Evolution Biol 4802

Lecture 4

 

Objectives for today

  1. Steps in parismony
  2. Testing phylogenetic hypotheses
  3. Molecular clocks
  4. Problems in tree building
  5. Group work on EvoBeaker Dogs

Why is parsimony a useful concept?

  1. Ancestral states are not knowable with certainty
  2. All you can know is current state
  3. Patterns of branching inferred from current states suggest what the ancestral state probably was
  4. You need a rule

Maximum Parsimony

  1. The process
    1. Chose an “outgroup” to compare “ingroup”

                                                               i.      Known to be ancestral (i.e. fossil record, biogeographical patterns)

    1. Build all possible trees
    2. Map traits on to the tree
    3. Choose the tree with the fewest steps

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

Does evolution tick along like a clock?

1.      Adaptive change?

2.      Neutral molecular change?

a.   If true, can estimate time since divergence

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

c.   Ongoing evolution can obscure patterns

i.       Multiple hits at the same spot erase synapomorphies

ii.       Genes evolve at different rates

d. Rapid evolution may prevent synapomorphies to become established

e. Gene trees may produce incorrect trees if the “haplotypes” are not fixed in the species

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

f. Hybridization causes reticulate (net-like) trees

g. Horizontal gene transfer possible through uptake of DNA by bacteria and viral transfer of genes