Dietary similarity among jaguars (Panthera onca) in a high-density population.

Prey remains found in carnivore scats provide generalised dietary profiles of sampled populations. The profile may be biased if individual diets differ and some individuals are over- or under-represented in the sample. Quantifying individual contributions allows us to recognise these potential biases and better interpret generalised profiles. Knowing the dietary differences or similarity between individuals can help us to understand selection pressures and identify drivers of distribution and abundance. Using the results of individual faecal genotyping, we re-interpreted our previously-published generalised dietary profile of an elusive, neotropical felid, the jaguar (Panthera onca; Foster et al. (2010)). We quantified individual sample sizes, assessed whether the generalised profile was influenced by the inclusion of scats originating from the same individual and prey carcass (pseudo-replication), and quantified the distribution of prey species among individuals. From an original sample of 322 jaguar scats from a high-density jaguar population in Belize, we identified 206 prey items (individual prey animals) in 176 independent scats representing 32 jaguars (26 males, 3 females, 3 unknown sex). The influence of pseudo-replication in the original dietary profile was minimal. The majority of scats (94%) came from male jaguars. Eight males accounted for two-thirds of the prey items, while 24 jaguars each contributed <5% of the prey items. With few exceptions, the jaguars followed the same broad diet, a 2:1:1 ratio of nine-banded armadillos (Dasypus noveminctus), other vertebrates ≤10kg, and ungulates, primarily peccaries (Tayassu pecari and Pecari tajacu). We noted prey switching between wild and domestic ungulates for individuals spanning protected forests and farmland. This first scat-based study exploring individual variation in jaguar diet highlights the importance of armadillos and peccaries for male jaguars in Belize, the need for research on their roles in supporting high-density jaguar populations, and the need for more data on female diet from across the jaguar range.

Long-term monitoring of margays (Leopardus wiedii): Implications for understanding low detection rates.

Population assessments of wide-ranging, cryptic, terrestrial mammals rely on camera trap surveys. While camera trapping is a powerful method of detecting presence, it is difficult distinguishing rarity from low detection rate. The margay (Leopardus wiedii) is an example of a species considered rare based on its low detection rates across its range. Although margays have a wide distribution, detection rates with camera traps are universally low; consequently, the species is listed as Near Threatened. Our 12-year camera trap study of margays in protected broadleaf forest in Belize suggests that while margays have low detection rate, they do not seem to be rare, rather that they are difficult to detect with camera traps. We detected a maximum of 187 individuals, all with few or no recaptures over the years (mean = 2.0 captures/individual ± SD 2.1), with two-thirds of individuals detected only once. The few individuals that were recaptured across years exhibited long tenures up to 9 years and were at least 10 years old at their final detection. We detected multiple individuals of both sexes at the same locations during the same survey, suggesting overlapping ranges with non-exclusive territories, providing further evidence of a high-density population. By studying the sparse annual datasets across multiple years, we found evidence of an abundant margay population in the forest of the Cockscomb Basin, which might have been deemed low density and rare, if studied in the short term. We encourage more long-term camera trap studies to assess population status of semi-arboreal carnivore species that have hitherto been considered rare based on low detection rates.

The differential genetic signatures related to climatic landscapes for jaguars and pumas on a continental scale.

Modern and paleoclimate changes may have altered species dynamics by shifting species' niche suitability over space and time. We analyze whether the current genetic structure and isolation of the two large American felids, jaguar (Panthera onca) and puma (Puma concolor), are mediated by changes in climatic suitability and connection routes over modern and paleoclimatic landscapes. We estimate species distribution under 5 climatic landscapes (modern, Holocene, last maximum glaciations [LMG], average suitability, and climatic instability) and correlate them with individuals' genetic isolation through causal modeling on a resemblance matrix. Both species exhibit genetic isolation patterns correlated with LMG climatic suitability, suggesting that these areas may have worked as "allele refuges." However, the jaguar showed higher vulnerability to climate changes, responding to modern climatic suitability and connection routes, whereas the puma showed a continuous and gradual transition of genetic variation. Despite differential responsiveness to climate change, both species are subjected to the climatic effects on genetic configuration, which may make them susceptible to future climatic changes, since these are progressing faster and with higher intensity than changes in the paleoclimate. Thus, the effects of climatic changes should be considered in the design of conservation strategies to ensure evolutionary and demographic processes mediated by gene flow for both species.

