Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Comparing diel activity patterns of wildlife across latitudes and seasons: Time transformations using day length
Vazquez, Carmen ; Rowcliffe, Marcus ; Spoelstra, Kamiel ; Jansen, Patrick A. - \ 2019
Methods in Ecology and Evolution (2019). - ISSN 2041-210X
activity level - activity pattern - camera trapping - day length - diel activity - double anchoring - equinoctial anchoring - mouflon - red deer - seasonal variation

Camera trapping allows scientists to study activity patterns of animals under natural conditions. However, comparisons of activity patterns across seasons or latitudes can be biased, because activity is often attuned to sunrise and sunset, the timing of which varies with latitude and season. Existing transformation methods to solve this problem have limitations. Here, we explore whether and how activity patterns can be transformed more accurately using two alternative ‘double anchoring’ transformations – equinoctial and average anchoring – that anchor activity time to two chosen anchor points during the study period. Using simulated noisy datasets mimicking species with either crepuscular, diurnal or cathemeral activity patterns, we compared the ability of different transformation methods to extract the latent pattern and activity levels under different study conditions. We found that average anchoring best retrieved the original diel activity pattern and yielded accurate estimates of activity level. Two alternative transformation methods – single anchoring and equinoctial anchoring – performed less well. Bias in estimates from using untransformed clock times was most marked (up to 2.5-fold overestimation) for longer studies covering 4–5 months either side of an equinox at high latitude, and focusing on crepuscular species. We applied the average anchoring method to 9 months of data on Red deer Cervus elaphus, Wild boar Sus scrofa and Mouflon Ovis amon musimon activity as captured by camera traps in National Park Hoge Veluwe, the Netherlands. Average anchoring revealed more pronounced peaks of activity after sunset than was apparent from untransformed data in red deer and wild boar, but not for mouflon, a cathemeral species. Similarly, activity level was lower when calculated using average anchored time for red deer and wild boar, but no difference was observed for mouflon. We conclude that transformation of time might not be necessary at latitudes below 20°, or in studies with a duration of less than a month (below 40° latitude). For longer study periods and/or higher latitudes, average anchoring resolves the problem of variable day length. Code is provided. The transformation functions are incorporated in the r-package ‘activity’.

Prey availability and temporal partitioning modulate felid coexistence in Neotropical forests
Santos, Fernanda ; Carbone, Chris ; Wearn, Oliver R. ; Rowcliffe, J.M. ; Espinosa, Santiago ; Moreira, Marcela Guimarães ; Ahumada, Jorge A. ; Gonçalves, André Luis Sousa ; Trevelin, Leonardo C. ; Alvarez-Loayza, Patricia ; Spironello, Wilson R. ; Jansen, Patrick A. ; Juen, Leandro ; Peres, Carlos A. - \ 2019
PLoS ONE 14 (2019)3. - ISSN 1932-6203

Carnivores have long been used as model organisms to examine mechanisms that allow coexistence among ecologically similar species. Interactions between carnivores, including competition and predation, comprise important processes regulating local community structure and diversity. We use data from an intensive camera-trapping monitoring program across eight Neotropical forest sites to describe the patterns of spatiotemporal organization of a guild of five sympatric cat species: jaguar (Panthera onca), puma (Puma concolor), ocelot (Leopardus pardalis), jaguarundi (Herpailurus yagouaroundi) and margay (Leopardus wiedii). For the three largest cat species, we developed multi-stage occupancy models accounting for habitat characteristics (landscape complexity and prey availability) and models accounting for species interactions (occupancy estimates of potential competitor cat species). Patterns of habitat-use were best explained by prey availability, rather than habitat structure or species interactions, with no evidence of negative associations of jaguar on puma and ocelot occupancy or puma on ocelot occupancy. We further explore temporal activity patterns and overlap of all five felid species. We observed a moderate temporal overlap between jaguar, puma and ocelot, with differences in their activity peaks, whereas higher temporal partitioning was observed between jaguarundi and both ocelot and margay. Lastly, we conducted temporal overlap analysis and calculated species activity levels across study sites to explore if shifts in daily activity within species can be explained by varying levels of local competition pressure. Activity patterns of ocelots, jaguarundis and margays were similarly bimodal across sites, but pumas exhibited irregular activity patterns, most likely as a response to jaguar activity. Activity levels were similar among sites and observed differences were unrelated to competition or intraguild killing risk. Our study reveals apparent spatial and temporal partitioning for most of the species pairs analyzed, with prey abundance being more important than species interactions in governing the local occurrence and spatial distribution of Neotropical forest felids.

