Strong spatial segregation between wildcats and domestic cats may explain low hybridization rates on the Iberian Peninsula

Genetic swamping of the critically endangered Scottish wildcat was recent and accelerated by disease

The European wildcat population in Scotland is considered critically endangered as a result of hybridization with introduced domestic cats,1,2 though the time frame over which this gene flow has taken place is unknown. Here, using genome data from modern, museum, and ancient samples, we reconstructed the trajectory and dated the decline of the local wildcat population from viable to severely hybridized. We demonstrate that although domestic cats have been present in Britain for over 2,000 years,3 the onset of hybridization was only within the last 70 years. Our analyses reveal that the domestic ancestry present in modern wildcats is markedly over-represented in many parts of the genome, including the major histocompatibility complex (MHC). We hypothesize that introgression provides wildcats with protection against diseases harbored and introduced by domestic cats, and that this selection contributes to maladaptive genetic swamping through linkage drag. Using the case of the Scottish wildcat, we demonstrate the importance of local ancestry estimates to both understand the impacts of hybridization in wild populations and support conservation efforts to mitigate the consequences of anthropogenic and environmental change.

Applications of non-intrusive methods to study the sand cat: a field study in the Sahara Desert

Surveys based on indirect signs and camera trapping are two non-invasive methods extensively used for monitoring elusive mammals. Both approaches can be useful to obtain key information on wildlife in remote areas, since they may allow for the logistically viable design of optimal field frameworks. The sand cat (Felis margarita) is a feline that inhabits the Sahara Desert, the Arabian Peninsula, and western Asian deserts. Its basic ecology is poorly known and the status and impacts of threats are difficult to assess. Some local population declines have been detected, and more research is needed. Based on field surveys carried out in the Atlantic Sahara, we have evaluated the applications of both methods to study this species. Our results show that (a) camera trapping provided reliable data on several key aspects of its ecology, (b) walking surveys to collect feces for molecular data failed completely, and (c) for footprints, identification problems and the marked effects of the absence of optimal substrates and the prevalence of wind are relevant handicaps. Beyond this evaluation, we provide for the first time some key aspects of the ecology of sand cats in the Sahara Desert, including habitat selection, density, diel activity, and predator–prey relationships.

Human impact on the recent population history of the elusive European wildcat inferred from whole genome data

BACKGROUND

The extent and impact of evolutionary change occurring in natural populations in response to rapid anthropogenic impact is still poorly understood on the genome-wide level. Here, we explore the genetic structure, demographic history, population differentiation, and domestic introgression based on whole genome data of the endangered European wildcat in Germany, to assess potential genomic consequences of the species' recent spread across human-dominated cultural landscapes.

RESULTS

Reconstruction of demographic history and introgression rates based on 47 wildcat and 37 domestic cat genomes suggested late introgression between wild and domestic cat, coinciding with the introduction of domestic cat during the Roman period, but overall relatively low rates of hybridization and introgression from domestic cats. Main population divergence found between an eastern and central German wildcat clade was found to be of rather recent origin (200 y), and thus the likely consequence of anthropogenic persecution and resulting isolation in population refugia. We found similar effective population sizes and no substantial inbreeding across populations. Interestingly, highly differentiated genes between wild cat populations involved in the tryptophan-kynurenine-serotonin pathway were revealed, which plays a role in behavioral processes such as stress susceptibility and tolerance, suggesting that differential selection acted in the populations.

CONCLUSIONS

We found strong evidence for substantial recent anthropogenic impact on the genetic structure of European wildcats, including recent persecution-driven population divergence, as well as potential adaptation to human-dominate environments. In contrast, the relatively low levels of domestic introgression and inbreeding found in this study indicate a substantial level of "resistance" of this elusive species towards major anthropogenic impacts, such as the omnipresence of domestic cats as well as substantial habitat fragmentation. While those findings have strong implications for ongoing conservation strategies, we demand closer inspection of selective pressures acting on this and other wildlife species in anthropogenic environments.

