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BIS2C_2020. Lecture 7. The Domains of Life.

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Slides for BIS2C "Biodiversity and the Tree of Life"
Class at UC Davis Spring 2020.
Lecture 7. The Domains of Life.

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BIS2C_2020. Lecture 7. The Domains of Life.

  1. 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 BIS2C Biodiversity & the Tree of Life Spring 2019 Lecture 7: The Domains of Life Prof. Jonathan Eisen
  2. 2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Anna’s Hummingbird in Davis, CA. April 7, 2020 • In previous classes I would leave my screen saver on with pictures from around UC Davis and Davis area as people walked into class •
  3. 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Learning Goals 1. Understand ways in which the view of the tree of life has changed over time 2. Understand similarities and differences between prokaryotic and eukaryotic cell structures 3. Understand the uses of sequence alignments and comparisons in inferring the structure of the tree of life 4. Compare the structure and implications of the two current main competing models for the tree of life
  4. 4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 !6: The Tree of Life !7: The Domains of Life !8: Phylogenetic Diversity of Microbes Lecture 7 Context
  5. 5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 7 Outline • Background and Context • The Domains of Life !Introduction !“Prokaryotes” vs. Eukaryotes !Three Domain Tree of Life !Two Domain Tree of Life
  6. 6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 7 Outline • Background and Context • The Domains of Life !Introduction !“Prokaryotes” vs. Eukaryotes !Three Domain Tree of Life !Two Domain Tree of Life
  7. 7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Background: Lab Connections • Lab 2: Tree of life and LUCA • Lab 1: Classification and the tree of life • Lab 1: Monophyletic groups and Linnaean ranks • Lab 1: Phylogenetic terminology
  8. 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Background: Review of Lecture 6
  9. 9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Single Tree? L6: Tree of Life vs. Trees of Life
  10. 10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 L6: Tree of Life vs. Trees of Life Multiple Trees?
  11. 11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Hypothesis 1: Separate Origins Hypothesis 2: Common Origin Two Hypotheses L6: Tree of Life vs. Trees of Life How Can We Choose Which Hypothesis is Best?
  12. 12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 List traits found in all organisms. • 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 • Acquires energy from environment • Store energy in chemicals L6: Universal Traits Yes: not evidence for common ancestry. No: evidence for common ancestry. Could trait have evolved with a reasonable probability in separate origins of life?
  13. 13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 L6: Homology vs. Homoplasy: Ribosome for Translation
  14. 14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Recreate conditions of early Earth • Model and theory • Study Earth history • Inferences from comparing organisms L6: How Do We Study The Origin(s) of Life? Absolutely no way a separate origin of life would use the same ribosomes, with 50+ proteins, multiple rRNAs, and similar 3D structures and mechanisms
  15. 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 NO WAY: “uses ribosome for translation” could have evolved in separate origins of life. Then only possibility is a single tree. L6: Homology vs. Homoplasy: Ribosome for Translation Ribosome For Translation
  16. 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Universal Trait Trait shared by all organisms. L6: Universal Homology
  17. 17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Universal Homology Trait shared by all organisms that could not have arisen in separate origins of life and thus is evidence for common ancestry. L6: Universal Homology
  18. 18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Hypothesis 2: Common Origin Hypothesis 1: Separate Origins Two Hypotheses L6: Tree of Life vs. Trees of Life The existence of Universal Homologies means all life on Earth is related.
