系统发生分析.ppt

第五章
系谱分析
生物信息学
2. 系统发生分析(ic analysis)
分析基因或蛋白质的进化关系
系统发生(进化)树(ic tree)
A tree showing the evolutionary relationships among various biological species or other entities that are believed to have mon 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 up in different sequences are considered to share mon ancestry (., they are derived from mon ancestral residue).
An Alignment is an hypothesis of positional homology between bases/Amino Acids
Easy
only with substitutions
Difficult
also with indels
= ((A, (B,C)), (D, E))
Newick format
节点Node
分支
Branch
A
B
C
D
E
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
HTU
A clade(进化支) is a group anisms that includes an ancestor and all descendents of that ancestor.
ic change
no meaning
Phylogram
Cladogram
time
Taxon A
Taxon B
Taxon C
Taxon D
1
1
1
6
3
5
Taxon A
Taxon B
Taxon C
Taxon D
Taxon A
Taxon B
Taxon C
Taxon D
Ultrametric tree
超度量树
进化树
分支树
系统发生树术语
Rooted tree vs. Unrooted tree
two major ways to root trees:
A
B
C
D
10
2
3
5
2
d (A,D) = 10 + 3 + 5 = 18
Midpoint = 18 / 2 = 9
By midpoint or distance
有根树
A
C
B
D
无根树
系统发生树术语
outgroup
外群、外围支
plant
plant
plant
fungus
animal
animal
animal
Unrooted tree
root
Rooted tree
bacterium
animal
animal
animal
fungus
plant
plant
plant
Monophyletic group
Monophyletic
group
Rooted tree vs. Unrooted tree
选择外群(Outgroup)
选择一个或多个已知与分析序列关系较远的序列作为外类群
外类群可以辅助定位树根
外类群序列必须与进化树上其它序列同源,但外类群序列与这些序列间的差异必须比这些序列之间的差异更显著。
eukaryote
eukaryote
eukaryote
eukaryote
archaea
archaea
archaea
bacteria 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
Bootstrap
Likelihood Ratio Test
……
UPGMA
邻近法
(Neighbor-joining, NJ)
最小进化法
(minimum evolution)