Listeria monocytogenes is responsible for severe foodborne disease and major economic losses, but... more Listeria monocytogenes is responsible for severe foodborne disease and major economic losses, but its potential reservoirs in natural ecosystems remain poorly understood. Here, we report the draft genome sequences of 158 L. monocytogenes strains isolated from black bears ( Ursus americanus ) in the southeastern United States between 2014 and 2017.
International Journal of Primatology, May 21, 2016
Primate populations, including Madagascar's lemurs, are threatened worldwide and conservationists... more Primate populations, including Madagascar's lemurs, are threatened worldwide and conservationists need accurate population estimates to develop targeted conservation plans. We sought to fill knowledge gaps for three lemur taxa-whitefronted brown lemur (Eulemur albifrons); eastern woolly lemur (Avahi laniger); and Allocebus/Microcebus, a category combining observations of hairy-eared dwarf lemurs (Allocebus trichotis) and mouse lemurs (Microcebus spp.)-in northeastern Madagascar by estimating their density, examining how their encounter rates and densities vary across three different forest types, and monitoring trends in encounter rates and densities at resurveyed sites, using data from surveys at six forest sites over a 4-year period (2010-2013). Landscape density for white-fronted brown lemur, eastern woolly lemur, and Allocebus/Microcebus was 21.5 (SE 3.67), 57.7 (SE 9.17), and 39.1 (SE 9.55) individuals/km 2 , respectively. There was no difference in density estimates at intact and intermediately degraded forest sites; however, we encountered white-fronted brown lemurs more often in intact forest (1.64 ± SE 0.40 individuals/km) than in intermediately degraded and degraded forest (0.15 ± SE 0.06 and 0.16 ± SE 0.06 individuals/km). In addition, we encountered white-fronted brown lemurs at lower rates in 2013 (0.15 ± SE 0.06 individuals/km) compared to 2010 (0.82 ± SE 0.12 individuals/km) at a resurveyed site. Our findings emphasize that primate researchers must account for variation in how lemur encounter rates and densities differ between intact Int J Primatol
Data are presented on the demography and reproductive success of cheetahs (Acinonyx jubatus) livi... more Data are presented on the demography and reproductive success of cheetahs (Acinonyx jubatus) living on the Serengeti Plains, Tanzania over a 25-year period. Average age at independence was 17.1 months, females gave birth to their first litter at approximately 2.4 years old, inter-birth interval was 20.1 months, and average litter size at independence was 2.1 cubs. Females who survived to independence lived on average 6.2 years while minimum male average longevity was 2.8 years for those born in the study area and 5.3 years for immigrants, with a large proportion of males dispersing out of the Plains population. Females produced on average only 1.7 cubs to independence in their entire lifetime and their average reproductive rates were 0.36 cubs per year or 0.17 litters per year to independence. Variance in lifetime reproductive success in the cheetah is similar to that of other mammals. No significant negative correlations were found between adult cheetah population size and numbers of cubs reaching independence, implying that the Plains population had not reached carrying capacity. Annual numbers of adult female cheetahs only were correlated with rainfall. Adult female cheetah numbers were not correlated with adult female lion numbers on the Plains, however, reproductive rates of cheetahs were negatively correlated with the presence of lions while cheetahs had cubs. Moreover, cheetah reproductive success was lower during the period of high lion abundance (1980±1994) than during the earlier period of relatively few lions (1969±1979). Litter size at independence dropped from 2.5 to 2.0, lifetime reproductive success declined from 2.1 to 1.6 cubs reared to independence, and the reproductive rate (cubs/year) decreased from 0.42 to 0.36 from the earlier to the later period. Cheetah reproductive success showed little association with the presence of Thomson's gazelle at sightings except for a negative correlation between large numbers of gazelle (200±500) and reproductive success possibly because hunting success decreases with increasing prey herd size, or because cheetahs always lose in direct competition with other predators which are attracted to large congregations of prey. In addition, cheetah reproductive success was negatively correlated with the presence of Grant's gazelles (11 or more) perhaps because Grant's gazelles were more likely to occur consistently in dry areas.
Madagascar's native small mammals (Tenrecidae and Nesomyinae) are understudied. To help fill thes... more Madagascar's native small mammals (Tenrecidae and Nesomyinae) are understudied. To help fill these knowledge gaps, we analyzed 1,575 detections of small mammals obtained during camera-trap surveys at 7 sites in northeastern Madagascar (2008-2011) using single-season occupancy analyses in program PRESENCE. We estimated landscape occupancy and detection probabilities of tufted-tailed rats (Eliurus spp.), red forest rats (Nesomys spp.), greater hedgehog tenrecs (Setifer setosus), and common tenrecs (Tenrec ecaudatus) and examined how these parameters responded to habitat characteristics, habitat degradation, and the trap success of native and exotic carnivorans. Only Nesomys showed a marked difference in mean occupancy between intact (ψ = 0.71 ± SE 0.06), intermediately degraded (ψ = 0.23 ± SE 0.05), and degraded (ψ = 0.34 ± SE 0.06) forest sites. Only Nesomys and Setifer occupancy was strongly influenced by habitat characteristics; Nesomys occupancy was positively related to distance away from forest edge (β = 1.39 ± SE 0.27) and percent rainforest cover (β = 1.89 ± SE 0.39), and Setifer occupancy negatively related to average canopy height (β = −0.52 ± SE 0.25). We found trap success of exotic carnivorans had little influence on small mammal occupancy and detection probabilities (with the exception of Eliurus). We suggest that camera traps are a valid method for studying aspects of small mammal ecology, but caution researchers to consider characteristics of camera traps (e.g., trigger speed) to increase potential inference.
