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Over the last decades, the study of the microbiome has been receiving increasing attention as a major driver of individual health and wellbeing. The accumulation of knowledge on microbiomes sparked new research lines, from which the association between oral microbiome composition and taste perception is of great interest. Taste plays a paramount role in food and beverage choice as well as emotions. For wine tasters, the smell is also part of the tasting evaluation. However, the nasal microbiome is relatively unexplored. The relation between the microorganisms residing in the nostrils is still poorly known despite their leading role in flavor perception. Therefore, characterizing the composition of nasal microbiomes represents a fundamental prerequisite to elucidate their relationship with taste. To improve our understanding of the relationship between taste and the microorganism inhabiting the nostrils, the nasal microbiome of 5 wine tasters versus 5 non-tasters was analyzed through the sequencing of the V3-V4 region of the16S rRNAgene. The taxonomic composition of these nasal microbiomes was characterized, and the comparison of diversity indexes revealed no significant differences. However, the experimental group showed a lower number of identified taxa (171) when compared to the control group (287). Another interesting result was the higher presence of Krebs Cycle pathways in wine tasters, which could indicate the importance of the nostril bacterial community in alcohol oxidation. Regarding smoking habits, smokers presented a lower microbiome diversity. These preliminary results should be confirmed in a larger sample dataset of wine tasters and controls.

Over the last two decades, vocal and genetic data have been extensively used in avian studies addressing taxonomic and systematic issues. However, even when multiple lines of evidence lean toward lumping or splitting of species, some taxonomic committees refuse to acknowledge their validity until convincing genetic evidence is produced and integrated with other sources of data. As a case in point, the genus Pseudocolaptes (Furnariidae) consists of three mostly allopatric and overtly distinct neotropical taxa differing in plumage and vocal features: the Streaked Tuftedcheek (P. boissonneautii), the Buffy Tuftedcheek (P. lawrencii), and the contentious Pacific Tuftedcheek (P. johnsoni). In this study, we assemble already available mitochondrial and nuclear DNA sequences to assess their taxonomy and to provide appointed committees with specific proof to ascertain the number of Pseudocolaptes species. Phylogenetic inference and species delimitation analysis indicate three species equally divergent from each other. We hope that this work will contribute to resolve the long-lasting taxonomical confusion regarding this genus, and that proper future conservation plans will be adopted to preserve each species within the inhabited biodiversity hotspot.

Taste plays a paramount role in food and beverage choice, with recent studies pointing to a potential influence of the microorganisms from the tongue dorsum - particularly bacteria - on flavor perception. Thus, the association between tongue dorsum biofilm and taste is a fundamental prerequisite for a better understanding of the role played by these bacteria in wine tasting. To study this impact, we have analyzed the microbiomes from 58 samples of the tongue dorsum surface from professional wine tasters and 30 samples from non professional wine tasters. The microbiome of each sample was characterized through metagenome sequencing of the 16S rRNA gene for taxonomic discrimination of bacteria. A total of 497 taxa were identified in the tongue dorsum, and significant differences in diversity were observed between the wine taster and the control group. The comparison of bacterial diversity between samples collected before and after wine tasting along with the presence of new bacterial taxa indicates a direct effect of wine on the microbiome of frequent wine tasters, particularly in those tasting sparkling wines.

The study of diel and seasonal variation in vocal interactions of Crested Francolin Ortygornis sephaena territorial males helps clarify its purpose, thus delivering insights into the behavioural ec...

The red junglefowl Gallus gallus is the ancestor of the domestic chicken and arguably the most important bird species on Earth. Continual gene flow between domestic and wild populations has compromised its gene pool, especially since the last century when human encroachment and habitat loss would have led to increased contact opportunities. We present the first combined genomic and morphological admixture assessment of a native population of red junglefowl, sampled from recolonized parts of its former range in Singapore, partly using whole genomes resequenced from dozens of individuals. Crucially, this population was genomically anchored to museum samples from adjacent Peninsular Malaysia collected ~110–150 years ago to infer the magnitude of modern domestic introgression across individuals. We detected a strong feral–wild genomic continuum with varying levels of domestic introgression in different subpopulations across Singapore. Using a trait scoring scheme, we determined morphological thresholds that can be used by conservation managers to successfully identify individuals with low levels of domestic introgression, and selected traits that were particularly useful for predicting domesticity in genomic profiles. Our study underscores the utility of combined genomic and morphological approaches in population management and suggests a way forward to safeguard the allelic integrity of wild red junglefowl in perpetuity.

