2.9 | Gene family expansion and contraction
The expansion and contraction of gene families were determined by
comparing the cluster size differences between the ancestor and each
species using the CAFE program
(http://sourceforge.net/projects/cafehahnlab/).
A random birth-and-death model was used to evaluate changes in gene
families of the phylogenetic tree. A probabilistic graphical model (PGM)
was used to calculate the transfer probability of each gene family from
parent to child nodes in the phylogeny. The conditional likelihood was
used as the test statistics to calculate the correspondingP -value of each lineage, and a P -value of or below 0.05
was considered significant.