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BIS2C. Biodiversity and the Tree of Life. 2014. L2. Trees, taxa and groups.

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BIS2C. Biodiversity and the Tree of Life.
At UC Davis Spring 2014.

Lecture 2.
Trees, taxa and groups.

Slides for Lectures by Jonathan Eisen

Published in: Science
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BIS2C. Biodiversity and the Tree of Life. 2014. L2. Trees, taxa and groups.

  1. 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 2 ! BIS 002C Biodiversity & the Tree of Life Spring 2014 ! Lecture 2: ! Phylogeny 2: Trees, Taxa, and Groups ! Prof. Jonathan Eisen 1
  2. 2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Where we are going and where we have been • Previous lecture: ! 1: Introduction & Overview • Current Lecture: ! 2: Trees, taxa and groups • Next Lecture: ! 3: Characters and traits 2
  3. 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Reading • Previous lecture: ! 1: Chapter 22 • Current Lecture: ! 2: Chapter 22 • Next Lecture: ! 3: Chapter 22 3
  4. 4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 2 Outline • Rotating phylogenetic trees ! • Components of a phylogenetic tree ! • Rotating branches in trees ! • Groupings in trees 5
  5. 5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 2 Outline 6 • Rotating phylogenetic trees ! • Components of a phylogenetic tree ! • Rotating branches in trees ! • Groupings in trees
  6. 6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Figure 22.1 The Components of a Phylogenetic Tree 7
  7. 7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept Entire phylogenetic trees can be rotated in any direction without changing their meaning. Ch. 25.1 8
  8. 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 9
  9. 9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree Present Past 9
  10. 10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree Present Past Vertical Tree 9
  11. 11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree Present Past Vertical Tree Draw This Tree 9
  12. 12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 A model phylogenetic tree 10 a b c d e f g hPresent Past
  13. 13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 A model phylogenetic tree 10 a b c d e f g hPresent Past
  14. 14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 A model phylogenetic tree 10 abcdefghPresent Past
  15. 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 A model phylogenetic tree 11 a b c d e f g h PresentPast Horizontal Tree
  16. 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Horizontal tree 12 Horizontal Tree
  17. 17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Horizontal tree 12 Horizontal Tree
  18. 18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Horizontal tree 12 Horizontal Tree
  19. 19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Horizontal tree 12 Horizontal TreeVertical Tree
  20. 20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 2 Outline • Rotating phylogenetic trees ! • Components of a phylogenetic tree ! • Rotating branches in trees ! • Groupings in trees 13
  21. 21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept A phylogenetic tree is made up by combining together a few simple units. Ch. 25.1 14
  22. 22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 15 Present Past
  23. 23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 16 a b c d e f g h
  24. 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 17 a b c d e f g h ????
  25. 25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree a b c d e f g h taxa taxon: any group of species that we designate a name (p543) (e.g., a) taxa: multiple taxons (e.g., a and b) 18
  26. 26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Taxa 19 four taxa (species) three taxa (domains)
  27. 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 20 ????
  28. 28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 21 nodes f g h i j k
  29. 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 22 nodes node: (1) common ancestor of taxa “above” the node (e.g., f is common ancestor of a & b) (2) splits in branches from one lineage into more f g h i j k
  30. 30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 23 ????
  31. 31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 24 internal nodes
  32. 32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 25 ????
  33. 33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 26 root node
  34. 34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 27 root node root node: (1) common ancestor of all taxa in the tree (2) point of earliest split in the tree
  35. 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 28 ????
  36. 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 29 branches: represent the evolution of taxa over time branches
  37. 37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 30 ????
  38. 38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 31 internal branches
  39. 39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 32 ????
  40. 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 33 terminal branches
  41. 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 34 ????
  42. 42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 35 root or root branch
  43. 43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h A model phylogenetic tree 36 root: branch leading up to the root node (i.e., the common ancestor of all taxa in tree) root or root branch
  44. 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g hPresent Past A model phylogenetic tree 37 taxa internal branches internal nodes root node terminal branches root
  45. 45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g hPresent Past A model phylogenetic tree 38 taxa internal branches internal nodes root node terminal branches root Questions ?????????
