Occupancy modeling of ruffed grouse in the Black Hills National Forest

Ruffed grouse (Bonasa umbellus) are a popular game bird and the management indicator species for quaking aspen (Populus tremuloides) in the Black Hills National Forest (BHNF), which requires development of a robust monitoring protocol to evaluate trends in ruffed grouse populations. We used roadside drumming surveys in spring 2007 and 2008 to estimate ruffed grouse occupancy and detection probabilities in the BHNF while simultaneously assessing the influence of sampling and site covariates on these processes. Ruffed grouse occupancy estimates were constant between spring 2007 and 2008 (Ψ = 0.12, SE = 0.03) and were positively influenced by the amount of aspen surrounding the site. Detection probability estimates were constant between spring 2007 and 2008 (p = 0.27, SE = 0.06) and were influenced by survey date in a quadratic form and negatively influenced by wind speed and time of the survey. Collectively, our results demonstrated that ruffed grouse occupancy and detection probabilities in the BHNF were low. Occupancy could be increased by increasing the extent of aspen. To improve monitoring efficiency and maximize probability of detecting ruffed grouse, ruffed grouse monitoring should be conducted during the peak of drumming (mid-May), during favorable weather conditions such as low wind speeds and little precipitation, and during early morning, near sunrise. © 2010 The Wildlife Society.     

Use of classical bird census transects as spatial replicates for hierarchical modeling of an avian community

New monitoring programs are often designed with some form of temporal replication to deal with imperfect detection by means of occupancy models. However, classical bird census data from earlier times often lack temporal replication, precluding detection‐corrected inferences about occupancy. Historical data have a key role in many ecological studies intended to document range shifts, and so need to be made comparable with present‐day data by accounting for detection probability. We analyze a classical bird census conducted in the region of Murcia (SE Spain) in 1991 and 1992 and propose a solution to estimating detection probability for such historical data when used in a community occupancy model: the spatial replication of subplots nested within larger plots allows estimation of detection probability. In our study, the basic sample units were 1‐km transects, which were considered spatial replicates in two aggregation schemes. We fit two Bayesian multispecies occupancy models, one for each aggregation scheme, and evaluated the linear and quadratic effect of forest cover and temperature, and a linear effect of precipitation on species occupancy probabilities. Using spatial rather than temporal replicates allowed us to obtain individual species occupancy probabilities and species richness accounting for imperfect detection. Species‐specific occupancy and community size decreased with increasing annual mean temperature. Both aggregation schemes yielded estimates of occupancy and detectability that were highly correlated for each species, so in the design of future surveys ecological reasons and cost‐effective sampling designs should be considered to select the most suitable aggregation scheme. In conclusion, the use of spatial replication may often allow historical survey data to be applied formally hierarchical occupancy models and be compared with modern‐day data of the species community to analyze global change process.     

Modelling large spotted genet (Genetta tigrina) and slender mongoose (Galerella sanguinea) occupancy in a heterogeneous landscape of South Africa

Drivers of distribution patterns of poorly known species are among the most important aspects in conservation biology. We studied the proportion of area occupied by the large spotted genet (Genetta tigrina) and the slender mongoose (Galerella sanguine) in response to land use variables using camera-trapping data in Drakensberg Midlands, South Africa. Average estimated occupancy of large spotted genet and slender mongoose were 0.42 ± 0.10 and 0.41 ± 0.04 respectively using single season occupancy models. Altitudinal variation was found to be significant in the distribution of both species, along with human abundance for genet and availability of bushland for mongoose. Autumn influenced detection probability of both species negatively, while summer influenced slender mongoose positively. Relative human abundance was positively associated with detection probability of slender mongoose, and for large spotted genet, availability of bushland influenced positively while relative abundance of jackal (Canis mesomelas) influenced negatively. Occurrence of both species suggests that high elevations may not provide favourable ecological conditions, and bush cover appeared to be favourable habitats for both species. Either positive occurrence or detection of small carnivores to human abundance indicated their tendency to subsist in low-lying human populated areas. The present study shows the influence of a range of factors on the distribution of lesser known carnivores.     