Human and environmental factors driving Toxoplasma gondii prevalence in wild boar (Sus scrofa)

As one of the most relevant foodborne diseases, it is essential to know the factors related to the transmission, persistence and prevalence of Toxoplasma gondii infection. Eurasian wild boar (Sus scrofa) might play a relevant role in T.gondii's life cycle. This species is the most consumed big game animal in Spain and may act as a source of infection if the meat is eaten raw or undercooked or due to cross-contaminations. Additionally, wild boar can act as an excellent bioindicator of T.gondii circulation in the ecosystem, because its natural behaviour leads to exposure to oocysts from the soil when rooting and tissular bradyzoites when scavenging. A total of 1003 wild boar were sampled from 2010 to 2017 in Mediterranean Spain. Blood samples were tested with an indirect ELISA test giving a total of 14.1% (95% confidence interval 12.0-16.4%) positive results. The prevalence was not homogeneous in neither the animals nor the sampled districts. Significant differences were found regarding age, climatic conditions and human space occupancy. Human population aggregation, assessed by Demangeon's index, was identified as an influential factor in T.gondii infection risk. This multiple approach allows us to evaluate local risks for human and environmental contamination.

Abundance and use pattern of wildcats of ancient human-modified cattle pastures in northern Iberian Peninsula

The wildcat is typically found in low densities. Here, we estimated wildcat abundance in cattle pastures interspersed between forests in northern Iberian Peninsula, and their patterns of intra-annual and daily use. We censused wildcats three times daily (morning, afternoon, and night) from a car during 4 years in summer season. We also carried out four monthly tracks (two in the morning and two in the afternoon) for a complete year. Overall, we recorded 191 wildcats in pastures and 5 on the road in forest zones. Thirteen different individual wildcats were identified during the summer censuses, but only 29.9% of the wildcats observed (n = 196) could be assigned to an individual wildcat. The number of wildcats sighted decreased especially during the last year, when sightings were 52–67% lower than in previous years. Wildcats were seen significantly more during the morning and night censuses than during the afternoon ones. Estimated annual summer densities in pasture areas ranged between 0.11 and 0.46 sightings/km2. Throughout the year, wildcats were observed 5.9 times more during summer-autumn than during winter-spring, and they could be observed in any time of the day, but more often close to dusk. It is noteworthy that the ancient human-transformed landscapes for cattle pastures could be an important habitat for wildcats in northern Iberian Peninsula, and conserving these areas should be important to maintaining wildcat populations.

Projecting introgression from domestic cats into European wildcats in the Swiss Jura

Hybridization between wild and domesticated organisms is a worldwide conservation issue. In the Jura Mountains, threatened European wildcats (Felis silvestris) have been demographically spreading for approximately the last 50 years, but this recovery is coupled with hybridization with domestic cats (Felis catus). Here, we project the pattern of future introgression using different spatially explicit scenarios to model the interactions between the two species, including competition and different population sizes. We project the fast introgression of domestic cat genes into the wildcat population under all scenarios if hybridization is not severely restricted. If the current hybridization rate and population sizes remain unchanged, we expect the loss of genetic distinctiveness between wild and domestic cats at neutral nuclear, mitochondrial and Y chromosome markers in one hundred years. However, scenarios involving a competitive advantage for wildcats and a future increase in the wildcat population size project a slower increase in introgression. We recommend that future studies assess the fitness of these hybrids and better characterize their ecological niche and their ecological interactions with parental species to elucidate effective conservation measures.

Spatial Segregation between Red Foxes (Vulpes vulpes), European Wildcats (Felis silvestris) and Domestic Cats (Felis catus) in Pastures in a Livestock Area of Northern Spain

Red foxes, European wildcats and domestic cats share cattle pastures for hunting in La Pernía Valley, northern Spain. To understand the mechanisms that allow the coexistence of these mesopredators in a habitat characterized by its anthropogenic modifications, we recorded sightings of these species in pastures in the summers of 2016, 2017, 2018 and 2019. We tested if the species preferred specific areas of pastures and if they exhibited any spatial segregation in the use of pastures. Red foxes did not show consistent preferences for any area of the pastures. European wildcats preferred pasture areas closer to streams and forest edges, whereas domestic cats preferred areas closer to buildings and paved roads whilst avoiding forest edges. All species pairs showed strong spatial segregation with less than 7% overlap. We hypothesize that spatial segregation is the mechanism used by European wildcats and domestic cats to avoid dangerous interactions with other predators and which characterizes their preference of specific areas on pastures, using areas near places that may protect them from other predators. Ultimately, the influence of fox presence (and probably that of other larger potential predators) on the use of pastures by European wildcats and domestic cats is decreasing the number of interactions between them and may help to prevent hybridization in this area.