Quantifying the availability of vertebrate hosts to ticks : A camera-trapping approach
Hofmeester, Tim R. ; Marcus Rowcliffe, J. ; Jansen, Patrick A. - \ 2017
Frontiers in Veterinary Science 4 (2017)JUL. - ISSN 2297-1769
Contact rate - Forest wildlife - Gas theory - Host availability - Ixodes ricinus - Passage rate - Remote sensing - Tick-borne disease
The availability of vertebrate hosts is a major determinant of the occurrence of ticks and tick-borne zoonoses in natural and anthropogenic ecosystems and thus drives disease risk for wildlife, livestock, and humans. However, it remains challenging to quantify the availability of vertebrate hosts in field settings, particularly for medium-sized to large-bodied mammals. Here, we present a method that uses camera traps to quantify the availability of warm-bodied vertebrates to ticks. The approach is to deploy camera traps at questing height at a representative sample of random points across the study area, measure the average photographic capture rate for vertebrate species, and then correct these rates for the effective detection distance. The resulting "passage rate" is a standardized measure of the frequency at which vertebrates approach questing ticks, which we show is proportional to contact rate. A field test across twenty 1-ha forest plots in the Netherlands indicated that this method effectively captures differences in wildlife assemblage composition between sites. Also, the relative abundances of three life stages of the sheep tick Ixodes ricinus from drag sampling were correlated with passage rates of deer, which agrees with the known association with this group of host species, suggesting that passage rate effectively reflects the availability of medium- to large-sized hosts to ticks. This method will facilitate quantitative studies of the relationship between densities of questing ticks and the availability of different vertebrate species-wild as well as domesticated species-in natural and anthropogenic settings.
A simple method for estimating the effective detection distance of camera traps
Hofmeester, Tim R. ; Rowcliffe, J.M. ; Jansen, Patrick A. - \ 2017
Remote Sensing in Ecology and Conservation 3 (2017)2. - ISSN 2056-3485 - p. 81 - 89.
Body mass - camera traps - distance sampling - passive infrared sensor - sensor sensitivity - trail camera

Estimates of animal abundance are essential for understanding animal ecology. Camera traps can be used to estimate the abundance of terrestrial mammals, including elusive species, provided that the sensitivity of the sensor, estimated as the effective detection distance (EDD), is quantified. Here, we show how the EDD can be inferred directly from camera trap images by placing markers at known distances along the midline of the camera field of view, and then fitting distance-sampling functions to the frequency of animal passage between markers. EDD estimates derived from simulated passages using binned detection distances approximated those obtained from continuous detection distance measurements if at least five intervals were used over the maximum detection distance. A field test of the method in two forest types with contrasting vegetation density, with five markers at 2.5 m intervals, produced credible EDD estimates for 13 forest-dwelling mammals. EDD estimates were positively correlated with species body mass, and were shorter for the denser vegetation, as expected. Our findings suggest that this simple method can produce reliable estimates of EDD. These estimates can be used to correct photographic capture rates for difference in sampling effort resulting from differences in sensor sensitivity between species and habitats. Simplifying the estimation of EDD will result in less biased indices of relative abundance, and will also facilitate the use of camera trap data for estimating animal density.

Wildlife speed cameras: measuring animal travel speed and day range using camera traps
Rowcliffe, J.M. ; Jansen, P.A. ; Kays, R. ; Kranstauber, B. ; Carbone, C. - \ 2016
Remote Sensing in Ecology and Conservation 2 (2016)2. - ISSN 2056-3485 - p. 84 - 94.
Travel speed (average speed of travel while active) and day range (average speed over the daily activity cycle) are behavioural metrics that influence processes including energy use, foraging success, disease transmission and human-wildlife interactions, and which can therefore be applied to a range of questions in ecology and conservation. These metrics are usually derived from telemetry or direct observations. Here, we describe and validate an entirely new alternative approach, using camera traps recording passing animals to measure movement paths at very fine scale. Dividing the length of a passage by its duration gives a speed observation, and average travel speed is estimated by fitting size-biased probability distributions to a sample of speed observations. Day range is then estimated as the product of travel speed and activity level (proportion of time spent active), which can also be estimated from camera-trap data. We field tested the procedure with data from a survey of terrestrial mammals on Barro Colorado Island, Panama. Travel speeds and day ranges estimated for 12 species scaled positively with body mass, and were higher in faunivores than in herbivores, patterns that are consistent with those obtained using independent estimates derived from tracked individuals. Comparisons of our day range estimates with independent telemetry-based estimates for three species also showed very similar values in absolute terms. We conclude that these methods are accurate and ready to use for estimating travel speed and day range in wildlife. Key advantages of the methods are that they are non-invasive, and that measurements are made at very high resolution in time and space, yielding estimates that are comparable across species and studies. Combined with emerging techniques in computer vision, we anticipate that these methods will help to expand the range of species for which we can estimate movement rate in the wild.