Solar Radiation Determines Site Occupancy of Coexisting Tropical and Temperate Deer Species Introduced to New Zealand Forests

Assemblages of introduced taxa provide an opportunity to understand how abiotic and biotic factors shape habitat use by coexisting species. We tested hypotheses about habitat selection by two deer species recently introduced to New Zealand’s temperate rainforests. We hypothesised that, due to different thermoregulatory abilities, rusa deer (Cervus timorensis; a tropical species) would prefer warmer locations in winter than red deer (Cervus elaphus scoticus; a temperate species). Since adult male rusa deer are aggressive in winter (the rut), we also hypothesised that rusa deer and red deer would not use the same winter locations. Finally, we hypothesised that in summer both species would prefer locations with fertile soils that supported more plant species preferred as food. We used a 250 × 250 m grid of 25 remote cameras to collect images in a 100-ha montane study area over two winters and summers. Plant composition, solar radiation, and soil fertility were also determined for each camera location. Multiseason occupancy models revealed that direct solar radiation was the best predictor of occupancy and detection probabilities for rusa deer in winter. Multistate, multiseason occupancy models provided strong evidence that the detection probability of adult male rusa deer was greater in winter and when other rusa deer were present at a location. Red deer mostly vacated the study area in winter. For the one season that had sufficient camera images of both species (summer 2011) to allow two-species occupancy models to be fitted, the detection probability of rusa deer also increased with solar radiation. Detection probability also varied with plant composition for both deer species. We conclude that habitat use by coexisting tropical and temperate deer species in New Zealand likely depends on the interplay between the thermoregulatory and behavioural traits of the deer and the abiotic and biotic features of the habitat.     

Dynamic occupancy models reveal within‐breeding season movement up a habitat quality gradient by a migratory songbird

The timing of settlement decisions likely influences the quality of breeding site choices.This is particularly the case in migratory birds, because the conditions that enhance breeding success are often not apparent upon arrival after migration. A strategy that addresses this problem is to adjust settlement decisions when reliable information becomes available. We used a new indirect method – dynamic site occupancy modeling – to estimate apparent movement of black‐throated blue warblers Dendroica caerulescens among sites within a breeding season. Because individuals should disperse to sites that maximize their fitness, we hypothesized that warblers would move up a habitat quality gradient when opportunities arose. For our study species, that would involve moving into sites with greater shrub density and at higher elevation within northern hardwoods forest, as these two features are positively correlated with reproduction and apparent survival in this species. Although the probability of site occupancy in our study landscape remained consistent throughout the breeding season (range: 0.66–0.69), occupancy models revealed substantial support for apparent movement of individuals within the breeding season. The mean probability of emigration from a point count site was 0.21 (±0.03 SE), and the mean probability of immigration to a site not previously occupied was 0.51 (±0.05 SE). The spatial distribution of this movement was a function of habitat quality. A portion of the black‐throated blue warbler population appears to arrive on the breeding grounds and settle initially in sub‐optimal habitat, moving subsequently into high quality densely shrubbed habitat at higher elevations. This modeling approach provides a new means to test hypotheses about habitat selection and movement by using presence–non‐detection data.     

Diversity and occupancy of small carnivores within oil palm plantations in central Sumatra,Indonesia

In Southeast Asia, the conversion of native forests to oil palm plantations threatens tropical biodiversity, but very little is known about the impacts of oil palm cultivation on small carnivore species. To determine the diversity and occupancy of small carnivores within oil palm plantations and to investigate possible factors that might affect their presence within oil palm, we used camera-traps within two oil palm plantations in central Sumatra, analysed the data using occupancy modelling and tested whether two covariates (distance to the edge of the oil palm habitat and distance from extensive areas of lowland forest) affected the model parameters for each small carnivore species. From 3164 camera-trap days, we detected only three small carnivores: leopard cat (Prionailurus bengalensis), common palm civet (Paradoxurus hermaphroditus) and Malay civet (Viverra tangalunga), which indicates that there was a low diversity of small carnivores within the oil palm plantations. Both the leopard cat and common palm civet were found deep within the oil palm, whereas the Malay civet was only detected near the edge in one of the plantations. The leopard cat and common palm civet had very high occupancy values, whereas the Malay civet had low values for both occupancy and detection probability. Neither covariate affected occupancy of the leopard cat and common palm civet, but distance from the edge of the oil palm habitat did influence their detection probabilities. Malay civet occupancy decreased with distance from the oil palm edge, and detection probability was affected by distance from extensive areas of lowland forest. Forests and rest/den site availability are suggested to be important features for small carnivores with oil palm-dominated landscapes.     

