Summary1. Under increasing environmental and financial constraints, ecologists are faced with making decisions about dynamic and uncertain biological systems. To do so, stochastic dynamic programming (SDP) is the most relevant tool for determining an optimal sequence of decisions over time.2. Despite an increasing number of applications in ecology, SDP still suffers from a lack of widespread understanding. The required mathematical and programming knowledge as well as the absence of introductory material provide plausible explanations for this. 3. Here, we fill this gap by explaining the main concepts of SDP and providing useful guidelines to implement this technique, including R code. 4. We illustrate each step of SDP required to derive an optimal strategy using a wildlife management problem of the French wolf population. 5. Stochastic dynamic programming is a powerful technique to make decisions in presence of uncertainty about biological stochastic systems changing through time. We hope this review will provide an entry point into the technical literature about SDP and will improve its application in ecology.

The extent to which the fitness costs of infection are mediated by key life‐history traits such as age or social status is still unclear. Within populations, individual heterogeneity in the outcome of infection is the result of two successive processes; the degree of contact with the pathogen (exposure) and the immune response to infection. In social mammals, because individuals holding high social status typically interact more frequently with group members, they should be more often in contact with infected individuals than those of low social status. However, when access to resources is determined by social status, individuals with a high social status are often better nourished, have a greater opportunity to allocate resources to immune processes and therefore should have a smaller chance of succumbing to infection than individuals with low social status. We investigated the risk and fitness costs of infection during a virulent epidemic of canine distemper virus (CDV) in a social carnivore, the spotted hyena, in the Serengeti National Park. We analysed two decades of detailed life‐history data from 625 females and 816 males using a multi‐event capture–mark–recapture model that accounts for uncertainty in the assignment of individual infection states. Cubs of mothers with a high social status had a lower probability of CDV infection and were more likely to survive infection than those with low social status. Subadult and adult females with high social status had a higher infection probability than those with low social status. Subadult females and pre‐breeder males that had recovered from CDV infection had a lower survival than susceptible ones. Our study disentangles the relative importance of individual exposure and resource allocation to immune processes, demonstrates fitness costs of infection for juveniles, particularly for those with low social status, shows that patterns of infection can be driven by different mechanisms among juveniles and adults and establishes a negative relationship between infection and fitness in a free‐ranging mammal. A http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.13059/suppinfo is available for this article.

Interaction networks are central elements of ecological systems and have very complex structures. Historically, much effort has focused on niche-mediated processes to explain these structures, while an emerging consensus posits that both niche and neutral mechanisms simultaneously shape many features of ecological communities. However, the study of interaction networks still lacks a comprehensive neutral theory. Here we present a neutral model of predator-prey interactions and analyze the structural characteristics of the simulated networks. We find that connectance values (complexity) and complexity-diversity relationships of neutral networks are close to those observed in empirical bipartite networks. High nestedness and low modularity values observed in neutral networks fall in the range of those from empirical antagonist bipartite networks. Our results suggest that, as an alternative to niche-mediated processes that induce incompatibility between species (“niche forbidden links”), neutral processes create “neutral forbidden links” due to uneven species abundance distributions and the low probability of interaction between rare species. Neutral trophic networks must be seen as the missing endpoint of a continuum from niche to purely stochastic approaches of community organization.

Effective species management and conservation relies on accurate estimates of vital rates and an understanding of their link to environmental variables. We used multistate capture-mark-recapture models to directly quantify effects of predation on age-specific survival of black-tailed deer Odocoileus hemionus columbianus in California, USA. Survival probabilities were derived from individual encounter histories of 136 fawns and 57 adults monitored over 4 years. Based on results from our survival analysis we parameterized a Lefkovitch matrix and used elasticity analyses to investigate contributions of mortality due to predation to changes in population growth. We found strong evidence for age-specific survival including senescence. Survival of females [1 year old was consistently low (0.56 ± 0.18 for yearlings, 0.77 ± 0.13 for prime-aged females, and 0.55 ± 0.08 for senescent individuals), primarily due to high puma Puma concolor predation during summer. Predation from black bears Ursus americanus and coyotes Canis latrans was the primary cause for low annual survival of fawns (0.24 ± 0.16). Resulting estimates of population growth rates were indicative of a strongly declining population (k = 0.82 ± 0.13). Despite high sensitivity to changes in adult survival, results from a lower-level elasticity analysis suggested that predation on fawns was the most significant individual mortality component affecting population decline. Our results provide a rare, direct link between predation, age-specific survival and the predicted population decline of a common ungulate species. The magnitude of predation was unexpected and suggests that ungulates in multi-predator systems struggle to cope with simultaneous reductions in survival probabilities from predators targeting different age classes.

