分子進化樹構建方法

1、第五章系譜分析,生物信息學,2. 系統(tǒng)發(fā)生分析（Phylogenetic analysis),分析基因或蛋白質的進化關系系統(tǒng)發(fā)生（進化）樹（phylogenetic tree）,A tree showing the evolutionary relationships among various biological species or other entities that are believed to have a comm

2、on ancestor.,經(jīng)典進化生物學：比較：形態(tài)、生理結構、化石分子進化生物學：比較DNA和蛋白質序列,研究系統(tǒng)發(fā)生的方法,Residues that are lined up in different sequences are considered to share a common ancestry (i.e., they are derived from a common ancestral residue).,An

3、 Alignment is an hypothesis of positional homology between bases/Amino Acids,Easyonly with substitutions,Difficultalso with indels,,,,,,,,,,,,,,= ((A, (B,C)), (D, E)),Newick format,節(jié)點Node,系統(tǒng)發(fā)生樹術語,A clade（進化支） is a grou

4、p of organisms that includes an ancestor and all descendents of that ancestor.,Phylogram,Cladogram,Ultrametric tree,超度量樹,系統(tǒng)發(fā)生樹術語,Rooted tree vs. Unrooted tree,two major ways to root trees:,By midpoint or distance,有根樹,系統(tǒng)發(fā)

5、生樹術語,plant,plant,plant,Unrooted tree,Rooted tree vs. Unrooted tree,選擇外群（Outgroup）,選擇一個或多個已知與分析序列關系較遠的序列作為外類群外類群可以輔助定位樹根外類群序列必須與進化樹上其它序列同 源，但外類群序列與這些序列間的差異必須比這些序列之間的差異更顯著。,How to root a tree?,系統(tǒng)發(fā)育樹構建步驟,多序列比對（自動比對、手

6、工校正）,選擇建樹方法（替代模型）,建立進化樹,進化樹評估,最大簡約法(maximum parsimony, MP)距離法(distance)最大似然法(maximum likelihood, ML)貝葉斯法(Bayesian inference),,統(tǒng)計分析BootstrapLikelihood Ratio Test ……,距離法,距離法又稱距離矩陣法，首先通過各個序列之間的比較，根據(jù)一定的假設（進化距離模型）推導

7、得出分類群之間的進化距離，構建一個進化距離矩陣。進化樹的構建則是基于這個矩陣中的進化距離關系 。,,計算序列的距離，建立距離矩陣,通過距離矩陣建進化樹,Step1. 計算序列的距離，建立距離矩陣,對位排列，去除空格,由進化距離構建進化樹的方法有很多，常見有：1. Unweighted Pair Group Method with Arithmetic mean (UPGMA)2. Neighbor-Joining Method

8、 (NJ法/鄰位連接法)3.Minimum Evolution (MP法/最小進化法),Step2. 通過矩陣建樹,最大簡約法（MP）最早源于形態(tài)性狀研究，現(xiàn)在已經(jīng)推廣到分子序列的進化分析中。最大簡約法的理論基礎是奧卡姆（Ockham）哲學原則，對所有可能的拓撲結構進行計算，找出所需替代數(shù)最小的那個拓撲結構，作為最優(yōu)樹。,最大簡約法 (Maximum Parsimony),Find the tree that explains t

9、he observed sequences with a minimal number of substitutions,MP法建樹流程,,If 1 and 2 are grouped a total of four changes are needed. If 1 and 3 are grouped a total of five changes are needed. If 1 and 4 are grouped a tot

10、al of six changes are needed.,Position 1 (1,2): 1 change; (1,3) or (1,4): 2 changes,Position 2 (1,3): 1 change; (1,2) or (1,4): 2 changes,Position 3 (1,2): 1

11、 change; (1,3) or (1,4): 2 changes,,BEST,,MP法建樹步驟,最大似然法 (Maximum Likelihood),最大似然法(ML) 最早應用于對基因頻率數(shù)據(jù)的分析上。其原理為選取一個特定的替代模型來分析給定的一組序列數(shù)據(jù)，使得獲得的每一個拓撲結構的似然率都為最大值，然后再挑出其中似然率最大的拓撲結構作為最優(yōu)樹。,ML法建樹流程,,Pick an E

12、volutionary Model For each position, Generate all possible tree structures Based on the Evolutionary Model, calculate Likelihood of these Trees and Sum them to get the Column Likelihood for each OTU cluster.Calculate