Occupancy and detectability of Snowy Plovers in western Utah: an application to a low density population

Occupancy modeling can be used to identify habitat characteristics associated with species occurrence. Additionally, occupancy sampling can provide measures of detection probability, increasing confidence in monitoring efforts. Little is known about the distribution and habitat preferences of a small population of Snowy Plovers (Charadrius nivosus) in western Utah. We conducted a study to estimate occupancy and detection probability of Snowy Plovers in western Utah during 2011 and 2012. We made repeated visits to randomly selected survey plots during the breeding period, sampling 84 64‐ha plots in 2011 and 100 64‐ha plots in 2012 and recording the number of adults and habitat characteristics in each plot. We then modeled the relationship between detection, occupancy, and covariates that included distance to water, distance to roads, land cover types, and characteristics of the vegetation. We also included covariates for observer, Julian date, temperature, cloud cover, and wind speed when modeling detection probability. Detection probability was high (0.74, 95% CI = 0.57–0.86) and positively influenced by temperature. Occupancy of 64‐ha plots was low (0.27, 95% CI = 0.18–0.39) and did not vary by year. Occupancy of Snowy Plovers was negatively associated with distance to water (β = ?0.62 ± 0.31, 95% CI = ?1.23 to ?0.01) and percent shrub cover (β = ?0.28 ± 0.02, 95% CI = ?0.58 to ?0.01). Land cover types also influenced plot occupancy. Management actions that conserve shallow water and adjacent habitats or minimize disturbance in these areas are likely to have conservation benefits for Snowy Plovers where water is scarce. Because our detection probabilities were high, investigators involved in future monitoring efforts can achieve reasonable precision with limited revisits to sample plots.     

Conservation Assessments of Arboreal Mammals in Difficult Terrain: Occupancy Modeling of Pileated Gibbons (Hylobates pileatus)

Long-term monitoring programs, wildlife surveys, and other research involving species population assessment require reliable data on population status. Given the logistically challenging nature of some species’ habitats and cryptic behaviors, collecting these data can prove to be a considerable barrier. We used detection/nondetection data from pileated gibbons (Hylobates pileatus) in the Cardamom Mountains of southwest Cambodia to estimate their population occupancy and detectability. We modeled occupancy using elevation, tree height, tree density, tree diversity, and disturbance covariates. Modeling demonstrated that 83% of the sites are occupied by Hylobates pileatus and that the detectability of the species varies positively with elevation. No clear relationship between habitat quality covariates and occupancy of Hylobates pileatus emerged. Effort analysis based on model estimates demonstrated that at high elevations, less than half the number of site visits is needed to attain the same detectability estimate precision as across all elevations. We suggest that human activities at low elevations, which affect forest composition, are the central factors impacting the detectability and occupancy of Hylobates pileatus. Longer sampling durations and/or a higher number of site visits, especially at lower elevations, increase precision of the occupancy estimator for the least effort. For effective future monitoring and research for this and similar species, using this relatively simple method, applied with repeat site visits, would allow a longitudinal comparison of detection at sites in difficult terrain.     

Eurasian lynx hunting red deer: is there an influence of a winter enclosure system?

