Ozzie Vilhelmsson Zoology Building, Room 213 Tel.: (01224 27) 2867 Email: o.vilhelmsson@abdn.ac.uk

1. Ozzie Vilhelmsson Zoology Building, Room 213 Tel.: (01224 27) 2867 Email: o.vilhelmsson@abdn.ac.uk Estimating and using phylogenies

2. Taxonomy and Phylogeny • What fossils tell us • What living organisms tell us • Cladistics • Constructing phylogenies • Classification & Evolutionary Relationships • Molecular Analyses - the way ahead!

3. Fossils • Incompleteness of fossil record • Fossilization an unlikely event • Only found in sedimentary rocks • Habitat bias • Age known • Intermediates observed • Can access extinct lines

4. PHYLOGENETIC TREES • Pedigree of a lineage • Evidence of dates of separation (trees) Time Time

5. Tree construction Gather data: • Morphology • Development • Metabolic • Biochemical • Genetic • Anything, really Similarity matrix (numerical taxonomy) Tree Simple, right?

6. But, .... Turtle/birds/crocodile picture ... Different data can yield different trees!

7. CLADISTICS • Aims to distinguish reliable from unreliable characters: • Homologies vs. Homoplasies • Derivedvs. ancestral homologies

8. CLADISTICS • Method of determining evolutionary histories - displayed as trees • Clade: entire portion of phylogeny from a common ancestor = Monophyletic group • Cladogram: unrooted evolutionary tree (no ancestors but points where lineages diverged)

9. HOMOLOGIES • A trait shared between species and inherited from their common ancestor = homologous • Ancestral (general) homologies:shared byall species in lineage - eg. vertebrae in vertebrates • Derived (special) homologies: shared by few species in lineage - eg. indeterminate incisors in vertebrates

10. Only this one is useful! Why the fuss?

11. To reiterate: • Derived homologous traits order TIME of separation • Ancestral homologous traits no use for this -all members of lineage have them

12. Identifying non-useful traits • Divergence = traits unrecognizable • eg. plant leaves

13. (fig. 23.4 in textbook)

14. Identifying non-useful traits • Divergence = traits unrecognizable • eg. plant leaves • Homoplasy = trait evolves more than once • different structures resemble each other by convergent evolutioneg. bat/bird/insect wings • Both cases = analogous traits

15. Hennig’s Method • Same trait in 2 species = provisionally homologousie. innocent, until proven guilty • Ancestral homology = found in group and outside in species = outgroup • Outgroup = branched off from below base of lineage

16. What about wings? Homoplaseous? Ancestral? Derived? Fig. 23.2 in textbook Homoplasy/homology depends on reference/outgroup

17. Three methods: • Distance • Parsimony • Maximum likelihood Rooting the tree Having figured out which traits are important, we can draw a cladogram. But, where does it root? (Possible roots picture)

18. Distance • Simple principle: How similar are the species? (similarity matrix/measurement) • Works well for simple molecular methods, such as DNA:DNA hybridization data • “Molecular clock” assumption

19. (Panda example)

20. PARSIMONY • Simple distance rooting assumes: • trait evolution irreversible, ie. ancestral to derived • trait can change only once per lineage UNREALISTIC • But, cladogram requiring fewest reversals/changes most likely to be correct • PARSIMONY = simplest is correct!

21. PARSIMONY (“counting changes” picture)

22. Maximum likelihood • Requires a lot of data, massive computing power • Need model of evolutionary change to calculate probabilities • Probably the most widely used method today (sequence homologies, etc.)

23. Drawing a cladogram • 8 vertebrates • traits +/- • hagfish = outgroup • derived traits = acquired since hagfish • cladistics minimizes branching - ie. assumes minimal homoplasy

24. Drawing a cladogram

25. Lungs Claws or nails Feathers Four-chambered heart Fur, mammary glands Relative evolutionary time Ancient events Recent events A phylogenetic tree Hagfish Perch Salamander Lizard Crocodile Pigeon Mouse Chimpanzee Jaws

26. Properties of cladogams • Temporal order of splits • Horizontal axis NOT correlated with similarity • 8 vertibrates cladogram = perfect because traits arose & not lost - BUT SNAKES???

27. Classification & Evolutionary Relationships • Linnaeus - predated evolution as central concept of biology • but what features natural? important? • Modern taxonomists - classification reflects evolutionary relationships • BUT should classification reflect time or rate of evolution??

28. Defining clades • Monophyletic - share common ancestor • Polyphyletic - NO common ancestor • Paraphyletic - some, but not all, from common ancestor

29. (mon/para/polyphyletic picture; similar to 23.12 in textbook)

30. The problem of paraphyly • Birds and crocodiles - more recent ancestor than crocs. and snakes/lizards • Crocs. evolved more slowly than birds since lineages separated • Birds as separate class recognizes their rapid evolution = major unique derived traits

31. Systematicists • Still many polyphylectic groups • Detect convergent evol. ==> change classification • BUT favour retaining paraphyletic groups to underscore rapid evolution • STABILITY of taxonomic system

32. Future of Systematics • Molecular genetics & powerful computers • Fossil history - dating and derived vs ancestral traits • Molecular = more traits than ever before • Combining two lines of evidence produces accurate dated phylogenies