In this study, we focused on common quails (Coturnix coturnix) from the Azores archipelago and used morphological, stable isotope, genetic and genomic data to characterise this lineage and to assess the divergence from neighbouring common quail populations. We detected the presence of a large chromosomal inversion that had been already described in other populations and we studied its role in this remote archipelago. The genotyping-by-sequencing data generated in this project were analysed together with those from Sanchez-Donoso et al. 2022 (https://doi.org/10.1016/j.cub.2021.11.019).  

We captured common quail males during the breeding season in Spain, Portugal, Morocco, Italy, Netherlands and the Atlantic archipelagos of Madeira, Canary Islands and Azores. About 100 µl of blood was extracted from each individual from the jugular vein for genomic analyses.

DNA was extracted by using the DNeasy Blood & Tissue Kit of QIAGEN. We built a shotgun genotyping-by-sequencing library from DNA of 90 common quails from 10 localities, two domestic Japanese quails and three hybrids between common and Japanese quails (plus a control) after digestion with the restriction enzymeEcoT22I. This library was sequenced using Illumina HiSeq 2500 (1x100bp) at Cornell University, Biotechnology Resource Center.

We called SNPs using the TASSEL-5-GBS pipeline52 and mapped them against the Japanese quail genome (Coturnix japonica, RefSeq assembly accession number: GCF_001577835.2) using bowtie2 v.2.4.1. We filtered for biallelic SNPs with minor allele frequency higher than 0.03, missing data less than 25% and depth higher than 5 and lower than 100 using VCFTOOLS v.0.1.13.