DOI: 10.5061/dryad.n8pk0p31k
title: Podarcis bocagei vs P. carbonelli hybrid zone SNP datasets from ddRADseq

description: We used double digestion restriction site associated DNA (ddRAD)
 sequencing to discover SNPs in samples across a transect including a
 hybrid zone between Podarcis carbonelli and Podarcis carbonelli.
 We used P. bocagei and P. carbonelli samples from the locations
 at the extremes of the transect as references. We obtained a SNP dataset
 including all SNPs after removing loci with depth coverage &lt;8,
 missing data &gt;20%, removing loci containing more than five SNPs,
 and with more than 70% heterozygosity (complete dataset; 6905 SNPs, 329
 individuals). Additionally, we obtained from the complete dataset two
 other datasets, prior to apply a missing data filter. One dataset
 contained loci with allele frequencies higher than 0.8 in the reference
 population containing only parental individuals of one species and lower
 than 0.2 in the reference population of the other species
 ("80/20" dataset; 2300 SNPs, 329 individuals); the other dataset
 comprised diagnostic SNPs between reference populations (diagnostic
 dataset; 1241 SNPs, 236 individuals) but excluding private alleles from
 references, i.e. excluding alleles that are not present in the populations
 of contact. Individuals with missing data &gt;35% were removed from
 all datasets (the number of individuals reported for each dataset is after
 applying this filter, but note that the 80/20 and the diagnostic datasets
 were obtained before applying this filter to the complete dataset). Across
 datasets, average depth of coverage by individuals was 28 (median = 26.8,
 min = 12.5, max = 85.8) and by loci was 29 (median = 28.8; min = 15.6; max
 = 48.6). The analysis of replicate samples (four samples were replicated
 twice, i.e. were amplified and sequenced in independent libraries and SNP
 calling was performed independently) showed high levels (99.87%) of
 multilocus genotype replicability.
description: Samples were collected between spring and autumn of 2013 in a
 contact zone between <em>Podarcis bocagei and P.
 carbonelli</em>. We collected samples across a transect with 8
 locations, including the hybrid zone. Sampling scheme aimed at capturing
 all the individuals encountered, avoiding bias towards species, sex or
 age. We used 20 <em>P.
 bocagei</em> and 23 <em>P. carbonelli</em> samples from
 the locations at the extremes of the transect as references. We obtained
 SNP datasets from ddRAD sequencing from 356 samples by preparing one
 library following the modifications described by Brelsford <em>et
 al.</em> (2016) to the protocols from Parchman et al. (2013),
 Peterson <em>et al.</em> (2012) and Purcell <em>et al.
 </em>(2014), and sequenced on a Illumina<sup>®</sup>
 HiSeq 2000. Individual raw reads were demultiplexed using the
 process_radtags module of Stacks version 2.2 (Catchen <em>et
 al.</em>, 2013). SNP calling was
 performed using the Stacks pipeline, following Rochette and
 Catchen (2017) recommendations, by running consecutivelly ustacks (build
 loci), cstacks (create a catalogue of loci), sstacks (match individual
 samples against the catalogue), tsv2bam (transpose data) and gstacks
 (align each read to a locus and call SNPs) units. SNP filtering was done
 with populations unit from Stacks, VCFtools 0.1.15 (Danecek <em>et
 al.</em>, 2011) and a custom Python script (available at https://github.com/catpinho/filter_RADseq_data).