Estimating coyote (Canis latrans) density and other demographic parameters is difficult, particul... more Estimating coyote (Canis latrans) density and other demographic parameters is difficult, particularly for populations that exist at low density. This is the situation for recently established coyote populations in the eastern United States where populations may be below carrying capacity and growth unregulated. We used non-invasive fecal DNA collected from 5 scat sampling sessions over 2.5 years to estimate population parameters (i.e., density, apparent survival, recruitment, and population growth) for coyotes at 2 different sites in the Ridge and Valley region of the central Appalachians in Virginia, USA. We identified individuals using microsatellite genotypes and estimated apparent survival for the local population at both sites across the 5 sessions in a single Cormack-Jolly-Seber model. We estimated density for each site and session separately using single session spatial replicates of 0.5-km transect segments as traps in a spatial capture-recapture model. Finally, we derived estimates of recruitment and population growth using an ad hoc robust design approach. We were able to estimate population parameters, even though coyote densities at both sites were low. Generally, derived recruitment and apparent survival were inversely related across sites, however, precision in estimates was poor. Thus, although there appeared to be some differences in demographic estimates for local coyote populations, uncertainty in parameters was too great to detect changes in demographic rates over short periods of time using ad hoc robust design. However, the non-invasive genetic sampling and spatial capture-recapture approach provides a useful methodology and framework for future research intended to estimate population dynamics for coyotes. This method will also be useful for other species that occur at low densities, over large spatial scales, and lack distinguishing marks for cameratrap surveys. Finally, we believe this method will allow for detection of population trends over greater periods of time, and we consider alternate sampling strategies and modeling approaches that may improve the ability to estimate demographic rates of change for coyote populations using noninvasive genetics and spatial capture-recapture.
Herniation of viscera induced by medical intervention has been described in carnivores, yet occur... more Herniation of viscera induced by medical intervention has been described in carnivores, yet occurrence of hernias causing wild carnivore mortality, including in bears, remains unknown. We describe an inguinal hernia, intestinal entrapment and rupture, and peritonitis causing mortality in a male American black bear (Ursus americanus). In the autumn of 2014, a free-ranging, adult bear was housed at Virginia Tech's Black Bear Research Center. After 13 days in captivity, the bear showed signs of lethargy and intermittent inappetence consistent with the onset of hibernating behaviors. However, the bear suddenly displayed rapid deterioration and died before medical assistance could be provided. During necropsy examination, a devitalized portion of small intestine was found entrapped in the left inguinal ring. An intestinal perforation was evident near the entrapment area, which caused a subsequent peritonitis. To our knowledge this is the first report of bear mortality due to inguinal herniation with subsequent perforation and peritonitis.
Sparse detections in camera trap surveys commonly hinder density estimation for threatened specie... more Sparse detections in camera trap surveys commonly hinder density estimation for threatened species. By combining detections across multiple surveys, or using informative priors in Bayesian model fitting, researchers can improve parameter estimation from sparse capture–recapture data. Using a spatial mark–resight model that incorporates site‐level heterogeneity in the spatial scale parameter via a hierarchical process and prior information, we estimated the density of a threatened carnivore (fosa, Cryptoprocta ferox) from multiple sparse datasets collected during extensive camera trapping surveys in northeastern Madagascar (2008–2015). Our objectives were to estimate density for six sites, examine the response of fosa density and movement to habitat degradation, monitor annual density trends across 7 years at two sites, and estimate fosa abundance in the Makira–Masoala protected area complex. We obtained a mean of 16.1 (se = 0.52; range = 2–49) fosa detections and three observers identified a mean of 3.62 (se = 0.09; range = 1–8) marked individuals per survey. Fosa daily baseline encounter rate was very low (λ0 = 0.004; 0.003–0.006) and density/movement estimates were similar across forest types. Density estimates at resurveyed sites suggested annual variability in density, with estimates trending lower during the final surveys [e.g. D = 0.39 (0.14–1.11) versus 0.08 (0.05–0.31) individuals per km2]. We estimated fosa abundance across the Makira–Masoala region to be 1061 (95% HPDI: 596–1780) adult individuals. On the basis of our estimate and the size of the region, we believe Makira–Masoala harbors a significant portion of the global fosa population. The conservation and management of rare species is commonly limited due to lack of population estimates. By combining detections across surveys, we overcame estimation issues and obtained valuable information on a threatened carnivore, allowing us to better assess its status and prioritize conservation actions. We advocate for practical use of sparse datasets for such data‐deficient species.
The presence of exotic predators in ecosystems across the world is a leading driver of native spe... more The presence of exotic predators in ecosystems across the world is a leading driver of native species' declines. Exotic predators largely influence native species through predation and harassment, which may cause native species to avoid them spatially. We used a camera trap dataset from seven sites in Madagascar's largest protected area complex to investigate spatial co-occurrence patterns between three exotic predators (free-ranging domestic dogs Canis familiaris and cats Felis silvestris, and small Indian civet Viverricula indica) and native ground-dwelling forest birds (n = 5) and small mammals (n = 4). We created 216 two-species occupancy models for 27 exotic predator-native species pairings to examine how habitat, exotic predator presence or both, influenced each native species' occupancy and/or detection. We found that native bird and small mammal occupancy and/or detection were strongly related to an exotic predator's presence 52% of the time (i.e. 14 of 27 exotic predator-native species pairings). Six of the 14 species pairings (i.e. 43%) had non-independent co-occurrence patterns, four of which were habitatmediated. The effect of exotic predator presence on native species' detection was largely negative, depressing native species' detection in seven out of 12 instances (i.e. 58% of the time). The small Indian civet and free-ranging cats each strongly influenced the occupancy and/or detection of six species for a combined impact on seven native species, while domestic dogs strongly influenced two species. By including habitat covariates in two-species occupancy models, we gained deeper insight into the effect exotic predator presence has on native species' distribution. We also note that the strong effect of exotic predator presence on our ability to detect native species can hinder the ability of researchers to provide accurate parameter estimates. We recommend future research into the synergistic effects that habitat degradation and exotic species presence has on native species.
