The effect of incongruence on molecular dates

Abstract

Despite what is known about processes that can cause topological incongruence among datasets, combined analysis of concatenated datasets (simultaneous analysis) without examination of congruence is still advocated and practiced. Although the danger in such cases of inferring the incorrect topology is known (and sometimes ignored), here I examine an under-appreciated effect of the combined analysis of incongruent datasets on molecular date inferences. Using simulated character matrices, a bias towards either increased or decreased dates is demonstrated that increases in its effect with greater proportion of incongruent characters. A general prediction is made regarding the behaviour of molecular date estimates based on the phylogenetic position of taxa that are incongruent. This prediction is borne out in a case study using real data from incongruent nuclear genes in Medicago (Fabaceae).