Environmental and anthropogenic factors synergistically affect space use of jaguars

Development of a SNP Panel for Geographic Assignment and Population Monitoring of Jaguars (Panthera onca)

The jaguar (Panthera onca) is an iconic top predator that is threatened by habitat loss and fragmentation, along with an emerging expansion of poaching for the illegal trade of live individuals and their parts. To address the need for tools that improve surveillance and monitoring of its remaining populations, we have developed a genome-enabled single nucleotide polymorphism (SNP) panel targeting this species. From a dataset of 58 complete jaguar genomes, we identified and selected highly informative SNPs for geographic traceability, individual identification, kinship, and sexing. Our panel, named "Jag-SNP", comprises 459 SNPs selected from an initial pool of 13,373,949 markers based on the inter-biome F ST, followed by rigorous filtering and addition of eight sex-linked SNPs. We then randomly selected subsets of this panel and identified an 84-SNP set that exhibited a similar resolving power. With both the 459-SNP panel and its 84-SNP subset, samples were assigned with 98% success to their biomes of origin and 65%-69% of them were assigned to within 500 km of their origin. Furthermore, ca. 10-18 SNPs within these panels were sufficient to distinguish individuals, whereas 6 sex-linked SNPs perfectly separated males and females. We used whole-genome data from an additional 18 jaguars to further test these panels, which provided insights into kinship relationships and allowed inference of geographic origin of samples collected outside the spatial scope of the original sample set. These results support the strong potential of these panels as an efficient tool for application in forensic, genetic, ecological, behavioral and conservation projects targeting jaguars.

A reliance on human habitats is key to the success of an introduced predatory reptile

Understanding the success of animals in novel environments is increasingly important as human-mediated introductions continue to move species far beyond their natural ranges. Alongside these introductions, inhabited and agricultural areas are spreading, and correspondingly most animal introductions occur in populated areas. Commensal species which can live alongside humans by making use of specific conditions, structures, or prey, have a significant advantage. Introduced mammal species often use anthropogenic features in their environment and demonstrate a higher tolerance of human disturbance, but their importance remains understudied in ectotherms. The Aesculapian snake (Zamenis longissimus) is an ectotherm which has been introduced beyond the northern extremities of its natural range. To understand their persistence, we radio-tracked snakes daily over two active seasons, including high-frequency tracking of a subset of males. We investigated snake home range size using Autocorrelated Kernel Density Estimators (AKDE). Using AKDE-weighted Habitat Selection Functions we identified preferences for habitat features in a mosaic of habitats, and we used Integrated Step Selection Functions to further explore how these features influence movement. We revealed a particular preference for buildings in male snakes, while females preferred woodland. We demonstrate that the success of this ectothermic predator is likely tied to a willingness to use human features of the landscape.

Most Random-Encounter-Model Density Estimates in Camera-Based Predator-Prey Studies Are Unreliable

Identifying population-level relationships between predators and their prey is often predicated on having reliable population estimates. Camera-trapping is effective for surveying terrestrial wildlife, but many species lack individually unique natural markings that are required for most abundance and density estimation methods. Analytical approaches have been developed for producing population estimates from camera-trap surveys of unmarked wildlife; however, most unmarked approaches have strict assumptions that can be cryptically violated by survey design characteristics, practitioner choice of input values, or species behavior and ecology. Using multi-year datasets from populations of an unmarked predator and its co-occurring unmarked prey, we evaluated the consequences of violating two requirements of the random encounter model (REM), one of the first developed unmarked methods. We also performed a systematic review of published REM studies, with an emphasis on predator-prey ecology studies. Empirical data analysis confirmed findings of recent research that using detections from non-randomly placed cameras (e.g., on trails) and/or borrowing movement velocity (day range) values caused volatility in density estimates. Notably, placing cameras strategically to detect the predator, as is often required to obtain sufficient sample sizes, resulted in substantial density estimate inflation for both the predator and prey species. Systematic review revealed that 91% of REM density estimates in published predator-prey ecology studies were obtained using camera-trap data or velocity values that did not meet REM requirements. We suggest considerable caution making conservation or management decisions using REM density estimates from predator-prey ecology studies.

