bme 130 – genomes lecture 26 molecular phylogenies i
Post on 20-Dec-2015
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BME 130 – Genomes
Lecture 26
Molecular phylogenies I
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Cacao genome sequenced
http://www.cacaogenomedb.org/
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A phylogeny
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How can we construct a phylogeny?
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Convergent evolution (homoplasy)
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apomorphicplesiomorphicplesiomorphic
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Molecular phylogenies with sequence data
Benefits?
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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
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Outgroup can root a tree
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Anc: ACGTCGAGTTATTA
A: ATGTCGGGTTATTA
B: ACGTCGAGTCATTC
C: ACGCTGAGTCATTA
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Patterson and Reich (2006) Nature
441(7097):1103
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Sequence alignment is necessary for phylogenetic analysis
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Distance methods for phylogenetic reconstruction:UPGMA: pick two closest nodes, collapse, continueNeighbor-joining (NJ): pick two nodes that minimize total branch length, collapse, continue
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Bootstrapping to measure robustness of phylogenetic tree
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Phylogenetic methods that search tree-space
Maximum parsimony: correct tree is the one requiring the fewest changes
Maximum-likelihood: p(D|tree, M)
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The molecular clock
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