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BiS2C: Lecture 8: The Tree of Life II

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

Published in: Science
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BiS2C: Lecture 8: The Tree of Life II

  1. 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Lecture 8: The Tree of Life:II 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 Where we are going and where we have been • Previous Lecture: !7: The Tree of Life I • Current Lecture: !8: The Tree of Life II • Next Lecture: !9: Culture 2
  3. 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Thought Questions & Main Topics • How can the Tree of Life be rooted? • What is the overall structure of the Tree of Life? • How can we use this structure to better understand life? • What diversity (form, function, phylogeny) is there within each Domain? 3
  4. 4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Key Concepts • Rooting, ingroups and outgroups • Domains and Classification • Characters: states, ancestral, derived • Gene trees & species trees • Competing Trees of Life • Office Hours today 4-5 pm in 3089 SLB (CLC) 4
  5. 5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Thought Questions & Main Topics 5 • How can the Tree of Life be rooted? • What is the overall structure of the Tree of Life? • How can we use this structure to better understand life? • What diversity (form, function, phylogeny) is there within each Domain?
  6. 6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Woese Tree of Life 6 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
  7. 7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Unrooted Tree of Life from Woese 7
  8. 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 8 Eukaryotes Archaea Bacteria
  9. 9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Table 26.1: Features of the Three Domains of Life 9
  10. 10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 10 TEST HINT: STUDY THESE Table 26.1: Features of the Three Domains of Life
  11. 11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 11 Eukaryotes Archaea Bacteria
  12. 12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 12 Eukaryotes Archaea Bacteria D Domain K Kingdom P Phylum C Class O Order F Family G Genus S Species
  13. 13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Unrooted Tree of Three Primates 19 Humans Chimps Gorilla
  14. 14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 20 Resolving the Primate HCG Polytomy Humans GorillasChimps
  15. 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 22 Outgroup for the Tree of Life? Humans GorillasChimpsOrangutans
  16. 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Unrooted Tree of Three Primates w/ Outgroup 23 H C O G H O C G H G O C
  17. 17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Which of these Trees is Unique Compared to the Others 26 H C O G G O H C C G O H H O C G G H O C C G H O 1 2 3 6 5 4 A: 1 B: 3 C: 4 D: 5 E: none
  18. 18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Unrooted Tree of Three Primates w/ Outgroup 29 H C O G H O C G H G O C H GCO
  19. 19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Simplified Three Domain Unrooted Tree of Life 30 Eukaryotes Archaea Bacteria
  20. 20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 31 Outgroup Bacteria Archaea Eukaryotes Outgroup for the Tree of Life?
  21. 21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 32 Bacteria Archaea Eukaryotes Outgroup for the Tree of Life?
  22. 22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 33 Bacteria Archaea Eukaryotes Outgroup for the Tree of Life?
  23. 23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 34 Outgroup for the Tree of Life Bacteria Archaea Eukaryotes INGROUP Bacteria Archaea Eukaryotes OUTGROUP
  24. 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 35 Bacteria Archaea Eukaryotes Lots of Genes Within Each Species / Lineage
  25. 25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 36 Bacteria Archaea Eukaryotes Lots of Genes Within Each Species / Lineage Gene Trees & Species Trees Genes Within Genomes Have An Evolutionary History Too This Can Be Represented by a Phylogenetic Tree
  26. 26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 37 Bacteria Archaea Eukaryotes If Species Tree has AE Group, So Should Gene Tree
  27. 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 37 Bacteria Archaea Eukaryotes If Species Tree has AE Group, So Should Gene Tree
  28. 28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 38 Bacteria Archaea Eukaryotes If Species Tree Has AB Group So Should Gene Tree
  29. 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 39 Bacteria Archaea Eukaryotes EF EF-G EF-Tu Taxa Characters B1 EFG ACUGCACCUAUCGUUCG B2 EFG ACUCCACCUAUCGUUCG E1 EFG ACUCCAGCUAUCGAUCG E2 EFG ACUCCAGGUAUCGAUCG A1 EFG ACCCCAGCUCUCGCUCG A2 EFG ACCCCAGCUCUGGCUCG B1 EF2 ACAACAGCUCUGACUGG E1 EF2 CCAACAGCUCUGACUGG A1 EF2 ACAACAGUUUUGACUGG INGROUP OUTGROUP Gene Duplications Prior to MRCA of All Life Sandra Baldauf
  30. 30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 40 Semi-resolved Phylogeny of Elongation Factors Bacteria Archaea Eukaryotes EF-TU Bacteria Archaea Eukaryotes EFG
  31. 31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 41 If AB Together Should Be For Both EF2 and EFG Bacteria Archaea Eukaryotes EF-TU Bacteria Archaea Eukaryotes EFG
  32. 32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 42 If AE Together Should Be For Both EF2 and EFG Bacteria Archaea Eukaryotes EF-TU Bacteria Archaea Eukaryotes EFG
  33. 33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Thought Questions & Main Topics 43 • How can the Tree of Life be rooted? • What is the overall structure of the Tree of Life? • How can we use this structure to better understand life? • What diversity (form, function, phylogeny) is there within each Domain?
