANG Analytics Engineer 李宗煦 采样员 Zong-xv LEE Specimen Manager 许小娥 实验员 Xiao-e XU Laboratory Technician SCDBC co-chaired the global DNA barcoding on Amphibians and Reptiles project – Cold Code. Since its releasing on the fourth iBOL Meeting, 12 countries from Asia, Europe, Africa, America, Australia had been joined in. 4. Judicial Forensic Identification using DNA Barcoding Technology. As the molecular branch of Yunnan CITES Judicial Forensic Center (JFC), SCDBC developed and advanced species identifying methodology using DNA barcoding technology. These applications involved 21cases from Forest Police Service (some artifactitious wild animal meats), Nature Reserves (some residual hairs from wild animal(s)) and Administration of Industrial and Commercial Products (so called mutton or beef meats selling in markets or restaurants). SCDBC provides DNA barcoding is so useful to identify species from hairs, bones, muscles or even processed, where lacks morphologic features for taxonomists. 38 谭 婧 助理司法鉴定师 Jing TAN Assistant Judicial Appraiser 遗传资源与进化国家重点实验室 2012 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） 一、基因组学分析平台 许绍斌 工程师 Mr. Shaobin Xu Engineer xushao@mail.kiz.ac.cn 1. 基因芯片扫描系统 Affymetrix 基因芯片技术平台是用 于基因组学和转录组学研究的整合平台， 既 可 以 分 析 基 因 组 DNA， 也 可 以 分 析 RNA，在 DNA 水平上既可以做 SNP 分 析，也可以做 DNA 再测序。 2. 基因分型系统 Beckman GenomeLab SNPstream 系 统 是 一 套 自 动 化、 通 量 可 升 级 的 SNP 分型工具。在特制 384 孔板的每 个微孔中可分析 12 个或 48 个 SNP 位 点。 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。 杨 梅 助理工程师 Mrs. Mei Yang Assistant Engineer yangmei39030@163.com 唐 嘉 助理实验师 Mrs. Jia Tang Assistant Experimentalist tangj@mail.kiz.ac.cn 杨双娟 助理实验师 Ms. Shuangjuan Yang Assistant Experimentalist yangsj@mail.kiz.ac.cn 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。 39 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 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/ 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. The Three Technical Platforms I. Genomic Analysis Platform 1. Affymetrix GeneChip scanner The GeneChip® Scanner 3000 7G allows you to scan nextgeneration higher-density arrays, including SNP arrays with up to 900,000 SNPs, tiling arrays for transcription and all-exon arrays for whole-genome analysis. The GCS 3000 7G combines space-saving and other design improvements with speed, superior performance and lower scanner-to-scanner variation to dramatically improve throughput and efficiency in your genetic analysis. II. Proteomic Analysis Platform 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 post- and co-translational modifications. III. High Performance Computing Platform 2. SNPstream Genotyping System The GenomeLab Genetic Analysis System is capable of determining the base sequence and fragment length of DNA samples labeled with the dye from Beckman Coulter, Inc. 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. 40 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 2012 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: 2013-2017; 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. 人类智力的基因组及遗传学基础，973 课题 ; 执行年限：2011-2012；项目负责人：宿兵；金额：306 万元。 