分子系统学的新进展.ppt

分子系统学的新进展,黄原2006-9,主要内容,1 DNA条形码2 组装生命之树3 谱系基因组学4 系统发育信息学5 系统发育分类学6 系统发育生物学,DNA条形码DNA barcode,什么是DNA条形码?,能够用于识别和鉴定某一类群所有物种的一段DNA序列.DNA条形码是由DNA序列上A、C、G和T 4种碱基组成及其次序决定的。,DNA条形码标记的要求,在某一类群的所有物种中都有这段DNA序列.必须是物种特异性的.可以使用简便的方法进行研究.在物种之间长度变异不大.,建议的DNA条形码标记,COI gene18S rRNA gene16S rRNA gene,COI基因是首选标记,COI 基因5约648bp.COI 不适用于植物.COI在两栖类进化速度很高,不适用于两栖类.,DNA条形码识别原理,建立地球上所有物种的DNA条形码数据库测定待鉴定标本的条形码序列将待鉴定标本的条形码序列与条形码数据库中的所有记录进行比对根据比对结果中与最近邻居的条形码差异做出结论：已知物种或未知物种。,DNA条形码的意义,快速而准确的识别和鉴定物种使非专业人员也能鉴定物种野外物种识别,DNA条形码是技术而非科学,DNA条形码仅供物种识别.DNA条形码应该跟物种学名一样有承载它的凭证标本(vouchered specimen)或在微小型种类中有数码图象凭证.DNA条形码序列应该提交到专门的条形码数据库中.根据DNA条形码进行物种识别的前提条件是已经测得并建立了相关类群所有物种的条形码标记的数据库.,DNA条形码识别中存在的困难,Input order alters resultsEuclidean distances?Mitochondrial heteroplasmyIdentical sequences in different speciesIntrogressionHybrid speciationIncomplete lineage sortingNUMTs-Nuclear Pseudogenes,DNA条形码国际组织,生物条形码联合体CBOL-Consortium for the Barcode of Life：22国家的45 研究机构2004年首届会议：London meeting(7th-9th of February)有46个国家的220名代表参加。目标Goals 加速DNA条形码的研究建立向公众开放的DNA条形码数据库促进条形码识别根据的开发http:/Funded by Sloan Foundation,The Barcode of Life Database(BoLD)has 32,000+sequences,(12,000 spp+).,Projects examples,Birds of the World:DNA barcodes have been determined for most of the bird species of North America and a new effort has been mounted by Rockefeller University,the University of Guelph,and the Smithsonian Institution.Their collective goal is to obtain DNA barcodes for 10,000 bird species by 2010.Fish-Bol:An“All Fishes”initiative has been undertaken by an international collaboration organized by Paul Hebert at the University of Guelph.The Sloan Foundation has awarded support for a June 2005 workshop aimed at planning a barcode project for 500,000 specimens and more than 20,000 species.,Neighbor-Joining Tree of Genetic Distances in COIAmong and Within 100 Hominidae.,Ten species in one:DNA barcoding reveals cryptic species in the neotropical skipper butterfly,Differences in DNA barcodes help create trees showing genetic distances between species.,DNA分类学（DNA Taxonomy）,定义：应用DNA序列作为唯一数据来描述和定义分类单元。,2.组装生命之树,Assembling the Tree of Life(ATOL),Tree of Life:10M species,David Hillis,Science 300:1687(2003),现在是组装地球上所有生物的系统发育树的时候,基因组学和DNA测序技术已经能够满足组装生命之树所需要的数据.生物信息学的理论和方法已经能够满足组装生命之树需要的计算和数据管理任务,Assembling the Tree of Life,NSF Proposal：Phylogeny&predictive classification for life on earthin 10-15 years,The Assembling the Tree of Life(AToL)Program,construct a universal Tree of Life for all 1.7 million named species of living organisms on earth.capitalize on new computational and genomic technologies.encompass all microbes,fungi,protists,animals and plants.,Funding with Core programs,Funding with AToL,Two Types of Proposals,Taxon BasedAddress complex phylogenetic problems for a major taxon that have been resistant to solution using past approaches Tree-building method not specifiedManagement plan,Analytical or PhyloinformaticsData analysisData acquisitionData sharingData storage,BIO Homepage-http:/www.nsf/bio,2002 AToL Awards:7 Projects Funded,Bacteria Non-seed Plants Fungi Nematodes Spiders and Scorpions Birds Dinosaurs,NSF:ASSEMBLING THE TREE OF LIFE(ATOL)PROGRAM,Bacteria.Tree of Life for bacteria.Eu-Tree.Assembling the Tree of eukaryotic microbial diversity(protists).Chloroplast Genomics.Sequence and analyse whole chloroplast genomes of 55 species of land plants(Embryophytes).The Green Tree of Life.Tree of Life for Green Plants(Chlorobionta).Angiosperms.Tree of Life for Flowering Plants.AFToL.Assembling the Fungal Tree of Life,i.e.for mushrooms,yeasts,molds etc.Cypriniformes.Phylogeny of cypriniform fishes.AmphibiaTree.Tree of Life for amphibians.Deep Scaly Project.Tree of Life for squamate reptiles(lizards and snakes).Archosauria.Phylogeny