DOI: 10.5061/dryad.sj3tx96b9
title: SNP data for Northern Alligator Lizards

description: 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.
description: # 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 migration \(MSC\-M\) analyses \(bpp\.zip\)\. The folders are organized by population pairs using the same abbreviations in the manuscript \(nine folders; \#\_pop1\_pop2\)\. Each of the nine folders contains aligned loci \(data\.phy\)\, assignments of samples to populations \(imap\.txt\)\, and the bpp commands file \(bpp\.ctl\)\. ## Sharing/Access information The demultiplexed data are available at the NCBI Sequence Read Archive (BioProject ID: PRJNA903883). https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA903883