Phylogenetic Analysis – Part I

1. Spring 2013 Phylogenetic Analysis – Part I

2. Outline • Systematics • Phenetics (brief review) • Phylogenetics & Characters • Evolutionary Trees

3. Systematics • Science of organismal diversity. • Discovery, description and interpretation of biological diversity. • Discovery and description of the evolutionary tree of life. • Synthesis of information in the form of predictive classification systems. • Production of identification tools (e.g., keys, floras and faunas, monographs, etc.)

4. Some important definitions Systematics = the study of the biological diversity on Earth and its evolutionary history. Taxon (pl. taxa) = a group of organisms distinct enough to be distinguished by a name and ranked in a definite category. Classification = the delimitation, ordering and ranking of taxa. Taxonomy = the theory and practice of classifying organisms.

5. Phylogenetics • Greek: • phylon = tribe, race • genetikos = refers to birth • (from genesis = birth) • = the study of the evolutionary relationships of organisms • Phylogeny = evolutionary relationships; • genealogical (through time)

6. Phenetics:Historically, systematists relied on similarities to classify organisms Pheno = Greek for display, referring to visible characteristics Phenetics = method of classifying organisms based on overall similarity

7. Were originally designed to reflect God’s plan of creation [“natural order”] Later systems were considered “natural” in that presumably related plants were grouped together. Were based on many characters selected from experience, not from a pre-existing theory Overall similarity was the main criterion; all characters had equal weight Phenetic Classification Systems

8. Phenetics vs. Phylogenetics Vertebrate limbs

9. A plant example: cacti euphorbs

10. Phenetics is not Sufficient…. • Modern systematists seek an evolutionary interpretation for the relationships between organisms. • Simple “matching” or relationships based on superficial similarity may not reflect evolutionary relationships. • Testability and identification of specific characters used to group taxa is lacking in most phenetic methods. • Character-based, evolutionarily interpreted inter-taxon comparisons deemed superior!

11. Phylogenetics & Characters • Based on an explicit set of a priori assumptions on how the characters used have evolved. Relies heavily on evolutionary information. • Data are scored and analyzed following testable methods using shared derived character states to build evolutionary trees (phylogenies). • Methods are continually being developed that enhance the reliability of the analyses, and that provide tests for statistical support for the groups determined by the process. (More on this later…)

12. Character = any feature of the organism, especially one with variation that helps to define groups. E.g., flower color. Character state = one of the various conditions or values of a character observed across a given group of taxa. E.g., red, white, pink, yellow are states for flower color. What is a character?

13. Another example: Character = leaf arrangement. Character states = ???

14. Another example: Character = leaf arrangement. Character states (depending on the group) = -alternate -opposite -whorled

15. Phylogenetic Analyses Philosophy: Determine relationships based upon uniquely derived and shared character state changes as evidence of common ancestry. Relies on the principle of homology.

16. What is HOMOLOGY?

17. What is HOMOLOGY? Similarity due to inheritance of a feature from a common ancestor; may be associated with a change in function.

18. a a a • Homologous characters (homology) • Character states of 2 or more taxa are homologous if the character is found in their common ancestor • 2 character states (or features) are homologous if one is directly (or sequentially) derived from another Characters a’ a

19. Leaf modified as: -pitcher for catching insects -jaws for catching insects -colored, petal-like bracts for attracting pollinators -spines for protection

20. Homologous characters • example: perianth (petal & sepal) modification Characters

21. An animal example Forelimbs of human, cat, whale, bat

22. Homoplasious characters (homoplasy) • Result of convergence, parallelisms, or reversals • Describes a character state found in 2 taxa if the common ancestor did not have this character or one character state is not the precursor of another (= superficial similarity) Characters

23. Remember this? Euphorbs (vegetative) Cacti (vegetative)

24. cacti • euphorbs Flowers and fruits show that these are two groups with different origins.

25. Homologous vs. Homoplasious • Similarity – includes detailed structure • Position • Development • Congruence – various types of evidence give • the same answer Characters

26. Characters Homologous characters • molecular evidence: genetic basis for homology (or not!) of basic features and how they have been modified ABC model of floral organ identity

27. Evolutionary Trees CBA TIME

28. Evolutionary Trees Petal number Stem shape CBA TIME

29. Evolutionary Trees CBA Petal number Stem shape

30. Evolutionary Trees Petal number Stem shape CBA 5 petals TIME square stem

31. Terminology Apomorphy = derived character state Plesiomorphy = ancestral character state In the example we just looked at, which character states are apomorphic? Plesiomorphic?

32. Terminology Apomorphy = derived character state Plesiomorphy = ancestral character state In the example we just looked at, which character states are apomorphic? Plesiomorphic? Apomorphic: square stems, 5 petals Plesiomorphic: round stems, 4 petals

33. Terminology Synapomorphy – shared derived character for two or more taxa or lineages; defines clades. Symplesiomorphy – shared ancestral (underived) character – uninformative. Autapomorphy – derived character state occurring in only ONE taxon – uninformative. Clade – group of taxa defined by at least one synapomorphy; branch of an evolutionary tree; a lineage.

34. Terminology For our purposes: an evolutionary tree = phylogeny = cladogram The shape of the tree (the branching order) is known as the topology.

35. Equivalent (Congruent) Cladograms Cladograms 1, 2, and 3 have the same topology.

36. The Same Cladogram… …these trees are topologically congruent.

37. Common Phylogenetic Tree Terminology Clades or Branches or lineages Terminal nodes Ancestral node or root Sister groups Internal nodes or divergence points Polytomy

39. (apomorphic) (plesiomorphic)

40. Monophyletic taxon – contains a common ancestor and all of its descendents Phylogenetic definitions of groups/taxa

41. A clade by definition is monophyletic!

42. Paraphyletic taxon – contains a common ancestor and some, but not all of its descendents Phylogenetic definition of groups/taxa

43. Example of Paraphyly The term “invertebrate” is used to describe all metazoans without a vertebral column— This is a group that does not include all descendents of animals.

44. Polyphyletic taxon – a composite taxon derived from 2 or more ancestral sources (taxa) Phylogenetic definition of groups/taxa

45. Examples of monophyly and paraphyly

46. Example of polyphyly Traditional concept of plants included: Euglenas Blue-green algae (cyanobacteria) Green plants Red algae Diatoms Fungi

47. Tree of Life Showing Groups Previously Classified as Plants (see Fig. 1.1 in Simpson)

48. Another way to think about it. monophyletic paraphyletic polyphyletic Source: Stuessy (1990)