  19. 19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 7 Outline • Background and Context • The Domains of Life !Introduction !“Prokaryotes” vs. Eukaryotes !Three Domain Tree of Life !Two Domain Tree of Life
  20. 20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 7 Outline • Background and Context • The Domains of Life !Introduction !“Prokaryotes” vs. Eukaryotes !Three Domain Tree of Life !Two Domain Tree of Life
  21. 21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Single Tree A Single Tree of Life
  22. 22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Now, we care about the order. A Single Tree of Life
  23. 23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Now, we care about the order. A Single Tree of Life
  24. 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 The Tree of Life
  25. 25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Ernst Haeckel 1866 www.mblwhoilibrary.org Plantae AnimaliaProtista
  26. 26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Whittaker – Five Kingdoms 1969 Plantae Animalia Protista Fungi Monera
  27. 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 EukaryotesProkaryotes Chatton 1937 & others: Prokaryotes vs. Eukaryotes
  28. 28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 7 Outline • Background and Context • The Domains of Life !Introduction !“Prokaryotes” vs. Eukaryotes !Three Domain Tree of Life !Two Domain Tree of Life
  29. 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Cell Structure Observations Prokaryotes vs. Eukaryotes
  30. 30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures
  31. 31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures What Other Differences Are There?
  32. 32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures What Other Differences Are There? Mitochondria Endoplasmic Reticulum Diploid MeiosisBinary Fission Mitosis Golgi Linear DNACircular DNA Haploid Chromatin
  33. 33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 EukaryotesProkaryotes Prokaryotes vs. Eukaryotes Interpreted As Implying a Tree
  34. 34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic Eukaryotic P1 P2 P3 E1 E2 E3P4 Prokaryotes vs. Eukaryotes Interpreted as implying this tree because this would require only one event for the nucleus origin
  35. 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic Eukaryotic P1 P2 P3 E1 E2 E3P4 Prokaryotes vs. Eukaryotes Interpreted as implying this tree because this would require only one event for the nucleus origin
  36. 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic Eukaryotic P1 P2 P3 E1 E2 E3P4 Prokaryotes vs. Eukaryotes Interpreted as implying this tree because this would require only one event for the nucleus origin
  37. 37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 Prokaryotic Eukaryotic Prokaryotes vs. Eukaryotes Interpreted As Implying This Tree Because That Would Require Only One Event For Nucleus Origin But this is a mistake since this tree, also only requires one event for origin of the nucleus
  38. 38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 Prokaryotic Eukaryotic Prokaryotes vs. Eukaryotes As does this tree
  39. 39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic Eukaryotic P1 P2 P3 E1 E2 E3P4 Prokaryotes vs. Eukaryotes So no reason to assume this is the correct tree, even though many did
  40. 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Side lesson — Defining groups based on the absence of a trait is a bad idea … Prokaryotes vs. Eukaryotes
  41. 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 7 Outline • Background and Context • Problems with Life v11’s Tree of Life • The Domains of Life !Introduction !“Prokaryotes” vs. Eukaryotes !Three Domain Tree of Life !Two Domain Tree of Life
  42. 42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Three Domain Tree of Life • There is a better way …
  43. 43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Diversity of Life of Earth
  44. 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 http://mcb.illinois.edu/faculty/profile/1204 1970s - Woese et al. Carl Woese
  45. 45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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 Woese rRNA Tree of Life
  46. 46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Skeletons !All vertebrates have skeletons !The structure of the skeleton differs between species and skeletal comparisons can be used to infer phylogeny • rRNA !All organisms have ribosomal RNA !The sequence of the ribosomal RNA genes differ between species and sequence comparisons can be used to infer phylogeny Woese rRNA Tree of Life vs Skeletons
  47. 47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic Eukaryotic Woese rRNA Tree of Life
  48. 48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic Eukaryotic Tree is unrooted. Why? Woese rRNA Tree of Life
  49. 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Slide from Professor Moore’s Lecture 3
  50. 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic Eukaryotic What is Our Outgroup? Woese rRNA Tree of Life
  51. 51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic Eukaryotic What is Our Outgroup? Woese rRNA Tree of Life