Population density estimates are necessary to inform management and conservation, yet are difficu... more Population density estimates are necessary to inform management and conservation, yet are difficult to obtain for cryptic species such as carnivores, and often require intensive sampling. We implemented a single-survey, closed session, scat sampling protocol to estimate bobcat density using fecal DNA and spatial capture-recapture at two sites over five sessions in Virginia, USA. We employed a Poisson encounter model to allow for multiple detections on scat transect segments over a single collection interval, and compared single session and multistrata (closed, multi-site, multisession) spatial capturerecapture (SCR) approaches to estimate density for each site and session. We found improved precision for most estimates using the multistrata SCR approach, sharing data on baseline detection and individual movement across sites and sessions. We suggest the summer session estimates are representative of the resident population, that differences in density between summer and winter are representative of potential net recruitment, and that differences between consecutive summer sessions are representative of the net recruitment realized for the population (dependent on survival and emigration). Finally, we assessed factors affecting precision in single session model estimates and provide recommendations to improve detection and reduce credible intervals that may be applicable across the bobcat range and to other carnivore species. The single survey transect methodology provides flexibility in monitoring carnivore populations specifically, or as part of concurrent monitoring for multiple carnivore species. This methodology has potential to dramatically increase the effectiveness of conservation and management dollars, improving our ability to monitor carnivore populations and assess conservation needs and actions.
Diet studies are frequently used to improve understanding of predator ecology, potential effects ... more Diet studies are frequently used to improve understanding of predator ecology, potential effects of carnivores on prey populations, and competition among predators. However, field identification of carnivore scat typically relies on scat morphology, size, and contents resulting in possible subjective predator identification and potentially biased results. Advancements in noninvasive genetic sampling allow for molecular identification of predator scat, eliminating many issues associated with field identification methods. We collected scat samples once per month from June 2011 to May 2012 in western Virginia, USA, using morphological characteristics for field identification of the predator. We then used mitochondrial DNA to identify the predator species of each scat and identified prey remains visually. Using confusion matrices, we found a range of accuracy in field identification for the 3 target species: coyotes (Canis latrans; 54.0%), bobcats (Lynx rufus; 57.1%), and black bears (Ursus americanus; 95.2%), even though we only considered samples with high-confidence field identification. We found a high coyote false-positive rate (52.7%), indicating we often incorrectly identified scats as coyote (98% of misidentified bobcat scats and 75% of misidentified black bear scats were recorded as coyote in the field). This asymmetrical bias in predator identification resulted in inaccurate estimates of dietary niche breadth and overlap between competitors. Our results suggest that caution should be exercised when interpreting results from studies in which carnivore species are identified by scat morphology. Future studies should employ noninvasive genetic sampling for carnivore scat identification, especially in areas with sympatric predator species that have similar scat morphology.
Despite exceptionally high levels of biodiversity and endemism found in Madagascar, much of its w... more Despite exceptionally high levels of biodiversity and endemism found in Madagascar, much of its wildlife remains little studied, particularly the carnivore community. The recently described, little-known black forest cat (locally known as "fitoaty") is believed to be restricted to NE Madagascar and has been investigated only through village surveys and anecdotal accounts. From 2008 to 2012, we photographically sampled 7 forest sites with varying degrees of degradation and fragmentation across Makira Natural Park with the goals of: 1) estimating landscape occupancy for fitoaty (Felis spp.), 2) identifying variables influencing fitoaty occupancy, and 3) comparing fitoaty and feral cat (Felis spp.) occupancy across the landscape. We observed higher occupancy for fitoaty, minimal co-occurrence between fitoaty and feral cats (n = 2 sites), and strong divergence in habitat use. We provide the 1st assessment of fitoaty morphology, including comparisons with anecdotal reports, and the 1st population assessment of Madagascar's exotic cat community with insights into factors associated with carnivore population trends in Madagascar. We suggest the described fitoaty is a phenotypically different form of the feral cat, but additional research is needed. Targeted management plans are needed to diminish the spread and potential negative effects of invasive cats across this important biologically diverse ecoregion.
Borner and others at FZS, as well as T. Mariki. AH thanks Ulrike Hilborn for data entry and gener... more Borner and others at FZS, as well as T. Mariki. AH thanks Ulrike Hilborn for data entry and general support and Ray Hilborn for help with R. We also thank Dr. Matt Hayward and an anonymous reviewer for their helpful comments.
