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BiS2C: Lecture 7: The Tree of Life

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Slides for BIS2C at UC Davis Spring 2016.
Lecture by Jonathan Eisen.
Topic: The Tree of Life.

Publicado en: Ciencias
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BiS2C: Lecture 7: The Tree of Life

  1. 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Lecture 7: The Tree of Life: I BIS 002C Biodiversity & the Tree of Life Spring 2016 Prof. Jonathan Eisen 1
  2. 2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 About Me • At UC Davis since 2005 ! UC Davis Genome Center ! Dept. of Evolution and Ecology ! Dept. of Medical Microbiology and Immunology • Research: Evolution, ecology and function of communities of microbes • Open Science • More info ! Tree of Life blog: phylogenomics.blogspot.com ! Lab page: phylogenomics.wordpress.com ! Twitter: @phylogenomics 2
  3. 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Where we are going and where we have been • Previous Lecture: !6: Inferring Trees • Current Lecture: !7: The Tree of Life I • Next Lecture: !8: The Tree of Life II 3
  4. 4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 • Brad Pitt movie • Natural food remedies • Art by the arboretum • Name of my blog !4 Tree of Life Imagery is Everywhere 4
  5. 5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Thought Questions & Main Topics • If you found life on another planet, how could you determine if it was related to life on Earth? • What is the evidence that all life on Earth is related by a common descent and thus is on a single “Tree of Life”? • What is the structure of the Tree of Life? 5
  6. 6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Key Concepts from Previous Lectures • Groupings in trees: monophyly, sister taxa, outgroup, ingroup • Phylogeny inference • Trees: polytomies, rooted, unrooted • Trait evolution: ancestral & derived, homology • Traits: data matrices, alignments 6
  7. 7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Thought Questions & Main Topics • If you found life on another planet, how could you determine if it was related to life on Earth? • What is the evidence that all life on Earth is related by a common descent and thus is on a single “Tree of Life”? • What is the structure of the Tree of Life? 7
  8. 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Life on Mars 8
  9. 9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Life on Mars 8
  10. 10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Life on Mars 8
  11. 11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 • How would one determine if the Martian organisms are related to the Earth ones? 9 Life on Mars
  12. 12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Are These Separate Trees or Connected? 10 Life on EarthLife on Mars
  13. 13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Are These Separate Trees or Connected? 11 Life on EarthLife on Mars
  14. 14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Are These Separate Trees or Connected? 12 Life on EarthLife on Mars
  15. 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Evidence? • How could one determine if organisms on Mars were related to organisms on Earth? • (Assuming of course that Donald Trump is alive) 13
  16. 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Not Just A Thought Experiment 14
  17. 17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Dawn Sumner - UC Davis Geology Professor 15 http://geology.ucdavis.edu/people/faculty/sumner.php
  18. 18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Thought Questions & Main Topics • If you found life on another planet, how could you determine if it was related to life on Earth? • What is the evidence that all life on Earth is related by a common descent and thus is on a single “Tree of Life”? • What is the structure of the Tree of Life? 16
  19. 19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Diversity of Life 17
  20. 20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Darwin - Tree or maybe Trees of Life 18 “There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and wonderful have been, and are being, evolved.”
  21. 21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 19 “There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and wonderful have been, and are being, evolved.” Darwin - Tree or maybe Trees of Life
  22. 22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Are These Separate Trees or Connected? 20 Life on EarthLife on Earth Multiple Origins of Life on Earth
  23. 23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Are These Separate Trees or Connected? 21 Life on EarthLife on Earth Single Origin of Life on Earth
  24. 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Are These Separate Trees or Connected? 22 Life on EarthLife on Earth Single Origin of Life on Earth EVIDENCE????
  25. 25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Diversity of Life 23
  26. 26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Universal Traits: Examples 24
  27. 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Universal Traits: Examples ! Made up of cells ! Use of DNA as a genetic material ! Use of ACTG in DNA ! Use of ACUG in RNA ! Three letter genetic code ! Central dogma (DNA -> RNA -> protein) ! Use water as a solvent ! Lipoprotein cell envelope ! 20 core amino acids in proteins ! Live on Earth ! Ribosome for translation ! RNA polymerase proteins ! Store energy in chemicals ! Pump compounds in and out of cells 25
  28. 28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Homology vs. Homoplasy • Homology: similarity that is due to inheritance from a common ancestor • Homoplasy: similarity that has evolved independently • For a trait to be evidence that all organisms are related it must be universal AND homologous 26
  29. 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 ! Made up of cells ! Use of DNA as a genetic material ! Use of ACTG in DNA ! Use of ACUG in RNA ! Three letter genetic code ! Central dogma (DNA -> RNA -> protein) ! Use water as a solvent ! Lipoprotein cell envelope ! 20 core amino acids in proteins ! Live on Earth ! Ribosome for translation ! RNA polymerase proteins ! Store energy in chemicals ! Pump compounds in and out of cells 27 Universal Homologies The existence of Universal Homologies means all life on Earth is related.