  46. 46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 2 Outline • Rotating phylogenetic trees ! • Components of a phylogenetic tree ! • Rotating branches in trees ! • Groupings in trees 39
  47. 47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: Rotation of Branches Each node in a tree can be rotated/spun around without changing the meaning of the tree. This is known as “branch rotation”. Ch. 25.1 40
  48. 48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h Branch rotation 41
  49. 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f g h Branch rotation 42 “Order” left-to-right has no specific meaning on a vertical tree
  50. 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 h ggha b c d e f Branch rotation 43 Consider this node g h The node can rotate around freely “Order” left-to-right has no specific meaning on a vertical tree
  51. 51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 h ggha b c d e f Branch rotation 43 Consider this node The node can rotate around freely “Order” left-to-right has no specific meaning on a vertical tree
  52. 52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 After rotation tree has same meaning a b c d e f h g Branch rotation 44 “Order” left-to-right has no specific meaning on a vertical tree
  53. 53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Figure 22.2 How to Read a Phylogenetic Tree (Part 2) 45
  54. 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Practice Question Practice Question 46
  55. 55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Consider the following three trees: Which of these statements is true? ! A) Tree #1 = Tree #2 B) Tree #1 = Tree #3 C) All three trees are equivalent D) All three trees are different Tree #1 U V W X Y Z Tree #2 W V U Y Z X Tree #3 U V W X Y Z 47 Practice Question
  56. 56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Consider the following three trees: Which of these statements is true? ! A) Tree #1 = Tree #2 B) Tree #1 = Tree #3 C) All three trees are equivalent D) All three trees are different Tree #1 U V W X Y Z Tree #2 W V U Y Z X Tree #3 U V W X Y Z 48 Practice Question
  57. 57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Consider the following three trees: Which of these statements is true? ! A) Tree #1 = Tree #2 B) Tree #1 = Tree #3 C) All three trees are equivalent D) All three trees are different Tree #1 U V W X Y Z Tree #2 W V U Y Z X Tree #3 U V W X Y Z 49 Practice Question
  58. 58. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Consider the following three trees: Which of these statements is true? ! A) Tree #1 = Tree #2 B) Tree #1 = Tree #3 C) All three trees are equivalent D) All three trees are different Tree #1 U V W X Y Z Tree #2 W V U Y Z X Tree #3 U V W X Y Z 50 Practice Question
  59. 59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Consider the following three trees: Which of these statements is true? ! A) Tree #1 = Tree #2 B) Tree #1 = Tree #3 C) All three trees are equivalent D) All three trees are different Tree #1 U V W X Y Z Tree #2 W V U Y Z X Tree #3 U V W X Y Z 51 Practice Question
  60. 60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Consider the following three trees: Which of these statements is true? ! A) Tree #1 = Tree #2 B) Tree #1 = Tree #3 C) All three trees are equivalent D) All three trees are different Tree #1 U V W X Y Z Tree #2 W V U Y Z X Tree #3 U V W X Y Z 52 Practice Question
  61. 61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Consider the following three trees: Which of these statements is true? ! A) Tree #1 = Tree #2 B) Tree #1 = Tree #3 C) All three trees are equivalent D) All three trees are different Tree #1 U V W X Y Z Tree #2 W V U Y Z X Tree #3 U V W X Y Z 53 Practice Question
  62. 62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Consider the following three trees: Which of these statements is true? ! A) Tree #1 = Tree #2 B) Tree #1 = Tree #3 C) All three trees are equivalent D) All three trees are different Tree #1 U V W X Y Z Tree #2 W V U Y Z X Tree #3 U V W X Y Z 54 Practice Question
  63. 63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Consider the following three trees: Which of these statements is true? ! A) Tree #1 = Tree #2 B) Tree #1 = Tree #3 C) All three trees are equivalent D) All three trees are different Tree #1 U V W X Y Z Tree #2 W V U Y Z X Tree #3 U V W X Y Z 55 Practice Question
  64. 64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Consider the following three trees: Which of these statements is true? ! A) Tree #1 = Tree #2 B) Tree #1 = Tree #3 C) All three trees are equivalent D) All three trees are different Tree #1 U V W X Y Z Tree #2 W V U Y Z X Tree #3 U V W X Y Z 56 Practice Question
  65. 65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Consider the following three trees: Which of these statements is true? ! A) Tree #1 = Tree #2 B) Tree #1 = Tree #3 C) All three trees are equivalent D) All three trees are different Tree #1 U V W X Y Z Tree #2 W V U Y Z X Tree #3 U V W X Y Z 57 Practice Question
  66. 66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Consider the following three trees: Which of these statements is true? ! A) Tree #1 = Tree #2 B) Tree #1 = Tree #3 C) All three trees are equivalent D) All three trees are different Tree #1 U V W X Y Z Tree #2 W V U Y Z X Tree #3 U V W X Y Z 58 Practice Question
  67. 67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 2 Outline • Rotating phylogenetic trees ! • Components of a phylogenetic tree ! • Rotating branches in trees ! • Groupings in trees 5959
  68. 68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 For many purposes it is useful to identify and name organisms that all share a common ancestry to the exclusion of other organisms Common ancestry and naming 60
  69. 69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 61 Where did HIV Come From?
