Coalescent Species Delimitation in Milksnakes (genus Lampropeltis) and Impacts on Phylogenetic Comparative Analyses

1. Sara Ruane¹,²,*,
2. Robert W. Bryson Jr.³,
3. R. Alexander Pyron⁴ and
4. Frank T. Burbrink¹,²

+ Author Affiliations

1. 1. Department of Biology, College of Staten Island, 2800 Victory Blvd., Staten Island, NY 10314
2. 2. The Graduate Center, City University of New York, 365 5^th Avenue, NY, NY 10016
3. 3. Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Box 351800, Seattle, WA 98195-1800
4. 4. Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052

1. ↵*Corresponding author: email:sruane@amnh.org; phone: (212)-769-5734

• Received August 21, 2012.
• Revision received June 12, 2013.
• Revision received November 2, 2013.
• Revision received November 19, 2013.
• Accepted November 27, 2013.

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 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 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 of 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. 

http://sysbio.oxfordjournals.org/content/early/2013/12/10/sysbio.syt099.abstract