Homology : a character shared between two or more species that was present in their common ancestor.

2. Homology: a character shared between two or more species that was present in their common ancestor. Analogy: “shared” character not present in common ancestory (I.e., the character evolved twice, independently): convergent evolution.

4. Classification of Biological Diversity: • Phenetics • Phylogenetics (Cladistics)

5. PHENETICS • Classic approach (Linnaeus) • Group species based upon phenotypic similarity • Use ALL traits

6. PHYLOGENETICS • New (Hennig, 1966) • Based on patterns of ancestry (species are groups based on most recent ancestory) • Uses only shared, derived characters (i.e., derived homologues) • Therefore, it aims to reval actual evolutionary history (the “real” phylogeny; “the tree”)

7. “The Actual Events” Horse Beetle Butterfly

8. Horse Horse Beetle Beetle Butterfly Butterfly Phenetics Phylogenetics

9. “The Actual Events” Dragonfly Lizard Bird

10. Phenetics Phylogenetics Dragonfly Lizard Bird Lizard Dragonfly Bird

11. Equivalent Trees

12. Characters Used

14. Species: Character State: 1 2 3 4 Ancestral state Analogy In Sp. 1 and 3 is an analogy; ‘red’ arose independently twice

15. Species: Character State: 1 2 3 4 Ancestral state Ancestral Homology In Sp. 1, 2 and 3 is an ancestral homology; It’s ancestral because it’s present at the base of the tree.

16. Species: Character State: 1 2 3 4 Ancestral state Derived Homology is homologous in Sp. 1 and 2 and it’s derived (i.e., there has been a transition from the “basal” state).

17. Building a “tree” (aka phylogeny or cladogram) • Obtain data (shared derived characters)

18. Building a “tree” (aka phylogeny or cladogram) • Obtain data (shared derived characters) • Determine ancestral state (“0”)

19. Building a “tree” (aka phylogeny or cladogram) • Obtain data (shared derived characters • Determine ancestral state (“0”) • Assign derived states (“1”, “2”, “3”), which defines the character matrix

20. Building a “tree” (aka phylogeny or cladogram) • Obtain data (shared derived characters) • Determine ancestral state (“0”) • Assign derived states (“1”, “2”, “3”), which defines the character matrix • Build trees (many are possible)

21. Building a “tree” (aka phylogeny or cladogram) • Obtain data (shared derived characters) • Determine ancestral state (“0”) • Assign derived states (“1”, “2”, “3”), which defines the character matrix • Build trees (many are possible) • Pick the “best” (i.e., most parsimonious) -- fewest evolutionary steps (fewest convergences and reversals)

22. Convergence: independent origin of trait (i.e., two lineages independently evolve similar phenotype).Reversal: origin and subsequent loss of character (i.e., reversion to ancestral state).

23. Sunfishes

24. Sunfish Character Matrix

25. LMB BC WM BG RE b-1 a-1

26. LMB BC WM BG RE d-1 c-1 b-1 a-1

27. LMB BC WM BG RE g-1 f-1 e-1 d-1 c-1 b-1 a-1

28. 7 Steps LMB BC WM BG RE g-1 f-1 e-1 Note: characters f-1 and g-1 are not shared: i.e., they are non-informative d-1 c-1 b-1 a-1

29. LMB WM RE BC BG f-1 c-0, d-0, e-0, g-0 g-1 e-1 d-1 c-1 b-1 a-1 Another possible tree: 11 Steps (4 reversals)

30. X X X X X O Y Z

31. Y X X X X Z O X

32. O X Y Z b-1 a-1

33. O X Y Z d-1 c-1 b-1 a-1

34. O X Y Z e-1 f-1 e-1 g-1 f-1 g-1 d-1 c-1 b-1 a-1 10 steps (3 convergences)

35. An Alternative Tree

36. O Z X Y g-1 f-1 e-1 b-1 a-1

37. O Z Y X d-1 d-1 c-1 c-1 g-1 f-1 e-1 b-1 a-1 9 steps (2 convergences)

38. O Z Y X Four of the possible trees d-1 d-1 c-1 c-1 g-1 f-1 e-1 b-1 9 steps (2 convergences) a-1 O X Y Z e-1 O X Z Y O Z X Y f-1 e-1 e-0 d-0 g-1 f-1 f-0 c-0 g-1 g-0 g-1 d-1 d-1 f-1 c-1 c-1 e-1 d-1 g-1 c-1 b-1 f-1 b-1 e-1 9 steps (2 reversals) 10 steps (3 reversals) a-1 b-1 a-1 a-1 10 steps (3 convergences)

39. Fitting Linnaean systematics into phylogenetics C1 Class: O1 O1 Order: F1 F2 F3 F4 Family: G1 G2 G3 G4 G5 G6 Genus: A B C D E F G H I J Species:

40. A monophyletic group:is a group of taxa that includes all descendants of the most recent common ancestor of the group members

41. An example of a non-monophyletic group: Reptiles Lizard Snake Croc. Fish Amphib. Turtle Mammal Bird The most recent common ancestor of reptiles also gave rise to mammals and birds

42. An example of a non-monophyletic group: Fish Sturgeon X Sharks + Rays Coelacanth Teleosts lungfish X = all other vertebrates (e.g., mammals, birds, amphibians, reptiles)!