As in several Central European areas, in the Bohemian Forest Ecosystem (Germany and the Czech Republic), fenced feeding enclosures are used for the winter management of red deer (Cervus elaphus), which is an important component of the Eurasian lynx’s (Lynx lynx) winter diet. Using GPS telemetry data, we tested whether (1) lynx hunted red deer mainly selecting for high prey densities and environmental characteristics like a good level of habitat heterogeneity, independently of the enclosures’ presence; (2) enclosures attracted lynx and (3) positively influenced their predation on red deer, being predictable and abundant prey sources throughout the winter; or (4) extremely high deer densities inside the enclosures rather negatively influenced lynx predation on this species. We first compared lynx space usage and predation on red deer inside and outside the enclosures. Then, we investigated the effects of the environment, prey densities and the enclosure distance for the area outside of enclosures. Prey densities positively influenced lynx space usage, whilst the probability of predation on red deer was highest at medium to low red deer densities. Habitat heterogeneity and terrain ruggedness influenced both lynx space usage and probability of predation on red deer. Regarding the effect of enclosures, the ratio “area used during night vs. daytime” was larger by a factor of 2 inside compared to outside enclosures, and the probability of predation on red deer was three times higher inside rather than outside of enclosures; however, these differences were not statistically significant, suggesting that the influence of the enclosures is not very pronounced.     

Edge effects created by clear-cutting on habitat use by sika deer on Mt. Goyo,northern Honshu,Japan

Clear-cutting increased the species diversity and amount of undergrowth plants in a habitat of Sika deer (Cervus nippon) on Mt. Goyo, northern Japan. The number of species increased from 15 to 48 as a result of clear-cutting. Among the plants,Sasa nipponica (a dwarf bamboo), an important forage plant for Sika deer, was predominant. Fecal pellets of deer were abundant in the forest and at the “adjacent zone” (from the edge to 150 m out of the forest) and thereafter decreased suddenly. The intensity of utilization ofSasa nipponica was also heavy in the forest, moderate at the adjacent zone and light 200 m from the forest edge. Since the amount of the bamboo in the forest was small, the removal of bamboo was greatest at the adjacent zone. Clear-cutting creates a favorable feeding area for Sika deer in this zone by increasing the available plant production and securing forest cover.     

Influence of interspecific competition on mule deer birthing and rearing site selection

Ungulates often alter behavior and space use in response to interspecific competition. Despite observable changes in behavior caused by competitive interactions, research describing the effects of competition on survival or growth is lacking. We used spatial modeling to determine if habitat use by female mule deer (Odocoileus hemionus) was affected by other ungulate species prior to, during, and after parturition. We conducted our study in the Book Cliffs region of eastern Utah, USA, during 2019 and 2020. We used resource selection function (RSF) analysis to model space use of 4 ungulate species that potentially competed with mule deer: bison (Bos bison), cattle, elk (Cervus canadensis), and feral horses. We incorporated RSF models for competing species into a random forest analysis to determine if space use by mule deer was influenced by these other ungulate species. We used survival and growth data from neonate mule deer to directly assess potential negative effects of other ungulates. Habitat use by elk was an important variable in predicting use locations of mule deer during birthing and rearing. The relationship was positive, suggesting interference competition was not occurring. Survival of neonate mule deer increased as the probability of use by elk increased (hazard ratio = 0.185 ± 0.497 [SE]). Further, probability of use by elk in rearing habitat had no influence on growth of neonate mule deer from birth to 6 months of age, suggesting that exploitative competition was not occurring.     

Risk factors affecting the probability of damage by sika deer in plantation forests in Yamanashi Prefecture, Japan

Using a generalized linear mixed model approach, we determined the most important risk factors affecting the probability of damage by sika deer in a forest plantation in Japan. Candidate risk factors included tree species, stand age, peripheral dwarf bamboo community, topographical factors, snow depth, and human disturbance factors. Based on this model, we developed a risk map of forest damage. The model indicated that the most important risk factor was stand age, followed by tree species and maximum snow depth. Our predictive model has practical use due to its high classification accuracy (83.9%). To decrease damage from sika deer, an afforestation plan that incorporates these factors should be implemented. Because it is based on common, forest GIS data that have recently been compiled by several local governments in Japan, our modeling method of deer damage can easily be adapted to other areas.     

