Additive vs ultrametric: triangle inequality Additive vs ultrametric ...

Phenetic vs patristic distances
• Assessing agreement between tree and original
distance matrix:
– Patristic distance: predicted between two taxa by
tree.
• UPGMA: 2 x distance to nearest common node.
• NJ: sum of horizontal branch lengths between taxa.
UPGMA
2
Neighbor-joining
7
1
6
3
3
5
2
4
1
1
0.8
0.6 0.4
Distance
0.2
7
6
0
4
5
Correlations between
phenetic and patristic distances
• Ex: phenetic distances calculated from clocklike
tree:
– Add noise.
– Calculate cophenetic correlation between phenetic
and patristic distances.
8
r = 0.59
UPGMA, 7 taxa
8
7.5
r = 0.82
Neighbor-joining tree, 7 taxa
7
Patristic distanc ce
7
6
5
4
3
ce
Patristic distanc
6.5
6
5.5
5
4.5
4
3.5
4 4.5 5 5.5 6 6.5 7 7.5 8 8.5 9
Original phenetic distance
3 3.5 4 4.5 5 5.5 6 6.5 7 7.5 8
Original phenetic distance
6