SNP data for Northern Alligator Lizards
Data files
Nov 17, 2023 version files 179.88 MB
-
bpp.zip
-
coerulea10percent.vcf
-
coerulea50percent.vcf
-
elgaria.phy
-
hhsd.zip
-
README.md
-
snapp.xml
Abstract
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.
README: SNP data for Northern Alligator Lizards (Elgaria coerulea)
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