Phylogeny and Systematics: Understanding the Evolutionary History of Species

1. Exam I: Friday afternoon • Exam covers lecture material and corresponding readings • Chapter 22: Descent with modification: a Darwinian view of life • Chapter 23 The evolution of populations • Chapter 24 The origin of Species • Chapter 25 Tracing phylogeny (omit last subunit; The science of phylogenetic systematics) • Two additional readings • Coverage of topics on exam is approximately proportional to time spent in lecture to those topics

2. Phylogeny and Systematics

4. Taxonomic classification is hierarchical and nested • Linnean classification called binomial nomenclature, in reference to genus and specific epithet • Taxon is a generic term for any taxonomic unit (level) • Most inclusive taxon, not shown here, is Domain

5. Systematics • Study of biodiversity • Inter-related goals of systematists and taxonomists • Formally name and describe species • Classify taxa; assign species to genera, genera to families, etc., which may require establishing new taxa • Determine evolutionary relationships among lineages; establish nested hierarchical classifications (taxonomies) that superimpose precisely on the branching pattern of the corresponding phylogenetic tree

6. Bass Frog Snake Bird Phylogeny evolutionary history of a species or a group of related species “Basal” or “Ancestral” Lineage Phylogenetic Tree or Cladogram. Depiction of a phylogeny. Carries information only on order of branching (= speciation = cladogenesis); no information about passage of time or amount of phenotypic change.

7. Tunicate Bass Frog Snake Bird • Subphylum Vertebrata (fish, amphibians,reptiles, birds) • Tetrapoda (frog, snake, bird) • Amniota (snake, bird)

8. Vertebrata Tetrapoda Amniota Tunicate Bass Frog Snake Bird

9. Determining monophyletic taxa is key to classifying organisms according to their evolutionary history: • Monophyletic taxon is one in which a single ancestor gave rise to all species, and which includes all descendents of that single ancestor • Paraphyletic taxonexcludes one or more species descended from a single ancestor • Polyphyletic taxon includes species descended from two or more ancestral forms not common to all members

10. Systematists classify organisms based on homologous characters (traits) • Remember; classify organisms ~ establish taxa ~ determine evolutionary history • Homologouscharacter; character that is shared by two or more taxa because those taxa inherited the character from a common ancestor • Expect shared character to be quite similar, perhaps, but not identical among taxa, as a result of descent with modification • Homology indicates common ancestry, which is information with which one can determine evolutionary history • Analagous character; character occurring in two or more taxa because it evolved independently in each of those taxa, • Analagies may arise through convergent evolution: taxa occupy similar ecological roles and similar selective forces

11. Divergent Evolution of Homologous Characters Homologous characters may “evolve away” from each other in structure

12. Aardvark, native to central, southern and eastern Africa Giant Anteater (at a termite mound), native to Latin America from Southern Mexico to Northern Argentina Pangolin, native to Africa and southern and southeastern Asia Convergent Evolution of Analogous Characters. Three distantly related mammals have structural similarities (analogous characters, homoplasious characters) due to convergent evolution. Each taxon independently evolved morphological traits for feeding on ants and termites.

13. The supporting structure of bird and bat wings are homologous structures; derived from a common ancestor The supporting structures of insect wings are analogous to the structures of bird and bat wings; evolved independently. Systematic investigation is based on analysis of homologous characters (traits). Characters may be morphological, molecular, behavioral, physiological..

14. Shoot develops from axillary bud Thorn develops from axillary bud Spine develops from midrib of leaf Thorn of downy hawthorn is a modified stem Spine of Japanese barberry is a modified leaf Analagous traits, or homoplasies, in two distantly related plant taxa

15. Evolutionary relationships can also be determined through analysis of macromolecules; DNA, RNA and proteins • Molecular biology provides powerful tools for systematics • Nucleotide sequences and therefore amino acid sequences, are inherited; both undergo descent with modification following divergence of one lineage into two • Extent of sequence differences between taxa is an indicator, an estimator, of time since divergence from a common ancestor • DNA , RNA and proteins are used to classify organisms and determine evolutionary relationships

16. Phylogenetic Analyses Based On DNA-DNA Hybridizations

17. Melting tempertature curve for DNA of T4 bacteriophage. T50 = 84 deg C % Dissociated DNA

18. Phylogenetic tree based on systematics. • Data used in this analysis includes comparison of genomes by DNA-DNA hybridization • Note: this molecular approach help determine that lesser panda isn’t a bear (an Ursid) – it’s a racoon relative (a Procyonid)

19. Pattern of speciation that explains the diversity of Galapagos Finches

20. Seed Eaters

21. Seed Eaters ?

22. 2 of the 3 competing hypotheses on phylogeny of seed eating Galapagos Finches G. fuliginosa diverged first; G. fortis and G. magnirostris are sister species G. magnirostris diverged first; G. fortis and G. fuliginosa are sister species Seed Eaters Seed Eaters

27. Phylogenetic Systematics Dr. Willi Hennig (1913-1976) • The history of diversification is recorded through descent with modification • Modification exists in the form of evolutionary transformation of characters from one state to another state. • Plesiomorphy: Ancestral character state • Apomorphy: Derived character state • Synapomorphy Derived character state that is exclusively shared by a subset of taxa under investigation. • A synapomorphy is evidence that taxa bearing it are descended from the same common ancestor -- the ancestor in which the derived character arose.

