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Evolutionary Analysis PowerPoint Presentation
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Evolutionary Analysis

Evolutionary Analysis

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Evolutionary Analysis

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  1. Evolutionary Analysis • Tara Harmer Luke • The Richard Stockton College of NJ

  2. Tree • Mathematical structure • Model evolutionary history

  3. Taxon 1 Taxon 2 Taxon 3 Taxon 4 Taxon 5 Taxon 6

  4. Taxon 1 Outgroup Taxon 2 Root Sister taxa Taxon 3 Branch Taxon 4 Node Taxon 5 Polytomy (more than one branch emerging from one node) Taxon 6 Tip

  5. (a) The astragalus is a synapomorphy that identifies artiodactyls as a monophyletic group. (b) If whales are related to hippos, then two changes occurred in the astragalus. ARTIODACTYLS Camel Whale Gain of pulley- shaped astragalus ARTIODACTYLS Peccary Camel Pig Peccary Gain of pulley- shaped astragalus Hippo Pig Whale Hippo Loss of pulley- shaped astragalus Astragalus (ankle bone) Deer Deer Cow Cow (c) Data on the presence and absence of SINE genes support the close relationship between whales and hippos. Locus 1 = gene present 0 = gene absent ? = still undetermined Cow Deer Whale Whales and hippos share four unique SINE genes (4, 5, 6, and 7) Hippo Pig Peccary Camel

  6. Phylogenetic Tree • shows ancestor-descendent relationships among populations or species • clarifies evolutionary relationships

  7. Root • Ancestor of all sequences on tree

  8. Taxon 1 Outgroup Taxon 2 Root Sister taxa Taxon 3 Branch Taxon 4 Node Taxon 5 Polytomy (more than one branch emerging from one node) Taxon 6 Tip

  9. 2 4 5 1 2 3 6 3 1 4 5 6 (a) (b) (c) 1 6 5 4 3 2

  10. 2 4 5 1 2 3 6 3 1 4 5 6 (a) (b) (c) 1 6 5 = = 4 3 2

  11. Types of Trees • Rooted • Unrooted

  12. Rooted Trees • Node identified as root, from which all other nodes descend • Have direction corresponding to evolutionary time

  13. Taxon 1 Outgroup Taxon 2 Root Sister taxa Taxon 3 Branch Taxon 4 Node Taxon 5 Polytomy (more than one branch emerging from one node) Taxon 6 Tip

  14. Unrooted Trees • Lacks root • Does not specify evolutionary relationships • Nothing about ancestors and descendents

  15. Unrooted Trees • Lacks root • Does not specify evolutionary relationships • Nothing about ancestors and descendents • Many tree-building programs generate unrooted trees!

  16. Number of possible phylogenetic trees

  17. Types of Trees • Cladogram • Phylogram

  18. Cladogram

  19. Cladogram • Relative recency of common ancestry

  20. Cladogram

  21. Cladogram • Relative recency of common ancestry • Does not show amount of evolutionary change

  22. Phylogram

  23. Phylogram • Also contains branch lengths • Numbers associated with branches • Amount of evolutionary change

  24. Phylogram

  25. Cladogram Phylogram

  26. Constructing a Tree • Construct multiple sequence alignment • Determine Tree reconstruction method • Build Tree • Evaluate Tree

  27. Constructing a Tree • Construct multiple sequence alignment • Determine Tree reconstruction method • Build Tree • Evaluate Tree

  28. Methods for Tree Reconstruction • Distance methods • Discrete methods

  29. Distance methods • measures sequence dissimilarity • UPGMA • Neighbor Joining (NJ)

  30. UPGMA(Unweighted Pair-Group Method with Arithmetic Mean) • Assumes constant rate of evolution • Sequential clustering algorithm

  31. Neighbor Joining (NJ) • also uses distance matrix • Sequentially find neighbors that minimize length of tree

  32. Neighbor Joining (NJ) • also uses distance matrix • Sequentially find neighbors that minimize length of tree A H B G C F D E

  33. Neighbor Joining (NJ) • also uses distance matrix • Sequentially find neighbors that minimize length of tree A A H H B B I G G C C F D F D E E

  34. Discrete methods • Maximum parsimony • Maximum likelihood

  35. Maximum Parsimony

  36. Maximum Parsimony Possible Trees: ((1,2),(3,4)) ((1,3),(2,4)) ((1,4),(2,3))

  37. Newick Format • represented in linear form by nested parentheses • how computers store trees A C B D E (((A,C)B)(D,E))

  38. Maximum Parsimony Possible Trees: ((1,2),(3,4)) ((1,3),(2,4)) ((1,4),(2,3))

  39. Maximum Parsimony 1 2 3 4

  40. Maximum Parsimony 1 + 1 + 2 + 1 + 0 =5 1 2 3 4

  41. Maximum Parsimony 2 + 2 + 1 + 1 + 0 =6 1 3 2 4

  42. Maximum Parsimony 1 3 2 4 1 2 3 4 Tree length: 5 6

  43. Maximum Parsimony 1 + 1 + 2 + 1 + 0 =5 1 2 3 4