Habitat modification destabilizes spatial associations and persistence of Neotropical carnivores

Spatial relationships between sympatric species underpin biotic interactions, structure ecological communities, and maintain ecosystem health. However, the resilience of interspecific spatial associations to human habitat modification remains largely unknown, particularly in tropical regions where anthropogenic impacts are often greatest. We applied multi-state multi-species occurrence models to camera trap data across nine tropical landscapes in Colombia to understand how prominent threats to forest ecosystems influence Neotropical carnivore occurrence and interspecific spatial associations, with implications for biotic interactions. We show that carnivore occurrence represents a delicate balance between local environmental conditions and interspecific interactions that can be compromised in areas of extensive habitat modification. The stability of carnivore spatial associations depends on forest cover to mediate antagonistic encounters with apex predators and structurally intact forests to facilitate coexistence between competing mesocarnivores. Notably, we demonstrate that jaguars play an irreplaceable role in spatially structuring mesocarnivore communities, providing novel evidence on their role as keystone species. With increasing global change, conserving both the extent and quality of tropical forests is imperative to support carnivores and preserve the spatial associations that underpin ecosystem stability and resilience.

Ranging behaviours across ecological and anthropogenic disturbance gradients: a pan-African perspective of giraffe (Giraffa spp.) space use

Animal movement behaviours are shaped by diverse factors, including resource availability and human impacts on the landscape. We generated home range estimates and daily movement rate estimates for 149 giraffe (Giraffa spp.) from all four species across Africa to evaluate the effects of environmental productivity and anthropogenic disturbance on space use. Using the continuous time movement modelling framework and a novel application of mixed effects meta-regression, we summarized overall giraffe space use and tested for the effects of resource availability and human impact on 95% autocorrelated kernel density estimate (AKDE) size and daily movement. The mean 95% AKDE was 359.9 km2 and the mean daily movement was 14.2 km, both with marginally significant differences across species. We found significant negative effects of resource availability, and significant positive effects of resource heterogeneity and protected area overlap on 95% AKDE size. There were significant negative effects of overall anthropogenic disturbance and positive effects of the heterogeneity of anthropogenic disturbance on daily movements and 95% AKDE size. Our results provide unique insights into the interactive effects of resource availability and anthropogenic development on the movements of a large-bodied browser and highlight the potential impacts of rapidly changing landscapes on animal space-use patterns.

Jaguar density in the most threatened ecoregion of the Amazon

Population parameters provide essential information for conservation efforts aimed at target species. We used the spatially explicit capture-recapture method to estimate the jaguar density and population size in the Gurupi Jaguar Conservation Unit (JCU), located in the most threatened ecoregion of the Amazon. The estimated density of 2.62 individuals/100 km2 in a continuous forest of over 10,000 km2 implies a small effective population size, underscoring the threat to the long-term viability of the Gurupi JCU’s jaguar population. We recommend urgent forest restoration actions to reduce fragmentation and improve connectivity between Gurupi JCU and other forest fragments to facilitate jaguar gene flow.

A review of environmental and anthropogenic variables used to model jaguar occurrence

Jaguars (Panthera onca) are a landscape species of conservation importance and our understanding of environmental and anthropogenic drivers of jaguar occurrence is necessary to improve conservation strategies. We reviewed available literature to simply describe environmental and anthropogenic variables used and found to be significant in occurrence modeling. We reviewed 95 documents published from 1980 to 2021 that focused on jaguar occurrence and that used 39 variable types (21 anthropogenic, 18 environmental) among different techniques, scales, and approaches. In general, these variables included both anthropogenic (roads, land use, human activities, and population) and environmental (climate, vegetation, ecological interactions, topographic, water, and others) factors. Twelve variables were identified as affecting jaguar occurrence overall, eleven at local scale and seven at broad scales (regional and continental). Focusing more specifically on the variables that correlate with occurrence should help researchers to make better predictions in areas without quantitative jaguar data.

