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BIS2C_2020. Lecture 6. The Tree of Life.

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Slides for BIS2C "Biodiversity and the Tree of Life"
Class at UC Davis Spring 2020.
Lecture 6. The Tree of Life.

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BIS2C_2020. Lecture 6. The Tree of Life.

  1. 1. BIS2C Biodiversity & the Tree of Life Spring 2020 Lecture 6: The Tree of Life Prof. Jonathan Eisen
  2. 2. !5: Inferring Trees !6: The Tree of Life !7: The Domains of Life Lecture 6 Context
  3. 3. 1.Give examples of universal traits shared by all organisms 2.Understand how to determine which of these are evidence for common ancestry of life 3.Understand what “universal homologies” are 4.Understand why the existence of universal homologies means all life on earth has a common origin 5.Understand how to determine if life on another planet has common origin to life on Earth Lecture 6 Learning Goals
  4. 4. Lecture 6 Outline • Background and Context • Tree of Life vs. Trees of Life - Concept - Universal traits - Homology vs. Homoplasy - Universal homologies
  5. 5. Lecture 6 Outline • Background and Context • Tree of Life vs. Trees of Life - Concept - Universal traits - Homology vs. Homoplasy - Universal homologies
  6. 6. Background: About Me
  7. 7. Background: About Me • Jonathan Eisen • At UC Davis since 2005 • Evolution & Ecology • Medical Microbiology and Immunology • Genome Center • Center for Population Biology • Web site: phylogenomics.me • Tree of Life Blog: phylogenomics.blogspot.com • Twitter: @phylogenomics • Ted: tinyurl.com/EisenTed
  8. 8. • Lab 1: Introduction to Phylogeny !Phylogenetic methods !Phylogenetic trees !Homology, homoplasy !Characters, character states Background: Lab Connections
  9. 9. Lecture 6 Outline • Background and Context • Tree of Life vs. Trees of Life - Concept - Universal traits - Homology vs. Homoplasy - Universal homologies
  10. 10. Lecture 6 Outline • Background and Context • Tree of Life vs. Trees of Life - Concept - Universal traits - Homology vs. Homoplasy - Universal homologies
  11. 11. Diversity of Life of Earth
  12. 12. Diversity of Life of Earth Ignoring viruses for now
  13. 13. Tree of Life vs. Trees of Life “As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever- branching and beautiful ramifications.” Darwin, 1872
  14. 14. “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.” Tree of Life vs. Trees of Life
  15. 15. Key Questions for Today: • Is there a single tree of life or are there multiple trees of life? • Is there a single origin for all of life, or are there multiple origins? Tree of Life vs. Trees of Life
  16. 16. Tree of Life vs. Trees of Life Connect These on a Single Tree of Life
  17. 17. Connect These on a Single Tree of Life Tree of Life vs. Trees of Life
  18. 18. Branch Order Does Not Matter As Long As There Is A Single Common Ancestor Tree of Life vs. Trees of Life Connect These on a Single Tree of Life
  19. 19. Tree of Life vs. Trees of Life Connect These on a Single Tree of Life Branch Order Does Not Matter As Long As There Is A Single Common Ancestor
  20. 20. Tree of Life vs. Trees of Life Connect These on a Multiple Trees of Life
  21. 21. Tree of Life vs. Trees of Life Connect These on a Multiple Trees of Life
  22. 22. Tree of Life vs. Trees of Life Connect These on a Multiple Trees of Life Branch Order Does Not Matter As Long As There Is A Single Common Ancestor
  23. 23. Tree of Life vs. Trees of Life Connect These on a Multiple Trees of Life Branch Order Does Not Matter As Long As There Is A Single Common Ancestor
  24. 24. Tree of Life vs. Trees of Life Connect These on a Multiple Trees of Life Branch Order Does Not Matter As Long As There Is A Single Common Ancestor
  25. 25. Tree of Life vs. Trees of Life Connect These on a Multiple Trees of Life Branch Order Does Not Matter As Long As There Is A Single Common Ancestor
  26. 26. Thought Question In theory, how many separate Origins of Life could we have for these five taxa? A: 1 B: 2 C: 3 D: 4 E: 5
  27. 27. In theory, how many separate Origins of Life could we have for these five taxa? A: 1 B: 2 C: 3 D: 4 E: 5 Thought Question
  28. 28. Hypothesis 1: Separate Origins Hypothesis 2: Common Origin Two Hypotheses Tree of Life vs. Trees of Life How Can We Choose Which Hypothesis is Best?