The Genomic and Genetic Basis of Human Intelligence, National Basic Research Program (973) project, Period: 20112012; Head of project, Bing Su; Amount: RMB 3.06 million microRNA 或 microRNA 基因簇在干细胞多能性维持与分化过程中的作用与调控机制；973 课题；执行年限： 2011-2012；项目负责人：郑萍；金额：125 万元。 The Functions and Regulation of MicroRNA or MicroRNA Clusters in Stem Cell Pluripotency Maintenance and Differentiation. National Basic Research Program (973) project, Period: 2011-2012; Head of project, Ping Zheng; Amount: RMB 1.25 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. 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. 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. 41 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 ANNUAL REPORT 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. 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. 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: 20122016; 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. 极原始的原生动物－－贾第虫的核仁功能基因组与核仁的起源进化探讨，国家自然科学基金重点项目；执行年 限：2009-2012；项目负责人：文建凡；金额：160 万。 Giardia Nucleolar Genome and the Evolution of Nucleus, Key project of National Science Foundation of China, Period: 2009-2012; Head of project, Wen Jian-Fan; Amount: RMB 1.6 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, 2010-2012; 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. 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 42 遗传资源与进化国家重点实验室 2012 年 度 报 告 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. 猪转基因操作技术的改进，中科院百人计划项目；执行年限：2010-2013；项目负责人：郑萍；金额：200 万元。 Improvement of the Transgenic Techniques in Pigs. One Hundred Talents Project of Chinese Academy of Sciences, 2010-2013; Head of project, Ping Zheng; Amount: RMB2.00 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. 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. 抗 PVY、抗黑胫病候选基因的发掘鉴定，企业委托；执行年限：2012；项目负责人：王文；金额：500 万。 Excavation and Identification of Candidate Genes of Anti-PVY and Anti-blackleg. Company Supported, Period, 2012; Head of project, Wen Wang; Amount: RMB 5.0 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; Head of project, Wen Wang; Amount: RMB 4.2 million. 阿墨江珍惜特有鱼类繁殖育苗放流研究，企业委托项目；执行年限：2010-2012；项目负责人：杨君兴；金额： 320 万元。 Breeding and Releasing of Endemic Fishes in AMo River. Company supported, Period, 2010-2012; Head of project, Junxing Yang; Amount: RMB 3.20 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. JingFei Huang; Amount: RMB 2.0 million. 43 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 ANNUAL REPORT 发表论文 Publications 1. Abnet CC#*, Wang Z#, Song X#, Hu N#, Zhou FY#, Freedman ND#, Li XM#, Yu K, ...Kong QP, ...Wang LD*. Genotypic variants at 2q33 and risk of esophageal squamous cell carcinoma in China: a meta- analysis of genomewide association studies. Hum Mol Genet, 2012, 1:21(9):2132-41. 2. Bonasio R, Li Q, Lian J, Mutti NS, Jin L, Zhao H, Zhang P, Wen P, Xiang H, Ding Y, Jin Z, Shen SS, Wang Z, Wang W, Wang J, Berger SL*, Liebig J*, Zhang G*, Reinberg D*.Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator. Curr Biol, 2012, 22(19):1755-64. 