  52. 52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Rooted using a special method that is similar to using an outgroup but is a little different • Involves using ancient gene duplication events Rooting the Tree of Life
  53. 53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic Rooted Woese rRNA Tree of Life
  54. 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic Thought Question Given this tree, if you group prokaryotic organisms together into “prokaryotes” this group can be described as: A: Not monophyletic B: A clade C. A natural grouping D: Prophyletic E: None of the above
  55. 55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic Given this tree, if you group prokaryotic organisms together into “prokaryotes” this group can be described as: A: Not monophyletic B: A clade C. A natural grouping D: Prophyletic E: None of the above Thought Question
  56. 56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Key Result #1: “Prokaryotes” Not Monophyletic “Prokaryotes” Eukaryotes Prokaryotic Eukaryotic Rooted Woese rRNA Tree of Life
  57. 57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Key Result #1: “Prokaryotes” Not Monophyletic “Prokaryotes” Eukaryotes Prokaryotic Eukaryotic Rooted Woese rRNA Tree of Life We Put Unnatural Groupings in Quotes
  58. 58. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Key Result #1: “Prokaryotes” Not Monophyletic “Prokaryotes” Eukaryotes Prokaryotic Eukaryotic FOCUS ON THESE KEY RESULTS Rooted Woese rRNA Tree of Life
  59. 59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic G1 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic Key Result #2: Two Major Monophyletic Groups of “Prokaryotes” Prokaryotic G2 Rooted Woese rRNA Tree of Life
  60. 60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic Key Result #3: Three Major Monophyletic Groups Rooted Woese rRNA Tree of LifeRooted Woese rRNA Tree of Life Prokaryotic G1 Prokaryotic G2 Eukaryotes
  61. 61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic Eukaryotes Rooted Woese rRNA Tree of Life Key Result #3: Three Major Monophyletic Groups Prokaryotic G1 Prokaryotic G2
  62. 62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic New Classification Level? Rooted Woese rRNA Tree of Life Key Result #3: Three Major Monophyletic Groups EukaryotesProkaryotic G1 Prokaryotic G2
  63. 63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Slide from Professor Moore’s Lecture 2
  64. 64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Domain: ???? Slide from Professor Moore’s Lecture 2
  65. 65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic New Classification Level? Rooted Woese rRNA Tree of Life Key Result #3: Three Major Monophyletic Groups EukaryotesProkaryotic G1 Prokaryotic G2
  66. 66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic The Three Domain Tree of Life The Three Domain Tree of Life EukaryotesProkaryotic G1 Prokaryotic G2 The Three Domains
  67. 67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryotesEubacteria Prokaryotic G2 Domain 1: Named “Eubacteria” (aka “true” bacteria)
  68. 68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryotesEubacteria Prokaryotic G2 Domain 2: What Should We Call It?
  69. 69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Figure 25.16 Some Crenarchaeotes Like It Hot
  70. 70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Figure 25.17 Extreme Halophiles
  71. 71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryotesEubacteria Archaebacteria Domain 2: Named “Archaebacteria” (Archae from Greek for ancient)
  72. 72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryotesEubacteria Archaebacteria BAD BAD Domain 2: Named “Archaebacteria” (Archae from Greek for ancient)
  73. 73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryotesEubacteria Archaea Domain 2: Renamed Archaea (Archae from Greek for Ancient)
  74. 74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryotesEubacteria Archaea Domain 2: Renamed Archaea (Archae from Greek for Ancient) BAD BAD BAD BAD
 BAD BAD BAD BAD
  75. 75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryotesEubacteria Archaea
  76. 76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryotesEubacteria Archaea Domain 1: Named “Eubacteria” (aka “true” bacteria)
  77. 77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryotesBacteria Archaea Domain 1: Removed the “Eu” part of the name
  78. 78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryaBacteria Archaea Domain 3: Named Eukarya
  79. 79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryotesBacteria Archaea Domain 3: Many Use Eukaryotes
  80. 80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryaBacteria Archaea Three Domains
  81. 81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 A3 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryaBacteria Archaea Three Domains Re-labelled individual taxa
  82. 82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 A3 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryaBacteria Archaea Key Result #4: Archaea closer to Eukarya than to Bacteria
  83. 83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 A3 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryaBacteria Archaea Key Result #4: Archaea closer to Eukarya than to Bacteria Some shared derived traits