Wildfires disproportionately affected jaguars in the Pantanal

The Pantanal wetland harbours the second largest population of jaguars in the world. Alongside climate and land-use changes, the recent mega-fires in the Pantanal may pose a threat to the jaguars' long-term survival. To put these growing threats into perspective, we addressed the reach and intensity of fires that have affected jaguar conservation in the Pantanal ecoregion over the last 16 years. The 2020 fires were the most severe in the annual series, burned 31% of the Pantanal and affected 45% of the estimated jaguar population (87% of these in Brazil); 79% of the home range areas, and 54% of the protected areas within home ranges. Fires consumed core habitats and injured several jaguars, the Pantanal's apex predator. Displacement, hunger, dehydration, territorial defence, and lower fecundity are among the impacts that may affect the abundance of the species. These impacts are likely to affect other less mobile species and, therefore, the ecological stability of the region. A solution to prevent the recurrence of mega-fires lies in combating the anthropogenic causes that intensify drought conditions, such as implementing actions to protect springs, increasing the number and area of protected areas, regulating fire use, and allocating fire brigades before dry seasons.

Collaborative behaviour and coalitions in male jaguars (Panthera onca)—evidence and comparison with other felids

Abstract

Most large felids are classified as solitary species, with only lions (Panthera leo) and cheetahs (Acinonyx jubatus) exhibiting social, collaborative behaviours. Herein, we present evidence of the formation of male coalitions by jaguars (Panthera onca), based on data from five studies conducted with camera trapping, GPS telemetry, and direct observations in the Venezuelan Llanos and Brazilian Pantanal. Out of 7062 male records obtained with camera traps or visual observations, we detected 105 cases of male-male interactions, of which we classified 18 as aggression, nine as tolerance, 70 as cooperation/coalition, and eight as unidentified. In two studies, two male jaguars formed stable coalitions lasting over 7 years each. In the Llanos, each coalition male paired and mated with several females. For male jaguar coalitions, we documented similar behaviours as recorded earlier in lions or cheetahs, which included patrolling and marking territory together, invading territories of other males, collaborative chasing and killing other jaguars, and sharing prey. However, different from lions or cheetahs, associated male jaguars spent less time together, did not cooperate with females, and did not hunt cooperatively together. Our analysis of literature suggested that male jaguar coalitions were more likely to form when females had small home range size, a proxy of females’ concentration, while in lions, the male group size was directly correlated with the female group size. Similarly, locally concentrated access to females may drive formation of male coalitions in cheetahs. We conclude that high biomass and aggregation of prey are likely drivers of sociality in felids.

Significance statement

The division into social and solitary species in large felids has so far seemed unambiguous, with only lions and cheetahs classified as social species, in which male coalitions also occurred. Our data show that, under certain conditions, male coalitions may also form in jaguar populations. Factors that drive formation of male coalitions in lions and cheetahs, but not in other species of large cats, have not been clear until now. Our analyses indicate that in jaguars, lions, and cheetahs, the concentration of females likely plays the most important role. In jaguars, the probability of male coalition occurrence is highest in populations with the smallest mean female home range size (and thus likely high local density of females), while in lions, male group size is most strongly correlated with female group size.

Jaguars in the matrix: population, prey abundance and land-cover change in a fragmented landscape in western Mexico

Habitat fragmentation threatens biodiversity worldwide, particularly affecting large-bodied species that require vast territories and move across long distances, including most large felids. The jaguar Panthera onca has lost more than half of its habitat throughout its range and its subpopulations are becoming isolated, making them susceptible to local extinction. Knowledge about the status of its subpopulations in highly fragmented environments is lacking but urgently needed. Using camera traps during 2019–2020, we estimated number of individuals, age classes and sex ratio, occupancy, relative abundance and density of jaguars in Nayarit, western Mexico. We also determined the relative abundance of potential prey and estimated the land-cover change rate during 1999–2019, using GIS. We found that a resident subpopulation of five adult females, two adult males and one cub, at a high density (5.3 individuals/100 km2), is supported by at least 14 wild prey species. Natural habitat in the area is rapidly decreasing because of expanding agriculture and shrimp farming: agricultural areas increased from 39 to 50% and mangroves decreased from 35 to 26% of the study area over 20 years. The high jaguar population density and the diversity and relative abundance of remaining wild prey are remarkable, considering that natural habitat in the area is highly fragmented, shrinking rapidly and embedded in a matrix of human-dominated land-cover types. Effective conservation actions are needed urgently, including the protection of patches with native vegetation, reforestation to maintain connectivity between these patches, and the involvement of local communities.

