1. Lecture 19 – Non-tree Based Methods
Increasing molecular evidence indicates that hybridization is far more
common in animals than has traditionally been recognized. A B C D
Hybridization
Non-Introgressed Genes
Introgressed Genes
Between Sister Species
Between Non-Sister Species

2. Horizontal Gene Transfer
HGT is usually used to refer to reticulations among potentially strongly diverged organisms (i.e., large spans of evolutionary time).

3. For n taxa, there are 2(n-1) possible bipartitions.
Spectral Analysis
Examines all possible bipartitions of taxa, and examines the data for support and conflict.
A ATCGAGCAGCCTGGGAGAGAGACTTATTTGACAAACGTAA
B ATTGGGGAGTAGCGTAAACACTCTTATTTGACGAAATTAT
C ATCGTGGGTTAGAGTAGAGACTCTCATTTGACGAAATTAT
D AACGTGGCGAATAGTAGTCAAAAAATGTGTACCAGATTAC
A RYYRRRYRRYYYRRRRRRRRRRYYYRYYYRRYRRRYRYRR
B RYYRRRRRRYRRYRYRRRYRYYYYYRYYYRRYRRRRYYRY
C RYYRYRRRYYRRRRYRRRRRYYYYYRYYYRRYRRRRYYRY
D RRYRYRRYRRRYRRYRRYYRRRRRRYRYRYRYYRRRYYRY
For n taxa, there are 2(n-1) possible bipartitions.
{A} = 6 {AB} = 2
{B} = 1 {AC} = 1
{C} = 1 {AD} = 3
{D} = 12 Constant = 14

4. Spectral Analysis
Support for competing hypotheses.

5. Split Decomposition
A network-based method that incorporates reticulations into the network at points where the data have conflicting signals.
The idea is similar to Spectral Analysis in that the data are not forced into a single tree. Instead, each site is examined for the split that it supports.
Human T C C T T A A A A
Chimp T T C T A T A A A
Gorilla T T A C A A T A A
Oranutan C C A C A A A T A
Gibbon C C A C A A A A T

6. Split Decomposition This network contains two bifurcating trees Go C HGi C H Go O Gi
Orange tree has more support.

7. These can get very complicated.
Split Decomposition
These can get very complicated.
These address where the data are not tree-like, but not why.