BIOL 102 Chp 26: Phylogeny and the Tree of Life

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This is a lecture presentation for my BIOL 102 General Biology II students on Chapter 26: Phylogeny and the Tree of Life (Biology 9E by Campbell et al).

Rob Swatski, Assistant Professor of Biology, Harrisburg Area Community College - York Campus, York, PA.
Email: rjswatsk@hacc.edu

Please visit my website, BioGeekiWiki, for more biology learning resources: http://robswatskibiology.wetpaint.com

Visit my Flickr photostream for anatomy model photographs!
http://www.flickr.com/photos/rswatski/

Thanks for looking!

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BIOL 102 Chp 26: Phylogeny and the Tree of Life

  1. 1. BIOL 102: General Biology II Rob Swatski Assoc. Prof. Biology HACC-York Chapter 26 Phylogeny & the Tree of Life 1
  2. 2. 2 New Species of 2015!
  3. 3. 3 Balanophora coralliformis – parasitic plant
  4. 4. 4 Cebrennus rechenbergi – cartwheeling spider
  5. 5. 5 Dendrogramma enigmatica – cnidarian relative?
  6. 6. 6 Deuteragenia ossarium – bone-house wasp
  7. 7. SnakeThis is NOT a Common Scaly-Foot Legless Lizard! 7
  8. 8. The Science of Classification Phylogeny Systematics: fossil, molecular, & genetic Taxonomy Binomial nomenclature 8
  9. 9. 9
  10. 10. 10
  11. 11. 11
  12. 12. 12
  13. 13. 13
  14. 14. 14
  15. 15. 15
  16. 16. Carolus Linnaeus (1707-1778) 1st “modern” taxonomy system based on physical appearances Two key features we still use: 1. Two-part scientific names 2. Hierarchical classification 16
  17. 17. 17
  18. 18. Systema Naturae 18
  19. 19. 19
  20. 20. Binomial Nomenclature The 1st part of the name is the Genus (always Capitalized) The 2nd name is the specific epithet (unique for each species in the Genus) The entire species name is italicized or underlined Both words together make up the scientific name of a species 2020
  21. 21. “Linnea, a plant of Lapland, lowly, insignificant, disregarded, flowering but for a brief space” - from Linnaeus who resembles it… 21
  22. 22. {“little chief nipple twister” (Greek)} Creative Scientific Names Brachyanax thelestrephones (fly) 22
  23. 23. {“vampire squid from Hell”} Vampyroteuthis infernalis 23
  24. 24. 24 Dinohyus hollandi “Holland is a terrible pig”
  25. 25. iago {“James”}, badius {Brown”}, {“King of Funk”} Funkotriplogynium iagobadius (mite) 25
  26. 26. Mackenziurus johnnyi, M. joeyi, M. deedeei, M. ceejayi 26
  27. 27. Metallichneumon neurospatarchus (icneumonid wasp) 27
  28. 28. Anophthalmus hitleri (blind cave beetle) Satan eurystomus (blind cave fish) {big-mouthed Prince of Darkness} Darthvaderum (mite) Han solo (trilobite) Bangiomorpha pubescens (fossil red alga) {1st recorded sex act} Cuterebra emasculator (bot flies) {eat testes of rodent hosts} More Creative Scientific Names! 28
  29. 29. Domain Kingdom Phylum Class Order Family Genus Species Hierarchical Classification 29
  30. 30. Do Keep Pot Clean Or Family Get Sick Hierarchical Classification 30
  31. 31. Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Domain: Bacteria Kingdom: Animalia Domain: Archaea Domain: Eukarya 31 Linnaean Classification
  32. 32. Order Family Panthera pardus (leopard) Genus Species Canis latrans (coyote) Taxidea taxus (American badger) Lutra lutra (European otter) Canis lupus (gray wolf) Felidae Carnivora PantheraTaxidea Mustelidae Lutra Canidae Canis Phylogenetic Tree 32
  33. 33. 33
  34. 34. 34
  35. 35. Modern Systematics Phylogeny-based Cladistics: PhyloCode (International Code of Phylogenetic Nomenclature) Recognizes only groups that include a common ancestor … … & all its descendents 3535
  36. 36. Phylogenetic Trees Represents a hypothesis about evolutionary relationships Each branch point represents the divergence of 2 species Sister taxa: groups sharing an immediate common ancestor Rooted tree: includes a branch representing the last common ancestor of all related taxa Polytomy: a branch from which more than 2 groups emerge (unresolved) 3636
  37. 37. Branch point: where lineages diverge ANCESTRAL LINEAGE This branch point represents the common ancestor of taxa A–G. (ROOT) This branch point forms a polytomy: an unresolved pattern of divergence. Sister taxa Basal taxon Taxon A Taxon B Taxon C Taxon D Taxon E Taxon F Taxon G 37
  38. 38. What Can We Learn from Phylogenetic Trees? Show patterns of descent They do NOT indicate when species evolved… … or how much genetic change occurred in a lineage We can’t assume that a taxon evolved from the taxon next to it on a tree 3838
