题目： Genomic and evolutionary insights from molecular clocks 报告人： Simon Ho 教授 School of Life and Environmental Sciences, University of Sydney 时间： 2016年10月26日15:30 地 点： 中国科学院动物研究所 会议室： C101 联系人： 罗阿蓉（luoar@ioz.ac.cn）、朱朝东（zhucd@ioz.ac.cn） Molecular clocks are models that describe variation in rates of genetic change among organisms, allowing us to infer evolutionary timescales using phylogenetic analyses of DNAsequence data. A wide variety of clock models are now available, including those that allow rates to vary across branches in the tree. Over the past five decades, molecular clocks have been pivotal in resolving the timescale of the Tree of Life. Genome-scale data are now being produced at an astonishing rate, opening up exciting prospects for gaining detailed insights into the molecular evolutionary process. They also present anopportunity for refining our estimates of evolutionary timescales. I provide an overview of some of the approaches that have been used to estimate evolutionarytimescales from genome-scale data, drawing on several recent examples from mywork. I also describe how a phylogenetic approach can be used to provide insight into molecular evolutionary dynamics, with particular reference to the “pacemaker” models of genome evolution. About the speaker Simon is a Professor of Molecular Evolution at the University of Sydney. He received his PhD in 2006 (University of Oxford), then did postdoctoral work at Oxford and the Australian National University. Simon joined the University of Sydney in 2010, where he now leads the Molecular Ecology, Evolution, and Phylogenetics Lab. His research interests include phylogenetic methods, evolutionary models, and molecular clocks. The focus of Simon’s recent work has been on describing patterns of evolutionary rate variation across genomes and on phylogenomic estimation of evolutionary timescales. http://sydney.edu.au/science/people/simon.ho.php 看看Simon教授是哪位帅哥？ （图片来自：http://www.shsobu.org.au）
Systems biology institutes EUROPE Biosystems Informatics Institute, Newcastle upon Tyne, UK http://www.biiuk.com Centre for Modelling and Simulation in the Biosciences (BIOMS), University of Heidelberg, Heidelberg, Germany http://www.bioms.de Centre for Systems Biology, Trinity College, Dublin, Ireland http://www.systemsbiologyireland.org Computational Medicine, Linköping University Karolinska Institute, Linköping Stockholm, Sweden http://www.computationalmedicine.se Computational Neurobiology Group, European Bioinformatics Institute, Hinxton, UK http://www.ebi.ac.uk/compneur-srv Computational Systems Biology, University of Edinburgh, Edinburgh, UK http://www.bioinformatics.ed.ac.uk/csb Computational Systems Biology, University of Sheffield, Sheffield, UK http://www.shef.ac.uk/dcs/research/groups/compbio Computational Systems Biology of Cell Signalling (COSBICS), Europe http://www.sbi.uni-rostock.de/cosbics/index.html Department of Plant Systems Biology, University of Ghent, Ghent, Belgium http://www.psb.ugent.be European Molecular Biology Laboratory (EMBL) - Cell Biology and Biophysics Unit, Heidelberg, Germany http://www-db.embl.de/jss/EmblGroupsHD/p_9.html EMBL - Structural and Computational