1. Phylogeny reconstruction How do we reconstruct the tree of life? Outline: Terminology Methods distance parsimony maximum likelihood bootstrapping Problems homoplasy hybridisation Dr. Sean Graham, UBC.

2. Phylogenetic reconstruction

3. Rooted trees Phylogenetic reconstruction

4. Rooted trees Outgroup: Phylogenetic reconstruction

5. Introduction

6. Birds Crocodiles Turtles Amphibians Mammals Lizards Snakes Turtles Amphibians MammalsLizards Snakes Crocodiles Birds Understanding Trees

7. Do these phylogenies agree? Figure 14.17

8. Branch lengths A B C D A B C D 1 nt change

9. Understanding Trees ABCDE Monophyletic ABCDE Paraphyletic ABCDE Polyphyletic Trees can be used to describe taxonomic groups

10. What is the relationship between taxonomic names and phylogenetic groups? BirdsCrocodilesTurtles Amphibians Mammals Lizards Snakes Amnion Amniotes

11. What is the relationship between taxonomic names and phylogenetic groups? BirdsCrocodilesTurtles Lizards Snakes Cold Blooded Reptiles

12. What is the relationship between taxonomic names and phylogenetic groups? Birds CrocodilesTurtles Amphibians Rodents Lizards Snakes Wings Bats

13. Polyphyletic example: Amentiferae

14. Ancestor with separate flowers Willows Walnuts Oaks Evolution of catkins

15. Vertebrate Phylogeny Are these groups monophyletic, paraphyletic or polyphyletic? fish? tetrapods? (= four limbed) amphibians? mammals? ectotherms (= warm blooded)?

16. Constructing Trees Methods: distance (UPGMA, Neighbor joining) parsimony maximum likelihood (Bayesian)

17. Distance Methods (phenetics)

18. Distance methods rely on clustering algorithms (e.g. UPGMA) Trait 1 Trait 2 A B C D Distance matrix ABCD A 1.03.04.9 B 3.33.0 C D Example 1: morphology

19. UPGMA Trait 1 Trait 2 A B C D Distance matrix ABCD A 1.03.04.9 B 3.33.0 C D A B Example 1: morphology

20. UPGMA Trait 1 Trait 2 A B C D Distance matrix ABCD A 1.03.04.9 B 3.33.0 C D A B C D Example 1: morphology

21. Distance matrix ABCD A 135 B 37 C 7 D Distance methods with sequence data A: ATTGCAATCGG B: ATTACGATCGG C: GTTACAACCGG D: CTCGTAGTCGA A B

22. New Distance matrix: take averages ABCD 36 C 7 D Distance methods with sequence data A B ABCD A 135 B 37 C 7 D

23. ABCD 36 C 7 D Distance methods with sequence data A B ABCD A 135 B 37 C 7 D C A B C D

24. ABCD 36 C 7 D Distance methods with sequence data A B ABCD A 135 B 37 C 7 D C A B C D

25. Assumptions of distance methods

26. Strengths and weaknesses of distance methods

27. II. Parsimony Methods (Cladistics) Hennig (German entomologist) wrote in 1966 Translated into English in 1976: very influential

28. Applying parsimony Consider four taxa (1-4) and four characters (A-D) Ancestral state: abcd ABCD 1a’bcd 2 b’cd’ 3a’b’c’d 4a’b’cd Trait Taxon

29. Applying parsimony Consider four taxa (1-4) and four characters (A-D) Ancestral state: abcd ABCD 1a’bcd 2 b’c’d’ 3a’b’c’d 4a’b’cd Trait Taxon 1234 a’bcda’b’c’d’a’b’c’da’b’cd a’ d’ c’ b Unique changes Convergences or reversals b’ 5 steps abcd

30. Applying parsimony Consider four taxa (1-4) and four characters (A-D) Ancestral state: abcd ABCD 1a’bcd 2 b’c’d’ 3a’b’c’d 4a’b’cd Trait Taxon 1432 a’bcda’b’cda’b’c’da’b’c’d’ a’ d’ c’ Unique changes Convergences or reversals b’ 4 steps abcd

31. Strengths and weaknesses of parsimony Strengths Weaknesses.

32. Parsimony practice Position Taxon1234567 KAGTACCG LAAGACTA MAACCTTA NAAAGTTA Which unrooted tree is most parsimonious? L M N K L KN M N L M K Plot each change on each tree. Positions 1 and 2 are done. Which positions help to determine relationships? 2 2 2

33. Inferring the direction of evolution Chimp Human Gorilla Bonobo Orangutan Mouse ACGCTAGCTACG ACGCTAGCTAGG Where did the mutation occur, and what was the change?

