Habitat use and sensitivity to fragmentation in America’s smallest wildcat

Assessing micro-macroparasite selective pressures and anthropogenic disturbance as drivers of immune gene diversity in a Neotropical wild cat

Anthropogenic environmental change is reducing available habitat for wild species, providing novel selection pressures such as infectious diseases and causing species to interact in new ways. The potential for emerging infectious diseases and zoonoses at the interface between humans, domestic animals, and wild species is a key global concern. In vertebrates, diversity at the major histocompatibility complex MHC is critical to disease resilience, and its study in wild populations provides insights into eco-evolutionary dynamics that human activities alter. In natural populations, variation at MHC loci is partly maintained by balancing selection, driven by pathogenic selective pressures. We hypothesize that MHC genetic diversity differs between guigna populations inhabiting human-dominated landscapes (higher pathogen pressures) versus more natural habitats (lower pathogen pressures). We predict that MHC diversity in guignas would be highest in human-dominated landscapes compared with continuous forest habitats. We also expected to find higher MHC diversity in guignas infected with micro and macro parasites (higher parasite load) versus non infected guignas. We characterized for the first time the genetic diversity at three MHC class I and II exons in 128 wild guignas (Leopardus guigna) across their distribution range in Chile (32-46° S) and Argentina, representing landscapes with varying levels of human disturbance. We integrated MHC sequence diversity with multiple measures of anthropogenic disturbance and both micro and macro parasite infection data. We also assessed signatures of positive selection acting on MHC genes. We found significantly higher MHC class I diversity in guignas inhabiting landscapes where houses were present, and with lower percentage of vegetation cover, and also in animals with more severe cardiorespiratory helminth infection (richness and intensity) and micro-macroparasite co-infection. This comprehensive, landscape-level assessment further enhances our knowledge on the evolutionary dynamics and adaptive potential of vertebrates in the face of emerging infectious disease threats and increasing anthropogenic impacts.

Habitat use by the endangered spotted-tailed quoll in a fragmented landscape

The spotted-tailed quoll (Dasyurus maculatus) is an endangered mesopredator endemic to Australia. It is generally considered a forest-dependent species associated with large, intact forested habitats. In Australia’s mainland, quoll research has typically been conducted in contiguous forest, and consequently, the species’ presumed forest-dependency might reflect sampling bias rather than preferred habitat niche. Recent studies have revealed that quolls also persist in fragmented agricultural landscapes, raising questions about their true habitat requirements and preferences. In this study, we investigated quoll habitat use within a fragmented agricultural landscape in mainland Australia. We deployed 42 lured camera traps to determine quoll habitat preferences across four broad vegetation types (open grassland, grassy woodland, dry sclerophyll forest, and wet sclerophyll forest) based on quoll activity and occupancy. Quolls were detected in all vegetation types, and quoll activity indicated a preference for dry sclerophyll forest and grassy woodlands, although this preference varied depending on the time of year. Our results suggest that quoll habitat use in mainland Australia is more flexible than previously assumed, and we recommend further research on factors that may influence habitat preference such as prey availability and seasonal behavior. Understanding the factors that drive habitat use by quolls outside of contiguous forested landscapes will inform and improve conservation and management strategies to ensure critical habitat for the species is protected and retained in an increasingly fragmented landscape.

Sampling and modelling rare species: Conceptual guidelines for the neglected majority

Biodiversity conservation faces a methodological conundrum: Biodiversity measurement often relies on species, most of which are rare at various scales, especially prone to extinction under global change, but also the most challenging to sample and model. Predicting the distribution change of rare species using conventional species distribution models is challenging because rare species are hardly captured by most survey systems. When enough data are available, predictions are usually spatially biased towards locations where the species is most likely to occur, violating the assumptions of many modelling frameworks. Workflows to predict and eventually map rare species distributions imply important trade-offs between data quantity, quality, representativeness and model complexity that need to be considered prior to survey and analysis. Our opinion is that study designs need to carefully integrate the different steps, from species sampling to modelling, in accordance with the different types of rarity and available data in order to improve our capacity for sound assessment and prediction of rare species distribution. In this article, we summarize and comment on how different categories of species rarity lead to different types of occurrence and distribution data depending on choices made during the survey process, namely the spatial distribution of samples (where to sample) and the sampling protocol in each selected location (how to sample). We then clarify which species distribution models are suitable depending on the different types of distribution data (how to model). Among others, for most rarity forms, we highlight the insights from systematic species-targeted sampling coupled with hierarchical models that allow correcting for overdispersion and spatial and sampling sources of bias. Our article provides scientists and practitioners with a much-needed guide through the ever-increasing diversity of methodological developments to improve the prediction of rare species distribution depending on rarity type and available data.

