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CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Consensus Trees Anders Gorm Pedersen Molecular Evolution Group Center for Biological Sequence Analysis Technical.

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1 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Consensus Trees Anders Gorm Pedersen Molecular Evolution Group Center for Biological Sequence Analysis Technical University of Denmark gorm@cbs.dtu.dk

2 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Strict Consensus Tree HuChGoOrGiHuChGoOrGi Tree 1 Tree 3 HuChGoOrGi Tree 2 HuChGoOrGi Strict consensus

3 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree HuChGoOrGiHuChGoOrGi Tree 1 Tree 3 Majority rule consensus HuChGoOrGi Tree 2 HuChGoOrGi

4 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F

5 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount

6 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount

7 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-

8 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I

9 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I

10 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I *-*-*-

11 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I *-*-*-I

12 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I *-*-*-I

13 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I *-*-*-I *-*-**I

14 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I *-*-*-I *-*-**I

15 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I *-*-*-I *-*-**I

16 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I *-*-*-I *-*-**I *-*---I

17 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I *-*-*-I *-*-**I *-*---I

18 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I *-*-*-I *-*-**I *-*---I

19 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I *-*-*-I *-*-**I *-*---I

20 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I *-*-*-II *-*-**I *-*---I

21 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I *-*-*-II *-*-**I *-*---I

22 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I *-*-*-II *-*-**I *-*---I

23 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I *-*-*-II *-*-**I *-*---I ***-*-I

24 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-I *-*-*-II *-*-**I *-*---I ***-*-I

25 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-II *-*-*-II *-*-**I *-*---I ***-*-I

26 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-II *-*-*-II *-*-**I *-*---I ***-*-I

27 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-II *-*-*-II *-*-**I *-*---I ***-*-I *---**I

28 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-II *-*-*-II *-*-**I *-*---I ***-*-I *---**I

29 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-II *-*-*-II *-*-**I *-*---I ***-*-I *---**I *--***I

30 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-II *-*-*-II *-*-**I *-*---I ***-*-I *---**I *--***I

31 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-II *-*-*-II *-*-**I *-*---I ***-*-I *---**I *--***I --*-*-I

32 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-II *-*-*-II *-*-**I *-*---I ***-*-I *---**I *--***I --*-*-I

33 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-II *-*-*-III *-*-**I *-*---I ***-*-I *---**I *--***I --*-*-I

34 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-II *-*-*-III *-*-**I *-*---I ***-*-I *---**I *--***I --*-*-I

35 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-II *-*-*-III *-*-**I *-*---I ***-*-II *---**I *--***I --*-*-I

36 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-II *-*-*-III *-*-**I *-*---I ***-*-II *---**I *--***I --*-*-I

37 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-III *-*-*-III *-*-**I *-*---I ***-*-II *---**I *--***I --*-*-I

38 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-III *-*-*-III *-*-**I *-*---I ***-*-II *---**I *--***I --*-*-I

39 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-III *-*-*-III *-*-**I *-*---I ***-*-III *---**I *--***I --*-*-I

40 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-III *-*-*-III *-*-**I *-*---I ***-*-III *---**I *--***I --*-*-I

41 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F ABCDEFCount *---*-III *-*-*-III *-*-**I *-*---I ***-*-III *---**I *--***II --*-*-I

42 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree ABCDEFCount *---*-III *-*-*-III *-*-**I *-*---I ***-*-III *---**I *--***II --*-*-I

43 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree ABCDEFFreq *---*-60 *-*-*-60 *-*-**20 *-*---20 ***-*-60 *---**20 *--***40 --*-*-20

44 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree ABCDEFFreq *-*-*-60 *---*-60 ***-*-60 *--***40 *-*-**20 *-*---20 *---**20 --*-*-20

45 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree ABCDEFFreq *-*-*-60 *---*-60 ***-*-60 *--***40 *-*-**20 *-*---20 *---**20 --*-*-20 E A B D F C

46 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree ABCDEFFreq *-*-*-60 *---*-60 ***-*-60 *--***40 *-*-**20 *-*---20 *---**20 --*-*-20 E A B D F C

47 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree ABCDEFFreq *-*-*-60 *---*-60 ***-*-60 *--***40 *-*-**20 *-*---20 *---**20 --*-*-20 E A B D F C 60

48 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree ABCDEFFreq *-*-*-60 *---*-60 ***-*-60 *--***40 *-*-**20 *-*---20 *---**20 --*-*-20 E A B D F C 60

49 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree E A B D F C 60 ABCDEFFreq *-*-*-60 *---*-60 ***-*-60 *--***40 *-*-**20 *-*---20 *---**20 --*-*-20

50 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree ABCDEFFreq *-*-*-60 *---*-60 ***-*-60 *--***40 *-*-**20 *-*---20 *---**20 --*-*-20 E A B D F C 60

51 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree ABCDEFFreq *-*-*-60 *---*-60 ***-*-60 *--***40 *-*-**20 *-*---20 *---**20 --*-*-20 E A B D F C 60

52 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree ABCDEFFreq *-*-*-60 *---*-60 ***-*-60 *--***40 *-*-**20 *-*---20 *---**20 --*-*-20  E A B D F C 60

53 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree ABCDEFFreq *-*-*-60 *---*-60 ***-*-60 *--***40 *-*-**20 *-*---20 *---**20 --*-*-20  E A B D F C 60

54 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree ABCDEFFreq *-*-*-60 *---*-60 ***-*-60 *--***40 *-*-**20 *-*---20 *---**20 --*-*-20  E A B D F C 60