Biology, Heidelberg, Germany http://www-db.embl.de/jss/EmblGroupsHD/p_7.html EMBL/Centre for Genomic Regulation (CRG) Research Unit in Systems Biology, Barcelona, Spain This is in progress. http://www.embl.org/aboutus/news/press/2006/07sept06 European Systems Biology Initiative combating complex diseases (ESBIC-D), Europe http://pybios.molgen.mpg.de/ESBIC-D/index_html Freiburg Center for Data Analysis and Modeling (FDM), Albert-Ludwigs-Universität Freiburg, Freiburg, Germany http://www.fdm.uni-freiburg.de/groups/timeseries/biocs/index.php HepatoSys, Systems biology of hepatocytes, Germany http://www.systembiologie.de/de/index.html Institute for Atomic and Molecular Physics (AMOLF), Amsterdam, the Netherlands http://www.amolf.nl/index.html Institute of Molecular Systems Biology, Swiss Federal Institute of Technology Zurich, Zurich, Switzerland http://www.imsb.ethz.ch Intelligent Bioinformatics Systems (iBioS), The German Cancer Research Institute, Heidelberg, Germany http://www.dkfz-heidelberg.de/tbi Interdisciplinary Research Institute, Institut de Biologie de Lille, Lille, France http://iri.ibl.fr Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, UK http://www.mcisb.org Max-Plank Institute for Physics of Complex Systems, Dresden, Germany http://www.mpipks-dresden.mpg.de/pages/institut/frames_institut.html Physical Chemistry 'Curie' - UMR 168 CNRS/Institute Curie, Paris, France http://www.curie.fr/recherche/themes/detail_unites.cfm/lang/_gb/id/45.htm Systems Biology, Hamilton Institute, National University of Ireland, Maynooth, Ireland http://www.hamilton.ie/SystemsBiology Systems Biology, University of Stuttgart, Stuttgart, Germany http://www.sysbio.de Systems Biology and Bioinformatics, Academy of Finland, Finland http://www.aka.fi/sysbio SystemsX, The Swiss Initiative in Systems Biology, ETH Zurich, University of Basel and University of Zurich, Switzerland http://www.systemsx.ch/M1_WhatIsSystemsX?menu_id=90 The Quantitative Analysis of Molecular and Cellular Biosystems Center (BIOQUANT), University of Heidelberg , Heidelberg, Germany To open in February 2007. http://www.bioquant.uni-heidelberg.de/proposal.php Yeast Systems Biology Network (YSBN), Europe http://www.ysbn.org top of page USA AND CANADA Bio-X Program, Stanford University, Stanford, CA, USA http://biox.stanford.edu California Institute for Quantitative Biomedical Research, CA, USA http://www.qb3.org Cell Signaling Team, Los Alamos National Laboratory, Los Alamos, NM, USA http://bionetgen.lanl.gov Center for Cell Decision Processes, Massachusetts Institute of Technology, Cambridge, MA, USA http://www.cdpcenter.org Center for Cell Dynamics, University of Washington Friday Harbor Laboratories, Friday Harbor, WA, USA http://raven.zoology.washington.edu/celldynamics Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, ME, USA http://www.genomedynamics.org Center for Modeling Integrated Metabolic Systems, Case Western Reserve University, Cleveland, OH, USA http://www.csuohio.edu/mims/contact.htm Center for Modular Biology, Harvard University, Cambridge, MA, USA http://www.cgr.harvard.edu/cmb Center for Nonlinear Dynamics in Physiology and Medicine, McGill University, Montreal, Canada