Branches can be rotated at a node, without changing the relationships among the otus. D C B A
Branches can be rotated at a node, without changing the relationships among the OTU’s
Rooted: unique path from root. Unrooted: degree of kinship, no evolutionary path Rooted tree Root Unrooted tree G Fig 2.6 Rooted and unrooted Root trees for human(H), chimp C), gorilla(G), orang-utan rooted tree(top) corresponds to the unrooted tree below
Rooted: unique path from root. Unrooted: degree of kinship, no evolutionary path
Assumptions about rate of change in branches of tree May assume constant rate of change throughout tree -then branch length is proportional to no of changes and we can easily root the tree using a simple algorithm May have variable rate no ancestor sequence ancestor sequence
Assumptions about rate of change in branches of tree • May assume constant rate of change throughout tree - then branch length is proportional to no. of changes and we can easily root the tree using a simple algorithm •May have variable rate no ancestor sequence ancestor sequence
Tree reconstruction as optimization Number of possible trees is 2. Considering branch lengths makes the problem harder Want the tree that maximizes some quality score. Score based on either Characters(e.g. sites in a sequence)directly, or Distances between character sets(e.g alignment scores
Tree reconstruction as optimization • Number of possible trees is 2S . Considering branch lengths makes the problem harder. • Want the tree that maximizes some quality score. Score based on either • Characters (e.g. sites in a sequence) directly, or • Distances between character sets (e.g. alignment scores)
Ronted (a) loTUs b) 3 ons (cl loTUs Number of possible phylogenetic trees KV/ 3 OTUs: 1 unrooted tree 3 rooted trees 4 OTUs:3 unrooted trees 15 rooted trees m three OTUs it is possible to construct only a single unrooted different rooted ones (b). From four OTUs it is possible to con- oted trees (c) and 15 rooted ones id)
Number of possible phylogenetic trees 3 OTU’s: 1 unrooted tree 3 rooted trees 4 OTU’s: 3 unrooted trees 15 rooted trees. 实用分类单位(operational taxonomic units，OTU)