1. BME 130 – Genomes Lecture 26 Molecular phylogenies I

2. Cacao genome sequenced http://www.cacaogenomedb.org/

3. A phylogeny

4. How can we construct a phylogeny?

5. Convergent evolution (homoplasy)

6. apomorphic plesiomorphic

7. Molecular phylogenies with sequence data Benefits?

9. Number of trees # taxa# unrooted trees # rooted trees 313 4315 5 105 6 945 7 10395 8 135135 9 2027025 10202702534459425

10. Outgroup can root a tree

14. Anc: ACGTCGAGTTATTA A: ATGTCGGGTTATTA B: ACGTCGAGTCATTC C: ACGCTGAGTCATTA

15. Patterson and Reich (2006) Nature 441(7097):1103

16. Sequence alignment is necessary for phylogenetic analysis

18. 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

19. Bootstrapping to measure robustness of phylogenetic tree

20. Phylogenetic methods that search tree-space Maximum parsimony: correct tree is the one requiring the fewest changes Maximum-likelihood: p(D|tree, M)

21. The molecular clock