BME 130 – Genomes

Lecture 26

Molecular phylogenies I

Cacao genome sequenced

http://www.cacaogenomedb.org/

A phylogeny

How can we construct a phylogeny?

Convergent evolution (homoplasy)

apomorphicplesiomorphicplesiomorphic

Molecular phylogenies with sequence data

Benefits?

Number of trees# taxa # unrooted

trees# rooted trees

3 1 3

4 3 15

5 15 105

6 105 945

7 945 10395

8 10395 135135

9 135135 2027025

10 2027025 34459425

Outgroup can root a tree

Anc: ACGTCGAGTTATTA

A: ATGTCGGGTTATTA

B: ACGTCGAGTCATTC

C: ACGCTGAGTCATTA

Patterson and Reich (2006) Nature

441(7097):1103

Sequence alignment is necessary for phylogenetic analysis

Distance methods for phylogenetic reconstruction:UPGMA: pick two closest nodes, collapse, continueNeighbor-joining (NJ): pick two nodes that minimize total branch length, collapse, continue

Bootstrapping to measure robustness of phylogenetic tree

Phylogenetic methods that search tree-space

Maximum parsimony: correct tree is the one requiring the fewest changes

Maximum-likelihood: p(D|tree, M)

The molecular clock