34. III. Maximum likelihood (and Bayesian)

35. Maximum likelihood: a starting sketch Probabilities –transition: 0.2transversion: 0.1no change 0.7 A CT G Transitions Transversions A T A G G C A G G A A C G G G A G G G G Find the tree with the highest probability

36. Maximum likelihood: a starting sketch Probabilities –transition: 0.2transversion: 0.1no change 0.7 A CT G Transitions Transversions A T A G G C A G G A A C G G G A G G G G A T G G G A T A G G Find the tree with the highest probability P = (.7)(.1)(.2)(.7)(.7)

37. Maximum likelihood: a starting sketch Probabilities –transition: 0.2transversion: 0.1no change 0.7 A CT G Transitions Transversions A T A G G C A G G A A C G G G A G G G G A T A G G A A G G G A A G G A C A G G A P = (.7)(.1)(.2)(.7)(.7) P = (.7)(.1)(.7)(.7)(.7) P = (.1)(.2)(.7)(.7)(.2) Find the tree with the highest probability

38. Assessment of Maximum Likelihood (also Bayesian) Strengths Weaknesses

39. Characters to use in phylogeny Morphology DNA sequence

40. Challenges of using DNA data Alignment can be very challenging! Taxon 1AATGCGC Taxon 2AATCGCT Taxon 1AATGCGC Taxon 2

41. Informative sequences evolve at moderate rates Too slow? –not enough variation –Taxon 1AATGCGC –Taxon 2AATGCGC –Taxon 3AATGCGC Polytomy

42. Example of insufficient evidence: metazoan phylogeny Fungi Metazoans

43. Challenges: sunflower phylogeny = 15 spp! = 12 spp! Recent radiation (200,000 years) Many species, much hybridization Need more rapidly evolving markers!!

44. Informative sequences evolve at moderate rates Too fast? –homoplasy likely –“saturation” – only 4 possible states for DNA –Taxon 1ATTCTGA –Taxon 2GTAGTGG –Taxon 3CGTGCTG Polytomy

45. Saturation Imagine changing one nucleotide every hour to a random nucleotide Split the ancestral population in 2. ACGTGCT One hour Four hours 12 hours ACTTGCT ACGAGCT ACCTGAA GCGATCC ACCAGAA AGCCTCC 8 hours AGCGGAA GAGCTCC Red indicates multiple mutations at a site 24 hours?

46. Saturation: mammalian mitochondrial DNA

47. Forces of evolution and phylogeny reconstruction How does each force affect the ability to reconstruct phylogeny? mutation? drift? selection? non-random mating? migration?

48. Phylogeny case study I: whales Are whales ungulates (hoofed mammals)? Figure 14.4

49. Whales: DNA sequence data Hillis, D. A. 1999. How reliable is this tree? Bootstrapping.

50. How consistent are the data? Take the dataset (5 taxa, 10 characters) Create a new data set by sampling characters at random, with replacement Taxon12345678910 HumanACGTTGTACT ChimpAGGTTCTATT BonoboAGGTTCTATG GorillaACTTGCTGTC OrangTCGTGTACCC Taxon382610 58873 HumanGACGTTTAATG ChimpGAGCTTTAATG Bonob o GAGCGGTAATG GorillaTGCCCCGGGTT OrangGCCTCCGCCAG

51. Whales: DNA sequence data Hillis, D. A. 1999.

52. Molecular clocks

53. Basic idea of molecular clocks chimps humans whales hippos 56 mya 60 substitutions 6 substitutions

54. Challenges for phylogeny: gene flow

55. Sunflower annuals

56. Different genes may have different histories!

57. Phylogeny summary

58. Phylogeny study questions 1)Explain in words the difference between monophyletic, paraphyletic, and polyphyletic taxa. Draw a hypothetical phylogeny representing each type. Give an actual example of a commonly recognized paraphyletic taxon in both animals and in plants. 2) How can a reconstructed phylogeny be used to determine if a similar character in two taxa is due to homoplasy? 3) Whales are classified as cetaceans, not artiodactyl ungulates. This makes artiodactyls paraphyletic – why? What is the evidence that whales belong in the artiodactyls? 4)Phenetics (distance methods) and cladistics (parsimony) differ in the ways they recognize and use similarities among taxa to form phylogenetic groupings. What types of similarity does each school recognize, and how useful is each type of similarity considered to be for identifying groups?

59. Phylogeny study questions 5) What is “bootstrapping” in the context of phylogenetic analysis, and why is this procedure performed? 6) Why are maximum likelihood methods increasing in popularity for reconstructing phylogenies? In your answer, include a short description of how this method identifies the best phylogeny. 7) For what kinds of data can maximum likelihood methods of phylogeny construction be used? Why is this so? What types of data are typically not used, and why? 8) Would animal mitochondrial DNA provide a reasonable molecular tool for evaluating deep phylogenetic relationships between animal phyla? What about ribosomal DNA? Justify your answers. 9) Integrative question: Draw a pair of axes with “Time since divergence” on the x axis and “percent of sites that are the same” on the y axis. Draw a graph that shows the basic pattern for third codon sites: is your graph linear? Explain why or why not.

60. Phylogeny study questions 10) You are studying a group of species that lives in two very different environments. You build two phylogenies: one is based on a locus that is probably under divergent selection in the two environments, while the other phylogeny is based on a neutral locus. Which phylogeny would be more likely to represent the species history? why? 11) For a number of years, Anolis lizards are found in similar micro- habitats on many separate islands in the Carribean are very similar to each other (for example, large lizards that feed on the ground, smaller lizards that feed on tree trunks, and very small lizards that feed at the tops of branches). Two different, historical explanations have been proposed to explain this pattern: each morph has evolved repeatedly on each island, or each morph has evolved just once, then dipsersed. Sketch a phylogeny that would support each hypothesis. 12) Integrative question: the Cameroon lake cichlid phylogeny, showing that the lake species were monophyletic, was based on mitochondrial DNA. Explain why this might not reflect the species history. How could you be more certain about the phylogeny? 13) Explain why allopolyploid taxa pose problems for phylogenies.