Assessment of game restocking contributions to anthropogenic hybridization: the case of the Iberian red-legged partridge

Unexpected genetic integrity boosts hope for the conservation of the red-legged partridge (Alectoris rufa, Galliformes) in Italy

The red-legged partridge (Alectoris rufa) is a medium-sized galliform endemic to southwestern Europe. In the easternmost part of the species' range, the population inhabiting Elba Island (Tuscan Archipelago National Park, Italy) is of undisputed conservation value. While we found nuclear and maternal DNA introgression with the exotic chukar partridge (A. chukar) in previous studies based on microsatellite DNA (n = 25) and two mitochondrial markers (n = 103), respectively, we disclosed a limited or null admixture in a few Elban partridges (n = 4) in a recent genomic investigation relying on 168,675 Single Nucleotide Polymorphisms (SNPs). We herein carried out an extended microsatellite DNA survey including additional 65 samples (total, 90) and six loci (total, 11) to determine both spatial structure and genetic integrity of local A. rufa. A sharp divergence between the subpopulations inhabiting the two sides of the island was disclosed, and the microsatellites indicated that all Elban partridges were not admixed with the chukar, thus fully reflecting the picture inferred using SNPs. We hypothesized that the spreading of chukar genes was constrained by negative selection, with the persistence of only the maternal lineage being indicative of thermal adaptation. The two subpopulations should be treated as distinct Management Units, and an envisaged plan to secure a stock onto nearby Pianosa Island could not only warrant endurance of the Elban population but also establish a source of valuable founders for the ex-situ management of the species in Italy. Our study exemplifies how a suitable samples/loci combination is the key to solve wildlife issues dealing with introgression.

Gastrointestinal parasites in red-legged partridges (Alectoris rufa) hunted in Spain: a warning to game managers

Red-legged partridge (Alectoris rufa) populations are currently declining in the Iberian Peninsula, mainly due to habitat degradation and hunting pressure. In addition, the release of farm-reared partridges may introduce pathogens, including parasites, to wild populations. The presence of digestive parasites in red-legged partridges hunted in fifteen Spanish provinces was studied. Fecal samples and gastrointestinal tracts were collected, analyzed, and the morphometric identification of parasites was carried out. Eimeria spp. oocysts, nematode, cestode and trematode eggs were observed in fecal samples. Adult nematodes (Ascaridia galli, Ascaridia compar, Heterakis gallinarum, Heterakis tenuicauda, Trichostrongylus tenuis, Subulura spp., Cyrnea spp. and Aonchotheca caudinflata), tapeworms (Raillietina tetragona, R. echinobothrida, R. micracantha, Rhabdometra nigropunctata, and Choanotaenia infundibulum), and trematodes (Brachylaima spp., Brachylecithum spp., Dicrocoelium spp.) were identified in the gastrointestinal tracts. Significant statistical differences were found among climatic regions in the prevalence and intensity of Eimeria spp. infection, median intensity and the prevalence of indirect life cycle helminths, with Southern areas always showing higher infection values. The study provides information of the health status of red-legged partridges in Spain, highlighting the risk associated with the release of farm-reared partridges for restocking purposes. This should be taken into account to improve management strategies for the long-term conservation of the species.

Assessing the origin, genetic structure and demographic history of the common pheasant (Phasianus colchicus) in the introduced European range

The common pheasant, a game species widely introduced throughout the world, can be considered as an ideal model to study the effects of introduction events on local adaptations, biogeographic patterns, and genetic divergence processes. We aimed to assess the origin, spatial patterns of genetic variation, and demographic history of the introduced populations in the contact zone of Central and Southeast Europe, using mitochondrial DNA control region sequences and microsatellite loci. Both types of molecular markers indicated relatively low to moderate levels of genetic variation. The mtDNA analyses revealed that common pheasants across the study area are divided into two distinct clades: B (mongolicus group) and F (colchicus group). Analyses of the microsatellite data consistently suggested a differentiation between Hungary and Serbia, with the pheasant population in Hungary being much more genetically homogeneous, while that of Serbia has much more genetic mixture and admixture. This cryptic differentiation was not detected using a non-spatial Bayesian clustering model. The analyses also provided strong evidence for a recent population expansion. This fundamental information is essential for adequate and effective conservation management of populations of a game species of great economic and ecological importance in the studied geographical region.

