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Abstract
<p class="first" id="d4978712e59">Most approaches to species delimitation to date
have considered divergence-only models.
Although these models are appropriate for allopatric speciation, their failure to
incorporate many of the population-level processes that drive speciation, such as
gene flow (e.g., in sympatric speciation), places an unnecessary limit on our collective
understanding of the processes that produce biodiversity. To consider these processes
while inferring species boundaries, we introduce the R-package delimitR and apply
it to identify species boundaries in the reticulate taildropper slug (Prophysaon andersoni).
Results suggest that secondary contact is an important mechanism driving speciation
in this system. By considering process, we both avoid erroneous inferences that can
be made when population-level processes such as secondary contact drive speciation
but only divergence is considered, and gain insight into the process of speciation
in terrestrial slugs. Further, we apply delimitR to three published empirical datasets
and find results corroborating previous findings. Finally, we evaluate the performance
of delimitR using simulation studies, and find that error rates are near zero when
comparing models that include lineage divergence and gene flow for three populations
with a modest number of Single Nucleotide Polymorphisms (SNPs; 1500) and moderate
divergence times (<100,000 generations). When we apply delimitR to a complex model
set (i.e., including divergence, gene flow, and population size changes), error rates
are moderate (∼0.15; 10,000 SNPs), and, when present, misclassifications occur among
highly similar models.
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