The transition zones between and within biogeographic realms are a topical issue. Long ascribed to eastern Palaearctic, Iran was recently proposed as entirely pertaining to its western counterpart ...

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 entireA. rufarange, 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.

The mouflon (Ovis gmelini ophion) is the largest wild terrestrial mammal of Cyprus. Regarded as the local flagship species, its population range is limited to the mountainous Paphos Forest and adjacent areas including part of Troodos National Forest Park (> 700 Km2). This species, protected by both national and international legislation, is classified as Endangered by the IUCN, with livestock intrusion, poaching and habitat loss as the main threatening factors. We determined the spatial genetic structure by investigating sexes separately and shed further light on the Cyprus mouflon placement among Ovis haplogroups (HGs) to enforce its protection within an adaptive conservation framework. We genotyped 108 samples collected across the entire species’ range at both14 loci of the microsatellite DNA and the mitochondrial DNA Control Region (CR). Microsatellite genotyping indicated that the wild population retained low genetic variability, which, however, was not associated with a level of inbreeding raising particular concern (FIS = 0.12). An overall weak spatial genetic structure was disclosed, consistently with the limited extension of the mouflon range, the lack of significant physical barriers to dispersal and the intense gene flow mostly occurring along a northeast-southwest axis across the forest. Nevertheless, evidences of structure were found for females in compliance with their philopatric behaviour. The disclosure of unique features compared to Mediterranean and Near East conspecifics, such as the occurrence of a six-fold 76 bp-long repeated motif in the Cyprus mouflon CR, along with the outcome of a phylogenetic reconstruction (based on a far higher number of Ovis GenBank records and Cyprus haplotypes than in previous studies) inspired the proposal of a new haplogroup (HGC2) which included the Anatolian mouflon (O. g. anatolica, former HGX) as sister taxon. While both high habitat heterogeneity and low human disturbance were the main drivers in determining the overall spatial structure, future conservation efforts to preserve this valuable genetic resource should focus on avoiding possible introgressive hybridisation with co-grazing livestock to the edge of its range.

Reconstructing the demographic history of endangered taxa is paramount to predict future fluctuations and disentangle the contributing factors. Extinct taxa or populations might also provide key insights in this respect by means of the DNA extracted from museum specimens. Nevertheless, the degraded status of biological material and the limited number of records may pose some constraints. For this reason, identifying all available sources, including private and public biological collections, is a crucial step forward. In this study, we reconstructed the demographic history based on cytochrome-b sequence data of the Pyrenean ibex (Capra pyrenaica pyrenaica), a charismatic taxon of the European wildlife that became extinct in the year 2000. Moreover, we built a database of the museum specimens available in public biological collections worldwide and genotyped a privately owned 140-year-old trophy from the Spanish Pyrenees to confirm its origin. We found that the population of the Pyrenean ibex underwent a recent expansion approximately 20,000 years ago, after which trophy hunting and epizootics triggered a relentless population decline. Our interpretations, based on the genetic information currently available in public repositories, provide a solid basis for more exhaustive analyses relying on all the new sources identified. In particular, the adoption of a genome-wide approach appears a fundamental prerequisite to disentangle the multiple contributing factors associated with low genetic diversity, including inbreeding depression, acting as extinction drivers.

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.

