More Like this

1. Guidelines for estimating occupancy from autocorrelated camera trap detections

   https://doi.org/10.1111/2041-210X.14359  

   Goldstein, Benjamin_R; Jensen, Alex_J; Kays, Roland; Cove, Michael_V; McShea, William_J; Rooney, Brigit; Kierepka, Elizabeth_M; Pacifici, Krishna (May 2024, Methods in Ecology and Evolution)

   Abstract Site occupancy models (SOMs) are a common tool for studying the spatial ecology of wildlife. When observational data are collected using passive monitoring field methods, including camera traps or autonomous recorders, detections of animals may be temporally autocorrelated, leading to biased estimates and incorrectly quantified uncertainty. We presently lack clear guidance for understanding and mitigating the consequences of temporal autocorrelation when estimating occupancy models with camera trap data.We use simulations to explore when and how autocorrelation gives rise to biased or overconfident estimates of occupancy. We explore the impact of sampling design and biological conditions on model performance in the presence of autocorrelation, investigate the usefulness of several techniques for identifying and mitigating bias and compare performance of the SOM to a model that explicitly estimates autocorrelation. We also conduct a case study using detections of 22 North American mammals.We show that a join count goodness‐of‐fit test previously proposed for identifying clustered detections is effective for detecting autocorrelation across a range of conditions. We find that strong bias occurs in the estimated occupancy intercept when survey durations are short and detection rates are low. We provide a reference table for assessing the degree of bias to be expected under all conditions. We further find that discretizing data with larger windows decreases the magnitude of bias introduced by autocorrelation. In our case study, we find that detections of most species are autocorrelated and demonstrate how larger detection windows might mitigate the resulting bias.Our findings suggest that autocorrelation is likely widespread in camera trap data and that many previous studies of occupancy based on camera trap data may have systematically underestimated occupancy probabilities. Moving forward, we recommend that ecologists estimating occupancy from camera trap data use the join count goodness‐of‐fit test to determine whether autocorrelation is present in their data. If it is, SOMs should use large detection windows to mitigate bias and more accurately quantify uncertainty in occupancy model parameters. Ecologists should not use gaps between detection periods, which are ineffective at mitigating temporal structure in data and discard useful data. 

   more » « less
2. Multi‐species occupancy models as robust estimators of community richness

   https://doi.org/10.1111/2041-210X.13378  

   Tingley, Morgan W.; Nadeau, Christopher P.; Sandor, Manette E.; Baselga, ed., Andrés (March 2020, Methods in Ecology and Evolution)

   Abstract Understanding patterns of diversity is central to ecology and conservation, yet estimates of diversity are often biased by imperfect detection. In recent years, multi‐species occupancy models (MSOM) have been developed as a statistical tool to account for species‐specific heterogeneity in detection while estimating true measures of diversity. Although the power of these models has been tested in various ways, their ability to estimate gamma diversity—or true community size,Nis a largely unrecognized feature that needs rigorous evaluation.We use both simulations and an empirical dataset to evaluate the bias, precision, accuracy and coverage of estimates ofNfrom MSOM compared to the widely applied iChao2 non‐parametric estimator. We simulated 5,600 datasets across seven scenarios of varying average occupancy and detectability covariates, as well as varying numbers of sites, replicates and true community size. Additionally, we use a real dataset of surveys over 9 years (where species accumulation reached an asymptote, indicating trueN), to estimateNfrom each annual survey.Simulations showed that both MSOM and iChao2 estimators are generally accurate (i.e. unbiased and precise) except under unideal scenarios where mean species occupancy is low. In such scenarios, MSOM frequently overestimatedN. Across all scenarios, MSOM estimates were less certain than iChao2, but this led to over‐confident iChao2 estimates that showed poor coverage. Results from the real dataset largely confirmed the simulation findings, with MSOM estimates showing greater accuracy and coverage than iChao2.Community ecologists have a wide choice of analytical methods, and both iChao2 and MSOM estimates ofNare substantially preferable to raw species counts. The simplicity of non‐parametric estimators has obvious advantages, but our results show that in many cases, MSOM may provide superior estimates that also account more accurately for uncertainty. Both methods can show strong bias when average occupancy is very low, and practitioners should show caution when using estimates derived from either method under such conditions. 

   more » « less
3. Relative bee abundance varies by collection method and flowering richness: Implications for understanding patterns in bee community data

   https://doi.org/10.1002/2688-8319.12071  

   Kuhlman, Marirose P.; Burrows, Skyler; Mummey, Daniel L.; Ramsey, Philip W.; Hahn, Philip G. (May 2021, Ecological Solutions and Evidence)

