TABLE 5.1 Numbers of possible rooted and unrooted trees for up to 20 OTUs Number of OTUs Number of rooted trees Number of unrooted trees 3456789 15 3 105 15 954 105 10395 135,135 10395 2027025 135,135 10 34459425 2027025 654,729075 34,459425 12 13749310575 654729075 13 316234143225 13749310575 14 7905853580,625 316,234143,225 213458046,676,875 7905853580625 6,190,283353629375 213458046676875 17 191898783962510625 6,190,283353629375 6332659870762850625 191898783962510625 221,643,095,476699,771,875 6332659,870,762,850,625 20 8,200794532637891559375221,643,095476699771875 Data from Felsenstein(1978b)
Phylogeny Cladogram B C TYPES OF TREES Additive tree B Fig 2.5 A phylogeny and the Character change three basic kinds of tree used to depict that phylogeny. The Ultrametric tree cladogram represents relative A B C recency of common ancestry; the additive tree depicts the amount of evolutionary change that has occurred along the different branches and the ultrametric tree depicts times of divergence
TYPES OF TREES
Newick(shorthand) format text based representation of relationships A B Fig. 2. 4 A nd its (((A, B),C),(D, E)) horthand representation using nested parentheses
Newick (shorthand) format --- text based representation of relationships
5.2 Construction of phylogenetic tree UPGMA法 距离法 邻接法 最小进化法 基于SNP 最大似然法 简约法 系统发生树构建 贝叶斯法 基于字符串 基因组组份矢量法
5.2 Construction of phylogenetic tree
目前应用最为广泛方法 Distance methods Probabilistic methods: maximum likelihood ML
• Distance methods • Probabilistic methods: maximum likelihood (ML) 目前应用最为广泛方法