Assessing heterogeneity in transition propensity in multi-state capture-recapture data

Multi-state capture-recapture models are a useful tool to help understand the dynamics of movement within discrete capture-recapture data. The standard multi-state capture-recapture model however relies on assumptions of homogeneity within the population with respect to survival, capture and transition probabilities. There are many ways in which this model can be generalized so that some guidance as to what is really needed is highly desirable. Within this paper we derive a new test capable of detecting heterogeneity in transition propensity and show its good power using simulation and application to a Canada goose data set. We also demonstrate that existing tests which have traditionally been used to diagnose memory are in fact sensitive to other forms of transition heterogeneity and we propose modified tests which are able to distinguish between memory and other forms of transition heterogeneity

Estimation of lifetime reproductive success when reproductive status cannot always be assessed

International audienceThe Lifetime Reproductive Success (LRS) of an individual i.e. the number of young raised during its lifespan is an indicator of its contribution t o future generations and thus a measure of fitness. Nevertheless, the LRS is hard to estimate because of the difficulty to keep track of the outcome of each breed- ing attempt (successful or failed and, if successful, number of young raised). We propose two new methods to estimating the LRS that takes into account the uncertainty about the reproductive status when the individuals are not de- tected or when the reproductive status cannot be assessed. We illustrate these two methods using roe deer reproductive histories and discuss their advantages and disadvantages

Multi-event capture-recapture analysis reveals individual foraging specialization in a generalist species

© 2015 by the Ecological Society of America. Populations of species typically considered trophic generalists may include specialized individuals consistently feeding on certain resources. Optimal foraging theory states that individuals should feed on those resources most valuable to them. This, however, may vary according to individual differences in detecting or processing resources, different optimization criteria, and competitive abilities. White Storks (Ciconia ciconia) are trophic generalists at the population level. Their European population recovery has been attributed to increased wintering in southern Europe (rather than Africa) where they feed upon new anthropogenic food subsidies: predictable dumps and less predictable and more difficult to detect, but abundant, invasive Procambarus clarkii crayfishes in ricefields. We studied the foraging strategies of resident and wintering storks in southwestern Spain in ricefields and dumps, predicting that more experience in the study area (residents vs. immigrants, old vs. young) would increase ricefield specialization. We developed the first multi-event capture- recapture model to evaluate behavioral consistency, analyzing 3042 observations of 1684 banded storks. There were more specialists among residents (72%) than immigrants (40%). All resident specialists foraged in ricefields, and ricefield use increased with individual age. In contrast, some immigrants specialized on either dumps (24%) or ricefields (16%), but the majority were generalists (60%). Our results provide empirical evidence of high individual foraging consistency within a generalist species and a differential resource selection by individuals of different ages and origins, probably related to their previous experience in the foraging area. Thus, future changes in food resource availability at either of the two anthropogenic subsidies (ricefields or dumps) may differentially impact individuals of different ages and origins making up the wintering population. The use of multi-event capture- recapture modeling has proven useful for studying interindividual variability in behavior.Peer Reviewe

A Test for the Underlying State-Structure of Hidden Markov Models: Partially Observed Capture-Recapture Data

Hidden Markov models (HMMs) are being widely used in the field of ecological modeling, however determining the number of underlying states in an HMM remains a challenge. Here we examine a special case of capture-recapture models for open populations, where some animals are observed but it is not possible to ascertain their state (partial observations), whilst the other animals' states are assigned without error (complete observations). We propose a mixture test of the underlying state structure generating the partial observations, which assesses whether they are compatible with the set of states observed in the complete observations. We demonstrate the good performance of the test using simulation and through application to a data set of Canada Geese

Sex-specific costs of reproduction on survival in a long-lived seabird

Costs of reproduction on survival have captured the attention of researchers since life history theory was formulated. Adults of long-lived species may increase survival by reducing their breeding effort or even skipping reproduction. In this study, we aimed to evaluate the costs of current reproduction on survival and whether skipping reproduction increases adult survival in a long-lived seabird. We used capture-mark-recapture data (1450 encounters) from two populations of Bulwer's petrel (Bulweria bulwerii), breeding in the Azores and Canary Islands, North Atlantic Ocean. Using a multi-event model with two different breeding statuses (breeders versus non-breeders), we calculated probabilities of survival and of transitions between breeding statuses, evaluating potential differences between sexes. Females had lower survival probabilities than males, independent of their breeding status. When considering breeding status, breeding females had lower survival probabilities than non-breeding females, suggesting costs of reproduction on survival. Breeding males had higher survival probabilities than non-breeding males, suggesting that males do not incur costs of reproduction on survival and that only the highest quality males have access to breeding. The highest and the lowest probabilities of skipping reproduction were found in breeding males from the Azores and in breeding males from the Canary Islands, respectively. Intermediate values were observed in the females from both populations. This result is probably due to differences in the external factors affecting both populations, essentially predation pressure and competition. The existence of sex-specific costs of reproduction on survival in several populations of this long-lived species may have important implications for species population dynamics