Fragmentation and low density as major conservation challenges for the southernmost populations of the European wildcat

Knowledge of population dynamics of threatened species in the wild is key to effective conservation actions. However, at present, there are many examples of endangered animals for which their current situation is unknown, and not just in remote areas and less developed countries. We have explored this topic by studying the paradigmatic case of the European wildcat (Felis silvestris silvestris), an endangered small carnivore whose status has been subjectively established on the basis of non-systematic approaches and opportunistic records. Little is known about its demographic situation, prompting the need for information to improve conservation measures. However, the secretive behaviour of felines along with its low density in natural conditions have prevented the gathering of sufficient data. We developed a field sampling strategy for one of the largest populations (Andalusia, South Spain, 87,268 km2), based on a logistically viable systematic non-intrusive survey by camera-trapping. This study offers the first large-scale estimation for any European wildcat population, based on analytical approaches applied on Species Distribution Models. A hierarchical approach based on a Maxent model for distribution estimation was used, along with Generalised Linear Models for density estimation from explicit spatial capture-recapture data. Our results show that the distribution range is smaller and more highly fragmented than previously assumed. The overall estimated density was very low (0.069 ±0.0019 wildcats/km2) and the protected areas network seems to be insufficient to cover a significant part of the population or a viable nucleus in demographic terms. Indeed, the most important areas remain unprotected. Our main recommendations are to improve the protected area network and/or vigilance programs in hunting estates, in addition to studying and improving connectivity between the main population patches.

Range-wide patterns of human-mediated hybridisation in European wildcats

Hybridisation between wild taxa and their domestic congeners is a significant conservation issue. Domestic species frequently outnumber their wild relatives in population size and distribution and may therefore genetically swamp the native species. The European wildcat (Felis silvestris) has been shown to hybridise with domestic cats (Felis catus). Previously suggested spatially divergent introgression levels have not been confirmed on a European scale due to significant differences in the applied methods to assess hybridisation of the European wildcat. We analysed 926 Felis spp. samples from 13 European countries, using a set of 86 selected ancestry-informative SNPs, 14 microsatellites, and ten mitochondrial and Y-chromosome markers to study regional hybridisation and introgression patterns and population differentiation. We detected 51 hybrids (four F1 and 47 F2 or backcrosses) and 521 pure wildcats throughout Europe. The abundance of hybrids varied considerably among studied populations. All samples from Scotland were identified as F2 hybrids or backcrosses, supporting previous findings that the genetic integrity of that wildcat population has been seriously compromised. In other European populations, low to moderate levels of hybridisation were found, with the lowest levels being in Central and Southeast Europe. The occurrence of distinct maternal and paternal markers between wildcat and domestic cat suggests that there were no severe hybridisation episodes in the past. The overall low (< 1%) prevalence of F1 hybrids suggests a low risk of hybridisation for the long-term genetic integrity of the wildcat in most of Europe. However, regionally elevated introgression rates confirm that hybridisation poses a potential threat. We propose regional in-depth monitoring of hybridisation rates to identify factors driving hybridisation so as to develop effective strategies for conservation.

