Phylogenies & Classifying species (AKA Cladistics & Taxonomy)

1. Phylogenies & Classifying species (AKA Cladistics & Taxonomy) What are phylogenies? How do we read them? How do we estimate them?

2. Carolus Linneaus:Systema Naturae (1735) • Swedish botanist & natural theologist • Hierarchicalclassification based on “ideal of unchanging types”. • Binomial nomenclature - replaced polynomials • Categories: • K, P,C, O, F, G, S • Assumes a static, unchanging Universe

3. Charles Darwin and Fig. 1 • Origin of Species (1859) • Species diverge; they do so gradually • Articulated idea of sharedancestry, branching of lineages (cladogenesis) and change along branches (anagenesis) • Only figure in OS: a dendrogram

4. Problems with Linnean system • It does NOT represent evolutionary history. • Hierarchical categories do not imply degree of evolutionary change or divergence. • Are Rabbits as different from Rodents as they are from Elephants? • When and how should we split groups into separate categories? - splitting vs. lumping • How different is different enough to warrant separate groupings? • Ex: Dogs & wolves

5. Dendrogram ~ Phylogenies • Phylogeny: Interpretation of the evolutionary history and relationships between a group of organisms • Phylogenetictree: Hypothesis of ancestor-descendent relationships among populations, species, or larger groups*

6. Why construct phylogenies? • Understand evolutionary history • System of classifying organisms & organizing diversity • Most biologists agree: most efficient way to classify organisms is based on phylogenetic relatedness

7. All species coalesce to a common ancestor: • Recall our lab: • Just as all genes coalesce to a single ancestral gene, all individuals coalesce to a single ancestor. • Like tracing a family tree

8. 1 1 1 1 1 2 2 2 2 2 3 3 3 3 3 3 10 10 10 10 10 1 1 1 2 2 3 3 10 10 10 10 1 1 2 2 2 2 3 3 3 10 10 7 7 7 7 7 7 7 7 7 7 7 1 4 4 4 4 8 8 8 8 4 8 4 4 4 4 8 8 8 8 4 5 5 5 5 5 5 6 6 6 6 6 6 8 4 5 6 8 5 5 6 6 5 5 6 6 9 9 9 9 9 9 9 9 9 9 9 10 9 8 7 6 5 4 3 2 1 0

9. 3 10 1 2 3 8 10 10 10 2 10 10 10 1 1 2 2 3 4 7 10 2 2 3 3 4 6 7 8 1 1 2 2 3 3 3 8 10 1 1 2 3 6 1 2 3 10 1 4 4 7 7 7 7 8 8 9 7 7 9 4 4 7 7 1 4 4 5 5 8 10 2 3 6 7 8 9 6 6 9 1 4 8 8 5 5 8 5 6 9 5 5 5 9 4 5 6 6 6 8 9 6 6 9 5 5 4 9 9 9 10 9 8 7 6 5 4 3 2 1 0

10. 4 7 10 2 6 3 3 8 2 3 7 4 2 3 1 3 4 2 7 4 2 8 2 3 5 7 10 1 7 7 8 10 1 8 10 2 10 10 6 7 4 5 8 9 10 1 4 9 9 10 1 3 8 2 4 5 5 2 3 6 6 1 4 8 10 3 3 9 4 8 5 7 7 9 10 1 1 7 8 8 9 2 5 9 8 6 9 4 5 5 6 7 1 6 9 3 6 1 9 6 6 2 9 10 1 5 4 5 6 5 10 9 8 7 6 5 4 3 2 1 0

11. 10 2 6 5 1 2 8 5 1 3 3 3 3 4 10 3 3 1 2 2 2 4 5 6 7 10 10 2 5 7 2 2 4 8 5 2 1 1 7 7 9 10 10 8 10 1 4 5 9 10 4 4 8 9 3 5 5 7 8 1 3 7 7 7 7 7 10 1 3 3 3 4 6 10 5 9 1 2 4 6 7 8 9 1 4 5 6 8 8 2 6 10 6 4 6 5 8 6 8 8 9 1 4 9 6 9 6 9 9 9 10 9 8 7 6 5 4 3 2 1 0

12. 2 10 2 2 10 7 8 10 1 1 8 10 10 1 1 3 2 8 10 1 2 3 8 10 10 2 2 3 3 3 8 10 2 2 3 3 7 10 2 1 4 4 4 5 7 7 7 1 1 1 2 3 3 4 6 7 7 9 10 1 3 3 5 7 8 5 7 4 6 8 9 4 8 5 5 6 6 7 4 4 6 7 4 6 6 6 5 5 6 5 5 6 8 9 9 1 4 4 8 8 9 9 5 9 9 9 5 6 9 9 10 9 8 7 6 5 4 3 2 1 0

13. 10 9 8 7 6 5 4 3 2 1 0

14. 10 9 8 7 6 5 4 3 2 1 0

15. 10 9 8 7 6 5 4 3 2 1 0 • Tips • Branches • Nodes • Root • Most Recent Common Ancestor (MRCA)

