Lecture 4: Phylogeny and the Tree of Life   Campbell & Reece:  Chapter 26
All life is interconnected by descent How to determine the pattern of descent? Humans Rattlesnake Pine tree Amoeba Bacterium
Systematics -  field of biology dealing with diversity and evolutionary history of life <ul><li>Includes  Taxonomy :  DINC...
Description <ul><li>= assign features </li></ul><ul><li>Character  = a feature (e.g., “petal color”) </li></ul><ul><li>Cha...
Identification <ul><li>= associate an unknown with a known </li></ul><ul><li>How?  One way:  </li></ul><ul><li>Taxonomic K...
Nomenclature <ul><li>Naming, according to a formal system. </li></ul><ul><li>Binomial: Species are two names (Linnaeus): <...
Nomenclature <ul><li>Hierarchical Ranks: </li></ul><ul><li>Domain </li></ul><ul><li>Kingdom </li></ul><ul><li>Phylum </li>...
Classification <ul><li>Placing objects, e.g., life, into some type of order. </li></ul><ul><li>Taxon = a taxonomic group (...
How to classify life <ul><li>Phenetic classification </li></ul><ul><ul><li>Based on overall similarity </li></ul></ul><ul>...
Problem with phenetic classification: <ul><li>Can be arbitrary,  e.g., classify these: </li></ul>
Phylogenetic classification <ul><li>Based on known (inferred) evolutionary history. </li></ul><ul><li>Advantage: </li></ul...
= representation of the history of life
 
 
Ingroup  – group studied Outgroup  – group not part of ingroup, used to “root” tree
Fig. 26-5 Sister taxa ANCESTRAL LINEAGE Taxon A Polytomy Common ancestor of taxa A–F Branch point (node) Taxon B Taxon C T...
Apomorphy (derived trait) <ul><li>= a new, derived feature E.g., for this evolutionary transformation   scales  --------> ...
Taxa are grouped by apomorphies <ul><li>Apomorphies are the result of evolution. </li></ul><ul><li>Taxa sharing apomorphie...
Principle of Parsimony <ul><li>That cladogram (tree) having the fewest number of “steps” (evolutionary changes) is the one...
Other methods of phylogeny reconstruction: <ul><li>Maximum Likelihood  or  Bayesian  analysis </li></ul><ul><ul><li>Uses p...
 
Fig. 26-11 TAXA Lancelet (outgroup) Lamprey Salamander Leopard Turtle Tuna Vertebral column (backbone) Hinged jaws Four wa...
Fig. 26-8a Deletion Insertion 1 2 DNA sequence data  – most important type of data
Fig. 26-8b 3 4 DNA sequence data - alignment  Each nucleotide position =  Character Character states  = specific nucleotide
Homology <ul><li>Similarity resulting from common ancestry. </li></ul><ul><ul><li>E.g., the forelimb bones of a bird, bat,...
 
Homoplasy (analogy) <ul><li>Similarity  not  due to common ancestry </li></ul><ul><li>Reversal  – loss of new (apomorphic)...
Convergent evolution : spines of cacti & euphorbs <ul><li>Cactus </li></ul>Euphorb
Convergent evolution: spines of cacti & euphorbs euphorb spines cactus spines
Both examples of  reversal  within Tetrapods:  loss of a derived feature – forelimbs. Leg-less lizards Snake Example of  c...
Convergent evolution: wings of some animals evolved independently
Fig. 26-7 Convergent evolution: Australian “mole” and N. Am. “mole”
Fig. 26-18 (b) Paralogous genes (a) Orthologous genes Ancestral gene Paralogous genes Ancestral species Speciation with di...
Common ancestry
Monophyletic Group <ul><li>a group consisting of:  </li></ul><ul><ul><li>a  common ancestor  + </li></ul></ul><ul><ul><li>...
 
 
 
 
 
 
C  B   F   E   D   A Cladograms can be “flipped” at nodes, show same relationships
Fig. 26-13 Drosophila Lancelet Zebrafish Frog Human Chicken Mouse CENOZOIC Present 65.5 MESOZOIC 251 Millions of years ago...
Relationship <ul><li>= recency of common ancestry i.e., taxa sharing a common ancestor  more recent in time  are more clos...
Example: <ul><li>Are fish more closely related to sharks or to humans? </li></ul>
 
 
 
Example: <ul><li>Are crocodyles more closely related to lizards or to birds? </li></ul>
 
 
Paraphyletic group <ul><li>Consist of common ancestor but  not  all descendents </li></ul><ul><li>Paraphyletic groups are ...
 
“ Reptilia” here paraphyletic
Re-defined Reptilia  monophyletic
 
Importance of a name: Did humans evolve from apes?
 
