A Comment on Priors for Bayesian Occupancy Models

Understanding patterns of species occurrence and the processes underlying these patterns is fundamental to the study of ecology. One of the more commonly used approaches to investigate species occurrence patterns is occupancy modeling, which can account for imperfect detection of a species during surveys. In recent years, there has been a proliferation of Bayesian modeling in ecology, which includes fitting Bayesian occupancy models. The Bayesian framework is appealing to ecologists for many reasons, including the ability to incorporate prior information through the specification of prior distributions on parameters. While ecologists almost exclusively intend to choose priors so that they are “uninformative” or “vague”, such priors can easily be unintentionally highly informative. Here we report on how the specification of a “vague” normally distributed (i.e., Gaussian) prior on coefficients in Bayesian occupancy models can unintentionally influence parameter estimation. Using both simulated data and empirical examples, we illustrate how this issue likely compromises inference about species-habitat relationships. While the extent to which these informative priors influence inference depends on the data set, researchers fitting Bayesian occupancy models should conduct sensitivity analyses to ensure intended inference, or employ less commonly used priors that are less informative (e.g., logistic or t prior distributions). We provide suggestions for addressing this issue in occupancy studies, and an online tool for exploring this issue under different contexts

Elevated potential for intraspecific competition in territorial carnivores occupying fragmented landscapes

The distribution of mammals is determined by a suite of endogenous and exogenous factors. In territorial, polygynous species like tigers (Panthera tigris), males often center their space-use around female territories, repelling competitors from these areas. Competition among males for females leads to increased mortality of both sexes and infanticide of unrelated cubs, which can lead to population declines. We hypothesized that increased territorial overlap among adult male tigers and elevated levels of inter and intra-sex competition would be manifest in populations with male-biased adult sex ratios (ASR). We also assessed whether inter-sex variation in adult survival or degree of habitat connectivity resulted in skewed ASR. We evaluated these hypotheses using camera trap data from three tiger populations occupying habitat patches with varying levels of connectivity and ASRs. Data were analyzed using multi-state occupancy models, where states were defined as habitat use by one or more male tigers in sites with and without female use. As predicted, in populations with male-biased or even ASR we found evidence for increased spatial overlap between male tigers, particularly pronounced in areas adjacent to female territories. Given parity in adult survival, habitat fragmentation likely caused male-biased ASR. Our results suggest that the persistence of small tiger populations in habitat patches with male-biased ASR may be significantly compromised by behavior-mediated endogenous demographic processes that are often overlooked. In habitat fragments with pronounced male biased ASR, population recovery of territorial carnivores may require timely supplementation of individuals to compensate for population losses from intraspecific competition

Behavioral and Demographic Responses of Mule Deer to Energy Development on Winter Range

Anthropogenic habitat modification is a major driver of global biodiversity loss. In North America, one of the primary sources of habitat modification over the last 2 decades has been exploration for and production of oil and natural gas (hydrocarbon development), which has led to demographic and behavioral impacts to numerous wildlife species. Developing effective measures to mitigate these impacts has become a critical task for wildlife managers and conservation practitioners. However, this task has been hindered by the difficulties involved in identifying and isolating factors driving population responses. Current research on responses of wildlife to development predominantly quantifies behavior, but it is not always clear how these responses scale to demography and population dynamics. Concomitant assessments of behavior and population‐level processes are needed to gain the mechanistic understanding required to develop effective mitigation approaches. We simultaneously assessed the demographic and behavioral responses of a mule deer population to natural gas development on winter range in the Piceance Basin of Colorado, USA, from 2008 to 2015. Notably, this was the period when development declined from high levels of active drilling to only production phase activity (i.e., no drilling). We focused our data collection on 2 contiguous mule deer winter range study areas that experienced starkly different levels of hydrocarbon development within the Piceance Basin. We assessed mule deer behavioral responses to a range of development features with varying levels of associated human activity by examining habitat selection patterns of nearly 400 individual adult female mule deer. Concurrently, we assessed the demographic and physiological effects of natural gas development by comparing annual adult female and overwinter fawn (6‐month‐old animals) survival, December fawn mass, adult female late and early winter body fat, age, pregnancy rates, fetal counts, and lactation rates in December between the 2 study areas. Strong differences in habitat selection between the 2 study areas were apparent. Deer in the less‐developed study area avoided development during the day and night, and selected habitat presumed to be used for foraging. Deer in the heavily developed study area selected habitat presumed to be used for thermal and security cover to a greater degree. Deer faced with higher densities of development avoided areas with more well pads during the day and responded neutrally or selected for these areas at night. Deer in both study areas showed a strong reduction in use of areas around well pads that were being drilled, which is the phase of energy development associated with the greatest amount of human presence, vehicle traffic, noise, and artificial light. Despite divergent habitat selection patterns, we found no effects of development on individual condition or reproduction and found no differences in any of the physiological or vital rate parameters measured at the population level. However, deer density and annual increases in density were higher in the low‐development area. Thus, the recorded behavioral alterations did not appear to be associated with demographic or physiological costs measured at the individual level, possibly because populations are below winter range carrying capacity. Differences in population density between the 2 areas may be a result of a population decline prior to our study (when development was initiated) or area‐specific differences in habitat quality, juvenile dispersal, or neonatal or juvenile survival; however, we lack the required data to contrast evidence for these mechanisms. Given our results, it appears that deer can adjust to relatively high densities of well pads in the production phase (the period with markedly lower human activity on the landscape), provided there is sufficient vegetative and topographic cover afforded to them and populations are below carrying capacity. The strong reaction to wells in the drilling phase of development suggests mitigation efforts should focus on this activity and stage of development. Many of the wells in this area were directionally drilled from multiple‐well pads, leading to a reduced footprint of disturbance, but were still related to strong behavioral responses. Our results also indicate the likely value of mitigation efforts focusing on reducing human activity (i.e., vehicle traffic, light, and noise). In combination, these findings indicate that attention should be paid to the spatial configuration of the final development footprint to ensure adequate cover. In our study system, minimizing the road network through landscape‐level development planning would be valuable (i.e., exploring a maximum road density criteria). Lastly, our study highlights the importance of concomitant assessments of behavior and demography to provide a comprehensive understanding of how wildlife respond to habitat modification