Genetic variability has been widely neglected as a measure of biodiversity for conservation and management over the last decades. However, major technical advances in molecular biology coupled with increased public awareness have recently marked the opening of a new era. Estimates and tracking of genetic variability in species and populations are now mandates for governments. However, this obligation is difficult to implement. There is no agreement on the most appropriate way to assess genetic diversity, yet the urgent need for comparability among different studies calls for the adoption of standardized molecular tools in biodiversity monitoring. Here, we take stock of the plethora of techniques and tools that have been historically adopted for monitoring genetic diversity in mammals and evaluate their strengths and weaknesses. We focus on the opportunities offered by new genomic approaches and touch upon the major bioinformatics challenges posed by the impressive amount of data that they deliver, suggesting current trends and future prospects.

Background and aims Wildlife conservation has focused primarily on species for the last decades. Recently, popular perception and laws have begun to recognize the central importance of genetic diversity in the conservation of biodiversity. How to incorporate genetic diversity in ongoing monitoring and management of wildlife is still an open question. Methods We tested a panel of multiplexed, high-throughput sequenced introns in the small mammal communities of two UNESCO World Heritage Sites on different continents to assess their viability for large-scale monitoring of genetic variability in a spectrum of diverse species. To enhance applicability across other systems, the bioinformatic pipeline for primer design was outlined. Results The number of loci amplified and amplification evenness decreased as phylogenetic distance increased from the reference taxa, yet several loci were still variable across multiple mammal orders. Conclusions Genetic variability found is informative for population genetic analyses and for addressing phylogeographic and phylogenetic questions, illustrated by small mammal examples here., Conservation, Genetics, Intron, High-throughput sequencing NGS, Multiplex, Wildlife management, Agricultural science, Environmental science, Earth sciences, Biological sciences, Veterinary medicine.

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.

Social networks are the result of interactions between individuals at different temporal scales. Thus, sporadic intergroup encounters and individual forays play a central role in defining the dynamics of populations in social species. We assessed the rate of intergroup encounters for three western lowland gorilla ( Gorilla gorilla gorilla ) groups with daily observations over 5 years, and non-invasively genotyped a larger population over four months. Both approaches revealed a social system much more dynamic than anticipated, with non-aggressive intergroup encounters that involved social play by immature individuals, exchanges of members between groups likely modulated by kinship, and absence of infanticide evidenced by infants not fathered by the silverback of the group where they were found. This resulted in a community composed of groups that interacted frequently and not-aggressively, contrasting with the more fragmented and aggressive mountain gorilla ( G. beringei beringei ) societies. Such extended sociality can promote the sharing of behavioural and cultural traits, but might also increase the susceptibility of western lowland gorillas to infectious diseases that have decimated their populations in recent times.

The mouflon population of Cyprus (Ovis orientalis ophion) comprises historically preserved feral descendants of sheep domesticated during the Neolithic. We determined genetic identity of this taxon in order to elucidate its systematic placement and enforce its protection. We used 12 loci of microsatellite DNA to infer genetic relationships between the Cypriot mouflon and either long-time isolated (Corsica, Sardinia) or recently introduced (central Italy) European mouflons (O. o. musimon). We also sequenced the mitochondrial DNA (mtDNA) Cytochrome-b gene to infer the origin of the Cypriot mouflon including many National Centre for Biotechnology Information (NCBI) entries of European and Near Eastern conspecifics. Microsatellites disclosed net divergence between Western Mediterranean and Cypriot mouflon. The latter was included in the highly heterogeneous Near Eastern O. orientalis mtDNA group, Iran representing the most credited region as the source for its ancient introduction to Cyprus. Both internationa...

The ever-increasing human-mediated wildlife reshuffling is raising concern for the conservation of biodiversity. The loss of biological distinctiveness among regions lessens the genetic diversity and consequently the evolutionary potential of local biotas to tackle present-day global change and human disturbance. This process may be sometimes cryptic unless investigated by means of a molecular approach. In this respect, game birds are a paradigmatic case. The black francolin (Francolinus francolinus, Phasianidae) is a medium-sized galliform whose distribution range stretches from Cyprus to the Gulf of Bengal. Six morphologic subspecies are known, with three of which occurring in Pakistan, where the species is heavily hunted and used as pet for chirping competitions. We genotyped 98 samples (feathers) at both the entire mitochondrial DNA Control Region gene and nine microsatellite loci to get a deeper insight into the genetic diversity of the black francolin in Pakistan in order to offer cogent recommendations for its conservation management. We identified several mtDNA lineages that were consistent with the currently described subspecies/taxonomy whose pattern of co-occurrence is compatible with the geological history and the faunal movement routes of the region under study. However, the biparentally inherited microsatellites returned a quite discordant picture of an extensive, sex-biased genetic mixing due to the intensive relocations of already overharvested male individuals for chirping competitions. Our results indicated that the genetic integrity of the black francolin in Pakistan could be seriously at risk and call for monitoring and limiting its trade other than enhancing the public awareness of the importance of local biodiversity resources.