Density estimation using camera trap surveys: the Random Encounter Model
Rowcliffe, J.M. ; Carbone, C. ; Kays, R. ; Kranstauber, B. ; Jansen, P.A. - \ 2014
In: Camera Trapping in Wildlife Management and Research / Meek, P., Ballard, A.G., Melbourne : CSIRO Publishing - p. 317 - 323.
Quantifying levels of animal activity using camera trap data
Rowcliffe, J.M. ; Kays, R. ; Kranstauber, B. ; Carbone, C. ; Jansen, P.A. - \ 2014
Methods in Ecology and Evolution 5 (2014)11. - ISSN 2041-210X - p. 1170 - 1179.
home-range size - predator avoidance - circadian activity - microtus-arvalis - activity pattern - common vole - time - food - determinants - ecology
1.Activity level (the proportion of time that animals spend active) is a behavioural and ecological metric that can provide an indicator of energetics, foraging effort and exposure to risk. However, activity level is poorly known for free-living animals because it is difficult to quantify activity in the field in a consistent, cost-effective and non-invasive way. 2.This article presents a new method to estimate activity level with time-of-detection data from camera traps (or more generally any remote sensors), fitting a flexible circular distribution to these data to describe the underlying activity schedule, and calculating overall proportion of time active from this. 3.Using simulations and a case study for a range of small- to medium-sized mammal species, we find that activity level can reliably be estimated using the new method. 4.The method depends on the key assumption that all individuals in the sampled population are active at the peak of the daily activity cycle. We provide theoretical and empirical evidence suggesting that this assumption is likely to be met for many species, but may be less likely met in large predators, or in high-latitude winters. Further research is needed to establish stronger evidence on the validity of this assumption in specific cases; however, the approach has the potential to provide an effective, non-invasive alternative to existing methods for quantifying population activity levels.
Food aquisition and predator avoidance in a Neotropical rodent
Suselbeek, L. ; Emsens, W.J. ; Hirsch, B.T. ; Kays, R. ; Rowcliffe, J.M. ; Zamore-Gutierrez, V. ; Jansen, P.A. - \ 2014
Animal Behaviour 88 (2014). - ISSN 0003-3472 - p. 41 - 48.
agouti dasyprocta-punctata - ocelot leopardus-pardalis - scatter-hoarding rodent - barro-colorado island - antipredator behavior - allocation hypothesis - moonlight avoidance - foraging behavior - time allocation - habitat use
Foraging activity in animals reflects a compromise between acquiring food and avoiding predation. The Risk Allocation Hypothesis predicts that prey animals optimize this balance by concentrating their foraging activity at times of relatively low predation risk, as much as their energy status permits, but empirical evidence is scarce. We used a unique combination of automated telemetry, manual radio telemetry and camera trapping to test whether activity at high-risk times declined with food availability, as predicted, in a Neotropical forest rodent, the Central American agouti (Dasyprocta punctata). We found that the relative risk of predation by the main predator, the Ocelot (Leopardus pardalis), estimated as the ratio of ocelot to agouti activity on camera trap footage, was up to four orders of magnitude higher between sunset and sunrise than during the rest of the day. Kills of radio-tracked agoutis by ocelots during this high-risk period far exceeded expectations given agouti activity. Both telemetric monitoring of radio-tagged agoutis and camera monitoring of burrow entrances indicated that agoutis exited their burrows later at dawn, entered their burrows earlier at dusk, and had lower overall activity levels, as they lived in areas with higher food abundance. Thus, agoutis avoided activity during the high-risk period more strongly as access to food was higher. Our study provides quantitative empirical evidence of prey animals concentrating their activity at times of relatively low predation risk.
Letter to the Editor : Clarifying Assumptions Behind the Estimation of Animal Density From Camera Trap Rates
Rowcliffe, J.M. ; Carbone, C. ; Jansen, P.A. - \ 2013
Journal of Wildlife Management 77 (2013)6. - ISSN 0022-541X - p. 876 - 876.
