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The locus of identity for phylogeographic species delimitation and integrative taxonomy in seal salamanders (Desmognathus monticola)

Citation

Pyron, Robert et al. (2022), The locus of identity for phylogeographic species delimitation and integrative taxonomy in seal salamanders (Desmognathus monticola), Dryad, Dataset, https://doi.org/10.5061/dryad.sbcc2fr7s

Abstract

Significant empirical and theoretical advances have been made regarding species delimitation. Numerous methods have been developed to test precisely defined models of speciation, and the philosophical basis of species ontology has several robust definitions. However, there are still at least two distinct areas in which this synthesis is incomplete. First, computational algorithms alone are unable to settle the theory-laden question of whether a sample of individuals consists of one or more species; this is an ontological value judgement, rather than an empirical determination. Second, the thresholds for making this determination are often idiosyncratic and incompletely defined relative to speciation processes. We refer to what we call the “locus of identity” when in the sequence of analytical investigations into population differentiation (an epistemological query) does one expect to make conclusion about species-level distinctiveness (an ontological query)? As datasets increase in size towards full genomes, they frequently converge on stable estimates of significantly distinct genetic clusters. This, we suggest, is strong initial evidence of species-level distinctiveness in most cases; an a priori locus of identity as opposed to an a posteriori locus conditioned on empirical thresholds or differentiation by cumulation or congruence along arbitrarily defined trait axes. A truly integrative taxonomy can consequently test these newly erected hypotheses of multiple species by linking trait differentiation to specific mechanisms of divergence. Some axes may still be incompletely linked to an integrative taxonomy; significant differences therein may be confirmatory, but absence thereof is not evidence against speciation. We illustrate this approach here with Seal Salamanders (Desmognathus monticola) and introduce a new unsupervised machine-learning method for species delimitation.

Methods

GBS data to generate SNPs - seal_in_c90

Linear morphometrics  - seal_morph

Usage Notes

Analyses were performed on the seal_in.str file, not the NEXUS alignment. Morphology data are in CSV format.

Funding

National Science Foundation, Award: DEB-1655737