1. Estimating and using phylogenies
Ozzie Vilhelmsson
Zoology Building, Room 213
Tel.: ( ) 2867
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 Similarity matrix Tree Simple, right? 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
Derived vs. 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 by all species in lineage - eg. vertebrae in vertebrates
Derived (special) homologies: shared by few species in lineage - eg. indeterminate incisors in vertebrates

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

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 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 evolution eg. bat/bird/insect wings
Both cases = analogous traits

15. Hennig’s Method
Same trait in 2 species = provisionally homologous ie. 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? Homoplasy/homology depends on reference/outgroup
Homoplaseous? Ancestral? Derived?
Fig in textbook
Homoplasy/homology depends on reference/outgroup

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

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

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