Using Continuous-Time Spatial Capture-Recapture models to make inference about animal activity patterns.

Quantifying the distribution of daily activity is an important component of behavioral ecology. Historically, it has been difficult to obtain data on activity patterns, especially for elusive species. However, the development of affordable camera traps and their widespread usage has led to an explosion of available data from which activity patterns can be estimated.Continuous-time spatial capture-recapture (CT SCR) models drop the occasion structure seen in traditional spatial and nonspatial capture-recapture (CR) models and use the actual times of capture. In addition to estimating density, CT SCR models estimate expected encounters through time. Cyclic splines can be used to allow flexible shapes for modeling cyclic activity patterns, and the fact that SCR models also incorporate distance means that space-time interactions can be explored. This method is applied to a jaguar dataset.Jaguars in Belize are most active and range furthest in the evening and early morning and when they are located closer to the network of trails. There is some evidence that females have a less variable pattern than males. The comparison between sexes demonstrates how CT SCR can be used to explore hypotheses about animal behavior within a formal modeling framework.SCR models were developed primarily to estimate and model density, but the models can be used to explore processes that interact across space and time, especially when using the CT SCR framework that models the temporal dimension at a finer resolution.

Spatially explicit capture recapture density estimates: Robustness, accuracy and precision in a long-term study of jaguars (Panthera onca).

Camera trapping is the standard field method of monitoring cryptic, low-density mammal populations. Typically, researchers run camera surveys for 60 to 90 days and estimate density using closed population spatially explicit capture-recapture (SCR) models. The SCR models estimate density, capture probability (g0), and a scale parameter (σ) that reflects ranging behaviour. We used a year of camera data from 20 camera stations to estimate the density of male jaguars (Panthera onca) in the Cockscomb Basin Wildlife Sanctuary in Belize, using closed population SCR models. We subsampled the dataset into 276 90-day sessions and 186 180-day sessions. Estimated density fluctuated from 0.51 to 5.30 male jaguars / 100 km2 between the 90-day sessions, with comparatively robust and precise estimates for the 180-day sessions (0.73 to 3.75 male jaguars / 100 km2). We explain the variation in density estimates from the 90-day sessions in terms of temporal variation in social behaviour, specifically male competition and mating events during the three-month wet season. Density estimates from the 90-day sessions varied with σ, but not with the number of individuals detected, suggesting that variation in density was almost fully attributable to changes in estimated ranging behaviour. We found that the models overestimated σ when compared to the mean ranging distance derived from GPS tracking data from two collared individuals in the camera grid. Overestimation of σ when compared to GPS collar data was more pronounced for the 180-day sessions than the 90-day sessions. We conclude that one-off ('snap-shot') short-term, small-scale camera trap surveys do not sufficiently sample wide-ranging large carnivores. When using SCR models to estimate the density from these data, we caution against the use of poor sampling designs and/or misinterpretation of scope of inference. Although the density estimates from one-off, short-term, small-scale camera trap surveys may be statistically accurate within each short-term sampling period, the variation between density estimates from multiple sessions throughout the year illustrate that the estimates obtained should be carefully interpreted and extrapolated, because different factors, such as temporal stochasticity in behaviour of a few individuals, may have strong repercussions on density estimates. Because of temporal variation in behaviour, reliable density estimates will require larger samples of individuals and spatial recaptures than those presented in this study (mean +/- SD = 14.2 +/- 1.2 individuals, 37.7 +/- 4.7 spatial recaptures, N = 276 sessions), which are representative of, or higher than published sample sizes. To satisfy the need for larger samples, camera surveys will need to be more expansive with a higher density of stations. In the absence of this, we advocate longer sampling periods and subsampling through time as a means of understanding and describing stability or variation between density estimates.

Consequences Matter: Compassion in Conservation Means Caring for Individuals, Populations and Species.

