Parts of a phylogenetic tree

1. Parts of a phylogenetic tree sister taxa Taxon 3 Taxon 1 Taxon 6 Taxon 2 Taxon 4 Taxon 5 More recent Tips or terminal nodes C Time D Branches Nodes B More ancient A root

2. “Reading” a phylogenetic tree sister taxa Taxon 3 Taxon 1 Taxon 6 Taxon 2 Taxon 4 Taxon 5 More recent C D Time B More ancient A Start at the bottom and work up. A is the common ancestor of all taxa 1-6. It split into two groups. One evolved into taxon 1, and the other into the population indicated by node B. This is the common ancestor of taxa 2-5...

3. Taxon 1 Often, a tree is drawn on its side, with time increasing left to right. Branches are drawn as “forks” on cladograms. These are trees drawn using cladistic methods. Taxon 2 C sister taxa A B Taxon 3 Taxon 4 D Taxon 5 Taxon 6 More recent More ancient Time

4. Taxon 1 On cladograms, only the relative branching order is important. So taxon 2 and 3 split from their ancestor (C) earlier than taxon 4, 5, and 6 did from (D), but the tree does not show how much earlier. Branches are not scaled to time on cladograms. Taxon 2 sister taxa C A B Taxon 3 Taxon 4 D Taxon 5 Taxon 6 More recent More ancient Time

5. given a molecular clock of 2% per million years, 10% ≈ 5 million years Genetic distance = 10% Often the branches are “squared off” instead of drawn as diagonal forks. This is common for phylogenies called phylograms, in which branch lengths are scaled to time (they represent genetic distance). Taxon 1 Taxon 2 A sister taxa D Taxon 3 B Taxon 4 Taxon 5 C Phylograms are generated by phenetic methods. Taxon 6

6. Phenetic methods • Group taxa based on their overall similarities and differences • No explicit evolutionary hypothesis

7. Phenetic methods • Often used for DNA data, from which genetic distancesare calculated • The preferred tree is the one that minimizes the total distance along the tree

8. Phenetic methods “neighbor-joining”: the most popular method for building trees from distance data

9. Cladistic methods • cladistics: the branch of systematics that builds phylogenies based on hypotheses for evolutionary relationships

10. Cladistic methods • cladistics and cladograms are based on clades—monophyletic groups defined by shared, derived homologous characters: synapomorphies

11. Shared derived homologous characters amniotic egg homologous = similar due to common descent derived = evolved later, in a recent common ancestor

12. Cladistic methods • a synapomorphy for the artiodactyl mammals is the trochleated astragulus

13. Perissodactyla odd-toed ungulates, e.g. rhino and horse 1 or 3 toes Artiodactyla even toed ungulates, e.g. hippo and deer most 2, some 4 toes The ungulates or hoofed mammals

14. Synapomorphies arise from independent evolution after speciation (branching events). When gene flow stops, populations evolve shared derived characters by selection and drift. Fig. 4.2

15. Synapomorphies appear in a nested fashion that “naturally” produces hierarchical ancestor-descendant relationships. You can see this by tracing the tree upwards in (b).

16. Synapomorphies in tetrapods

17. Selection between alternative cladistic trees is often based on parsimony. Parsimony is a logical criterion that prefers the tree with the fewest evolutionary changes. trochleated astragulus: gained lost

18. A problem Modern whales lack ankles, so presence/absence of astragulus is impossible to evaluate

19. Solution: fossil whales have ankle bones! Image from Thewissen lab (Kent State Univ.)

20. Philip Gingerich: fossil whale research in Egypt and Pakistan Univ. of MI camp in Egypt, source of > 400 fossil whales! Basilosaurus isis skeleton images P. Gingerich

21. Fossil whale ankle bones Artiocetus Pronghorn antelope Rhodocetis images P. Gingerich

22. Independent analyses of DNA sequences agree Milk protein (-casein) DNA sequences from Gatesy et al. (1999)

23. Using parsimony to distinguish homology from convergence

26. “Reading” trees to determine branching order Does the “subtree” in (b) show the same relationships as the tree in (a)? Figure 14.19

27. Applications of phylogenies in biology • tests of hypotheses often are based on the following features of a tree • sister taxon relationships • identity of monophyletic groups • branching order

28. Applications of phylogenies in systematics sister taxon relationships

29. Issues in systematics: identifying sister taxa

30. Phylogenetic analysis of mitochondrial cytochrome oxidase II sequences by Ruvolo et al. (1994) revealed that chimps were the sister taxon to humans.

31. Applications of phylogenies in systematics identifying monophyletic groups

32. The goal of phylogenetic systematics is to produce taxonomic categories that accurately depict evolutionary history. According to this field, “valid” catagories are monophyletic groups. A monophyletic group contains an ancestor and all of its decendants

33. The goal of phylogenetic systematics is to produce taxonomic categories that accurately depict evolutionary history. Paraphyletic groups are not valid categories. A paraphyletic group contains an ancestor and some but not all of its decendants

34. Resolving human-chimp relationships produced a paraphyletic group Pongidae baboon whales orangutan human sharks skates chimp gorilla Hominidae if this phylogeny is true, the Pongidae is a paraphyletic group (and should be discarded?)

35. Reptiles are a paraphyletic group • Reptilia includes its common ancestor and most descendents, but not the birds

36. Another famous paraphyletic group…

37. Applications for testing hypotheses for speciation Sister taxa and branching order

38. Allopatric speciation • The Isthmus of Panama closed ~ 3.1 MYA • About 150 “geminate” (twin) species now exist

39. Proof for allopatric speciation in snapping shrimps Knowlton et al.(1993): a phylogeny of Pacific (P) and Carribean (C) species pairs of Alpheus In 6 out of 7 cases, the closest relative of a species was in the other ocean

40. Proof for allopatric speciation in snapping shrimps The phylogeny suggests that the ancestor of P1/C1, P2/C2, P3/C3, P4/C4, P5/C5, and P6/C6 was split into descendant species when the Isthmus of Panamá closed

41. A phylogeny of Hawaiian Drosophila D. heteroneura D. silvestris

42. Hawaiian Laupala crickets

43. Applications to studies of pathogen evolution and disease outbreaks Sister taxa, branching order, monophyletic groups

44. Influenza pandemics

45. Influenza biology and evolution • RNA virus (Orthomyxoviridae) • Genome of 8 single stranded RNA molecules • Key to infection and to immunity are viral envelope proteins hemagglutinin and neuraminidase

46. Hemagglutinin (HA)* • Controls attachment to host cell (by binding to a receptor) • Mediates membrane fusion *Origin of its name: HA binds to red blood cells, causing agglutination

47. HA • 15 known serotypes in influenza A (e.g. H1, H5) • A single amino acid in HA position 226 determines host species (mostly) • HA226Gln Bird flu • HA226Leu Human flu

48. HA • Antibodies to HA neutralize virus infectivity • But variability in HA amino acid sequence helps overcome this immune response

49. Neuraminidase (NA) • Involved in replication and virus “spreading” • Enzymatically digests cell receptors and releases new virions

50. Neuraminidase (NA) • 9 known serotypes in influenza A • e.g. H5N1 “bird flu”