Once widespread in Italy, in the last century the Eurasian otter (Lutra lutra) went to the brink of extinction in this country, only surviving in a few southern river basins. Being included in the Habitats Directive 92/43/EEC, it is mandatory for State Members to monitor its conservation status over time, making cost effective and accurate monitoring protocols a relevant issue. We compared the efficiency of environmental DNA (eDNA) and traditional field survey techniques in detecting the presence of Eurasian otter at the border of the current expansion range of the Eurasian otter in Latium, Central Italy. Water sampling for eDNA detection through species-specific assay and systematic field surveys were run in six river basins. Results from the two approaches were compared at the scale of sampling site, 5 km and 10 km radius upstream. Both techniques agreed in revealing the expansion of Eurasian otter in southern Latium and in confirming otter absence in the northern part of the study area. eDNA allowed to detect otters at two more river catchments compared to field surveys, one of which is located northward in a tributary of the river Tiber, and showed a higher detection rate (0.41), both at sampling site (0.06, p = 0.01), 5 km (0.23) or 10 km radius (0.35) scale. These results suggest that eDNA is a more sensitive method in revealing Eurasian otter presence, providing a useful reference for future standardized monitoring of the species at the country level, especially in expansion areas.

Comparative landscape genetics studies provide insights on the impact of landscape elements on gene flow patterns of different species inhabiting the same geographic area. We investigated the population genetic structure of two sympatric ungulates, roe deer Capreolus capreolus and Northern chamois Rupicapra rupicapra, in a mountain area of the central Italian Alps (Trentino, northern Italy). A total of 122 chamois and 72 roe deer samples were genotyped by two species-specific panels of 11 polymorphic microsatellite loci and analyzed by aspatial and spatially explicit analyses. While the roe deer population resulted unstructured, a clear population structure was detected in chamois, with two main groups, one inhabiting the eastern and the other spread in the western part of the study area. Landscape genetics analysis confirmed these scenarios and revealed a different effect of landscape on gene flow. An IBD (Isolation-By-Distance) model best explained genetic variation in roe deer, while IBR (Isolation-By-Resistance) was found as the process underlying genetic variation patterns in chamois, suggesting arable lands, coniferous forests, watercourses, and main roads as potential barriers. Species distribution and landscape use might explain these results: roe deer mostly occupy valley floors relatively connected to each other, and their spatial behavior may promote gene flow across areas. On the other hand, chamois prefer higher elevations and their movements may be hindered by valleys, rivers, and road networks. This study highlights the different impacts of natural and anthropic landscape elements on gene flow in two sympatric species, resulting from their different ecological requirements.

This comprehensive species-specific chapter covers all aspects of the mammalian biology, including paleontology, physiology, genetics, reproduction and development, ecology, habitat, diet, mortality, and behavior. The economic significance and management of mammals and future challenges for research and conservation are addressed as well. The chapter includes a distribution map, a photograph of the animal, and a list of key literature.

AbstractPatterns of genetic differentiation within and among animal populations might vary due to the simple effect of distance or landscape features hindering gene flow. An assessment of how landscape connectivity affects gene flow can help guide management, especially in fragmented landscapes. Our objective was to analyze population genetic structure and landscape genetics of the native wild boar (Sus scrofa meridionalis) population inhabiting the island of Sardinia (Italy), and test for the existence of Isolation‐by‐Distance (IBD), Isolation‐by‐Barrier (IBB), and Isolation‐by‐Resistance (IBR). A total of 393 Sardinian wild boar samples were analyzed using a set of 16 microsatellite loci. Signals of genetic introgression from introduced non‐native wild boars or from domestic pigs were revealed by a Bayesian cluster analysis including 250 reference individuals belonging to European wild populations and domestic breeds. After removal of introgressed individuals, genetic structure in the population was investigated by different statistical approaches, supporting a partition into five discrete subpopulations, corresponding to five geographic areas on the island: north‐west (NW), central west (CW), south‐west (SW), north‐central east (NCE), and south‐east (SE). To test the IBD, IBB, and IBR hypotheses, we optimized resistance surfaces using genetic algorithms and linear mixed‐effects models with a maximum likelihood population effects parameterization. Landscape genetics analyses revealed that genetic discontinuities between subpopulations can be explained by landscape elements, suggesting that main roads, urban settings, and intensively cultivated areas are hampering gene flow (and thus individual movements) within the Sardinian wild boar population. Our results reveal how human‐transformed landscapes can affect genetic connectivity even in a large‐sized and highly mobile mammal such as the wild boar, and provide crucial information to manage the spread of pathogens, including the African Swine Fever virus, endemic in Sardinia.

