Copyright c © Society of Systematic Biologists DOI:10.1093/sysbio/syp061 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 esti-mation procedure. Rather than equating a gene tree with the phylogenetic history, the new approaches ex-plicitly consider the relationships between gene trees and the underlying history of species divergence, pro-viding direct estimates of species trees (Fig. 1). The inherent appeal of these approaches is 2-fold. Incor-porating information contained in the distribution of gene trees not only extracts phylogenetic signal, but modeling the relationship between the gene trees embedded in a species tree also reveals the biologi-cal processes that have influenced the diversification history and shaped organismal genomes. In contrast