The influence of study design on the ability to detect the effects of landscape pattern on gene flow is one of the most pressing methodological gaps in landscape genetic research. To investigate the effect of study design on landscape genetics inference, we used a spatially‐explicit, individual‐based program to simulate gene flow in a spatially continuous population inhabiting a landscape with gradual spatial changes in resistance to movement. We simulated a wide range of combinations of number of loci, number of alleles per locus and number of individuals sampled from the population. We assessed how these three aspects of study design influenced the statistical power to successfully identify the generating process among competing hypotheses of isolation‐by‐distance, isolation‐by‐barrier, and isolation‐by‐landscape resistance using a causal modelling approach with partial Mantel tests. We modelled the statistical power to identify the generating process as a response surface for equilibrium and non‐equilibrium conditions after introduction of isolation‐by‐landscape resistance. All three variables (loci, alleles and sampled individuals) affect the power of causal modelling, but to different degrees. Stronger partial Mantel r correlations between landscape distances and genetic distances were found when more loci were used and when loci were more variable, which makes comparisons of effect size between studies difficult. Number of individuals did not affect the accuracy through mean equilibrium partial Mantel r, but larger samples decreased the uncertainty (increasing the precision) of equilibrium partial Mantel r estimates. We conclude that amplifying more (and more variable) loci is likely to increase the power of landscape genetic inferences more than increasing number of individuals.

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Predator species identification is an important step in understanding predator-prey interactions, but predator identifications using kill site observations are often unreliable. We used molecular tools to analyse predator saliva, scat and hair from caribou calf kills in Newfoundland, Canada to identify the predator species, individual and sex. We sampled DNA from 32 carcasses using cotton swabs to collect predator saliva. We used fragment length analysis and sequencing of mitochondrial DNA to distinguish between coyote, black bear, Canada lynx and red fox and used nuclear DNA microsatellite analysis to identify individuals. We compared predator species detected using molecular tools to those assigned via field observations at each kill. We identified a predator species at 94% of carcasses using molecular methods, while observational methods assigned a predator species to 62.5% of kills. Molecular methods attributed 66.7% of kills to coyote and 33.3% to black bear, while observations assigned 40%, 45%, 10% and 5% to coyote, bear, lynx and fox, respectively. Individual identification was successful at 70% of kills where a predator species was identified. Only one individual was identified at each kill, but some individuals were found at multiple kills. Predator sex was predominantly male. We demonstrate the first large-scale evaluation of predator species, individual and sex identification using molecular techniques to extract DNA from swabs of wild prey carcasses. Our results indicate that kill site swabs (i) can be highly successful in identifying the predator species and individual responsible; and (ii) serve to inform and complement traditional methods.

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An understanding of a species’ diet is required to make sound conservation and management decisions. Traditionally, morphological analyses of undigested hard parts from food items remaining in scats have been used to assess diets. More recently, molecular analyses of scats have been used to identify plant and prey species’ DNA, but no studies have compared morphological and molecular diet analyses for large, terrestrial carnivores. We used molecular tools to determine the percentage of black bear and coyote scats that contained 3 common prey species (caribou, moose, and snowshoe hares) in Newfoundland and compared the results to a traditional morphological analysis. We found that a ranking of relative prey frequencies was consistent between the 2 methods, but molecular methods tended to detect prey species in a greater percentage of scats for all prey species. However, there were individual scats in which a prey species was detected by morphological methods only, and we provide evidence that molecular methods could result in false negatives if prey DNA is not uniformly distributed throughout a scat or as a result of PCR inconsistency. We also found that the per sample cost comparison between morphological and molecular analyses was dependent upon whether or not a molecular test was needed to identify scats to the predator species, the cost of developing molecular methods, and the number of samples being processed. We recommend that controlled feeding studies be performed to validate molecular methods and investigate the utility of molecular techniques to estimate the proportions of food items consumed.

