A Phylogenetic Approach to the Problem of Differential Lineage Sorting

A test that can detect the influence of differential lineage sorting on phylogenetic signal in integrated studies with two or more loci is presented. Hitherto unexplored consequences of relationships among gene trees and species trees are made explicit, revealing potential influences of differential lineage sorting on phylogenetic signal. These influences can result in observable consequences, in particular an increase in signal when sequences or characters are combined among taxa to create a mixed-character taxon. Simulations of nucleotide evolution reflecting two gene phylogenies within a five-taxon species phylogeny were used to demonstrate and justify the mixed-character taxon test. An empirical example of lineage sorting during the evolution of Robineae is presented that appears to resolve conflict between morphological and organellar chloroplast DNA (cpDNA) signal.