Cross-species transmission of retroviruses among domestic and wild felids in human-occupied landscapes in Chile

Human transformation of natural habitats facilitates pathogen transmission between domestic and wild species. The guigna (Leopardus guigna), a small felid found in Chile, has experienced habitat loss and an increased probability of contact with domestic cats. Here, we describe the interspecific transmission of feline leukemia virus (FeLV) and feline immunodeficiency virus (FIV) between domestic cats and guignas and assess its correlation with human landscape perturbation. Blood and tissue samples from 102 free-ranging guignas and 262 domestic cats were collected and analyzed by PCR and sequencing. Guigna and domestic cat FeLV and FIV prevalence were very similar. Phylogenetic analysis showed guigna FeLV and FIV sequences are positioned within worldwide domestic cat virus clades with high nucleotide similarity. Guigna FeLV infection was significantly associated with fragmented landscapes with resident domestic cats. There was little evidence of clinical signs of disease in guignas. Our results contribute to the understanding of the implications of landscape perturbation and emerging diseases.

New records of Leopardus guigna in its northern-most distribution in Chile: implications for conservation

We report new records of the wild felid Leopardus guigna in its northern-most distribution, in the southern Coquimbo and northern Valparaíso regions, in northern-central Chile. To our knowledge, these are the northern-most confirmed guigna records to date. We discuss implications for the conservation of these fragile populations in the face of different anthropic threats.

Epidemiology and molecular characterization of Carnivore protoparvovirus-1 infection in the wild felid Leopardus guigna in Chile

Landscape anthropization has been identified as one of the main drivers of pathogen emergence worldwide, facilitating pathogen spillover between domestic species and wildlife. The present study investigated Carnivore protoparvovirus-1 infection using molecular methods in 98 free-ranging wild guignas (Leopardus guigna) and 262 co-occurring owned, free-roaming rural domestic cats. We also assessed landscape anthropization variables as potential drivers of infection. Protoparvovirus DNA was detected in guignas across their entire distribution range, with observed prevalence of 13.3% (real-time PCR) and 9% (conventional PCR) in guignas, and 6.1% (conventional PCR) in cats. Prevalence in guigna did not vary depending on age, sex, study area or landscape variables. Prevalence was higher in juvenile cats (16.7%) than in adults (4.4%). Molecular characterization of the virus by amplification and sequencing of almost the entire vp2 gene (1,746 bp) from one guigna and five domestic cats was achieved, showing genetic similarities to canine parvovirus 2c (CPV-2c) (one guigna and one cat), feline panleukopenia virus (FPV) (one cat), CPV-2 (no subtype identified) (two cats), CPV-2a (one cat). The CVP-2c-like sequence found in a guigna clustered together with domestic cat and dog CPV-2c sequences from South America, suggesting possible spillover from a domestic to a wild species as the origin of infection in guigna. No clinical signs of disease were found in PCR-positive animals except for a CPV-2c-infected guigna, which had haemorrhagic diarrhoea and died a few days after arrival at a wildlife rescue centre. Our findings reveal widespread presence of Carnivore protoparvovirus-1 across the guigna distribution in Chile and suggest that virus transmission potentially occurs from domestic to wild carnivores, causing severe disease and death in susceptible wild guignas.

Gastrointestinal and cardiorespiratory endoparasites in the wild felid guigna (Leopardus guigna) in Chile: Richness increases with latitude and first records for the host species

