Dataset for "A range-wide assessment of genetic diversity, structure and inbreeding in the threatened Olrog’s Gull (Larus atlanticus)"

Assessing genetic differentiation and its drivers among populations is essential for informing localized conservation management. Here we study Olrog's Gull (Larus atlanticus), a threatened seabird which breeds in two sectors of coastal Argentina separated by approximately 700 km (Buenos Aires and Chubut provinces). We used a reduced-representation genomic approach to genotype 59 individuals from five colonies at thousands of single-nucleotide polymorphisms (SNPs) to study patterns of connectivity across the species range. While individuals from the four northern colonies are genetically indistinguishable, the single colony located in the Patagonian province of Chubut is highly genetically differentiated. These individuals also have low genetic diversity, high inbreeding, and are closely related (higher than first-order relatives). For a subset of individuals, we generated whole genome sequences to assess the possible effects of inbreeding on the depletion of genetic variation across the genome (i.e., the number and length of runs of homozygosity, ROH). We found an exceptionally high number of ROH in the Chubut colony compared to its northern counterparts. This southern colony is genetically isolated from the panmictic northern colonies containing most of the breeding population of Orlog’s Gull, and at risk of suffering from inbreeding depression and therefore of significant conservation concern.List of attached files:Olrog.snps.vcf: VCF file of filtered SNPs used for analysis.Olrog_COI.phy: Aligned COI sequences for a subset of individuals.Demultiplexed raw reads per individual.zip: This compressed folder contains the demultiplexed reads for each individual included in the study. The files are named with a number (1 to 60), the species code "GO", a two to four letter code indicating the breeding colony and a final two letter code indicating the breeding sector (for details see Figure 1 in the paper).Olrog Assembly: Compressed folders with the assembly files from STACKS that can be used to export SNP datasets under different filtering conditions.olrogs_tags_bi_qual_dp_nmiss_exhet_renamed_auto.vcf.gz: VCF file with filtered SNPs used as input for the ROH analyses.