A genetic linkage map of microsatellites in the domestic cat (Felis catus)

A multidisciplinary approach to analyze the antimicrobial resistance in natural ecosystems

Antimicrobial Resistance (AMR) poses a global threat to both human health and environmental well-being. Our study delved into Costa Rican wildlife reserves, uncovering a substantial human impact on these ecosystems and underscoring the imperative to pinpoint AMR hotspots. Embracing a One Health perspective, we advocated for a comprehensive landscape analysis that intricately intertwined geographic, climatic, forest, and human factors. This study illuminated the link between laboratory results and observed patterns of antimicrobial use, thereby paving the way for sustainable solutions. Our innovative methodology involved deploying open-ended questions to explore antimicrobial usage across livestock activities, contributing to establishing a comprehensive methodology. Non-invasive sampling in wildlife emerged as a critical aspect, shedding light on areas contaminated by AMR. Feline species, positioned at the apex of the food chain, acted as sentinels for environmental health due to heightened exposure to improperly disposed waste. Regarding laboratory findings, each sample revealed the presence of at least one antimicrobial resistance gene (ARG). Notably, genes encoding resistance to tetracyclines dominated (94.9%), followed by beta-lactams (75.6%), sulfonamides (53.8%), aminoglycosides (51.3%), quinolones (44.9%), phenicols (25.6%), and macrolides (20.5%). Genes encoding polymyxins were not detected. Moreover, 66% of samples carried a multi-resistant microbiome, with 15% exhibiting resistance to three antimicrobial families and 51% to four. The absence of a correlation between forest coverage and ARG presence underscored the profound human impact on wildlife reserves, surpassing previous estimations. This environmental pressure could potentially modify microbiomes and resistomes in unknown ways. As not all antimicrobial families encoding ARGs were utilized by farmers, our next step involved evaluating other human activities to identify the primary sources of contamination. This comprehensive study contributed crucial insights into the intricate dynamics of AMR in natural ecosystems, paving the way for targeted interventions and sustainable coexistence.

Can genetic rescue help save Arabia's last big cat?

Genetic diversity underpins evolutionary potential that is essential for the long-term viability of wildlife populations. Captive populations harbor genetic diversity potentially lost in the wild, which could be valuable for release programs and genetic rescue. The Critically Endangered Arabian leopard (Panthera pardus nimr) has disappeared from most of its former range across the Arabian Peninsula, with fewer than 120 individuals left in the wild, and an additional 64 leopards in captivity. We (i) examine genetic diversity in the wild and captive populations to identify global patterns of genetic diversity and structure; (ii) estimate the size of the remaining leopard population across the Dhofar mountains of Oman using spatially explicit capture-recapture models on DNA and camera trap data, and (iii) explore the impact of genetic rescue using three complementary computer modeling approaches. We estimated a population size of 51 (95% CI 32-79) in the Dhofar mountains and found that 8 out of 25 microsatellite alleles present in eight loci in captive leopards were undetected in the wild. This includes two alleles present only in captive founders known to have been wild-sourced from Yemen, which suggests that this captive population represents an important source for genetic rescue. We then assessed the benefits of reintroducing novel genetic diversity into the wild population as well as the risks of elevating the genetic load through the release of captive-bred individuals. Simulations indicate that genetic rescue can improve the long-term viability of the wild population by reducing its genetic load and realized load. The model also suggests that the genetic load has been partly purged in the captive population, potentially making it a valuable source population for genetic rescue. However, the greater loss of its genetic diversity could exacerbate genomic erosion of the wild population during a rescue program, and these risks and benefits should be carefully evaluated. An important next step in the recovery of the Arabian leopard is to empirically validate these conclusions, implement and monitor a genomics-informed management plan, and optimize a strategy for genetic rescue as a tool to recover Arabia's last big cat.

Ancestry dynamics and trait selection in a designer cat breed

The Bengal cat breed was developed from intercrosses between the Asian leopard cat, Prionailurus bengalensis, and the domestic cat, Felis catus, with a last common ancestor approximately 6 million years ago. Predicted to derive ∼94% of their genome from domestic cats, regions of the leopard cat genome are thought to account for the unique pelage traits and ornate color patterns of the Bengal breed, which are similar to those of ocelots and jaguars. We explore ancestry distribution and selection signatures in the Bengal breed by using reduced representation and whole-genome sequencing from 947 cats. The mean proportion of leopard cat DNA in the Bengal breed is 3.48%, lower than predicted from breed history, and is broadly distributed, covering 93% of the Bengal genome. Overall, leopard cat introgressions do not show strong signatures of selection across the Bengal breed. However, two popular color traits in Bengal cats, charcoal and pheomelanin intensity, are explained by selection of leopard cat genes whose expression is reduced in a domestic cat background, consistent with genetic incompatibility resulting from hybridization. We characterize several selective sweeps in the Bengal genome that harbor candidate genes for pelage and color pattern and that are associated with domestic, rather than leopard, cat haplotypes. We identify the molecular and phenotypic basis of one selective sweep as reduced expression of the Fgfr2 gene, which underlies glitter, a trait desired by breeders that affects hair texture and light reflectivity.

A method for noninvasive individual genotyping of black-footed cat (Felis nigripes)

The black-footed cat (Felis nigripes) is endemic to the arid regions of southern Africa. One of the world's smallest wild felids, the species occurs at low densities and is secretive and elusive, which makes ecological studies difficult. Genetic data could provide key information such as estimates on population size, sex ratios, and genetic diversity. In this study, we test if microsatellite loci can be successfully amplified from scat samples that could be noninvasively collected from the field. Using 21 blood and scat samples collected from the same individuals, we statistically tested whether nine microsatellites previously designed for use in domestic cats can be used to identify individual black-footed cats. Genotypes recovered from blood and scat samples were compared to assess loss of heterozygosity, allele dropout, and false alleles resulting from DNA degradation or PCR inhibitors present in scat samples. The microsatellite markers were also used to identify individuals from scats collected in the field that were not linked to any blood samples. All nine microsatellites used in this study were amplified successfully and were polymorphic. Microsatellite loci were found to have sufficient discriminatory power to distinguish individuals and identify clones. In conclusion, these molecular markers can be used to monitor populations of wild black-footed cats noninvasively. The genetic data will be able to contribute important information that may be used to guide future conservation initiatives.

