Application of Spatial and Closed Capture-Recapture Models on Known Population of the Western Derby Eland (Taurotragus derbianus derbianus) in Senegal

Camera trapping with capture-recapture analyses has provided estimates of the abundances of elusive species over the last two decades. Closed capture-recapture models (CR) based on the recognition of individuals and incorporating natural heterogeneity in capture probabilities are considered robust tools; however, closure assumption is often questionable and the use of an M_h jackknife estimator may fail in estimations of real abundance when the heterogeneity is high and data is sparse. A novel, spatially explicit capture-recapture (SECR) approach based on the location-specific capture histories of individuals overcomes the limitations of closed models. We applied both methods on a closed population of 16 critically endangered Western Derby elands in the fenced 1,060-ha Fathala reserve, Senegal. We analyzed the data from 30 cameras operating during a 66-day sampling period deployed in two densities in grid and line arrays. We captured and identified all 16 individuals in 962 trap-days. Abundances were estimated in the programs CAPTURE (models M₀, M_h and M_h Chao) and R, package secr (basic Null and Finite mixture models), and compared with the true population size. We specified 66 days as a threshold in which SECR provides an accurate estimate in all trapping designs within the 7-times divergent density from 0.004 to 0.028 camera trap/ha. Both SECR models showed uniform tendency to overestimate abundance when sampling lasted shorter with no major differences between their outputs. Unlike the closed models, SECR performed well in the line patterns, which indicates promising potential for linear sampling of properly defined habitats of non-territorial and identifiable herbivores in dense wooded savanna conditions. The CR models provided reliable estimates in the grid and we confirmed the advantage of M_h Chao estimator over M_h jackknife when data appeared sparse. We also demonstrated the pooling of trapping occasions with an increase in the capture probabilities, avoiding violation of results.     

Estimating Black Bear Density Using DNA Data From Hair Snares

ABSTRACT DNA-based mark-recapture has become a methodological cornerstone of research focused on bear species. The objective of such studies is often to estimate population size; however, doing so is frequently complicated by movement of individual bears. Movement affects the probability of detection and the assumption of closure of the population required in most models. To mitigate the bias caused by movement of individuals, population size and density estimates are often adjusted using ad hoc methods, including buffering the minimum polygon of the trapping array. We used a hierarchical, spatial capture-recapture model that contains explicit components for the spatial-point process that governs the distribution of individuals and their exposure to (via movement), and detection by, traps. We modeled detection probability as a function of each individual's distance to the trap and an indicator variable for previous capture to account for possible behavioral responses. We applied our model to a 2006 hair-snare study of a black bear (Ursus americanus) population in northern New York, USA. Based on the microsatellite marker analysis of collected hair samples, 47 individuals were identified. We estimated mean density at 0.20 bears/km². A positive estimate of the indicator variable suggests that bears are attracted to baited sites; therefore, including a trap-dependence covariate is important when using bait to attract individuals. Bayesian analysis of the model was implemented in WinBUGS, and we provide the model specification. The model can be applied to any spatially organized trapping array (hair snares, camera traps, mist nests, etc.) to estimate density and can also account for heterogeneity and covariate information at the trap or individual level.     

Trap Array Configuration Influences Estimates and Precision of Black Bear Density and Abundance

