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 1.2 Figure 25.2

8. bat, bird, insect wings - not homologs Figure 25.2

9. leaf homologs in flowering plants Figure 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 EuphrobiaceaeCactaceae Asclepiadaceae Figure: three plants that all look like cactus but come from Three distinct families -

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 vertebrates Figure 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 between taxa with little adult similarity Figure 25.4

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

27. Dendroica fusca hierarchy Figure 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 hierarchy Figure 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 Endymion sp. Liliaceae Three different species, all called “Bluebells”

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

34. Arabidopsis thaliana the primary flowering plant molecular model system a.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