  34. 34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 46 A B E EFG A E B EFG E B A EFG EFG Rooted Tree of 3 Domains from EFTu (EFG Outgroup) Bacteria Archaea Eukaryotes EF-Tu
  35. 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Unrooted Tree of 3 Domains from EFG (EFTu Outgroup) 49 A B E EFTu A E B EFTu E B A EFTu EFTu Bacteria Archaea Eukaryotes EF-G
  36. 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 50 Phylogenetic Tree of Elongation Factors Bacteria Archaea Eukaryotes EF-TU Bacteria Archaea Eukaryotes EFG
  37. 37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 51 Bacteria Archaea Eukaryotes EF EF-G EF-Tu Taxa Characters B1 EFG ACUGCACCUAUCGUUCG B2 EFG ACUCCACCUAUCGUUCG E1 EFG ACUCCAGCUAUCGAUCG E2 EFG ACUCCAGGUAUCGAUCG A1 EFG ACCCCAGCUCUCGCUCG A2 EFG ACCCCAGCUCUGGCUCG B1 EF2 ACAACAGCUCUGACUGG E1 EF2 CCAACAGCUCUGACUGG A1 EF2 ACAACAGUUUUGACUGG INGROUP OUTGROUP Gene Duplications Prior to MRCA of All Life Sandra Baldauf
  38. 38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Elongation Factor Rooting 52
  39. 39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 54 Bacteria Archaea Eukaryotes Winner Three Domain Tree of Life
  40. 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Prokaryotes 55 Bacteria Archaea Eukaryotes Paraphyletic Rooted Three Domain Tree of Life
  41. 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Unrooted Tree of Life from Woese 56
  42. 42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Unrooted Tree of Life from Woese 57 ROOT
  43. 43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 58 Bacteria Archaea Eukaryotes Rooted Three Domain Tree of Life
  44. 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Unrooted Tree of Life from Woese 59 ROOT MAJOR DEBATE/AMBIGUITIES
  45. 45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Alternative Position of Eukaryote Branch 60 ROOT
  46. 46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 63 Bacteria Archaea Eukaryotes Eocyte Tree New Winner (maybe)
  47. 47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 64 Bacteria Archaea Eukaryotes Eocyte Tree TACK New Winner (maybe)
  48. 48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Loki 65
  49. 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Thought Questions & Main Topics 66 • How can the Tree of Life be rooted? • What is the overall structure of the Tree of Life? • How can we use this structure to better understand life? • What diversity (form, function, phylogeny) is there within each Domain?