Generation of Fel d 1 chain 2 genome-edited cats by CRISPR-Cas9 system

Allergens from domestic cats (Felis catus) cause allergy-related health problems worldwide. Fel d 1 is a major allergen that causes severe allergic reactions in humans, including rhinitis, conjunctivitis, and life-threatening asthma. Therefore, patients with cat allergies anticipate hypoallergenic cats. We successfully generated Fel d 1 chain 2 (CH2) genome-edited cats using the CRISPR-Cas9 system in this study. T7 endonuclease 1 assay and Sanger sequencing were used to confirm the mutation in CH2 genome-edited cats. Fel d 1 level in CH2 genome-edited cats were assessed by enzyme-linked immunosorbent assay (ELISA). Remarkably, ELISA showed that the level of Fel d 1 in the CH2 homozygous genome-edited cat (Name: Alsik) was extremely low compared with that in wild type domestic cats and could be hypoallergenic cats. Additionally, we successfully cloned the CH2 homozygous genome-edited cat using cytoplasm injection clone technology. The cloned CH2 homozygous genome-edited cat was verified using microsatellite analysis. Creating hypoallergenic cats using the CRISPR-Cas9 system is a significant step forward because these cats can safely approach allergic patients.

Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution

The role of structurally dynamic genomic regions in speciation is poorly understood due to challenges inherent in diploid genome assembly. Here we reconstructed the evolutionary dynamics of structural variation in five cat species by phasing the genomes of three interspecies F1 hybrids to generate near-gapless single-haplotype assemblies. We discerned that cat genomes have a paucity of segmental duplications relative to great apes, explaining their remarkable karyotypic stability. X chromosomes were hotspots of structural variation, including enrichment with inversions in a large recombination desert with characteristics of a supergene. The X-linked macrosatellite DXZ4 evolves more rapidly than 99.5% of the genome clarifying its role in felid hybrid incompatibility. Resolved sensory gene repertoires revealed functional copy number changes associated with ecomorphological adaptations, sociality and domestication. This study highlights the value of gapless genomes to reveal structural mechanisms underpinning karyotypic evolution, reproductive isolation and ecological niche adaptation.

Morphological and Genetics Support for a Hitherto Undescribed Spotted Cat Species (Genus Leopardus; Felidae, Carnivora) from the Southern Colombian Andes

In 1989, a skin of a small spotted cat, from the Galeras Volcano in southern Colombia (Nariño Department), was donated to the Instituto Alexander von Humboldt (identification, ID 5857) at Villa de Leyva (Boyacá Department, Colombia). Although originally classified as Leopardus tigrinus, its distinctiveness merits a new taxonomic designation. The skin is distinct from all known L. tigrinus holotypes as well as from other Leopardus species. Analysis of the complete mitochondrial genomes from 44 felid specimens (including 18 L. tigrinus and all the current known species of the genus Leopardus), the mtND5 gene from 84 felid specimens (including 30 L. tigrinus and all the species of the genus Leopardus), and six nuclear DNA microsatellites (113 felid specimens of all the current known species of the genus Leopardus) indicate that this specimen does not belong to any previously recognized Leopardus taxon. The mtND5 gene suggests this new lineage (the Nariño cat as we name it) is a sister taxon of Leopardus colocola. The mitogenomic and nuclear DNA microsatellite analyses suggest that this new lineage is the sister taxon to a clade formed by Central American and trans-Andean L. tigrinus + (Leopardus geoffroyi + Leopardus guigna). The temporal split between the ancestor of this new possible species and the most recent ancestor within Leopardus was dated to 1.2-1.9 million years ago. We consider that this new unique lineage is a new species, and we propose the scientific name Leopardus narinensis.

Time is running out: Microsatellite data predict the imminent extinction of the boreal lynx (Lynx lynx) in France

The Eurasian lynx reappeared in the French Jura Mountains, in the late 1970s, as the result of the dispersion of lynxes from the Carpathian region reintroduced in Switzerland in the early 1970s. Since then, the state of this population has remained poorly known. One estimate gives the number of individuals between 120 and 150. Opportunistic observation and monitoring suggest poor connectivity with the populations in Germany or in other parts of Switzerland. Forty years after its comeback in France, we could expect a higher number of individuals, but possible inbreeding depression as well as threats such as poaching and collisions with cars may explain the limitation of number of individuals observed and may lead to a new extinction of the specie in this region. We used 23 microsatellite markers and 78 DNA samples, collected between 2008 and 2020, to establish the genetic state of the French Jura Mountain lynx population. Our results show extremely low genetic diversity with an observed heterozygosity (Ho) of 0.36 and an effective population size (Ne) of 38.2. When comparing the source population (Carpathian), the inbreeding level is very worrying (Fe = 0.41). These results are among the lowest recorded for the Eurasian lynx. To avoid extinction, which we estimate will occur in approximately 30 years, we recommend the introduction of new genetic material. Although reintroduction is controversial, solutions such as the replacement of poached lynxes and the exchange of orphan lynxes between care centers are good initial actions for population strengthening. This offers a rapid intervention while studying solutions for more sustainable conservation

Application of genetic and Spatially Explicit Capture-Recapture analyses to design adaptive feral cat control in a large inhabited island

Faunas of oceanic islands have a high proportion of endemic species which contribute to the uniqueness of island communities. Island species are particularly naïve and vulnerable to alien predators, such as cats (Felis catus). On large, inhabited islands, where the complete eradication of feral cat populations is not considered feasible, control represents the best management option to lower their detrimental effects on native fauna. The first objective of our study was to investigate population genetics of feral cats of Réunion Island. The second objective was to understand the space use of feral cats established near the breeding colonies of the two endemic and endangered seabirds of Réunion Island, the Barau’s Petrel (Pterodroma baraui) and the Mascarene Petrel (Pseudobulweria aterrima). We evaluated genetic diversity, population structure and gene flow amongst six groups of feral cats located at a maximum of 10 km from known petrel colonies. We also analysed the behaviour and space use of one of these feral cat groups using camera-trap data and Spatially Explicit Capture-Recapture (SECR) models. Genetic analyses revealed that feral cats were structured in three genetic clusters explained mostly by the island topography. Two clusters were observed at five sampled sites, suggesting high connectivity amongst these sites. The last cluster was found in only one site, suggesting high isolation. This site was a remote mountain area located in the vicinity of one of the main Barau’s Petrel colonies. The behavioural study was conducted on this isolated feral cat population. Mark recapture analysis suggested that feral cats were present at low density and had large home ranges, which is probably explained by reduced food availability. Finally, we make several recommendations for refining feral cat management programmes on inhabited islands.