Spatial capture-recapture (SCR) models have advanced our ability to estimate population density for wide ranging animals by explicitly incorporating individual movement. Though these models are more robust to various spatial sampling designs, few studies have empirically tested different large-scale trap configurations using SCR models. We investigated how extent of trap coverage and trap spacing affects precision and accuracy of SCR parameters, implementing models using the R package secr. We tested two trapping scenarios, one spatially extensive and one intensive, using black bear (Ursus americanus) DNA data from hair snare arrays in south-central Missouri, USA. We also examined the influence that adding a second, lower barbed-wire strand to snares had on quantity and spatial distribution of detections. We simulated trapping data to test bias in density estimates of each configuration under a range of density and detection parameter values. Field data showed that using multiple arrays with intensive snare coverage produced more detections of more individuals than extensive coverage. Consequently, density and detection parameters were more precise for the intensive design. Density was estimated as 1.7 bears per 100 km² and was 5.5 times greater than that under extensive sampling. Abundance was 279 (95% CI = 193–406) bears in the 16,812 km² study area. Excluding detections from the lower strand resulted in the loss of 35 detections, 14 unique bears, and the largest recorded movement between snares. All simulations showed low bias for density under both configurations. Results demonstrated that in low density populations with non-uniform distribution of population density, optimizing the tradeoff among snare spacing, coverage, and sample size is of critical importance to estimating parameters with high precision and accuracy. With limited resources, allocating available traps to multiple arrays with intensive trap spacing increased the amount of information needed to inform parameters with high precision.     

Effect of the odour of weasels (Mustela nivalis L.) on trapped samples of their prey

Summary The presence of weasel anal gland secretion on rodent live traps substantially depresses population estimate by greatly reducing the catch of Microtus agrestis. The catch of Apodemus sylvaticus remains almost unaffected.     

The influence of trap density and sampling duration on the detection of small mammal species richness

Assessing species richness of small mammal communities is an important research objective for many live-trapping studies designed to assess or monitor biological diversity. We tested the effectiveness and efficiency of various trap densities for determining estimates and counts of small mammal species richness. Trapping was conducted in grassland habitats in northeastern Kansas during spring and fall of 2002 and 2003. Estimates and counts of species richness were higher at increased trap densities. This effect appeared to be primarily due to the higher number of individuals sampled at higher trap densities. At least 3 nights duration was needed to produce a stable estimate of species richness for the range of trap densities tested (9–144 trap stations/ha). Higher trap densities generally reached stable richness estimates in fewer nights than low density trapping arrangements. Given that counts and estimates of species richness were influenced by trap density and sampling duration, it is critical that these parameters are selected to most effectively meet research objectives.     

Geographically differentiating morphology of genetically similar dogroses: consequences of canina meiosis

Despite their genetic homogeneity, many taxonomic species are described as European dogroses (Rosa L. section Caninae (DC.) Ser.) with consistent morphological variability. Here we report a morphometric study of 27 hip and leaf characters of proximate dogrose populations that include Rosa agrestis, a member of the subsection Rubigineae, in Flanders. In principal components analysis one R. agrestis population in Kanne had intermediate morphology between R. canina and R. corymbifera, on the one hand, and three other R. agrestis populations, on the other, suggesting hybridogenic origin. Half-sib R. agrestis seedlings were grown under controlled conditions and their leaf characters were studied. A tendency toward deviating morphology in seedlings from the Kanne population, analogous to the mother plants in the field, and a correlation for specific leaf characters between mother plants and their corresponding seedlings reinforce a genetic basis for the observed divergence in the Kanne population. The assumed hybridogenic mother plants did not produce fewer seeds per hip than the others of the pure populations. In addition, for all sampled dogroses, which included six species, the diameter of the discus was correlated with the number of seeds per hip, whereas the diameter of the orifice was not correlated with this character. This implies that only the diameter of the orifice and not the diameter of the discus might be decisive for species identification among European dogroses.     

Eurasian otter (<Emphasis Type="Italic">Lutra lutra</Emphasis>) density estimate based on radio tracking and other data sources

