分子進(jìn)化樹(shù)構(gòu)建方法

1、第五章系譜分析,生物信息學(xué),2. 系統(tǒng)發(fā)生分析（Phylogenetic analysis),分析基因或蛋白質(zhì)的進(jìn)化關(guān)系系統(tǒng)發(fā)生（進(jìn)化）樹(shù)（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(jìn)化生物學(xué)：比較：形態(tài)、生理結(jié)構(gòu)、化石分子進(jìn)化生物學(xué)：比較DNA和蛋白質(zhì)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(diǎn)Node,系統(tǒng)發(fā)生樹(shù)術(shù)語(yǔ),A clade（進(jìn)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(shù),系統(tǒng)發(fā)生樹(shù)術(shù)語(yǔ),Rooted tree vs. Unrooted tree,two major ways to root trees:,By midpoint or distance,有根樹(shù),系統(tǒng)發(fā)

5、生樹(shù)術(shù)語(yǔ),plant,plant,plant,Unrooted tree,Rooted tree vs. Unrooted tree,選擇外群（Outgroup）,選擇一個(gè)或多個(gè)已知與分析序列關(guān)系較遠(yuǎn)的序列作為外類(lèi)群外類(lèi)群可以輔助定位樹(shù)根外類(lèi)群序列必須與進(jìn)化樹(shù)上其它序列同 源，但外類(lèi)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(shù)構(gòu)建步驟,多序列比對(duì)（自動(dòng)比對(duì)、手

6、工校正）,選擇建樹(shù)方法（替代模型）,建立進(jìn)化樹(shù),進(jìn)化樹(shù)評(píng)估,最大簡(jiǎn)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(jì)分析BootstrapLikelihood Ratio Test ……,距離法,距離法又稱(chēng)距離矩陣法，首先通過(guò)各個(gè)序列之間的比較，根據(jù)一定的假設(shè)（進(jìn)化距離模型）推導(dǎo)

7、得出分類(lèi)群之間的進(jìn)化距離，構(gòu)建一個(gè)進(jìn)化距離矩陣。進(jìn)化樹(shù)的構(gòu)建則是基于這個(gè)矩陣中的進(jìn)化距離關(guān)系 。,,計(jì)算序列的距離，建立距離矩陣,通過(guò)距離矩陣建進(jìn)化樹(shù),Step1. 計(jì)算序列的距離，建立距離矩陣,對(duì)位排列，去除空格,由進(jìn)化距離構(gòu)建進(jìn)化樹(shù)的方法有很多，常見(jiàn)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(jìn)化法),Step2. 通過(guò)矩陣建樹(shù),最大簡(jiǎn)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(jìn)化分析中。最大簡(jiǎn)約法的理論基礎(chǔ)是奧卡姆（Ockham）哲學(xué)原則，對(duì)所有可能的拓?fù)浣Y(jié)構(gòu)進(jìn)行計(jì)算，找出所需替代數(shù)最小的那個(gè)拓?fù)浣Y(jié)構(gòu)，作為最優(yōu)樹(shù)。,最大簡(jiǎn)約法 (Maximum Parsimony),Find the tree that explains t

9、he observed sequences with a minimal number of substitutions,MP法建樹(shù)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(shù)步驟,最大似然法 (Maximum Likelihood),最大似然法(ML) 最早應(yīng)用于對(duì)基因頻率數(shù)據(jù)的分析上。其原理為選取一個(gè)特定的替代模型來(lái)分析給定的一組序列數(shù)據(jù)，使得獲得的每一個(gè)拓?fù)浣Y(jié)構(gòu)的似然率都為最大值，然后再挑出其中似然率最大的拓?fù)浣Y(jié)構(gòu)作為最優(yōu)樹(shù)。,ML法建樹(shù)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(gòu)建進(jìn)化樹(shù)的新方法——貝葉斯推斷(Bayesian inference),與ML相比，BI的優(yōu)勢(shì)：,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(píng)估進(jìn)化樹(shù)的可靠性——自展法（bootstrapping method）,從排列的多序列中隨機(jī)有放回的抽取某一列，構(gòu)成相同長(zhǎng)度的新的排列序列重復(fù)上面的過(guò)程，得到多組新的序列

19、對(duì)這些新的序列進(jìn)行建樹(shù)，再觀察這些樹(shù)與原始樹(shù)是否有差異，以此評(píng)價(jià)建樹(shù)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(yàn)流程,Bootstrapping doesn’t really assess

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

21、的關(guān)鍵步驟,分子進(jìn)化樹(shù)構(gòu)建（ClustalW）,,,頁(yè)面下方 顯示Cladogram Tree,,點(diǎn)擊“Show as Phylogram Tree”展示Phylogram Tree,不推薦：僅提供距離法建樹(shù)，且沒(méi)有進(jìn)行評(píng)估,輸入比對(duì)后的序列（或上載Alignments文件）,看圖工具,,下載“Phylip tree file”（ph文件）,,TreeView 進(jìn)化樹(shù)編輯打印軟件（在http://taxonomy.zoology.g

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

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

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

25、 ML建樹(shù)工具Tree-puzzle http://www.tree-puzzle.de/ 較快的ML建樹(shù)工具M(jìn)rBayes http://mrbayes.csit.fsu.edu/

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

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