The release of exotic genotypes into the wild can lead to the extinction of local demes through the hybridization among distinct gene pools. This may occur between wild specimens and their domesticated relatives. Escaped pets represent a well-known pathway for the introduction of allochtonous resources, and island environments require major attention as they include small-sized and naive populations that may be prone to extinction. We characterized the genetic make-up of the black francolin ( Francolinus francolinus , Phasianidae) resident to Cyprus using microsatellite and mitochondrial DNA for the purpose of sustainable use and long-term protection of this game species. We collected 59 samples of specimens hunted in the districts of Nicosia and Paphos, while others ( n = 18) were obtained from birds of unknown origin. These had been imported to a pet-centre in Nicosia, the largest in the capital offering animals either for production or leisure purposes. Both genetic systems pointed to the occurrence of distinct wild district populations that could be treated as separate management units. The non-significant value of the inbreeding coefficient ( F IS ) computed for Nicosia and Paphos populations (−0.039 and −0.189, respectively: P > 0.05) and the lack of evidence for recent genetic bottlenecks did not indicate a serious risk of over-hunting. The microsatellites revealed the birds in the pet-centre as highly genetically divergent with respect to the wild ones, the mtDNA pointed to their assignment to alien Asian subspecies once they were compared to141 sequences of allopatric francolins. We advised the Game & Fauna Service to consider law enforcement to ban the import, detention and sale of these subspecies to protect the black francolin population native to Cyprus. The results are discussed in the context of a bibliographic frame including the partridges of the genus Alectoris (Phasianidae) as a model group with reference to genetic characterization and conservation of game bird island populations.

International audience

Molecular DNA techniques in combination with appropriate reference population database and statistical methods are fundamental tools to forensic wildlife investigations. This is even more relevant when taxa with uncertain systematics are involved, as is the case of the genus Ovis (Bovidae), whose evolution has been influenced by multiple events of domestication. The Cypriot mouflon, Ovis orientalis ophion, a protected subspecies endemic to Cyprus, is threatened by poaching. This study deals with a case of alleged poaching that occurred in Cyprus (September, 2010). A car did not stop at a checkpoint and when finally blocked by the police, several bloodstained exhibits (n=12) were recovered. Three recently deceased mouflons were found by game wardens at the roadside. The Cyprus Veterinary Services established that these animals had been killed by gunshot. As part of the investigation, DNA testing was performed to establish if there was a link between the dead mouflons and the bloodstained exhibits. The mitochondrial Cytochrome-b gene (Cyt-b) and 12 loci of microsatellite DNA were used as markers. The Cyt-b sequences were obtained from 11 exhibits. They were the same as each other and the same as the single haplotype obtained from the three dead mouflons and all the investigated wild Cypriot mouflons (20 individuals). A database of wild mouflons (47 individuals) from which the unknown samples may have originated was generated. The probability of identity (P(ID)) of the microsatellite panel, computed by genotyping all 47 wild mouflons (10 selected loci, P(ID)=10(-5)), allowed us to assign nine exhibits to two out of the three carcasses (seven with very strong support: Likelihood Ratio, LR>3000 and Random Match Probability, RMP

