Single nucleotide polymorphism (SNPs) data for Scurria scurra, Scurria variabilis, Scurria ceciliana and Scurria araucana

The distribution of genetic diversity is often heterogeneous in space, and it usually correlates with environmental transitions or historical processes that affect demography. The coast of Chile encompasses two biogeographic provinces and spans a broad environmental gradient together with oceanographic processes linked to coastal topography that can affect species' genetic diversity. Here, we evaluated the genetic connectivity and historical demography of four Scurria limpets, S. scurra, S. variabilis, S. ceciliana and S. araucana, between ca. 19° S and 53° S in the Chilean coast using genome-wide SNPs markers. Genetic structure varied among species which was evidenced by species-specific breaks together with two shared breaks. One of the shared breaks was located at 22–25° S and was observed in S. araucana and S. variabilis, while the second break around 31–34° S was shared by three Scurria species. Interestingly, the identified genetic breaks are also shared with other low-disperser i..., These data were retrieved by restriction-site associate DNA sequencing of muscle (foot) tissue using the enzyme pstI. 
Raw reads were demultiplexed using Stacks. Scurria scurra, Scurria ceciliana and Scurria araucana RAD loci were mapped to the reference genome of Scurria scurria (Saenz-Agudelo P., unpublished) using the ref_map.pl pipeline of Stacks, while for Scurria variabilis loci were called de novo using the denovo_map.pl pipline of Stacks.
VCF files were generated in populations from Stacks, keeping only 80% as the minimum percentage of all individuals to process a locus. Further filtering steps were made in VCFtools, namely mean minimum read depth per locus (15), maximum mean depth per site (62-73, depending on the species) and a final genotype call rate of 90%. No individuals with more than 20% missing data were kept. The final filter consisted of removing loci with evidence of linkage disequilibrium, which was estimated using the function snpgdsLDpruning from the R package SNP..., To open VCF files, any program that read such files can be used, such as VCFtools, snpR package in R, etc., # Single nucleotide polymorphism (SNPs) data for Scurria scurra, Scurria variabilis, Scurria ceciliana and Scurria araucana

VCF files used in the analyses of the in press article \"Comparative population genetics of congeneric limpets across a biogeographic transition zone reveals common patterns of genetic structure and demographic history\", to be published in Molecular Ecology.

## Description of the data and file structure

This dataset contains VCF files for the four species of limpets analyzed, Scurria scurra, Scurria variabilis, Scurria ceciliana and Scurria araucana.
A separate vcf file containing all loci (\"All.vcf\"), only outlier loci (\"Outs.vcf\"), and all loci except the outliers (\"NoOuts.vcf\") are given for each species. Note that for the demographic history analyses, only a subset of the \"NoOuts.vcf\" files were used since only few sites were considered (check article Materials and Methods section for more information).
In the metadata file, sample information concerning spe...