Coalescent species delimitation in milksnakes (genus Lampropeltis) and impacts on phylogenetic comparative analyses

Abstract.—Both gene-tree discordance and unrecognized diversity are sources of error for accurate estimation of species trees, and can affect downstream diversification analyses by obscuring the correct number of nodes, their density, and the lengths of the branches subtending them. Although the theoretical impact of gene-tree discordance on evolutionary analyses has been examined previously, the effect of unsampled and cryptic diversity has not. Here, we examine how delimitation of previously unrecognized diversity in the milksnake (Lampropeltis triangulum) and use of a species-tree approach affects both estimation of the Lampropeltis phylogeny and comparative analyses with respect to the timing of diversification. Coalescent species delimitation indicates that L. triangulum is not monophyletic and that there are multiple species of milksnake, which increases the known species diversity in the genus Lampropeltis by 40%. Both genealogical and temporal discordance occurs between gene trees and the species tree, with evidence that mitochondrial DNA (mtDNA