Assessing Asiatic cheetah’s individual diet using metabarcoding and its implication for conservation

Knowledge on diet composition allows defining well-targeted conservation measures of large carnivores. Little is known about ecology of critically endangered Asiatic cheetah, especially the overall diet and its possible regional differences. We used cheetah scats, metabarcoding technique and microsatellite markers to assess the individual and overall diet composition of the species across its entire range in Asia. Cheetahs were primarily predating on mouflon; following by ibex, cape hare and goitered gazelle. Despite their high availability, small-sized livestock was never detected. Goitered gazelles were only detected in an area where the habitat is mainly flatlands. In hilly areas, mouflon was the most frequent prey item taken. Ibex was typically taken in rugged terrain, but mouflon was still the most frequently consumed item in these habitats. High consumption of mouflon in comparison to goitered gazelle suggests that human pressure on lowland habitats has possibly forced Asiatic cheetahs to occupy suboptimal habitats where gazelles are less abundant. The protection of flatlands and the removal of livestock from them are needed to ensure the long-term survival of Asiatic cheetah. The laboratory and bioinformatics pipelines used in this study are replicable and can be used to address similar questions in other threatened carnivores.

DNA matchmaking in captive facilities: a case study with tigers

BACKGROUND

Genetics driven interventions if adopted in conservation breeding projects may enhance the overall success by prioritizing breeding among genetically most competent individuals and delaying or completely diminishing the ill effects of inbreeding.

METHODS AND RESULTS

In the present study, we investigated genetic make-up of 15 tigers housed at five different captive facilities of West Bengal in India and report the moderate level of genetic variation. We identified five tigers based on individual genetic attributes that may be prioritized for future breeding or animal exchange programmes. The occurrence of first and second order related individuals in captivity require management attention and they should be paired considering their immediate genetic background.

CONCLUSION

Considering tiger as a case study, we highlight the use of genetic assessment and necessity to validate the studbook records in formulating adaptive management strategies for long-term conservation and management of species of interest.

Novel hair snare and genetic methods for non-invasive bobcat detection

Over the past 20 years, the use of non-invasive hair snare surveys in wildlife research and management has become more prevalent. While these tools have been used to answer important research questions, these techniques often fail to gather information on elusive carnivores, such as bobcats (Lynx rufus). Due to the limited success of previous bobcat studies using hair snares which required active rubbing, this technique has largely fallen out of use, in favor of camera trapping. The goal of our study was to construct a novel, passive bobcat hair snare that could be deployed regardless of terrain or vegetation features, which would be effective for use in capture-recapture population estimation at a large spatial scale. This new hair snare was deployed in 1500 10-km2 cells across West Virginia (USA) between two sampling seasons (2015-2016). Collected hair samples were analyzed with newly developed mitochondrial DNA primers specifically for felids and qPCR to determine species of origin, with enough sensitivity to identify samples as small as two bobcat hairs. Over the two years of the study, a total of 378 bobcat detections were recorded from 42,000 trap nights of sampling, for an overall rate of 0.9 detections/100 trap nights-nearly 2-6 times greater than any previous bobcat hair snare study. While the overall number of recaptured animals was low (n = 9), continued development of this platform should increase its usefulness in capture-recapture studies.

Genetic diversity and population structure for ocelots (Leopardus pardalis) in Costa Rica

Ocelots (Leopardus pardalis) are a wide-ranging felid species, occurring from southern United States to northern Argentina. They occupy various habitats and are usually considered the most abundant wild cat species in the Neotropics. However, genetic studies that include free-ranging Mesoamerican ocelots are rare and generally based on small sample sizes. This is the first conservation genetics study on ocelots in Costa Rica and the second one in Mesoamerica that has conducted a genetic assessment of the species at a countrywide scale. We evaluated genetic diversity and population structure of ocelots using 15 microsatellite loci in 28 successfully genotyped individuals from throughout the country. We also compared genetic diversity of Costa Rican ocelots with that of jaguars (Panthera onca) and pumas (Puma concolor) in the country, and with ocelots in Belize. Genetic diversity of ocelots in Costa Rica was relatively high as measured by rarified allelic richness (AR = 5.50 ± 1.36) and expected heterozygosities (HE = 0.79 ± 0.08). We did not detect patterns of genetic substructure, suggesting high levels of gene flow throughout the country and no strong barriers to movement. As expected, genetic diversity of Costa Rican ocelots was higher than co-occurring jaguars and pumas. Additionally, levels of genetic diversity were slightly higher in Costa Rican ocelots when compared with their counterparts in Belize, confirming the south to north decrease in genetic diversity reported in other studies. Our study provides critical baseline information to understand the status of wild ocelot populations in Costa Rica. Future studies on ocelots and other threatened or keystone species should also integrate genetic monitoring and conservation genetics analysis to properly inform management decisions, guarantee their long-term survival, and improve the resilience of ecosystems.

Population genetic attributes of common leopard (Panthera pardus fusca) from Uttarkashi, Western Himalayas

BACKGROUND

The common leopard (Panthera pardus fusca), which persists in most of its historic range, is experiencing steady population decline due to habitat loss, anthrophonic disturbances, illegal poaching for their body parts, and retaliatory killings in response to the leopard-human conflicts.

METHODS AND RESULTS

We analysed 143 scats samples and identified 32 unique leopards following a selected panel of seven loci with cumulative P_ID sibs 5.30E-04. We observed moderate genetic diversity at nuclear (Ho = 0.600 ± 0.06) and mitochondrial markers (Hd = 0.569 ± 0.009; π = 0.001 ± 0.0002) and found sub-structuring in the leopard population at Uttarkashi, Western Himalayas.

CONCLUSIONS

The present study exhibits the utility of non-invasive genetics in monitoring the leopard population and paves the path to investigate population genetic parameters in further studies.