3. Che J, Chen HM, Yang JX, Jin JQ, Jiang K, Yang ZY, Murphy RW, Zhang YP*. Universal COI primers for DNA barcoding amphibians. Mol Ecol Resour, 2012, 12: 247–258. 4. Chen R, Irwin DM, Zhang YP*. Differences in selection drive olfactory receptor genes in different directions in dogs and wolf. Mol Biol Evol, 2012, 29(11):3475-3484. 5. Chen SY, Gomes R, Costa V, Rocha I, Zsolnai A, Anton I, Charneca R, Santos P, Nunes JL, Buzgo J, Varga G, Zhang YP, Beja-Pereira A. Novel coding genetic variants of the GBP1 gene in wild and domestic pigs (Susscrofa). Livest Sci, 2012, 146(1):1-4. 6. Chen XY, David AN*.Schistura albirostris, a new nemacheiline loach (Teleostei: Balitoridae) from the Irrawaddy River drainage of Yunnan Province, China. Zootaxa, 2012, 3586: 222–227. 7. Chen ZM#, Yang J#*, Yang JX*. Description of a new species of the genus Yunnanilus Nichols, 1925 (Teleostei: Nemacheilidae) from Yunnan, China. Zootaxa, 2012, 3569: 57–64. 8. Dai SX, Zhang AD, Huang JF*. Evolution, expansion and expression of the Kunitz/BPTI gene family associated with long-term blood feeding in Ixodes Scapularis. BMC Evol Biol, 2012,12:4. 9. Ding Y, Zhou Q, Wang W*. Origins of new genes and evolution of their novel functions. Annu Rev EcolEvolution S, 2012, 43:345-363. 10. Ding ZL#, Oskarsson M#, Ardalan A, Angleby H, Dahlgren LG, Tepeli C, Kirkness E, Savolainen P*, Zhang YP*. Origins of domestic dog in Southern East Asia is supported by analysis of Y-chromosome DNA. Heredity, 2012, 108(5):507-514. 11. Dong BJ, Che J, Ding L, Huang S, Murphy RW, Zhao EM*, Zhang YP*.Testing Hypotheses of Pleistocene Population History Using Coalescent Simulations: Refugial Isolation and Secondary Contact in Pseudepidalearaddei (Amphibia: Bufonidae). Asian Herpetol Res, 2012, 3(2):103-113. 12. Du LN, Yang JX*, Thomas VR*, Chen XY, David A. Molecular Phylogenetic Evidence that the Chinese Viviparid Genus Margarya (Gastropoda: Viviparidae) is Polyphyletic. Chinese Sci Bull, 2012,57(1): 1-9. 13. Feng JM#, Sun J#, Xin DD, Wen JF*. Comparative Analysis of the 5S rRNA and Its Associated Proteins Reveals Unique Primitive Rather Than Parasitic Feature in Graidia lamblia. PloS ONE, 2012 7(6):e36978. 14. Fu Y, He F, Tang NLS, Tam CWC, Lui VWC, Chiu HFK, Lam LCW: NEDD9 Gene Polymorphism Influences the Risk of Alzheimer Disease and Cognitive Function in Chinese Older Persons. Alz Dis Assoc Dis, 2012, 26(1):88-90. 15. Gajer P#, Brotman RM#, Bai G, Sakamoto J, Schütte UM, Zhong X, Koenig SS, Fu L, Ma ZS, Zhou X, Abdo Z, Forney LJ*, Ravel J*. Temporal dynamics of the human vaginal microbiota. Sci Transl Med, 2012, 4:(132): 132ra52. 16. Gao Y#, Wang SY#, Luo J, Murphy RW, Du R, Wu SF, Zhu CL, Li Y, Poyarkov AD, Nguyen SN, Luan PT, Zhang YP*. Quaternary palaeoenvironmental oscillations drove the evolution of the Eurasian Carassius auratus complex (Cypriniformes, Cyprinidae). J Biogeogr, 2012, 02755.x. 17. Gou ZH#, Wang X#, Wang W*.Evolution of neurotransmitter gamma-aminobutyric acid, glutamate and their receptors. Zool Res, 33 (E5−6): E75−E81. 18. Grazziotin FG, Zaher H, Murphy RW, Scrocchi G, Benavides MA, Zhang YP, Bonatto SL: Molecular phylogeny of the New World Dipsadidae (Serpentes: Colubroidea): a reappraisal. Cladistics, 2012, 28(5):437-459. 