Surveys across multiple seasons or years are necessary to evaluate the effects of dynamic process... more Surveys across multiple seasons or years are necessary to evaluate the effects of dynamic processes on long-term persistence of wildlife populations, such as effects of exotic species on native species populations. Unfortunately, multi-year surveys are rare, particularly for rainforest carnivore populations, and managers often rely on singleseason/year, 'snapshot' surveys that produce static estimates of population parameters. Here we provide results using single-species, multi-year occupancy modeling from a six-year survey (2008-2013) of a rainforest carnivore community at a 15 km 2 area study site within the newly established Makira Natural Park, Madagascar. We demonstrate a precipitous decline in the native carnivore community with four of the six native carnivores (falanouc Eupleres goudotii, ring-tailed vontsira Galidia elegans, broad-striped vontsira Galidictis fasciata, and brown-tailed vontsira Salanoia concolor) decreasing by at least 60% over this six-year period. In addition, we observed two exotic carnivores (small Indian civet Viverricula indica and feral cat Felis species) colonize this study site with Felis species increasing in occupancy from 0 to 0.68 by the final year. Further, we demonstrate how variables associated with human encroachment (i.e. distance to forest edge and nearest village) are most important for explaining these trends in native carnivore extirpation and exotic carnivore colonization. These findings provide additional evidence on the threat posed to native carnivore populations by the expansion of exotic carnivores worldwide. We highlight the striking increase in extirpation, and the factors influencing such changes, for native carnivores. In this manuscript, we point to the limited number of multi-year surveys to evaluate dynamic processes on long-term persistence of native wildlife populations, as well as the lack of exotic carnivore control programs in threatened ecosystems in many developing nations as factors limiting our ability to effectively conserve biodiversity across the globe.
With fewer than 200 tigers (Panthera tigris tigris) left in Nepal, that are generally confined to... more With fewer than 200 tigers (Panthera tigris tigris) left in Nepal, that are generally confined to five protected areas across the Terai Arc Landscape, genetic studies are needed to provide crucial information on diversity and connectivity for devising an effective country-wide tiger conservation strategy. As part of the Nepal Tiger Genome Project, we studied landscape change, genetic variation, population structure, and gene flow of tigers across the Terai Arc Landscape by conducting Nepal's first comprehensive and systematic scat-based, non-invasive genetic survey. Of the 770 scat samples collected opportunistically from five protected areas and six presumed corridors, 412 were tiger (57%). Out of ten microsatellite loci, we retain eight markers that were used in identifying 78 individual tigers. We used this dataset to examine population structure, genetic variation, contemporary gene flow, and potential population bottlenecks of tigers in Nepal. We detected three genetic clusters consistent with three demographic sub-populations and found moderate levels of genetic variation (H e = 0.61, A R = 3.51) and genetic differentiation (F ST = 0.14) across the landscape. We detected 3-7 migrants, confirming the potential for dispersal-mediated gene flow across the landscape. We found evidence of a bottleneck signature likely caused by large-scale landuse change documented in the last two centuries in the Terai forest. Securing tiger habitat including functional forest corridors is essential to enhance gene flow across the landscape and ensure long-term tiger survival. This requires cooperation among multiple stakeholders and careful conservation planning to prevent detrimental effects of anthropogenic activities on tigers.
This article has been accepted for publication and undergone full peer review but has not been th... more This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record. Please cite this article as
Better conservation planning requires updated information about leopard distribution to prioritiz... more Better conservation planning requires updated information about leopard distribution to prioritize and allocate limited resources available. The long-term persistence of leopards and sympatric tigers can be compromised by linear infrastructure development such as roads that fragment habitat. We used detection and non-detection data collected along walking search paths (~4140 km) in 96 grid cells (each cell 15 km by 15 km) spread across potential habitat (~13,845 km 2) in the Terai Arc Landscape, Nepal. Multi-season occupancy models allowed us to make both spatial and temporal inferences between two surveys in 2009 and 2013, based on ecologically relevant covariates recorded in the field or remotely sensed. Additionally, we used 2013 data to make inferences on co-occurrence between tigers and leopards at the landscape level. We found the additive model containing deforestation and district roads negatively influenced leopard detection across the landscape. Although weak, we found anthropogenic factors such as extent of deforestation (decrease in forest cover) negatively affected leopard occupancy. Road abundance, especially for the east-west highway and district roads, also negatively (but weakly) influenced leopard occupancy. We found substantially lower occupancy in the year 2013 (0.59 (SE 0.06)) than in 2009 (0.86 (SE 0.04)). Tigers and leopards co-occurred across the landscape based on the species interaction factor (SIF) estimated at 1.47 (0.13) but the amount of available habitat and the prey index mediated co-occurrence. The SIF decreased as habitat availability increased, reaching independence at large habitat patches, but leopard occupancy declined in sites with tigers, primarily in large patches. The prey index was substantially lower outside of protected areas and leopards and tigers co-occurred more strongly in small patches and at low prey indices, indicating potential attraction to the same areas when prey is scarce. Mitigation measures should focus on preventing loss of
We assessed the effects of cub age, litter size, and sex, on body mass (BM), absolute and relativ... more We assessed the effects of cub age, litter size, and sex, on body mass (BM), absolute and relative growth rates (AGR, RGR), opening of ears and eyes, and deciduous teeth eruption from 129 cubs of American black bears (Ursus americanus) born at Virginia Tech’s Black Bear Research Center. Specific ages, related to maternal food consumption, and litter size, best described BM, AGR, RGR, and ear and eye development. Overall, newborns weighed ~0.44 kg at birth and increased ~9-fold by ~14 weeks. Twins were greater in BM than single cubs and triplets. Single and triplet cubs had higher AGR and RGR than twins after mothers resumed food consumption post-hibernation. Newborns displayed RGR > 3.5% that decreased until den emergence (RGR < 3.5% after emergence). RGR differed among litter sizes, particularly after den emergence. Ear and eye opening occurred concurrently at ~44 days of age, while teeth erupted ~10 days later. Single cubs experienced delayed development of these organs comp...
