@ARTICLE{TreeBASE2Ref22109, author = {Sara Ruane and R. W. Bryson and Robert Alexander Pyron and Frank T. Burbrink}, title = {Coalescent Species Delimitation in Milksnakes (genus Lampropeltis) and Impacts on Phylogenetic Comparative Analyses}, year = {2013}, keywords = {Divergence-time estimation, mtDNA introgression, Lampropeltini, diversification rates, Pleistocene diversification}, doi = {}, url = {http://}, pmid = {}, journal = {Systematic Biology}, volume = {}, number = {}, pages = {}, 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. While the theoretical impact of gene-tree discordance on evolutionary analyses has been previously examined, the effect of unsampled or 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 mtDNA introgression is a main factor. This discordance is further manifested in the preferred models of diversification, where the concatenated gene tree strongly supports an early burst in speciation during the Miocene, in contrast to species-tree estimates where diversification follows a birth-death model and speciation occurs mostly in the Pliocene and Pleistocene. This study highlights the crucial interaction among coalescent-based phylogeography and species delimitation, systematics, and species diversification analyses. } }

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