http://www.cnd.mcgill.ca Center for Plant Cell Biology, University of California, Riverside, CA, USA http://www.cepceb.ucr.edu Center for Quantitative Biology, Princeton University, Princeton, NJ, USA http://quantbio.princeton.edu Center for Systems Biology, Institute for Systems Biology, Seattle, WA, USA http://www.systemsbiology.org Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA http://www.utsouthwestern.edu/GCSB Center for Systems Synthetic Biology, University of Texas, Austin, TX, USA http://cssb.icmb.utexas.edu Computational Systems Biology, Keck Institute, Claremont, CA, USA http://sbw.kgi.edu/ Computational Systems Biology Group, Carnegie Mellon University, University of Pittsburgh, University of West Florida Institute for Human and Machine Cognition, USA http://www.phil.cmu.edu/projects/genegroup Department of Systems Biology, Harvard Medical School, Boston, MA, USA http://sysbio.med.harvard.edu/faculty/index.html Kaern Dynamical Systems Biology, University of Ottawa, Ottawa, Canada http://www.sysbiolab.uottawa.ca Molecular Sciences Institute, Berkeley, CA, USA http://www.molsci.org Ottawa Institute of Systems Biology, Ottawa, Canada http://mededu.med.uottawa.ca/oisb Systems Biology, Pacific Northwest National Laboratory, Richland, WA, USA http://www.sysbio.org Systems Biology Research Group, University of California San Diego, San Diego, CA, USA http://systemsbiology.ucsd.edu top of page ASIA Cellular Systems Biology Team, RIKEN Genomic Sciences Center (GSC), Kanagawa, Japan http://csb.gsc.riken.jp Chinese Academy of Science (CAS)/Max-Planck-Gesellschaft (MPG) Partner Institute for Computational Biology, Shanghai, China http://www.icb.ac.cn/snews3.htm Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan http://www.cbrc.jp/index.eng.html Department of Computational Biology, University of Tokyo, Tokyo, Japan http://www.cb.k.u-tokyo.ac.jp/cb Genome Institute of Singapore, Singapore http://www.gis.a-star.edu.sg/internet/site/ Kitano Symbiotic Systems Project, Tokyo, Japan http://www.symbio.jst.go.jp/symbio2/index.html Laboratory for Bioinformatics, Keio University, Kanagawa, Japan http://www.bioinfo.sfc.keio.ac.jp Laboratory for Molecular Cell Network, Waseda University, Tokyo, Japan http://www.f.waseda.jp/hideo-iwasaki Laboratory on Signal Transduction, Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan http://www.bi.s.u-tokyo.ac.jp/kuroda-lab National Centre for Biological Sciences, Bangalore, India http://www.ncbs.res.in Okinawa Institute of Science and Technology, Okinawa, Japan http://www.oist.jp/index.html RIKEN Genomic Sciences Center, Yokohama, Japan http://www.gsc.riken.go.jp/indexE.html Systems Biology Laboratory, Seoul National University, Seoul, Korea http://systemsbiology.snu.ac.kr/index.html Systems Biology Laboratory of Mammalian Circadian Clocks, Center for Developmental Biology, RIKEN, Kobe, Japan http://www.cdb.riken.jp/en/index.html?CDBdirect#02_research/ 0202_creative20.html The Systems Biology Institute, Tokyo, Japan http://sbi.jp REST OF THE WORLD The Kahn Family Research Center for Systems Biology of the Human Cell, The Weizmann Institute of Science, Rehovot, Israel http://www.weizmann.ac.il/centers/system_biology.html