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BIS2C_2020. Lecture 13 Organelles and Endosymbiosis

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Slides for BIS2C 2020 at UC Davis by Jonathan Eisen

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BIS2C_2020. Lecture 13 Organelles and Endosymbiosis

  1. 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 BIS2C Biodiversity & the Tree of Life Spring 2020 Lecture 13: Organelles and Endosymbiosis Prof. Jonathan Eisen
  2. 2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Black necked stilt
  3. 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Yellow headed blackbird
  4. 4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Sora
  5. 5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Calidrid
  6. 6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Great horned owl
  7. 7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Ruddy Duck
  8. 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 American avocet
  9. 9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 White tailed kite
  10. 10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Anna’s hummingbird
  11. 11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Black chinned hummingbird
  12. 12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 White faced ibis
  13. 13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Hover fly
  14. 14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Skipper
  15. 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Gulf fritillary
  16. 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Tiger swallowtail
  17. 17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Mytila crescent
  18. 18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Damsel fly
  19. 19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 River otter
  20. 20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Learning Goals • Understand the models and the evidence that supports those models, that explain the origin of the nucleus, mitochondria and chloroplasts • Understand the differences between primary, secondary and tertiary endosymbioses • Understand how to track the multiple evolutionary histories within eukaryotic genomes that result from endosymbioses
  21. 21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 !12: Mutualisms and Microbiomes !13: Endosymbiosis and Organelles !14: Plants Lecture 13 Context
  22. 22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 13 Outline • Background and Context • Endosymbiosis and Organelles !Origin and evolution of the nucleus !Origin and evolution of mitochondria !Origin and evolution of chloroplasts
  23. 23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 13 Outline • Background and Context • Endosymbiosis and Organelles !Origin and evolution of the nucleus !Origin and evolution of mitochondria !Origin and evolution of chloroplasts
  24. 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Background: Lab • Many parts of Lab 3
  25. 25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Background: Lecture 12 Review
  26. 26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 12 Outline • Background and Context • Mutualisms • The Human Microbiome
  27. 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 12 Outline • Background and Context • Mutualisms • The Human Microbiome
  28. 28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Classes of symbiosis Organism Class of symbiosis A B Mutualism + +
  29. 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Mutualistic Symbioses of Bacteria w/ Eukaryotes • Digestive ! Ruminants ! Cellulolytic insects • Defensive • Behavioral ! Squid light organs • Autotrophic ! Photosynthetic (many) ! Chemosynthetic in deep sea • Nutritional ! Aphids ! Nitrogen fixation in legumes
  30. 30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 These worms with their symbionts function as chemolithoautotrophs. This is weird because “normal" worms and most other animals are A: Chemolithoheterotrophs B: Chemoorganoautotrophs C: Chemoorganoheterotrophs D: Photolithoautotrophs Thought Question
  31. 31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 12 Outline • Background and Context • Mutualisms • The Human Microbiome
  32. 32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Classes of symbiosis Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Microbes in human microbiome likely benefit. Many interactions with human microbiome likely “commensalism” because we do not know effect on humans
  33. 33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Classes of symbiosis Organism Class of symbiosis A B Mutualism + + Some associations in the human microbiome appear to be mutualistic
  34. 34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Story 1: The Obese Mouse
  35. 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Story 2: Disturbing the Microbiome Antibiotics Diet Changes Hygiene C-sections Story 2: Disturbing the Microbiome (vs expected)
  36. 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Story 3: Restoring the Microbiome • C-section story is an example of attempting to restore a disturbed microbiome • Many other examples
