Phylogenies

1. Phylogenies Reconstructing the Past

2. The field of systematics • Studies • the mechanisms of evolution • evolutionary agents • the process of evolution • speciation events • the products of evolution • discovery, nomenclature, classification, tools for identification of extant organisms

3. Phylogenetic Analysis • Phylogeny • chronicle of the descent of a group of organisms from a common ancestor • illustrated as a branching, tree-like diagram • anagenesis operating along branches • cladogenesis producing new branches • shows the origins of different groups from an ancestral group

4. Phylogenetic Reconstruction • a phylogenetic tree (cladogram) is a hypothesis of events in the evolution of a group • based on the analysis of characters of extant organisms • identifies the speciation events (branch points) in the evolution of the group • estimation of time spans or identification of ancestral organisms is extraneous

5. Phylogenetic Reconstruction • an ideal data set… • the complete morphological and genetic description of each member of the lineage • better than nothing… • the complete fossilized remains of each member of a lineage • One approach that’s always feasible… • inference from extant members

6. Phylogenetic Reconstruction • clues to the phylogenetic history of a group • homologies • two features descended from a common ancestral feature are homologous • may or may not resemble each other • may or may not perform the same functions

7. tetrapod limbs - homologs Figure 25.2 Figure 1.2

8. bat, bird, insect wings - not homologsFigure 25.2

9. leaf homologs in flowering plantsFigure 25.3

10. Phylogenetic Reconstruction • clues to the phylogenetic history of a group • common ancestry is inferred from the presence of homologous traits • traits inherited from a distant ancestor are shared by many taxa • traits inherited from a recent ancestor are shared by few taxa

11. Homoplasies • traits that are similar due to something other than inheritance from a common ancestor • convergent evolution • parallel evolution • evolutionary reversal

12. Homoplasies • traits that are similar due to something other than inheritance from a common ancestor • convergent evolution Figure: three plants that all look like cactus but come from Three distinct families - Euphrobiaceae Cactaceae Asclepiadaceae

13. Homoplasies • traits that are similar due to something other than inheritance from a common ancestor • convergent evolution • parallel evolution Figure: butterfly/moth wings with similar patterns

14. Homoplasies • traits that are similar due to something other than inheritance from a common ancestor • convergent evolution • parallel evolution • evolutionary reversal Figure: Magnolia & grass

15. Phylogenetic Reconstruction • steps in the reconstruction of a phylogeny • identification of members of the group • key homologous traits e.g. a vertebral column • selection of characters • characters with traits that differ in the group • ancestral vs. derived • (plesiomorphies vs. apomorphies)

16. Phylogenetic Reconstruction =>during the history of a lineage, some traits change from the ancestral condition ancestral => derived =>taxa that change pass on the changes =>closely related taxa share traits from a recent ancestor and a distant ancestor =>distantly related taxa share traits from a distant ancestor only

17. Phylogenetic Reconstruction • steps in the reconstruction of a phylogeny • identification of ancestral and derived character states • select an outgroup • traits shared with the outgroup are ancestral • distinguish between homologies and homoplasies • assume similar traits are homologous • other characters will test the assumption

18. Table 25.1

19. phylogeny of selected vertebratesFigure 25.5

20. dealing with the real world • unrecognized homoplasies happen • multiple trait changes, reversals, convergence, parallels • each analysis produces multiple possible trees • some trees explain the evolution of the group by assuming many speciation events • some trees explain the evolution of the group by assuming few speciation events • how to select the right tree?

21. dealing with the real world • selecting the right tree • can’t be done (with certainty) • Principle of Parsimony • the best hypothetical tree is the one that requires the fewest unverified assumptions (events) • the best tree is the shortest tree, for now • new data, new insights, may provide evidence supporting a different tree

22. dealing with the real world • selecting the right tree • Maximum Likelihood • analyzes trees using additional information • certain possible events are more likely than others and are given greater weight e.g. transitions are more likely than tranversions

23. dealing with the real world • final trees are often inconclusive, so • consensus trees combine results from several best-scoring trees • “unresolved” nodes support multiple branches

24. dealing with the real world • cladistic analysis is a highly documented hypothetical process • assumptions are explicit • taxon selection criteria are explicit • character/trait selection criteria are explicit • homoplasy identification is explicit • software choices are explicit • tree reconciliation is explicit

25. shared developmental features may demonstrate links betweentaxa with little adult similarityFigure 25.4

26. Useful Characters for Phylogenies • heritable, quantifiable characters • morphological characters • anatomical characters • developmental biology • molecular traits • proteins • nucleic acids

27. Dendroica fusca hierarchyFigure 25.6

28. Classification of Organisms • Biological Classification uses a hierarchical system • a taxon is identified by diagnostic characteristics • lower taxa belong to higher taxa along with sister taxa

29. Rosa gallica hierarchyFigure 25.6

30. Classification of Organisms • Biological Classification uses a hierarchical system • the taxonomic hierarchy is information rich • diagnostic characters are reliable as predictors

31. Classification of Organisms • Biological Classification applies a unique name to each species • A binomial is applied to each species • every known species possesses a binomial • each binomial is applied to only one species • binomial nomenclature is accepted universally among scientists

32. Mertensia sp.Boraginaceae Campanula sp. Campanulaceae Three different species, all called “Bluebells” Endymion sp. Liliaceae

33. Classification of Organisms • Biological Classification applies a unique binomial to each species • common names are insufficient • unregulated • incomplete

34. Arabidopsis thalianathe primary flowering plant molecular model systema.k.a.Arabidopsis thaliana

35. Classification of Organisms • Biological Classification applies a unique binomial to each species • binomials consist of two parts • Genus name: e.g. Echinocactus • specific epithet: E. enneacanthus

36. Classification of Organisms • Biological Classification applies a unique binomial to each species • binomials replaced polynomial phrase names • Linnaeus is credited with development of binomial nomenclature, ~1750