Use of molecular scatology to assess the diet of feral cats living in urban colonies

The overpopulation of domestic cats (Felis catus) presents a serious concern for wildlife conservationists, animal welfare advocates, public health officials, and community members alike. In cities, free-ranging, unowned cats often form high-density groups (commonly called ‘colonies’) around human provisioned food sources. While previous diet studies have primarily utilized morphology-based methods, molecular techniques offer a higher resolution alternative. In this study, we used next-generation sequencing techniques to examine the diet composition of feral cats living in five Trap-Neuter-Return colonies located in urban parks on Staten Island, a borough of New York City. We hypothesized that (1) cats living in urban colonies would still consume natural prey despite being regularly fed and (2) that the composition of taxa represented in the diet of each colony would vary, possibly due to differences in prey availability across sites. In total, 16 vertebrate prey taxa were identified in the diet, 13 at the genus level and 3 at the family level. Despite being regularly fed, 58.2% of cat scats contained DNA from natural prey. The diet composition of the cat colonies differed depending on the land cover composition surrounding the colony with the frequency of native prey positively correlated with the proportion of green space and that of non-native prey with developed land cover types. The use of molecular techniques combined with environmental DNA methods offers a promising, non-invasive approach to assessing the diet and consequently, impact of a highly abundant and non-native predator on the persistence of wildlife communities in cities.

Do all roads lead to resistance? State road density is the main impediment to gene flow in a flagship species inhabiting a severely fragmented anthropogenic landscape

AIM

Connectivity conservation is ideally based on empirical information on how landscape heterogeneity influences species-specific movement and gene flow. Here, we present the first large-scale evaluation of landscape impacts on genetic connectivity in the European wildcat (Felis silvestris), a flagship and umbrella species for connectivity conservation across Europe.

LOCATION

The study was carried out in the core area of the distributional range of wildcats in Germany, covering about 186,000 km2 of a densely populated and highly fragmented landscape.

METHODS

We used data of 975 wildcats genotyped at 14 microsatellites and an individual-based landscape genetic framework to assess the importance of twelve landscape variables for explaining observed genetic connectivity. For this, we optimized landscape resistance surfaces for all variables and compared their relative impacts using multiple regression on distance matrices and commonality analysis.

RESULTS

Genetic connectivity was best explained by a synergistic combination of six landscape variables and isolation by distance. Of these variables, road density had by far the strongest individual impact followed by synergistic effects of agricultural lands and settlements. Subsequent analyses involving different road types revealed that the strong effect of road density was largely due to state roads, while highways and federal roads had a much smaller, and county roads only a negligible impact.

MAIN CONCLUSIONS

Our results highlight that landscape-wide genetic connectivity in wildcats across Germany is strongly shaped by the density of roads and in particular state roads, with higher densities providing larger resistance to successful dispersal. These findings have important implications for conservation planning, as measures to mitigate fragmentation effects of roads (e.g., over- or underpasses) often focus on large, federally managed transportation infrastructures. While these major roads exert local barrier effects, other road types can be more influential on overall connectivity, as they are more abundant and more widespread across the landscape.

Population structure and gene flow of Geoffroy’s cat (Leopardus geoffroyi) in the Uruguayan Savanna ecoregion

Felids are among the species most threatened by habitat fragmentation resulting from land-use change. In the Uruguayan Savanna ecoregion, about 30% of natural habitats have been lost, large felids have been eradicated from most of the region, and the impact of anthropogenic threats over the smaller species that remain is unknown. To develop management strategies, it is important to enhance knowledge about species population structure and landscape connectivity, particularly when land-use change will continue and intensify in the next years. In this study, we evaluate the population structure and gene flow of Geoffroy’s cat in the Uruguayan Savanna ecoregion. We generated a matrix of 11 microsatellite loci for 70 individuals. Based on Bayesian approaches we found that within the Uruguayan Savanna, Geoffroy’s cat shows high levels of genetic variability and no population structure. However, we observed genetic differences between individuals from the Uruguayan Savanna and those from the contiguous ecoregion, the Argentinian Humid Pampa. Four first-generation migrants from Humid Pampa were identified in the Uruguayan Savanna, suggesting a stronger gene flow in the west-east direction. We detected a past bottleneck followed by a subsequent recovery in Geoffroy’s cat populations in both ecoregions. These results lay the groundwork to understand the population dynamics and conservation status of Geoffroy’s cat in the Uruguayan Savanna ecoregion, and provide baseline data to establish population monitoring.

Multiscale patterns of isolation by ecology and fine-scale population structure in Texas bobcats

Patterns of spatial genetic variation can be generated by a variety of ecological processes, including individual preferences based on habitat. These ecological processes act at multiple spatial and temporal scales, generating scale-dependent effects on gene flow. In this study, we focused on bobcats (Lynx rufus), a highly mobile, generalist felid that exhibits ecological and behavioral plasticity, high abundance, and broad connectivity across much of their range. However, bobcats also show genetic differentiation along habitat breaks, a pattern typically observed in cases of isolation-by-ecology (IBE). The IBE observed in bobcats is hypothesized to occur due to habitat-biased dispersal, but it is unknown if this occurs at other habitat breaks across their range or at what spatial scale IBE becomes most apparent. Thus, we used a multiscale approach to examine isolation by ecology (IBE) patterns in bobcats (Lynx rufus) at both fine and broad spatial scales in western Texas. We genotyped 102 individuals at nine microsatellite loci and used partial redundancy analysis (pRDA) to test if a suite of landscape variables influenced genetic variation in bobcats. Bobcats exhibited a latitudinal cline in population structure with a spatial signature of male-biased dispersal, and no clear barriers to gene flow. Our pRDA tests revealed high genetic similarity in similar habitats, and results differed by spatial scale. At the fine spatial scale, herbaceous rangeland was an important influence on gene flow whereas mixed rangeland and agriculture were significant at the broad spatial scale. Taken together, our results suggests that complex interactions between spatial-use behavior and landscape heterogeneity can create non-random gene flow in highly mobile species like bobcats. Furthermore, our results add to the growing body of data highlighting the importance of multiscale study designs when assessing spatial genetic structure.