Summary 1.Mark-recapture studies are often used to estimate adult survival probability / ð Þ, which is an important demographic parameter for long-lived species, as it can have a large impact on the population growth rate. We consider the impact of variation in capture probability among individuals (capture heterogeneity) on the estimation of / from a mark-recapture study and thence on estimation of the asymptotic population growth rate k ð Þ. 2. We review the mechanisms by which capture heterogeneity arises, methods of allowing for it in the analysis, and use simulation to assess the power of detecting three types of capture heterogeneity (two-group heterogeneity, trap-response and temporary emigration) using standard mark-recapture lack-of-fit tests. 3. We use simulation to assess the bias that can arise in the estimation of / from a mark-recapture study when we do not allow for capture heterogeneity. Using a generic population model, we assess the effect this bias has on estimation of k. 4. We use our results on the power of the lack-of-fit tests, together with a measure of the size of the bias relative to the standard error of the estimate of /, to assess which situations might lead to an important level of undetected bias. Our results suggest that undetected bias is not likely to be an issue when there is trap-response, owing to the lack-of-fit tests having sufficient power to detect any trap-response that could lead to non-negligible bias. For two-group heterogeneity, the worst bias generally occurs when the difference between the capture probabilities for the two groups is moderate and both capture probabilities are low. For temporary emigration, the worst bias generally occurs when the rate of emigration and the capture probability are both low. 5. We illustrate the issues for conservation management using data from studies of Hector's dolphin (Cephalorhynchus hectori) in New Zealand and wolves (Canis lupus) in France. 6. Previous studies have suggested that capture heterogeneity will generally lead to a relatively small bias in the estimate of /. However, given the high sensitivity of the asymptotic population growth rate to adult survival, a small bias in / might lead to nontrivial bias in the estimate of k.

Determining the 'space race' between co-occurring species is crucial to understand the effects of interspecific interactions on the extinction risk of species threatened by poachers and predators. Dynamic two-species occupancy models provide a flexible framework to decompose complex species interaction patterns, while accounting for imperfect detection. These models can describe poachers-wildlife interactions, as they allow estimating occupancy, extinction and colonisation probabilities of wildlife conditional on the occurrence of poachers and vice versa. We applied our model to a case study on wildlife poaching in the eastern plains of Cambodia. We used co-occurrence data extracted from the database of the SMART partnership to study the distribution dynamics between poachers and six ungulate species pooled together into the tiger prey guild. We used four years of survey data reporting the locations of snares and of presence signs of the ungulates recorded by rangers during their monthly multi-patrolling sessions. Our results showed that a substantial proportion of the sites occupied by ungulate species went extinct over the years of the study while the proportion of sites colonised by poachers increased. We also showed, for the first time, that spatiotemporal heterogeneity in the patrolling effort explains a great deal of the variation in the detection of poachers and ungulates. Our approach provides practitioners with a flexible and robust tool to assess conservation status of species and extinction risk of wildlife populations. It can assist managers in better evaluating, learning and adapting the patrolling strategies of rangers.

Managing large carnivores is one of the most controversial issues in wildlife conservation, as the sociopolitical challenges it raises are as important as the biological ones. Such controversial issues in wildlife conservation require objective biological components to be implemented within the management decision process, in particular, a reliable way of estimating trends in abundance. However, these species usually exhibit territoriality, low densities, and social constraints that can generate individual detection heterogeneity (IDH) of methodological (sampling) or biological (social status, marking behavior) origin. If not accounted for, IDH can lead, in turn, to strong bias in the estimation of population abundance. As a complement to population size, we propose to use the population growth rate (λ) estimated with capture–recapture (CR) data, a robust method to detect and account for IDH, to monitor and manage elusive species. As a case study, we consider the natural recovery of the wolf (Canis lupus) population in France, for which a previous study has shown strong IDH leading to a 27% underestimation of abundance. Analyzing a nine‐year data set based on a noninvasive sampling protocol relying on wolf scat genotyping, we adopt a new CR approach to estimate λ while explicitly accounting for IDH. The annual population growth rate was estimated at 1.271 ± 0.087 (mean ± SE) vs. 1.270 ± 0.095 when not accounting for IDH, indicating that λ is much less sensitive to IDH than is abundance. We evaluated the robustness of our approach in a simulation study using increasing levels of IDH. The bias in λ increased with detection heterogeneity but was low whether we used a model with IDH or not. Finally, we discuss the management implications of our findings in terms of sampling protocols and management strategies of elusive species.

Introduction Various processes contribute to shaping the local assemblage of species in hyperdiverse tropical forest. The relative contribution of environmental factors and dispersal limitation in determining the spatial distribution of saplings at local scale is unclear. & Methods We examined two types of environmental factors: (a) soil type reflecting drainage regime and (b) past logging damages reflecting light regime in a neotropical moist forest site. We used a logistic model to predict presence or absence of a given species in a network of elementary small plots. & Results The effect of mapped environmental factors and a spatial correlation term were jointly estimated providing a direct measure of the relative role of habitat specialisation and dispersal limitation. At community level, dispersal limitation was the most important determinant of species absence at local scale. The two environmental factors examined played a balanced role. Different species however showed different degrees of dispersal limitation and habitat specialisation. The distribution of a large proportion of species-the majority of the most abundant species-was significantly affected by at least one environmental factor. We provide a ranking of 49 species sensitive to canopy disturbance (from shade specialist to pioneer) and 41 species affected by seasonal flooding (either positively or negatively). (Résumé d'auteur