  37. 37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 13 Outline • Background and Context • Endosymbiosis and Organelles !Origin and evolution of the nucleus !Origin and evolution of mitochondria !Origin and evolution of chloroplasts
  38. 38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 13 Outline • Background and Context • Endosymbiosis and Organelles !Origin and evolution of the nucleus !Origin and evolution of mitochondria !Origin and evolution of chloroplasts
  39. 39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Nucleus: An organelle found in all eukaryotes
  40. 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Common Features of Eukaryotic Cells
  41. 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Additional Traits Common To Eukaryotes • Cell Structure !Cytoskeleton !Phagocytosis !Diverse organelles and compartments • Molecular Processes !Mitosis (vs. binary fission) !Sexual reproduction (vs. gene transfer) " Meiosis " Haploidy vs. Diploidy " Fertilization !Linear chromosomes & telomeres !Chromosomes packaged into chromatin !Decoupling of transcription and translation !Introns and splicing
  42. 42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 An ancestor of all eukaryotes Cell membrane Genome
  43. 43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Cell membrane Genome Nucleus An ancestor of all eukaryotes
  44. 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Cell membrane Genome Other Eukaryotic Features Nucleus An ancestor of all eukaryotes
  45. 45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Formation of nucleus & invention of many eukaryotic traits 1 1
  46. 46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Traits Shared by Eukaryotes and Asgard Archaea • Cell Structure !Cytoskeleton !Phagocytosis !Diverse organelles and compartments • Molecular Processes !Mitosis (vs. binary fission) !Sexual reproduction (vs. gene transfer) " Meiosis " Haploidy vs. Diploidy " Fertilization !Linear chromosomes & telomeres !Chromosomes packaged into chromatin !Decoupling of transcription and translation !Introns and splicing
  47. 47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Formation of nucleus & invention of many eukaryotic traits 1 1 Some key traits may have originated here
  48. 48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 13 Outline • Introduction • Origin and evolution of the nucleus • Origin and evolution of mitochondria • Origin and evolution of chloroplasts
  49. 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Mitochondrion: Organelle in (Almost) All Eukaryotes Respiration and production of ATP for eukaryotes
  50. 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Many similarities to bacteria / prokaryotic archaea But morphology not useful for phylogeny of bacteria & prokaryotic archaea Origin and evolution of mitochondria
  51. 51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 DNA Origin and evolution of mitochondria
  52. 52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thought Question • T/F • The fact that mitochondria have DNA genomes shows that they are derived from bacteria
  53. 53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thought Question • T/F • The fact that mitochondria have DNA genomes shows that they are derived from bacteria
  54. 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thought Question • T/F • The fact that mitochondria have DNA genomes shows that they are derived from bacteria • Prokaryotic Archaea have DNA genomes too and some look a lot like mitochondria
  55. 55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Origin and evolution of mitochondria
  56. 56. 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 PB AMito B Origin and evolution of mitochondria
  57. 57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 PB AMito B All mitochondrial trace a common ancestry to a single lineage within the alpha subgroup of the Proteobacteria phylum of Bacteria Origin and evolution of mitochondria
  58. 58. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lynn Margulis Konstantin Mereschkowski Origin and evolution of mitochondria Endosymbiotic Theory
  59. 59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 A common ancestor of eukaryotes Cell membrane Genome Nucleus
  60. 60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 A Proteobacterium αProteo Genome Bacterial cell envelope
  61. 61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Proteobacteria are Gram negative • Two major ways it is used in bacteria • Gram-positive bacteria - thick peptidoglycan layer outside 1 cell membrane • Gram-negative bacteria - thin peptidoglycan layer outside between two cell membranes • This has many impacts on biology, including sensitivity to antibiotics
  62. 62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 A Proteobacterium αProteo Genome Bacterial cell envelope
  63. 63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 A Symbiosis Between Eukaryote and a Proteobacterium Genome Bacterial cell envelope Cell membrane Genome Nucleus αProteo
  64. 64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Engulfment Nucleus Cell membrane Genome Genome Bacterial cell envelope αProteo