Hybridization between Felis silvestris silvestris and Felis silvestris catus in two contrasted environments in France

European wildcat (Felis silvestris silvestris) populations are fragmented throughout most of the whole range of the subspecies and may be threatened by hybridization with the domestic cat F.s. catus. The underlying ecological processes promoting hybridization remain largely unknown. In France, wildcats are mainly present in the northeast and signs of their presence in the Pyrenees have been recently provided. However, no studies have been carried out in the French Pyrenees to assess their exposure to hybridization. We compared two local populations of wildcats, one living in a continuous forest habitat in the French Pyrenees, the other living in a highly fragmented forest-agricultural landscape in northeastern France to get insights into the variability of hybridization rates. Strong evidence of hybridization was detected in northeastern France and not in the Pyrenees. Close kin in the Pyrenees were not found in the same geographic location contrary to what was previously reported for females in the northeastern wildcat population. The two wildcat populations were significantly differentiated (F ST = 0.072) to an extent close to what has been reported (F ST = 0.103) between the Iberian population, from which the Pyrenean population may originate, and the German population, which is connected to the northeastern population. The genetic diversity of the Pyrenean wildcats was lower than that of northeastern wildcat populations in France and in other parts of Europe. The lower hybridization in the Pyrenees may result from the continuity of natural forest habitats. Further investigations should focus on linking landscape features to hybridization rates working on local populations.

Assessing Risks to Wildlife from Free-Roaming Hybrid Cats: The Proposed Introduction of Pet Savannah Cats to Australia as a Case Study

Simple Summary

The domestic cat, Felis catus, is often cross-bred with other species in the cat family to produce hybrid or ‘designer’ cats that are sought by people as pets. However, hybrid cats are often surrendered to wildlife shelters, or released, which leads to concern that they may establish free-roaming populations and damage native wildlife. In 2008, the Australian government rejected an application, on precautionary grounds, to import savannah cats (hybrids of the domestic cat and serval Leptailurus serval) into the country. We review the limited information informing this decision and then present a framework that identifies the native mammal species likely to have been most at risk of predation from savannah cats if importation and establishment had occurred. Assuming that savannah cats hunt similar prey to those that are hunted by both parent species, we estimate that 91% of Australia’s extant terrestrial mammal fauna would likely face some risk of predation from savannah cats, including 93% of non-volant mammal species that have threatened conservation status. The framework results strongly validate the decision to ban savannah cats from Australia. We suggest that our framework approach could be adapted to assess the likely risks that are posed by the arrival of other hybrid cats or hybrids of other animals.

Abstract

Hybrid cats—created by crossing different species within the family Felidae—are popular pets, but they could potentially threaten native species if they escape and establish free-roaming populations. To forestall this possibility, the Australian government imposed a specific ban on importation of the savannah cat, a hybrid created by crossing the domestic cat Felis catus and serval Leptailurus serval, in 2008. We develop a decision–framework that identifies those species of non-volant native mammals in Australia that would likely have been susceptible to predation by savannah cats if importation and establishment had occurred. We assumed that savannah cats would hunt ecologically similar prey to those that are depredated by both the domestic cat and the serval, and categorised native mammals as having different levels of susceptibility to predation by savannah cats based on their size, habitat range, and behaviour. Using this framework, we assessed savannah cats as likely to add at least 28 extant native mammal species to the 168 that are known already to be susceptible to predation by the domestic cat, posing a risk to 91% of Australia’s extant non-volant terrestrial mammal species (n = 216) and to 93% of threatened mammal species. The framework could be generalised to assess risks from any other hybrid taxa.

Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations

The survival of indigenous European wildcat (Felis silvestris silvestris) populations can be locally threatened by introgressive hybridization with free-ranging domestic cats. Identifying pure wildcats and investigating the ancestry of admixed individuals becomes thus a conservation priority. We analyzed 63k cat Single Nucleotide Polymorphisms (SNPs) with multivariate, Bayesian and gene-search tools to better evaluate admixture levels between domestic and wild cats collected in Europe, timing and ancestry proportions of their hybrids and backcrosses, and track the origin (wild or domestic) of the genomic blocks carried by admixed cats, also looking for possible deviations from neutrality in their inheritance patterns. Small domestic ancestry blocks were detected in the genomes of most admixed cats, which likely originated from hybridization events occurring from 6 to 22 generations in the past. We identified about 1,900 outlier coding genes with excess of wild or domestic ancestry compared to random expectations in the admixed individuals. More than 600 outlier genes were significantly enriched for Gene Ontology (GO) categories mainly related to social behavior, functional and metabolic adaptive processes (wild-like genes), involved in cognition and neural crest development (domestic-like genes), or associated with immune system functions and lipid metabolism (parental-like genes). These kinds of genomic ancestry analyses could be reliably applied to unravel the admixture dynamics in European wildcats, as well as in other hybridizing populations, in order to design more efficient conservation plans.