Estimating animal population size is a critical task in both wildlife management and conservation biology. Precise and unbiased estimates are nonetheless mostly difficult to obtain, as estimates based on abundance over unit area are frequently inflated due to the “edge effect” bias. This may lead to the implementation of inappropriate management and conservation decisions. In an attempt to obtain an as accurate and conservative as possible picture of Eurasian otter (Lutra lutra) numbers, we combined radio tracking data from a subset of tracked individuals from an extensive project on otter ecology performed in Southern Portugal with information stemming from other data sources, including trapping, carcasses, direct observation of tagged and untagged individuals, relatedness estimates among genotyped individuals, and a minor contribution from non-invasive genetic sampling. In 158 km of water network, which covers a sampling area of 161 km² and corresponds to the minimum convex polygon constructed around the locations of five radio-tracked females, 21 animals were estimated to exist. They included the five radio-tracked, reproducing females and six adult males. Density estimates varied from one otter per 3.71–7.80 km of river length (one adult otter per 7.09–14.36 km) to one otter per 7.67–7.93 km² of range, depending on the method and scale of analysis. Possible biases and implications of methods used for estimating density of otters and other organisms living in linear habitats are highlighted, providing recommendations on the issue.     

Demography,density, and survival of an endemic and near threatened cottontail<Emphasis Type="Italic">Sylvilagus cunicularius</Emphasis> in central Mexico

A 3-year live trapping investigation was carried out in a temperate forest in central Tlaxcala, México from 2002 to 2004. During a total of 504 trap nights, 87Silvilagus cunicularius Waterhouse, 1848 individuals were captured and marked, and age-specific survival models using demographic parameters were tested using the JOLLYAGE program. We evaluated population density of this species over a 1-year period. The age structure of the population varied among years, and the proportion of adults was relatively constant among years, whereas the proportion of juvenile showed high fluctuations. The sex ratio of juveniles that were recaptured as adults, did not differ from unity neither did the sex ratio for adults. We found no sex bias among cottontails during all 3 years of the study. When data for both sexes were combined, mean survival probability of juveniles was lower than that of adults. Although our line transect counts showed a mean density of 27 ± 5.4 individuals per km², the obtained results from trapping suggests that this species is low in abundance at La Malinche. Further studies are needed to evaluate demographical aspects of this species at different protected and unprotected areas to obtain robust information about their status.     

The selfie trap: A novel camera trap design for accurate small mammal identification

Camera traps are a popular tool for monitoring wildlife though they can fail to capture enough morphological detail for accurate small mammal species identification. Camera trapping small mammals is often limited by the inability of camera models to: (i) record at close distances; and (ii) provide standardised photos. This study aims to provide a camera trapping method that captures standardised images of the faces of small mammals for accurate species identification, with further potential for individual identification. A novel camera trap design coined the ‘selfie trap’ was developed. The selfie trap is a camera contained within an enclosed PVC pipe with a modified lens that produces standardised close images of small mammal species encountered in this study, including: Brown Antechinus (Antechinus stuartii), Bush Rat (Rattus fuscipes) and Sugar Glider (Petaurus breviceps). Individual identification was tested on the common arboreal Sugar Glider. Five individual Sugar Gliders were identified based on unique head stripe pelage. The selfie trap is an accurate camera trapping method for capturing detailed and standardised images of small mammal species. The design described may be useful for wildlife management as a reliable method for surveying small mammal species. However, intraspecies individual identification using the selfie trap requires further testing.     

No Effect of Host Species on Phenoloxidase Activity in a Mycophagous Beetle

Ecological immunology is an interdisciplinary field that helps elucidate interactions between the environment and immune response. The host species individuals experience have profound effects on immune response in many species of insects. However, this conclusion comes from studies of herbivorous insects even though species of mycophagous insects also inhabit many different host species. The goal of this study was to determine if fungal host species as well as individual, sex, body size, and host patch predict one aspect of immune function, phenoloxidase activity (PO). We sampled a metapopulation of Bolitotherus cornutus, a mycophagous beetle in southwestern Virginia. B. cornutus live on three species of fungus that differ in nutritional quality, social environment, and density. A filter paper phenoloxidase assay was used to quantify phenoloxidase activity. Overall, PO activity was significantly repeatable among individuals (0.57) in adult B. cornutus. While there was significant variance among individuals in PO activity, there were surprisingly no significant differences in PO activity among subpopulations, beetles living on different host species, or between the sexes; there was also no effect of body size. Our results suggest that other factors such as age, genotype, disease prevalence, or natal environment may be generating variance among individuals in PO activity.     