  65. 65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis Cell membrane Genome Genome Bacterial cell envelope Host membrane αProteo Endosymbiosis: when an organism (the host) bring another organism (the symbiont) inside of its cell. Nucleus
  66. 66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis Cell membrane Genome Genome Bacterial cell envelope Host membrane Endosymbiosis: when an organism (the host) bring another organism (the symbiont) inside of its cell. Is a “Primary symbiosis” because symbiont has not experienced a prior symbiosis Nucleus αProteo
  67. 67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis Cell membrane Genome Genome Bacterial cell envelope Host membrane αProteo Endosymbiosis: when an organism (the host) bring another organism (the symbiont) inside of its cell. Lost a membrane Nucleus
  68. 68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis Cell membrane Genome Genome Bacterial cell envelope Host membrane αProteo Endosymbiosis: when an organism (the host) bring another organism (the symbiont) inside of its cell. Lost cell wall Nucleus
  69. 69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Eukaryote with a Mitochondrion N Mitochondrion Genome M Nucleus Cell membrane Genome
  70. 70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Formation of nucleus & invention of many eukaryotic traits 1 1
  71. 71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Formation of nucleus & invention of many eukaryotic traits 1 Endosymbiosis with a Proteobacterium that became the mitochondrion 2 2 1 Note - Proteobacteria were already diverse at this point even though this tree does not show this
  72. 72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Eukaryotic Parts Have Different Histories Nucleus A model of a eukaryotic cell Bacteria Eukaryotes“Prok. Archaea” Nuclear Tree Mitochondrial Tree Eukaryotes Bacteria “Prok. Archaea”PB Mitochondrion
  73. 73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Eukaryotic Parts Have Different Histories Nucleus MitochondrionA model of a eukaryotic cell Bacteria Eukaryotes“Prok. Archaea” Nuclear Tree Mitochondrial Tree Eukaryotes Bacteria “Prok. Archaea”PB
  74. 74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Eukaryotic Parts Have Different Histories Nucleus MitochondrionA model of a eukaryotic cell Bacteria Eukaryotes“Prok. Archaea” Nuclear Tree Mitochondrial Tree Eukaryotes Bacteria “Prok. Archaea”PB
  75. 75. More Detailed Phylogeny of Eukaryotes Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Phylogeny of Eukaryotic Groups The exact phylogeny here does not matter and you do not need to know this full phylogeny.
  76. 76. N M N M N M N M N M N M N M N M N + + + + - + + + + Presence/Absence of Mitochondria Some eukaryotes do not have mitochondria Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Giardia = Diplomonad Trichomonas = Parabisalid Best explanation is that they lost their mitochondria
  77. 77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 13 Outline • Introduction • Origin and evolution of the nucleus • Origin and evolution of mitochondria • Origin and evolution of chloroplasts
  78. 78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Chloroplast: Organelle Found in Photosynthetic Eukarya
  79. 79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Many similarities to bacteria / prokaryotic archaea But morphology not useful for phylogeny of bacteria & prokaryotic archaea Origin and evolution of chloroplasts
  80. 80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 DNA Origin and evolution of chloroplasts
  81. 81. 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 Cyano “pA”CPST B Origin and evolution of chloroplasts
  82. 82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Chloroplast Phylogeny Conclusion: All Chloroplasts Have a Common Ancestry and Are Derived from A Single Cyanobacterial Lineage
  83. 83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Extending the Endosymbiosis Model …
  84. 84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Eukaryotic Cell N M Mitochondrion Mitochondrial Genome Nucleus Cell membrane Nuclear Genome
  85. 85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Cyanobacterium Cyano
  86. 86. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Cyanobacteria are Gram negative • Two major ways it is used in bacteria • Gram-positive bacteria - thick peptidoglycan layer outside 1 cell membrane • Gram-negative bacteria - thin peptidoglycan layer outside between two cell membranes • This has many impacts on biology, including sensitivity to antibiotics
  87. 87. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Symbiosis with Free Living Cyanobacterium N Mitochondrion Mitochondrial Genome M Nucleus Cell membrane Nuclear Genome Cyanobacterial Cell envelope Cyanobacterial Genome Cyano
  88. 88. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Engulfment N Mitochondrion Mitochondrial Genome M Nucleus Cell membrane Nuclear Genome Cyanobacterial Cell envelope Cyanobacterial Genome Cyano
  89. 89. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis N Mitochondrion Mitochondrial Genome M Nucleus Cell membrane Nuclear Genome Cyanobacterial Cell envelope Cyanobacterial Genome Cyano Is a “Primary symbiosis” because the symbiont has not experienced a prior symbiosis.