  70. 70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Birds ARE Dinosaurs 62
  71. 71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Groupings in Trees: Monophyletic Groups • Groupings in trees ! Monophyletic groups 63
  72. 72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Monophyletic group: (1) a group of organisms consisting of a single node and ALL the descendants of that node in a tree and nothing else (2) a group of organisms consisting of their most recent common ancestor (MRCA) and all its descendants and nothing else ! Clade = a monophyletic group Key Concept: Monophyletic Group 64
  73. 73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f Monophyly 65
  74. 74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f Monophyly 65 Consider node k k
  75. 75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 The group enclosed in the yellow triangle is a monophyletic group for node k a b c d e h g f Monophyly 65 Consider node k k
  76. 76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Practice Question Practice Questions 66
  77. 77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 How many monophyletic groups in this tree?* a b c d e h g f 67 *In some senses, each taxon can be considered to be a clade, we ignore these here A: 1 B: 3 C: 5 D: 7 67 Practice Question
  78. 78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 How many monophyletic groups in this tree?* a b c d e h g f 68 *In some senses, each taxon can be considered to be a clade, we ignore these here A: 1 B: 3 C: 5 D: 7 68 Practice Question
  79. 79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 69 1: GH How many monophyletic groups in this tree?* 69 Practice Question
  80. 80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 70 1: GH 2: GHF How many monophyletic groups in this tree?* 70 Practice Question
  81. 81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 71 1: GH 2: GHF 3: EFGH How many monophyletic groups in this tree?* 71 Practice Question
  82. 82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 72 1: GH 2: GHF 3: EFGH 4: DEFGH How many monophyletic groups in this tree?* 72 Practice Question
  83. 83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 73 1: GH 2: GHF 3: EFGH 4: DEFGH 5: AB 1: GH 2: GHF 3: EFGH 4: DEFGH 5: AB How many monophyletic groups in this tree?* 73 Practice Question
  84. 84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 74 1: GH 2: GHF 3: EFGH 4: DEFGH 5: AB 6: ABC How many monophyletic groups in this tree?* 74 Practice Question
  85. 85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 75 1: GH 2: GHF 3: EFGH 4: DEFGH 5: AB 6: ABC 7: ABCDEFGH How many monophyletic groups in this tree?* 75 Practice Question
  86. 86. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Figure 22.3. Clades Represent an Ancestor and All of Its Descendants 76
  87. 87. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Groupings in Trees: Monophyletic Groups • Groupings in trees ! Monophyletic groups ! Non monophyletic groups 77
  88. 88. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Non-monophyletic groups are groups that include some but not all descendants of the most recent common ancestor of that group Non-Monophyletic groups a b c d e h g f Non monophyly 78
  89. 89. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 MRCA e, h, g, f are excluded Paraphyletic group a b c d e h g f Key Concept: Paraphyletic Group 79 Paraphyletic group: a group of organisms consisting of their MRCA but excluding some of its descendants
  90. 90. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 MRCA Polyphyletic group a b c d e h g f Key Concept: Polyphyletic Group Polyphyletic group: a group of organisms that excludes the MRCA of the group 80
  91. 91. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Practice Question Practice Questions 81
  92. 92. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 82 Lizards (including snakes) TurtlesCrocodilians Birds Why are Reptiles (in the traditional sense) paraphyletic? Reptiles (in red, not including birds) Example of a paraphyletic group: Reptiles (traditional sense) What kind of grouping are “reptiles”? Practice Question
  93. 93. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lizards (including snakes) TurtlesCrocodilians Birds Why are Reptiles (in the traditional sense) paraphyletic? Reptiles (in red, not including birds) Example of a paraphyletic group: Reptiles (traditional sense) What kind of grouping are “reptiles”? 83 Practice Question
  94. 94. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lizards (including snakes) TurtlesCrocodilians Birds Why are Reptiles (in the traditional sense) paraphyletic? Reptiles (in red, not including birds) Example of a paraphyletic group: Reptiles (traditional sense) Paraphyletic Group 84 Practice Question
  95. 95. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Practice Question Practice Questions 85