Listeria monocytogenes is responsible for severe foodborne disease and major economic losses, but... more Listeria monocytogenes is responsible for severe foodborne disease and major economic losses, but its potential reservoirs in natural ecosystems remain poorly understood. Here, we report the draft genome sequences of 158 L. monocytogenes strains isolated from black bears ( Ursus americanus ) in the southeastern United States between 2014 and 2017.
International Journal of Primatology, May 21, 2016
Primate populations, including Madagascar's lemurs, are threatened worldwide and conservationists... more Primate populations, including Madagascar's lemurs, are threatened worldwide and conservationists need accurate population estimates to develop targeted conservation plans. We sought to fill knowledge gaps for three lemur taxa-whitefronted brown lemur (Eulemur albifrons); eastern woolly lemur (Avahi laniger); and Allocebus/Microcebus, a category combining observations of hairy-eared dwarf lemurs (Allocebus trichotis) and mouse lemurs (Microcebus spp.)-in northeastern Madagascar by estimating their density, examining how their encounter rates and densities vary across three different forest types, and monitoring trends in encounter rates and densities at resurveyed sites, using data from surveys at six forest sites over a 4-year period (2010-2013). Landscape density for white-fronted brown lemur, eastern woolly lemur, and Allocebus/Microcebus was 21.5 (SE 3.67), 57.7 (SE 9.17), and 39.1 (SE 9.55) individuals/km 2 , respectively. There was no difference in density estimates at intact and intermediately degraded forest sites; however, we encountered white-fronted brown lemurs more often in intact forest (1.64 ± SE 0.40 individuals/km) than in intermediately degraded and degraded forest (0.15 ± SE 0.06 and 0.16 ± SE 0.06 individuals/km). In addition, we encountered white-fronted brown lemurs at lower rates in 2013 (0.15 ± SE 0.06 individuals/km) compared to 2010 (0.82 ± SE 0.12 individuals/km) at a resurveyed site. Our findings emphasize that primate researchers must account for variation in how lemur encounter rates and densities differ between intact Int J Primatol
Data are presented on the demography and reproductive success of cheetahs (Acinonyx jubatus) livi... more Data are presented on the demography and reproductive success of cheetahs (Acinonyx jubatus) living on the Serengeti Plains, Tanzania over a 25-year period. Average age at independence was 17.1 months, females gave birth to their first litter at approximately 2.4 years old, inter-birth interval was 20.1 months, and average litter size at independence was 2.1 cubs. Females who survived to independence lived on average 6.2 years while minimum male average longevity was 2.8 years for those born in the study area and 5.3 years for immigrants, with a large proportion of males dispersing out of the Plains population. Females produced on average only 1.7 cubs to independence in their entire lifetime and their average reproductive rates were 0.36 cubs per year or 0.17 litters per year to independence. Variance in lifetime reproductive success in the cheetah is similar to that of other mammals. No significant negative correlations were found between adult cheetah population size and numbers of cubs reaching independence, implying that the Plains population had not reached carrying capacity. Annual numbers of adult female cheetahs only were correlated with rainfall. Adult female cheetah numbers were not correlated with adult female lion numbers on the Plains, however, reproductive rates of cheetahs were negatively correlated with the presence of lions while cheetahs had cubs. Moreover, cheetah reproductive success was lower during the period of high lion abundance (1980±1994) than during the earlier period of relatively few lions (1969±1979). Litter size at independence dropped from 2.5 to 2.0, lifetime reproductive success declined from 2.1 to 1.6 cubs reared to independence, and the reproductive rate (cubs/year) decreased from 0.42 to 0.36 from the earlier to the later period. Cheetah reproductive success showed little association with the presence of Thomson's gazelle at sightings except for a negative correlation between large numbers of gazelle (200±500) and reproductive success possibly because hunting success decreases with increasing prey herd size, or because cheetahs always lose in direct competition with other predators which are attracted to large congregations of prey. In addition, cheetah reproductive success was negatively correlated with the presence of Grant's gazelles (11 or more) perhaps because Grant's gazelles were more likely to occur consistently in dry areas.
Madagascar's native small mammals (Tenrecidae and Nesomyinae) are understudied. To help fill thes... more Madagascar's native small mammals (Tenrecidae and Nesomyinae) are understudied. To help fill these knowledge gaps, we analyzed 1,575 detections of small mammals obtained during camera-trap surveys at 7 sites in northeastern Madagascar (2008-2011) using single-season occupancy analyses in program PRESENCE. We estimated landscape occupancy and detection probabilities of tufted-tailed rats (Eliurus spp.), red forest rats (Nesomys spp.), greater hedgehog tenrecs (Setifer setosus), and common tenrecs (Tenrec ecaudatus) and examined how these parameters responded to habitat characteristics, habitat degradation, and the trap success of native and exotic carnivorans. Only Nesomys showed a marked difference in mean occupancy between intact (ψ = 0.71 ± SE 0.06), intermediately degraded (ψ = 0.23 ± SE 0.05), and degraded (ψ = 0.34 ± SE 0.06) forest sites. Only Nesomys and Setifer occupancy was strongly influenced by habitat characteristics; Nesomys occupancy was positively related to distance away from forest edge (β = 1.39 ± SE 0.27) and percent rainforest cover (β = 1.89 ± SE 0.39), and Setifer occupancy negatively related to average canopy height (β = −0.52 ± SE 0.25). We found trap success of exotic carnivorans had little influence on small mammal occupancy and detection probabilities (with the exception of Eliurus). We suggest that camera traps are a valid method for studying aspects of small mammal ecology, but caution researchers to consider characteristics of camera traps (e.g., trigger speed) to increase potential inference.
