The common quail (Coturnix coturnix) is a popular game species for which restocking with farm-reared individuals is a common practice. In some areas, the number of released quails greatly surpasses the number of wild breeding common quail. However, common quail are difficult to raise in captivity and this casts suspicion about a possible hybrid origin of the farmed individuals from crosses with domestic Japanese quail (C. japonica). In this study we used a panel of autosomal microsatellite markers to characterize the genetic origin of quails reared for hunting purposes in game farms in Spain and of quails from an experimental game farm which was founded with hybrids that have been systematically backcrossed with wild common quails. The genotypes of these quail were compared to those of wild common quail and domestic strains of Japanese quail. Our results show that more than 85% of the game farm birds were not common quail but had domestic Japanese quail ancestry. In the experimental farm a larger proportion of individuals could not be clearly separated from pure common quails. We conclude that the majority of quail sold for restocking purposes were not common quail. Genetic monitoring of individuals raised for restocking is indispensable as the massive release of farm-reared hybrids could represent a severe threat for the long term survival of the native species.

Interbreeding of two species in the wild implies introgression of alleles from one species into the other only when admixed individuals survive and successfully backcross with the parental species. Consequently, estimating the proportion of first generation hybrids in a population may not inform about the evolutionary impact of hybridization. Samples obtained over a long time span may offer a more accurate view of the spreading of introgressed alleles in a species' gene pool. Common quail (Coturnix coturnix) populations in Europe have been restocked extensively with farm quails of hybrid origin (crosses with Japanese quails, C. japonica). We genetically monitored a common quail population over 15 years to investigate whether genetic introgression is occurring and used simulations to investigate our power to detect it. Our results revealed that some introgression has occurred, but we did not observe a significant increase over time in the proportion of admixed individuals. However, simulations showed that the degree of admixture may be larger than anticipated due to the limited power of analyses over a short time span, and that observed data was compatible with a low rate of introgression, probably resulting from reduced fitness of admixed individuals. Simulations predicted this could result in extensive admixture in the near future.

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Highlights d A chromosomal inversion of 115 Mbp, 12% of the genome, is found in common quails d Birds with the inversion are darker, heavier, and have rounder wings d These birds do not undertake the characteristic longdistance migration d The sequence in the inversion is highly divergent and originated before speciation

Background:The common quail, Coturnix coturnix, is a migratory bird hunted extensively across Europe. To satisfy this hunting interest, thousands of farm-reared birds are restocked every year. However, restocked individuals are not common quail but hybrids with domestic Japanese quail, C. japonica. Interbreeding between restocked and native birds in the wild allows the entry of alien alleles to the native populations, which could lead to the loss of adaptive phenotypes and behaviours, such as migratory drive. Sedentary individuals may face wintering conditions to which they are not adapted, suffering higher mortality. Some individuals have been observed to remain in northern latitudes during winter.Question: Does game restocking contribute to the sedentarization of the common quail population?Method: We sampled 42 quail during the autumn migration and 50 quail during winter in Spain. We genetically analysed them using a set of autosomal microsatellites and also sequenced a fragment of the mitochondrial DNA control region. We evaluated the proportion of admixed quail found and compared it with that previously found in a breeding population.Results: None of the migratory quail were admixed individuals, although two of them showed introgression of Japanese mitochondrial DNA. Among wintering quail, only three individuals had a genetic composition compatible with a farm origin, while the rest were common quail. Thus, the proportion of admixed quail during winter was not higher than during the breeding season.Conclusion: Restocking individuals with domestic Japanese quail ancestry is not directly associated with the presence of quail during winter in northern latitudes. The almost complete absence of individuals of farm origin among the migratory and wintering quail populations indicates that the vast majority of the restocked individuals probably die soon after release.

Farm-reared quails are released to the wild in Europe in vast numbers every year to increase hunting bag quotas. Experimental studies indicate that rather than the native common quail (Coturnix coturnix), the restocking is often done with domestic Japanese quail (Coturnix japonica) or with hybrids of domestic Japanese quail and common quail. Such practices are thought to be a severe threat for the native species as it could lead to introgression of domestic Japanese quail alleles into the wild common quail genome and potentially alter the migratory and reproductive behaviour in wild populations. In this study, we assessed the genetic purity of a captive population of common quail that was established from wild-caught founders caught on the Southern Italian coast in Sicily (Italy). We evaluated the proportion of ancestry to common and Japanese quail in this captive population via genetic screening using nuclear microsatellite markers and mitochondrial DNA analyses. We showed that the captive farm quail in our study had no sign of admixture with domestic Japanese quail and had similar genotype frequencies relative to wild common quail, confirming the success of the breeding programme for the native species. We propose that raising common quails in captivity for restocking purposes rather than domestic Japanese quails or hybrids would be a feasible alternative that could minimise the risk of genetic pollution of wild common quail populations.

Detection of hybridization and introgression is important in ecological research as in conservation and evolutionary biology. STRUCTURE is one of the most popular software to study introgression and allows estimating what proportion of the genome of each individual belongs to each ancestral population, even in cases where no reference sample from the ancestral nonadmixed populations is previously identified. In spite of its frequent use, some studies have indicated that ancestry estimates may not always be reliable. We simulated population data under different conditions with regard to the genetic differentiation between ancestral populations, number of loci considered, number of alleles per marker and hybridization rate, and analysed data with STRUCTURE. When reference samples were not included, the comparison of the known degree of admixture for each simulated individual and the value estimated with STRUCTURE revealed a strong underestimation of the level of introgression, classifying many admixed individuals as nonadmixed. This derives from an inaccurate estimation of the ancestral allele frequencies. When samples from the nonadmixed ancestral population were included as reference in the analyses, the bias in the estimations was reduced. The most accurate estimates were obtained when potentially admixed samples were few in relation to reference samples. Thus, whenever possible, a very large proportion of nonadmixed reference samples should be included in admixture assessments and different approaches should be combined. The misestimate of the amount of introgression can impair our understanding of the evolutionary history of species and misguide conservation efforts.

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