Microbial Phylogenomics (EVE161) Class 4
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Microbial Phylogenomics (EVE161) at UC Davis Spring 2016. Co-taught by Jonathan Eisen and Holly Ganz. Class 4: Background on Phylogeny
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Microbial Phylogenomics (EVE161) Class 4
- 1. Lecture 3: EVE 161: Microbial Phylogenomics Lecture #4: Background on Phylogeny UC Davis, Winter 2016 Instructors: Jonathan Eisen & Holly Ganz
- 2. Where we are going and where we have been • Previous lecture: !3. Woese and the Tree of Life • Current Lecture: !4. Background on Phylogeny • Next Lecture: !5. Modern view of Tree of Life !2
- 4. Internal nodes represent hypothetical ancestral taxa a b c d e f g h root, root node terminal (or tip) taxa internal nodes internal branches u v w x y z t Terminal branches Parts of a phylogenetic tree !4
- 5. Characters • A heritable feature of an organism is known as a character (also character trait or trait). • The form that a character takes is known as its state (also known as character state). ! Note: Presence/absence can be a state • Example: ! Character = heart ! Character state = present/absent ! Character state = # of chambers !5
- 6. Characters ancestry is critical to understand • Characters that are inherited from a common ancestor are homologous. • Species change over time ! Known (generally) as divergence, or divergent evolution. ! Species change over time due to the combined processes of mutation, recombination, drift, selection, etc !6
- 11. UPGMA Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm
- 12. The True Tree
- 13. Distance Matrix For True Tree
- 15. Identify Lowest D OTUs A B C D E B 2 C 4 4 D 6 6 6 E 6 6 6 4 F 8 8 8 8 8
- 16. Join Those Two Taxa • Create branch with length = D • 2 • A--------------B
- 17. Make D from Node Equal
- 18. Create New Distance Matrix • Merge Two OTUs joined in previous step (AB) • Dx, AB = 0.5 * (Dx, A + Dx, B)
- 19. New Matrix
- 20. UPGMA
- 21. Compare to True Tree
- 22. But … • What is evolutionary rates not equal
- 23. Unequal rates
- 24. UPGMA with Unequal rates
- 25. Compare to True Tree
- 26. Likelihood • Based on Bayes’ Theorem • Prob(H|D) = Prob(H and D) ÷ Prob(D) • Prob(H|D) = Prob(D|H) x Prob(H) ÷ Prob(D)
- 27. Bayesian • Based on Bayes’ Theorem • Prob(H|D) = Prob(H and D) ÷ Prob(D) • Prob(H|D) = Prob(D|H) x Prob(H) ÷ Prob(D)
- 29. Rooting !29
- 31. Woese 1987 - rRNA Microbiological Reviews 51:221 Woese
- 32. The Tree of Life 2006 adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
- 33. The Tree of Life 2006 adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
- 34. Simplified, Rooted Tree of Life
- 35. TTwo different kinds of elongation factors Elongation Factor Tu (EF-Tu) Elongation Factor G (EF-G) From Steitz Nature Reviews MCB 9: 242. 2008 Translation
- 36. TTwo different kinds of elongation factors in all organisms Who has two EFs?
- 37. EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G MRCA EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G Elongation Factor Evolution
- 38. Zoom in ... EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G MRCA EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF Gene duplication event Elongation Factor Evolution
- 40. MRCA Gene duplication event EF-Tu EF-G EF EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G Elongation Factor Evolution
- 41. MRCA Gene duplication event EF-Tu EF-G EF EF-Tu EF-Tu EF-Tu EF-G EF-G EF-G Elongation Factor Evolution
- 42. EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G Gene duplication event EF EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G Elongation Factor Evolution
- 43. Lecture 7 Outline • Extracting the gene tree from the species tree Genes trees in species trees
- 44. EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G Gene duplication event EF We can extract the gene tree from the species tree Step 1: Remove species tree Elongation Factor Evolution
- 45. EF-G EF-G EF-G EF-G EF-G EF-G EF-G EF-G Gene duplication event EF-Tu EF-Tu EF-Tu EF-Tu EF-Tu EF-Tu EF-Tu EF-Tu EF We can extract the gene tree from the species tree Step 2: Untangle gene trees Elongation Factor Evolution
- 46. EF-G Gene duplication event EF-Tu EF We can extract the gene tree from the species tree Step 2: Untangle gene trees 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 EF-Tu EF-Tu EF-Tu EF-Tu EF-Tu EF-Tu EF-Tu EF-G EF-G EF-G EF-G EF-G EF-G EF-G Elongation Factor Evolution
- 47. EF-G Gene duplication event EF-Tu EF 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 EF-Tu EF-Tu EF-Tu EF-Tu EF-Tu EF-Tu EF-Tu EF-G EF-G EF-G EF-G EF-G EF-G EF-G Any/all EF-TUs are Outgroup of EF-Gs Which taxa are an outgroup to EF-Gs? Elongation Factor Evolution
- 48. EF-G Gene duplication event EF-Tu EF 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 EF-Tu EF-Tu EF-Tu EF-Tu EF-Tu EF-Tu EF-Tu EF-G EF-G EF-G EF-G EF-G EF-G EF-G Any/all EF-Gs are Outgroup of EF-TUs Which taxa are an outgroup to EF-Tus? Elongation Factor Evolution
- 49. • For 9 species ! Three archaea (A1, A2, A3) ! Three eukaryotes (E1, E2, E3) ! Three bacteria (B1, B2, B3) • Take their EF-TU and EF-G genes • Align them to each other ! This is your data matrix ! Note - there are lots of phylogenetically informative positions in the alignment • Build unrooted tree Elongation Factor Evolution
- 50. Alignment of EF-G and EF-Tu Elongation Factor Evolution
- 52. Identify different Elongation Factors E2 E3 B3 B1 B2 A1 A3 A2 E1 E1 E2 E3 B3 B1 B2 A1 A3 A2 EF-Tu EF-G Each species has one of each EF-G and EF-Tu Elongation Factor Evolution
- 53. • Rooting???? Rooting this tree?
- 54. Identify different Elongation Factors E1 E2 E3 B3 B1 B2 A1 A3 A2 E1 E2 E3 B3 B1 B2 A1 A3 A2 EF-Tu EF-G Root between the two forms Elongation Factor Evolution
- 55. Identify different Elongation Factors E1 E2 E3 B3 B1 B2 A1 A3 A2 E1 E2 E3 B3 B1 B2 A1 A3 A2 EF-Tu EF-G 1 2 3 E E E A A A B B B E E E A A A B B B EF-G EF-Tu 1 2 3 4 4 5 5 6 6 Trees are equivalent Elongation Factor Evolution
- 56. E1 E2 E3 A1 A2 A3 B1 B3 B2 E1 E2 E3 A1 A2 A3 B1 B3 B2 EF-G EF-Tu Gene duplication event Elongation Factor Evolution
- 57. E1 E2 E3 A1 A2 A3 B1 B3 B2 E1 E2 E3 A1 A2 A3 B1 B3 B2 EF-G EF-Tu Gene duplication event Outgroup Elongation Factor Evolution
- 59. E1 E2 E3 A1 A2 A3 B1 B3 B2 E1 E2 E3 A1 A2 A3 B1 B3 B2 EF-G EF-Tu Gene duplication event Outgroup Outgroup Elongation Factor Evolution
- 63. EF-Tu EF-G EF-Tu EF-G EF-Tu EF-G Gene duplication event EF Eukaryotes Archaea Bacteria Elongation Factor Evolution
- 64. Homoplasy !64
- 66. Jacknifing !66
- 67. Congruence !67
- 68. Masking !68