Human activity affecting the welfare of wild vertebrates, widely accepted to be sentient, and therefore deserving of moral concern, is widespread. A variety of motives lead to the killing of individual wild animals. These include to provide food, to protect stock and other human interests, and also for sport. The acceptability of such killing is widely believed to vary with the motive and method. Individual vertebrates are also killed by conservationists. Whether securing conservation goals is an adequate reason for such killing has recently been challenged. Conventional conservation practice has tended to prioritise ecological collectives, such as populations and species, when their interests conflict with those of individuals. Supporters of the 'Compassionate Conservation' movement argue both that conservationists have neglected animal welfare when such conflicts arise and that no killing for conservation is justified. We counter that conservationists increasingly seek to adhere to high standards of welfare, and that the extreme position advocated by some supporters of 'Compassionate Conservation', rooted in virtue ethics, would, if widely accepted, lead to considerable negative effects for conservation. Conservation practice cannot afford to neglect consequences. Moreover, the do-no-harm maxim does not always lead to better outcomes for animal welfare.

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.

Open population maximum likelihood spatial capture-recapture.

Open population capture-recapture models are widely used to estimate population demographics and abundance over time. Bayesian methods exist to incorporate open population modeling with spatial capture-recapture (SCR), allowing for estimation of the effective area sampled and population density. Here, open population SCR is formulated as a hidden Markov model (HMM), allowing inference by maximum likelihood for both Cormack-Jolly-Seber and Jolly-Seber models, with and without activity center movement. The method is applied to a 12-year survey of male jaguars (Panthera onca) in the Cockscomb Basin Wildlife Sanctuary, Belize, to estimate survival probability and population abundance over time. For this application, inference is shown to be biased when assuming activity centers are fixed over time, while including a model for activity center movement provides negligible bias and nominal confidence interval coverage, as demonstrated by a simulation study. The HMM approach is compared with Bayesian data augmentation and closed population models for this application. The method is substantially more computationally efficient than the Bayesian approach and provides a lower root-mean-square error in predicting population density compared to closed population models.

Ecological correlates of the spatial co-occurrence of sympatric mammalian carnivores worldwide.

The composition of local mammalian carnivore communities has far-reaching effects on terrestrial ecosystems worldwide. To better understand how carnivore communities are structured, we analysed camera trap data for 108 087 trap days across 12 countries spanning five continents. We estimate local probabilities of co-occurrence among 768 species pairs from the order Carnivora and evaluate how shared ecological traits correlate with probabilities of co-occurrence. Within individual study areas, species pairs co-occurred more frequently than expected at random. Co-occurrence probabilities were greatest for species pairs that shared ecological traits including similar body size, temporal activity pattern and diet. However, co-occurrence decreased as compared to other species pairs when the pair included a large-bodied carnivore. Our results suggest that a combination of shared traits and top-down regulation by large carnivores shape local carnivore communities globally.

Scraping marking behaviour of the largest Neotropical felids.

BACKGROUND: Details of how, why and in what conditions large felids make scrapes is unknown. Here, we examined the general hypothesis about the use of scrapes for marking proposals, as well as to communicate with other individuals to signalize particular points or areas of interest, by studying scrape-marking behaviour of jaguars and pumas. METHODS: We surveyed by scrapes between five days and two months mainly during dry season in five study areas from Mexico (El Edén and San Ignacio), Belize (Cockscomb) and Brazil (Angatuba and Serra das Almas), which differed in presence and/or abundance of jaguars and pumas. Paths were slowly walked while searching for scrapes by teams normally composed of two people and tracks were stored in GPS, distinguishing the type of path surveyed (unpaved track roads, trails and cross-country). RESULTS: We found a total of 269 felid scrapes along 467 km of paths surveyed, obtaining a finding rate of 0.576 scrapes per km. Most scrapes were found in car tracks (0.629 scrapes per km), followed by trails (0.581 scrapes per km), and rarely did we find scrapes in cross country (0.094 scrapes per km). In trails, scrapes were found in a similar frequency in the centre and edge, whereas in car tracks they were mainly found in the edge. There were also clear differences in the position of the scrapes between study areas that differed in presence and/or abundance of pumas and jaguars, with scrapes located mainly in the centre in areas only with pumas, in the centre and in the edge in areas with a similar number of jaguars and pumas, and in the edge in area mainly dominated by jaguars. The remarking rate tended to be higher in one of the areas with only pumas where natural vegetation was scarcer. Felids chose sites mainly covered by leaves and located in paths less wide, clean and rarely used. DISCUSSION: Scraping was a frequent behaviour in the largest felids of America, although in some areas, scraping behaviour was rare. Scrapes seem to be signalizing some specific areas within territories and data suggest that they are made with the proposal of communication between individuals. It seems that a high scraping behaviour in pumas is not related to the presence of jaguars.