16. Phylogeny of Vertebrates Name another tip Name another node

17. Monophyletic groupings Who is the MRCA of Mammals and Crocodiles?

18. Monophyletic groupings Nodes name monophyleticgroups: An ancestor and ALL of its descendents

19. Reading phylogenies • 5 of these are identical • Which one is not the same?*

20. Paraphyletic groupings

21. Tree of Life

22. What data should we use to generate trees? • What data do you use? • Often do it without understanding why

23. What data should we use to determine evolutionary relationships? • Characters: distinguishable variations of an organism • Morphologic • Developmental • Genetic • Quantifiable • Independent of each other • Homologous: due to common ancestry ACGTTGAA ACCTTGTA

24. Phenetic approach • Sokal (1950) Made classification rigorous. Based groupings on many characters rather than few “important” ones. • Calculated overall SIMILARITY. Generated phenograms (Basically, phylogenetic trees) • Characters: Vary independently of other features. Homologous among ingroups. • Character states: alternative versions of character. • Presence/absence • 1/2/3/4…etc.

25. Characters • Are the bones of the upper limb homologous structures? • Are wings of bats, birds and pterosaurs homologous structures?

26. PitfallsWhen Similarity ≠ Close Relationship! • 2 taxa may share a derived character state • OR may share an ancestral character state • OR may share a character state due to convergence to same phenotype (MRCA did not have the character) These are analogous traits • Bird and bat wings • Dermopterans, Flying squirrels, Sugar gliders • Only if first case is true will you ALWAYS infer correct phylogenetic relationship.

27. AnuraCaudata Caecilians Mammals Turtles Crocs Birds Tuatara Lizards Snakes Diapsida Where is the MRCA of Tuatara and Crocs?

28. AnuraCaudata Caecilians Mammals Turtles Crocs Birds Tuatara Lizards Snakes A B C D The Monophyletic group that includes Birds, Crocs & Turtles begins at node:

29. Willi Hennig and Cladistics • Grouping scheme based ONLY on phylogenetic relationships • Not on degree of similarity and adaptive divergence • Used presence of sharedderived characters (synapomorphies) to infer evolutionary relationships • Based trees upon total weight of ALL synapomorphies

30. Phylogenetic terms* • Plesiomorphy: Ancestral character state • Symplesiomorphy: Ancestral character state shared by many taxa - phylogenetically uninformative • Apomorphy: Derived (novel) character - phylogenetically uninformative • Synapomorphy: Shared derived character - GOLD • ”Hennig has indeed emphasized and defined some procedures of phylogenetic analysis that have long been used by systematists. He might even have clarified them if he had not unnecessarily replaced the usual plain-language terms by a bizarre and idiosyncratic new terminology." (1978) G. G. Simpson

31. Similarity ≠ Relationship synapomorphy • 2 taxa may share a derived character state • OR may share an ancestral character state • OR may share a state due to convergence • Bird and bat wings • Dermopterans, Flying squirrels, Sugar gliders • Only if first case is true will you infer the phylogenetic relationship correctly. symplesiomorphy analogy

32. Synapomorphies identify monophyletic groups • Unite groups with shared, (only among each other)derived(from some ancestral group)characters

33. Problems • What characters (traits) are “best” for assessing evolutionary relationships? • Skull length, body size, pelage color, limb modification and specialization, chromosome #? • When and how should we split groups into separate categories? - splitting vs. lumping • How different is different enough to warrant separate groupings? • Can/should hierarchical categories imply degree of evolutionary change or divergence? • Are Hyraxes as different from Manatees as they are from Bats? • Are dogs as different from cats as they are from humans?

34. Problems with characters • Which characters are phylogenetically informative? • How do we quantify # of possible states & frequency of change among them? • How do we establish polarity? • How do we deal with continuous traits: Quantify or discard them?

35. Ideal character • States are discrete • # of states are knowable (across taxa) • Transition frequencies (rates of change) are estimable DNA ONLY 4 states; A C G T No polarity Can measure transition frequencies

36. Method of inferring a tree • Choose the most parsimonious one • Parsimony: Methodological reductionism; Explanation which requires the fewest undocumented assumptions is probably correct. • Occam’s Razor: The easiest explanation is probably the correct one. • William of Occam: 14th century Franciscan monk • In cladistics/phylogeny: The tree which requires us to postulate the least evolutionary change & fewest homoplasies is probably correct

37. Parsimony • Find all possible tree topologies; calculate total number of changes required to produce each topology. • Topology with fewest changes = the most parsimonious tree* C ABD AB C D Taxa: A, B, C, D Characters: › › ›

38. Placement of Cetaceans • Morphology of astragalus unites Artiodactyls • Most parsimonious placement = one gain of pulley-shaped astragalus

39. Placement of Cetaceans • Mounting genetic evidence suggests Hippos have shared genes with Cetaceans morerecently than they have with other Artiodactyls (e.g. deer)

40. Placement of Cetaceans • Appearance of SINE’s (mutations) throughout the genome suggests that Cetaceans & Hippos are close relatives • Rare; Selectively neutral; Once established, lost only via drift