Guignas (Leopardus guigna) are small felids closely associated with native forest habitats. In fragmented landscapes, they use vegetation corridors and forest remnants to move across the landscape. In these contexts, guignas may increase contact probabilities with domestic animals, being therefore relevant to assess their pathogens and parasites. The aim of this study was to characterize the helminth fauna in the gastrointestinal tract and cardiorespiratory system of guignas from central and southern Chile. Between 2015 and 2018, 33 dead free-ranging guignas were found road-killed or were collected from wildlife rescue centers. Thirty-two gastrointestinal tracts and 32 cardiorespiratory organs were analyzed through direct analysis and artificial digestion. We found 81.8% (27/33) guignas were positive for helminth endoparasites (84.4% (27/32) positive for gastrointestinal parasites, 37.5% (12/32) positive for cardiorespiratory parasites). Fourteen parasites were identified (7 at genus level and 7 at species level), with Angiostrongylus sp., Molineus sp., Oslerus sp. and Troglostrongylus sp. as first records in guignas. The most prevalent parasites were the species Toxascaris leonina, Toxocara cati and Uncinaria stenocephala. Uncinaria stenocephala showed the highest intensity of infection. Multiparasitism was observed in 76% of the animals. Significant differences in richness of endoparasites and prevalence of cardiorespiratory parasites were found between geographic zones; higher values in the southern zone are possibly due to favorable environmental characteristics for endoparasite development. There were no statistically significant differences between sexes. All the parasites found in this study have been previously reported in domestic cats. These results are valuable to understand parasite transmission at the domestic-wildlife interface; the possibility of endoparasite transmission between domestic cats and guignas should be clarified with molecular analysis.

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The 81.8% of analyzed Leopardus guigna were positive for helminth parasites.

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First report of Angiostrongylus sp., Molineus sp., Oslerus sp. and Troglostrongylus sp. in guignas.

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Higher prevalence and diversity of cardiorespiratory parasites in guignas from southern Chile.

Antibiotic resistance genes as landscape anthropization indicators: Using a wild felid as sentinel in Chile

Antimicrobial resistance is a global emerging public health issue whose presence and impact in wildlife are widely unknown. Antimicrobial resistance genes (ARGs) are considered environmental contaminants, suitable to evaluate the degree of anthropic impact on wildlife and the environment. We used a wild felid, the guigna (Leopardus guigna), as a sentinel for the presence of ARGs in anthropized and pristine areas across their entire distribution range in Chile. We evaluated fecal samples from 51 wild guignas, collected between 2009 and 2018. Real-time PCR essays were employed to detect and quantify 22 selected ARGs in their fecal microbiome. All animals (100%) were positive for at least one ARG. The most prevalent ARG families were those that confer resistance to tetracycline (88.2%) and beta-lactamase (68.9%), with tet(Q) (60.8%), tet(W) (60.8%), and bla_TEM (66.7%) as the most prevalent ARGs. Multi-resistance profiles were observed in 43% of the guignas. Statistically significant differences were found between anthropized and pristine areas for tet(Q) (p = 0.014), tet(W) (p = 0.0037), tetracycline family (p = 0.027), multi-resistance profile prevalence (p = 0.043) and tet(W) quantification (p = 0.004). Two animals from anthropized landscapes were positive for mecA, a gene associated with Staphylococcus aureus and other staphylococci resistant to methicillin, while three animals from anthropized areas were positive for bla_CTX-M, that encodes class A extended-spectrum beta-lactamase. Both genes have been identified in bacteria causing relevant nosocomial infections worldwide. This is the first study on ARGs in wild felids from Chile and the first detection of mecA in South American wild felids. We observed an association between the degree of landscape anthropization and ARG prevalence, confirming that ARGs are important indicators of wildlife exposure to human activity/presence, with a widespread distribution.

Remnants of native forests support carnivore diversity in the vineyard landscapes of central Chile

Carnivores play an important role in ecosystem functioning as apex predators. However, most carnivore species are threatened or have been extirpated in human-dominated landscapes. The Mediterranean region of central Chile is a biodiversity hotspot, but expansion of agricultural areas such as vineyards is degrading wildlife habitat. We estimated the species richness and composition of carnivore communities in remnant fragments of sclerophyllous forest-shrubland in the vineyard landscapes of central Chile to evaluate the effects of human disturbance at different spatial scales. We tested two hypotheses: (1) vineyard landscapes with higher levels of human disturbance support a lower diversity of native carnivores in fragments of remnant native vegetation compared to landscapes with larger areas of natural habitat, and (2) habitat specialists and generalists respond differentially to human influence at the habitat vs landscape spatial scale. We used camera traps at 12 sites across the study area and evaluated the impact of human disturbance indicators on the richness and detection frequency of carnivore species. We found that human population density negatively affected carnivore richness and was associated with a lower detection frequency of the Vulnerable guiña Leopardus guigna. The presence of domestic dogs also had a negative effect on the detection frequency of the guiña and the two native species of foxes, the culpeo Lycalopex culpaeus and South American grey fox Lycalopex griseus. We conclude that protecting remnants of native forest in vineyard landscapes is crucial for carnivore conservation in central Chile.