Estimating coyote (Canis latrans) density and other demographic parameters is difficult, particul... more Estimating coyote (Canis latrans) density and other demographic parameters is difficult, particularly for populations that exist at low density. This is the situation for recently established coyote populations in the eastern United States where populations may be below carrying capacity and growth unregulated. We used non-invasive fecal DNA collected from 5 scat sampling sessions over 2.5 years to estimate population parameters (i.e., density, apparent survival, recruitment, and population growth) for coyotes at 2 different sites in the Ridge and Valley region of the central Appalachians in Virginia, USA. We identified individuals using microsatellite genotypes and estimated apparent survival for the local population at both sites across the 5 sessions in a single Cormack-Jolly-Seber model. We estimated density for each site and session separately using single session spatial replicates of 0.5-km transect segments as traps in a spatial capture-recapture model. Finally, we derived estimates of recruitment and population growth using an ad hoc robust design approach. We were able to estimate population parameters, even though coyote densities at both sites were low. Generally, derived recruitment and apparent survival were inversely related across sites, however, precision in estimates was poor. Thus, although there appeared to be some differences in demographic estimates for local coyote populations, uncertainty in parameters was too great to detect changes in demographic rates over short periods of time using ad hoc robust design. However, the non-invasive genetic sampling and spatial capture-recapture approach provides a useful methodology and framework for future research intended to estimate population dynamics for coyotes. This method will also be useful for other species that occur at low densities, over large spatial scales, and lack distinguishing marks for cameratrap surveys. Finally, we believe this method will allow for detection of population trends over greater periods of time, and we consider alternate sampling strategies and modeling approaches that may improve the ability to estimate demographic rates of change for coyote populations using noninvasive genetics and spatial capture-recapture.
Herniation of viscera induced by medical intervention has been described in carnivores, yet occur... more Herniation of viscera induced by medical intervention has been described in carnivores, yet occurrence of hernias causing wild carnivore mortality, including in bears, remains unknown. We describe an inguinal hernia, intestinal entrapment and rupture, and peritonitis causing mortality in a male American black bear (Ursus americanus). In the autumn of 2014, a free-ranging, adult bear was housed at Virginia Tech's Black Bear Research Center. After 13 days in captivity, the bear showed signs of lethargy and intermittent inappetence consistent with the onset of hibernating behaviors. However, the bear suddenly displayed rapid deterioration and died before medical assistance could be provided. During necropsy examination, a devitalized portion of small intestine was found entrapped in the left inguinal ring. An intestinal perforation was evident near the entrapment area, which caused a subsequent peritonitis. To our knowledge this is the first report of bear mortality due to inguinal herniation with subsequent perforation and peritonitis.
Sparse detections in camera trap surveys commonly hinder density estimation for threatened specie... more Sparse detections in camera trap surveys commonly hinder density estimation for threatened species. By combining detections across multiple surveys, or using informative priors in Bayesian model fitting, researchers can improve parameter estimation from sparse capture–recapture data. Using a spatial mark–resight model that incorporates site‐level heterogeneity in the spatial scale parameter via a hierarchical process and prior information, we estimated the density of a threatened carnivore (fosa, Cryptoprocta ferox) from multiple sparse datasets collected during extensive camera trapping surveys in northeastern Madagascar (2008–2015). Our objectives were to estimate density for six sites, examine the response of fosa density and movement to habitat degradation, monitor annual density trends across 7 years at two sites, and estimate fosa abundance in the Makira–Masoala protected area complex. We obtained a mean of 16.1 (se = 0.52; range = 2–49) fosa detections and three observers identified a mean of 3.62 (se = 0.09; range = 1–8) marked individuals per survey. Fosa daily baseline encounter rate was very low (λ0 = 0.004; 0.003–0.006) and density/movement estimates were similar across forest types. Density estimates at resurveyed sites suggested annual variability in density, with estimates trending lower during the final surveys [e.g. D = 0.39 (0.14–1.11) versus 0.08 (0.05–0.31) individuals per km2]. We estimated fosa abundance across the Makira–Masoala region to be 1061 (95% HPDI: 596–1780) adult individuals. On the basis of our estimate and the size of the region, we believe Makira–Masoala harbors a significant portion of the global fosa population. The conservation and management of rare species is commonly limited due to lack of population estimates. By combining detections across surveys, we overcame estimation issues and obtained valuable information on a threatened carnivore, allowing us to better assess its status and prioritize conservation actions. We advocate for practical use of sparse datasets for such data‐deficient species.
The presence of exotic predators in ecosystems across the world is a leading driver of native spe... more The presence of exotic predators in ecosystems across the world is a leading driver of native species' declines. Exotic predators largely influence native species through predation and harassment, which may cause native species to avoid them spatially. We used a camera trap dataset from seven sites in Madagascar's largest protected area complex to investigate spatial co-occurrence patterns between three exotic predators (free-ranging domestic dogs Canis familiaris and cats Felis silvestris, and small Indian civet Viverricula indica) and native ground-dwelling forest birds (n = 5) and small mammals (n = 4). We created 216 two-species occupancy models for 27 exotic predator-native species pairings to examine how habitat, exotic predator presence or both, influenced each native species' occupancy and/or detection. We found that native bird and small mammal occupancy and/or detection were strongly related to an exotic predator's presence 52% of the time (i.e. 14 of 27 exotic predator-native species pairings). Six of the 14 species pairings (i.e. 43%) had non-independent co-occurrence patterns, four of which were habitatmediated. The effect of exotic predator presence on native species' detection was largely negative, depressing native species' detection in seven out of 12 instances (i.e. 58% of the time). The small Indian civet and free-ranging cats each strongly influenced the occupancy and/or detection of six species for a combined impact on seven native species, while domestic dogs strongly influenced two species. By including habitat covariates in two-species occupancy models, we gained deeper insight into the effect exotic predator presence has on native species' distribution. We also note that the strong effect of exotic predator presence on our ability to detect native species can hinder the ability of researchers to provide accurate parameter estimates. We recommend future research into the synergistic effects that habitat degradation and exotic species presence has on native species.