The red-legged partridge, Alectoris rufa (Phasianidae), is a game bird hunted throughout its range (Italy, France with Corsica Island, Iberian Peninsula). The release into the wild of farmed birds of unknown origin coupled to the hybridization with the exotic chukar Alectoris chukar (East Mediterranean to East Asia) has led to the reduction of the spatial component of genetic variability and to the pollution of the genome of A. rufa, respectively. On the mainland, A. chukar genes occur according a decreasing gradient from Italy to the Iberian Peninsula. Corsica hosts a number of A. rufa×A. chukar hybrids, but at a much lower incidence than nearby Italy. We sampled 97 red-legged partridges in different habitats of Corsica [lower-Mediterranean: Desertu di l'Agriate; rural: Nessa-Felicetu; mountainous: Vivariu-Venacu and Fium'Orbu-Taravu (FT)]. We investigated kinship between Corsican and continental A. rufa populations by sequencing the mitochondrial DNA (mtDNA) Cytochrome-b gene in a subset (n=60) of island specimens as well as in 105 partridges sampled on mainland Europe. All 97 Corsican partridges were genotyped at eight microsatellite DNA loci in order to estimate intraspecific relationships at a finer scale. We also used microsatellite data from previous studies to compare the genotypes of A. rufa reared in the only island farm with those of wild conspecifics. Corsican partridges grouped in the only statistically reliable and diverging mtDNA clade. Microsatellites provided evidence for the genetic isolation of the FT mountain population, whose low level of hybridization with A. chukar had been unveiled in a former paper. Both mtDNA and microsatellite markers revealed that released captive partridges did not enter the wild breeding populations to any great extent. We suggested banning A. rufa translocation from Corsica to the continent to comply with the disclosed genetic kinship, and vice versa to contain the spreading of A. chukar genes in to the A. rufa population.

1. The conservation of small aquatic habitats is fundamental to preserving diversity in Mediterranean freshwater ecosystems. Amphibians are particularly endangered, as their chemical world, represented by both abiotic and biotic scent trails, is highly susceptible to environmental changes. 2. Breeding site fidelity in the northern spectacled salamander, Salamandrina perspicillata, an Italian endemic vertebrate, was investigated with respect to the ability of this species to locate its own home water rather than that from other places. The choice of aquatic habitat for spawning was investigated in dark conditions by comparing different types of experimental water (home breeding water vs. breeding water of allopatric populations vs. mineral water vs. distilled water). Fifty-eight reproductive females were collected at four breeding sites in the Lepini Mountains (Latium, central Italy). The number of eggs spawned by each specimen in the different types of experimental water was counted. 3. The very large majority of the eggs were found in the home breeding water. When the eggs counted in the other types of water were compared, no differences were found. 4. These findings revealed that in the northern spectacled salamander the choice of spawning site was affected by the scent trail of its own aquatic habitat. This new information has improved knowledge of the auto-ecology of S. perspicillata, thus contributing to strategies for its conservation. Copyright © 2007 John Wiley & Sons, Ltd.

Humans have a long history of moving wildlife that over time has resulted in unprecedented biotic homogenization. It is, as a result, often unclear whether certain taxa are native to a region or naturalized, and how the history of human involvement in species dispersal has shaped present-day biodiversity. Although currently an eastern Palaearctic galliform, the black francolin ( Francolinus francolinus ) was known to occur in the western Mediterranean from at least the time of Pliny the Elder, if not earlier. During Medieval times and the Renaissance, the black francolin was a courtly gamebird prized not only for its flavor, but also its curative, and even aphrodisiac qualities. There is uncertainty, however, whether this important gamebird was native or introduced to the region and, if the latter, what the source of introduction into the western Mediterranean was. Here we combine historical documentation with a DNA investigation of modern birds and archival (13th–20th century) specimens from across the species’ current and historically documented range. Our study proves the black francolin was nonnative to the western Mediterranean, and we document its introduction from the east via several trade routes, some reaching as far as South Asia. This finding provides insight into the reach and scope of long-distance trade routes that serviced the demand of European aristocracy for exotic species as symbols of wealth and prestige, and helps to demonstrate the lasting impact of human-mediated long-distance species dispersal on current day biodiversity.