Hominidae Pongidae “ Great Apes”
Pongidae “ Great Apes” Pongidae  or Hominidae
Pongidae  or Hominidae
Pongidae  or Hominidae
 
We are human, but we are also apes. <ul><li>We share unique human features. </li></ul><ul><li>We also share features with ...
Importance of systematics & evolution:   <ul><li>1) Foundation of biology - study of biodiversity </li></ul><ul><li>2) Bas...
E.g., schistosomiasis
 
Schistosomiasis: knowledge of species diversity and evolutionary history of primary host can aid in controlling parasite (...
All of life is interconnected by descent.
There are no “higher” or “lower” species.
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4 phylogeny-ch26

  1. 1. Lecture 4: Phylogeny and the Tree of Life Campbell & Reece: Chapter 26
  2. 2. All life is interconnected by descent How to determine the pattern of descent? Humans Rattlesnake Pine tree Amoeba Bacterium
  3. 3. Systematics - field of biology dealing with diversity and evolutionary history of life <ul><li>Includes Taxonomy : DINC </li></ul><ul><li>D escription </li></ul><ul><li>I dentification </li></ul><ul><li>N omenclature </li></ul><ul><li>C lassification </li></ul><ul><li>Goal: </li></ul><ul><ul><li>Determine Evolutionary History (Phylogeny) of Life </li></ul></ul>
  4. 4. Description <ul><li>= assign features </li></ul><ul><li>Character = a feature (e.g., “petal color”) </li></ul><ul><li>Character states = two or more forms of a character (e.g., “red,” “white”). </li></ul>
  5. 5. Identification <ul><li>= associate an unknown with a known </li></ul><ul><li>How? One way: </li></ul><ul><li>Taxonomic Key , e.g., </li></ul><ul><li>Tree …………………………………….…………… Species A </li></ul><ul><li> Leaves simple …….………………………… Species B </li></ul><ul><li> Leaves pinnate …….………..…..…..…… Species C </li></ul><ul><li>Herb </li></ul><ul><li> Flowers red …….…………………………… Species D </li></ul><ul><li> Flowers white …….…………………..…… Species E </li></ul>
  6. 6. Nomenclature <ul><li>Naming, according to a formal system. </li></ul><ul><li>Binomial: Species are two names (Linnaeus): </li></ul><ul><li>E.g., Homo sapiens </li></ul><ul><li>Homo = genus name </li></ul><ul><li>sapiens = specific epithet </li></ul><ul><li>Homo sapiens = species name </li></ul>
  7. 7. Nomenclature <ul><li>Hierarchical Ranks: </li></ul><ul><li>Domain </li></ul><ul><li>Kingdom </li></ul><ul><li>Phylum </li></ul><ul><li>Class </li></ul><ul><li>Order </li></ul><ul><li>Family </li></ul><ul><li>Genus </li></ul><ul><li>Species </li></ul>
  8. 8. Classification <ul><li>Placing objects, e.g., life, into some type of order. </li></ul><ul><li>Taxon = a taxonomic group (plural = taxa). </li></ul>
  9. 9. How to classify life <ul><li>Phenetic classification </li></ul><ul><ul><li>Based on overall similarity </li></ul></ul><ul><ul><li>Those organisms most similar are classified more “closely” together. </li></ul></ul>
  10. 10. Problem with phenetic classification: <ul><li>Can be arbitrary, e.g., classify these: </li></ul>
  11. 11. Phylogenetic classification <ul><li>Based on known (inferred) evolutionary history. </li></ul><ul><li>Advantage: </li></ul><ul><ul><li>Classification reflects pattern of evolution </li></ul></ul><ul><ul><li>Classification not ambiguous </li></ul></ul>
  12. 12. = representation of the history of life
  13. 15. Ingroup – group studied Outgroup – group not part of ingroup, used to “root” tree
  14. 16. Fig. 26-5 Sister taxa ANCESTRAL LINEAGE Taxon A Polytomy Common ancestor of taxa A–F Branch point (node) Taxon B Taxon C Taxon D Taxon E Taxon F
  15. 17. Apomorphy (derived trait) <ul><li>= a new, derived feature E.g., for this evolutionary transformation scales --------> feathers (ancestral feature) (derived feature) </li></ul><ul><li>Presence of feathers is an apomorphy for birds. </li></ul>
  16. 18. Taxa are grouped by apomorphies <ul><li>Apomorphies are the result of evolution. </li></ul><ul><li>Taxa sharing apomorphies underwent same evolutionary history should be grouped together . </li></ul>
  17. 19. Principle of Parsimony <ul><li>That cladogram (tree) having the fewest number of “steps” (evolutionary changes) is the one accepted. </li></ul><ul><li>Okham’s razor: the simplest explanation, with fewest number of “ad hoc” hypotheses, is accepted. </li></ul>
  18. 20. Other methods of phylogeny reconstruction: <ul><li>Maximum Likelihood or Bayesian analysis </li></ul><ul><ul><li>Uses probabilities </li></ul></ul><ul><ul><li>Advantage: can use evolutionary models . </li></ul></ul>