Monitoring compliance of CITES lion bone exports from South Africa

From 2008 to 2018, South Africa permitted the export of captive-bred African lion (Panthera leo) skeletons to Southeast Asia under CITES Appendix II. Legal exports rose from approximately 50 individuals in 2008 to a maximum of 1,771 skeletons in 2016, and has led to ongoing concerns over possible laundering of non-lion, multiple-source and wild-sourced bones. South Africa is required under its obligations to CITES to employ mechanisms for monitoring and reporting trade, and to limit the potential for illegal trade and laundering of lion and other large felid bones. Monitoring tools for legal trade are critical to compliance with CITES. Here we evaluate the CITES-compliance procedure implemented by South Africa for export of lion bones and identify six essential general points for consideration in the implementation of animal export quota compliance protocols. We provide specific insight into the South African lion bone export monitoring system through: i) outlining the protocols followed; ii) assessing the utility of cranial morphology to identify species; iii) evaluating skeleton consignment weight as a monitoring tool; and iv) presenting molecular (DNA) species assignment and pairwise-comparative sample matching of individuals. We describe irregularities and illicit behaviour detected in the 2017 and 2018 lion bone quotas. Notably, we report that the compliance procedure successfully identified and prevented the attempted laundering of a tiger (P. tigris) skeleton in 2018. We emphasise the utility of mixed-method protocols for the monitoring of compliance in CITES Appendix II export quota systems.

Ultracontinuous Single Haplotype Genome Assemblies for the Domestic Cat (Felis catus) and Asian Leopard Cat (Prionailurus bengalensis)

In addition to including one of the most popular companion animals, species from the cat family Felidae serve as a powerful system for genetic analysis of inherited and infectious disease, as well as for the study of phenotypic evolution and speciation. Previous diploid-based genome assemblies for the domestic cat have served as the primary reference for genomic studies within the cat family. However, these versions suffered from poor resolution of complex and highly repetitive regions, with substantial amounts of unplaced sequence that is polymorphic or copy number variable. We sequenced the genome of a female F1 Bengal hybrid cat, the offspring of a domestic cat (Felis catus) x Asian leopard cat (Prionailurus bengalensis) cross, with PacBio long sequence reads and used Illumina sequence reads from the parents to phase >99.9% of the reads into the 2 species' haplotypes. De novo assembly of the phased reads produced highly continuous haploid genome assemblies for the domestic cat and Asian leopard cat, with contig N50 statistics exceeding 83 Mb for both genomes. Whole-genome alignments reveal the Felis and Prionailurus genomes are colinear, and the cytogenetic differences between the homologous F1 and E4 chromosomes represent a case of centromere repositioning in the absence of a chromosomal inversion. Both assemblies offer significant improvements over the previous domestic cat reference genome, with a 100% increase in contiguity and the capture of the vast majority of chromosome arms in 1 or 2 large contigs. We further demonstrated that comparably accurate F1 haplotype phasing can be achieved with members of the same species when one or both parents of the trio are not available. These novel genome resources will empower studies of feline precision medicine, adaptation, and speciation.

Genetic analysis indicates spatial-dependent patterns of sex-biased dispersal in Eurasian lynx in Finland

Conservation and management of large carnivores requires knowledge of female and male dispersal. Such information is crucial to evaluate the population's status and thus management actions. This knowledge is challenging to obtain, often incomplete and contradictory at times. The size of the target population and the methods applied can bias the results. Also, population history and biological or environmental influences can affect dispersal on different scales within a study area. We have genotyped Eurasian lynx (180 males and 102 females, collected 2003-2017) continuously distributed in southern Finland (~23,000 km2) using 21 short tandem repeats (STR) loci and compared statistical genetic tests to infer local and sex-specific dispersal patterns within and across genetic clusters as well as geographic regions. We tested for sex-specific substructure with individual-based Bayesian assignment tests and spatial autocorrelation analyses. Differences between the sexes in genetic differentiation, relatedness, inbreeding, and diversity were analysed using population-based AMOVA, F-statistics, and assignment indices. Our results showed two different genetic clusters that were spatially structured for females but admixed for males. Similarly, spatial autocorrelation and relatedness was significantly higher in females than males. However, we found weaker sex-specific patterns for the Eurasian lynx when the data were separated in three geographical regions than when divided in the two genetic clusters. Overall, our results suggest male-biased dispersal and female philopatry for the Eurasian lynx in Southern Finland. The female genetic structuring increased from west to east within our study area. In addition, detection of male-biased dispersal was dependent on analytical methods utilized, on whether subtle underlying genetic structuring was considered or not, and the choice of population delineation. Conclusively, we suggest using multiple genetic approaches to study sex-biased dispersal in a continuously distributed species in which population delineation is difficult.

The role of the environment in the spatial dynamics of an extensive hybrid zone between two neotropical cats

Identifying factors that create and maintain a hybrid zone is of great interest to ecology, evolution and, more recently, conservation biology. Here, we investigated the role of environmental features in shaping the spatial dynamics of a hybrid zone between the southern tigrina, Leopardus guttulus, and Geoffroy's cat, L. geoffroyi, testing for exogenous selection as the main force acting on its maintenance. These Neotropical felid species are mainly allopatric, with a restricted area of sympatry in the ecotone between the Atlantic Forest and Pampa biomes. As both biomes have experienced high rates of anthropogenic habitat alteration, we also analysed the influence of habitat conversion on the hybrid zone structure. To do this, we used 13 microsatellite loci to identify potential hybrids and generated ecological niche models for them and their parental species. We compared the influence of variables on parental species and hybrid occurrence and calculated the amount of niche overlap among them. Parental species showed different habitat requirements and predicted co-occurrence was restricted to the forest-grassland mosaic of the ecotone. However, hybrids were found beyond this area, mainly in the range of L. geoffroyi. Hybrids demonstrated higher tolerance to habitat alteration than parental types, with a probability of occurrence that was positively related with mosaics of cropland areas and remnants of natural vegetation. These results indicate that exogenous selection alone does not drive the dynamics of the hybrid zone, and that habitat conversion influences its structure, potentially favouring hybrids over parental species.

