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.
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.

粗鳞绿蛇（Rough Greensnake，学名Opheodrys aestivus）是一种体型中等的半树栖蛇类，广泛分布于北美东部地区。此前已有多项研究表明，诸多分布范围相似的类群实则由多个物种构成，但截至目前，尚未有研究在详细的系统生物地理学（phylogeographic）框架下对O. aestivus展开系统性探讨。本研究采集了O. aestivus整个分布范围内的样本，利用1个线粒体基因座与3个核基因座的桑格测序（Sanger-sequence）数据，解析该物种的系统生物地理学格局；同时结合部分样本的ddRADseq数据，以在更全面的基因组尺度下验证相关格局。两套数据集的分析结果均显示，O. aestivus内存在3个深度分化的演化支：佛罗里达半岛支、德克萨斯中部支，以及涵盖其余分布区域的主干演化支；其中佛罗里达半岛支是3个支系中最早分化的类群。分化时间估算结果显示，德克萨斯中部支与主干演化支的分化时间约为134万年前（Mya），佛罗里达半岛支与其余支系的分化时间约为294万年前（Mya）；上述支系与其姐妹类群O. vernalis的分化时间则约为643万年前（Mya）。本研究结果同时提示，历史上被认定的佛罗里达亚种O. a. carinatus可被提升至物种层级。尽管在有鳞类爬行动物（squamates）中，佛罗里达半岛或德克萨斯中部种群的分化并非罕见现象，从大西洋沿岸至德克萨斯东部种群间的低分化水平也同样常见，但这种格局的组合形式却较为特殊，这为理解北美生物群的生物地理学特征提供了重要见解。此外，本研究的研究方法也佐证了：通过密集的地理采样配合有限的基因组测序，可以为全面验证系统生物地理学格局的样本选择提供有效指导。