Toward reliable population density estimates of partially marked populations using spatially explicit mark-resight methods

Estimating density of forest bats and their long-term trends in a climate refuge

For many species, estimating density is challenging, but it is important for conservation planning and understanding the functional role of species. Bats play key ecological roles, yet little is known about their free-ranging density. We used a long-term banding study of four species caught in an extensively forested climate refuge and spatial capture-recapture models (SCR) to estimate density and its change over time. Between 1999 and 2020, there were 3671 captures of four bat species, which were all edge-space foragers. Recaptures represented 16% (n = 587) of all captures, of which 89 were between-trap-cluster movements. Closed spatial mark-recapture models estimated plausible densities that varied with elevation. Preferred elevations differed between species, with density averaging 0.63 ha-1 for Vespadelus darlingtoni (high elevation), 0.43 ha-1 for V. pumilus (low elevation), 0.19 ha-1 for Chalinolobus morio (high elevation), and 0.08 ha-1 for V. regulus (high elevation). Overall, densities were higher than most previous published estimates for bats. Forest disturbance history (past timber harvesting) had no detectable effect on density. Density also varied substantially across years, and although annual maximum temperature and rainfall were not supported in models, some time periods showed an apparent relationship between density and annual rainfall (+ve) and/or annual maximum temperature (-ve). The most notable change was an increase in the density of V. pumilus after 2013, which tracked an increase in annual temperature at the site, reflecting a warming climate. Bat densities in forests outside of climate refugia are likely to be more sensitive to climate change, but more studies are needed in different habitats and continents and outside climate refugia to place the densities we estimated into a broader context.

Counting the Capital's cats: Estimating drivers of abundance of free-roaming cats with a novel hierarchical model

Free-roaming cats are a conservation concern in many areas but identifying their impacts and developing mitigation strategies requires a robust understanding of their distribution and density patterns. Urban and residential areas may be especially relevant in this process because free-roaming cats are abundant in these anthropogenic landscapes. Here, we estimate the occupancy and density of free-roaming cats in Washington D.C. and relate these metrics to known landscape and social factors. We conducted an extended camera trap survey of public and private spaces across D.C. and analyzed data collected from 1483 camera deployments from 2018 to 2020. We estimated citywide cat distribution by fitting hierarchical occupancy models and further estimated cat abundance using a novel random thinning spatial capture-recapture model that allows for the use of photos that can and cannot be identified to individual. Within this model, we utilized individual covariates that provided identity exclusions between photos of unidentifiable cats with inconsistent coat patterns, thus increasing the precision of abundance estimates. This combined model also allowed for unbiased estimation of density when animals cannot be identified to individual at the same rate as for free-roaming cats whose identifiability depended on their coat characteristics. Cat occupancy and abundance declined with increasing distance from residential areas, an effect that was more pronounced in wealthier neighborhoods. There was noteworthy absence of cats detected in larger public spaces and forests. Realized densities ranged from 0.02 to 1.75 cats/ha in sampled areas, resulting in a district-wide estimate of ~7296 free-roaming cats. Ninety percent of cat detections lacked collars and nearly 35% of known individuals were ear-tipped, indicative of district Trap-Neuter-Return (TNR) programs. These results suggest that we mainly sampled and estimated the unowned cat subpopulation, such that indoor/outdoor housecats were not well represented. The precise estimation of cat population densities is difficult due to the varied behavior of subpopulations within free-roaming cat populations (housecats, stray and feral cats), but our methods provide a first step in establishing citywide baselines to inform data-driven management plans for free-roaming cats in urban environments.

Monitoring small mammal abundance using NEON data: are calibrated indices useful?

Small mammals are important to the functioning of ecological communities with changes to their abundances used to track impacts of environmental change. While capture–recapture estimates of absolute abundance are preferred, indices of abundance continue to be used in cases of limited sampling, rare species with little data, or unmarked individuals. Improvement to indices can be achieved by calibrating them to absolute abundance but their reliability across years, sites, or species is unclear. To evaluate this, we used the US National Ecological Observatory Network capture–recapture data for 63 small mammal species over 46 sites from 2013 to 2019. We generated 17,155 absolute abundance estimates using capture–recapture analyses and compared these to two standard abundance indices, and three types of calibrated indices. We found that neither raw abundance indices nor index calibrations were reliable approximations of absolute abundance, with raw indices less correlated with absolute abundance than index calibrations (raw indices overall R2 < 0.5, index calibration overall R2 > 0.6). Performance of indices and index calibrations varied by species, with those having higher and less variable capture probabilities performing best. We conclude that indices and index calibration methods should be used with caution with a count of individuals being the best index to use, especially if it can be calibrated with capture probability. None of the indices we tested should be used for comparing different species due to high variation in capture probabilities. Hierarchical models that allow for sharing of capture probabilities over species or plots (i.e., joint-likelihood models) may offer a better solution to mitigate the cost and effort of large-scale small mammal sampling while still providing robust estimates of abundance.

