Lecture V How to Determine Evolutionary Relationships: Concepts in Phylogeny and Systematics

1. Lecture V How to Determine Evolutionary Relationships: Concepts in Phylogeny and Systematics Textbook Reading: pp 425-433, 435-437 in chapter 23: Reconstructing and using Phylogenies

2. Nature 413, 277 - 281 (2001) Skeletons of terrestrial cetaceans and the relationship of whales to artiodactyls. J. G. M. Thewissen, E. M. Williams, L. J. Roe & S. T. Hussain. See webpage for link to pdf of this paper, and summary/persptive of this paper

4. Taxonomic classification is hierarchical and nested • Taxonomy is the science of the classification (=naming) of organisms • 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. Bass FrogSnake Bird “Basal” lineage Phylogenyhistory of descent of a group of organisms from their common ancestor Phylogenetic Tree or Cladogram. Depiction of a phylogeny. Carries information only on branching relationships; no information about passage of time or amount of phenotypic change. Each branching point (node) reflects a divergence (ie, speciation, cladogenesis) event that took place in the species that is the most recent common ancestor to the descendents of that cladogenesis event Lineage Organisms in an ancestor-descendent relationship

6. Tunicate Bass Frog Snake Bird • Vertebrata (fish, amphibians,reptiles, birds) • Tetrapoda (frog, snake, bird) • Amniota (snake, bird) The nested polygons here show taxonomic groupings, but with no regard for “inclusion” or “exclusion” of ancestors common to the groupings

7. Vertebrata Tetrapoda Amniota Tunicate Bass Frog Snake Bird The nested polygons here do show taxonomic groupings, but with regard for “inclusion” or “exclusion” of ancestors common to the groupings

8. Determining monophyletic taxa is key to classifying organisms according to their evolutionary history: • Monophyletic taxon is one in which a single ancestorgives rise toall species, and which includes all descendents of that single ancestor • Paraphyletic taxonexcludes one or more species descended from the most recent common ancestor of the taxon • Polyphyletic taxon excludes the most recent common ancestor of all members of the taxon A taxon that includes only A and B would be paraphyletic A taxon that includes B, C and D would be polyphyletic A taxon that includes D, E and F would be monophyletic

9. “SCHOOLS” OF SYSTEMATICS • TRADITIONAL EVOLUTIONARY TAXONOMY [Simpson and others] • Establish taxa based on common ancestry (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 • Powerful methodological and analytic tool for determining relationships • The tools of cladistics now represent the prevailing approach to determining relationships; the philosophy of strict monophyly wrt classification is still under debate -- bears on definition - concept- of species George Gaylord Simpson (1902-1984). Mammalian Paleontologist, regarded as one of the architects of the modern synthesis. Formulated the principles of evolutionary taxonomy Willi Hennig (1913-1976). Hennig is best known for developing phylogenetic systematics, a coherent theory of the investigation and presentation of the relations that exist among species. http://www.cladistics.org/about/hennig.html

12. Systematists classify organisms and determine evolutionary relationships based on analysis of homologous characters (traits) • Systematic investigation is based on analysis of homologous characters (traits); characters may be morphological, molecular, behavioral, physiological.. • Homologous character; 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 Divergent Evolution of Homologous Characters Homologous characters may “evolve away” from each other in structure

13. Analagous character; character occurring in two or more lineages because it evolved independently in each of those lineages, • Analagies may arise through convergent evolution: lineages occupy similar ecological roles and similar selective forces • Misinterpretation of analagous characters for homologus ones may lead to erroneous conclusions regarding phylogenetic relationships and unintended taxanomic groupings Giant Anteater (at a termite mound), native to Latin America from Southern Mexico to Northern Argentina Aardvark, native to central, southern and eastern Africa 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.

14. The supporting structures 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.

15. Spine develops from midrib of leaf Shoot develops from axillary bud Thorn develops from axillary bud 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

16. 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. • “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) to produce an optimal tree, perhaps a concensus tree • Seek congruence • Product: Phylogenetic Hypothesis

17. 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. • “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) to produce an optimal tree, perhaps a concensus tree • Seek congruence • Product: Phylogenetic Hypothesis

18. Reconstruct the phylogeny of three closely related bird species Species A Species B Species C • 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)

19. 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

20. A B C ?

21. Outgroup Closely related species that we know diverged from ancestral lineage before our three species of interest diverged Ingroup

22. 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) H=hooked billC=crestW=webbed toes +=species has trait -=species lacks trait Assume character state seen in outgroup is ancestral character state.

23. 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.

24. 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

25. Evolutionary relationships may be determined through analysis of molecular characters; 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

27. Normal RBC’s and normal hemoglobin Sickled RBC’s and sickle-cell hemoglobin Phenotypic consequence of a point mutation - a substitution

28. Molecules evolve at different rates, some, at constant rates Raven and Johnson 1999)

29. Hemoglobin Evolution • Gene duplication Multigene Families • Evolution of molecular function Tetrameric Human hemoglobin

30. Gene family • -two or more genes in a genome, identical or highly similar in nucleotide sequence • -descended from the same ancestral gene • Origin of gene families • -Repeated gene duplication from errors during DNA replicationand recombination

31. Globin gene families are well-studied across taxa for sequence, structure and function • Hemoglobin multigene families in humans • Alpha globin family (on chr. 16) • Beta globin family (on chr. 13) • Hemoglobin families probably descended from a myoglobin-like ancestral gene

32. Evolutionary Time

33. Evolution of the Globin Gene • Genes encoding proteins have undergone continual evolution, accumulating increasing numbers of changes over time • Length of lines corresponds to number of nucleotide substitutions in the gene • Raven and Johnson 1999