Population density estimates are necessary to inform management and conservation, yet are difficu... more Population density estimates are necessary to inform management and conservation, yet are difficult to obtain for cryptic species such as carnivores, and often require intensive sampling. We implemented a single-survey, closed session, scat sampling protocol to estimate bobcat density using fecal DNA and spatial capture-recapture at two sites over five sessions in Virginia, USA. We employed a Poisson encounter model to allow for multiple detections on scat transect segments over a single collection interval, and compared single session and multistrata (closed, multi-site, multisession) spatial capturerecapture (SCR) approaches to estimate density for each site and session. We found improved precision for most estimates using the multistrata SCR approach, sharing data on baseline detection and individual movement across sites and sessions. We suggest the summer session estimates are representative of the resident population, that differences in density between summer and winter are representative of potential net recruitment, and that differences between consecutive summer sessions are representative of the net recruitment realized for the population (dependent on survival and emigration). Finally, we assessed factors affecting precision in single session model estimates and provide recommendations to improve detection and reduce credible intervals that may be applicable across the bobcat range and to other carnivore species. The single survey transect methodology provides flexibility in monitoring carnivore populations specifically, or as part of concurrent monitoring for multiple carnivore species. This methodology has potential to dramatically increase the effectiveness of conservation and management dollars, improving our ability to monitor carnivore populations and assess conservation needs and actions.
Diet studies are frequently used to improve understanding of predator ecology, potential effects ... more Diet studies are frequently used to improve understanding of predator ecology, potential effects of carnivores on prey populations, and competition among predators. However, field identification of carnivore scat typically relies on scat morphology, size, and contents resulting in possible subjective predator identification and potentially biased results. Advancements in noninvasive genetic sampling allow for molecular identification of predator scat, eliminating many issues associated with field identification methods. We collected scat samples once per month from June 2011 to May 2012 in western Virginia, USA, using morphological characteristics for field identification of the predator. We then used mitochondrial DNA to identify the predator species of each scat and identified prey remains visually. Using confusion matrices, we found a range of accuracy in field identification for the 3 target species: coyotes (Canis latrans; 54.0%), bobcats (Lynx rufus; 57.1%), and black bears (Ursus americanus; 95.2%), even though we only considered samples with high-confidence field identification. We found a high coyote false-positive rate (52.7%), indicating we often incorrectly identified scats as coyote (98% of misidentified bobcat scats and 75% of misidentified black bear scats were recorded as coyote in the field). This asymmetrical bias in predator identification resulted in inaccurate estimates of dietary niche breadth and overlap between competitors. Our results suggest that caution should be exercised when interpreting results from studies in which carnivore species are identified by scat morphology. Future studies should employ noninvasive genetic sampling for carnivore scat identification, especially in areas with sympatric predator species that have similar scat morphology.
Despite exceptionally high levels of biodiversity and endemism found in Madagascar, much of its w... more Despite exceptionally high levels of biodiversity and endemism found in Madagascar, much of its wildlife remains little studied, particularly the carnivore community. The recently described, little-known black forest cat (locally known as "fitoaty") is believed to be restricted to NE Madagascar and has been investigated only through village surveys and anecdotal accounts. From 2008 to 2012, we photographically sampled 7 forest sites with varying degrees of degradation and fragmentation across Makira Natural Park with the goals of: 1) estimating landscape occupancy for fitoaty (Felis spp.), 2) identifying variables influencing fitoaty occupancy, and 3) comparing fitoaty and feral cat (Felis spp.) occupancy across the landscape. We observed higher occupancy for fitoaty, minimal co-occurrence between fitoaty and feral cats (n = 2 sites), and strong divergence in habitat use. We provide the 1st assessment of fitoaty morphology, including comparisons with anecdotal reports, and the 1st population assessment of Madagascar's exotic cat community with insights into factors associated with carnivore population trends in Madagascar. We suggest the described fitoaty is a phenotypically different form of the feral cat, but additional research is needed. Targeted management plans are needed to diminish the spread and potential negative effects of invasive cats across this important biologically diverse ecoregion.
Borner and others at FZS, as well as T. Mariki. AH thanks Ulrike Hilborn for data entry and gener... more Borner and others at FZS, as well as T. Mariki. AH thanks Ulrike Hilborn for data entry and general support and Ray Hilborn for help with R. We also thank Dr. Matt Hayward and an anonymous reviewer for their helpful comments.