A Novel Use of Camera Traps to Study Demography and Life History in Wild Animals: A Case Study of Spider Monkeys (Ateles belzebuth)

Demographic and life history data from wild populations of long-lived primate species are difficult to acquire but are critical for evaluating population viability and the success of conservation efforts. Camera trapping provides an opportunity for researchers to monitor wild animal populations indirectly and could help provide demographic and life history data in a way that demands fewer person-hours in the field, is less disruptive to the study population because it requires less direct contact, and may be cost effective. Using data on group composition collected concurrently though both direct observation and camera trap monitoring, we evaluate whether camera traps can provide reliable information on population dynamics (births, disappearances, interbirth intervals, and other demographic variables) for a wild population of white-bellied spider monkeys (Ateles belzebuth), an Endangered species. We placed camera traps focused on the sole access point used by the monkeys to visit a geophagy site located roughly in the center of one group’s home range, and we reviewed all of the photos collected at that site over a roughly 3-yr period to identify the individual monkeys recorded in the pictures. Group composition based on 2947 photos containing 3977 individual monkey images matched perfectly data collected concurrently through direct observation. The camera traps also provided estimates of the dates when individuals disappeared from the study group, and of infant births during the study. We conclude that long-term camera trap monitoring of wild populations of white-bellied spider monkeys—and other animals that are individually recognizable and that regularly visit predictable resources—can be a useful tool for monitoring their population dynamics indirectly.     

Intra- and interspecific interactions of Apodemus sylvaticus (L.) and A. flavicollis (Melchoir) under laboratory conditions

Miller (1967) has indicated that the coexistence of Apodemus sylvaticus and A. flavicollis may be possible if A. flavicollis, a species with a more restricted niche, is competitively superior in interspecific encounters. Intra- and interspecific behaviour of male and female A. sylvaticus and A. flavicollis was examined in dyadic encounters in a small arena. Interactions between conspecifics indicate that intraspecific behaviour in A. sylvaticus and A. flavicollis is similar but, in interspecific interactions there were more submissive and agonistic acts, and less introductory and amicable behaviour. A. flavicollis was dominant to A. sylvaticus in 63 out of 70 encounters and A. sylvaticus dominant in only one. This superiority may contribute to the persistence of small, localized populations of A. flavicollis despite the presence of A. sylvaticus.     

Trapping Elusive Cats: Using Intensive Camera Trapping to Estimate the Density of a Rare African Felid

Camera trapping studies have become increasingly popular to produce population estimates of individually recognisable mammals. Yet, monitoring techniques for rare species which occur at extremely low densities are lacking. Additionally, species which have unpredictable movements may make obtaining reliable population estimates challenging due to low detectability. Our study explores the effectiveness of intensive camera trapping for estimating cheetah (Acinonyx jubatus) numbers. Using both a more traditional, systematic grid approach and pre-determined, targeted sites for camera placement, the cheetah population of the Northern Tuli Game Reserve, Botswana was sampled between December 2012 and October 2013. Placement of cameras in a regular grid pattern yielded very few (n = 9) cheetah images and these were insufficient to estimate cheetah density. However, pre-selected cheetah scent-marking posts provided 53 images of seven adult cheetahs (0.61 ± 0.18 cheetahs/100km²). While increasing the length of the camera trapping survey from 90 to 130 days increased the total number of cheetah images obtained (from 53 to 200), no new individuals were recorded and the estimated population density remained stable. Thus, our study demonstrates that targeted camera placement (irrespective of survey duration) is necessary for reliably assessing cheetah densities where populations are naturally very low or dominated by transient individuals. Significantly our approach can easily be applied to other rare predator species.     