We investigated the evolution of the Asian francolins, five little known species in the genus Francolinus (Phasianidae). Evolutionary affinities of two of these species, F. gularis (swamp francolin) and F. pondicerianus (grey francolin), has long remained unclear. In contrast, the other three species, F. pintadeanus (Chinese francolin), F. pictus (painted francolin) and F. francolinus (black francolin) have been cast among the “spotted francolins” on a morphological and ecological basis. Previous molecular DNA investigations including Asian francolins mostly relied upon partial gene sequencing of one specimen per species (no more than three species and with the exclusion of F. pictus). Therefore, fundamental questions do persist. What relationship exists among the spotted and the other Asian francolins? What is the geographic origin of the black francolin, the species with the largest distribution range? How did the geological history influence the diversification of francolins across Asia? We sequenced the entire Control Region of the mitochondrial DNA in 228 samples of all five Asian francolin species, which were collected in 16 countries (from East Europe to East Asia). We constructed a molecular phylogeny according to four different procedures. We showed the monophyly of each of the Asian francolins and the spotted group, while that of the entire Asian group was presumed according to a biogeographical model we proposed. The splitting of the genus Francolinus occurred ∼17.4 Ma (95% HPD: 13.4–22.1) while the spotted francolins diverged ∼10.5 Ma (7.0–14.9). We resolved the most recent common ancestor to painted and black francolin as being in the Indian sub-continent, thus suggesting a westwards adaptive radiation of the latter. In Pakistan, we identified F. f. asiae representatives in the Northern Areas and in the Sindh. The latter represents a relict population of Indian fauna within the Pakistani range of the Great Rann of Kachchh.

Introduction of wildlife for game restocking is one major pathway of genetic homogenization. The red-legged partridge (Alectoris rufa, Phasianidae), a small game bird native to south-western Europe, is in high demand by hunters and natural populations are constantly supplemented by commercial stocks of captive-bred individuals. Also, in recent years human-mediated hybridization with congeneric chukar partridges (Alectoris chukar: Greece, Cyprus, from Middle East to East Asia) has been frequently documented in the wild and in captivity. This study attempts to evaluate the genetic consequences of intensive captive breeding and restocking in the A. rufa species. We investigated A. rufa genetic diversity by making comparisons in both a spatial (across the entire species’ range) and a temporal framework. We accomplished this latter by comparing modern vs. ancient partridges resident in museums and collected 1856–1934, well before supplemental stocking became common. Using mtDNA we found significant changes in the haplotype profile of modern vs. ancient A. rufa, and widespread introgression with chukar genes across the entire species range only in modern representatives, with the relevant exception of Corsican populations. However, Random Amplified Polymorphic DNA (RAPD), as opposed to microsatellite DNA markers, showed also modern Corsican populations to harbour many A. rufa × A. chukar hybrids. We conclude that captive breeding programs should make strict use of time-saving and comparatively low cost DNA barcodes to minimize genetic pollution, such as those provided by diagnostic RAPD markers. We also recommend that the active ban on import of exotics and/or hybrids be extended to non-local populations. Altogether this would represent a substantial step forward to preserve A. rufa as well as other game species subjected to similar intensive management.

Historical and modern natural museum collections are storehouses of extraordinary value for scientific research in a wide range of fields. Recent advances in molecular biotechnology (e.g., next generation genomics) have increased the range of collection material employable for DNA-based analyses to unprecedented levels. Nevertheless, the value of museum specimens strictly depends on reliability of data associated with them. We report on investigations of ancient DNA from specimens of smooth-coated otter (Lutrogale perspicillata, Mustelidae), the largest otter species living in Asia, in US and European mammal collections. Mitochondrial DNA Cytochrome-b gene sequencing proved that the studied specimens were not the expected taxon. Indeed, they actually belonged to three different species, namely the Asian small-clawed (Aonyx cinereus), Eurasian (Lutra lutra) and African clawless (Aonyx capensis) otters. This represents the first record of mustelid misidentification from museum collections. Detection of errors can be extremely difficult when based only on collectors’ notes and data. Hence, we warn scientists involved in otter research about potential challenges when dealing with museum specimens. We recommend curators pursue a multidisciplinary approach, including DNA analyses, to accurately catalogue the resources under their management and uphold the value of biodiversity information.