44 遗传资源与进化国家重点实验室 2012 年 度 报 告 19. Guo P, Liu Q, Xu Y, Jiang K, Hou M, Ding L, Pyron RA, Burbrink FT: Out of Asia: Natricine snakes support the Cenozoic Beringian Dispersal Hypothesis. Mol Phylogenet Evol, 2012, 63(3):825-833. 20. Han ZQ, Yanagimoto T, Zhang YP, Gao TX*. Phylogeography study of Ammodytespersonatus in Northwestern Pacific: Pleistocene isolation, temperature and current conducted secondary contact. PloS ONE, 2012, 7(5):e37425. 21. He JD#, Peng MS#, Quang HH, Dang KP, Trieu AV, Wu SF, Jin JQ, Murphy RW, Yao YG, Zhang YP*. Patrilineal Perspective on the Austronesian Diffusion in Mainland Southeast Asia. PloS ONE, 2012, 7(5). e36437. 22. He K#, Chen JH#, Gould GC#, Yamaguchi N, Ai HS, Wang YX, Zhang YP, Jiang XL*. An Estimation of Erinaceidae Phylogeny: A Combined Analysis Approach. PLoS ONE, 2012, 7(6): e39304. 23. He K, Hu NQ, Orkin JO, Nyein DT, Ma C, Xiao W, Fan PF, Jiang XL*. Molecular phylogeny and divergence time of Trachypithecus: with implications for the taxonomy of T. phayrei. 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Replicated associations of TNFAIP3, TNIP1 and ETS0 with systemic lupus erythematosus in a southwestern Chinese population. Arthritis Res Ther, 2012, 13: R186. 114. Zhou MJ, Xiao JH, Bian SN, Li YW, Niu LM, Hu HY, Wu WS, Murphy RW, Huang DW*. Molecular approaches identify known species, reveal cryptic species and verify host specificity of Chinese Philotrypesis (Hymenoptera: Pteromalidae). Mol Ecol Resour, 2012, 12(4):598-606. 115. Zhou WW, Wen Y, Fu J, Xu YB, Jin JQ, Ding L, Min MS, Che J*, Zhang YP*. Speciation in the Rana chensinensis complex and its relationship to the uplift of the Qinghai–Tibetan Plateau. Mol Ecol, 2012, 21: 960–973. 116. 杜丽娜， 杨君兴 *， Thomas VR*， 陈小勇 . David A. 中国特有腹足类 —— 螺蛳属 (Margarya) 的 系统发育学研究 . 科学通报 , 2012, 57(1):1-9. 117. 冯金梅，孙隽，文建凡 *. 核仁研究新进展 . 动物学研究 , 2012, 33(6):549-556. 118. 何锴， 邓可， 蒋学龙 *. 中国兽类鼩鼱科一新纪录—高氏缺齿鼩 . 动物学研究，2012, 33(5):542-544. 119. 李朝晖， 郭琨，郑萍 *. 哺乳动物卵巢生殖干细胞研究的现状与未来 . 动物学研究 , 2012, 33(6): 586590. 120. 王金焕，苏榕，苏伟婷，成诚，魏曙光，丁海华，段英，李生斌，佴文惠 *. 朱鹮细胞系的建立及其 生物学特性观察 . 动物学研究，2012, 33(6): 591-596. 121. 叶丹丹， 樊萌萌， 关琼， 陈红菊， 马占山 *. 宏基因组研究的生物信息学平台现状 . 动物学研究 , 2012, 33(6):574-585. 122. 张玉娟，文建凡 *.YidC/Oxa/Alb3 蛋白家族 . 生命的化学 , 2012, 32(4). 123. 仇国新，杨晓君 主编 . 云南会泽黑颈鹤国家级保护区 . 云南科技出版社 , 昆明 . 2012, 1-228. 49 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 ANNUAL REPORT 获 奖 Awards ２０１２ 王文，杨爽，周琦，蔡晶，李昕 ． 国家自然科学二等奖（年轻新基因起源和遗传进化的机制研究） ２０１２ Wen Wang, Shuang Yang, Qi Zhou, Jing Cai, Xin Li. The second prize for State Natural Science Award. ( Mechanism of origin and genetic evolution of newly evolved genes) ２０１２ 肖春杰，宿兵，郑冰蓉，石宏，胡卫红，俞海菁 ． 云南省自然科学一等奖（基因结构变异与人类进化 和疾病发生的分子机制研究） ２０１２ Chunjie Xiao, Bin Su, Binrong Zhen, Hong Shi, Weihong Hu, Haijing Yu. The first prize for Natural Science of Yunnan province. (The molecular mechanisms of gene structural variation in human evolution and disease) ２０１１ 杨君兴，潘晓赋，李再云，陈小勇，崔桂华，张汝斌 ． ２０１１ 年度云南省自然科学三等奖 （ 滇池金 线鲃的人工驯养繁殖研究 ， ２０１２ 年 ５ 月颁奖 ） ２０１１ Junxing Yang, Xiaofu Pan, Zaiyun Li, Xiaoyong Chen, Guihua Cui, Rubing Zhang. The third prize for Natural Science of Yunnan province 2011.