Anthropogenic hybridization is recognized as a major threat to the long-term survival of natural populations. While identifying F1 hybrids might be simple, the detection of older admixed individuals is far from trivial and it is still debated whether they should be targets of management. Examples of anthropogenic hybridization have been described between wolves and domestic dogs, with numerous cases detected in the Italian wolf population. After selecting appropriate wild and domestic reference populations, we used empirical and simulated 39-autosomal microsatellite genotypes, Bayesian assignment and performance analyses to develop a workflow to detect different levels of wolf x dog admixture. Membership proportions to the wild cluster (qiw) and performance indexes identified two q-thresholds which allowed to efficiently classify the analysed genotypes into three assignment classes: pure (with no or negligible domestic ancestry), older admixed (with a marginal domestic ancestry) and recent admixed (with a clearly detectable domestic ancestry) animals. Based on their potential to spread domestic variants, such classes were used to define three corresponding management categories: operational pure, introgressed and operational hybrid individuals. Our multiple-criteria approach can help wildlife managers and decision makers in more efficiently targeting the available resources for the long-term conservation of species threatened by anthropogenic hybridization.

Anthropogenic hybridization is widely perceived as a threat to the conservation of biodiversity. Nevertheless, to date, relevant policy and management interventions are unresolved and highly convoluted. While this is due to the inherent complexity of the issue, we hereby hypothesize that a lack of agreement concerning management goals and approaches, within the scientific community, may explain the lack of social awareness on this phenomenon, and the absence of effective pressure on decision-makers. By focusing on wolf x dog hybridization in Europe, we hereby (a) assess the state of the art of issues on wolf x dog hybridization within the scientific community, (b) assess the conceptual bases for different viewpoints, and (c) provide a conceptual framework aiming at reducing the disagreements. We adopted the Delphi technique, involving a three-round iterative survey addressed to a selected sample of experts who published at Web of Science listed journals, in the last 10 years on wolf x dog hybridization and related topics. Consensus was reached that admixed individuals should always be defined according to their genetic profile, and that a reference threshold for admixture (i.e., q-value in assignment tests) should be formally adopted for their identification. To mitigate hybridization, experts agreed on adopting preventive, proactive and, when concerning small and recovering wolf populations, reactive interventions. Overall, experts' consensus waned as the issues addressed became increasingly practical, including the adoption of lethal removal. We suggest three non-mutually exclusive explanations for this trend: (i) value-laden viewpoints increasingly emerge when addressing practical issues, and are particularly diverging between experts with different disciplinary backgrounds (e.g., ecologists, geneticists); (ii) some experts prefer avoiding the risk of potentially giving carte blanche to wolf opponents to (illegally) remove wolves, based on the wolf x dog hybridization issue; (iii) room for subjective interpretation and opinions result from the paucity of data on the effectiveness of different management interventions. These results have management implications and reveal gaps in the knowledge on a wide spectrum of issues related not only to the management of anthropogenic hybridization, but also to the role of ethical values and real-world management concerns in the scientific debate.

Density estimation is a key issue in wildlife management but is particularly challenging and labour-intensive for elusive species. Recently developed approaches based on remotely collected data and capture-recapture models, though representing a valid alternative to more traditional methods, have found little application to species with limited morphological variation. We implemented a camera trap capture-recapture study to survey wolf packs in a 560-km2 area of Central Italy. Individual recognition of focal animals (alpha) in the packs was possible by relying on morphological and behavioural traits and was validated by non-invasive genotyping and inter-observer agreement tests. Two types (Bayesian and likelihood-based) of spatially explicit capture-recapture (SCR) models were fitted on wolf pack capture histories, thus obtaining an estimation of pack density in the area.

