Relationship between wintering site and survival in a migratory waterbird using different migration routes.

When wintering at different sites, individuals from the same breeding population can experience different conditions, with costs and benefits that may have implications throughout their lifetime. Using a dataset from a longitudinal study on Eurasian Spoonbills from southern France, we explored whether survival rate varied among individuals using different wintering sites. In the last 13 years, more than 3000 spoonbills have been ringed as chicks in Camargue. These birds winter in five main regions that vary in both migratory flyway (East Atlantic vs. Central European) and migration distance (long-distance vs. short-distance vs. resident). We applied Cormack-Jolly-Seber models and found evidence for apparent survival to correlate with migration distance, but not with flyway. During the interval between the first winter sighting and the next breeding period, long-distance migrants had the lowest survival, independently of the flyway taken. Additionally, as they age, spoonbills seem to better cope with migratory challenges and wintering conditions as no differences in apparent survival among wintering strategies were detected during subsequent years. As dispersal to other breeding colonies was rarely observed, the lower apparent survival during this period is likely to be partly driven by lower true survival. This supports the potential role of crossing of natural barriers and degradation of wintering sites in causing higher mortality rates as recorded for a variety of long-distance migrants. Our work confirms variation in demographic parameters across winter distribution ranges and reinforces the importance of longitudinal studies to better understand the complex demographics of migratory species.

Age-Specific Demographic Response of a Long-Lived Scavenger Species to Reduction of Organic Matter in a Landfill.

Food availability shapes demographic parameters and population dynamics. Certain species have adapted to predictable anthropogenic food resources like landfills. However, abrupt shifts in food availability can negatively impact such populations. While changes in survival are expected, the age-related effects remain poorly understood, particularly in long-lived scavenger species. We investigated the age-specific demographic response of a Griffon vulture (Gyps fulvus) population to a reduction in organic matter in a landfill and analyzed apparent survival and the probability of transience after initial capture using a Bayesian Cormack-Jolly-Seber model on data from 2012-2022. The proportion of transients among newly captured immatures and adults increased after the reduction in food. Juvenile apparent survival declined, increased in immature residents, and decreased in adult residents. These results suggest that there was a greater likelihood of permanent emigration due to intensified intraspecific competition following the reduction in food. Interestingly, resident immatures showed the opposite trend, suggesting the persistence of high-quality individuals despite the food scarcity. Although the reasons behind the reduced apparent survival of resident adults in the final four years of the study remain unclear, non-natural mortality potentially plays a part. In Europe landfill closure regulations are being implemented and pose a threat to avian scavenger populations, which underlines the need for research on food scarcity scenarios and proper conservation measures.

Extreme polygyny results in intersex differences in age-dependent survival of a highly dimorphic marine mammal.

Developmental differences in vital rates are especially profound in polygamous mating systems. Southern elephant seals (Mirounga leonina) are highly dimorphic and extremely polygynous marine mammals. A demographic model, supported by long-term capture-mark-recapture records, investigated the influence of sex and age on survival in this species. The study revealed clear differences between female and male age-dependent survival rates. Overall juvenile survival estimates were stable around 80-85% for both sexes. However, male survival estimates were 5-10% lower than females in the same age classes until 8 years of age. At this point, male survival decreased rapidly to 50% ± 10% while female estimates remained constant at 80% ± 5%. Different energetic requirements could underpin intersex differences in adult survival. However, the species' strong sexual dimorphism diverges during early juvenile development when sex-specific survival rates were less distinct. Maximizing growth is especially advantageous for males, with size being a major determinant of breeding probability. Maturing males may employ a high-risk high-reward foraging strategy to compensate for extensive sexual selection pressures and sex-specific energetic needs. Our findings suggest sex-specific adult survival is a result of in situ ecological interactions and evolutionary specialization associated with being a highly polygynous marine predator.

Post-weaning survival in kangaroos is high and constant until senescence: Implications for population dynamics.