Estimating population size by spatially explicit capture–recapture

The number of animals in a population is conventionally estimated by capture–recapture without modelling the spatial relationships between animals and detectors. Problems arise with non‐spatial estimators when individuals differ in their exposure to traps or the target population is poorly defined. Spatially explicit capture–recapture (SECR) methods devised recently to estimate population density largely avoid these problems. Some applications require estimates of population size rather than density, and population size in a defined area may be obtained as a derived parameter from SECR models. While this use of SECR has potential benefits over conventional capture–recapture, including reduced bias, it is unfamiliar to field biologists and no study has examined the precision and robustness of the estimates. We used simulation to compare the performance of SECR and conventional estimators of population size with respect to bias and confidence interval coverage for several spatial scenarios. Three possible estimators for the sampling variance of realised population size all performed well. The precision of SECR estimates was nearly the same as that of the null‐model conventional population estimator. SECR estimates of population size were nearly unbiased (relative bias 0–10%) in all scenarios, including surveys in randomly generated patchy landscapes. Confidence interval coverage was near the nominal level. We used SECR to estimate the population of a species of skink Oligosoma infrapunctatum from pitfall trapping. The estimated number in the area bounded by the outermost traps differed little between a homogeneous density model and models with a quadratic trend in density or a habitat effect on density, despite evidence that the latter models fitted better. Extrapolation of trend models to a larger plot may be misleading. To avoid extrapolation, a large region of interest should be sampled throughout, either with one continuous trapping grid or with clusters of traps dispersed widely according to a probability‐based and spatially representative sampling design.     

Sex ratios and population persistence in the rare shrub Lindera subcoriacea Wofford

Biased sex ratios can have conservation consequences for dioecious plant species with small population sizes because of an increased risk of single sex populations. Biased sex ratios have been observed in two of the three species of Lindera (Lauraceae) in the eastern United States, but have not been documented for Lindera subcoriacea, a rare shrub of the southeastern USA. We inventoried 78 of 118 populations in North Carolina over a 3 year period, documenting the location, community type, and sex, of 299 individuals. In addition, we measured the stem height and diameter for 245 individuals. We examined population persistence relative to historical population size estimates. Average population size was 7.9 individuals and 72 % of visited populations were extant. There was a significant positive correlation between historical estimates of population size and persistence. Lindera subcoriacea consistently had male-biased (58 %) sex ratios across all population sizes and vegetation communities. Males and females had similar stem heights (mean 200.4 vs. 187.8 cm, respectively) and diameters (1.3 vs. 1.2 cm, respectively) across years and were not spatially segregated within populations. It is unclear at what stage biased sex ratios arise in L. subcoriacea, but results suggest that the causes operate across vegetation communities and population sizes. The weak bias exhibited in L. subcoriacea sex ratios has limited implications for the species’ conservation except where spatially isolated populations are unisexual. Given the vulnerability of small L. subcoriacea populations to extirpation, they should be high priority targets for management.     

Intra‐ and inter‐specific variation in size and habitus of two sibling spider species (Araneae: Lycosidae): taxonomic and biogeographic insights from sampling across Europe

Discriminating closely related species can become a taxonomical challenge if a clear morphological diagnosis is lacking. Two subspecies have been recognized in Pardosa agrestis (Westring, 1861); however, their validity is still debated. To resolve this dilemma, quantitative and qualitative traits were measured for 30 females and 30 males per site from ten localities throughout Western Europe (11 measurements on each individual) and compared between subspecies. Mean annual temperature and geographical coordinates from all sites were also included in the statistical models in order to test for variations in size over the distribution range of each subspecies. We found significant differences in body size and size of copulatory organs as well as accurate criteria of discrimination between P. a. agrestis and P. a. purbeckensis F.O.P. Cambridge, 1895, suggesting that these taxa are two valid morphological species, occurring sympatrically. We also showed that temperatures did not directly influence the size of individuals, but that one species had smaller individuals at higher latitudes (following the converse Bergmann's rule), and that both species had larger individuals in centrally sampled populations (fitting to the centre hypothesis). © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113, 85–96.     