  90. 90. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis N Mitochondrion Mitochondrial Genome M Nucleus Cell membrane Nuclear Genome Chloroplast Cell envelope Chloroplast Genome Chloroplast Becomes the Chloroplast
  91. 91. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis N Mitochondrion Mitochondrial Genome M Nucleus Cell membrane Nuclear Genome Chloroplast Cell envelope Chloroplast Genome Chloroplast Outer chloroplast membrane lost in some
  92. 92. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis N Mitochondrion Mitochondrial Genome M Nucleus Cell membrane Nuclear Genome Chloroplast Cell envelope Chloroplast Genome Chloroplast Outer chloroplast membrane lost in some
  93. 93. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis N Mitochondrion Mitochondrial Genome M Nucleus Cell membrane Nuclear Genome Chloroplast Cell envelope Chloroplast Genome Chloroplast Chloroplast cell wall lost in some
  94. 94. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis N Mitochondrion Mitochondrial Genome M Nucleus Cell membrane Nuclear Genome Chloroplast Cell envelope Chloroplast Genome Chloroplast Chloroplast cell wall lost in some
  95. 95. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Formation of nucleus & invention of many eukaryotic traits 1 1
  96. 96. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Formation of nucleus & invention of many eukaryotic traits 1 Endosymbiosis with a Proteobacterium that became the mitochondrion 2 2 1
  97. 97. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Formation of nucleus & invention of many eukaryotic traits 1 Endosymbiosis with a Proteobacterium that became the mitochondrion 2 Endosymbiosis with a Cyanobacterium that became the chloroplast 3 3 2 1
  98. 98. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Eukaryotes with Chloroplasts: Three Histories Nucleus MITO CPST Bacteria “Pr. Archaea” Eukaryotes Nuclear Tree Mitochondrial Tree Eukaryotes Bacteria “Pr. Archaea”PB Chloroplast Tree Bacteria CBEukaryotes “Pr. Archaea”
  99. 99. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Eukaryotes with Chloroplasts: Three Histories Nucleus MITO CPST Bacteria “Pr. Archaea” Eukaryotes Nuclear Tree Mitochondrial Tree Eukaryotes Bacteria “Pr. Archaea”PB Chloroplast Tree Bacteria CBEukaryotes “Pr. Archaea”
  100. 100. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Scattered distribution of chloroplasts
  101. 101. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M C N M C N M C N M C N M C N M C Scattered distribution of chloroplasts Hypothesis 1: Ancestral AND Loss
  102. 102. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M C N M C N M C N M C N M C N M C Scattered distribution of chloroplasts Hypothesis 1: Ancestral AND Loss Not supported by analysis of phylogeny of chloroplasts. X
  103. 103. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M C N M N M N M N M N M Scattered distribution of chloroplasts Hypothesis 2: Diversification of Major Lineages Symbiosis in Plantae Ancestor And then other organisms with chloroplasts got them later …
  104. 104. The Plantae consist of several clades; all chloroplasts trace back to a single incidence of endosymbiosis. Plantae group w/in Eukaryotes Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  105. 105. Plantae group only have “simple” membrane around their chloroplasts Plantae group w/in Eukaryotes Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  106. 106. N M C N M C N M C N M C Each lineage accumulates some unique properties, such as sequences of some of their genes (N, M or C genes). N M C N M C N M C N M C N M C Plantae group w/in Eukaryotes Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  107. 107. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M C Scattered distribution of chloroplasts Hypothesis 2: Diversification of Major Lineages Symbiosis in Plantae Ancestor And then “Secondary Symbiosis” in other lineages
  108. 108. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Models and Examples • For the following topic you need to know the general models for additional symbioses in the history of chloroplasts and how to infer history of symbioses • You should also know which taxa are involved in the main examples covered
  109. 109. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Model for “Secondary” Symbiosis
  110. 110. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Symbiosis between two eukaryotic cells N M “Normal” eukaryote Blue membranes to help track
  111. 111. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Symbiosis between two eukaryotic cells Plantae representative with chloroplast Black Membranes to Help Track N M C
  112. 112. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Symbiosis between two eukaryotic cells N M “Normal” eukaryote Plantae representative with chloroplast N M C
  113. 113. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Engulfment N M N M C
  114. 114. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis N M N M C Symbiont Host Endosymbiosis: when an organism (the host) bring another organism (the symbiont) inside of its cell.
  115. 115. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis N M N M C Symbiont Host This is a “secondary” symbioses because the symbiont itself already was a host of other symbionts.
  116. 116. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thought Question N M N M C Symbiont Host This is a “secondary” symbioses because the symbiont itself already was a host of other symbionts. How many different histories could there be after a secondary endosymbiosis?