Microsatellite characterization and development of unified STR panel for big cats in captivity: a case study from a Seoul Grand Park Zoo, Republic of Korea

The zoos manage small populations of endangered big cat species like tiger, lion, and leopard for display, research, and conservation breeding. Genetic management of these populations is essential to ensure long term survival and conservation utility. Here we propose a simple and cost effective microsatellite based protocol for the genetic management of captive big cats. We sampled 36 big cat individuals from Seoul Grand Park Zoo (Republic of Korea) and amplified 33 published microsatellite loci. Overall, allelic richness and gene diversity was found highest for leopards, followed by lions and tigers. Twelve of the thirty-three markers showed a high degree of polymorphism across all target species. These microsatellites provide a high degree of discrimination for tiger (1.45 × 10^-8), lion (1.54 × 10^-10), and leopard (1.88 × 10^-12) and thus can be adopted for the genetic characterization of big cats in accredited zoos globally. During captive breeding, zoo authorities rely on pedigree records maintained in studbooks to ensure mating of genetically fit unrelated individuals. Several studies have reported errors in studbook records of big cat species. Microsatellites are simple and cost effective tool for DNA fingerprinting, estimation of genetic diversity, and paternity assessment. Our unified microsatellite panel (12-plex) for big cats is efficient and can easily be adopted by zoo authorities for regular population management.

Canada lynx (Lynx canadensis) gene flow across a mountain transition zone in western North America

Mountain ecotones have the potential to cause multiple patterns in divergence, from simple barrier effects to more fundamental ecological divergence. Most work in mountain ecotones in North America has focused on reinforcement between refugial populations, making prediction of how mountains impact species that are not restricted to separate glacial refugia remains difficult. This study focused on the Canada lynx (Lynx canadensis Kerr, 1792), a highly mobile felid considered to be a habitat and dietary specialist. Specifically, we used 14 microsatellite loci and landscape genetic tools to investigate if the Rocky Mountains and associated climatic transitions influence lynx genetic differentiation in western North America. Although lynx exhibited high gene flow across the region, analyses detected structuring of neutral genetic variation across our study area. Gene flow for lynx most strongly related to temperature and elevation compared with other landscape variables (terrain roughness, percent forest cover, and habitat suitability index) and geographic distance alone. Overall, genetic structure in lynx is most consistent with barrier effects created by the Rocky Mountains rather than ecological divergence. Furthermore, warmer temperatures had a measurable impact on gene flow, which suggests connectivity may further decrease in peripheral or fragmented populations as climate warms.

The role of kinship and demography in shaping cooperation amongst male lions

The influence of kinship on animal cooperation is often unclear. Cooperating Asiatic lion coalitions are linearly hierarchical; male partners appropriate resources disproportionately. To investigate how kinship affect coalitionary dynamics, we combined microsatellite based genetic inferences with long-term genealogical records to measure relatedness between coalition partners of free-ranging lions in Gir, India. Large coalitions had higher likelihood of having sibling partners, while pairs were primarily unrelated. Fitness computations incorporating genetic relatedness revealed that low-ranking males in large coalitions were typically related to the dominant males and had fitness indices higher than single males, contrary to the previous understanding of this system based on indices derived from behavioural metrics alone. This demonstrates the indirect benefits to (related) males in large coalitions. Dominant males were found to 'lose less' if they lost mating opportunities to related partners versus unrelated males. From observations on territorial conflicts we show that while unrelated males cooperate, kin-selected benefits are ultimately essential for the maintenance of large coalitions. Although large coalitions maximised fitness as a group, demographic parameters limited their prevalence by restricting kin availability. Such demographic and behavioural constraints condition two-male coalitions to be the most attainable compromise for Gir lions.

Genome-based development of 15 microsatellite markers in fluorescent multiplexes for parentage testing in captive tigers

As one of the most endangered species, tiger (Panthera tigris) inbreeding has become an urgent issue to address. Using a microsatellite (short tandem repeat, STR) identification system, paternity testing may be helpful to avoid inbreeding in captive breeding programs. In this study, we developed a genome-based identification system named tiger pedigree identification multiplex system (TPI-plex). By analyzing the entire tiger genome, 139,967 STR loci were identified and 12.76% of these displayed three to six alleles among three re-sequenced individual tiger genomes. A total of 204 candidate STRs were identified and screened with a reference population containing 31 unrelated captive tigers. Of these, 15 loci were chosen for inclusion in the multiplex panel. The mean allele number and mean expected heterozygosity (He) were 7.3333 and 0.7789, respectively. The cumulative probability of exclusion (CPE) and total probability of discrimination power (TDP) reached 0.999999472 and 0.999999999999995, respectively. The results showed that the TPI-plex system can be applied in routine pedigree identification for captive tigers. We also added a sex identification marker named TAMEL into the TPI-plex for sex determination.

The rise of a large carnivore population in Central Europe: genetic evaluation of lynx reintroduction in the Harz Mountains

Large carnivores have made a successful comeback across human-dominated landscapes in Central Europe. The Eurasian lynx, for instance, has been actively reintroduced in different regions. Genetic diversity is quickly eroding in these isolated, small populations, questioning the long-term success of lynx reintroductions. To track population development and genetic diversity in a reintroduced lynx population, we used microsatellite analysis and mtDNA haplotyping based on 379 samples collected during the initial 15 year period of lynx reintroduction in the Harz mountains National Park, Germany. The Harz lynx population shows higher genetic diversity relative to other lynx reintroductions, due to initial cross-breeding of divergent captive source lineages and a comparably high founder size. While the population shows significant population growth and spread into adjacent regions, genetic diversity is continiously declining. Expected heterozygosity values dropped from 0.63 after reintroduction (2006/2007) to 0.55 within a 10 year period. Despite this, the Harz lynx population is currently a viable component to an envisioned lynx metapopulation spanning across Central Europe. The ongoing genetic erosion in the Harz population along with a lack of geneflow from adjacent populations indicates that such connectivity is urgently needed to ensure long-term population persistence.