Estate-level decision-making and socioeconomics determine annual harvest in the European Turtle-dove in central Spain

Designing evidence-based policies that regulate harvest levels is essential to avoid unsustainable hunting. This requires a good understanding of the relationship between bag sizes and regulatory mechanisms of harvest, and particularly of how these mechanisms are implemented locally and how they vary between game estates. The European Turtle-dove (Streptopelia turtur) has decreased by 30-49% since the late 1990s. The three main identified threats for the species are habitat loss, illegal killing and unsustainable legal hunting. We assessed how turtle dove estate-level harvest varies in relation to hunter density, number of hunting days, the adopted hunting method, game management intensity and the economic investment of the estate. Additionally, we assessed whether estate-level harvest had declined concomitantly with the population decline, and whether trends had been similar in relation to hunting method. We analysed Hunting Management Plans and Annual Hunting Reports of several thousand estates in central Spain, one of the main breeding and hunting areas of the species. Annual estate harvest was positively associated with hunter density, and was higher on estates that offered fixed-position hunting compared to those that only provided walked-up shooting. Importantly, these decisions are made by managers at the estate level and are not directly regulated by policy. We also found that more turtle doves are harvested on estates that invest more money in management, suggesting that the socioeconomic characteristics of the estate also influence local decisions on harvest intensity. Average annual estate-level harvest declined by 27% between 2007 and 2018, accompanied by a switch from fixed-position to walked-up hunting practices. Our study indicates that reducing hunting density or the number of fixed-position hunting days may be the most efficient ways to reduce turtle dove harvest, and that factors influencing estate-level decision-making have to be understood if reduction of hunting pressure in declining species is sought.

Novel genome reveals susceptibility of popular gamebird, the red-legged partridge (Alectoris rufa, Phasianidae), to climate change

We produced a high-quality de novo genome assembly of the red-legged partridge A. rufa, the first reference genome of its genus, by utilising novel 10× Chromium technology. The estimated genome size was 1.19 Gb with an overall genome heterozygosity of 0.0022; no runs of homozygosity were observed. In total, 21,589 protein coding genes were identified and assigned to 16,772 orthologs. Of these, 201 emerged as unique to Alectoris and were enriched for positive regulation of epithelial cell migration, viral genome integration and maturation. Using PSMC analysis, we inferred a major demographic decline commencing ~140,000 years ago, consistent with forest expansion and reduction of open habitats during the Eemian interglacial. Present-day populations exhibit the historically lowest genetic diversity. Besides implications for management and conservation, this genome also promises key insights into the physiology of these birds with a view to improving poultry husbandry practices.

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

Heavily managed wildlife may suffer from genetic homogenization 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 (Alectoris 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 hybridization worldwide.

An open platform system based on SNP type genetic markers for discrimination between Alectoris rufa and Alectoris chukar

The red-legged partridge (Alectoris rufa) is one of the most emblematic game species in Southern Europe. For the conservation of its natural populations against hybridization with chukar partridges (Alectoris chukar) a public and agreed control system able to detect genetic introgression between the two species should be established. As the already available method has not been implemented yet, this paper presents an improvement of the genetic analysis technique by using an open platform system to optimize the diagnostic procedure. Here we present the results obtained from the design of an Open Array™ platform with the available SNPs with proved diagnosis capacity between the two species of interest. By this procedure we genotyped 380 partridge samples, both from farms and field populations, which resulted in an overall percentage of genotyping performed with success of 99.64%. The Open Array genotyping plates showed high performance, specificity and an easy reproducibility compared to conventional techniques of genotyping.

Non-native and hybrid in a changing environment: conservation perspectives for the last Italian red-legged partridge (Alectoris rufa) population with long natural history