  19. 22. Fig. 26-11 TAXA Lancelet (outgroup) Lamprey Salamander Leopard Turtle Tuna Vertebral column (backbone) Hinged jaws Four walking legs Amniotic (shelled) egg CHARACTERS Hair (a) Character table Hair Hinged jaws Vertebral column Four walking legs Amniotic egg (b) Phylogenetic tree Salamander Leopard Turtle Lamprey Tuna Lancelet (outgroup) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Sequentially group taxa by shared derived character states (apomorphies)
  20. 23. Fig. 26-8a Deletion Insertion 1 2 DNA sequence data – most important type of data
  21. 24. Fig. 26-8b 3 4 DNA sequence data - alignment Each nucleotide position = Character Character states = specific nucleotide
  22. 25. Homology <ul><li>Similarity resulting from common ancestry. </li></ul><ul><ul><li>E.g., the forelimb bones of a bird, bat, and cat. </li></ul></ul>
  23. 27. Homoplasy (analogy) <ul><li>Similarity not due to common ancestry </li></ul><ul><li>Reversal – loss of new (apomorphic) feature, resembles ancestral (old) feature. </li></ul><ul><li>Convergence (parallelism) – gain of new, similar features independently . </li></ul>
  24. 28. Convergent evolution : spines of cacti & euphorbs <ul><li>Cactus </li></ul>Euphorb
  25. 29. Convergent evolution: spines of cacti & euphorbs euphorb spines cactus spines
  26. 30. Both examples of reversal within Tetrapods: loss of a derived feature – forelimbs. Leg-less lizards Snake Example of convergence relative to one another! Independently evolved. snakes leg-less lizards legged lizards * * * = loss of legs gain of legs (Tetrapods)
  27. 31. Convergent evolution: wings of some animals evolved independently
  28. 32. Fig. 26-7 Convergent evolution: Australian “mole” and N. Am. “mole”
  29. 33. Fig. 26-18 (b) Paralogous genes (a) Orthologous genes Ancestral gene Paralogous genes Ancestral species Speciation with divergence of gene Gene duplication and divergence Species A after many generations Species A Species B Species A Orthologous genes Orthology – genes homologous Paralogy – genes not homologous Gene Duplication can occur!
  30. 34. Common ancestry
  31. 35. Monophyletic Group <ul><li>a group consisting of: </li></ul><ul><ul><li>a common ancestor + </li></ul></ul><ul><ul><li>all descendents of that common ancestor </li></ul></ul>
  32. 42. C B F E D A Cladograms can be “flipped” at nodes, show same relationships
  33. 43. Fig. 26-13 Drosophila Lancelet Zebrafish Frog Human Chicken Mouse CENOZOIC Present 65.5 MESOZOIC 251 Millions of years ago PALEOZOIC 542 One can date divergence times with molecular clock and fossils
  34. 44. Relationship <ul><li>= recency of common ancestry i.e., taxa sharing a common ancestor more recent in time are more closely related than those sharing common ancestors more distant in time. </li></ul>
  35. 45. Example: <ul><li>Are fish more closely related to sharks or to humans? </li></ul>
  36. 49. Example: <ul><li>Are crocodyles more closely related to lizards or to birds? </li></ul>
  37. 52. Paraphyletic group <ul><li>Consist of common ancestor but not all descendents </li></ul><ul><li>Paraphyletic groups are unnatural, distort evolutionary history, and should not be recognized. </li></ul>
  38. 54. “ Reptilia” here paraphyletic
  39. 55. Re-defined Reptilia monophyletic
  40. 57. Importance of a name: Did humans evolve from apes?
  41. 59. Hominidae Pongidae “ Great Apes”
  42. 60. Pongidae “ Great Apes” Pongidae or Hominidae
  43. 61. Pongidae or Hominidae
  44. 62. Pongidae or Hominidae
  45. 64. We are human, but we are also apes. <ul><li>We share unique human features. </li></ul><ul><li>We also share features with other apes (and with other animals, plants, fungi, bacteria, etc.). </li></ul><ul><li>Humans didn’t evolve from apes, humans are apes. </li></ul>
  46. 65. Importance of systematics & evolution: <ul><li>1) Foundation of biology - study of biodiversity </li></ul><ul><li>2) Basis for classification of life </li></ul><ul><li>3) Gives insight into biological processes: speciation processes adaptation to environment </li></ul><ul><li>4) Can be aesthetically/intellectually pleasing! </li></ul>
  47. 66. E.g., schistosomiasis
  48. 68. Schistosomiasis: knowledge of species diversity and evolutionary history of primary host can aid in controlling parasite ( Schistosoma , a fluke) Phylogeny of Oncomelania snails
  49. 69. All of life is interconnected by descent.
  50. 70. There are no “higher” or “lower” species.
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