28. Seed Eaters ?

29. Species A Species B Species C • Reconstruct the phylogeny of three closely related bird species • Determine characters to use for analysis • bill shape (derived character state: hooked;ancestral= not hooked) • head feathers (derived = crest; ancestral = no crest) • toe condition (derived = webbed; ancestral = no webbing)

30. Species A Species B Species C • Hooked Bill Hooked Bill No Hooked Bill • Crested Head No Crested Head Crested Head • Webbed Toes Webbed Toes No Webbed Toes • Character states variously arise in lineages. • Character states variously accumulate in lineages, in descendents of the ancestor in which the character states arose

31. A B C ?

32. “Cladistic” or “Phylogenetic” Analysis: Procedural Outline • SELECT ORGANISMS • Identify the ingroup • Select an appropriate outgroup • BUILD TRANSFORMATION MATIX • Select characters for analysis • Assign character states • Determine polarity of character states • ANALYZE AND INTERPRET DATA • Subject data to optimization algorithm • (usually parsimony criteria) • Product: optimal tree, perhaps a concensus tree • Seek congruence • Product: Phylogenetic Hypothesis

33. Closely related species that we know diverged from ancestral lineage before our three species of interest diverged (outgroup) ? (ingroup)

34. Outgroup Species A Species B Species C Transformation Series Closely related species that diverged from ancestral lineage before our three species of interest diverged (outgroup) Bill Shape Head Plumage Toe Condition Outgroup H- C- W- Species A H+ C+ W+ Species B H+ C- W+ Species C H- C+ W- ? (ingroup) Assume character state seen in outgroup is ancestral character state.

35. H- C- W- H+ C+ W+ H+ C- W+ H- C+ W- OG A B C C+ Outgroup Species A Species B Species C Transformation Series Closely related species that diverged from ancestral lineage before our three species of interest diverged (outgroup) W+ C+ H+ Bill Shape Head Plumage Toe Condition Outgroup H- C- W- Species A H+ C+ W+ Species B H+ C- W+ Species C H- C+ W- ? (ingroup) This phylogenetic hypothesis requires four evolutionary transformations to explain the distribution of character states among taxa under investigation W- C- H- Assume character state seen in outgroup is ancestral.

36. H- C- W- H+ C- W+ H+ C+ W+ H- C+ W- OG B A C W+ C+ Outgroup Species A Species B Species C Transformation Series W+ H+ Closely related species that diverged from ancestral lineage before our three species of interest diverged (outgroup) W+ C+ H+ H+ Bill Shape Head Plumage Toe Condition Outgroup H- C- W- Species A H+ C+ W+ Species B H+ C- W+ Species C H- C+ W- C+ ? (ingroup) This phylogenetic hypothesis requires five evolutionary transformations to explain the distribution of character states among taxa under investigation This phylogenetic hypothesis requires four evolutionary transformations to explain the distribution of character states among taxa under investigation W- W- C- H- C- H- Assume character state seen in outgroup is ancestral.

37. Choosing Among Competing Hypotheses: The Parsimony Principle • The Parsimony Principle holds that, all other things being equal, the hypothesis requiring the fewest number of evolutionary transformations has the highest likelihood of being the correct hypothesis

38. Using Phylogenies to Test Hypotheses McGregor’s Viper, Phillipines

40. not (Scanlon and Lee 2000)

45. George Gaylord Simpson (1902-1984) Mammalian Paleontologist, regarded as one of the architects of the modern synthesis Formulated the principles of evolutionary taxonomy

46. “SCHOOLS” OF SYSTEMATICS • TRADITIONAL EVOLUTIONARY TAXONOMY [Simpson] • Establish taxa based on common descent (clades) and or extent of adaptive evolutionary change: • evolutionary groups that represent adaptive zone constitute legitimate higher taxa -- a grade • adaptive zone; “…characteristic reaction and mutual relationship between environment and organism, a way of life and not a place where life is led.” • paraphyletic taxa may be acceptable • PHYLOGENETIC SYSTEMATICS (CLADISTICS) [Hennig] • Establish taxa based on: • clades; monophyletic taxa only

47. Tunicate Bass Frog Snake Bird You establish the taxon... PHYLUM: REPTILAVES snake bird

48. Tunicate Bass Frog Snake Bird You establish the taxon... Monophyletic taxon: Includes all and only all the descendents of the most recent common ancestor of the group (taxon) PHYLUM: REPTILAVES snake bird

49. Tunicate Bass Frog Snake Bird You establish the taxon... PHYLUM: AMPHIREPTA frog snake

50. Tunicate Bass Frog Snake Bird You establish the taxon... Paraphyletic taxon: Includes common ancestor to all members of the group (taxon), but not all descendents of the common ancestor PHYLUM: AMPHIREPTA frog snake