  96. 96. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 gha b c d e f Practice Question 86
  97. 97. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Are h and g monophyletic? gha b c d e f Practice Question 86
  98. 98. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Are h and g monophyletic? gha b c d e f Practice Question 86 1) Trace to most recent common ancestor (MRCA)
  99. 99. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Are h and g monophyletic? 2) Create group that includes MRCA and all descendants gha b c d e f Practice Question 86 1) Trace to most recent common ancestor (MRCA)
  100. 100. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Are h and g monophyletic? 2) Create group that includes MRCA and all descendants gha b c d e f Practice Question 86 1) Trace to most recent common ancestor (MRCA)3) Determine if any other modern taxa are in group
  101. 101. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Are h and g monophyletic? 2) Create group that includes MRCA and all descendants gha b c d e f Practice Question 86 1) Trace to most recent common ancestor (MRCA)3) Determine if any other modern taxa are in group 4) Answer?
  102. 102. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Practice Question Practice Question 87
  103. 103. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ga b c d e f 88 h Practice Question
  104. 104. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Are h and f monophyletic? h ga b c d e f 88 h Practice Question
  105. 105. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Are h and f monophyletic? h ga b c d e f 88 1) Trace to most recent common ancestor (MRCA) h Practice Question
  106. 106. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Are h and f monophyletic? h 2) Create group that includes MRCA and all descendants ga b c d e f 88 1) Trace to most recent common ancestor (MRCA) h Practice Question
  107. 107. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Are h and f monophyletic? h 2) Create group that includes MRCA and all descendants ga b c d e f 88 1) Trace to most recent common ancestor (MRCA)3) Determine if any other modern taxa are in group h Practice Question
  108. 108. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Are h and f monophyletic? h 2) Create group that includes MRCA and all descendants ga b c d e f 88 1) Trace to most recent common ancestor (MRCA)3) Determine if any other modern taxa are in group 4) Answer? h Practice Question
  109. 109. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Practice Question Practice Questions 89
  110. 110. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Which of the following are NOT monophyletic? A) ehgf B) dehgf C) bc D) abcdehgf a b c d e h g f 90 Practice Question
  111. 111. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 91 Which of the following are NOT monophyletic? A) ehgf B) dehgf C) bc D) abcdehgf Practice Question
  112. 112. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Practice Question Practice Question 92
  113. 113. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Unicellular eukaryotes 93 Practice Question
  114. 114. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 In the previous slide and lecture, a summary of the tree of life was presented ! Based on that tree, which of the following groups is NOT monophyletic? ! A. bacteria + archaea B. archaea + eukaryotes C. fungi D. animals E. plants 94 Practice Question
  115. 115. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 95 Unicellular eukaryotes Practice Question
  116. 116. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 96 Unicellular eukaryotes Bacteria + Archaea: includes MRCA but excludes some descendants Practice Question
  117. 117. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Unicellular eukaryotes Bacteria + Archaea: includes MRCA but excludes some descendants 97 This pattern is called? Practice Question
  118. 118. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Unicellular eukaryotes Bacteria + Archaea: includes MRCA but excludes some descendants Bacteria and archaea a non-monophyletic group 98 This pattern is called? Paraphyly
  119. 119. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 99 • Groupings in trees ! Monophyletic groups ! Non monophyletic groups ! Relatedness
  120. 120. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: Relatedness • Relatedness (in phylogenetics) is assessed by examining patterns of common ancestry on a tree 100
  121. 121. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Practice Question Practice Question 101
  122. 122. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f h g Is taxon e more closely related to d or g? 102 Practice Question
  123. 123. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f h g 103 This is answered to determining with which it shares a more recent common ancestor Is taxon e more closely related to d or g? Practice Question
