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 rece..., , , # SNP data for Northern Alligator Lizards (*Elgaria coerulea*)

[https://doi.org/10.5061/dryad.sj3tx96b9](https://doi.org/10.5061/dryad.sj3tx96b9)

## Description of the data and file structure

1\. VCF file containing all variants \(unfiltered\) using a 10% missing data assembly threshold \(coerulea10percent\.vcf\)\.
2\. VCF file containing all variants \(unfiltered\) using a 50% missing data assembly threshold \(coerulea50percent\.vcf\)\.
3\. Concatenated ddRADseq loci for all samples and the outgroups species in phylip format\. The data matrix contains 122 samples and 605\,616 aligned base pairs \(elgaria\.phy\)\.
4\. SNP data in XML format\, recoded for SNAPP analysis using BEAST2 \(snapp\.xml\)\.
5\. Species delimitation files for bpp/hhsd analysis \(hhsd\.zip\)\. Three files include the aligned loci \(data\.txt\)\, assignments of samples to species/populations \(imap\.txt\)\, and the hhsd commands file \(elgaria\_merge\.ctl\)\.
6\. BPP files for multispecies coalescent with migrat...