  117. 117. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M N M C Symbiont Host This is a “secondary” symbioses because the symbiont itself already was a host of other symbionts. How many different histories could there be after a secondary endosymbiosis? Thought Question
  118. 118. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M N M C Symbiont Host Loss of components Second mitochondria often lost
  119. 119. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis N M N C Symbiont Host Second mitochondria often lost
  120. 120. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis N M N C Symbiont Host Second nucleus often lost
  121. 121. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis N M C Symbiont Host Second nucleus often lost
  122. 122. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis N M C Symbiont Host Symbiont membrane sometimes lost
  123. 123. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis N M C Symbiont Host Symbiont membrane sometimes lost
  124. 124. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Examples
  125. 125. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Excavates: Euglenids • Have flagella. • Some are photosynthetic, some always heterotrophic, and some can switch. Movement in the euglenoid Eutreptia
  126. 126. N M N M N M N M N M N M C N M C N M C N M C N M C N M C N M C N M C N M C Euglena Nuclear DNA tells us what its phylogenetic backbone is Excavates: Euglenid Chloroplast Origins Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  127. 127. Euglena plastid DNA says its plastid is related to those of chlorophytes Excavates: Euglenid Chloroplast Origins Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  128. 128. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Model to explain this … 130
  129. 129. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 A lonely Excavate ... 131 N M
  130. 130. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M C Chlorophyte
  131. 131. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M C N M C N M C N M C N M C N M C N M C N M C N M C Chlorophyte
  132. 132. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M C Chlorophyte
  133. 133. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Symbiosis N M N M C
  134. 134. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Engulfment N M N M C
  135. 135. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis N M N M C
  136. 136. N M N M N M N M N M N M C N M C N M C N M C N M C N M C N M C N M C N M C Excavates: Euglenid Chloroplast Origins Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  137. 137. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Stramenopiles: Diatoms A colony of the diatom, Bacillaria paradoxa •Unicellular, but many associate in filaments. •Have carotenoids and appear yellow or brown. •Excellent fossil record •Most are photoautotrophic •Responsible for 20% of all carbon fixation. •Oil, gas source
  138. 138. N M N M N M N M N M Many lines of evidence indicate that it occurred in the common ancestor of the “Plantae” lineage. One line of evidence for this is that all organisms on this branch have chloroplasts and the cells of these organisms resemble the “primary” symbiotic cell. N M C N M C N M C N M C N M C N M C N M C N M C N M C Diatom nuclear DNA tells us what its phylogenetic backbone is Diatom Chloroplast Origins Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  139. 139. Diatom plastid DNA says its plastid is related to those of red algae Diatom Chloroplast Origins Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  140. 140. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 A lonely Stramenopile ... 142 N M
  141. 141. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 A lonely red algae ... 143 N M C
  142. 142. Red algae Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M C N M C N M C N M C N M C N M C N M C N M C N M C
  143. 143. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 A lonely red algae ... 145 N M C
  144. 144. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Symbiosis N M N M C
  145. 145. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Engulfment N M N M C
  146. 146. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Endosymbiosis N M N M C
  147. 147. N M N M N M N M N M N M C N M C N M C N M C N M C N M C N M C N M C N M C Diatom Chloroplast Origins Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  148. 148. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M N M N M N M N M N M C N M C N M C N M C N M C N M C N M C N M C N M C Many other secondary endosymbioses Apicomplexans Dinoflagellates Amoebozoans
  149. 149. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M N M N M N M N M N M C N M C N M C N M C N M C N M C N M C N M C N M C Many other secondary endosymbioses Apicomplexans Dinoflagellates Amoebozoans
  150. 150. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 •Most are marine and are important photoautotrophic primary producers •Mixture of pigments give them a golden brown color. •Have two flagella, one in an equatorial groove, the other in a longitudinal groove. Alveolates: Dinoflagellates Certium tenue Coral symbiont Tour - Don’t Need to Know These Details
  151. 151. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Alveolates: Apicomplexans • All parasitic • Have a mass of organelles at one tip —the apical complex that help the parasite enter the host’s cells. Apical complex • Plasmodium falciparum- Malaria kills 700,000-2,000,000 people per year—75% of them are African children 152 Tour - Don’t Need to Know These Details