The impact of forest logging and fragmentation on the species richness and density of Malagasy rainforest carnivores

Despite significant efforts to understand and conserve Madagascar’s unique biodiversity, relatively little is known about the island’s carnivore populations. We sampled four rainforest sites to explore the effects of forest logging and fragmentation on carnivore species richness and the density of the two largest endemic carnivores, the Fossa (Cryptoprocta ferox) and Malagasy Civet (Fossa fossana). Our rainforest sites were selected across a gradient of increasing anthropogenic disturbance from primary to selectively-logged to fragmented forest < 2.5 km from primary forest, to fragmented forest > 20 km from primary forest. We deployed a minimum of 26 passive infrared camera stations at each forest site to non-invasively sample carnivores. By identifying C. ferox and F. fossana individuals based on unique pelage patterns, we were able to apply capture-recapture analyses using the Huggins model in Program MARK and Program DENSITY. We used a buffer of full mean-maximum-distance-moved (MMDM) and a spatially-explicit capture-recapture (SECR) method to estimate density. A total of 5,579 camera-trap nights yielded detections of five endemic carnivores (C. ferox, F. fossana, ring-tailed mongoose Galidia elegans, broad-striped mongoose Galidictus fasciata, small-toothed civet Eupleres goudotii). We found variation in carnivore species richness among the four sites. All endemic carnivores were present in the primary and selectively-logged rainforest, while overall endemic species richness was greatly reduced in the fragmented forests. Density also varied significantly among the rainforest sites. F. fossana density (individuals/km-2 ± SE) decreased significantly between the primary rainforest (SECR 3.19 ±0.55, MMDM 2.47 ±0.13) and selectively-logged rainforest (SECR 1.38 ± 0.223, MMDM 1.22 ± 0.055). F. fossana was absent from both fragmented sites. C. ferox density also decreased significantly between the primary rainforest (SECR 0.12 ± 0.05, MMDM 0.14 ± 0.001) and the selectively-logged rainforest (SECR 0.09 ±0.04, MMDM 0.09 ±0.002). C. ferox was absent from the fragmented rainforest > 20 km from primary forest, yet we did detect a single individual at the fragmented rainforest < 2.5 km from the primary forest. Our results suggest that forest logging and fragmentation negatively impact C. ferox and F. fossana populations in Malagasy rainforests. Unlike F. fossana, C. ferox appears to be able to occupy rainforest fragments near primary forest. Our study provides the first assessment of carnivore population parameters in the eastern rainforests of Madagascar and will be of importance to Malagasy governmental and non-governmental agencies seeking to more accurately assess the status of these species and to best set management goals

Accounting for Location Uncertainty in Azimuthal Telemetry Data Improves Ecological Inference

