Data for: Morphological species delimitation in the Western Pond Turtle (Actinemys): Can machine learning methods aid in cryptic species identification?

<p>As the discovery of cryptic species has increased in frequency, there has been interest in whether geometric morphometric data can detect fine-scale patterns of variation that can be used to morphologically diagnose such species. We used a combination of geometric morphometric data and an ensemble of five supervised machine learning methods to investigate whether plastron shape can differentiate two putative cryptic turtle species, <em>Actinemys marmorata</em> and <em>Actinemys pallida</em>. <em>Actinemys</em> has been the focus of considerable research due to its biogeographic distribution and conservation status. Despite this work, reliable morphological diagnoses for its two species are still lacking. We validated our approach on two datasets, one consisting of eight morphologically disparate emydid species, and the other consisting of two subspecies of <em>Trachemys</em> (<em>T. scripta scripta</em>, <em>T. scripta elegans</em>). The validation tests returned near-perfect classification rates, demonstrating that plastron shape is an effective means for distinguishing taxonomic groups of emydids via machine learning methods. By contrast, the same methods did not return high classification rates for a set of alternative phylogeographic and morphological binning schemes in <em>Actinemys</em>. All classification hypotheses performed poorly relative to the validation datasets and no single hypothesis was unequivocally supported for <em>Actinemys</em>. Two hypotheses had machine learning performance that was marginally better than our remaining hypotheses. In both cases, those hypotheses favored a two-species split between <em>A. marmorata</em> and <em>A. pallida</em> specimens, lending tentative morphological support to the hypothesis of two <em>Actinemys</em> species. However, the machine learning results also underscore that <em>Actinemys</em> as a whole have lower levels of plastral variation than other turtles within Emydidae, but the reason for this morphological conservatism is unclear.</p>