Visitation of artificial watering points by the red fox (Vulpes vulpes) in semiarid Australia

The introduced red fox (Vulpes vulpes) now occupies most of the Australian continent outside the tropics, including arid and semiarid ecosystems. Information on the water requirements of foxes is scant, but free water is not thought to be required if adequate moisture-containing food is available. The frequency and duration of visits by foxes fitted with GPS collars to known artificial watering points in semiarid Australia were recorded for 22 individual foxes across four austral seasons between October 2015 and November 2017, providing >93,000 location fixes. We modeled home range and the distance traveled by range-resident foxes beyond their home range to reach known water sources. We used recurse analysis to determine the frequency of visitation and step-selection functions to model the speed and directionality of movement inside and outside the home range. Our study demonstrates that some foxes in this semiarid environment utilize free-standing water. The findings suggest that artificial watering points can be used as a focal point for conducting strategic fox control in arid and semiarid environments. Additionally, strategies that restrict access to water by foxes may reduce their duration of occupancy and/or long-term abundance in parts of the landscape, thus providing benefits for conservation and agriculture.

Dingo Density Estimates and Movements in Equatorial Australia: Spatially Explicit Mark-Resight Models

Australia is currently free of canine rabies. Spatio-ecological knowledge about dingoes in northern Australia is currently a gap that impedes the application of disease spread models and our understanding of the potential transmission of rabies, in the event of an incursion. We therefore conducted a one-year camera trap survey to monitor a dingo population in equatorial northern Australia. The population is contiguous with remote Indigenous communities containing free-roaming dogs, which potentially interact with dingoes. Based on the camera trap data, we derived dingo density and home range size estimates using maximum-likelihood, spatially explicit, mark-resight models, described dingo movements and evaluated spatial correlation and temporal overlap in activities between dingoes and community dogs. Dingo density estimates varied from 0.135 animals/km² (95% CI = 0.127-0.144) during the dry season to 0.147 animals/km² (95% CI = 0.135-0.159) during the wet season. The 95% bivariate Normal home range sizes were highly variable throughout the year (7.95-29.40 km²). Spatial use and daily activity patterns of dingoes and free-roaming community dogs, grouped over ~3 month periods, showed substantial temporal activity overlap and spatial correlation, highlighting the potential risk of disease transmission at the wild-domestic interface in an area of biosecurity risk in equatorial northern Australia. Our results have utility for improving preparedness against a potential rabies incursion.

The value of camera traps in monitoring a feral-cat and fox reduction program

Abstract ContextWe examined the effectiveness of camera traps to monitor the success of a feral-cat (Felis catus) and fox (Vulpes vulpes) reduction program near Ravensthorpe, Western Australia. AimsTo determine whether camera traps are an effective tool to measure a reduction in the abundance of F. catus and V. vulpes at a local scale. MethodsIn all, 201 Foxoff® baits (i.e. 1080) were laid along the edge of unsealed tracks for each of three periods (i.e. opened 13–15 May 2017, Period 1 closed 29–31 May 2017, Period 2 closed 12–13 June 2017, Period 3 closed 25–26 June 2017), and 98 bait sites were monitored by camera traps during each period. In addition, 150 baited cage traps were deployed to catch F. catus for the same three periods. Vulpes vulpes and F. catus were also shot in the adjacent paddocks before traps were opened and during the laying of traps and bait replacement. We used the first 13 days of camera-trapping data for each period to examine whether there was a significant reduction in V. vulpes and F. catus. Key resultsCamera traps recorded a significant reduction in V. vulpes images, but knock-down with Foxoff® baits was not as effective as in other programs, and there was no change in the measured abundance of F. catus. Numerous baits were taken and not recorded by camera traps. Multiple V. vulpes moved past or investigated, but did not take baits and a V. vulpes was recorded regurgitating a bait. ConclusionsCamera traps were not effective for recording bait-take events. Vulpes vulpes knock-down was low and slow compared with other studies, did not reflect the number of baits taken and Foxoff® baits appeared unpalatable or unattractive to many V. vulpes. ImplicationsCamera traps did not record a high proportion of bait-take, appeared to be insensitive to small changes in fox and cat abundance and Foxoff® baits were less effective in reducing the abundance of V. vulpes than in other studies.