55 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree ABCDEFFreq *-*-*-60 *---*-60 ***-*-60 *--***40 *-*-**20 *-*---20 *---**20 --*-*-20  E A B D F C 60

56 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree ABCDEFFreq *-*-*-60 *---*-60 ***-*-60 *--***40 *-*-**20 *-*---20 *---**20 --*-*-20  E A B D F C 60

57 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Majority Rule Consensus Tree E A B D F C 60 A E C F B D C A E B D F A E F D B C A E B C D F C E A B D F

58 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Anders Gorm Pedersen Molecular Evolution Group Center for Biological Sequence Analysis Technical University of Denmark gorm@cbs.dtu.dk

59 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Sankoff: length of 4 possible subtrees starting at internal node? CACAG A CGT

60 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Sankoff: length of subtree having nucleotide “A” at internal node CA 1 10 TGCA

61 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Sankoff: length of subtree having nucleotide “C” at internal node CA 1 1 0 1 TGCA

62 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS 1 12 1 1 CA Sankoff: length of subtree having nucleotide “G” at internal node TGCA

63 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS 1 122 1 1 CA Sankoff: length of subtree having nucleotide “T” at internal node TGCA

64 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS C A CAG 1 122 Sankoff: length of 4 possible subtrees starting at internal node?

65 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS 1 122 1212 C A C A G Sankoff: length of 4 possible subtrees starting at internal node?

66 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS 1 122 1212 A C A CA G Sankoff: length of shortest possible subtree having “A” at internal node?

67 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS 1 122 1212 A C A CA G Sankoff: length of shortest possible subtree having “A” at internal node? 1 0 length of subtree = 1+0+1 = 2

68 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS 1 122 1212 A C A CA G Sankoff: length of shortest possible subtree having “A” at internal node? 1 1 length of subtree = 1+1+2 = 4

69 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS 1 122 1212 A C A CA G Sankoff: length of shortest possible subtree having “A” at internal node? 1 1 length of subtree = 1+1+1 = 3

70 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS 1 122 1212 A C A CA G Sankoff: length of shortest possible subtree having “A” at internal node? 1 1 length of subtree = 1+1+2 = 4

71 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS 1 122 1212 A C A CA G Sankoff: length of shortest possible subtree having “A” at internal node? 1 0 length of subtree = 1+0+1 = 2

72 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS 1 122 1212 2 C A CA G Ancestral Reconstruction Step I: Keep Track of Shortest Subtrees

73 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step I: Keep Track of Shortest Subtrees 1 122 1212 22 C A CA G

74 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step I: Keep Track of Shortest Subtrees 1 122 1212 2223 C A CA G

75 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step I: Keep Track of Shortest Subtrees 1 122 1212 2223 3345 C A CA G

76 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step I: Keep Track of Shortest Subtrees 1 122 1212 2223 3345 C A CA G

77 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step II: BacktrackingA C A CA G

78 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step II: Backtracking A A A C A CA G

79 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step II: Backtracking A A A C A CA G

80 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step II: Backtracking A A A A C A CA G

81 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step II: Backtracking A A A A C A CA G

82 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step III: Placement of Changes A A A A C A CA G

83 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step II: Backtracking A A A AC C A CA G

84 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step II: Backtracking A C A AC AC C A CA G

85 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step II: Backtracking A C A AC AC C A CA G

86 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step II: Backtracking A C ACG AC AC C A CA G

87 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step II: Backtracking A C ACG AC AC C A CA G

88 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step III: Placement of Changes A C ACG AC AC C A CA G

89 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step III: Placement of Changes A C ACG AC AC C A CA G

90 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction Step III: Placement of Changes A C ACG AC AC C A CA G

91 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral Reconstruction: State Sets A C ACG AC AC C A CA G

92 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral reconstruction: experimental analysis of extinct molecules

93 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral reconstruction

94 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral reconstruction: dinosaur night vision

95 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral reconstruction: thermostability of ancestral proteins

96 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Ancestral reconstruction: thermostability of ancestral proteins

97 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Phylogeny and ancestral reconstruction for manuscripts

98 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Branch Lengths 0.250.75 0 0.25 0.5 0 0.750.5

99 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Problems With Parsimony Anders Gorm Pedersen Molecular Evolution Group Center for Biological Sequence Analysis Technical University of Denmark gorm@cbs.dtu.dk

100 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Phylogenetically Informative Sites 1 3 42 1 2 43 1 2 34 1: A C G G G G G A A 2: A C G G G G C A A 3: A C G C C G T A A 4: A C G C T C A A A

101 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Phylogenetically Informative Sites G C CG G G CC G G CC 1: A C G G G G G A A 2: A C G G G G C A A 3: A C G C C G T A A 4: A C G C T C A A A GC C C C C

102 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Not Informative G C TG G G TC G G CT 1: A C G G G G G A A 2: A C G G G G C A A 3: A C G C C G T A A 4: A C G C T C A A A G G G G G G

103 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Not Informative G G CG G G CG G G GC 1: A C G G G G G A A 2: A C G G G G C A A 3: A C G C C G T A A 4: A C G C T C A A A G G G G G G

104 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Not Informative G T AC G C AT G C TA 1: A C G G G G G A A 2: A C G G G G C A A 3: A C G C C G T A A 4: A C G C T C A A A C C T T C C

105 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Long Branch Attraction 1 2 3 4

106 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Long Branch Attraction A A A A A

107 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Uninformative A A A A A AA

108 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Uninformative A A A A A CA

109 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Uninformative A A A A A CG

110 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Misinformative A A A A A GG

111 CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS Informative A A G G A AG

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