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Microbial Phylogenomics (EVE161) Class 4
The document is a lecture on microbial phylogenomics, discussing the importance of phylogenetic analysis and the evolution of species through various processes. It covers topics such as character states, homologous characters, divergence, tree reconstruction methods, and the extraction of gene trees from species trees. Key concepts include UPGMA for tree construction and the analysis of elongation factors in different organisms.
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Microbial Phylogenomics (EVE161) Class 4
- 1. Lecture 3: EVE 161: MicrobialPhylogenomics Lecture #4: Background on Phylogeny UC Davis, Winter 2016 Instructors: Jonathan Eisen & Holly Ganz
- 2. Where we aregoing 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
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- 4. Internal nodes representhypothetical 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 heritablefeature 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 iscritical 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
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- 11. UPGMA Unweighted Pair GroupMethod with Arithmetic mean (UPGMA) algorithm
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- 13. Distance Matrix ForTrue Tree
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- 15. Identify Lowest D OTUsA 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 TwoTaxa • Create branch with length = D • 2 • A--------------B
- 17. Make D fromNode Equal
- 18. Create New DistanceMatrix • Merge Two OTUs joined in previous step (AB) • Dx, AB = 0.5 * (Dx, A + Dx, B)
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- 21. Compare to TrueTree
- 22. But … • Whatis evolutionary rates not equal
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- 24. UPGMA with Unequalrates
- 25. Compare to TrueTree
- 26. Likelihood • Based onBayes’ Theorem • Prob(H|D) = Prob(H and D) ÷ Prob(D) • Prob(H|D) = Prob(D|H) x Prob(H) ÷ Prob(D)
- 27. Bayesian • Based onBayes’ Theorem • Prob(H|D) = Prob(H and D) ÷ Prob(D) • Prob(H|D) = Prob(D|H) x Prob(H) ÷ Prob(D)
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- 31. Woese 1987 -rRNA Microbiological Reviews 51:221 Woese
- 32. The Tree ofLife 2006 adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
- 33. The Tree ofLife 2006 adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
- 34. Simplified, Rooted Treeof Life
- 35. TTwo different kindsof elongation factors Elongation Factor Tu (EF-Tu) Elongation Factor G (EF-G) From Steitz Nature Reviews MCB 9: 242. 2008 Translation
- 36. TTwo different kindsof elongation factors in all organisms Who has two EFs?
- 37. EF-Tu EF-G EF-Tu EF-G EF-TuEF-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-TuEF-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
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- 42. EF-Tu EF-G EF-Tu EF-G EF-TuEF-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-TuEF-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 canextract 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 canextract 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-TUsare 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-Gsare Outgroup of EF-TUs Which taxa are an outgroup to EF-Tus? Elongation Factor Evolution
- 49. • For 9species ! 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-Gand EF-Tu Elongation Factor Evolution
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- 52. Identify different ElongationFactors 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
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- 54. Identify different ElongationFactors 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 ElongationFactors 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
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- 63. EF-Tu EF-G EF-Tu EF-G EF-TuEF-G Gene duplication event EF Eukaryotes Archaea Bacteria Elongation Factor Evolution
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