@article{7a7d497398fb4460848b24ea595dc0c6,
title = "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) 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.",
keywords = "Divergence-time estimation, Lampropeltini, Pleistocene diversification, diversification rates, gene-tree/species-tree discordance, mtDNA introgression",
author = "Sara Ruane and Bryson, {Robert W.} and Pyron, {R. Alexander} and Burbrink, {Frank T.}",
note = "Funding Information: ACKNOWLEDGEMENTS The authors thank the following for providing tissues and support during this project: American Museum of Natural History (D. Frost, C. Raxworthy, D. Kizirian, and J. Feinstein), Louisiana State University Museum of Natural Sciences (J. Boundy, D. Dittman, and R. Brumfeld, F. Sheldon), Museum of Vertebrate Zoology (J. McGuire and C. Spencer), the University of Texas, Arlington (J. Campbell, E. Smith, C. Franklin, C. Cox, J. Streicher, and R. Jadin), the Texas Cooperative Wildlife Collection, Texas A&M University (T. Hibbitts), the Senckenburg Museum of Natural History (U. Kuch), the United States National Museum (R. McDiarmid and K. de Queiroz), the North Carolina Museum Natural Sciences (J. Beane and C. Fisher), the University of Alabama (L. Rissler), the Peabody Museum, Yale University (G. Watkins-Colwell), the Florida Museum of Natural History (K. Krysko), the Texas Natural History Collection, the University of Texas, Austin (D. Cannatella, T. LaDuc, and D. Hall), Southeastern Louisiana Unviersity (B. Crother), the Sternberg Museum, Fort Hays State University (T. Taggart, C. Schmidt, and J. Collins), Swaim Biological, Inc. (K. Swaim), La Mica Biological Station (J. Ray), the University of Colorado Museum of Natural History (J. Lemos-Espinal), the Illinois Natural History Survey (C. Phillips), P. Warny, T. Guiher, D. Shepard, L. Vitt, K. Irwin, R. Hansen, D. Mulcahy, J. Jones, C. Grunwald, G. Weatherman, J. Harrison, E. Myers, X. Chen, A. McKelvy, R. Ruane, B. Ruane, G. Hancock, L. Clampitt, M. Ryan, D. Finnegan, J. Briggler, R. Highton, D. Heath, C. Stephen, K. Lodrigue, O. Torres Carjaval, S. Ballard, R. King, B. German, U.O. Garcia-Vasquez, the late F. Mendoza-Quijano, I. Solano-Zavaleta, R. Bezy, E. Enderson, M. Torroco, I. White Murray, W. Howell, G. Salmon, M. Ingrasci, A. Richmond, A. Stengle, C. Wollney, M. Walker, B. Edmond, A. Williams, R. Lovich, R. Gassaway, T. Tyning, J. Iverson, M. Graziano, J. Tucker, C. Jimenez, R. Staub, S. Joly, C. Newsom, J. Badman, J. Hernandez, N. Howe, F. Fontanella, J. Rowell, P. Frank, S. Marshall, and R. Walsh. They also thank E. Myers, R. Glor, F. Anderson, and three anonymous reviewers for comments that substantially improved this manuscript. S.R. would also like to thank her dissertation committee members (F.T.B., C. Raxworthy, M. Hickerson, E. Naro-Maciel, and J. Munshi-South), as this manuscript was in partial fulfillment of her dissertation. Photos in Figure 2 are credited as follows: S. Ruane (A, C), R. Hansen (B, D), D. Sheperd (E), M. Graziano (F), L. Porras (G), J. Streicher (H). This work was supported in part by the American Museum of Natural History (Theodore Roosevelt Memorial Fund), Graduate Women in Science (Vanessa Notchev Fund), The Explorer{\textquoteright}s Club, and CUNY-PSC. Support for this project was provided in part by the American Museum of Natural History (Theodore Roosevelt Memorial Fund), Graduate Women in Science (Vanessa Notchev Fund), The Explorer{\textquoteright}s Club, and CUNY-PSC. This research was also supported, in part, under National Science Foundation Grants [CNS-0958379 and CNS-0855217] to the City University of New York High Performance Computing Center; [DBI-0905765] R.A.P.; and the University of Texas at Arlington [DEB-0613802 to J.A. Campbell] for samples loaned from UTA-Arlington.",
year = "2014",
month = mar,
doi = "10.1093/sysbio/syt099",
language = "English (US)",
volume = "63",
pages = "231--250",
journal = "Systematic Biology",
issn = "1063-5157",
publisher = "Oxford University Press",
number = "2",
}