Bias in estimating animal travel distance: the effect of sampling frequency
Rowcliffe, J.M. ; Carbone, C. ; Kays, R. ; Kranstauber, B. ; Jansen, P.A. - \ 2012
Methods in Ecology and Evolution 3 (2012)4. - ISSN 2041-210X - p. 653 - 662.
bialowieza-primeval-forest - correlated random-walk - gps telemetry data - home ranges - movement data - body-size - behavior - models - poland - error
1. The distance travelled by animals is an important ecological variable that links behaviour, energetics and demography. It is usually measured by summing straight-line distances between intermittently sampled locations along continuous animal movement paths. The extent to which this approach underestimates travel distance remains a rarely addressed and unsolved problem, largely because true movement paths are rarely, if ever, available for comparison. Here, we use simulated movement paths parameterized with empirical movement data to study how estimates of distance travelled are affected by sampling frequency. 2. We used a novel method to obtain fine-scale characteristics of animal movement from camera trap videos for a set of tropical forest mammals and used these characteristics to generate detailed movement paths. We then sampled these paths at different frequencies, simulating telemetry studies, and quantified the accuracy of sampled travel distance estimation. 3. For our focal species, typical telemetry studies would underestimate distances travelled by 67–93%, and extremely high sampling frequencies (several fixes per minute) would be required to get tolerably accurate estimates. The form of the relationship between tortuosity, sample frequency, and distance travelled was such that absolute distance cannot accurately be estimated by the infrequent samples used in typical tracking studies. 4. We conclude that the underestimation of distance travelled is a serious but underappreciated problem. Currently, there is no reliable, widely applicable method to obtain approximately unbiased estimates of distance travelled by animals. Further research on this problem is needed.
Quantifying the sensitivity of camera traps:an adapted distance sampling approach
Rowcliffe, M. ; Carbone, C. ; Jansen, P.A. ; Kays, R.W. ; Kranstauber, B. - \ 2011
Methods in Ecology and Evolution 2 (2011)5. - ISSN 2041-210X - p. 464 - 476.
neotropical forests - photographic rates - estimate densities - cryptic mammals - population - tigers - landscape - design - birds
1. Abundance estimation is a pervasive goal in ecology. The rate of detection by motion-sensitive camera traps can, in principle, provide information on the abundance of many species of terrestrial vertebrates that are otherwise difficult to survey. The random encounter model (REM, Rowcliffe et al. 2008) provides a means estimating abundance from camera trap rate but requires camera sensitivity to be quantified. 2. Here, we develop a method to estimate the area effectively monitored by cameras, which is one of the most important codeterminants of detection rate. Our method borrows from distance sampling theory, applying detection function models to data on the position (distance and angle relative to the camera) where the animals are first detected. Testing the reliability of this approach through simulation, we find that bias depends on the effective detection angle assumed but was generally low at less than 5% for realistic angles typical of camera traps. 3. We adapted standard detection functions to allow for the possibility of smaller animals passing beneath the field of view close to the camera, resulting in reduced detection probability within that zone. Using a further simulation to test this approach, we find that detection distance can be estimated with little or no bias if detection probability is certain for at least some distance from the camera. 4. Applying this method to a 1-year camera trapping data set from Barro Colorado Island, Panama, we show that effective detection distance is related strongly positively to species body mass and weakly negatively to species average speed of movement. There was also a strong seasonal effect, with shorter detection distance during the wet season. Effective detection angle is related more weakly to species body mass, and again strongly to season, with a wider angle in the wet season. 5. This method represents an important step towards practical application of the REM, including abundance estimation for relatively small (
Camera traps as sensor networks for monitoring animal communities
Kays, R.W. ; Kranstauber, B. ; Jansen, P.A. ; Carbone, C. ; Rowcliffe, M. ; Fountain, T. ; Tilak, S. - \ 2009
In: Proceedings of the 4th IEEE International Workshop on Practical Issues in Building Sensor Network Applications (SenseApp) and the IEEE 34th Conference on Local Computer Networks (LCN 2009), Zurich, Switzerland, 20-23 October 2009. - - p. 811 - 818.
Studying animal movement and distribution is of critical importance to addressing environmental challenges including invasive species, infectious diseases, climate and land-use change. Motion sensitive camera traps offer a visual sensor to record the presence of a species at a location, recording their movement in the Eulerian sense. Modern digital camera traps that record video present new analytical opportunities, but also new data management challenges. This paper describes our experience with a year-long terrestrial animal monitoring system at Barro Colorado Island, Panama. The data gathered from our camera network shows the spatio-temporal dynamics of terrestrial bird and mammal activity at the site-data relevant to immediate science questions, and long-term conservation issues. We believe that the experience gained and lessons learned during our year long deployment and testing of the camera traps are applicable to broader sensor network applications and are valuable for the advancement of the sensor network research. We suggest that the continued development of these hardware, software, and analytical tools, in concert, offer an exciting sensor-network solution to monitoring of animal populations which could realistically scale over larger areas and time spans
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