  39. 39. Applications of Phylogeny Practical value! Provides valuable info about similar traits in closely-related species Ex: Identify species of food being sold as “whale” meat Ex: Identify source of a particular strain of bacteria 3939
  40. 40. 40 ??????
  41. 41. Minke (Southern Hemisphere) Unknowns #1a, 2, 3, 4, 5, 6, 7, 8 Minke (North Atlantic) Humpback (North Atlantic) Humpback (North Pacific) Gray Blue Unknowns #10, 11, 12 Unknown #13 Unknown #1b Unknown #9 Fin (Mediterranean) Fin (Iceland) RESULTS 41
  42. 42. A B A A B B C CC D D D (a) (b) (c) Which strain of Anthrax is it? 42
  43. 43. Sources of Phylogenetic Data Morphologies Genes Biochemistry Organisms with similar morphologies or DNA are likely to be more closely related than those with different morphologies or DNA 4343
  44. 44. Homology vs. Analogy Must distinguish between similarities when building a phylogeny Homology: similarity due to shared ancestry Analogy: similarity due to convergent evolution Convergent evolution 4444
  45. 45. Marsupial mole: develops in pouch Eutherian mole: develops in uterus Convergent Evolution of Burrowers 45
  46. 46. Convergent Evolution Occurs when similar enviro pressures & natural selection produce analogous adaptations in organisms from different evolutionary lineages Ex: Bat & bird wings are homologous as forelimbs … …. but analogous as functional wings Analogous traits that evolved independently are also called homoplasies 4646
  47. 47. 47 Why are most aliens in sci-fi movies hominids?
  48. 48. 48
  49. 49. Distinguishing Between Homology & Analogy Compare fossil evidence Compare the degree of complexity The more complex two similar structures are … … the more likely it is that they are homologous 4949
  50. 50. 50 Molecular Systematics Analyze comparable DNA segments (nuclear, mito, chloro) from different organisms Use computer programs & mathematical tools Recognizes only groups that include a common ancestor … Once homologous characters have been identified, they can be used to infer a phylogeny GenBank
  51. 51. Deletion Insertion 1 1 1 1 2 2 2 2 2 1 3 4 Aligning Segments of DNA (role of computers) 51
  52. 52. Molecular Homoplasies Two species that are not closely related can share 25% of their bases … … by coincidence! Mathematical tools are used to help identify homoplasies 5252
  53. 53. 53 Humans share… 7% of genes with bacteria 21% of genes with roundworms 36% of genes with fruitflies 85% of genes with zebrafish 98% of genes with chimpanzees
  54. 54. 54 http://www.ncbi.nlm.nih.gov/genbank/ A Molecular Homoplasy
  55. 55. Cladistics Grouping organisms by common descent Clade: a group of species that includes an ancestral species & all its descendants Clades can be nested into larger clades … … but not all groupings of organisms qualify as clades 5555 A B C D E F G Group I
  56. 56. 56
  57. 57. 57First appearance of specific traits
  58. 58. A B C D E F G Group I Monophyletic Clade (Group) Consists of the ancestor species & all its descendents 58
  59. 59. A B C D E F G Group II Paraphyletic Clade (Group) Consists of an ancestral species & some, but not all, of its descendents 59
  60. 60. Group  A B C D E F G Polyphyletic Clade (Group) Consists of various species that lack a common ancestor 60
  61. 61. 61 Prosimians (blue & red) Simians (yellow)Night-active primates (red)
  62. 62. 62 Lemurs
  63. 63. 63 Loris Tarsier *Lack a common ancestor
  64. 64. Shared Characters Shared ancestral character: originated in an ancestor of the taxon Shared derived character: an evolutionary novelty unique to a specific clade A character can be both ancestral & derived – it depends on the context Infer phylogenies knowing in which clade a shared derived character 1st appeared 6464
  65. 65. Ingroups & Outgroups Ingroup: the various species being studied Outgroup: A species (or group of species) closely related to the ingroup The goal is to differentiate between shared derived & shared ancestral characters Homologies shared by both the outgroup & ingroup are ancestral characters 6565
  66. 66. TAXA Leopard Bass Vertebral column (backbone) Hinged jaws Four walking legs Amniotic (shelled) egg Hair Character Table 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 11 111 1 11 1 1 11 11 Constructing a Phylogenetic Tree 66
  67. 67. 67 Do you see where this is headed… ?
