Objectives for today
How can we test phylogenetic hypotheses?
a. Add more genes
b. Compare independent data sets
c. Use computer simulation modeling to test problems
d. Experimental evolution
Trees based on morphological and molecular data often support each other
Fig. from Smith et al. 1992
The validity of parsimony can be tested experimentally
Fig. 2.12 (old Fig. 2.11)
Does evolution tick along like a clock?
1. Adaptive change?
2. Neutral molecular change?
a. If true, can estimate time since divergence
Fig. 2.10 (old Fig. 2.9)
What if there is no fossilized ancestor?
1. Use the rate estimated for other taxa to calculate time since divergence
2. This the beauty of the molecular clock concept
Nothing is easy
a. Scoring characters is difficult
vi. Anatomical features of fossils not apparent
a. 75 my older than Archeopteryx
b. Canadians say they are scales
vii. Number of characters not always obvious
viii. Not all base pairs evolve independently
b. Homoplasy is common
i.Several equally or almost equally good trees
Fig. from Hibbett et al. 2000.
c. Ongoing evolution can obscure patterns
i.Multiple hits at the same spot erase synapomorphies
Fig. 2.17(old Fig. 2.12A)
ii.Genes evolve at different rates
Fig. 2.18 (old Fig. 2.16)
b. Rapid evolution may prevent synapomorphies to become established
Fig. 2.19 (old Fig. 2.17)
c. Gene trees may produce incorrect trees if the “haplotypes” are not fixed in the species
Fig. 2.20 (old Fig. 2.18)
a. Example of polymorphic mitochondrial haplotypes
1. Polymorphism throughout the tree
2. Same haplotype pops up in unrelated taxa
3. Ancestor must also have been polymorphic
4. Can’t use these genes to resolve relationships
d. Hybridization causes reticulate (net-like) trees
Fig. 2.23 (old Fig. 2.20)
e. Horizontal gene transfer possible through uptake of DNA by bacteria and viral transfer of genes
Fig. 2.24 (old Fig. 2.21)