(The the artificial domestication and breeding research of Dianchi Nemipterus, Awarded in May 2012). ２０１１ 司维，季维智，牛昱宇，郑萍，纪少珲，王宏，和协超，李亚辉 ． ２０１１ 年度云南省自然科学三等奖 （ 生 物医学实验动物精子超低温冷冻保存的研究 ， ２０１２ 年 ５ 月颁奖 ） ２０１１ Wei Si, Weizhi Ji, Yuyu Niu, Ping Zhen, Shaohui Ji, Hong Wang, Xiechao He, Yahui Li. The third prize for Natural Science of Yunnan province 2011.( Research on cryopreservation of sperm from Biomedical experimental animal, Awarded in May 2012) ２０１２ 石宏博士荣获 “中国科学院王宽诚西部学者突出贡献奖” ２０１２ Dr. Hong Shi was awarded as “The outstanding contribution prize in Wang kuancheng western scholars, Chinese academy of sciences (CAS)” ２０１２ 吴世芳荣获“中国科学院技术能手”称号 ２０１２ Shifang Wu was awarded “Technical Expert of CAS”. ２０１２ 吴东东博士学位论文获得中国科学院优秀博士学位论文奖，导师张亚平院士获中国科学院优秀研究生 指导教师称号 ２０１２ Dongdong Wu’s doctoral thesis won the Outstanding Doctoral Dissertation Award of CAS. Academician Yaping Zhang was awarded Outstanding Graduate Student’s Instructor of CAS. ２０１２ 刘振、李明获中科院院长奖优秀奖；蒋万胜获中国科学院地奥奖学金一等奖，冯金梅、倪婷获中国科 学院地奥奖学金二等奖； 叶志强、张雁峰、周炜帏获朱李月华优秀博士生奖学金；任彦栋荣获 ２０１２ 年度中科院大学生奖学金 ２０１２ Zhen Liu, Ming Li won “the Excellent Award of the President Scholarship of CAS”. Wansheng Jiang won the First Prize of “Diao Scholarship of CAS” and Jinmei Feng won the second Prize. Zhiqiang Ye, Yanfeng Zhang and Weiwei Zhou won “Zhu Li Yuehua Outstanding PhD Graduate Scholarship of CAS”. Yandong Ren won “Undergraduate Scholarship in 2012 of CAS”. 50 遗传资源与进化国家重点实验室 2012 年 度 报 告 研究生优秀论文奖 Outstanding Paper Awards for Graduate Students 一等奖 （４ 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 (4, IF ≥ 9): 彭 忆 Yi Peng （Molecular Biology and Evolution，IF9.872） 李 明 Ming Li （American Journal of Psychiatry，IF12.522） 赵 莉 Li Zhao （PLoS Genetics，IF9.532） 徐 讯 Xun Xu （Nature Biotechnology，IF31.1） 三等奖 （８ 篇，４ ≤影响因子 ＜６）: The third prize (8, 4 ≤ IF<6): 李 明 Ming Li（2 篇，Schizophrenia Research，IF4.458） 彭旻晟 Minshen Peng（BMC Biology，IF5.64） 彭旻晟 Minshen Peng（BMC Evolutionary Biology，IF4.29） 叶志强 Zhiqiang Ye（BMC Evolutionary Biology，IF4.29） 李 明 Ming Li（The World Journal of Biological Psychiatry，IF5.564） 李杰晶 Jiejing Li（PLoS ONE，IF4.411） 刘 振 Zhen Liu（PLoS ONE，IF4.411） 51 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 ANNUAL REPORT 大事记 （1）2012 年 2 月 23 日，实验室组织召 开了国家重点实验室专项经费审计总结 分析会。 The meeting to analyze the audit results of State Key Laboratory was held on Feburary 23, 2012. Major Events （2）2012 年 5 月 19 日，实验室参与昆明动物所第八届“公 众科学日”活动。活动中，实验室 2 位科技人员作了科普 报告，各研究组还对外开放参观。 The lab participated in the eighth “Public Science Day” of Kunming Institute of Zoology on May19,2012. Two staff scientists gave talks and the lab was open to the public to visit. （3）2012 年 5 月 17-24 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 6 天的精彩授课。 On May17-24,2012, Prof. David Irwin, a well-known expert on molecular evolution from the University of Toronto, Canada, was invited to the lab and made ​​a series of lectures to graduate students. （4）2012 年 7 月 25 日，实验室举办了 2012 年研究生 Poster 比赛。 The 2012 Graduates’ Poster Competition of the lab was held on July 25, 2012. 