Genome-wide markers redeem the lost identity of a heavily managed gamebird

Heavily managed wildlife may suffer from genetic homogenisation and reshuffling of locally adapted genotypes with non-native ones. This phenomenon often affects natural populations by reducing their evolutionary potential and speeding up the ongoing biodiversity crisis. For decades, the red-legged partridge (Alectoris rufa), an intensively managed gamebird of conservation concern and considerable socio-economic importance, has been subjected to extensive releases of farm-reared hybrids with the chukar partridge (A. chukar) and translocations irrespective of subspecific affinity. These practices have led to serious concerns that the genetic integrity and biogeographic structure of most red-legged partridge populations are irreversibly affected, as suggested by previous studies based on few genetic markers. Using over 168,000 genome-wide loci and a sampling across the entire A. rufa range, we detected unexpectedly limited and spatially uneven chukar introgression as well as significant intraspecific structure. We demonstrate that species widely feared to have irretrievably lost their genetic identity are likely to be much less affected by unsuitable management practices than previously assumed. Our results spell the need for a radical re-think on animal conservation, possibly restoring native status to populations long treated as compromised. Our study exemplifies how the application of innovative conservation-genomic methods is key to solving wildlife management problems dealing with introgressive hybridisation worldwide.The data are Stacks files and logs for the SNP calling. There are two zipped foulders include dataset of two Alectoris species and only Alectoris rufa respectively. Funding provided by: Universidad de MálagaCrossref Funder Registry ID: http://dx.doi.org/10.13039/100009473Award Number: EURASIACAT ref. nr. 552067Funding provided by: Fundação para a Ciência e a TecnologiaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001871Award Number: PTDC/BAA-AGR/28866/2017Funding provided by: Provincia di Livorno*Crossref Funder Registry ID: Award Number: INTERREG III Toscana – Corsica – Sardegna (2002-2007)Funding provided by: Università di PisaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100007514Award Number: #PRA_2018_15Funding provided by: Provincia di LivornoCrossref Funder Registry ID: Award Number: INTERREG III Toscana – Corsica – Sardegna (2002-2007)The dataset is genome-wide Single Nucleotide Polymorphisms (SNPs) from 96 individuals of Alectoris patridges. Please refer to the publication and the supplimentery table for detailed sample information