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Many phylogeographic studies on species with large ranges have found genetic–geographic structure associated with changes in habitat and physical barriers preventing or reducing gene flow. These interactions with geographic space, contemporary and historical climate, and biogeographic barriers have complex effects on contemporary population genetic structure and processes of speciation. While allopatric speciation at biogeographic barriers is considered the primary mechanism for generating species, more recently it has been shown that parapatric modes of divergence may be equally or even more common. With genomic data and better modeling capabilities, we can more clearly define causes of speciation in relation to biogeography and migration between lineages, the location of hybrid zones with respect to the ecology of parental lineages, and differential introgression of genes between taxa. Here, we examine the origins of three Nearctic milksnakes (Lampropeltis elapsoides, Lampropeltis triangulum and Lampropeltis gentilis) using genome-scale data to better understand species diversification. Results from artificial neural networks show that a mix of a strong biogeographic barrier, environmental changes, and physical space has affected genetic structure in these taxa. These results underscore conspicuous environmental changes that occur as the sister taxa L. triangulum and L. gentilis diverged near the Great Plains into the forested regions of the Eastern Nearctic. This area has been recognized as a region for turnover for many vertebrate species, but as we show here the contemporary boundary does not isolate these sister species. These two species likely formed in the mid-Pleistocene and have remained partially reproductively isolated over much of this time, showing differential introgression of loci. We also demonstrate that when L. triangulum and L. gentilis are each in contact with the much older L. elapsoides, some limited gene flow has occurred. Given the strong agreement between nuclear and mtDNA genomes, along with estimates of ecological niche, we suggest that all three lineages should continue to be recognized as unique species. Furthermore, this work emphasizes the importance of considering complex modes of divergence and differential allelic introgression over a complex landscape when testing mechanisms of speciation. [Cline; delimitation; Eastern Nearctic; Great Plains; hybrids; introgression; speciation.]

List of specimens and sequences used for each species, with corresponding catalog numbers, country/island of origin, and GenBank accession number for each gene. ("*" denote sequences to be submitted in GenBank. Accession numbers will be added upon acceptance of the manuscript).

New Caledonia is the smallest global biodiversity hotspot, yet has one of the highest levels of endemism for an insular region of its size. Lizards are the dominant vertebrate fauna, and, while ecologically important, can be difficult to identify and many are in decline due to anthropogenic threats. As an aid to facilitate identification, we generated a near-complete DNA barcode dataset for New Caledonian lizards, consisting of 601 mitochondrial CO1 sequences of 100 of the 107 described lizards, and a number of yet undescribed species. We use this dataset to assess the performance of CO1 in delimiting species recognised by other, more extensive data and in recovering phylogenetic signal. Most species had intraspecific genetic distances ≤3.7%. Most comparisons between described species were at least ~5% divergent, with the exception of three pairwise species comparisons showing interspecific distances > 2.5%. Maximum likelihood CO1 trees of the six most speciose genera recovered each as monophyletic and, although discordant with previously published ND2 trees using quantitative topology tests, showed similar patterns of intraspecific and interspecific divergence, supporting the utility of CO1 in taxonomic identification and species delimitation. Some species showed overlap between intra- and interspecific pairwise distances, suggesting cryptic taxa, a finding also supported by species delimitation analyses using GMYC and mPTP. This dataset not only provides the basis for economical and reliable identification of New Caledonian lizards encountered during biodiversity assessments, but also provides a potential tool for investigating the identity of native lizards and their ecosystem interactions, even from partial remains.