Phylogeography of the Rough Greensnake, Opheodrys aestivus (Squamata: Colubridae), Using Multilocus Sanger Sequence and Genomic ddRADseq Data
The Rough Greensnake, Opheodrys aestivus, is a moderately sized, semi-arboreal snake broadly distributed throughout eastern North America. Although numerous taxa with similar distributions have been shown to comprise multiple species, O. aestivus has not been examined in a detailed phylogeographic context. Here, we use Sanger-sequence data (one mitochondrial, 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 data sets, 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. Estimates of divergence time suggest that the central Texas and Main clades diverged ∼1.3 million years ago (mya), while the peninsular Florida clade diverged from other lineages ∼2.9 mya, and these lineages diverged from the sister taxon, O. vernalis, ∼6.4 mya. 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, but 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. We conclude that elevating O. a. carinatus to species status may better describe the diversity of this genus.ABSTRACT
Sampling localities for Opheodrys aestivus included in this study, with the distribution of the species based on IUCN Red List data (Hammerson et al., 2007) shown in grey. Symbol color corresponds to clade: yellow: peninsular Florida clade, red: central Texas clade, blue: Main clade. Squares indicate samples included in both Sanger and ddRADseq datasets, circles indicate samples included only in Sanger data sets.
(A) Bayesian maximum clade credibility phylogeny of Opheodrys aestivus based on partitioned analysis of concatenated Sanger loci. (B) Maximum likelihood phylogeny of O. aestivus from analysis of mitochondrial cytochrome b (cytb) data, partitioned by codon position. (C) Maximum likelihood phylogeny of O. aestivus based on concatenated analyses of three nuclear loci from Sanger sequence data, partitioned by locus. Symbols on nodes correspond to branch support values: green indicates Bayesian posterior probability (BPP) >0.95 and Maximum likelihood bootstrap (MLBS) >75, yellow indicates BPP >0.95 and MLBS <75. Symbols at branch tips correspond to the sampling localities in Fig. 1: yellow: peninsular Florida clade, red: central Texas clade, blue: Main clade.
Calibrated species tree for Opheodrys aestivus from Bayesian multispecies coalescent analyses of Sanger data in *BEAST. Fossil calibration points are indicated with asterisks. Values above branches indicate mean estimated node age in millions of years before present (mya), bars on nodes correspond to 95% credibility intervals. Values below branches correspond to BPP branch support. Colors of symbols at branch tips correspond to major clades in Figures 1 and 2.
Bayesian maximum clade credibility phylogeny of Opheodrys aestivus based on ddRADseq data. Symbols on nodes correspond to branch support values: green indicates Bayesian posterior probability (BPP) >0.95 and Maximum likelihood bootstrap (MLBS) >75, yellow indicates BPP >0.95 and MLBS <75. Values below branches indicate BPP support from species tree analysis of ddRADseq data in SNAPP. Colors of symbols at branch tips correspond to the sampling localities in Figs. 1 and 2.
Contributor Notes