   Abstract Recent declines in wild bee populations have led to increases in conservation actions and monitoring of bee communities. Pan traps are a commonly used sampling method for monitoring bee populations due to their efficiency and low cost. However, potential biases inherent in different sampling techniques may result in misleading characterizations of bee communities across space and time.In this paper, we examined how bee communities sampled using pan traps and aerial nets changed seasonally, and if they were affected by the availability of floral resources.We found strong seasonal changes in the abundance, but not the richness, of bees captured in pan traps. Notably, we captured the fewest bees during weeks in spring when most flowering plant species were in bloom, suggesting that floral resource availability influences pan trap captures. We also compared patterns of bee abundance in pan traps to those captured by aerial netting. Bee richness in pans and nets was positively correlated, but relative abundances in pan and net samples were dominated by different bee genera. Furthermore, most genera decreased in pans with increasing floral richness, but patterns were mixed for nets. When using presence/absence data, rather than abundance, community composition was more similar between netted and pan‐trapped bee communities and changed less substantially across the floral richness gradient.Overall, these differences led to sampling substantially different bee community compositions in pan traps versus nets, especially when using abundance‐based methods to characterize the bee community. By examining multiple years of intensive seasonal sampling of plant and bee communities, we document potential pitfalls with methods commonly used to sample bee communities.We suggest that pan trapping and aerial netting provide similar estimates of bee species richness and community composition when using presence/absence data, but that practitioners should interpret pan‐trapped bee abundance data with caution especially when comparing bee communities between sites where plant communities may differ. 

   more » « less
4. Estimating animal size or distance in camera trap images: Photogrammetry using the pinhole camera model

   https://doi.org/10.1111/2041-210X.13880  

   Leorna, Scott; Brinkman, Todd; Fullman, Timothy (May 2022, Methods in Ecology and Evolution)

   Abstract As camera trapping has become a standard practice in wildlife ecology, developing techniques to extract additional information from images will increase the utility of generated data. Despite rapid advancements in camera trapping practices, methods for estimating animal size or distance from the camera using captured images have not been standardized. Deriving animal sizes directly from images creates opportunities to collect wildlife metrics such as growth rates or changes in body condition. Distances to animals may be used to quantify important aspects of sampling design such as the effective area sampled or distribution of animals in the camera's field‐of‐view.We present a method of using pixel measurements in an image to estimate animal size or distance from the camera using a conceptual model in photogrammetry known as the ‘pinhole camera model’. We evaluated the performance of this approach both using stationary three‐dimensional animal targets and in a field setting using live captive reindeerRangifer tarandusranging in size and distance from the camera.We found total mean relative error of estimated animal sizes or distances from the cameras in our simulation was −3.0% and 3.3% and in our field setting was −8.6% and 10.5%, respectively. In our simulation, mean relative error of size or distance estimates were not statistically different between image settings within camera models, between camera models or between the measured dimension used in calculations.We provide recommendations for applying the pinhole camera model in a wildlife camera trapping context. Our approach of using the pinhole camera model to estimate animal size or distance from the camera produced robust estimates using a single image while remaining easy to implement and generalizable to different camera trap models and installations, thus enhancing its utility for a variety of camera trap applications and expanding opportunities to use camera trap images in novel ways. 

   more » « less
5. Reaching new heights: Arboreal ant diversity in a North American temperate forest ecosystem

   https://doi.org/10.1111/icad.12788  

   Kirchner, Michelle; Sorenson, Clyde; Blaimer, Bonnie B; Youngsteadt, Elsa (November 2024, Insect Conservation and Diversity)

   Abstract Most canopy insect research takes place in tropical forests, where communities are highly vertically stratified. However, temperate forest canopies also provide critical resources to many species and are under intense pressure from global change drivers. The relative lack of knowledge regarding temperate canopy insect ecology impedes our forest management and conservation decisions such that we may be losing temperate canopy biodiversity before we know it exists.We directly compared ant diversity and community composition on the ground and in the tree canopy of North American temperate deciduous forests for the first time. We also evaluated two canopy sampling methods—baits and hand collections.We collected 34 ant species from 102 trees across seven sites. Ant diversity was greater on the ground than in the canopy, and species turnover created distinct communities across vertical strata. Only 12% of species were exclusively arboreal, but 47% were collected in both strata, indicating the canopy is an important resource for temperate ants, even if they are not restricted there.Baiting and hand‐collecting recovered similar species richness, but whether baits captured a subset of hand‐collected species or a unique assemblage was site‐dependent. Nevertheless, we suggest that these methods are most effective in conjunction.Hand collection allowed us to document arboreal nests of 10 species, including the invasive needle ant,Brachyponera chinensis, which was previously thought to be strictly terrestrial.Our results emphasise the importance of including the canopy in temperate forest ecology and conservation assessments. 

   more » « less