Winter site occupancy patterns of the northern flying squirrel in boreal mixed-wood forests

We assessed habitat use by the northern flying squirrel (Glaucomys sabrinus) to test the hypothesis that the species is not a late-seral coniferous forest specialist in boreal mixedwood forests of northwestern Québec. We monitored 149 pairs of nest boxes over 3 visits during February–April 2008. A total of 31 pairs of nest boxes were occupied during the study. The average (3.7, 2.8, and 1.8) and maximum (8, 6, and 4) numbers of individuals in nest boxes decreased from the first to last visit. Average air temperatures were below freezing and increased with the arrival of spring (?23.9, ?14.5, and ?3.7 °C). Using GIS software, we created a 430-m (median dispersal distance) buffer around each pair of nest boxes and extracted landscape composition variables from digital forest inventory maps. We created models that potentially explained site occupancy by the northern flying squirrel as well as detection probability. Model selection indicated that the area of coniferous forests negatively affected site occupancy by flying squirrels while temperature positively influenced detection probability. Our results support the hypothesis that the northern flying squirrel is not a habitat specialist, but can occupy a wider range of forest cover types than previously recognized in various landscape contexts.     

Towards the automated detection and occupancy estimation of primates using passive acoustic monitoring

Recent advancements in technology have made possible the use of novel, cost-efficient biomonitoring techniques which facilitate monitoring animal populations at larger spatial and temporal scales. Here, we investigated using passive acoustic monitoring (PAM) for wild primate populations living in the forest of Taï National Park, Côte d’Ivoire. We assessed the potential of using a customized algorithm for the automated detection of multiple primate species to obtain reliable estimates of species occurrence from acoustic data. First, we applied the algorithm on continuous rainforest recordings collected using autonomous recording units (ARUs) to detect and classify three sound signals: chimpanzee buttress drumming, and the loud calls of the diana and king colobus monkey. Using an occupancy modelling approach we then investigated to what extent the automated, probabilistic output needs to be listened to, and thus manually cleaned, by a human expert, to approach occupancy probabilities derived from ARU data fully verified by a human. To do this we explored the robustness of occupancy probability estimates by simulating ARU datasets with various degrees of cleaning for false positives and false negative detections. We further validated the approach by comparing it to data collected by human observers on point transects located within the same study area. Our study demonstrates that occurrence estimates from ARU data, combined with automated processing methods such as our algorithm, can provide results comparable to data collected by humans and require less effort. We show that occupancy probabilities are quite robust to cleaning effort, particularly when occurrence is high, and suggest that for some species even naïve occupancy, as derived from ARU data without any cleaning, could provide a quick and reliable indicator to guide monitoring efforts. We found detection probabilities to be most influenced by time of day for chimpanzee drums while temperature and, likely, poaching pressure, affected detection of diana monkey loud calls. None of the covariates investigated appeared to have strongly affected king colobus loud call detection. Finally, we conclude that the semi-automated approach presented here could be used as an early-warning system for poaching activity and suggest additional techniques for improving its performance.     

Use of Camera-Trapping to Estimate Puma Density and Influencing Factors in Central Brazil

Abstract: We used remotely triggered cameras to collect data on Puma (Puma concolor) abundance and occupancy in an area of tropical forest in Brazil where the species' status is poorly known. To evaluate factors influencing puma occupancy we used data from 5 sampling campaigns in 3 consecutive years (2005 to 2007) and 2 seasons (wet and dry), at a state park and a private forest reserve. We estimated puma numbers and density for the 2007 sampling data by developing a standardized individual identification method. We based individual identification on 1) time-stable parameters (SP; physical features that do not change over time), and 2) time-variable parameters (VP; marks that could change over time such as scars and botfly marks). Following individual identification we established a capture-recapture history and analyzed it using closed population capture-mark-recapture models. Puma capture probability was influenced by camera placement (roads vs. trails), sampling year, and prey richness. Puma occupancy was positively associated with species richness and there was a correlation between relative puma and jaguar (Panthera onca) abundance. Identifications enabled us to generate 8 VP histories for each photographed flank, corresponding to 8 individuals. We estimated the sampled population at 9 pumas (SE = 1.03, 95% CI = 8–10 individuals) translating to a density of 3.40 pumas/100 km². Information collected using camera-traps can effectively be used to assess puma population size in tropical forests. As habitat progressively disappears and South American felines become more vulnerable, our results support the critical importance of private forest reserves for conservation.     

