Genes are gained and lost throughout genome evolution. Gene family expands through horizontal gene transfers and the duplication of whole genome or individual genes, while genes are lost via the removal or pseudogenization of previously functional genes.
Comparative analyses of a growing number of completely sequenced genomes have provided strong evidence for the importance of gene duplications and losses in human evolution. Although the study of gene evolution is still in its early stage, several methods have been developed to enable researchers to infer gene gains and losses. One of the most popular methods for the task reconciles the gene tree inferred from the sequences of a gene family and the species tree that describes the evolutionary relationship of the taxa from which the genes are sampled. Although the concept of comparing gene tree and species tree is simple, reconciling non-binary gene trees and non-binary species trees present many challenging problems. In this talk, I shall present our recent work on reconciling gene tree and specie tress when polytomies and/or horizontal gene transfers are present.