Some important evolutionary system biology Labs Alon, Uri http://www.weizmann.ac.il/mcb/UriAlon/ Barkai, Naama http://barkai-serv.weizmann.ac.il/GroupPage/ Bergman, Aviv http://www.einstein.yu.edu/bergman/index.html Borenstein, Elhanan http://elbo.gs.washington.edu/ Fong, Stephen http://www.engineering.vcu.edu/fong-lab/ Foster, Kevin http://www.people.fas.harvard.edu/~kfoster/index.html Hurst, Laurence http://www.bath.ac.uk/bio-sci/research/profiles/hurst-l.html Jordan, King http://esbg.biology.gatech.edu/lab/ Kishony, Roy http://kishony.med.harvard.edu/ Landry, Christian ht tp://www.bio.ulaval.ca/landrylab/ Lehner, Ben http://www.crg.es/ben_lehner Lercher, Martin http://www.cs.uni-duesseldorf.de/AG/BI/Deutsch/Englisch Loewe, Laurence http://evolution.ws/people/loewe Maere, Steven http://www.psb.ugent.be/esb/ESB/Home.html MacLean, Craig http://www.zoo.ox.ac.uk/staff/academics/maclean_c.htm Moses, Alan http://www.moseslab.csb.utoronto.ca/research.html Palsson, Bernhard http://gcrg.ucsd.edu/ Pál, Csaba http://www.brc.hu/sysbiol Papp, Balázs http://www.brc.hu/sysbiol Peisajovich, Sergio http://labs.csb.utoronto.ca/peisajovich/ Ruppin, Eytan http://cns.cs.tau.ac.il/ Segrè, Daniel http://prelude.bu.edu/ Siegal, Mark http://homepages.nyu.edu/~ms4131/ Soyer, Orkun http://osslab.lifesci.warwick.ac.uk/ Tawfik, Dan http://www.weizmann.ac.il/Biological_Chemistry/scientist/Tawfik/ Van de Peer, Yves http://bioinformatics.psb.ugent.be/ Wagner, Andreas http://www.bioc.uzh.ch/wagner/ Wittkopp, Patricia http://www.umich.edu/~pwlab/ Yin, John http://www.engr.wisc.edu/che/faculty/yin_john.html
最新影响因子发布 Wiley进化生物学类期刊居分类榜首 欢迎阅读这些优秀期刊 影响因子：6.091 影响因子：5.84 影响因子：5.626 影响因子：4.659 热门文章： On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature 热门文章： The biogeography of mitochondrial and nuclear discordance in animals 热门文章： An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding 热门文章： The QTN program and the alleles that matter for evolution: all that's gold does not glitter ! 影响因子：4.569 影响因子：3.483 影响因子：2.684 影响因子：2.535 热门文章： Genetic erosion impedes adaptive responses to stressful environments 热门文章： Sex, outcrossing and mating types: unsolved questions in fungi and beyond 热门文章： Hox gene expression in the harvestman Phalangium opilio reveals divergent patterning of the chelicerate opisthosoma 热门文章： Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement
10月1日早晨收到Scientific Reports杂志邮件，被邀请参加生态学和进化生物学编委会。傍晚，收到第二封邮件和相关文档，填写并提交了5个专业最相关的关键词和注册信息。10月3日下午，收到编辑部来信安排了第一篇论文任务。我通过PubMed和ScienceDirect等，找到了5个相关同行，并通过系统发送了审稿邀请信。5分钟之内，一个同行就在线回复同意审稿。10月6日，3个同行同意评审稿件。系统自动给其他同行发信，说明已经找到足够的评委（3个）。 Scientific Reports（http://www.natureasia.com/zh-cn/srep/） 2011年创刊，多学科、在线发表、开放获取，内容覆盖自然科学的各个领域。和PLoS ONE（http://www.plosone.org/）一样，该杂志对投稿的论文重要性并不设最低门槛，而是由评审专家判断技术方案的可靠性。同时，该杂志和Journal of the Royal Society Interface（ http://rsif.royalsocietypublishing.org/） 一样鼓励多学科交叉。今年，该杂志影响因子上升到5.078，并成为多学科交叉领域前5。 多学科杂志列表 Scientific Reports杂志排名 国内自然科学工作者队伍较大。随着国家对科技经费投入的加大、科技人员经费越来越规范地用在研究工作上，产出成果必将越来越多。自然科学领域多个期刊目前已经以英文为刊用语言，既可以吸纳国内优秀成果，也可以发表国外一些成果。部分期刊已经进入SCI源期刊行列，影响在逐渐增长。这些期刊在短期时间，在科技界，乃至商业上均获得了巨大的成功，其经验值得借鉴。 Scientific Reports涵盖多个领域，每个领域都有一个编委指导委员会成员主持。