Hybridization between domestic and wild species is known to widely occur and it is reported to be one of the major causes of the current biodiversity crisis. Despite this, poor attention has been deserved to the behavioural ecology of hybrids, in particular in relation to their social behaviour. We carried out a camera trap study to assess whether phenotypically anomalous colouration in wild boar, i.e. potentially introgressed with domestic pigs, affected the hierarchical structure of wild boar social groups. Chromatically anomalous wild boars (CAWs) were detected in 32 out of 531 wild boar videos. In most videos (75%) CAWs were the latest of the group, independently from their age class and group composition. Aggressions by their wild type fellows were recorded in 31.25% videos; by contrast, no aggression among wild type individuals was observed. The lack of camouflage may expose CAWs, and thus their group, to a higher predation risk, compared to wild type groups. This individual loss of local adaptation may increase predation risk by the wolf or detection by hunters, being maladaptive for the whole social group.

Motion-activated video cameras and non-invasive genetic sampling are tools commonly used to obtain relevant information on wild populations of rare or elusive carnivores while minimizing disturbance. The two approaches are usually implemented separately, but they are occasionally integrated at a population level, mostly in order to estimate population size. Here we show the advantages of combining camera trapping and non-invasive genotyping at an individual level, in a monitored Italian wolf population affected by introgression from domestic dogs. After 24 defecation events recorded by camera traps located at marking sites, samples ('video-scats') were collected in order to determine the individuals' identity based on the analysis of sex markers, 11 autosomal microsatellites, two Y-chromosome microsatellites and the control region of the mitochondrial DNA. Genetic data for 19 successfully genotyped scat samples were combined with morphological and behavioural traits observed in the videos and compared to data from ongoing genetic monitoring, all of which enabled us to determine sex, pack membership, breeding status, morphological traits (including those used to assess hybridization), sampling history, and introgression level of each individual. Finally we discuss the advantages and possible drawbacks of 'video-scats', supporting their use as an opportunistic source of valuable data.

Y-chromosome markers are important tools for studying male-specific gene flow within and between populations, hybridization patterns and kinship. However, their use in non-human mammals is often hampered by the lack of Y-specific polymorphic markers. We identified new male-specific short tandem repeats (STRs) in Sus scrofa using the available genome sequence. We selected four polymorphic loci (5-10 alleles per locus), falling in one duplicated and two single-copy regions. A total of 32 haplotypes were found by screening 211 individuals from eight wild boar populations across Europe and five domestic pig populations. European wild boar were characterized by significantly higher levels of haplotype diversity compared to European domestic pigs (HD  = 0.904 ± 0.011 and HD  = 0.491 ± 0.077 respectively). Relationships among STR haplotypes were investigated by combining them with single nucleotide polymorphisms at two linked genes (AMELY and UTY) in a network analysis. A differentiation between wild and domestic populations was observed (FST  = 0.229), with commercial breeds sharing no Y haplotype with the sampled wild boar. Similarly, a certain degree of geographic differentiation was observed across Europe, with a number of local private haplotypes and high diversity in northern populations. The described Y-chromosome markers can be useful to track male inheritance and gene flow in wild and domestic populations, promising to provide insights into evolutionary and population genetics in Sus scrofa.

Domestication promotes the emergence of novel phenotypic and behavioural traits in domesticated animals compared to their wild ancestors. We analysed variation at the melanocortin receptor I ( MC1R ) and nuclear receptor subfamily 6, group A, member 1 ( NR6A1 ) genes in European wild boar populations, two loci which have been under strong artificial selection during domestication. These loci influence coat colour and number of vertebrae, respectively. A total of 145 wild boars were sampled throughout Europe, to evaluate frequency and spatial distribution of domestic alleles and patterns of hybridization between wild and domestic forms. Most of the wild boars (94%) were homozygous for the European wild-type (E + ) MC1R allele. We did not observe any synonymous substitution in the European E + allele, confirming its monomorphism even in areas known to be hotspots of wild boar genetic diversity. The remaining wild boars (6%) showed genetic introgression of three different European domestic alleles. No Asian MC1R allele was found in our sample. Furthermore, domestic NR6A1 alleles were observed in 6% of wild boars. Considering jointly the two loci analyzed, 11% of boars, sampled all over Europe, showed signs of recent or past introgression in their genome. These data agree with previous investigations on other molecular markers, confirming that, compared to Asian conspecifics, European wild boars have a relatively low genetic diversity, which is locally increased by the introgression of allelic variants from the domestic counterpart.

