Anthropogenic hybridization in wildlife has been identified as one of the main causes of genetic homogenization, highlighting the need for identification and evaluation of populations at risk. Relocation of wildlife for game management purposes is a widespread practice that may promote the admixing of genetically different populations, subspecies or species. We undertook a large-scale study on the Iberian Peninsula to assess the extent of hybridization in red-legged partridge Alectoris rufa populations, which have been subject to extensive restocking of farm-reared individuals. Using a polymerase chain reaction-restriction fragment length polymorphism technique to assess the prevalence of individuals with mtDNA from other species, we examined samples of A. rufa from museum specimens (229), extant wild populations (955) and game farms (530). We found widespread occurrence of chukar partridge Alectoris chukar mtDNA lineages in samples obtained from game farm partridges (63% of game farms) and from wild partridges (45% of populations), but no allochthonous mtDNA lineages were found in museum partridges. We also found that the probability of occurrence and the number of partridges with allochthonous lineages was higher in localities where recent restocking had occurred. In addition, investigation of trends in bag records and the numbers of game farms over the past 30 years suggests that the general decline of wild populations has been accompanied by an increase in game farm facilities. These results suggest that supplemental stocking practices are threatening the integrity of the wild population gene pool. We recommend that rural development policies and associated wildlife management programs focused on maintaining high stock densities for hunting also need to consider the impact of game management on the genetic integrity of game populations.

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The Pleistocene climatic oscillations promoted the diversification in avian species during the last glacial period. The red‐legged partridge (Alectoris rufa, Family Phasianidae) has a large natural distribution extending from the Mediterranean to humid temperate zones. However, the genetic structure for this species is unknown. The present study investigates the phylogeography, genetic structure and demographic history of A. rufa across its distribution, employing both mitochondrial DNA control region sequences and nuclear microsatellite loci. Our results propose that this species was greatly affected by Pleistocene glaciations. The mismatch analyses suggest that the current populations resulted from post‐glacial expansion and subsequent differentiation resulting in five diagnosable genetic clusters: Southwestern, Central‐eastern, Northwestern, Balearic and French and Italian. Further, we found evidence of three glacial refugia within the currently recognized Iberian glacial refugium. The intraspecific structure revealed by both maternal and biparental phylogeographic analyses was not resolved in the phylogenetic analyses. Based on all considerations, we recommended that five management units be recognized.

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We developed and tested 16 new polymorphic microsatellite markers for the red-legged partridge ( Alectoris rufa ): four dinucleotide, two trinucleotide, eight tetranucleotide and two pentanucleotide repeat loci. The number of alleles per locus ranged from two to 21, observed heterozygosity was from 0.03 to 1.00 and expected heterozygosity was comprised between 0.18 and 0.91. Cross-specific amplification in others members of the Phasianidae family highlighted the potential usefulness of these molecular markers for the study of related species.