Can Camera Traps Monitor Komodo Dragons a Large Ectothermic Predator?

Camera trapping has greatly enhanced population monitoring of often cryptic and low abundance apex carnivores. Effectiveness of passive infrared camera trapping, and ultimately population monitoring, relies on temperature mediated differences between the animal and its ambient environment to ensure good camera detection. In ectothermic predators such as large varanid lizards, this criterion is presumed less certain. Here we evaluated the effectiveness of camera trapping to potentially monitor the population status of the Komodo dragon (Varanus komodoensis), an apex predator, using site occupancy approaches. We compared site-specific estimates of site occupancy and detection derived using camera traps and cage traps at 181 trapping locations established across six sites on four islands within Komodo National Park, Eastern Indonesia. Detection and site occupancy at each site were estimated using eight competing models that considered site-specific variation in occupancy (ψ)and varied detection probabilities (p) according to detection method, site and survey number using a single season site occupancy modelling approach. The most parsimonious model [ψ (site), p (site*survey); ω = 0.74] suggested that site occupancy estimates differed among sites. Detection probability varied as an interaction between site and survey number. Our results indicate that overall camera traps produced similar estimates of detection and site occupancy to cage traps, irrespective of being paired, or unpaired, with cage traps. Whilst one site showed some evidence detection was affected by trapping method detection was too low to produce an accurate occupancy estimate. Overall, as camera trapping is logistically more feasible it may provide, with further validation, an alternative method for evaluating long-term site occupancy patterns in Komodo dragons, and potentially other large reptiles, aiding conservation of this species.     

No recent temporal changes in body size of three Danish rodents

We used museum collections to study temporal trends of possible changes in skull size, body mass and body length in three species of rodents in Denmark. Skulls of adult Microtus agrestis, Apodemus flavicollis and Apodemus sylvaticus, collected between 1895 and 2004, 1847 and 2002, and 1895 and 2002, respectively, were measured and data on body mass and length were taken from the museum registers. Principal component (PC) analysis was used to combine data of the four skull measurements taken. We tested the relationship of sex, latitude, longitude, month and year of collection to PC1 by a General Linear Model (GLM). PC1, body length and body mass of M. agrestis significantly increased from west to east. In addition, PC1, body mass and body length of M. agrestis declined from summer (August) through autumn and winter to spring (March), probably due to the decline in food availability towards winter. None of the other factors examined (sex, latitude and year) were significantly related to body size. PC1 of A. flavicollis and A. sylvaticus was not significantly related to any of the environmental factors examined.     

Monitoring of the saproxylic beetle Morimus asper (Sulzer, 1776) (Coleoptera: Cerambycidae) with freshly cut log piles

Quantitative information on population size, structure and dynamics are urgently needed for assessing species extinction risk and developing monitoring measures, especially for beetles belonging to the threatened guild of saproxylic organisms. Here freshly cut log piles (FCLP) were tested for the monitoring of the longhorn beetle Morimus asper (Sulzer, 1776) (Coleoptera: Cerambycidae). Novel mathematical models based on presence–absence or count data were compared with the most commonly used capture–recapture methods to investigate if less invasive and easier approaches may be suitable for large-scale monitoring of this species and other large saproxylic beetles. The use of FCLP as bait was reliable to detect the presence and abundance of M. asper, and capture events were not influenced by the phenomena of trap-happiness or trap-shyness. In order to obtain accurate presence–absence estimates of M. asper at a reasonable cost piles of at least 0.25 m³ are suggested. Models which take into account the abundance of the species without marking individuals were the best compromise between costs and accuracy of estimation. Therefore, a reliable assessment of the population size of M. asper, can be based on count data without marking individuals. Because FCLP attract adults of M. asper and other saproxylic beetles, they could act also as potential ecological traps if chipped and/or removed after the sampling season. Therefore, if FCLP are used in monitoring as a part of conservation programmes, the piles should be left until completely decayed.