Females know better: Sex-biased habitat selection by the European wildcat

The interactions between animals and their environment vary across species, regions, but also with gender. Sex-specific relations between individuals and the ecosystem may entail different behavioral choices and be expressed through different patterns of habitat use. Regardless, only rarely sex-specific traits are addressed in ecological modeling approaches. The European wildcat (Felis silvestris silvestris) is a species of conservation concern in Europe, with a highly fragmented and declining distribution across most of its range. We assessed sex-specific habitat selection patterns for the European wildcat, at the landscape and home range levels, across its Iberian biogeographic distribution using a multipopulation approach. We developed resource selection functions in a use-availability framework using radio-telemetry data from five wildcat populations. At the landscape level, we observed that, while both genders preferentially established home ranges in areas close to broadleaf forests and far from humanized areas, females selected mid-range elevation areas with some topographic complexity, whereas males used lowland areas. At the home range level, both females and males selected areas dominated by scrublands or broadleaf forests, but habitat features were less important at this level. The strength of association to habitat features was higher for females at both spatial levels, suggesting a tendency to select habitats with higher quality that can grant them enhanced access to shelter and feeding resources. Based on our results, we hypothesize that sex-biased behavioral patterns may contribute to the resilience of wildcats' genetic integrity through influencing the directionality of hybridization with domestic cats. Our study provides information about European wildcats' habitat use in an Iberian context, relevant for the implementation of conservation plans, and highlights the ecological relevance of considering sex-related differences in environmental preferences.

Low rates of hybridization between European wildcats and domestic cats in a human-dominated landscape

Hybridization between wild species and their domestic congeners is considered a major threat for wildlife conservation. Genetic integrity of the European wildcat, for instance, is a concern as they are outnumbered by domestic cats by several orders of magnitude throughout its range. We genotyped 1,071 individual wildcat samples obtained from hair traps and roadkills collected across the highly fragmented forests of western Central Europe, in Germany and Luxembourg, to assess domestic cat introgression in wildcats in human-dominated landscapes. Analyses using a panel of 75 autosomal SNPs suggested a low hybridization rate, with 3.5% of wildcat individuals being categorized as F1, F2, or backcrosses to either parental taxon. We report that results based on a set of SNPs were more consistent than on a set of 14 microsatellite markers, showed higher accuracy to detect hybrids and their class in simulation analyses, and were less affected by underlying population structure. Our results strongly suggest that very high hybridization rates previously reported for Central Europe may be partly due to inadequate choice of markers and/or sampling design. Our study documents that an adequately selected SNP panel for hybrid detection may be used as an alternative to commonly applied microsatellite markers, including studies relying on noninvasively collected samples. In addition, our finding of overall low hybridization rates in Central European wildcats provides an example of successful wildlife coexistence in human-dominated, fragmented landscapes.

Widespread introgression of mountain hare genes into Fennoscandian brown hare populations

In Fennoscandia, mountain hare (Lepus timidus) and brown hare (Lepus europaeus) hybridize and produce fertile offspring, resulting in gene flow across the species barrier. Analyses of maternally inherited mitochondrial DNA (mtDNA) show that introgression occur frequently, but unavailability of appropriate nuclear DNA markers has made it difficult to evaluate the scale- and significance for the species. The extent of introgression has become important as the brown hare is continuously expanding its range northward, at the apparent expense of the mountain hare, raising concerns about possible competition. We report here, based on analysis of 6833 SNP markers, that the introgression is highly asymmetrical in the direction of gene flow from mountain hare to brown hare, and that the levels of nuclear gene introgression are independent of mtDNA introgression. While it is possible that brown hares obtain locally adapted alleles from the resident mountain hares, the low levels of mountain hare alleles among allopatric brown hares suggest that hybridization is driven by stochastic processes. Interspecific geneflow with the brown hare is unlikely to have major impacts on mountain hare in Fennoscandia, but direct competition may.