生态学和进化生物学领域现在的召集人是University College London的Georgina Mace教授。 编委开始的任期一般两年，主要职责包括： 1、评估稿件是否应该送审； 2、安排稿件的专家评审并作最终编辑决定：接收、退稿或者重投； 3、支持并推动Scientific Reports的发展。 Scientific Reports编委手册 Scientific Reports等杂志鼓励科学家自由探索，通过开放获取加快科学成果分享和知识传播，得到了科技工作人员的广泛认同和支持。我希望通过这个平台，和来自不同国家的同领域专家和投稿人合作，了解并尽力掌握生态学和进化生物学方面的最新进展。同时，我也期待通过这个平台，本学科领域的专家 有更多 发布团队成果和提升科技水平的机会。 现在杂志主页上的编委信息表明，英国科学家有32位，美国10位，中国13位（包括香港4位）。 荷兰：2 美国：10 英国：32 加拿大：3 澳大利亚：5 瑞典：2 中国：13 日本：7 瑞士：2 芬兰：1 斐济：1 意大利：3 葡萄牙：3 法国：3 德国：3 比利时：2 ECOLOGY AND EVOLUTIONARY BIOLOGY Duur Aanen Wageningen University, Netherlands J. Marty Anderies Arizona State University, USA Paul Barrett Natural History Museum, UK Julia K. Baum University of Victoria, Canada Robin Beck University of New South Wales, Australia Andrea Belgrano Swedish University of Agricultural Sciences James Bullock Centre for Ecology Hydrology, United Kingdom Kathleen Campbell University of Auckland, New Zealand Daniele Canestrelli Tuscia University, Italy Susana Carvalho King Abdullah University of Science and Technology, Saudi Arabia Chengrong Chen Griffith University, Australia Andrew Clarke University of Warwick, UK Ben Collen University College London, UK Filipe Costa Universidade do Minho, Portugal Marina R. Cunha University of Aveiro, Portugal Andrew A. Cunningham ZSL Institute of Zoology, UK Darren Curnoe University of New South Wales, Australia Junhu Dai Institute of Geographical Sciences and Natural Resources Research Chinese Academy of Sciences, China Roberto Danovaro Università Politecnica delle Marche, Italy Mark de Bruyn Bangor University, UK Steven Degraer Royal Belgian Institute of Natural Sciences, Belgium Zhiqun (Daniel) Deng Pacific Northwest National Laboratory, USA Nicolas Desneux French National Institute for Agricultural Research (INRA), France Michael Doebeli University of British Columbia, Canada Gareth Dyke University of Southampton, UK Katrina Edwards University of Southern California, USA Felix Eigenbrod University of Southampton, UK Matthew Fisher Imperial College London, UK Toby Gardner University of Cambridge, UK Robbie Girling The Organic Research Centre, UK Stanislav Gorb Kiel University, Germany Frances Gulland The Marine Mammal Center, USA Geoff M Gurr Charles Sturt University, Australia Xavier Harrison ZSL Institute of Zoology, UK Simon I. Hay University of Oxford, UK Mariella Herberstein Macquarie University, Australia Satoshi Hirata Kyoto University, Japan Michael Hofreiter University of York, UK Michael A. Huffman Kyoto University, Japan Richard Inger University of Exeter, UK Nick Kamenos University of Glasgow, UK Michael Knapp University of Bangor, UK Judith Korb Universitat Regensburg, Germany Artem Kouchinsky Swedish Museum of Natural History, Sweden Kevin Laland University of St Andrews, UK Fu-Min Lei Institute of Zoology, Chinese Academy of Sciences, China Owen Lewis University of Oxford, UK Dejun Li Chinese Academy of Sciences, China Linghao Li Institute of Botany, Chinese Academy of Sciences, China Wen-Hsiung Li University of Chicago, USA Adrian Lister Natural History Museum, UK Xingzhong Liu State Key Laboratory of Mycology, China Mark Mainwaring Lancaster University, UK Mark Maslin University College London, UK Alice