LECTURE-7-分子系統(tǒng)學的新進展ppt課件

1、分子系統(tǒng)學的新進展,黃原 2011-4,主要內容,1 DNA條形碼 2 組裝生命之樹 3 譜系基因組學 4 系統(tǒng)發(fā)育信息學 5 系統(tǒng)發(fā)育分類學 6 系統(tǒng)發(fā)育生物學,DNA條形碼DNA barcode,什么是DNA條形碼,能夠用于識別和鑒定某一類群所有物種的一段DNA序列. DNA條形碼是由DNA序列上A、C、G和T 4種堿基組成及其次序決定的,DNA條形碼標記的要求,在某一類群的所有物種中都有這段DNA序列. 必須是物種特異性的. 可以使用簡便的方法進行研究. 在物種之間長度變異不大,建議的DNA條形碼標記,COI gene 18S rRNA gene 16S rRNA gene,COI基因是

2、首選標記,COI 基因5約648bp. COI 不適用于植物. COI在兩棲類進化速度很高, 不適用于兩棲類,DNA條形碼識別原理,建立地球上所有物種的DNA條形碼數(shù)據(jù)庫 測定待鑒定標本的條形碼序列 將待鑒定標本的條形碼序列與條形碼數(shù)據(jù)庫中的所有記錄進行比對 根據(jù)比對結果中與最近鄰居的條形碼差異做出結論：已知物種或未知物種,DNA條形碼的意義,快速而準確的識別和鑒定物種 使非專業(yè)人員也能鑒定物種 野外物種識別,DNA條形碼是技術而非科學,DNA條形碼僅供物種識別. DNA條形碼應該跟物種學名一樣有承載它的憑證標本( vouchered specimen)或在微小型種類中有數(shù)碼圖象憑證. DNA

3、條形碼序列應該提交到專門的條形碼數(shù)據(jù)庫中. 根據(jù)DNA條形碼進行物種識別的前提條件是已經(jīng)測得并建立了相關類群所有物種的條形碼標記的數(shù)據(jù)庫,DNA條形碼識別中存在的困難,Input order alters results Euclidean distances? Mitochondrial heteroplasmy Identical sequences in different species Introgression Hybrid speciation Incomplete lineage sorting NUMTs- Nuclear Pseudogenes,DNA條形碼國際組織,生物條

4、形碼聯(lián)合體CBOL- Consortium for the Barcode of Life： 22國家的45 研究機構 2004年首屆會議： London meeting (7th-9th of February) 有46個國家的220名代表參加。 目標Goals 加速DNA條形碼的研究 建立向公眾開放的DNA條形碼數(shù)據(jù)庫 促進條形碼識別根據(jù)的開發(fā) Funded by Sloan Foundation,http:/,The Barcode of Life Database (BoLD) has 32,000 + sequences, (12,000

5、 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 10,00

6、0 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 mor

7、e 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分類學（ DNA Tax

8、onomy,定義：應用DNA序列作為唯一數(shù)據(jù)來描述和定義分類單元,2. 組裝生命之樹,Assembling the Tree of Life (ATOL,Tree of Life: 10M species,David Hillis, Science 300:1687 (2003,現(xiàn)在是組裝地球上所有生物的系統(tǒng)發(fā)育樹的時候,基因組學和DNA測序技術已經(jīng)能夠滿足組裝生命之樹所需要的數(shù)據(jù). 生物信息學的理論和方法已經(jīng)能夠滿足組裝生命之樹需要的計算和數(shù)據(jù)管理任務,Assembling the Tree of Life,NSF Proposal：Phylogeny & predictive classi

9、fication 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 pl

10、ants,Funding with Core programs,Funding with AToL,Two Types of Proposals,Taxon Based Address complex phylogenetic problems for a major taxon that have been resistant to solution using past approaches Tree-building method not specified Management plan,Analytical or Phyloinformatics Data analysis Data

11、 acquisition Data sharing Data storage,BIO Homepage - http:/www.nsf/bio,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

12、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

13、. 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, v

14、ertebrates, 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.

