Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes

Discord among the gene trees of multilocus data has motivated the development of phylogenetic approaches that account for gene-tree heterogeneity in the estimation procedure. Rather than equating a gene tree with the phylogenetic history, the new approaches explicitly consider the relationships between gene trees and the underlying history of species divergence, providing direct estimates of species trees (Fig. 1). The inherent appeal of these...