  30. 30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Central Dogma in All Organisms 28 DNA, double stranded, w/ ACTG RNA w/ ACUG Transcription Translated into Proteins using tRNA using ribosomes using 3 letter code using 20 core amino acids Lipoprotein Cell Envelope Translation
  31. 31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Figure 14.6 The Genetic Code 29
  32. 32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Figure 14.14 Ribosome Structure 30
  33. 33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Thought Questions & Main Topics • If you found life on another planet, how could you determine if it was related to life on Earth? • What is the evidence that all life on Earth is related by a common descent and thus is on a single “Tree of Life”? • What is the structure of the Tree of Life? 31
  34. 34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Thought Questions & Main Topics • If you found life on another planet, how could you determine if it was related to life on Earth? • What is the evidence that all life on Earth is related by a common descent and thus is on a single “Tree of Life”? • What is the structure of the Tree of Life? • Historical Trees of Life 32
  35. 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 The Tree of Life 33
  36. 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Ernst Haeckel 1866 34www.mblwhoilibrary.org Plantae AnimaliaProtista
  37. 37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Whittaker – Five Kingdoms 1969 35 Plantae Animalia Protista Fungi Monera
  38. 38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Prokaryotes vs. Eukaryotes 36 EukaryotesProkaryotes
  39. 39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Prokaryotes vs. Eukaryotes 37 EukaryotesProkaryotes
  40. 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Limitations of This? • Are all prokaryotes the same? • Should we define organisms by the absence of a trait? 38
  41. 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Prokaryotes vs. Eukaryotes 39
  42. 42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Possible Trees 40 Tree 1 Prok Euk
  43. 43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 41 Tree 2 Alternative Trees Prok Euk
  44. 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 42 Tree 3 Alternative Trees Prok Euk
  45. 45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 43 Tree 4 Alternative Trees Prok Euk
  46. 46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Clicker 44
  47. 47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Which Tree is Most Parsimonious (character: nucleus)? 45 Tree 1 Tree 2 Tree 3 Tree 4 A)Tree 1 B)Tree 2 C)Tree 1&2 D)Tree 1&3 E)Tree 1,2,&3 P E
  48. 48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 46 Tree 1 Tree 2 Tree 3 Tree 4 P E Which Tree is Most Parsimonious (character: nucleus)? A)Tree 1 B)Tree 2 C)Tree 1&2 D)Tree 1&3 E)Tree 1,2,&3
  49. 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 21 1 Which Tree is Most Parsimonious? 47 Tree 1 Tree 2 Tree 3 Tree 4 P E 1
  50. 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 How many character state changes needed? 48 EukaryotesProkaryotes Tree 1
  51. 51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 49 Eukaryotes Ancestral Derived Prokaryotes Tree 1 Possible Ancestry #1 How many character state changes needed?
  52. 52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 50 Eukaryotes Given this tree … can we infer ancestral state? Ancestral Derived Prokaryotes Tree 1 Possible Ancestry #1
  53. 53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 51 Eukaryotes Given this tree … can we infer ancestral state? Derived Ancestral Prokaryotes Tree 1 Possible Ancestry #2
  54. 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 52 Eukaryotes Derived Ancestral Given this tree … can we infer ancestral state? Prokaryotes Tree 1 Possible Ancestry #2
  55. 55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Clicker 53
  56. 56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 In Which Tree are Prokaryotes Monophyletic 54 Tree 1 Tree 2 Tree 3 Tree 4 P E A) Tree 1 B) Tree 2 C) Trees 1 & 3 D) Trees 1 & 2 E) Trees 1,2,3
  57. 57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 In Which Tree are Prokaryotes Monophyletic? 55 Tree 1 Tree 2 Tree 3 Tree 4 P E A) Tree 1 B) Tree 2 C) Trees 1 & 3 D) Trees 1 & 2 E) Trees 1,2,3
  58. 58. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 In Which Tree are Prokaryotes Monophyletic? 56 Tree 1 Tree 2 P E Monophyletic Group = Clade A monophyletic group includes all of the descendant species of a given common ancestor
  59. 59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 In Which Tree are Eukaryotes Monophyletic 57 Tree 1 Tree 2 Tree 3 Tree 4 P E
  60. 60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Conclusion • Prokaryote vs eukaryote distinction does not tell us the topology of the tree 58
  61. 61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Thought Questions & Main Topics • If you found life on another planet, how could you determine if it was related to life on Earth? • What is the evidence that all life on Earth is related by a common descent and thus is on a single “Tree of Life”? • What is the structure of the Tree of Life? • Historical Trees of Life • The Modern Tree of Life 59
  62. 62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Diversity of Life 60
  63. 63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Carl Woese http://mcb.illinois.edu/faculty/profile/1204 61
  64. 64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62
  65. 65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62
  66. 66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62
  67. 67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62
  68. 68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62
  69. 69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62 rRNA rRNArRNA
  70. 70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62 rRNA rRNArRNA
  71. 71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG
  72. 72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG
  73. 73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG
  74. 74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG
  75. 75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG
  76. 76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG
  77. 77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG
  78. 78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG
  79. 79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG Eukaryotes
  80. 80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG Eukaryotes Eubacteria
  81. 81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG Eukaryotes Eubacteria
  82. 82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG Eukaryotes Eubacteria ????