15、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. 譜系基因組學,Phylogenomics,Complete genomes 1387 projects 261 published (01-03-05) 654 prokaryotes 472 eukaryotes,207,21,33,http:/www.geno

16、mesonline.or,Tree of life,基因樹與物種樹的不相合性,基因樹,物種樹,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

17、: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,原核

18、生物的系統(tǒng)發(fā)育網(wǎng)絡,A birds-eye view of the tree of life, showing the vines in red and the trees branches in grey Bacteria and green Archaea,生命之樹的基部分支關系,原核生物之間垂直遺傳和水平轉移的網(wǎng)絡表達方式,來自Dagan and Martin（2009）Figure 2e,線粒體的譜系基因組學mitochondrial phylogenomics,從1981年Anderson等人完成人類的線粒體基因組全序列測定以來，已有800余種生物完成了線粒體基因組全序列測定，其中，

19、NCBI Genebank數(shù)據(jù)庫中收錄的線粒體基因組序列中，后生動物751種，真菌41種，植物15種，原生生物34種。 動物線粒體基因組約14kb17kb，缺乏內含子，所有基因緊密的排列于2條鏈上?；蚪M成相對保守,直翅總目昆蟲的線粒體譜系基因組學,目的: 建立直翅目和直翅總目昆蟲高級階元之間的系統(tǒng)發(fā)育關系 方法: 線粒體全基因組測序、組裝、注釋及系統(tǒng)發(fā)育分析 資助: 已連續(xù)獲得3個國家自然科學基金 進展: 已測出20余種直翅目昆蟲的線粒體全基因組,直翅目昆蟲線粒體通用引物設計圖,霍山蹦蝗線粒體基因組的組成結構,意大利蝗線粒體基因組的組成結構,利用12條AA序列重建的部分六足類系統(tǒng)發(fā)育樹,5.

20、 系統(tǒng)發(fā)育信息學,系統(tǒng)發(fā)育信息學-定義,系統(tǒng)發(fā)育信息學是存貯、管理、注釋、開發(fā)和加工系統(tǒng)樹及其相關生物學信息的交叉學科。它所采用的方法是基于計算機和網(wǎng)絡技術，包括大型系統(tǒng)樹及其相關生物學數(shù)據(jù)庫的建立，系統(tǒng)樹數(shù)據(jù)庫網(wǎng)絡的構架，系統(tǒng)樹的可視化顯示，小系統(tǒng)樹的聯(lián)合與超樹的建立、用戶查詢、搜索和下載等，最終目的是要建立一個囊括地球上所有生物的系統(tǒng)樹和其相關的生物學數(shù)據(jù)庫，將各種生物在樹上精確定位,并進一步通過對系統(tǒng)發(fā)育信息的查詢、搜索、聯(lián)合與分析，從中獲取生命進化的知識和進行生物學的預測,系統(tǒng)發(fā)育信息學產生背景,組裝生命之樹計劃必需的的基礎建設 系統(tǒng)發(fā)育生物學知識整合的需要 系統(tǒng)發(fā)育數(shù)據(jù)爆炸,系統(tǒng)發(fā)育

21、信息學主要任務,發(fā)展算法、開發(fā)軟件、構建數(shù)據(jù)庫用于解決以下問題: 系統(tǒng)發(fā)育數(shù)據(jù)和系統(tǒng)樹貯存、搜索和查詢 超樹和超矩陣的構建方法(supertrees, supermatrices) 系統(tǒng)樹和網(wǎng)絡的可視化 meta analysis,Phyloloinformatic infrastructure,系統(tǒng)發(fā)育信息學網(wǎng)絡資源,系統(tǒng)發(fā)育信息學是近年來形成的新的學科方向，是系統(tǒng)學研究領域的一個新興生長點。目前可用的網(wǎng)絡資源有CIPRes和系統(tǒng)發(fā)育軟件（Phylogeny Programs）網(wǎng)站及數(shù)據(jù)庫資源，已有的系統(tǒng)發(fā)育信息學數(shù)據(jù)庫包括TreeBASE，Tree of Life, Species 200

22、0, NCBI Taxonomy數(shù)據(jù)庫等,生命之樹網(wǎng)站Tree of Life（,普及性網(wǎng)站 提供了大量的文字和圖象 無法進行系統(tǒng)樹分析 對系統(tǒng)學研究意義有限,TreeBASE,關系型數(shù)據(jù)庫 可以通過作者、分類單元等進行搜索 可以構建超樹 系統(tǒng)樹和數(shù)據(jù)集均NEXUS 格式,系統(tǒng)發(fā)育分析方法和軟件使用,5 系統(tǒng)發(fā)育分類學,Traditional versus Phylogenetic classification of Vertebrata,Phylogenetic nomenclature,The “PhyloCode”：/ De Queiroz & Gauthier, 1990. Systematic Biology 39:307-322. De