  152. 152. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Not colonial; live as single cells • Some secrete shells or glue sand grains together to form a casing. • Many pathogens Amoebozoans: Loboseans Tour - Don’t Need to Know These Details
  153. 153. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Rhizaria: Cercozoans Some cercozoans are aquatic, others live in soil. They have diverse forms and habitats. One group has chloroplasts derived from a green alga by secondary endosymbiosis. Euglyphid Chlorarachnion reptans Tour - Don’t Need to Know These Details
  154. 154. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates
  155. 155. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Formation of nucleus & invention of many eukaryotic traits 1 1
  156. 156. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Formation of nucleus & invention of many eukaryotic traits 1 Endosymbiosis with a Proteobacterium that became the mitochondrion 2 2 1
  157. 157. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Formation of nucleus & invention of many eukaryotic traits 1 Endosymbiosis with a Proteobacterium that became the mitochondrion 2 Endosymbiosis with a Cyanobacterium that became the chloroplast 3 3 2 1
  158. 158. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Formation of nucleus & invention of many eukaryotic traits 1 Endosymbiosis with a Proteobacterium that became the mitochondrion 2 Endosymbiosis with a Cyanobacterium that became the chloroplast 3 3 2 1 Secondary
  159. 159. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Still Can’t Fit Model to Some Eukaryotes
  160. 160. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Dinoflagellate Kryptoperidinium foliaceum http://onlinelibrary.wiley.com/doi/10.1111/j.1550-7408.2007.00245.x/full
  161. 161. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 •All are multicellular; some get very large (e.g., giant kelp). •The carotenoid fucoxanthin imparts the brown color. •Almost exclusively marine. Stramenopiles: Brown Algae A community of brown algae: The marine kelp forest
  162. 162. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Model to Explain These
  163. 163. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Diatom Doing It’s Thing N M N M C Diatom
  164. 164. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M A Lonely Stramenopile Stramenopile
  165. 165. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M Symbiosis N M N M C Stramenopile Diatom
  166. 166. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M Engulfment N M N M C
  167. 167. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M Endosymbsiosis Host Symbiont This is a “tertiary” symbiosis because the symbiont itself already underwent a secondary symbiosis. N M N M C
  168. 168. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M Endosymbsiosis Host Symbiont Note - many of these organelles and genomes will have been lost sometime in the history of such tertiary symbioses. I am showing all of them here so that you can track where they would go IF everything was kept N M N M C
  169. 169. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M Thought Question Host Symbiont How many different histories could thereby after a tertiary symbiosis? N M N M C
  170. 170. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M Thought Question Host Symbiont How many different histories could thereby after a tertiary symbiosis? N M N M C
  171. 171. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M Many of the genomes and components frequently lost Host Symbiont Can end up like this C
  172. 172. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 N M N M N M N M N M N M C N M C N M C N M C N M C N M C N M C N M C N M C Tertiary endosymbioses? Brown Algae Tertiary Endosymbsiosis
  173. 173. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates
  174. 174. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Formation of nucleus & invention of many eukaryotic traits 1 1
  175. 175. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Formation of nucleus & invention of many eukaryotic traits 1 Endosymbiosis with a Proteobacterium that became the mitochondrion 2 2 1
  176. 176. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Formation of nucleus & invention of many eukaryotic traits 1 Endosymbiosis with a Proteobacterium that became the mitochondrion 2 Endosymbiosis with a Cyanobacterium that became the chloroplast 3 3 2 1
  177. 177. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Formation of nucleus & invention of many eukaryotic traits 1 Endosymbiosis with a Proteobacterium that became the mitochondrion 2 Endosymbiosis with a Cyanobacterium that became the chloroplast 3 3 2 1 Secondary
  178. 178. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Formation of nucleus & invention of many eukaryotic traits 1 Endosymbiosis with a Proteobacterium that became the mitochondrion 2 Endosymbiosis with a Cyanobacterium that became the chloroplast 3 3 2 1 Secondary Tertiary
  179. 179. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Past, Present and Future !12: Mutualisms and Microbiomes !13: Endosymbiosis and Organelles !14: Plants
  180. 180. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thistle
  181. 181. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Poppy
  182. 182. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Salsify

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