Mauchline University of Reading, UK Kenneth Mei Yee Leung University of Hong Kong, Hong Kong Alexandru Milcu Imperial College London, UK Yolanda Morbey Western Science, Canada Akira Mori Yokohama National University, Japan Tadamichi Morisaka Tokai University, Japan Iain Morley University of Oxford, UK Pascal Niklaus University of Zürich, Switzerland Shuli Niu Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China Alf Norkko University of Helsinki,Finland Jingmai O'Connor Institute of Vertebrate Paleontology and Paleoanthropology, China Andrew Parker Natural History Museum, UK Dolores R. Piperno Smithsonian Tropical Research Institute, USA David Raichlen University of Arizona, USA Emily Rayfield University of Bristol, UK Andy Reynolds Rothamsted Research, UK Shane Richards Durham University, UK Ciro Rico University of the South Pacific, Fiji J Murray Roberts Heriot Watt University, UK Weiguo Sang Institute of Botany, Chinese Academy of Sciences, China Michele Scardi University of Rome Tor Vergata, Italy Ester A. Serrao University of the Algarve, Portugal Aaron Shafer Uppsala University, Sweden Martin Solan University of Southampton, UK Jay Stock University of Cambridge, UK Christopher Stojanowski Arizona State University, USA Koichi Takahashi Shinshu University, Japan Graham Taylor University of Oxford, UK Elisa Thebault Ecole Normale Supérieure, France Arne Traulsen Max Planck Institute for Evolutionary Biology, Germany Jasper van Ruijven Wageningen University, Netherlands Stefan Van Dongen Antwerp University, Belgium Jessica Ware Rutgers University, USA Geoff Williams University of Bern, Switzerland Rudolf Wu University of Hong Kong, Hong Kong Jianyang Xia University of Oklahoma, USA Akiyoshi Yamada Shinshu University, Japan Jin Yoshimura Shizuoka University, Japan Xuhui Zhou Fudan University, China Top of page
生物有很多学科，比如发育，细胞，生化，进化生物学，神经，植物学等，从一些杂志的分类大概也能看出一些，比如从我前面一篇文章“ 当前生物学研究的热门 ”有所介绍。这么多学科都属于生物学科，就是解决生物学问题，加深大家对生物的了解。 但是由于文化的原因，什么东西都要分出三六九等，主流非主流啥的。而这些学科也被国人分成了三六九等，认为某些学科才是主流。貌似国内对进化就不是很了解。碰到的一般现象是，如果你做进化研究，他人就来句“ 你这个研究有啥意义？有啥作用？”，有的人提问倒不是真的问你做的研究有啥意义，而是另外种目的，有的时候不知道想说什么。做研究就是做研究的，干嘛带进“政治”倾向。 这几天刚好看到黄晓磊老师的文章《 为什么做这样的研究?》， 我也来凑个热闹，试着从进化生物学本身的意义来叙述。 在黄老师文章中我回复了一个帖子 " 如今大家都觉得传统的生物实验很重要，比如遗传分析，细胞，生化等，这些是为了了解基因的功能，而了解这些功能的基础在于基因功能的保守性，比如了解小鼠一些功能希望以后能应用到人类中。 而进化生物学本身也是在了解基因的功能，从基因的进化历史能帮助我们了解到基因的功能及基因功能的多样性与保守性。 " 这些内容差不多从 杜布赞斯基的一句话中能体现出来： Dobzhansky (1973) noted that nothing in biology makes sense, except in the light of evolution, an understanding as to how evolution shaped the characteristics of these proteins will provide new insights into the roles of the proteins in the evolutionary success of organisms. 从这些差不多能看出进化生物学研究的意义，进化生物学本身也是解决生物问题。 生物学很多问题需要不同手段去解决，比如知道一个基因的表达信息和定位，只有借助于细胞，生化等手段，而想知道一个基因的起源，这个就是进化所要解决的问题。而这些问题的解答都是帮助我们对基因的了解。了解之后就想知道这些功能信息在生物体内有什么作用，比如眼前我们关注的物种的形成，就眼前来看物种的形成与基因功能的变化密切相关。 举个例子：开始有物种A，接着演化成A1与A2，A1和A2的遗传物质（基因组）与A不一样，我们可能说比较下A1和A2与A的基因组信息不就知道了，但是A一般是没有的。物种A1与A2的形成可能是A在某些时候某些下代的某些基因发生了丢失或者增加，或者某些基因发生了突变。这些基因的变化导致基因功能的变化形成了新性状就分化成了A1与A2. A1与A2是怎么形成的？这个问题是一个巨大的问题，要是能回答肯定是诺贝尔奖级别的，就眼前的技术还不能解决，但这个问题非常重要，是进化生物学与其他学科非常关注的。 从上面的一个例子就能看出进化生物学的重要性。有的人可能这么说上面的问题本身就是一个进化问题，但是我们眼前面对的那个生物学问题不是进化问题，那个问题最后与进化没有关系呢？
标签: 进化生物学