Surveys across multiple seasons or years are necessary to evaluate the effects of dynamic process... more Surveys across multiple seasons or years are necessary to evaluate the effects of dynamic processes on long-term persistence of wildlife populations, such as effects of exotic species on native species populations. Unfortunately, multi-year surveys are rare, particularly for rainforest carnivore populations, and managers often rely on singleseason/year, 'snapshot' surveys that produce static estimates of population parameters. Here we provide results using single-species, multi-year occupancy modeling from a six-year survey (2008-2013) of a rainforest carnivore community at a 15 km 2 area study site within the newly established Makira Natural Park, Madagascar. We demonstrate a precipitous decline in the native carnivore community with four of the six native carnivores (falanouc Eupleres goudotii, ring-tailed vontsira Galidia elegans, broad-striped vontsira Galidictis fasciata, and brown-tailed vontsira Salanoia concolor) decreasing by at least 60% over this six-year period. In addition, we observed two exotic carnivores (small Indian civet Viverricula indica and feral cat Felis species) colonize this study site with Felis species increasing in occupancy from 0 to 0.68 by the final year. Further, we demonstrate how variables associated with human encroachment (i.e. distance to forest edge and nearest village) are most important for explaining these trends in native carnivore extirpation and exotic carnivore colonization. These findings provide additional evidence on the threat posed to native carnivore populations by the expansion of exotic carnivores worldwide. We highlight the striking increase in extirpation, and the factors influencing such changes, for native carnivores. In this manuscript, we point to the limited number of multi-year surveys to evaluate dynamic processes on long-term persistence of native wildlife populations, as well as the lack of exotic carnivore control programs in threatened ecosystems in many developing nations as factors limiting our ability to effectively conserve biodiversity across the globe.
With fewer than 200 tigers (Panthera tigris tigris) left in Nepal, that are generally confined to... more With fewer than 200 tigers (Panthera tigris tigris) left in Nepal, that are generally confined to five protected areas across the Terai Arc Landscape, genetic studies are needed to provide crucial information on diversity and connectivity for devising an effective country-wide tiger conservation strategy. As part of the Nepal Tiger Genome Project, we studied landscape change, genetic variation, population structure, and gene flow of tigers across the Terai Arc Landscape by conducting Nepal's first comprehensive and systematic scat-based, non-invasive genetic survey. Of the 770 scat samples collected opportunistically from five protected areas and six presumed corridors, 412 were tiger (57%). Out of ten microsatellite loci, we retain eight markers that were used in identifying 78 individual tigers. We used this dataset to examine population structure, genetic variation, contemporary gene flow, and potential population bottlenecks of tigers in Nepal. We detected three genetic clusters consistent with three demographic sub-populations and found moderate levels of genetic variation (H e = 0.61, A R = 3.51) and genetic differentiation (F ST = 0.14) across the landscape. We detected 3-7 migrants, confirming the potential for dispersal-mediated gene flow across the landscape. We found evidence of a bottleneck signature likely caused by large-scale landuse change documented in the last two centuries in the Terai forest. Securing tiger habitat including functional forest corridors is essential to enhance gene flow across the landscape and ensure long-term tiger survival. This requires cooperation among multiple stakeholders and careful conservation planning to prevent detrimental effects of anthropogenic activities on tigers.
This article has been accepted for publication and undergone full peer review but has not been th... more This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record. Please cite this article as
Better conservation planning requires updated information about leopard distribution to prioritiz... more Better conservation planning requires updated information about leopard distribution to prioritize and allocate limited resources available. The long-term persistence of leopards and sympatric tigers can be compromised by linear infrastructure development such as roads that fragment habitat. We used detection and non-detection data collected along walking search paths (~4140 km) in 96 grid cells (each cell 15 km by 15 km) spread across potential habitat (~13,845 km 2) in the Terai Arc Landscape, Nepal. Multi-season occupancy models allowed us to make both spatial and temporal inferences between two surveys in 2009 and 2013, based on ecologically relevant covariates recorded in the field or remotely sensed. Additionally, we used 2013 data to make inferences on co-occurrence between tigers and leopards at the landscape level. We found the additive model containing deforestation and district roads negatively influenced leopard detection across the landscape. Although weak, we found anthropogenic factors such as extent of deforestation (decrease in forest cover) negatively affected leopard occupancy. Road abundance, especially for the east-west highway and district roads, also negatively (but weakly) influenced leopard occupancy. We found substantially lower occupancy in the year 2013 (0.59 (SE 0.06)) than in 2009 (0.86 (SE 0.04)). Tigers and leopards co-occurred across the landscape based on the species interaction factor (SIF) estimated at 1.47 (0.13) but the amount of available habitat and the prey index mediated co-occurrence. The SIF decreased as habitat availability increased, reaching independence at large habitat patches, but leopard occupancy declined in sites with tigers, primarily in large patches. The prey index was substantially lower outside of protected areas and leopards and tigers co-occurred more strongly in small patches and at low prey indices, indicating potential attraction to the same areas when prey is scarce. Mitigation measures should focus on preventing loss of
We assessed the effects of cub age, litter size, and sex, on body mass (BM), absolute and relativ... more We assessed the effects of cub age, litter size, and sex, on body mass (BM), absolute and relative growth rates (AGR, RGR), opening of ears and eyes, and deciduous teeth eruption from 129 cubs of American black bears (Ursus americanus) born at Virginia Tech’s Black Bear Research Center. Specific ages, related to maternal food consumption, and litter size, best described BM, AGR, RGR, and ear and eye development. Overall, newborns weighed ~0.44 kg at birth and increased ~9-fold by ~14 weeks. Twins were greater in BM than single cubs and triplets. Single and triplet cubs had higher AGR and RGR than twins after mothers resumed food consumption post-hibernation. Newborns displayed RGR > 3.5% that decreased until den emergence (RGR < 3.5% after emergence). RGR differed among litter sizes, particularly after den emergence. Ear and eye opening occurred concurrently at ~44 days of age, while teeth erupted ~10 days later. Single cubs experienced delayed development of these organs comp...
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