Unsustainable anthropogenic mortality disrupts natal dispersal and promotes inbreeding in leopards

Anthropogenic mortality of wildlife is typically inferred from measures of the absolute decline in population numbers. However, increasing evidence suggests that indirect demographic effects including changes to the age, sex, and social structure of populations, as well as the behavior of survivors, can profoundly impact population health and viability. Specifically, anthropogenic mortality of wildlife (especially when unsustainable) and fragmentation of the spatial distribution of individuals (home-ranges) could disrupt natal dispersal mechanisms, with long-term consequences to genetic structure, by compromising outbreeding behavior and gene flow. We investigate this threat in African leopards (Panthera pardus pardus), a polygynous felid with male-biased natal dispersal. Using a combination of spatial (home-range) and genetic (21 polymorphic microsatellites) data from 142 adult leopards, we contrast the structure of two South African populations with markedly different histories of anthropogenically linked mortality. Home-range overlap, parentage assignment, and spatio-genetic autocorrelation together show that historical exploitation of leopards in a recovering protected area has disrupted and reduced subadult male dispersal, thereby facilitating opportunistic male natal philopatry, with sons establishing territories closer to their mothers and sisters. The resultant kin-clustering in males of this historically exploited population is comparable to that of females in a well-protected reserve and has ultimately led to localized inbreeding. Our findings demonstrate novel evidence directly linking unsustainable anthropogenic mortality to inbreeding through disrupted dispersal in a large, solitary felid and expose the genetic consequences underlying this behavioral change. We therefore emphasize the importance of managing and mitigating the effects of unsustainable exploitation on local populations and increasing habitat fragmentation between contiguous protected areas by promoting in situ recovery and providing corridors of suitable habitat that maintain genetic connectivity.

Genetic analyses reveal population structure and recent decline in leopards (Panthera pardus fusca) across the Indian subcontinent

Background

Large carnivores maintain the stability and functioning of ecosystems. Currently, many carnivore species face declining population sizes due to natural and anthropogenic pressures. The leopard, Panthera pardus, is probably the most widely distributed and highly adaptable large felid globally, still persisting in most of its historic range. However, we lack subspecies-level data on country or regional scale on population trends, as ecological monitoring approaches are difficult to apply on such wide-ranging species. We used genetic data from leopards sampled across the Indian subcontinent to investigate population structure and patterns of demographic decline.

Methods

We collected faecal samples from the Terai-Arc landscape of northern India and identified 56 unique individuals using a panel of 13 microsatellite markers. We merged this data with already available 143 leopard individuals and assessed genetic structure at country scale. Subsequently, we investigated the demographic history of each identified subpopulations and compared genetic decline analyses with countrywide local extinction probabilities.

Results

Our genetic analyses revealed four distinct subpopulations corresponding to Western Ghats, Deccan Plateau-Semi Arid, Shivalik and Terai region of the north Indian landscape, each with high genetic variation. Coalescent simulations with microsatellite loci revealed a possibly human-induced 75–90% population decline between ∼120–200 years ago across India. Population-specific estimates of genetic decline are in concordance with ecological estimates of local extinction probabilities in these subpopulations obtained from occupancy modeling of the historic and current distribution of leopards in India.

Conclusions

Our results confirm the population decline of a widely distributed, adaptable large carnivore. We re-iterate the relevance of indirect genetic methods for such species in conjunction with occupancy assessment and recommend that detailed, landscape-level ecological studies on leopard populations are critical to future conservation efforts. Our approaches and inference are relevant to other widely distributed, seemingly unaffected carnivores such as the leopard.

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.

Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of postspeciation gene flow that can produce a mosaic of phylogenetic signals that interact with recombinational variation. Here, we tested the validity of this assumption with a phylogenomic analysis of 27 species of the cat family, assessing local effects of recombination rate on species tree inference and divergence time estimation across their genomes. We found that the prevailing phylogenetic signal within the autosomes is not always representative of the most probable speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within regions of low recombination, and notably enriched within large X chromosome recombination cold spots that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ∼40%. We conclude that existing phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic architecture of phylogenetic signal relative to recombination rate and its interplay with historical hybridization.

Population genetic structure and habitat connectivity for jaguar (Panthera onca) conservation in Central Belize

BACKGROUND

Connectivity among jaguar (Panthera onca) populations will ensure natural gene flow and the long-term survival of the species throughout its range. Jaguar conservation efforts have focused primarily on connecting suitable habitat in a broad-scale. Accelerated habitat reduction, human-wildlife conflict, limited funding, and the complexity of jaguar behaviour have proven challenging to maintain connectivity between populations effectively. Here, we used non-invasive genetic sampling and individual-based conservation genetic analyses to assess genetic diversity and levels of genetic connectivity between individuals in the Cockscomb Basin Wildlife Sanctuary and the Maya Forest Corridor. We used expert knowledge and scientific literature to develop models of landscape permeability based on circuit theory with fine-scale landscape features as ecosystem types, distance to human settlements and roads to predict the most probable jaguar movement across central Belize.

RESULTS

We used 12 highly polymorphic microsatellite loci to identify 50 individual jaguars. We detected high levels of genetic diversity across loci (HE = 0.61, HO = 0.55, and NA = 9.33). Using Bayesian clustering and multivariate models to assess gene flow and genetic structure, we identified one single group of jaguars (K = 1). We identified critical areas for jaguar movement that fall outside the boundaries of current protected areas in central Belize. We detected two main areas of high landscape permeability in a stretch of approximately 18 km between Sittee River Forest Reserve and Manatee Forest Reserve that may increase functional connectivity and facilitate jaguar dispersal from and to Cockscomb Basin Wildlife Sanctuary. Our analysis provides important insights on fine-scale genetic and landscape connectivity of jaguars in central Belize, an area of conservation concern.

CONCLUSIONS

The results of our study demonstrate high levels of relatively recent gene flow for jaguars between two study sites in central Belize. Our landscape analysis detected corridors of expected jaguar movement between the Cockscomb Basin Wildlife Sanctuary and the Maya Forest Corridor. We highlight the importance of maintaining already established corridors and consolidating new areas that further promote jaguar movement across suitable habitat beyond the boundaries of currently protected areas. Continued conservation efforts within identified corridors will further maintain and increase genetic connectivity in central Belize.

