Evolution Biol 4802

Lecture 4, Chapter 2


Objectives for today

  1. Testing phylogenetic hypotheses
  2. Molecular clocks
  3. Problems in tree building


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

  1. Sea urchins
    1. 81 morphological characters
    2. 380 bp sequence of 28s rRNA
    3. DNA tree has two unresolved bushes

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

1.      Problems

a.      Scoring characters is difficult

vi.           Anatomical features of fossils not apparent

a.      75 my older than Archeopteryx

b.      Canadians say they are scales

c.      Oregon State say they are feathers

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)