  84. 84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures What Other Differences Are There? Mitochondria Endoplasmic Reticulum Diploid MeiosisBinary Fission Mitosis Golgi Linear DNACircular DNA Haploid Chromatin
  85. 85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures What Other Differences Are There? Mitochondria Endoplasmic Reticulum Diploid MeiosisBinary Fission Mitosis Golgi Linear DNACircular DNA Haploid Chromatin
  86. 86. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 7 Outline • Background and Context • Problems with Life v11’s Tree of Life • The Domains of life !Introduction !“Prokaryotes” vs. Eukaryotes !Three Domain Tree of Life !Two Domain Tree of Life
  87. 87. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 A3 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryaBacteria Archaea Three Domain Tree of Life Supported Widely for Many Year
  88. 88. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Loki’s Castle • Loki’s Castle
  89. 89. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lokiarchaea named after Loki’s Castle Vent Site
  90. 90. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Loki Prokaryotic Eukaryotic EukaryaBacteria Archaea Phylogenetic Trees Using Genomes from Lokiarchaea Look Like This Alternative to Three Domain Tree of Life
  91. 91. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thorarchaeota http://sites.utexas.edu/baker-lab/2016/01/29/introducing-thorarchaeota/
  92. 92. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Loki Prokaryotic Eukaryotic EukaryaBacteria Archaea Lokiarchaea and Thorarchaea Together in Trees Alternative to Three Domain Tree of Life Thor
  93. 93. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Asgard Archaea
  94. 94. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic EukaryaBacteria Archaea A New Clade - The Asgard Archaea - and and Alternative Tree of Life Alternative to Three Domain Tree of Life
  95. 95. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Asgard Archaea
  96. 96. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Asgard Archaea Something is Wrong Here
  97. 97. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Complaining on Twitter …
  98. 98. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Response ..
  99. 99. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Helarchaeota
  100. 100. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Helarchaeota
  101. 101. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Freya not next … Helarchaeota
  102. 102. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Alternative to Three Domain Tree of Life
  103. 103. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 A3 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryaBacteria Archaea Three Domain Tree
  104. 104. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic EukaryaBacteria Archaea New Tree with Asgard Archaea Alternative to Three Domain Tree of Life
  105. 105. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 A3 Prokaryotic Eukaryotic The Three Domain Tree of Life EukaryaBacteria Archaea Three Domain Tree
  106. 106. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic EukaryaBacteria Archaea New Tree with Asgard Archaea Alternative to Three Domain Tree of Life
  107. 107. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Method developments !Same data, with different methods, sometimes gives different results !Some methods are more prone to artifacts and errors than others • Differences between genes • Better taxonomic sampling !Can improve resolution in trees !Can help get around some method problems Reasons for Changes in the Tree of Life Two Domain Tree of Life
  108. 108. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic EukaryaBacteria Archaea How Does This Differ From The Three Domain Tree of Life? Alternative to Three Domain Tree of Life
  109. 109. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic EukaryaBacteria "Archaea” Alternative to Three Domain Tree of Life Key Difference #1: Archaea not monophyletic
  110. 110. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic EukaryaBacteria “Archaea” Alternative to Three Domain Tree of Life Key Difference #2: Asgard “Archaea” Closer to Eukaryotes than to Other “Archaea”
  111. 111. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic EukaryaBacteria "Archaea” Alternative to Three Domain Tree of Life Key Difference #3: Two Major Monophyletic Groups
  112. 112. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic Bacteria Alternative to Three Domain Tree of Life Renaming The Groups Archaea
  113. 113. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic Bacteria Two Domain Tree of Life Two Domain Tree of Life Archaea
  114. 114. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic Bacteria Two Domain Tree of Life Two Domain Tree of Life Archaea Eukarya “Prokaryotic Archaea”
  115. 115. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Past, Present and Future !6: The Tree of Life !7: The Domains of Life !8: Phylogenetic Diversity of Microbes

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