Using Genetics to Evaluate the Success of a Feral Cat (Felis catus) Control Program in North-Western Australia

Simple Summary

The management of invasive species is a major challenge for the conservation of biodiversity globally. One technique that has been widely used to control feral cats (Felis catus) and red foxes (Vulpes vulpes) in Western Australia is the aerial broadcast of toxic baits, but assessing its efficacy can be difficult. Here, we report on a method of evaluating the effectiveness of this method for the abatement of feral cats using genetic analysis techniques. However, our results were unable to provide robust evidence that, over a five-year program, baiting had a detrimental impact on both genetics and demography in this population, and the results were not significant. Monitoring the impact of control programs in this way may provide valuable information to managers on the effectiveness of their management strategy, but further refinement of the methodology is recommended.

Abstract

The feral cat has been implicated in the decline and extinction of many species worldwide and a range of strategies have been devised for its control. A five-year control program using the aerial broadcast of toxic Eradicat^® baits was undertaken at Fortescue Marsh in the Pilbara region of north-western Australia, for the protection of biodiversity in this important wetland area. This program has been shown to have had a significant detrimental effect on cats in this landscape, but the long-term impact is difficult to ascertain. We assessed population genetics across three cohorts of feral cats sampled as part of the control program. We also compared cat populations in natural habitats and around human infrastructure. A key challenge in any study of wild animal populations is small sample sizes and feral cats are particularly difficult to capture and sample. The results of this study superficially appear to suggest promising trends but were limited by sample size and many were not statistically significant. We find that the use of genetic techniques to monitor the impact of invasive species control programs is potentially useful, but ensuring adequate sample sizes over a long enough time-frame will be critical to the success of such studies.

Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal

Bengal tigers (Panthera tigris tigris) serve a pivotal role as an apex predator in forest ecosystems. To increase our knowledge on factors impacting the viability and health of this endangered species, we studied the gut microbiota in 32 individual Bengal tigers from three geographically separated areas (Chitwan National Park (CNP), Bardia National Park (BNP) and Suklaphanta Wildlife Reserve (SWR)) in Nepal, using noninvasive genetic sampling methods. Gut microbiota influence the immune system, impact various physiological functions, and modulates metabolic reactions, that ultimately impact the host health, behavior and development. Across the tiger populations in Nepal, we found significant differences in the composition of microbial communities based on their geographic locations. Specifically, we detected significant differences between CNP and the other two protected areas (CNP vs BNP: pseudo t = 1.944, P = 0.006; CNP vs SWR: pseudo t = 1.9942, P = 0.0071), but no differences between BNP and SWR. This mirrors what has been found for tiger gene flow in the same populations, suggesting gut microbiota composition and host gene flow may be linked. Furthermore, predictive metagenome functional content analysis (PICRUSt) revealed a higher functional enrichment and diversity for significant gut microbiota in the Chitwan tiger population and the lowest enrichment and diversity in Suklaphanta. The CNP tiger population contained higher proportions of microbiota that are associated with predicted functions relevant for metabolism of amino acid, lipid, xenobiotics biodegradation, terpenoides and polyketides than the SWR population. We conclude the tiger population structure, gut microbiota profile and associated functional metabolic categories are correlated, with geographically most separated CNP and SWR tiger population having the most distinct and different host genotype and microbiota profiles. Our work dramatically expands the understanding of tiger microbiota in wild populations and provides a valuable case study on how to investigate genetic diversity at different hierarchical levels, including hosts as well as their microbial communities.

The Burmese cat as a genetic model of type 2 diabetes in humans

The recent extension of genetic tools to the domestic cat, together with the serendipitous consequences of selective breeding, have been essential to the study of the genetic diseases that affect them. Cats are increasingly presented for veterinary surveillance and share many of human's heritable diseases, allowing them to serve as natural models of these conditions. Feline diabetes mellitus is a common condition in domestic cats that bears close pathological and clinical resemblance to type 2 diabetes in humans, including pancreatic β-cell dysfunction and peripheral insulin resistance. In Australia, New Zealand and Europe, diabetes mellitus is almost four times more common in cats of the Burmese breed than in other breeds. This geographically based breed predisposition parallels familial and population clustering of type 2 diabetes in humans. As a genetically isolated population, the Australian Burmese breed provides a spontaneous, naturally occurring genetic model of type 2 diabetes. Genetically isolated populations typically exhibit extended linkage disequilibrium and increased opportunity for deleterious variants to reach high frequencies over many generations due to genetic drift. Studying complex diseases in such populations allows for tighter control of confounding factors including environmental heterogeneity, allelic frequencies and population stratification. The homogeneous genetic background of Australian Burmese cats may provide a unique opportunity to either refine genetic signals previously associated with type 2 diabetes or identify new risk factors for this disease.

Non-invasive faecal sampling reveals spatial organization and improves measures of genetic diversity for the conservation assessment of territorial species: Caucasian lynx as a case species

The Caucasian lynx, Lynx lynx dinniki, has one of the southernmost distributions in the Eurasian lynx range, covering Anatolian Turkey, the Caucasus and Iran. Little is known about the biology and the genetic status of this subspecies. To collect baseline genetic, ecological and behavioural data and benefit future conservation of L. l. dinniki, we monitored 11 lynx territories (396 km2) in northwestern Anatolia. We assessed genetic diversity of this population by non-invasively collecting 171 faecal samples and trapped and sampled 12 lynx individuals using box traps. We observed high allelic variation at 11 nuclear microsatellite markers, and found no signs of inbreeding despite the potential isolation of this population. We obtained similar numbers of distinct genotypes from the two sampling sources. Our results indicated that first order female relatives occupy neighbouring territories (female philopatry) and that territorial male lynx were highly unrelated to each other and to female territorial lynx, suggesting long distance male dispersal. Particular male and female resident territorial lynx and their offspring (kittens and subadults) were more likely to be trapped than resident floaters or dispersing (unrelated) lynx. Conversely, we obtained more data for unrelated lynx and higher numbers of territorials using non-invasive sampling (faeces). When invasive and non-invasive samples were analysed separately, the spatial organisation of lynx (in terms of female philopatry and females and males occupying permanent ranges) affected measures of genetic diversity in such a way that estimates of genetic diversity were reduced if only invasive samples were considered. It appears that, at small spatial scales, invasive sampling using box traps may underestimate the genetic diversity in carnivores with permanent ranges and philopatry such as the Eurasian lynx. As non-invasive sampling can also provide additional data on diet and spatial organisation, we advocate the use of such samples for conservation genetic studies of vulnerable, endangered or data deficient territorial species.