Data from: Pleistocene climatic fluctuations drive isolation and secondary contact in the red diamond rattlesnake (Crotalus ruber) in Baja California
Harrington, Sean M., San Diego State University
Hollingsworth, Bradford D., San Diego Natural History Museum
Higham, Timothy E., San Diego State University
Reeder, Tod W., San Diego State University
Published Oct 16, 2018 on Dryad.
Cite this dataset
Harrington, Sean M.; Hollingsworth, Bradford D.; Higham, Timothy E.; Reeder, Tod W. (2018). Data from: Pleistocene climatic fluctuations drive isolation and secondary contact in the red diamond rattlesnake (Crotalus ruber) in Baja California [Dataset]. Dryad. https://doi.org/10.5061/dryad.7hs0n
Aim: Many studies have investigated the phylogeographic history of species on the Baja California Peninsula, and they often show one or more genetic breaks that are spatially concordant among many taxa. These phylogeographic breaks are commonly attributed to vicariance as a result of geological or climatic changes, followed by secondary contact when barriers are no longer present. We use restriction-site associated DNA sequence data and a phylogeographic model selection approach to explicitly test the secondary contact hypothesis in the red diamond rattlesnake, Crotalus ruber. Location: Baja California and Southern California. Methods: We used phylogenetic and population clustering approaches to identify population structure. We then used coalescent methods to simultaneously estimate population parameters and test the fit of phylogeographic models to the data. We used ecological niche models to infer suitable habitat for C. ruber at the Last Glacial Maximum (LGM). Results: Crotalus ruber is composed of distinct northern and southern populations with a boundary near the town of Loreto in Baja California Sur. A model of isolation followed by secondary contact provides the best fit to the data, with both divergence and contact occurring in the Pleistocene. We also identify a genomic signature of northern range expansion in the northern population, consistent with LGM niche models showing that the northern-most portion of the range of C. ruber was not suitable habitat during the LGM. Main conclusions: We provide the first explicitly model-based test of the secondary contact model in Baja California and show that populations of C. ruber were isolated before coming back into contact near Loreto, a region that shows phylogeographic breaks for other taxa. Given the timing of divergence and contact, we suggest that climatic fluctuations have driven the observed phylogeographic structure observed in C. ruber and that they may have driven similar patterns in other taxa.
FSC2 input files
This zip archive contains all necessary input to run FastSimCoal2 analyses performed. See the included readme file in the zip archive for further details.
All other input files
This zip archive contains the input files for all analyses other than FSC2, which are contained in a separate zip archive. See the readme included in the archive for further details on individual files.
R code for sPCA, DAPC, and Mantel tests
This file contains the R script used for DAPC, sPCA, and Mantel test analyses. Input files are contained in the input files zip archive separately available on Dryad.