Predation risk is a driver of species’ distributions. Animals can increase risk avoidance in response to fluctuations in predation risk, but questions remain regarding individual variability and the capacity to respond to changes in spatial risk across human‐altered landscapes. In northeast British Columbia, Canada, boreal caribou populations declined as roads and seismic lines have increased, which are theorized to increase gray wolf predation. Our goal was to model risk and to evaluate individual variability and the development of risk perception by examining individual risk avoidance in response to reproductive status and age. We used locations from collared caribou and wolves to identify landscape features associated with the risk of a potential wolf‐caribou encounter and risk of being killed given an encounter. We built resource selection functions to estimate individual responses to risk. We used general linear regressions to evaluate individual risk and linear feature avoidance as a function of age and reproductive status (calf or no calf). Linear features increased the risk of encounter. Older caribou and caribou with calves demonstrated stronger avoidance of the risk of encounter and roads, but weaker avoidance in late summer to the risk of being killed relative to younger and calf‐less individuals. Mechanisms explaining the inverse relationships between the risk of encounter and risk of being killed are uncertain, but it is conceivable that caribou learn to avoid the risk of encounter and roads. Responses by females with vulnerable calves to the risk of encounter and risk of being killed might be explained by a trade‐off between these two risk types and a prioritization on the risk of encounter. Despite the capacity to alter their responses to risk, the global decline in Rangifer populations (caribou and wild reindeer) suggests these behaviors are insufficient to mitigate the impacts of anthropogenic disturbances.

Woodland caribou is a Threatened or Endangered subspecies across much of Canada. In many cases, these caribou are declining because of human‐mediated predation in the form of apparent competition. Provincial and federal agencies have employed a number of conservation actions to arrest the decline, but insufficient time and limited replication make it difficult to test the efficacy of those activities. We built a three‐species population model that served as a tool to integrate current knowledge, explore uncertainties, and assess activities focused on the recovery of caribou. We applied the model to interconnected populations of caribou, moose, and wolves at two locations in Canada (Chinchaga [British Columbia], Charlevoix [Québec]) and explored the efficacy of conservation actions unique to each population: predator control, restoration of linear features, reduction of habitat for moose, supplementation, maternal pens, and predator exclosures. Results confirmed that caribou at these two locations faced different recovery challenges, dictated by specific population dynamics and threats. Wolf predation, enhanced by seismic lines and resource roads, was responsible for the decline of the simulated Chinchaga population. The most cost‐effective recovery actions for that population were long‐term lethal wolf control (λ1–50 = 1.014, $25,665/caribou), a large‐scale predator exclosure (λ1–50 = 1.015, $170,767/caribou), and the aggressive restoration of linear features (λ1–50 = 1.002, $531,675/caribou). In contrast, simulations suggested that calf predation by black bears, a fixed source of mortality in the model, limited the growth of the Charlevoix population. Assuming high survival of adult caribou and poor recruitment of juveniles, a maternal pen was the most effective action for the recovery of those caribou (λ1–50 = 1.004, $148,473/caribou). Short‐term population supplementation provided only a temporary increase in abundance (λ1–50 = 0.994, $62,143/caribou). The model was limited by ecological and data uncertainties, but served as an effective platform for representing and testing our understanding of the complex interspecific interactions that underlie the recovery of woodland caribou.

Monitoring large carnivores is difficult because of intrinsically low densities and can be dangerous if physical capture is required. Noninvasive genetic sampling (NGS) is a safe and cost-effective alternative to physical capture. We evaluated the utility of two NGS methods (scat detection dogs and hair sampling) to obtain genetic samples for abundance estimation of coyotes, black bears and Canada lynx in three areas of Newfoundland, Canada. We calculated abundance estimates using program capwire, compared sampling costs, and the cost/sample for each method relative to species and study site, and performed simulations to determine the sampling intensity necessary to achieve abundance estimates with coefficients of variation (CV) of <10%. Scat sampling was effective for both coyotes and bears and hair snags effectively sampled bears in two of three study sites. Rub pads were ineffective in sampling coyotes and lynx. The precision of abundance estimates was dependent upon the number of captures/individual. Our simulations suggested that ~3.4 captures/individual will result in a < 10% CV for abundance estimates when populations are small (23-39), but fewer captures/individual may be sufficient for larger populations. We found scat sampling was more cost-effective for sampling multiple species, but suggest that hair sampling may be less expensive at study sites with limited road access for bears. Given the dependence of sampling scheme on species and study site, the optimal sampling scheme is likely to be study-specific warranting pilot studies in most circumstances.