52 遗传资源与进化国家重点实验室 2012 年 度 报 告 （5） 2012 年 8 月 17 日，实验室第二届学术委员会第一次会议在昆明召开。 The first meeting of the second academic committee of the lab was held in Kunming on August 17, 2012. （6）2012 年 8 月 18-20 日，实验室在昆明主办“遗传发育与进化”国际研讨会暨学科发展战略研究研讨会 On August 18-20, 2012, the International Symposium on “Genetics, Development and Evolution” and Discipline Developmental Strategic Meeting was held by the lab in Kunming. （7）2012 年 9 月，实验室经过征集、评选，确 定了实验室室徽。 In September 2012, the logo of the lab was selected. Developmental Strategic Meeting was held by the lab in Kunming. 53 （8）2012 年 9 月 30-10 月 2 日，实验室与中国灵 长类协会在云南景东联合主办“中国灵长类专家组 2012 年会暨黑冠长臂猿保护国际研讨会。 The 2012 Annual Meeting of the China Primate Specilist Group (CPSG) and the International Symposium on the Black Crested Gibbon Protection was held on September 30 to October 2, 2012, in Jingdong County organized by the lab and CPSG. State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 ANNUAL REPORT （9）2012 年 10 月 26-27 日，实验室在昆明召开了 2012 年学术交流年会。 The 2012 Annual Meeting of the key lab was held in Kunming, on October 26 to 27,2012. （10）2012 年 11 月 11-13 日，实验室召开 2012 年 PI 战略研讨会。 The strategic meeting of the key lab was held on November 11 to 13, 2012. （11）2012 年 11 月，由车静研究员负责的“两 栖爬行类多样性与进化研究组”加入实验室， 成为第 15 个研究组。 The 15th research group on “The diversity and evolution of amphibians and reptiles”, headed by Prof. Jing Che, joined the key lab in November, 2012. （12）2012 年 12 月 3-5 日，上海生科院计算生物 学研究所李海鹏研究员受邀来实验室为研究生教 授“群体遗传学”课程。 Between December 3 to 5, 2012, Prof. Haipeng Li from CAS-MPG Partner Institute for Computational Biology, CAS, was invited to give a 3-day course on population genetics to the graduate students. 54 遗传资源与进化国家重点实验室 2012 年 度 报 告 开放课题 Open Projects 课题编号 负责人 GREKF12-01 王 GREKF12-02 张佳进 讲师 云南农业大学 GREKF12-03 张德礼 教授 西北农林科技大学 GREKF12-04 边 巴 副教授 西藏大学 藏族人群对高原低氧适应的 关键候选基因 EPAS1 的功能研究 GREKF12-05 石 宇 助理 重庆医科大学 研究员 附属儿童医院 Wnt4 参与原肠期脊椎 动物胚胎发育分子机制研究 GREKF12-06 范朋飞 教授 大理学院 无量山菲氏叶猴的食性 和群体大小的季节性变化 11.54 万 GREKF12-07 孙国政 工程师 国家林业局自然保 护区及野生动植 物西南监测中心 黑冠长臂猿食物可获得性 季节性变化及行为生态适应 11.54 万 GREKF12-08 魏 强 讲师 西北农林科技大学 小鼠卵巢生殖 干细胞分子标记的筛选 11.54 万 GREKF12-09 吴 韬 副教授 昆明医学院 第一附属医院 胆石症相关人体 胆道微生物组及其起源研究 11.54 万 GREKF12-10 耿嘉蔚 副主任 医师 云南省第一人民医院 人体肠道微生物组 空间分布模式研究 11.54 万 GREKF12-11 陈万群 副教授 暨南大学医学院 冠心病相关遗传易感基因的研究 11.54 万 GREKF12-12 李 慧 副研究员 GREKF12-13 刘 强 讲师 璐 职称 助理 研究员 负责人单位 云南大学 课题名称 青藏高原家犬缺氧信号 通路基因的适应进化研究 基因组数据库 及其可视化平台构建 资助经费 11.54 万 11.54 万 高致病性猪蓝耳病病毒感染猪肺 泡 II 型上皮细胞过程中 miRNA 分子演化网络的系统生物学分析 中科院沈阳应用 长白山原始森林土壤 生态研究所 微生物多样性资源和进化初探 西南林业大学 基于 GIS 手段的 黑颈鹤空间行为研究 55 11.54 万 11.54 万 11.54 万 11.54 万 11.54 万 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 ANNUAL REPORT 专家学术报告 Invited Lectures 报告人：石磊教授 单 位：云南财经大学 时 间： 2012.1.10 题 目： 计算统计生物 报告人：龙继蓉博士 单 位：Vanderbilt University Medical Center 时 间： 2012.1.10 题 目：Genetic Epidemiology Study of Breast Cancer in Asia 报告人：Dr. David Cannatella 单 位：University of Texas at Austin 时 间：2012.5.30 题 目：Evolution and historical biogeography of Poison Frogs in South America 报告人：Dr. Theodore J. Papenfuss 单 位：University of California at Berkeley 时 间： 2012.5.30 题 目： Population Declines of Salam -anders in Guatemala and Mexico Between the 1970s and Now 报告人：许进超教授 单 位：Pennsylvania State University 时 间： 2012.7.4 题 目： Synergy Between Computational Mathematics and Computational Biology 报告人：周琦博士 单 位：University of California, Berkeley 时 间： 2012.7.11 题 目：Sex-specific adaptation drives early sex chromosome evolution in Drosophila. 