  124. 124. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f h g 104 e-g common ancestor Practice Question
  125. 125. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f h g 105 e-g common ancestor e-d common ancestor Practice Question
  126. 126. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f h g 106 e-g common ancestor e-d common ancestor e is more closely related to g than it is to d Practice Question
  127. 127. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 107 • Groupings in trees ! Monophyletic groups ! Non monophyletic groups ! Relatedness ! Ingroups and outgroups
  128. 128. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 108 a b c d e h g f Ingroup: the group of taxa under study Ingroup 108 Key Concept: Ingroup
  129. 129. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 109 Outgroup: one or more taxa that are not members of the ingroup. a b c d e h g f Ingroup m n Outgroups 109 Key Concept: Outgroup
  130. 130. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 2 Outline 110 • Groupings in trees ! Monophyletic groups ! Non monophyletic groups ! Relatedness ! Ingroups and outgroups ! “Sisters”
  131. 131. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f Sister groups: two clades or species that are each other’s closest relatives (the two descendants of a single node) Key Concept: Sister groups 111111
  132. 132. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f g and h are “sisters” or “sister taxa” 112112 Key Concept: Sister groups
  133. 133. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f 113 The group “g and h” is sister to f f is sister to the group “g and h” 113 Key Concept: Sister groups
  134. 134. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Practice Question Practice Question 114114
  135. 135. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f What is the sister group of defgh? 115115 Practice Question
  136. 136. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f Answer: abc 116116 Practice Question
  137. 137. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e h g f Answer: abc By definition sister groups originate as lineages at the same time. Time of origination 117117 Practice Question
  138. 138. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 2 Outline 118 • Groupings in trees ! Monophyletic groups ! Non monophyletic groups ! Relatedness ! Ingroups and outgroups ! “Sisters” ! Polytomies
  139. 139. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f h g Our default tree 119119
  140. 140. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 a b c d e f h g Key Concept: Polytomy 120 * Polytomies are used to indicate ambiguity in the branching patterns. * Here the branching order among d-e-f-h-g is unknown.
 * In a polytomy, more than three branches connect to a node. polytomy 120
  141. 141. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Polytomy 121 So far we have been discussing bifurcating trees These are trees in which each internal node gives rise to two descendant branches.
  142. 142. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Bifurcating Tree 122 Bifurcating trees - each internal node gives rise to two descendant branches.
  143. 143. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Polytomy 123 polytomy Polytomies - some nodes have three or more descendant branches - usually reflect uncertainty about phylogenetic relationships.
  144. 144. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Extreme Polytomy 124 polytomy
  145. 145. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Polytomy 125 polytomy Three possible resolutions
  146. 146. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 126 Resolution 1:The beetle is more closely related to (fly + moth) than the wasp is polytomy *
  147. 147. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 127 * Resolution 1:The beetle is more closely related to (fly + moth) than the wasp is
  148. 148. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 polytomy Resolution 2:The wasp is more closely related to (fly + moth) than the beetle *
  149. 149. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 129 Resolution 2:The wasp is more closely related to (fly + moth) than the beetle *
  150. 150. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 130 polytomy What is the third possibility?
  151. 151. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 131 Resolution 3: Wasp and beetle are each others closest relatives
  152. 152. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 132 A B C D A B C D A B C D Units of character divergence Units of time Cladogram Phylogram Chronogram Different kinds of trees Only the relative branching order is depicted. No meaning to branch lengths. Branch length is proportional to the amount of character change Branch length is proportional to time

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