1. BIOE 109 Summer 2009 Lecture 4- Part II Phylogenetic Inference

2. What is phylogeny?

3. A B (a)None (b)Both are phylogenetic trees (c)Only A is phylogenetic tree (d)Only B is phylogenetic tree

4. Phylogeny: evolutionary history of a group of species or a gene. What is phylogeny?

5. Phylogeny: evolutionary history of a group of species or a gene Phylogenetic tree: graphical summary of the evolutionary history What is phylogeny?

7. Phylogeny describes:- 1.Pattern and/or timing of events that occurred as species diversified. 2. Sequence in which lineages appeared 3. Which organisms are more closely or distantly related.

8. Phylogenetic Inference Two points to keep in mind:

9. Phylogenetic Inference Two points to keep in mind: 1.Phylogenetic trees are hypotheses -how reliable?

10. Phylogenetic Inference Two points to keep in mind: 1. Phylogenetic trees are hypotheses 2. Gene trees are not the same as species trees

11. Phylogenetic Inference Two points to keep in mind: 1. Phylogenetic trees are hypotheses 2. Gene trees are not the same as species trees a species tree depicts the evolutionary history of a group of species.

12. Phylogenetic Inference Two points to keep in mind: 1. Phylogenetic trees are hypotheses 2. Gene trees are not the same as species trees a species tree depicts the evolutionary history of a group of species. a gene tree depicts the evolutionary history of a specific locus.

13. Conflict between gene trees and species trees

15. Phylogenetic Inference phylogenetic trees are built from “characters”.

16. Phylogenetic Inference phylogenetic trees are built from “characters”. characters can be morphological, behavioral, physiological, or molecular.

17. Phylogenetic Inference phylogenetic trees are built from “characters”. characters can be morphological, behavioral, physiological, or molecular. there are two important assumptions about the characters used to build trees:

18. Phylogenetic Inference phylogenetic trees are built from “characters”. characters can be morphological, behavioral, physiological, or molecular. there are two important assumptions about the characters used to build trees: 1. they are independent.

19. Phylogenetic Inference phylogenetic trees are built from “characters”. characters can be morphological, behavioral, physiological, or molecular. there are two important assumptions about characters used to build trees: 1. they are independent. 2. they are homologous.

20. What is a homologous character?

21. a homologous character is shared by two species because it was inherited from a common ancestor.

22. What is a homologous character? a homologous character is shared by two species because it was inherited from a common ancestor. a character possessed by two species but was not present in their recent ancestors, it is said to exhibit “homoplasy”.

23. Types of homoplasy:

24. Types of homoplasy: 1. Convergent evolution Example: evolution of eyes, flight.

25. Examples of convergent evolution

26. Types of homoplasy: 1. Convergent evolution Example: evolution of eyes, flight. 2. Parallel evolution Example: drug resistance in HIV.

27. What is the difference between convergent and parallel evolution?

28. What is the difference between convergent and parallel evolution? Convergent Parallel

29. What is the difference between convergent and parallel evolution? Convergent Parallel Species compared: distantly closely related related

30. What is the difference between convergent and parallel evolution? Convergent Parallel Species compared: distantly closely related related Trait produced by: different genes/same genes/ developmental developmental pathwayspathways

31. Types of homoplasy: 1. Convergent evolution Example: evolution of eyes, flight. 2. Parallel evolution Example: lactose tolerance in human adults 3. Evolutionary reversals Example: back mutations at the DNA sequence level (C  A  C).

32.    Evolutionary reversals are common in DNA sequences

33. Our objective is to identify monophyletic groups

34. A monophyletic group is derived from a single ancestral species and includes all descendants (e.g., mammals).

35. Three monophyletic groups:

36. Two mistakes are possible: 1. A paraphyletic group is derived from a single ancestral species but does not include all descendants.

37. Reptiles are paraphyletic

38. Two mistakes are possible: 1. A paraphyletic group is derived from a single ancestral species but does not include all descendants (e.g., reptiles). 2. A polyphyletic group fails to include the most recent common ancestor.

39. “Warm blooded animals” is a polyphyletic group

40. Contending schools of systematics 1. Phenetics (Distance methods)

41. Contending schools of systematics 1. Phenetics (Distance methods) Objectives: 1. Tree should reflect overall degree of similarity.

42. Contending schools of systematics 1. Phenetics (Distance methods) Objectives: 1. Tree should reflect overall degree of similarity. 2. Tree should be based on as many characters as possible.

43. Contending schools of systematics 1. Phenetics (Distance methods) Objectives: 1. Tree should reflect overall degree of similarity. 2. Tree should be based on as many characters as possible. 3. Tree should minimize the distance among taxa.

44. Examples of distance trees-HIV strains Discrete character data is converted into a distance value

45. Distance tree—HIV strains - Captures overall degree of similarity - Branch lengths are important -Drawbacks: (a) loss of information about which traits have changed. (b) have to correct for multiple substitutions at the same site. (c) the tree may not reflect “true” phylogenetic relationship

46. Contending schools of systematics 2. Cladistics

47. Contending schools of systematics 2. Cladistics Objectives: 1. Tree should reflect the true phylogeny.

48. Contending schools of systematics 2. Cladistics Objectives: 1. Tree should reflect the true phylogeny. 2. Tree should use characters that are shared (among two or more taxa) and derived (from some inferred or known ancestral state).