The ever-increasing biotic homogenization - especially when associated with introgressive hybridization - raises concern for the reduction of the spatial component of diversity in wildlife worldwide. Nonetheless, there is a growing attention to the potential conservation value of hybridization in fastening the adaptive evolutionary responses to rapidly changing selective pressures. Under these premises, we investigated the genetic affinity of the red-legged partridge (Alectoris rufa) population inhabiting Elba Island (Italy) in the context of the overall species phylogeography and particularly of the nominate subspecies it is traditionally ascribed to. Although notoriously hybrid with the congeneric A. chukar, this island population is of undisputedly value because of its long natural history and self-sustainability. As such, its adaptive conservation management calls for a comprehensive knowledge including the assessment of its geographic origin. For this purpose, 110 fecal samples were collected across Elba, genotyped at their joint Cytochrome-b and Control Region genes (2,249 characters), and compared with 149 conspecifics from all over the species distribution range. We confirmed a widespread A. chukar mitochondrial DNA introgression in Elba partridges, whereas their expected formal assignment to the nominate subspecies from Italy and France was rejected, since these turned out to be closely related to conspecifics from the Iberian Peninsula. This counterintuitive result found support in a large variety of literary sources and compelling evidences from personal testimonies revealing recent intense management with farm-reared birds of Spanish origin. Although the nativeness of Elba partridges was disproved, we advise local authorities to keep warranting the ongoing conservation efforts - and especially restore the connectivity between the western and eastern island sub-populations - as this resource may still be conceived as the ultimate repository for part of the otherwise extinct Italian A. r. rufa genome. Indeed, the admixture with conspecifics from the Iberian Peninsula does not necessarily mean that the entirety of the native nuclear genome of Elba partridges has been wiped out. Furthermore, these latter represent an interesting case study in conservation biology to investigate the possible role played by introgressive hybridization in the adaptation to recent land use and vegetation cover changes associated with rural abandonment in an insular yet heavily anthropized context.

Anti-predator behavior in pure and hybrid red-legged partridges

The purpose of this study was to examine the anti-predator behavior in pure red-legged partridges (Alectoris rufa) and hybrids with chukar partridges (A. rufa × (A. rufa × A. chukar)). A total of 117 birds (66 pure and 51 hybrid partridges; 74 females and 43 males) maintained in outdoor cages were used at a range of 52 to 55 wk of age. Four active fear tests were performed (novel object test, fear of humans test, emergence test, and restraint test) in order to analyze differences between pure and hybrid populations regarding the escape response type (novel object test and fear of humans test), the withdrawal distance (fear of humans test), and the reaction time (emergence test and restraint test). These variables could determine the ability of pure partridges captive to survive when released into the wild for hunting. There were no significant differences in anti-predator behavior in pure and hybrid birds, only one trend was observed in withdrawal distance (P = 0.09), being greater in pure than in hybrids partridges. There was a significant difference between sexes in the response type in the novel object test (P = 0.05); whereby the females came closer to the object than the males. The results of the present study indicate that active anti-predatory behavior was not associated with the genotype. However, since captivity could reduce the active anti-predator behavior, the results could be different if the wild birds that were tested had been sourced from their natural environment. Both sexes had similar active anti-predator behavior, although the males showing less approach behavior to a novel object that could be related to the sex-dimorphic behavior in natural social structure.

Parallel introgression and selection on introduced alleles in a native species

As humans cause the redistribution of species ranges, hybridization between previously allopatric species is on the rise. Such hybridization can have complex effects on overall fitness of native species as new allelic combinations are tested. Widespread species introductions provide a unique opportunity to study selection on introgressed alleles in independent, replicated populations. We examined selection on alleles that repeatedly introgressed from introduced rainbow trout (Oncorhynchus mykiss) into native westslope cutthroat trout (Oncorhynchus clarkii lewisi) populations in western Canada. We found that the degree of introgression of individual single nucleotide polymorphisms from the invasive species into the native is correlated between independent watersheds. A number of rainbow trout alleles have repeatedly swept to high frequency in native populations, suggesting parallel adaptive advantages. Using simulations, we estimated large selection coefficients up to 0.05 favoring several rainbow trout alleles in the native background. Although previous studies have found reduced hybrid fitness and genome-wide resistance to introgression in westslope cutthroat trout, our results suggest that some introduced genomic regions are strongly favored by selection. Our study demonstrates the utility of replicated introductions as case studies for understanding parallel adaptation and the interactions between selection and introgression across the genome. We suggest that understanding this variation, including consideration of beneficial alleles, can inform management strategies for hybridizing species.

Anti-predator behaviour of adult red-legged partridge (Alectoris rufa) tutors improves the defensive responses of farm-reared broods

The aim of this work was to improve natural anti-predator behaviour of farm-reared gamebirds. We evaluated the anti-predator behaviour of reared red-legged partridge Alectoris rufa chicks kept in brooder houses in large groups (>350 chicks), trained and not trained by parent red-legged partridges acting as experienced tutors. The experiment consisted of two conditioned tests (a raptor model and a human) and two control tests, which were conducted during three consecutive phases of life (1-4, 15-17 and 30-32 d after hatching). The motor anti-predator behaviour, its duration, the intensity of response in chicks and alarm calls elicited by adults were recorded. Tutors elicited aerial alarm calls (76% of tests) and showed prolonged crouching (59% of tests) in response to the raptor model whereas uttering the ground alarm call (73% of tests) and showing vigilance behaviour (78% of tests) was the main pattern during the human test. Trained and not trained chicks showed similar motor behaviour in response to the raptor model (crouching) and the human test (escaping), but frequency of strong responses (all chicks responding) from chicks trained with tutors was double that of chicks trained without them, and chicks trained with tutors showed a higher frequency of long responses (41-60 s). This study indicates that anti-predator training programmes before release may improve behaviour of farm-reared partridges which may confer benefits to survival of birds.

