Phylogenetic Analysis – Part 2

1. Phylogenetic Analysis – Part 2 Spring 2014

2. Outline • Why do we do phylogenetics (cladistics)? • How do we build a tree? • Do we believe the tree? • Applications of phylogenetics (cladistics)

3. Why do we do phylogenetic analyses? Evolutionary interpretation of relationships between organisms. More reliable method of ascertaining the best hypothesis for how the organisms diverged from common ancestors. Provides a better rationale for circumscribing taxonomic groups. Enables testing of multiple hypotheses of relationships and character evolution based on specific character transformations.

4. Willi Hennig(1913-1976)German Entomologist (Diptera)

5. Warren Herbert Wagner(1920-2000)American Botanist (Pteridophytes, Dendrogrammaceae)

6. How do we build a tree? • Data: Types of characters • Look for synapomorphies • Assemble the hierarchy of synapomorphies according to the principle of parsimony

7. Parsimony • The idea that the simplest hypothesis is the best explanation given the assumptions of the analysis. • Also known as Occam’s Razor • In systematics, we look for the shortest trees in any given phylogenetic analysis (maximum parsimony)… • …even though we know that evolution doesn’t necessarily proceed in a parsimonious manner.

8. Data: type of characters Character Selection: Must study each individual character to assure comparisons of homologous characters, and interpretation of the direction of character state transformations. Some sources of characters: 1) morphology (external structure) or anatomy (internal structure) 2) biochemical (photosynthetic pathway, pigmentation pathways, etc.) 3) chromosome numbers 4) nucleotide sequence data ( a t c g )

9. Character states • Presence vs. absence (0 or 1): always binary (two states) • Other binary characters (0 or 1): yellow vs. white flowers; range of measurements (quantitative) • Multi-state characters (3 or more states): e.g., yellow, white, or pink flowers or a t g c for nucleotide sequence data • For binary or multi-state characters, can hypothesize the direction of evolutionary change (transformation series)

10. Pollen wall thickness µm (x axis) Fig. 2.2

11. Fig. 2.4 Examples of character state transformations

12. But how to hypothesize direction? • We usually have some working knowledge of the group under study (ingroup). • We choose a group thought to be closely related to the ingroup to serve as the outgroup as a basis of comparison. • Character states in the outgroup are assumed to be ancestral (plesiomorphic). • This allows us to establish the direction of character state transformation.

13. Phylogenetics or Cladistics Dixonia Dixonia

14. Cladistics Attigalea We need an outgroup, so we choose the closely related genus Attigalea(there is evidence for this from other studies). Dixonia Ingroup

15. Cladistics: characters 1. Leaf arrangement: alternate (0) or opposite (1) 2. Leaf midrib: white (0) or green (1) 3. Leaf apex: rounded (0) or spiny (1) 4. Sepals: present (0) or absent (1) 5. Flower color: yellow (0) or blue (1) 6. Subtending floral bracts: absent (0) or present (1)

16. Cladistics: characters 1. Leaf arrangement: alternate (0) or opposite (1) 2. Leaf midrib: white (0) or green (1) 3. Leaf apex: rounded (0) or spiny (1) 4. Sepals: present (0) or absent (1) 5. Flower color: yellow (0) or blue (1) 6. Subtending floral bracts: absent (0) or present (1)

17. Cladistics: matrix Outgroup (Attigalea) Ingroup(Dixonia)

18. Cladistics: matrix

19. Cladistics 3 2 6 4 5 1 7 8 Sepals absent Leaves opposite

20. Cladistics: matrix

21. Cladistics 3 2 6 4 5 1 7 8 Midrib green Sepals absent Leaves opposite

22. Cladistics: matrix

23. Cladistics 3 2 6 5 4 1 7 8 Floral bracts present Blue flowers Midrib green Sepals absent Leaves opposite

24. Cladistics: matrix

25. Dixonia Attigalea floral bracts present purple fringe midrib green sepals absent Length = 5 steps

26. Cladistics: matrix Homoplasy? Polymorphism in the outgroup

27. Attigalea Dixonia spiny leaf tip spiny leaf tip floral bracts present purple fringe midrib green sepals absent Length = 7 steps

28. Do we believe the tree? • Various programs to generate trees. • Various measures of statistical support for the clades and for the characters. • Can quantify the effects of homoplasy. • Can test alternate arrangements to examine the number of steps involved.

29. Attigalea Dixonia spiny leaf tip spiny leaf tip floral bracts present purple fringe midrib green sepals absent Length = 10 steps (7 - 1 + 4)

30. Phylogenetic Methodology 1. Selection of taxa to study - Individuals, populations, species, etc. identified as the units of comparison. One or more related groups (outgroups) necessary to “root” the trees. 2. The units under study described for as many characters as possible for which homology can be demonstrated or reasonably assumed. Character states assigned based on variation among the taxa in the ingroup and outgroup(s) and a priori hypotheses of the evolutionary direction of changes undergone by the character (character state polarization) are generated based on outgroup comparison. 3. A data matrix is assembled by scoring all taxa for all characters (ideally).

31. Phylogenetic Methodology(continued) 4. Using various analytical principles (maximum parsimony), a cladogram is constructed using synapomorphic character state changes to determine the tree topology. Systematists are seeking to define monophyletic groups (= clades). 5. Evaluation of the statistical confidence in how robustly the data support the grouping of organisms into clades is done next. 6. The subsequent grouping and ranking of the organisms in the resulting clades is then applied to classification systems or other questions.

32. Applications of phylogenetics • Classification • Biogeography • Many other possibilities (e.g., disease tracking, gene annotation)

33. Cladistics and Classification - Classifications based on tree topologies…Is it the best tree? Will new data and new tree topologies necessitate complete overhaul of classification? - Remember, systematists would like to define and name monophyletic groups (clades). Is this always possible? Must we accept paraphyletic groups? - Classifications must also be useful for communication. Do the groups truly represent the best evolutionary hypothesis, and yet are the classifications useful?

34. Phylogenetics and Classification

35. Phylogenetics and Classification Fig. 2.19A-C

36. Phylogenetics and Biogeography Adansonia (baobab tree) (Judd et al. 2008)

37. Fig. 2.22 Phylogenetics and Character Evolution

38. Phylogenetics and Conservation Anomochloa Grama grass Northern sea oats bamboo bluegrass Big bluestem Fig. 19.11