49. Contending schools of systematics 2. Cladistics Objectives: 1. Tree should reflect the true phylogeny. 2. Tree should use characters that are shared (among two or more taxa) and derived (from some inferred or known ancestral state). shared and derived characters are called synapomorphies.

50. Contending schools of systematics 2. Cladistics Objectives: 1. Tree should reflect the true phylogeny. 2. Tree should use characters that are shared (among two or more taxa) and derived (from some inferred or known ancestral state). shared and derived characters are called synapomorphies. 3. Ancestral state of characters inferred from an outgroup that roots the tree.

51. Contending schools of systematics 2. Cladistics Objectives: 1. Tree should reflect the true phylogeny. 2. Tree should use characters that are shared (among two or more taxa) and derived (from some inferred or known ancestral state). shared and derived characters are called synapomorphies. 3. Ancestral state of characters inferred from an outgroup that roots the tree. an outgroup is ideally picked from the fossil record.

52. Example of a cladogram

53. How do distance trees differ from cladograms?

54. Distance trees Cladograms

55. How do distance trees differ from cladograms? Distance trees Cladograms Characters used as many as synapomorphies possible only

56. How do distance trees differ from cladograms? Distance trees Cladograms Characters used as many as synapomorphies possible only Monophyly not required absolute requirement

57. How do distance trees differ from cladograms? Distance trees Cladograms Characters used as many as synapomorphies possible only Monophyly not required absolute requirement Emphasis branch lengths branch-splitting

58. How do distance trees differ from cladograms? Distance trees Cladograms Characters used as many as synapomorphies possible only Monophyly not required absolute requirement Emphasis branch lengths branch-splitting Outgroup not required absolute requirement

59. How do we select the “best” tree? No. of Taxa No. of possible trees 4 3

60. How do we select the “best” tree? No. of Taxa No. of possible trees 4 3 5 15

61. How do we select the “best” tree? No. of Taxa No. of possible trees 4 3 5 15 6 105

62. How do we select the “best” tree? No. of Taxa No. of possible trees 4 3 5 15 6 105 7 945

63. How do we select the “best” tree? No. of Taxa No. of possible trees 4 3 5 15 6 105 7 945 10 2 x 10 6

64. How do we select the “best” tree? No. of Taxa No. of possible trees 4 3 5 15 6 105 7 945 10 2 x 10 6 11 34 x 10 6

65. How do we select the “best” tree? No. of Taxa No. of possible trees 4 3 5 15 6 105 7 945 10 2 x 10 6 11 34 x 10 6 50 3 x 10 74

66. How do we select the “best” tree?

67. How do we select the “best” tree? A. Maximum parsimony: the “best” tree is that which minimizes the number of evolutionary steps (changes among characters).

68. How do we select the “best” tree? A. Maximum parsimony: the “best” tree is that which minimizes the number of evolutionary steps (changes among characters). -the simplest explanation is preferred over more complicated ones.

69. Examples of convergent evolution

70. Independent gain of camera eye requires two changes

71. Evolution and loss of camera eye requires six changes

72. How do we select the “best” tree? B. Maximum likelihood: the “best” tree is that which maximizes the likelihood of producing the observed data.

73. How do we select the “best” tree? B. Maximum likelihood: the “best” tree is that which maximizes the likelihood of producing the observed data. - likelihood scores are estimated from a specific model of base substitution and a specific tree.

74. How do we select the “best” tree? C. Bootstrapping

75. Evaluating tree support by bootstrapping Species 1 A A C G C C T… G Species 2 A T C G C C T… G Species 3 A T T G A C C… G Species 4 A T T G A C C… G

76. Evaluating tree support by bootstrapping Species 1 A A C G C C T… G Species 2 A T C G C C T… G Species 3 A T T G A C C… G Species 4 A T T G A C C… G Species 1 Species 2 Species 3 Species 4

77. Evaluating tree support by bootstrapping Species 1 A A C G C C T… G Species 2 A T C G C C T… G Species 3 A T T G A C C… G Species 4 A T T G A C C… G Step 1. Randomly select a base to represent position 1

78. Evaluating tree support by bootstrapping Species 1 A A C G C C T… G Species 2 A T C G C C T… G Species 3 A T T G A C C… G Species 4 A T T G A C C… G Step 1. Randomly select a base to represent position 1 Species 1 T Species 2 T Species 3 C Species 4 C 

79. Evaluating tree support by bootstrapping Species 1 A A C G C C T… G Species 2 A T C G C C T… G Species 3 A T T G A C C… G Species 4 A T T G A C C… G Step 2. Randomly select a base to represent position 2 Species 1 T G Species 2 T G Species 3 C G Species 4 C G 

80. Evaluating tree support by bootstrapping Step 3. Generate complete data set (sampling with replacement).

81. Evaluating tree support by bootstrapping Step 3. Generate complete data set (sampling with replacement). Step 4. Build tree and record if groupings match original tree.

82. Evaluating tree support by bootstrapping Step 3. Generate complete data set (sampling with replacement). Step 4. Build tree and record if groupings match original tree. Step 5. Repeat 1,000 times.

83. Species 1 Species 2 Species 3 Species 4 Evaluating tree support by bootstrapping 98 92