Background: Characterizing animal space use is critical for understanding ecological relationships. Animal telemetry technology has revolutionized the fields of ecology and conservation biology by providing high quality spatial data on animal movement. Radio-telemetry with very high frequency (VHF) radio signals continues to be a useful technology because of its low cost, miniaturization, and low battery requirements. Despite a number of statistical developments synthetically integrating animal location estimation and uncertainty with spatial process models using satellite telemetry data, we are unaware of similar developments for azimuthal telemetry data. As such, there are few statistical options to handle these unique data and no synthetic framework for modeling animal location uncertainty and accounting for it in ecological models. We developed a hierarchical modeling framework to provide robust animal location estimates from one or more intersecting or non-intersecting azimuths. We used our azimuthal telemetry model (ATM) to account for azimuthal uncertainty with covariates and propagate location uncertainty into spatial ecological models. We evaluate the ATM with commonly used estimators (Lenth (1981) maximum likelihood and M-Estimators) using simulation. We also provide illustrative empirical examples, demonstrating the impact of ignoring location uncertainty within home range and resource selection analyses. We further use simulation to better understand the relationship among location uncertainty, spatial covariate autocorrelation, and resource selection inference. Results: We found the ATM to have good performance in estimating locations and the only model that has appropriate measures of coverage. Ignoring animal location uncertainty when estimating resource selection or home ranges can have pernicious effects on ecological inference. Home range estimates can be overly confident and conservative when ignoring location uncertainty and resource selection coefficients can lead to incorrect inference and over confidence in the magnitude of selection. Furthermore, our simulation study clarified that incorporating location uncertainty helps reduce bias in resource selection coefficients across all levels of covariate spatial autocorrelation. Conclusion: The ATM can accommodate one or more azimuths when estimating animal locations, regardless of how they intersect; this ensures that all data collected are used for ecological inference. Our findings and model development have important implications for interpreting historical analyses using this type of data and the future design of radio-telemetry studies

Assessment of the Threatened Carnivore Community in the Recently Expanded Rainforest protected Area Anjanaharibe-Sud Special Reserve, Madagascar

Madagascar is an island nation renowned for its biodiversity and species endemism, yet it is still largely understudied despite intense anthropogenic threats including forest loss and edge effects. Anjanaharibe-Sud Special Reserve is a recently expanded rainforest protected area that is lacking detailed surveys and assessments of the native carnivore community of the endemic family Eupleridae. To identify which terrestrial carnivores occupy the reserve and what anthro- pogenic disturbances and factors best explain their occurrence patterns, we deployed 35 motion- activated cameras to detect native and introduced carnivores. From November 2018 to February 2019, we collected 2918 unique capture events (all species) and confirmed the presence of 5 eup- lerids: Galidia elegans, Galidictis fasciata, Eupleres goudotii, Fossa fossana, and Cryptoprocta ferox. These results extend the known range of E. goudotii and G. fasciata. In the reserve, F. fossana and G. elegans were the most common and widespread native carnivores, while E. goudotii was the rarest. We highlight the negative impact of edge effects on G. fasciata and F. fossana and the threat posed by the free-ranging non-native carnivore C. familiaris. This study represents the first detailed survey and occurrence estimates of the carnivore community of this protected area, allow- ing comparison with other protected areas in Madagascar. Our empirical findings show that anthro- pogenic disturbance negatively impacts carnivore existence within the Anjanaharibe-Sud Special Reserve and provide important management recommendations for protecting the carnivore com- munity and the co-occurring wildlife living within this area

Transboundary Cooperation Improves Endangered Species Monitoring and Conservation Actions: A Case Study of the Global Population of Amur Leopards

Political borders and natural boundaries of wildlife populations seldom coincide, often to the detriment of conservation objectives. Transnational monitoring of endangered carnivores is rare, but is necessary for accurate population monitoring and coordinated conservation policies. We investigate the benefits of collaboratively monitoring the abundance and survival of the critically endangered Amur leopard, which occurs as a single transboundary population across China and Russia. Country‐specific results overestimated abundance and were generally less precise compared to integrated monitoring estimates; the global population was similar in both years: 84 (70–108, 95% confidence interval). Uncertainty in country‐specific annual survival estimates were approximately twice the integrated estimates of 0.82 (0.69–0.91, 95% confidence limits). This collaborative effort provided a better understanding of Amur leopard population dynamics, represented a first step in building trust, and lead to cooperative agreements to coordinate conservation policies

Teeth, Sex, and Testosterone : Aging in the World's Smallest Primate

Peer reviewe