of theropod dinosaurs including birds.Early Bird.Phylogeny of birds.Protostomes.Tree of Life for the majority of Animalia,excluding jellyfish,echinoderms,tunicates,vertebrates,and a few others.NemAToL.Tree of Life for nematodes.Annelida.Tree of Life for annelid worms.Arthropoda.Tree of Life for Chelicerata,Myriapoda,Crustacea,and Hexapoda.Spiders.Tree of Life for Araneae.Hexapoda.Tree of Life for springtails,diplurans,proturans,and insects.HymAToL.Tree of Life for Hymenoptera(sawflies,horntails,wasps,ants,bees etc.)AntAToL.Tree of Life for ants(Formicidae).FLY-TREE.Tree of Life for true flies(Diptera).,4.谱系基因组学,Phylogenomics,Complete genomes 1387 projects261 published(01-03-05)654 prokaryotes 472 eukaryotes,207,21,33,Tree of life,GOLD,Cumulated number of available completely sequenced genomes,Completely sequenced Genomes that span the three domains of life are growing at a rapid rate,Martin&Embley,Nature 431:152-5.2004,The three-domain proposal based on the ribosomal RNA tree.Woese et al.PNAS.87:4576-4579.(1990),The two-empire proposal,separating eukaryotes from prokaryotes and eubacteria from archaebacteria.Mayr,D.PNAS 95:9720-23.(1998).,The three-domain proposal,with continuous lateral gene transfer among domains.Doolittle Science 284:2124-2128.(1999),The ring of life,incorporating lateral gene transfer but preserving the prokaryoteeukaryote divide.Rivera MC and Lake JA.Nature 431:152-155.(2004),Genome Tree,Profiles,Conservation,Orthologs,原核生物的系统发育网络,A birds-eye view of the tree of life,showing the vines in red and the trees branches in grey Bacteria and green Archaea,生命之树的基部分支关系,线粒体的谱系基因组学mitochondrial phylogenomics,从1981年Anderson等人完成人类的线粒体基因组全序列测定以来，已有800余种生物完成了线粒体基因组全序列测定，其中，NCBI Genebank数据库中收录的线粒体基因组序列中，后生动物751种，真菌41种，植物15种，原生生物34种。动物线粒体基因组约14kb17kb，缺乏内含子，所有基因紧密的排列于2条链上。基因组成相对保守。,直翅总目昆虫的线粒体谱系基因组学,目的:建立直翅目和直翅总目昆虫高级阶元之间的系统发育关系方法:线粒体全基因组测序、组装、注释及系统发育分析资助:已连续获得3个国家自然科学基金进展:已测出20余种直翅目昆虫的线粒体全基因组。,直翅目昆虫线粒体通用引物设计图,霍山蹦蝗线粒体基因组的组成结构,意大利蝗线粒体基因组的组成结构,利用12条AA序列重建的部分六足类系统发育树,5.系统发育信息学,系统发育信息学-定义,系统发育信息学是存贮、管理、注释、开发和加工系统树及其相关生物学信息的交叉学科。它所采用的方法是基于计算机和网络技术，包括大型系统树及其相关生物学数据库的建立，系统树数据库网络的构架，系统树的可视化显示，小系统树的联合与超树的建立、用户查询、搜索和下载等，最终目的是要建立一个囊括地球上所有生物的系统树和其相关的生物学数据库，将各种生物在树上精确定位,并进一步通过对系统发育信息的查询、搜索、联合与分析，从中获取生命进化的知识和进行生物学的预测。,系统发育信息学产生背景,组装生命之树计划必需的的基础建设系统发育生物学知识整合的需要系统发育数据爆炸,系统发育信息学主要任务,发展算法、开发软件、构建数据库用于解决以下问题:系统发育数据和系统树贮存、搜索和查询超树和超矩阵的构建方法(supertrees,supermatrices)系统树和网络的可视化meta analysis,Phyloloinformatic infrastructure,系统发育信息学网络资源,系统发育信息学是近年来形成的新的学科方向，是系统学研究领域的一个新兴生长点。目前可用的网络资源有CIPRes和系统发育软件（Phylogeny Programs）网站及数据库资源，已有的系统发育信息学数据库包括TreeBASE，Tree of Life,Species 2000,NCBI Taxonomy数据库等。,生命之树网站Tree of Life（tolweb.org）,普及性网站提供了大量的文字和图象无法进行系统树分析对系统学研究意义有限,TreeBASE,关系型数据库可以通过作者、分类单元等进行搜索可以构建超树系统树和数据集均NEXUS 格式,5 系统发育分类学,Traditional versus Phylogenetic classification of Vertebrata,Phylogenetic nomenclature,The“PhyloCode”：http:/De Queiroz&Gauthier,1990.Systematic Biology 39:307-322.De Queiroz&Gauthier,1992.Annual Review of Ecology and Systematics 23:449-480.,6 系统发育生物学,Phylogenetic Biology,系统发育生物学:定义,系统发育生物学是以系统树为基础的生物学研究，是比较生物学研究从种群（population thinking）思维向系统树思维（tree thinking）和网络思维（netkork thinking）发展的结果。,系统树思维方式,比较生物学研究范式的变化个体（1930s以前）群体（1930-1990s）系统树 和网络系统树思维,系统发育生物学研究的主要范围,1.小进化研究 基因谱系 谱系生物地理学 杂交研究 物种形成 kinship and parentage2.大进化研究 3.性状进化研究 4.祖先状态估计,5.分歧时间估计 6.协同进化 7.流行病学 8.分子进化（选择、重组、漂变、基因流、LGT、基因重复等）9.群体历史（瓶颈效应、奠基者效应、等）10.保护生物学,系统发育生物学研究范例,Phylogenetic Relationships of North American Field Crickets Inferred from Mitochondrial DNA Data Yuan Huang,Guillermo Ort,Marie Sutherlin,Amy Duhachek,and Anthony Zera Molecular Phylogenetics and Evolution Vol.17,No.1,October,pp.4857,2000,致谢Acknoledgments,学术道路上的导师：郑哲民、周尧、袁锋、G.Orti、F.Lang、G.Berg。研究生：叶海燕、叶维萍、芦荣胜、卢慧甍、陈茹冰、马兰、肖莉莉、刘艳、张辰艳、钱昭强、周志军，等,