The first description of population density and habitat use of the mainland clouded leopard Neofelis nebulosa within a logged-primary forest in South East Asia

The mainland clouded leopard (Neofelis nebulosa) is classified as vulnerable under the IUCN Red List, meaning that it faces a high risk of extinction in the wild. However, hardly any ecological research has been published on this species apart from several radiotelemetry studies in Thailand and Nepal, and one camera-trapping study in India. Here we present findings on the clouded leopard from a camera-trapping study conducted in Temengor forest reserve (a logged-over forest) and Royal Belum State Park (a primary forest) within Peninsular Malaysia. Using the spatially-explicit capture-recapture method, the density from Temengor forest reserve and Royal Belum State Park was estimated at 3.46 ± SE 1.00 and 1.83 ± SE 0.61, respectively. Clouded leopard habitat use was found to be highly influenced by the availability of small and medium prey species and therefore intrinsically highlights the potential conservation importance of species such as pig-tailed macaques, porcupine, mouse deer and small carnivores. These findings provide the first estimates of density and habitat use of this species in a logged-primary forest from both Peninsular Malaysia and South East Asia. Our study provides important baseline information on clouded leopards and contributes to filling up the knowledge gap that exists in understanding the population ecology of this species, not only within Peninsular Malaysia, but also on a regional level.     

Multi-species monitoring of rare wetland fishes should account for imperfect detection of sampling devices

Accuracy in estimating occupancy of a threatened species is important for conservation but false absences bias many monitoring programs. Imperfect detection is especially relevant to surveys of rare wetland fishes which are often small-bodied and cryptic. Many factors influence probability of detection, including fish size and abundance, habitat characteristics and sampling devices. Imperfect detection can be addressed by accounting for probability of detection when estimating occupancy by modelling detection/non-detection data collected in replicate surveys. Three ecological specialists were once common in habitats associated with Lake Alexandrina at the terminus of the Murray–Darling Basin, Australia. The threatened Murray Hardyhead (Craterocephalus fluviatilis), Southern Pygmy Perch (Nannoperca australis) and Yarra Pygmy Perch (N. obscura) are now rare in the region following population collapses during a prolonged drought, and ongoing monitoring aims to assess their statuses for management purposes. This study compares probability of detection of the rare wetland fishes and cohabiting species during 2 years of multi-species monitoring using contrasting sampling devices (fyke and seine). The findings suggest large variations in estimated probability of detection can occur between devices for Murray Hardyhead and Southern Pygmy Perch. Yarra Pygmy Perch was undetected during the study. Overall, the findings show multi-species monitoring programs using a single sampling device may wrongly estimate the occupancy of a target fish. By accounting for imperfect detection, multi-species monitoring programs will improve inferences regarding population status, recovery and habitat quality of fishes to more accurately inform wetland management.     

Large Forest Patches Promote Breeding Success of a Terrestrial Mammal in Urban Landscapes

Despite a marked increase in the focus toward biodiversity conservation in fragmented landscapes, studies that confirm species breeding success are scarce and limited. In this paper, we asked whether local (area of forest patches) and landscape (amount of suitable habitat surrounding of focal patches) factors affect the breeding success of raccoon dogs (Nyctereutes procyonoides) in Tokyo, Central Japan. The breeding success of raccoon dogs is easy to judge as adults travel with pups during the breeding season. We selected 21 forest patches (3.3–797.8 ha) as study sites. In each forest patch, we used infra-red-triggered cameras for a total of 60 camera days per site. We inspected each photo to determine whether it was of an adult or a pup. Although we found adult raccoon dogs in all 21 forest patches, pups were found only in 13 patches. To estimate probability of occurrence and detection for raccoon in 21 forest fragments, we used single season site occupancy models in PRESENCE program. Model selection based on AIC and model averaging showed that the occupancy probability of pups was positively affected by patch area. This result suggests that large forests improve breeding success of raccoon dogs. A major reason for the low habitat value of small, isolated patches may be the low availability of food sources and the high risk of being killed on the roads in such areas. Understanding the effects of local and landscape parameters on species breeding success may help us to devise and implement effective long-term conservation and management plans.