SNP data for Northern Alligator Lizards

Understanding the processes that shape genetic diversity by either
promoting or preventing population divergence can help identify geographic
areas that either facilitate or limit gene flow. Furthermore, broadly
distributed species allow us to understand how biogeographic and
ecogeographic transitions affect gene flow. We investigated these
processes using genomic data in the Northern Alligator Lizard (Elgaria
coerulea), which is widely distributed in Western North America across
diverse ecoregions (California Floristic Province and Pacific Northwest)
and mountain ranges (Sierra Nevada, Coastal Ranges, and Cascades). We
collected single nucleotide polymorphism (SNP) data from 120 samples of E.
coerulea. Biogeographic analyses of squamate reptiles with similar
distributions have identified several shared diversification patterns that
provide testable predictions for E. coerulea, including deep genetic
divisions in the Sierra Nevada, demographic stability of southern
populations, and recent post-Pleistocene expansion into the Pacific
Northwest. We use genomic data to test these predictions by estimating the
structure, connectivity, and phylogenetic history of populations. At least
ten distinct populations are supported, with mixed-ancestry individuals
situated at most population boundaries. A species tree analysis provides
strong support for the early divergence of populations in the Sierra
Nevada Mountains and recent diversification into the Pacific Northwest.
Admixture and migration analyses detect gene flow among populations in the
Lower Cascades and Northern California, and a spatial analysis of gene
flow identified significant barriers to gene flow across both the Sierra
Nevada and Coast Ranges. The distribution of genetic diversity in E.
coerulea is uneven, patchy, and interconnected at population boundaries.
The biogeographic patterns seen in E. coerulea are consistent with
predictions from co-distributed species.