  29. 29. • Recreate conditions of early Earth • Model and theory • Study Earth history • Inferences from comparing organisms How Do We Study The Origin(s) of Life?
  30. 30. • Recreate conditions of early Earth • Model and theory • Study Earth history • Inferences from comparing organisms How Do We Study The Origin(s) of Life?
  31. 31. Lecture 6 Outline • Background and Context • Tree of Life vs. Trees of Life - Concept - Universal traits - Homology vs. Homoplasy - Universal homologies
  32. 32. Universal Traits Universal Traits?
  33. 33. Which of the following is NOT a universal trait of all of life? A: Made up of cells B: Carry out transcription and translation C: Extract energy from the environment D: Universal molecular code to make proteins E: Contain genomes inside a nucleus Thought Question
  34. 34. Which of the following is NOT a universal trait of all of life? A: Made up of cells B: Carry out transcription and translation C: Extract energy from the environment D: Universal molecular code to make proteins E: Contain genomes inside a nucleus Thought Question
  35. 35. The basic structural and physiological unit of most living organisms is the A: Organelle B: Aggregate C: Genome D: Cell E: Membrane Thought Question
  36. 36. The basic structural and physiological unit of most living organisms is the A: Organelle B: Aggregate C: Genome D: Cell E: Membrane Thought Question
  37. 37. List traits found in all organisms. Universal Traits
  38. 38. List traits found in all organisms. Universal Traits Pause to Think
  39. 39. 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 Existence of universal traits does not prove all life has a common origin Universal Traits
  40. 40. Lecture 6 Outline • Background and Context • Tree of Life vs. Trees of Life - Concept - Universal traits - Homology vs. Homoplasy - Universal homologies • Martians
  41. 41. Homology Similarity that is due to inheritance from a common ancestor Homoplasy Similarity that has evolved independently Homology vs. Homoplasy
  42. 42. Slide by Brian Moore for BIS2C at UC Davis Spring 2018
  43. 43. Slide by Brian Moore for BIS2C at UC Davis Spring 2018
  44. 44. 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 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?
  45. 45. Homology vs. Homoplasy Assessment
  46. 46. Uses Water as Solvent Homology vs. Homoplasy: Water Could “uses water as a solvent" have evolved with a reasonable probability in separate origins of life?
  47. 47. Uses Water as Solvent Homology vs. Homoplasy: Water If YES: “uses water as a solvent" could have evolved with a reasonable probability in separate origins of life Thus this trait does not require a single tree of life. In other words, multiple trees are possible.
  48. 48. Uses Water as Solvent Homology vs. Homoplasy: Water If NO: “uses water as a solvent" could not have evolved with a reasonable probability in separate origins of life. Then only possibility is a single tree.
  49. 49. • Recreate conditions of early Earth • Model and theory • Study Earth history • Inferences from comparing organisms How Do We Study The Origin(s) of Life? Water abundant and likely only major available solvent for life.
  50. 50. Uses Water as Solvent Homology vs. Homoplasy: Water YES: “uses water as a solvent" could have evolved with a reasonable probability in separate origins of life. Thus this trait does not require a single tree of life. In other words, multiple trees are possible.
  51. 51. Uses Cells Homology vs. Homoplasy: Cells
  52. 52. Homology vs. Homoplasy: Cells Cells: Membrane bound compartments that are the fundamental building blocks of all organisms
  53. 53. Uses Cells Homology vs. Homoplasy: Cells Could “uses cells” have evolved with a reasonable probability in separate origins of life?
  54. 54. Homology vs. Homoplasy: Cells If YES: “uses cells" could have evolved with a reasonable probability in separate origins of life Thus this trait does not require a single tree of life. In other words, multiple trees are possible. Uses Cells
  55. 55. Homology vs. Homoplasy: Cells If NO: “uses cells” could not have evolved with a reasonable probability in separate origins of life. Then only possibility is a single tree. Uses Cells
  56. 56. • Recreate conditions of early Earth • Model and theory • Study Earth history • Inferences from comparing organisms How Do We Study The Origin(s) of Life? Cell-like structures can form from very simple components under early life conditions
  57. 57. Homology vs. Homoplasy: Cells YES: “uses cells” could have evolved with a reasonable probability in separate origins of life. Thus this trait does not require a single tree of life. In other words, multiple trees are possible. Uses Cells
  58. 58. Uses DNA as Genetic Material Homology vs. Homoplasy: DNA
  59. 59. Homology vs. Homoplasy: DNA Nucleic acids are made up of chains of nucleotides. Nucleotides are made up of a sugar, a base, and and a phosphate DNA = deoxyribonucleic acid RNA = ribonucleic acid
  60. 60. Uses DNA as Genetic Material Homology vs. Homoplasy: DNA Could “uses DNA” have evolved with a reasonable probability in separate origins of life?