Impacts of hydropower on the habitat of jaguars and tigers

The rapid expansion of hydropower across tropical landscapes has caused extensive habitat loss and degradation, triggering biodiversity loss. Despite known risks to freshwater biodiversity, the flooding of terrestrial habitats caused by dam construction, and associated impacts on terrestrial biota, have been rarely considered. To help fill this knowledge gap, we quantified the habitat loss following inundation of hydropower reservoirs across the range of two iconic species, jaguars and tigers. To do so, we compiled existing and planned dams intersecting the distribution of these apex predators. We found 164 dams intersecting the jaguar range, in total flooding 25,397 km². For tigers, we identified 421 dams, amounting to 13,750 km². As hydropower infrastructure is projected to expand in the decades ahead, these values are expected to increase greatly, particularly within the distribution of jaguars where the number of dams will nearly quadruple (429 planned dams). Despite the relatively few dams (41) planned across the range of tigers, most will intersect priority conservation areas for this species. We recommend a more cautious pursuit of hydropower in topographically flat regions, to avoid extensive habitat flooding which has occurred in the Neotropics, and avoiding dam construction in priority conservation landscapes for tigers.

Palmeirim and Gibson quantify the global habitat loss of jaguars and tigers due to existing and planned hydropower dams and relate these to published estimates of species densities from nearby regions. This analysis shows how dam construction intersects priority conservation areas for these apex predators.

Direct and indirect effects of roads on space use by jaguars in Brazil

Roads pose an imminent threat to wildlife directly through mortality and changes in individual behavior, and also indirectly through modification of the amount and configuration of wildlife habitat. However, few studies have addressed how these mechanisms interact to determine species response to roads. We used structural equation modeling to assess direct and indirect effects (via landscape modification) of roads on space use by jaguars in Brazil, using radio-tracking data available from the literature. We fit path models that directly link jaguars' space use to roads and to land cover, and indirectly link jaguars' space use to roads through the same land cover categories. Our findings show that space use by jaguars was not directly affected by roads, but indirect effects occurred through reductions in natural areas on which jaguars depend, and through urban sprawl. Males´ space use, however, was not negatively influenced by urban areas. Since jaguars seem to ignore roads, mitigation should be directed to road fencing and promoting safe crossings. We argue that planners and managers need to much more seriously take into account the deforestation and the unbridled urban expansion from roads to ensure jaguar conservation in Brazil.

Functional or Vestigial? The Genomics of the Pineal Gland in Xenarthra

Vestigial organs are historical echoes of past phenotypes. Determining whether a specific organ constitutes a functional or vestigial structure can be a challenging task, given that distinct levels of atrophy may arise between and within lineages. The mammalian pineal gland, an endocrine organ involved in melatonin biorhythmicity, represents a classic example, often yielding contradicting anatomical observations. In Xenarthra (sloths, anteaters, and armadillos), a peculiar mammalian order, the presence of a distinct pineal organ was clearly observed in some species (i.e., Linnaeus's two-toed sloth), but undetected in other closely related species (i.e., brown-throated sloth). In the nine-banded armadillo, contradicting evidence supports either functional or vestigial scenarios. Thus, to untangle the physiological status of the pineal gland in Xenarthra, we used a genomic approach to investigate the evolution of the gene hub responsible for melatonin synthesis and signaling. We show that both synthesis and signaling compartments are eroded and were probably lost independently among Xenarthra orders. Additionally, by expanding our analysis to 157 mammal genomes, we offer a comprehensive view showing that species with very distinctive habitats and lifestyles have convergently evolved a similar phenotype: Cetacea, Pholidota, Dermoptera, Sirenia, and Xenarthra. Our findings suggest that the recurrent inactivation of melatonin genes correlates with pineal atrophy and endorses the use of genomic analyses to ascertain the physiological status of suspected vestigial structures.