Used adaptML to look at the partitioning of bacteria by habitat and seasonal variation. This is an MC based method.
Ecological preferences are sufficient to produce speciation - what was defined as one species was found to have 17 different habitat locations and seasonal variations. Habitats are defined by net sizes or species in which they are present. Move from fish to squid means adaptation to the mucus membranes and so aquired new features.
Go from zooplankton to small particle associated. Looking for patterns of gene expression, between different lifestyles. Did 20 genomes how do you analyse a population of genomes?
- Where are the recombination break-points?
- Inconsistency of a phylogentic tree at a point with phylogentic trees from preceding bases.
- McDonald-Kreitman Test