  50. 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 67 Bacteria Archaea Eukaryotes Implications of the Rooted Tree of Life
  51. 51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 68 Bacteria Archaea Eukaryotes Similar to Implications of This Tree
  52. 52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Table 26.1 69
  53. 53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Evolution of Traits on a Tree • Tracing the Evolution of Traits and States • NOT using these characters to infer the branching patterns. • Branching patterns and rooting inferred from molecular sequence data. • Many of these characters would NOT be informative to infer the phylogenetic relationships among the groups 70
  54. 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Unique Bacterial Features 71
  55. 55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Unique Bacterial Features Cell envelope of bacteria contains peptidoglycan - a special polymer of amino sugars. Not seen in Archaea or Eukaryotes
  56. 56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 73 Bacteria Archaea Eukaryotes Peptidoglycan Has peptidoglycan No peptidoglycan
  57. 57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Unique Archaeal Features 75
  58. 58. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 77 Bacteria Archaea Eukaryotes Archaeal Membranes Ester Ether Read Ch 26 on the differences in membranes
  59. 59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 78 Bacteria Archaea Eukaryotes Ester Ether Archaeal Membranes
  60. 60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 79 Bacteria Archaea Eukaryotes Eocyte Tree TACK New Winner (maybe)
  61. 61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 80 Bacteria Archaea Eukaryotes Eocyte Tree TACK Ester Ether
  62. 62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Unique Eukaryotic Features
  63. 63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Nucleus 82
  64. 64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 83 Bacteria Archaea Eukaryotes N N N Has nucleus No nucleus Evolution of the Nucleus
  65. 65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 84 Bacteria Archaea Eukaryotes N N N N Has nucleus No nucleus Evolution of the Nucleus Gain of nucleus
  66. 66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Transcription and Translation in Eukaryotes 85 • Transcription by multiple
 RNA polymerases • Complex promoter and enhancer structures • Extensive splicing of RNA • Introns and Exons • Export of RNA out of nucleus • Translation in cytoplasm
  67. 67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Figure 9.19 Mitosis 86
  68. 68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Meiosis 87
  69. 69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Mitochondria 88
  70. 70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Fig 8-33 Telomerase carries a short RNA molecule that acts as a template for the addition of the complementary DNA sequence at the 3’ end of the double helix. In the ciliate Tetrahymena, the DNA sequence added is TTGGGG Telomeres 89
  71. 71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 90 Bacteria Archaea Eukaryotes Eukaryotes are Different … Many gains
  72. 72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 91 Bacteria Archaea Eukaryotes Features Shared by Bacteria and Archaea ++ ++ ++ ++
  73. 73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Binary Fission 92
  74. 74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 93 Bacteria Archaea Eukaryotes ++ ++ ++ ++ Evolution of Binary Fission No binary fission Has binary fission++ ++ ++ ++ ++ Loss of binary fission
  75. 75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 94 Bacteria Archaea Eukaryotes Evolution of Eukaryotes Many losses here too
  76. 76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 95 Bacteria Archaea Eukaryotes WHAT HAPPENED HERE? Eukaryotes are Different …
  77. 77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 96 Bacteria Archaea Eukaryotes Eocyte Tree SEARCH FOR THESE TACK
  78. 78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 97 Bacteria Archaea Eukaryotes Histones (for chromosome coiling) TACK - - - -
  79. 79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Thought Questions & Main Topics 98 • How can the Tree of Life be rooted? • What is the overall structure of the Tree of Life? • How can we use this structure to better understand life? • What diversity (form, function, phylogeny) is there within each Domain?
  80. 80. Figure 26.1 The Three Domains of the Living World Low-GC Gram-positives Origin of mitochondria ARCHAEA EUKARYA BACTERIA Origin of chloroplasts Origin of life Euryarchaeota Crenarchaeota All eukaryote phyla Proteo- bacteria Chlamydias Spirochetes Cyanobacteria Hadobacteria Hyperthermophilic bacteria High-GC Gram-positives
  81. 81. Figure 27.3 Precambrian Divergence of Major Eukaryote Groups
  82. 82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 101 Bacteria Archaea Eukaryotes Diversity Within Each Domain
  83. 83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 102 Bacteria Archaea Eukaryotes Diversity Within Each Domain
  84. 84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 103 Bacteria Archaea Eukaryotes Diversity Within Each Domain Tack
  85. 85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 104 Gram stains
  86. 86. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Gram stains • The gram stain method reveals two different types of bacterial cell walls. • Gram-positive bacteria have a thick layer of peptidoglycan outside the plasma membrane. • Gram-negative bacteria have a thin layer of peptidoglycan between the plasma membrane and another distinct outer membrane, in the periplasmic space. • Antibiotics such as penicillin interfere with the synthesis of the cell walls, but don’t affect eukaryote cells. 105
  87. 87. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Extreme Halophiles 106

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