DOI: 10.5061/dryad.brv15dv8w
title: Phylogeography of the Rough Greensnake, Opheodrys aestivus (Squamata: Colubridae), using multilocus Sanger sequence and genomic ddRADseq data

description: The Rough Greensnake, Opheodrys aestivus, is a moderately-sized,
 semi-arboreal snake broadly distributed throughout eastern North America.
 While numerous taxa with similar distributions have been shown to be
 comprised of multiple species, O. aestivus has yet to be examined in a
 detailed phylogeographic context. Here, we use Sanger-sequence data of one
 mitochondrial and three nuclear loci for samples from throughout the
 distribution of O. aestivus to elucidate phylogeographic patterns in this
 species. We combine this with ddRADseq data for a subset of samples to
 test patterns on a more genomically comprehensive scale. In both datasets,
 we find strong support for three deeply divergent clades within O.
 aestivus: peninsular Florida, central Texas, and a main clade comprising
 the rest of the distribution, with the Florida clade the earliest
 diverging lineage of the three. Estimates of divergence time suggest that
 the central Texas and main clades diverged approximately 1.34 million
 years ago (Mya), while the peninsular Florida clade diverged from other
 lineages approximately 2.94 Mya, and these lineages diverged from the
 sister taxon, O. vernalis, approximately 6.43 Mya. These results also
 suggest that the historically recognized Florida subspecies, O. a.
 carinatus, could be elevated to species status. While the divergence of
 peninsular Florida or central Texas populations is not unique among
 squamates, nor is low levels of divergence from the Atlantic coast to
 eastern Texas, this combination of patterns is unusual, and yields
 important insight into the biogeography of North American biota. Further,
 our approach helps illustrate how dense geographic sampling with limited
 genomic sequencing can be used as a guide for the selection of samples to
 test phylogeographic patterns comprehensively.
description: We obtained 47 samples of <i>Opheodrys aestivus
 </i>from throughout the distribution of the species, four samples
 from the sister taxon <i>O. vernalis</i>, and one sample from
 each of the more distantly related colubrid species <i>Cemophora
 coccinea</i>, <i>Lampropeltis getula</i>,<i>
 Pantherophis guttatus</i>, <i>Pituophis
 melanoleucus</i>, and the natricid <i>Nerodia
 sipedon</i> (Appendix 1). Whole genomic DNA was extracted for all
 samples using a Qiagen DNeasy Blood and Tissue kit and quantified using a
 Qubit 2.0 fluorometer with the High Sensitivity kit (Invitrogen, Inc.). we
 targeted one mitochondrial (cytochrome b, cytb) and three nuclear loci
 (LAT clone, LAT; neurotrophin 3, NT3; and prolactin receptor, PRLR). We
 used maximum likelihood (ML) and Bayesian inference (BI) methods to infer
 the phylogenetic relationships among populations of <i>O.
 aestivus</i>. To further evaluate putative species boundaries and
 clades recovered in the Sanger sequencing analyses in a more genomically
 comprehensive context, we also used a double-digest restriction associated
 DNA sequencing (ddRADseq) for a small subset of the samples, representing
 all clades identified from Sanger-sequence analyses. A subsample of 13
 samples of <i>O. aestivus</i>, spanning the distribution of
 the species and all lineages recovered in Sanger-data analyses, along with
 a single sample the sister species, <i>O.
 vernalis.</i>
description: Refer to the manuscript for descriptions of analyses leading to
 the supplementary figures here; figure captions for each supplementary
 figure are included (see read me file for additional details). In
 addition, the data files include a zipped folder with the raw ddRAD files,
 the processed ddRAD files, and a text file of the ddRAD stats. A nexus
 files of each locus, as described in the manuscript is included (as both a
 phased and unphased nexus for each nuclear locus).