Effect of Game Management on Wild Red-Legged Partridge Abundance

The reduction of game and fish populations has increased investment in management practices. Hunting and fishing managers use several tools to maximize harvest. Managers need to know the impact their management has on wild populations. This issue is especially important to improve management efficacy and biodiversity conservation. We used questionnaires and field bird surveys in 48 hunting estates to assess whether red-legged partridge Alectoris rufa young/adult ratio and summer abundance were related to the intensity of management (provision of supplementary food and water, predator control and releases of farm-bred partridges), harvest intensity or habitat in Central Spain. We hypothesized that partridge abundance would be higher where management practices were applied more intensively. Variation in young/adult ratio among estates was best explained by habitat, year and some management practices. Density of feeders and water points had a positive relationship with this ratio, while the density of partridges released and magpies controlled were negatively related to it. The variables with greatest relative importance were feeders, releases and year. Variations in post-breeding red-legged partridge abundance among estates were best explained by habitat, year, the same management variables that influenced young/adult ratio, and harvest intensity. Harvest intensity was negatively related to partridge abundance. The other management variables had the same type of relationship with abundance as with young/adult ratio, except magpie control. Variables with greatest relative importance were habitat, feeders, water points, releases and harvest intensity. Our study suggests that management had an overall important effect on post-breeding partridge abundance. However, this effect varied among tools, as some had the desired effect (increase in partridge abundance), whereas others did not or even had a negative relationship (such as release of farm-reared birds) and can be thus considered inefficient or even detrimental. We advise reconsidering their use from both ecological and economical points of view.

Market value of restocking and landscape in red-legged partridge hunting: a study based on advertisements

Context In Spain, the release of farm-reared partridges to hunt is increasingly used, despite being thought to affect sustainability of wild stocks and to reduce the need of natural habitats for game. Aims To explore the market value as a possible incentive for current management, we evaluated within a segment of the red-legged partridge hunting market whether the use of farm-reared birds (as opposed to wild stock) or the naturalisation of landscapes are affecting the hunt market price. Methods We considered estates that sell individual hunting days and contacted buyers through advertisements. We gathered all advertisements for the 2010 season in four top hunting magazines and two websites, and conducted a telephone survey to record price and associated characteristics of hunts. We looked for relationships between price and the characteristics of sold hunts, using general linear models. Key results Hunts varied largely in price, but neither restocking nor naturalisation of the landscape explained price variation, at least within our sample of estates. The absence of price difference between wild or released partridges could be reflecting the current difficulty to distinguish both kinds of products in the market. Conclusions Market forces alone might not be promoting the public interest of the sustainable use of wild stocks versus industrial hunting based on farm-reared birds. Implications If promoting conservation and sustainable use of wild stocks is considered a major goal of official institutions in charge of biodiversity conservation and game management, they should promote reliable ways of identifying estates selling wild or restocked partridges, and they should also evaluate benefits and costs associated with hunting farm-reared birds relative to wild birds, so as to help internalise these costs and benefits if necessary. A study of the determinants of hunter demands would also help explain variation in supply and market prices.

Are farm-reared quails for game restocking really common quails (Coturnix coturnix)?: a genetic approach

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.