Density-dependent parameters and demographic equilibrium in open populations

International audienceG. Tavecchia ([email protected]), R. Pradel, M. Genovart and D. Oro, IMEDEA (UIB-CSIC), 21 M. Marques, ES-07190 Esporles, Spain. Populations near their equilibrium are expected to show density-dependence through a negative feedback on at least one demographic parameter, e.g. survival and/or productivity. Nevertheless, it is not always clear which vital rate is affected the most, and even less whether this dependence holds in open populations in which immigration and emigration are also important. We assessed the relative importance of population density in the variation of local survival, recruitment, proportion of transients (emigrants) and productivity through the analysis of detailed life-histories of 4286 seabirds from a colony that reached an apparent demographic equilibrium after a period of exponential increase. We provide evidence that the role of population density and resource availability changes according to the demographic parameter considered. Estimates indicated that transients increased from 5% to 20% over the study period, suggesting an average turnover of about 1400 individuals per year. The parameters most influenced by population density alone were local survival and probability of transience. Recruitment was negatively associated with population density during the increasing phase but unexpected high values were also recorded at high population levels. These high values were explained by a combination of population size and food availability. Mean productivity varied with food availability, independently from population variations. The population density alone explained up to a third of the yearly variation of the vital rates considered, suggesting that open populations are equally influenced by stochastic and density-independent events (such as environmental perturbations) than by intrinsic (i.e. density-dependent) factors

Variations in band reporting rate and implications for kill rate in Greater Snow Geese

We assessed spatial and temporal variation in reporting probability of banded Greater Snow Geese (Chen caerulescens atlantica) shot by hunters in eastern North America and evaluated potential residual biases in kill rate estimation. Adult Greater Snow Geese were marked with reward (value: US$10,$20, $30,$50, and $100) and standard bands ($0, control) in the Canadian Arctic from 2003 to 2005. We used a spatially explicit multinomial model based on 200 direct recoveries from 4256 banded geese to estimate reporting rate and harvest rate. We found that reporting rate for standard bands varied over time whereas harvest rate was higher in Canada than in the U.S. The reporting probability increased from 0.40 ± 0.11 in the first year of the study to 0.82 ± 0.14 and 0.84 ± 0.13 the second and third years, respectively. Overall, these reporting rates are higher than two previous estimates for this population, which leads to lower estimates of kill rate. However, the large annual differences in reporting rates found in this study lead to uncertainty in the estimation of kill rate. We suggest that the increase in reporting rate in the last two year of the study may be due to the dissemination of information among hunters regarding the presence of reward bands on birds, resulting in increased reporting rate for all bands. This raises issues about the need to adequately inform the public in such large-scale studies to avoid undesirable temporal trends over the course of the study

Will climate change affect the survival of tropical and subtropical species? Predictions based on Bulwer's petrel populations in the NE Atlantic Ocean

Climate change has repeatedly been shown to impact the demography and survival of marine top predators. However, most evidence comes from single populations of widely distributed species, limited mainly to polar and subpolar environments. Here, we aimed to evaluate the influence of environmental conditions on the survival of a tropical and migratory seabird over the course of its annual cycle. We used capture-mark-recapture data from three populations of Bulwer's petrel (Bulweria bulwerii) spread across the NE Atlantic Ocean, from the Azores, Canary, and Cabo Verde Islands (including temperate to tropical zones). We also inferred how the survival of this seabird might be affected under different climatic scenarios, defined by the Intergovernmental Panel on Climate Change. Among the environmental variables whose effect we evaluated (North Atlantic Oscillation index, Southern Oscillation Index, Sea Surface Temperature [SST] and wind speed), SST estimated for the breeding area and season was the variable with the greatest influence on adult survival. Negative effects of SST increase emerged across the three populations, most likely through indirect trophic web interactions. Unfortunately, our study also shows that the survival of Bulwer's petrel will be profoundly affected by the different scenarios of climate change, even with the most optimistic trajectory involving the lowest greenhouse gas emission. Furthermore, for the first time, our study predicts stronger impacts of climate change on tropical populations than on subtropical and temperate ones. This result highlights the devastating effect that climate change may also have on tropical areas, and the importance of considering multi-population approaches when evaluating its impacts which may differ across species distributions

Dermal mycobacteriosis and warming sea surface temperatures are associated with elevated mortality of striped bass in Chesapeake Bay

Temperature is hypothesized to alter disease dynamics, particularly when species are living at or near their thermal limits. When disease occurs in marine systems, this can go undetected, particularly if the disease is chronic and progresses slowly. As a result, population-level impacts of diseases can be grossly underestimated. Complex migratory patterns, stochasticity in recruitment, and data and knowledge gaps can hinder collection and analysis of data on marine diseases. New tools enabling quantification of disease impacts in marine environments include coupled biogeochemical hydrodynamic models (to hindcast key environmental data), and multievent, multistate mark-recapture (MMSMR) (to quantify the effects of environmental conditions on disease processes and assess population-level impacts). We used MMSMR to quantify disease processes and population impacts in an estuarine population of striped bass (Morone saxatilis) in Chesapeake Bay from 2005 to 2013. Our results supported the hypothesis that mycobacteriosis is chronic, progressive, and, frequently, lethal. Yearly disease incidence in fish age three and above was 89%, suggesting that this disease impacts nearly every adult striped bass. Mortality of diseased fish was high, particularly in severe cases, where it approached 80% in typical years. Severely diseased fish also had a 10-fold higher catchability than healthy fish, which could bias estimates of disease prevalence. For both healthy and diseased fish, mortality increased with the modeled average summer sea surface temperature (SST) at the mouth of the Rappahannock River; in warmer summers (average SST29 degrees C), a cohort is predicted to experience \u3e90% mortality in 1year. Regression of disease signs in mildly and moderately diseased fish wa