Monophyletic groups

1
Characters Character states 0. A 1. D
Monophyletic groups Clades Sister groups Ingroup
2
autapomorphies
Synapomorphy shared DCSs
3
No
Homoplasy Independently derived
character states and reversals
A a b c d e f g h I j OG 1
0 0 0 0 0 0 0 0 0 Sp1 0 1 1 0
0 0 1 1 0 1 Sp2 0 1 1 1 1 1
0 1 0 0 Sp3 0 1 1 1 1 1 1 0 1
1
4

• Most phylogenetic analyses use the principle of
  parsimony.
• Best phylogenetic depiction is the one
  requiring the fewest evolutionary changes.

5
Principle of parsimony
Convergence
6
An example of phylogenetic analysis relationship
of whales to other mammals. Principle of
parsimony. Why is this a bad example?
7
Artiodactyl hypothesis
Whale-hippo hypothesis
Whale phylogeny
Competing hypotheses
10,395 trees
8
Perissodactyla
Artiodactyla
9
Gain of artiodactyl astragalus
Perissodactyl astragalus
10
Genetic resolution?
A sequence of 60 bases from the beta-casein gene
60 characters

• Characters
• (a) informative
• Character 166
• (b) uninformative
• no variation
• e.g., character 142
• 2. occur only once
• autapomorphy
• e.g., character 192
• (c) conflicting
• phylogenetic
• signals
• e.g., 162 and 177
• Homoplasy

11
Resolution of whale phylogeny
SINES and LINES Retrotransposable interspersed
elements RNA intermediate Contains info
for reverse transcriptase
12
Example of a phylogeny a globin pseudogene
13
A few difficulties Different genes may give
different results gene trees
14
A difficulty dataset could not resolve all
relationships
Polytomy
15
You hope for congruence