报告人：符建教授 单 位：浙江大学 时 间： 2012.7.18 题 目：高性能 GPU 计算应用于计算 生物学的关键问题 报告人： Prof. Suchinda Malaivijitnond 单 位： Chulalongkorn University, Tailand 时 间： 2012.8.22 题 目：Boundary zone between Northern and Southern Pig-tailed macaqu -es and their morphological differences 报告人： Prof. Yuzuru Hamada 单 位：Kyoto University, Japan 时 间： 2012.8.22 题 目：Variability of tail length and caudal vertebral composition in the hybrids of the Japanese macaque (Macaca fuscata) and the Taiwanese macaque (M. cyclopis): Implications for the evolution of macaque 56 遗传资源与进化国家重点实验室 2012 年 度 报 告 报告人：Prof. Richard Durbin 单 位：The Wellcome Trust Sanger Institute 时 间： 2012.8.28 题 目：Progress and opportunities in human population genome sequencing 报告人：Dr. Junjian Chen 单 位：McGill University Department of Surgery ,Canada 时 间： 2012.9.14 题 目：Novel molecular markers and platforms in early cancer detection. 报告人： Prof. Mukesh Kumar Chalise 单 位：Tribhuvan University, Nepal 时 间： 2012.9.28 题 目：Advances on Mammal Studies in Nepal 报告人：Dr. Ni Hong 单 位：DUKE-NUS Graduate Medical School, National University of Singapore 时 间： 2012.10.17 题 目：Fish haploid embryonic stem (ES) and semicloning 报告人：Prof. Dezhong Joshua Liao 单 位：Hormel Institute, University of Minnesota 时 间：2012.10.17 题 目：My challenge to the mainstr -eams of oncology and tumor supressor genes 报告人：韩珉教授 单 位：University of Colorado 时 间： 2012.11.7 题 目：存在就是合理的 — 一种无人 问津的脂肪酸在动物生长发育和觅食 行为中所拥有的巨大功能 报告人：夏雪山 教授 单 位：昆明理工大学 时 间： 2012.11.23 题 目：流行病的进化生物学研究 报告人：Prof. Axel Krings 单 位：University of Idaho, USA 时 间： 2012.12.3 题 目：Petri Nets and their Applications in Computation Biology and System Biology 57 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 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 文 张亚平 杨君兴 杨晓君 佴文惠 郑 萍 宿 兵 黄京飞 蒋学龙 琦 马云飞 牛昱宇 王 王国栋 王金焕 王文智 王华伟 王晓阳 王运宇 司 维 冯 庆 石 石 磊 任国鹏 任海清 许绍斌 刘 衡 刘立娜 刘鲁明 刘淑伟 纪少珲 吕永青 朱春玲 祁学斌 吴 飞 吴东东 吴世芳 孙艳波 何 季吟秋 闵 锐 余 蕊 余国华 张 张志刚 李功华 李 昕 李学燕 李桂梅 李朝翠 杨 杨 爽 杨鹏标 杨春燕 杨春先 杨 梅 杨双娟 杨利琴 苏伟婷 陈 睿 陈小勇 陈 兵 陈永昌 和协超 郑兰平 金洁琼 赵若苹 周 鑫 周炜帏 禹一川 饶定齐 施林明 相 辉 郝军军 唐 嘉 高 黄 蓓 韩树标 蒋 珂 董 锋 董 扬 谢海兵 舒树森 彭 忆 谭 韬 廖爱文 李家堂 李 艳 季林丹 周传江 黄 王伟营 冯金梅 石 磊 孙正华 孙艳波 张雁峰 李杰晶 陈 陈 鹏 周炜帏 贺军栋 郝晓丹 彭 彭应梅 Douglas W Yu 车 静 施 鹏 工作人员 于 宏 云 彭旻晟 林 慧 静 晖 潘晓赋 博士后 刘 斌 松 ２０１２ 年毕业研究生 博士生 忆 睿 蒋万胜 58 遗传资源与进化国家重点实验室 2012 年 度 报 告 硕士生 马云飞 安盟茵 邹 勇 罗伟雄 曹向宇 程菁菁 鲍学群 张文广 李贵生 徐 进 Nguyen Ngoc Sang Adeola Adeniyi Charles 马鹏程 王 王晓爱 王晓雄 王 刘 杰 刘 振 向 坤 吕 倪 婷 徐同美 茉 王姝妍 王荣兴 维 王鑫轶 叶志强 刘 刘 晖 刘鹤群 刘耀文 向志丹 俊 孙 健 江世友 何大健 张业胜 张 田 张晓明 张 斌 张 煦 李玉春 李 李毓劲 杨召辉 杨立新 杨军效 杨相彩 杨贺川 汪德勇 陈中正 周中银 胡玲玲 胡迺清 赵 博 倪庆永 徐 徐 桑伟建 袁智勇 曹 雪 梁 璐 程耀霆 董好岩 董 管振华 颜 芳 万 韬 寸益贤 王文敏 王晓磊 王 王 毅 卢广义 史妮妮 叶青青 叶凌群 宁文鹤 田娇阳 伊婷婷 关 刘杰伟 刘菲曾 刘 熙 汤济鑫 祁飞燕 许东明 吴 宋卢挺 张 凯 张景娟 李 权 李连伟 李欣磊 李 婷 李朝辉 李 杨 阳 杨坤凤 杨松霖 杨晏冬 杨晨雪 沈文菁 肖富辉 邵 勇 陈 垒 季 爽 林 罗 苟志恒 范 飞 郑智中 奎 玲 姚友旭 赵亚鹏 赵婷怡 夏 季 徐海波 涂小龙 秦 涛 郭 逯 翔 黄翠萍 曾 琳 曾燕妮 程 城 程菁菁 谢建新 谢钢琴 韩徐曼 廖志鹏 樊萌萌 霍永霞 博士后 任立晨 