  83. 83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG Eukaryotes Eubacteria
  84. 84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 62 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG Eukaryotes Eubacteria Archaebacteria
  85. 85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Unrooted Tree of Life from Woese 63
  86. 86. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 64 Eukaryotes Archaebacteria Eubacteria
  87. 87. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Archaea Dominate Extremely Hot Environments 65
  88. 88. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Archaea Dominate Extremely Salty Environments 66
  89. 89. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Table 26.1 The Three Domains of Life on Earth 67
  90. 90. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 68 Eukaryotes Archaebacteria Eubacteria
  91. 91. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 69 Eukaryotes Archaea Eubacteria
  92. 92. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 70 Eukaryotes Archaea Bacteria
  93. 93. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 71 Eukaryotes Archaea Bacteria
  94. 94. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 72 Eukaryotes Archaea Bacteria Can You Tell Which Groups are Sister Taxa from this?
  95. 95. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 73 Eukaryotes Archaea Bacteria What is Missing?
  96. 96. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Clicker 74
  97. 97. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Clicker How many different ways are there to root this tree? A: 0 B: 1 C: 2 D: 3 E: Not possible to determine 75 Eukaryotes Archaea Bacteria
  98. 98. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Clicker How many different ways are there to root this tree? A: 0 B: 1 C: 2 D: 3 E: Not possible to determine 76 Eukaryotes Archaea Bacteria
  99. 99. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 77 Eukaryotes Archaea Bacteria
  100. 100. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Eukaryotes BacteriaArchaea
  101. 101. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Eukaryotes BacteriaArchaea
  102. 102. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Eukaryotes BacteriaArchaea
  103. 103. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Eukaryotes BacteriaArchaea
  104. 104. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Eukaryotes BacteriaArchaea
  105. 105. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Eukaryotes Bacteria
  106. 106. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Eukaryotes Bacteria Archaea
  107. 107. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Eukaryotes Bacteria Archaea
  108. 108. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Eukaryotes Bacteria Archaea
  109. 109. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Eukaryotes Bacteria Archaea
  110. 110. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Eukaryotes Bacteria Archaea
  111. 111. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Bacteria Archaea
  112. 112. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Bacteria Archaea Eukaryotes
  113. 113. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Bacteria Archaea Eukaryotes
  114. 114. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Bacteria Archaea Eukaryotes
  115. 115. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Archaea Eukaryotes
  116. 116. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 78 Archaea BacteriaEukaryotes
  117. 117. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 79 Eukaryotes Archaea Bacteria
  118. 118. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 80 Eukaryotes Archaea Bacteria
  119. 119. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 81 Eukaryotes Archaea Bacteria
  120. 120. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 A Polytomous Three Domain Tree of Life 82 Bacteria Archaea Eukaryotes Polytomy
  121. 121. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Clicker Question 83
  122. 122. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Clicker 84 How Many Distinct Ways To Resolve this Polytomy? A: 1 B: 2 C: 3 D: 4 E: Can’t tell Bacteria EukaryotesArchaea
  123. 123. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Clicker 85 How Many Distinct Ways To Resolve this Polytomy? A: 1 B: 2 C: 3 D: 4 E: Can’t tell Bacteria Archaea Eukaryotes
  124. 124. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 86 Bacteria Eukaryotes Archaea and Bacteria as Sister Groups Archaea
  125. 125. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 87 Archaea Eukaryotes and Archaea as Sister Groups EukaryotesBacteria
  126. 126. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 88 Bacteria Eukaryotes and Bacteria as Sister Groups EukaryotesArchaea
  127. 127. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Resolving the Tree of Life Polytomy 89
  128. 128. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 90 Bacteria EukaryotesArchaea
  129. 129. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 91 Phylogenetic Inference polytomy
  130. 130. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 92 polytomy outgroup Phylogenetic Inference
  131. 131. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 93 outgroup Phylogenetic Inference
  132. 132. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 94 Outgroup Bacteria Archaea Eukaryotes Outgroup for the Tree of Life?
  133. 133. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 95 Bacteria Archaea Eukaryotes Outgroup for the Tree of Life?

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