LECTURE-7-分子系统学的新进展

分子系统学的新进展黄原2011-4主要内容1DNA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1.DNA条形码DNAbarcode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T4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COIgene18SrRNAgene16SrRNAgeneCOI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(voucheredspecimen)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InputorderaltersresultsEuclideandistances?MitochondrialheteroplasmyIdenticalsequencesindifferentspeciesIntrogressionHybridspeciationIncompletelineagesortingNUMTs-NuclearPseudogenesDNA条形码国际组织生物条形码联合体CBOL-ConsortiumfortheBarcodeofLife：22国家的45研究机构2004年首届会议：Londonmeeting(7th-9thofFebruary)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FundedbySloanFoundationTheBarcodeofLifeDatabase(BoLD)has32,000+sequences,(12,000spp+).Projectsexamples•BirdsoftheWorld:DNAbarcodeshavebeendeterminedformostofthebirdspeciesofNorthAmericaandanewefforthasbeenmountedbyRockefellerUniversity,theUniversityofGuelph,andtheSmithsonianInstitution.TheircollectivegoalistoobtainDNAbarcodesfor10,000birdspeciesby2010.••Fish-Bol:An“AllFishes”initiativehasbeenundertakenbyaninternationalcollaborationorganizedbyPaulHebertattheUniversityofGuelph.TheSloanFoundationhasawardedsupportforaJune2005workshopaimedatplanningabarcodeprojectfor500,000specimensandmorethan20,000species.Neighbor-JoiningTreeofGeneticDistancesinCOIAmongandWithin100Hominidae.Tenspeciesinone:DNAbarcodingrevealscrypticspeciesintheneotropicalskipperbutterflyDifferencesinDNAbarcodeshelpcreatetreesshowinggeneticdistancesbetweenspecies.DNA分类学（DNATaxonomy）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AssemblingtheTreeofLife(ATOL)TreeofLife:10MspeciesDavidHillis,Science300:1687(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AssemblingtheTreeofLifeNSFProposal：Phylogeny&predictiveclassificationforlifeonearthin10-15yearsTheAssemblingtheTreeofLife(AToL)ProgramconstructauniversalTreeofLifeforall1.7millionnamedspeciesoflivingorganismsonearth.capitalizeonnewcomputationalandgenomictechnologies.encompassallmicrobes,fungi,protists,animalsandplants.FundingwithCoreprogramsFundingwithAToLTwoTypesofProposalsTaxonBasedAddresscomplexphylogeneticproblemsforamajortaxonthathavebeenresistanttosolutionusingpastapproachesTree-buildingmethodnotspecifiedManagementplanAnalyticalorPhyloinformaticsDataanalysisDataacquisitionDatasharingDatastorageBIOHomepage-:ASSEMBLINGTHETREEOFLIFE(ATOL)PROGRAMBacteria.TreeofLifeforbacteria.Eu-Tree.AssemblingtheTreeofeukaryoticmicrobialdiversity(protists).ChloroplastGenomics.Sequenceandanalysewholechloroplastgenomesof55speciesoflandplants(Embryophytes).TheGreenTreeofLife.TreeofLifeforGreenPlants(Chlorobionta).Angiosperms.TreeofLifeforFloweringPlants.AFToL.AssemblingtheFungalTreeofLife,i.e.formushrooms,yeasts,moldsetc.Cypriniformes.Phylogenyofcypriniformfishes.AmphibiaTree.TreeofLifeforamphibians.DeepScalyProject.TreeofLifeforsquamatereptiles(lizardsandsnakes).Archosauria.Phylogenyoftheropoddinosaursincludingbirds.EarlyBird.Phylogenyofbirds.Protostomes.TreeofLifeforthemajorityofAnimalia,excludingjellyfish,echinoderms,tunicates,vertebrates,andafewothers.NemAToL.TreeofLifefornematodes.Annelida.TreeofLifeforannelidworms.Arthropoda.TreeofLifeforChelicerata,Myriapoda,Crustacea,andHexapoda.Spiders.TreeofLifeforAraneae.Hexapoda.TreeofLifeforspringtails,diplurans,proturans,andinsects.HymAToL.TreeofLifeforHymenoptera(sawflies,horntails,wasps,ants,beesetc.)AntAToL.TreeofLifeforants(Formicidae).FLY-TREE.TreeofLifefortrueflies(Diptera).4.谱系基因组学PhylogenomicsCompletegenomes•1387projects261published(01-03-05)•654prokaryotes•472eukaryotes2072133基因树与物种树的不相合性基因树物种树Martin&Embley,Nature431:152-5.2004Thethree-domainproposalbasedontheribosomalRNAtree.Woeseetal.PNAS.87:4576-4579.(1990)Thetwo-empireproposal,separatingeukaryotesfromprokaryotesandeubacteriafromarchaebacteria.Mayr,D.PNAS95:9720-23.(1998).Thethree-domainproposal,withcontinuouslateralgenetransferamongdomains.DoolittleScience284:2124-2128.(1999)Theringoflife,incorporatinglateralgenetransferbutpreservingtheprokaryote–eukaryotedivide.RiveraMCandLakeJA.Nature431:152-155.(2004)GenomeTree原核生物的系统发育网络Abird's-eyeviewofthetreeoflife,showingthevinesinredandthetree'sbranchesingrey[Bacteria]andgreen[Archaea]生命之树的基部分支关系原核生物之间垂直遗传和水平转移的网络表达方式来自DaganandMartin（2009）Figure2e线粒体的谱系基因组学mitochondrialphylogenomics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，NCBIGenebank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14kb~17kb，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