在读研究生 博士生 丹 讯 锋 佳 明 硕士生 琼 焕 戴 然 59 筱 强 越 杰 琨 State Key Laboratory of Genetic Resources and Evolution》 》 》 》 》 ■■■ 2012 ANNUAL REPORT Personnel Principal Investigators Douglas W Yu Zhanshan Ma Qingpeng Kong Jianfan Wen Bingyu Mao Wen Wang Jing Che Yaping Zhang Junxing Yang Xiaojun Yang Wenhui Nie Ping Zheng Peng Shi Bing Su Jingfei Huang Xuelong Jiang Qi Yu Yunfei Ma Yuyu Niu Lin Wang Guodong Wang Jinhuan Wang Wenzhi Wang Huawei Wang Xiaoyang Wang Yunyu Wang Wei Si Qing Feng Hong Shi Lei Shi Guopeng Ren Haiqing Ren Shaobin Xu Heng Liu Lina Liu Luming Liu Suwei Liu Saohui Ji Yongqin Lv Chunling Zhu Xuebin Qi Fei Wu Dongdong Wu Shifang Wu Yanbo Shun Jing He Yingqiu Ji Rui Min Rui Yu Guohua Yu Hui Zhang Zhigang Zhang Gonghua Li Xin Li Xueyan Li Guimei Li Chaocui Li Hui Yang Shuang Yang Pengbiao Yang Chunyan Yang Chunxian Yang Mei Yang Shuangjuan Yang Liqing Yang Weiting Su Rui Chen Xiaoyong Chen Bin Chen Yongchang Chen Xiechao He Lanping Zheng Jieqiong Jin Ruoping Zhao Xin Zhou Weiwei Zhou Yichuan Yu Dingqi Rao Linming Shi Hui Xiang Junjun Hao Jia Tang Yun Gao Bei Huang Shubiao Han Ke Jiang Feng Dong Yang Dong Minsheng Peng Haibing Xie Shusen Shu Yi Peng Tao Tan Aiwen Liao Jiatang Li Yan Li Lindan Ji Chuanjiang Zhou Song Huang Staff Xiaofu Pan Postdoctors Bin Liu Students Graduated in 2012 Dorctors Weiyin Wang Jinmei Feng Lei Shi Zhenghua Shun Yanbo Shun Yanfeng Zhang Jiejing Zhang Rui Chen Peng Chen Weiwei Zhou Jundong He Xiaodan He Yi Peng Yingmei Peng Wansheng Jiang 60 遗传资源与进化国家重点实验室 2012 年 度 报 告 Masters Yunfei Ma Mengyin An Yong Zhou Weixiong Luo Ting Ni Tongmei Xu Xiangyu Cao Jingjing Cheng Xuequn Bao Wenguang Zhang Guisheng Li Jin Xu Pengcheng Ma Mo Wang Shuyan Wang Rongxin Wang Postdoctors Lichen Ren Graduate students Doctors Nguyen Ngoc Sang Adeola Adeniyi Charles Xiaoai Wang Xiaoxiong Wang Wei Wang Xinyi Wang Zhiqiang Ye Jia Liu Jie Liu Zhen Liu Hui Liu Hequn Liu Yaowen Liu Zhidan Xiang Kun Xiang Jun Lv Jian Shun Shiyou Jiang Dajian He Yesheng Zhang Tian Zhang Xiaoming Zhang Bin Zhang Xu Zhang Yuchun Li Ming Li Yujin Li Zhaohui Yang Lixin Yang Junxiao Yang Xiangcai Yang Hechuan Yang Deyong Wang Zhongzheng Chen Zhongyin Zhou Lingling Hu Naiqing Hu Bo Zhao Qingyong Ni Dan Xu Xun Xu Weijian Shang Zhiyong Yuan Xue Cao Lu Liang Yaoting Cheng Haoyan Dong Feng Dong Zhenhua Guan Fang Yan Yi Peng Yingmei Peng Zhenhua Guan Fang Yan Tao Wan Yixian Chun Wenming Wang Xiaolei Wang Xiao Wang Yi Wang Guangyi Lu Nini Shi QingqingYe Lingqun Ye Wenhe Ning Jiaoyang Tian Tingting Yi Qiong Guan Jiewei Liu Feiceng Liu Xi Liu Jixin Tang Feiyan Qi Dongming Xu Huan Wu Luting Song Kai Zhang Jingjuan Zhang Quan Li Lianwei Li Xinlei Li Ting Li Zhaohui Li Yue Li Yang Yang Kunfeng Yang Songlin Yang Yandong Yang Chenxue Yang Wenjing Shen Fuhui Xiao Yong Zhou Lei Chen Shuang Ji Qiang Lin Jie Luo Zhiheng Gou Fei Fan Zhizhong Zhen Ling Kui Youxu Yao Yapeng Zhao Tingyi Zhao Ji Xia Haibo Xu Xiaolong Tu Tao Qing Kun Guo Xiang Lu Cuiping Huang Lin Zeng Yanni Zeng Cheng Cheng Jingjing Cheng Jianxin Xie Gangqin Xie Xuman Han Zhipeng Liao Mengmeng Fan Yongxia Huo Masters Ran Dai 61