Assessing cross-species transmission of hemoplasmas at the wild-domestic felid interface in Chile using genetic and landscape variables analysis

The co-occurrence of domestic cats (Felis silvestris catus) and wild felids in rural landscapes can facilitate pathogen transmission. However, in the relatively-isolated regions of southern South America there have been no comprehensive studies to assess disease transmission risks between domestic cats and forest-dwelling wild felids such as guigna (Leopardus guigna). We evaluated hemoplasma infection and the possibility of transmission between domestic cats and guignas by comparing spatial and phylogenetic patterns of pathogen prevalence. Blood/spleen samples were collected from 102 wild guignas and 262 co-occurring rural domestic cats across the entire distribution range of guigna in Chile. Hemoplasma infection was assessed by direct sequencing of the 16S RNA gene. Infection with hemoplasmas was common and geographically widespread across different bioclimatic areas for both species. The most common feline Mycoplasma species in guigna and domestic cats were Candidatus M. haemominutum (CMhm) (15.7% guigna; 10.3% domestic cat) and Mycoplasma haemofelis (Mhf) (9.8% guigna, 6.1% domestic cat). A previously undescribed Mycoplasma sp. sequence was found in two guignas and one cat. Continuous forest-landscapes were associated with higher hemoplasma-prevalence in guignas. Shared hemoplasma nucleotide sequence types between guigna and domestic cats were rare, suggesting that cross-species transmission between guignas and domestic cats may occur, but is probably uncommon. Ectoparasites, which have been linked with hemoplasma transmission, were not found on guignas and were infrequent on domestic cats. Our results suggest that transmission pathways vary among hemoplasma species and, contrary to our predictions, domestic cats did not appear to be the main driver of hemoplasma infection in guignas in these human-dominated landscapes.

A spatially integrated framework for assessing socioecological drivers of carnivore decline

Habitat loss, fragmentation and degradation are key threats to the long‐term persistence of carnivores, which are also susceptible to direct persecution by people. Integrating natural and social science methods to examine how habitat configuration/quality and human–predator relations may interact in space and time to effect carnivore populations within human‐dominated landscapes will help prioritise conservation investment and action effectively.

We propose a socioecological modelling framework to evaluate drivers of carnivore decline in landscapes where predators and people coexist. By collecting social and ecological data at the same spatial scale, candidate models can be used to quantify and tease apart the relative importance of different threats.

We apply our methodological framework to an empirical case study, the threatened güiña (Leopardus guigna) in the temperate forest ecoregion of southern Chile, to illustrate its use. Existing literature suggests that the species is declining due to habitat loss, fragmentation and persecution in response to livestock predation. Data used in modelling were derived from four seasons of camera‐trap surveys, remote‐sensed images and household questionnaires.

Occupancy dynamics were explained by habitat configuration/quality covariates rather than by human–predator relations. Güiñas can tolerate a high degree of habitat loss (>80% within a home range). They are primarily impacted by fragmentation and land subdivision (larger farms being divided into smaller ones). Ten per cent of surveyed farmers (N = 233) reported illegally killing the species over the past decade.

Synthesis and applications. By integrating ecological and social data, collected at the same spatial scale, within a single modelling framework, our study demonstrates the value of an interdisciplinary approach to assessing the potential threats to a carnivore. It has allowed us to tease apart effectively the relative importance of different potential extinction pressures for the güiña (Leopardus guigna), make informed conservation recommendations and prioritise where future interventions should be targeted. We have identified that human‐dominated landscapes with large intensive farms can be of conservation value, as long as an appropriate network of habitat patches is maintained within the matrix. Conservation efforts to secure the long‐term persistence of the species should focus on reducing habitat fragmentation rather than human persecution.

By integrating ecological and social data, collected at the same spatial scale, within a single modelling framework, our study demonstrates the value of an interdisciplinary approach to assessing the potential threats to a carnivore. It has allowed us to tease apart effectively the relative importance of different potential extinction pressures for the güiña (Leopardus guigna), make informed conservation recommendations and prioritise where future interventions should be targeted. We have identified that human‐dominated landscapes with large intensive farms can be of conservation value, as long as an appropriate network of habitat patches is maintained within the matrix. Conservation efforts to secure the long‐term persistence of the species should focus on reducing habitat fragmentation rather than human persecution.