1、 第五章系谱分析生物信息学2. 系统发生分析(Phylogenetic analysis)分析基因或蛋白质的进化关系系统发生(进化)树(phylogenetic tree)A tree showing the evolutionary relationships among various biological species or other entities that are believed to have a common ancestor. 经典进化生物学:比较:形态、生理结构、化石分子进化生物学:比较DNA和蛋白质序列研究系统发生的方法Residues that are lined
2、 up in different sequences are considered to share a common ancestry (i.e., they are derived from a common ancestral residue). An Alignment is an hypothesis of positional homology between bases/Amino AcidsEasyonly with substitutionsDifficultalso with indels= (A, (B,C), (D, E) Newick format节点Node分支 B
3、ranch ABCDE末端节点 可以是物种,群体,或者蛋白质、DNA、RNA分子等OTU祖先节点/树根Root系统发生树术语内部节点/分歧点该分支可能的祖先HTUA clade(进化支) is a group of organisms that includes an ancestor and all descendents of that ancestor. genetic changeno meaningPhylogramCladogramtimeTaxon ATaxon BTaxon CTaxon D111635Taxon ATaxon BTaxon CTaxon DTaxon ATax
4、on BTaxon CTaxon DUltrametric tree超度量树进化树分支树系统发生树术语Rooted tree vs. Unrooted treetwo major ways to root trees:A BCD102352d (A,D) = 10 + 3 + 5 = 18Midpoint = 18 / 2 = 9By midpoint or distance有根树A CB D无根树系统发生树术语outgroup 外群、外围支plantplantplantfungusanimalanimalanimalUnrooted treerootRooted treebacteriuma
5、nimalanimalanimalfungusplantplantplantMonophyletic groupMonophyleticgroupRooted tree vs. Unrooted tree选择外群(Outgroup) 一 或多 已知 分析序列 系 的序列作选择 个 个 与 关 较远 为外 群类外 群可以 助定位 根类 辅 树外 群序列必 化 上其 序列同 源,但类 须与进 树 它外 群序列 些序列 的差 必 比 些序列之 的类 与这 间 异 须 这 间差 更 著。异 显eukaryoteeukaryoteeukaryoteeukaryotearchaeaarchaeaarchaeabacteria outgroup 外群How to root a tree?系统发育树构建步骤多序列比对(自动比对、手工校正)选择建树方法(替代模型)建立进化树进化树评估最大简约法(maximum parsimony, MP)距离法(distance)最大似然法(maximum likelihood, ML)贝叶斯法(Bayesian inference)统计分析BootstrapLikelihood Ratio Test UPGMA邻近法(Neighbor-joining, NJ)最小进化法(minimum evolution)