BME 130 – Genomes Lecture 26 Molecular phylogenies I.

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Presentation transcript:

BME 130 – Genomes Lecture 26 Molecular phylogenies I

Cacao genome sequenced

A phylogeny

How can we construct a phylogeny?

Convergent evolution (homoplasy)

apomorphic plesiomorphic

Molecular phylogenies with sequence data Benefits?

Number of trees # taxa# unrooted trees # rooted trees

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, continue Neighbor-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