Long term monitoring of jaguars in the Cockscomb Basin Wildlife Sanctuary, Belize; Implications for camera trap studies of carnivores.

In this study, we estimate life history parameters and abundance for a protected jaguar population using camera-trap data from a 14-year monitoring program (2002-2015) in Belize, Central America. We investigated the dynamics of this jaguar population using 3,075 detection events of 105 individual adult jaguars. Using robust design open population models, we estimated apparent survival and temporary emigration and investigated individual heterogeneity in detection rates across years. Survival probability was high and constant among the years for both sexes (φ = 0.78), and the maximum (conservative) age recorded was 14 years. Temporary emigration rate for the population was random, but constant through time at 0.20 per year. Detection probability varied between sexes, and among years and individuals. Heterogeneity in detection took the form of a dichotomy for males: those with consistently high detection rates, and those with low, sporadic detection rates, suggesting a relatively stable population of 'residents' consistently present and a fluctuating layer of 'transients'. Female detection was always low and sporadic. On average, twice as many males than females were detected per survey, and individual detection rates were significantly higher for males. We attribute sex-based differences in detection to biases resulting from social variation in trail-walking behaviour. The number of individual females detected increased when the survey period was extended from 3 months to a full year. Due to the low detection rates of females and the variable 'transient' male subpopulation, annual abundance estimates based on 3-month surveys had low precision. To estimate survival and monitor population changes in elusive, wide-ranging, low-density species, we recommend repeated surveys over multiple years; and suggest that continuous monitoring over multiple years yields even further insight into population dynamics of elusive predator populations.

Ticks and rickettsiae from wildlife in Belize, Central America.

BACKGROUND: The agents of spotted fevers in Latin America are Rickettsia rickettsii, R. parkeri, Rickettsia sp. strain Atlantic rainforest, and R. massiliae. In Continental Central America, R. rickettsii remains the only known pathogenic tick-borne rickettsia. In the present study, ticks were collected from wild mammals in natural areas of Belize. Besides providing new data of ticks from Belize, we investigated rickettsial infection in some of these ticks. Our results provide ticks harboring rickettsial agents for the first time in Central America. METHODS: Between 2010 and 2015, wild mammals were lived-trapped in the tropical broadleaf moist forests of central and southern Belize. Ticks were collected from the animals and identified to species by morphological and molecular analysis (DNA sequence of the tick mitochondrial 16S RNA gene). Some of the ticks were tested for rickettsial infection by molecular methods (DNA sequences of the rickettsial gltA and ompA genes). RESULTS: A total of 84 ticks were collected from 8 individual hosts, as follows: Amblyomma pacae from 3 Cuniculus paca; Amblyomma ovale and Amblyomma coelebs from a Nasua narica; A. ovale from an Eira Barbara; A. ovale, Amblyomma cf. oblongoguttatum, and Ixodes affinis from a Puma concolor; and A. ovale, A. coelebs, A. cf. oblongoguttatum, and I. affinis from two Panthera onca. Three rickettsial agents were detected: Rickettsia amblyommii in A. pacae, Rickettsia sp. strain Atlantic rainforest in A. ovale, and Rickettsia sp. endosymbiont in Ixodes affinis. CONCLUSIONS: The present study provides unprecedented records of ticks harboring rickettsial agents in the New World. An emerging rickettsial pathogen of South America, Rickettsia sp. strain Atlantic rainforest, is reported for the first time in Central America. Besides expanding the distribution of 3 rickettsial agents in Central America, our results highlight the possible occurrence of Rickettsia sp. strain Atlantic rainforest-caused spotted fever human cases in Belize, since its possible vector, A. ovale, is recognized as one of the most important human-biting ticks in the Neotropical region.