Hybridization between wolves (Canis lupus) and domestic dogs (Canis familiaris) can represent a threat to wild populations via genetic introgression and ecological competition. Therefore understanding the ecological role of hybrids may be crucial for developing appropriate conservation strategies. The Italian wolf population has a peculiar genetic composition due to a long-lasting geographic isolation. Nowadays, however, its genetic integrity is threatened by the spread of canine genes as a result of the hybridization with stray dogs in the wild. The aim of the present study was to gain insights into the ecological role of free-ranging wolf–dog hybrids by investigating their winter food habits in comparison with wolves in a mountain area of Central Italy. Levels of genetic introgression from the dogs were assessed in two adjacent areas occupied by up to five different packs by analyzing non-invasive samples and carcasses collected therein with a set of uniparental and bi-parental molecular markers. The obtained results enabled us to classify the two areas as ‘hybrid’ and ‘wolf’ areas based on their level of genetic introgression. Trophic niche and similarity/dissimilarity analyses did not detect significant difference in the diet between the two areas: in both of them, wild boar was the main prey, followed by roe deer. Furthermore, the same age/body mass classes of the two ungulates were selected by wolves and hybrids. Our findings confirmed wolf–dog hybrids as potential competitors for wolves. Further studies on other aspects of their biology and ecology are recommended in order to better estimate the impact of hybridization on natural wolf populations.

Reproductive synchrony among gregarious mammals has a strong adaptive value and may lead to cooperative behaviors aimed at maximizing offspring survival. Additionally, temporal clustering of estrus has important implications on individual mating tactics and ultimately affects the degree of polygamy in a population. Although several studies have examined the reproductive biology of wild boar (Sus scrofa), much remains to be understood about the patterns of timing and synchrony of reproduction in natural populations. We analyzed the spatiotemporal distribution of conception dates in an Italian wild boar population taking into account the effects of environmental and individual factors, in order to determine the main variables influencing the timing of reproduction and to detect the signs of a socially-driven reproductive synchrony. Specifically, for each litter belonging to 354 pregnant sows culled between 2006 and 2013 in a mountain area of Tuscany, we determined the conception date (CD) from an estimate of the mean fetal age and the culling date. We then investigated which factors drove the variation in CD, by implementing linear mixed models, Mantel tests and spatial autocorrelation analyses. The selected model showed significant effects of rainfall, temperatures, and previous and current productivity on CD, as well as a strong correlation of CDs mong sows culled in close spatial and temporal proximity (i.e., in the same hunting ground and a hunting season). Likewise, autocorrelation analyses and Mantel tests consistently indicated that closer sows had similar conception dates. Overall, our results confirm the effect of resource availability and climate on wild boar reproductive phenology, and suggest socially-driven reproductive patterns, in spite of a high turn-over in social groups due to hunting. Finally, possible advantages and evolutionary implications of reproductive synchrony in wild boar are discussed.

Hybridization between wild boar (Sus scrofa) and domestic pig occurred in the past and still occurs today, having great evolutionary and management implications. In fact, genetic introgression from the domestic form may alter traits like behavior, reproduction rate, and immunology in wild populations, with likely demographic impacts. Thus, it is crucial to understand under what conditions hybridization occurs in S. scrofa. Captive crosses with domestic pigs (released or escaped) have been suggested to constitute the major source of the spread of domestic genes into wild boar populations. However, to date, few studies have assessed the degree of admixture in farmed animals in comparison to the surrounding wild populations. With this purpose, we analyzed microsatellite loci in wild boar sampled in breeding stations and in the local wild population in two Italian regions (Sardinia and Piedmont). Both captive populations had lower allelic richness than the corresponding wild population, but a similar expected heterozygosity. In Piedmont, introgression from the domestic form into the wild population seems to be extremely low, while there are significant signs of admixture in the sampled breeding stations. In Sardinia, instead, the captive sample did not differ significantly from the wild population, which showed moderate signs of introgression. We conclude that hybridization in nature seems to play the key role in Sardinia, while intentional hybridization in captivity is the major source of introgression in Piedmont. Our findings emphasize the need for a routine genetic monitoring of wild boar captive populations, coupled with reference data on the neighboring wild populations.