  61. 61. Homology vs. Homoplasy: DNA If YES: “uses DNA” could have evolved with a reasonable probability in separate origins of life Thus this trait does not require a single tree of life. In other words, multiple trees are possible. Uses DNA as Genetic Material
  62. 62. Homology vs. Homoplasy: DNA If NO: “uses DNA” could not have evolved with a reasonable probability in separate origins of life. Then only possibility is a single tree. Uses DNA as Genetic Material
  63. 63. • Recreate conditions of early Earth • Model and theory • Study Earth history • Inferences from comparing organisms How Do We Study The Origin(s) of Life? Nucleotides form in early Earth conditions. DNA might form too and thus could readily be used by different origins of life.
  64. 64. Homology vs. Homoplasy: DNA MAYBE: “uses DNA” could have evolved with a reasonable probability in separate origins of life. Thus it is unclear if this trait requires a single tree of life or if multiple trees are possible. Uses DNA as Genetic Material
  65. 65. Homology vs. Homoplasy: DNA Might be evidence that there is one tree. Uses DNA as Genetic Material
  66. 66. Homology vs. Homoplasy: Central Dogma Central Dogma CD CD CD CD CD
  67. 67. CD CD CD CD CD DNA»RNA»Protein Homology vs. Homoplasy: Central Dogma
  68. 68. Homology vs. Homoplasy: Central Dogma
  69. 69. Could “the central dogma” have evolved with a reasonable probability in separate origins of life? Central Dogma Homology vs. Homoplasy: Central Dogma CD CD CD CD CD
  70. 70. • Recreate conditions of early Earth • Model and theory • Study Earth history • Inferences from comparing organisms How Do We Study The Origin(s) of Life? No clear reason why or how a separate origin of life could or would end up with DNA»RNA»protein
  71. 71. Central Dogma CD CD CD CD CD CD CD CD CD Homology vs. Homoplasy: Central Dogma NO: “uses central dogma” likely could not have evolved with a reasonable probability in separate origins of life. Then only likely possibility is a single tree.
  72. 72. Thus multiple origins of life is not likely Central Dogma Homology vs. Homoplasy: Central Dogma CD CD CD CD CD CD CD CD
  73. 73. Homology vs. Homoplasy Assessment
  74. 74. Ribosome For Translation Homology vs. Homoplasy: Ribosome for Translation
  75. 75. Homology vs. Homoplasy: Ribosome for Translation
  76. 76. • Recreate conditions of early Earth • Model and theory • Study Earth history • Inferences from comparing organisms 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
  77. 77. NO WAY: “uses ribosome for translation” could have evolved in separate origins of life. Then only possibility is a single tree. Homology vs. Homoplasy: Ribosome for Translation Ribosome For Translation
  78. 78. List common traits of all organisms. Homology vs. Homoplasy Overview
  79. 79. List common traits of 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 Homology vs. Homoplasy
  80. 80. Easily could be homoplasious List common traits of 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 Homology vs. Homoplasy
  81. 81. Might be homoplasious List common traits of 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 Homology vs. Homoplasy
  82. 82. Likely Homologous List common traits of 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 Homology vs. Homoplasy
  83. 83. List common traits of 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 Definitely Homologous Homology vs. Homoplasy
  84. 84. Lecture 6 Outline • Background and Context • Tree of Life vs. Trees of Life - Concept - Universal traits - Homology vs. Homoplasy - Universal homologies • Martians
  85. 85. Universal Trait Trait shared by all organisms. Universal Homology
  86. 86. Universal Homology Trait shared by all organisms that could not have arisen in separate origins of life and thus is evidence for common ancestry. Universal Homology
  87. 87. Hypothesis 1: Separate Origins Hypothesis 2: Common Origin Two Hypotheses Tree of Life vs. Trees of Life How Can We Choose Which Hypothesis is Best?
  88. 88. Hypothesis 2: Common Origin Hypothesis 1: Separate Origins Two Hypotheses Tree of Life vs. Trees of Life The existence of Universal Homologies means all life on Earth is related.
  89. 89. “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.” Tree of Life vs. Trees of Life
  90. 90. “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.” Tree of Life vs. Trees of Life
  91. 91. !5: Inferring Trees !6: The Tree of Life !7: The Domains of Life Lecture 6 Context

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