Harvest of Red-Legged Partridge in Central Spain

A basic rule to attain sustainable use of harvested resources is to adjust take to availability. Populations of red-legged partridges in Spain have decreased in recent decades, and releases of farm-bred partridges to improve short-term availability are increasingly common. We used questionnaires and bird surveys to assess whether harvest was related to availability of wild partridges or intensity of farm-bred partridge releases. We studied 50 hunting estates, including 6 administratively labeled as intensive (with few numerical and temporal restrictions to releases). In addition, we considered hunting pressure (number of hunters × hunting days/km²) and habitat as explanatory variables in the analyses. In intensive estates, annual harvest was exclusively related to release intensity, indicating that in these estates hunting is detached from natural resources and approaches an industrial activity based on external inputs. In non-intensive estates, harvest was affected by wild stock availability, walked-up shooting pressure, and habitat (greater harvest in estates with more Mediterranean shrubland). In these estates, releases did not increase annual harvest, and can be considered an inefficient practice. Additionally, the relationship between abundance estimates and harvest disappeared in estates with low partridge abundance estimates, suggesting possibilities for overharvesting in a large proportion of estates. Increasing the abundance of wild red-legged partridge through techniques like habitat management, and improving the adjustment of harvest to availability, may be a good strategy to increase long-term harvest in non-intensive estates. Additionally, Government and managers must create ways to segregate and label the estates where only wild red-legged partridges are managed from those where releases are used, to reduce ecological costs of management decisions. © 2012 The Wildlife Society.

Effects of human perturbation on the genetic make-up of an island population: the case of the Sardinian wild boar

Game species are often manipulated by human beings, whose activities can deeply affect their genetic make-up and population structure. We focused on a geographically isolated wild boar population (Sardinia, Italy), which is classified, together with the Corsican population, as a separate subspecies (Sus scrofa meridionalis). Two hundred and ten wild boars collected across Sardinia were analysed with a set of 10 microsatellites and compared with 296 reference genotypes from continental wild populations and to a sample of domestic pigs. The Sardinian population showed remarkable diversity and a high proportion of private alleles, and strongly deviated from the equilibrium. A Bayesian cluster analysis of only the Sardinian sample revealed a partition into five subpopulations. However, two different Bayesian approaches to the assignment of individuals, accounting for different possible source populations, produced consistent results and proved the admixed nature of the Sardinian population. Indeed, introgressive hybridization with boars from multiple sources (Italian peninsula, central Europe, domestic stocks) was detected, although poor evidence of crossbreeding with free-ranging domestic pigs was unexpectedly found. After excluding individuals who carried exotic genes, the population re-entered Hardy-Weinberg proportions and a clear population structure with three subpopulations emerged. Therefore, the inclusion of introgressed animals in the Bayesian analysis implied an overestimation of the number of clusters. Nonetheless, two of them were consistent between analyses and corresponded to highly pure stocks, located, respectively, in north-west and south-west Sardinia. This work shows the critical importance of including adequate reference samples when studying the genetic structure of managed wild populations.

New directions in management strategy evaluation through cross-fertilization between fisheries science and terrestrial conservation

On 1 and 2 June 2010, an international meeting was held at the University of Paris Sud XI, France, organized within the framework of the EU FP7 consortium project HUNT, to bring together fisheries and conservation scientists to discuss a unified framework for the future of management strategies for harvested species.

The usefulness of field data and hunting statistics in the assessment of wild rabbit (Oryctolagus cuniculus) conservation status in Portugal

Context. The wild rabbit (Oryctolagus cuniculus) is a keystone species from the Iberian Peninsula that has suffered a strong decline in Spain during the past decades. Data on historical and current population trends in Portugal are virtually non-existent. Aims. To investigate changes in rabbit abundance at the national level so as to inform conservation status assessments, and to evaluate the usefulness of hunting bags as a rabbit abundance index. Methods. Field surveys based on latrine counts in linear transects were performed in two periods (1995 and 2002) to assess variation in population abundance. Hunting bags were also analysed for the same period to verify whether these data showed the same trends. General trends of rabbit abundance were estimated using TRIM software. Key results. Field data revealed that most of the sampling units across Portugal have low abundances, despite the observation of local high-density spots. A population reduction of 27% was estimated. Although some fluctuations were observed in hunting bags, global results obtained from these data suggest a slightly increasing trend in rabbit abundance. Conclusions. A discrepancy between field data and hunting statistics was observed. Because hunting bags may be influenced by sporadic management operations undertaken by hunters and the lack of systematic procedures in data collection, we believe that hunting statistics are not representative of real changes in rabbit populations. Thus, observed reduction in rabbit abundance estimated by field data, combined with the high initial morbidity due to rabbit haemorrhagic disease (RHD) after 1988 and the potential for continuing decline in population trends because of other factors, led to an inference of a reduction of >30% in rabbit abundance in Portugal during the past decade. Implications. Taking into account the estimated reduction, the species’ biology and socioeconomic implications, wild rabbit in Portugal was listed in 2005 in the Near Threatened category under IUCN criteria. Because of its ecological and economic importance, this classification prompted the definition of several conservation actions aimed at the recovery of the species in Portugal.