13、Tree Likelihood by multiplying the likelihood for each positionChoose Tree with Greatest Likelihood,Inferring the maximum likelihood tree,Holder&Lewis (2003) Nature Reviews Genetics 4, 275-284,Bayesian inference:

14、What is the probability that the model/theory is correct given the observed data? Pr(T|D),Maximum Likelihood: What is the probability of seeing the observed data (D) given a model/theory (T)? Pr(D|T),SpeedNo need

15、for bootstrapping,構建進化樹的新方法——貝葉斯推斷(Bayesian inference),與ML相比，BI的優(yōu)勢：,Comparison of Methods,Bioinformatics: Sequence and Genome Analysis, 2nd edition, by David W. Mount. p254,Choosing a Method for Phylogenetic Prediction

16、,http://cshprotocols.cshlp.org/cgi/content/full/2008/5/pdb.ip49,Molecular Biology and Evolution 2005 22(3):792-802,Assessing tree reliabilityPhylogenetic reconstruction is a problem of statistical inference. One must a

17、ssess the reliability of the inferred phylogeny and its component parts. Questions: (1) how reliable is the tree?(2) which parts of the tree are reliable? (3) is this tree significantly better than another one?,A s

18、tatistical technique that uses intensive random resampling of data to estimate a statistic whose underlying distribution is unknown.,評估進化樹的可靠性——自展法（bootstrapping method）,從排列的多序列中隨機有放回的抽取某一列，構成相同長度的新的排列序列重復上面的過程，得到多組新的序列

19、對這些新的序列進行建樹，再觀察這些樹與原始樹是否有差異，以此評價建樹的可靠性,The Bootstrap,Computational method to estimate the confidence level of a certain phylogenetic tree.,More replicates (between 100 - 1000),自展法檢驗流程,Bootstrapping doesn’t really assess

20、 the accuracy of a tree, only indicates the consistency of the data,對ML法而言，自展法太耗時，可用aLRT法檢驗進化樹的可靠性Anisimova&Gascuel (2006) Syst. Biol. 55(4):539-552,,,MSA程序可對任何序列進行比對，選擇什么樣的序列進行比對非常重要?。?用于構建進化樹的序列必須是同源序列,MSA是構建分子進化樹

21、的關鍵步驟,分子進化樹構建（ClustalW）,,,頁面下方 顯示Cladogram Tree,,點擊“Show as Phylogram Tree”展示Phylogram Tree,不推薦：僅提供距離法建樹，且沒有進行評估,輸入比對后的序列（或上載Alignments文件）,看圖工具,,下載“Phylip tree file”（ph文件）,,TreeView 進化樹編輯打印軟件（在http://taxonomy.zoology.g

22、la.ac.uk/rod/treeview.html）,,輸入比對后的序列（或上載Alignments文件）,用TreeView軟件打開上述文件,可以不同格式展示進化樹（1、2、3）,EBI的ClustalW2-phylogeny分析網(wǎng)頁,PHYLIP http://evolution.genetics.washington.edu/phylip.html 免費的集成進化

23、分析工具PAUP http://paup.csit.fsu.edu/ 商業(yè)軟件，集成的進化分析工具MEGA http://www.megasoftware.net/

24、 免費的圖形化集成進化分析工具PHYML http://atgc.lirmm.fr/phyml/ 最快的ML建樹工具PAML http://abacus.gene.ucl.ac.uk/software/paml.html

25、 ML建樹工具Tree-puzzle http://www.tree-puzzle.de/ 較快的ML建樹工具MrBayes http://mrbayes.csit.fsu.edu/

26、 基于貝葉斯方法的建樹工具,分子進化分析軟件,更多工具,http://evolution.gs.washington.edu/phylip/software.html,提供最大簡約法（MP）、最大似然法（ML）和距離法三種建樹方法。其中距離法包括鄰接法（NJ）、最小進化法（ME）和UPGMA三種算法。,分子進化樹構建方法,優(yōu)點：圖形界面，集序列查詢、比對、進化樹構建為一體，幫助文件詳盡，免費,http://www.mega

27、software.net/,,Buffon (1707-1788) Natural History of Animals,,始祖鳥化石,復原圖,,2.7% difference,,xl, Xenopus laevis; xt, Xenopus tropicalis; gg, Gallus gallus; rn, Rattus norvegicus; mm, Mus musculus; hs, Homo sapiens.,BMC