  68. 68. Lancelet (outgroup) Lamprey Bass Frog Turtle Leopard Vertebral column Hinged jaws Four walking legs Amnion Hair Phylogenetic Tree (created from Character Table) 68
  69. 69. Drosophila Lancelet Zebrafish Frog Human Chicken Mouse In some trees, the length of a branch can reflect the # of genetic changes that have occurred in a particular DNA sequence in that lineage 69
  70. 70. Drosophila Lancelet Zebrafish Frog Human Chicken Mouse CENOZOIC Present65.5 MESOZOIC 251 Millions of years ago PALEOZOIC 542 In other trees, branch length can represent chronological time & branching points can be determined from the fossil record 70
  71. 71. Assumes that the tree requiring the fewest shared derived characters is the most likely Maximum Parsimony 71 K I S S
  72. 72. A tree can be found that reflects the most likely sequence of evolutionary events, given certain rules about how DNA changes over time Maximum Likelihood 72
  73. 73. Percentage differences between sequences Human 40% 40% 30%0 0 0 Human Mushroom Mushroom Tulip Tulip 73 Trees with different likelihoods
  74. 74. 15% Tree 1: More likely Tree 2: Less likely 15% 15% 5% 5% 10% 25%20% Comparison of possible trees with different likelihoods 74
  75. 75. Phylogenetic Trees as Hypotheses The best hypotheses for phylogenetic trees fit the most data Use morphological, molecular, & fossil data Phylogenetic bracketing: use features of descendents to predict features of an ancestor (“reverse engineering”) Infer features of dinosaurs from their descendents: birds & crocodiles 7575
  76. 76. Common ancestor of crocodilians, dinosaurs, & birds Birds Lizards & snakes Crocodilians Ornithischian dinosaurs Saurischian dinosaurs Phylogenetic tree of birds & their close relatives 76
  77. 77. Fossil remains of Oviraptor & eggs (dinosaurs built nests & brooded their eggs) Eggs Front limb Hind limb 77
  78. 78. Artist’s reconstruction of the dinosaur’s egg-brooding posture 78
  79. 79. Molecular Evidence for Phylogeny DNA that codes for rRNA changes relatively slowly Useful for investigating distant branching points (bacteria  plants & animals) mtDNA (mitochondrial DNA): evolves rapidly Used to explore recent evolutionary events (animal & human evolution) 7979 Ribosome (rRNA) Mitochondria (mtDNA)
  80. 80. Gene Duplications Increase the # of genes in the genome Provides more opportunities for evolutionary changes Can be traced to a common ancestor Homologous genes (shared genes across generations) 8080
  81. 81. Orthologous Genes Found in a single copy in the genome Are homologous between species – genes diverged after a speciation event Can diverge only after speciation occurs Widespread & extend across many diverse species 8181 Human and Dog Hemoglobin
  82. 82. Ancestral gene Ancestral species Speciation with divergence of gene Species A Species BOrthologous genes Orthologous Genes 82
  83. 83. Paralogous Genes Result from gene duplication Found in multiple copies in the genome Can diverge within the clade that carries them Often evolve new functions 8383 Myoglobin evolved from Hemoglobin
  84. 84. Ancestral gene Species C Gene duplication and divergence Paralogous genes Species C after many generations Paralogous Genes 84 hemoglobin myoglobin
  85. 85. Genome Evolution Gene number & species complexity are not strongly linked (“quality over quantity”) Genes in complex organisms are very versatile Each gene can perform many functions (“multi- tasking genes”) 8585 mustard pufferfish rice
  86. 86. Revisions to the Tree of Life Only plants & animals, at first…then 5 kingdoms Monera, Protista, Fungi, Plantae, & Animalia The 3-domain system has been adopted: Bacteria, Archaea, Eukarya Eukarya & Archaea are more closely related to each other than to Bacteria (rRNA genes) 8686
  87. 87. Archaea Bacteria Eukarya COMMON ANCESTOR OF ALL LIFE Land plants Green algae Red algae Forams Ciliates Dinoflagellates Cellular slime molds Amoebas Animals Fungi Euglena Trypanosomes Leishmania Sulfolobus Thermophiles Halophiles Methanobacterium Green nonsulfur bacteria (Mitochondrion) Spirochetes Chlamydia Cyanobacteria Green sulfur bacteria (Plastids, including chloroplasts) Diatoms The 3 Domains of Life 87
  88. 88. 3 Archaea Bacteria Eukarya Billions of years ago 4 2 1 0 88 Horizontal Gene Transfer
  89. 89. 89 Endosymbiosis & a Ring of Life?
  90. 90. Archaea Eukarya Bacteria A Ring of Life 90
  91. 91. 91

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