In many areas, the management of overexploited populations of brown hare (Lepus europaeus) is based on annual restocking. While in some cases exotic hares are introduced, in some others hares are captured locally within protected areas and subsequently released into hunting grounds. We evaluated the genetic effects of this management regime in an Italian province where the brown hare population has recovered in the last few decades, by sequencing the hypervariable domain 1 of the mitochondrial control region and by genotyping eight autosomal microsatellites in hares sampled in both hunting and non-hunting areas. Both nuclear (H e = 0.68 and H o = 0.65) and mitochondrial variability (h = 0.853 and π = 0.012) were in line with other European populations. When comparing our data with mitochondrial sequences retrieved from GenBank, out of the 21 detected haplotypes, 14 were private to our study area. While 4.6 % of the individuals were found to carry haplotypes attributable to past introductions, 41.5 % grouped within a well-supported lineage, previously identified with a presumed native Italian taxon, L. e. meridiei. Despite the detectable geographic partitioning of mitochondrial haplotypes across the province, no genetic structure resulted from microsatellites analysis, indicating that no reproductive barriers exist among hares carrying different mitochondrial lineages. In conclusion, the local management seems to have contributed to the recovery of the species and to a full admixture of nuclear genes in the province. However, neither the extensive translocations nor the possible introductions of exotic heads seem to have completely undermined the local mitochondrial lineages.

Amphibians have emerged as a major conservation concern because of the global decline in their numbers in recent decades. Notwithstanding, they are often neglected in conservation planning respects to other less threatened vertebrate groups. In Italy, few studies have analyzed the effectiveness of amphibian protection regimes. The main aim of this paper is to estimate the contribution of the WWF oases network to amphibians conservation in Italy. Moreover, we conducted a prioritization of this network and we individuated additional areas that should be protected for implementing an oases role. We assembled the largest and most up-to-date dataset available for amphibians in the WWF oases, and we adopted a spatial approach based on gap and irreplaceability analyses. Our results provide a critical assessment of the oases importance for amphibians conservation. Many species that are completely uncovered by oases protection have been identified, and new areas suitable for filling the conservation gap have been recognized. We recommend designation of new reserves in these areas to help guarantee amphibian conservation. Moreover, we identified those oases that ensure the representation of the largest number of species. In this light, Monte Arcosu appeared to be the most important site for the achievement of the current degree of species representation. Together with six other oases that obtained high irreplaceability scores, Monte Arcosu represents a priority for the preservation of amphibian diversity. Specific initiatives should be primarily implemented in these oases, guaranteeing that highly irreplaceable sites will maintain their crucial role in the future.

Hares (Lepus capensis Linnaeus 1758) were probably introduced into Sardinia in historical times. Previous studies indicated North Africa as the most likely source area but did not exclude the occurrence of hybridization events with continental brown hares (L.similar to europaeus Pallas 1778) perhaps introduced for hunting purposes. We implemented both morphometric and genetic approaches to verify the genetic isolation of the Sardinian population. Specifically, we conducted a multivariate analysis of craniometric data and analysed 461 bp of the mitochondrial control region and 12 autosomal microsatellites in Sardinian hares, using North African cape hares and European brown hares as reference populations. Sardinian hares displayed a peculiar skull shape. In agreement, both nuclear and mitochondrial markers remarked the distinctiveness of this population. Observed and expected heterozygosity were 0.52 and 0.61, while haplotype and nucleotide diversity were 0.822 and 0.0129. Self-assignment based on Bayesian cluster analysis was high (average membership 0.98), and no evident signs of introgression from continental brown hares were found. Our results support the hypothesis that the Sardinian hares have been introduced from North Africa, remained genetically isolated since the founding event and evolved independently from the source population. This long-lasting isolation and the consequent genetic drift resulted in a differentiation, perhaps accompanied by an adaptation to local environmental conditions.

Although recent evidence of the species recovery has been reported for many European countries, in Italy the Eurasian otter Lutra lutra is still considered endangered. Otter populations are confined to few river basins in the southern part of the peninsula and these are both geographically and genetically isolated from other European populations. This critical situation led the Italian Ministry of Environment to promote the production of an Action Plan for the otter in Italy, whose methods, aims and actions are briefly summarized.