Large herbivores typically have consistently high prime-aged adult survival and lower, more variable, juvenile, and senescent survival. Many kangaroo populations undergo greater fluctuations in density compared with other large herbivores, but age- and sex-specific survival of kangaroos and their response to environmental variation remain poorly estimated. We used long-term capture-mark-recapture data on 920 individuals to investigate the survival component of eastern grey kangaroo (Macropus giganteus) population dynamics. Forage availability and population density were monitored quarterly and included as predictors of survival in Bayesian Cormack-Jolly-Seber models. Annual survival probabilities were estimated for five age classes: 0 years (juveniles), 1-2 years (subadults), 3-6 years (prime-aged adults), 7-9 years (presenescent adults), and ≥10 years (senescent adults). Survival of juveniles varied widely during our 12-year study, ranging from 0.07 to 0.90 for females and 0.05-0.92 for males. Subadult survival was 0.80-0.93 for females and 0.75-0.85 for males, while that of prime-aged adults was ≥0.94 for females and ≥0.83 for males, despite large fluctuations in forage and density. The survival of presenescent adults spanned 0.86-0.93 for females and 0.60-0.86 for males. Senescent survival was variable, at 0.49-0.90 for females and 0.49-0.80 for males. Male survival was significantly lower than female survival in prime-aged and presenescent adults, but not in other age classes. Although most of the models supported by Watanabe-Akaike Information Criterion selection included at least one environmental covariate, none of these covariates individually had a discernible effect on survival. Temporal variability in overall survival appeared mostly due to changes in the survival of juvenile and senescent kangaroos. Kangaroo survival patterns are similar to those of ungulates, suggesting a strong role of sex-age structure on population dynamics.

Understanding the impact of correlation within pair-bonds on Cormack-Jolly-Seber models.

The Cormack-Jolly-Seber (CJS) model and its extensions have been widely applied to the study of animal survival rates in open populations. The model assumes that individuals within the population of interest have independent fates. It is, however, highly unlikely that a pair of animals which have formed a long-term pairing have dissociated fates.We examine a model extension which allows animals who have formed a pair-bond to have correlated survival and recapture fates. Using the proposed extension to generate data, we conduct a simulation study exploring the impact that correlated fate data has on inference from the CJS model. We compute Monte Carlo estimates for the bias, range, and standard errors of the parameters of the CJS model for data with varying degrees of survival correlation between mates. Furthermore, we study the likelihood ratio test of sex effects within the CJS model by simulating densities of the deviance. Finally, we estimate the variance inflation factor c ^ for CJS models that incorporate sex-specific heterogeneity.Our study shows that correlated fates between mated animals may result in underestimated standard errors for parsimonious models, significantly deflated likelihood ratio test statistics, and underestimated values of c ^ for models taking sex-specific effects into account.Underestimated standard errors can result in lowered coverage of confidence intervals. Moreover, deflated test statistics will provide overly conservative test results. Finally, underestimated variance inflation factors can lead researchers to make incorrect conclusions about the level of extra-binomial variation present in their data.

An empirical Bayesian approach to incorporate directional movement information from a forage fish into the Arnason-Schwarz mark-recapture model.

BACKGROUND: Over the past two decades, various species of forage fish have been successfully implanted with miniaturized acoustic transmitters and subsequently monitored using stationary acoustic receivers. When acoustic receivers are configured in an array, information related to fish direction can potentially be determined, depending upon the number and relative orientation of the acoustic receivers. However, it can be difficult to incorporate directional information into frequentist mark-recapture methods. Here we show how an empirical Bayesian approach can be used to develop a model that incorporates directional movement information into the Arnason-Schwarz modeling framework to describe survival and migration patterns of a Pacific herring (Clupea pallasii) population in coastal Alaska, USA. METHODS: We acoustic-tagged 326 adult Pacific herring during April 2017 and 2018 while on their spawning grounds in Prince William Sound Alaska, USA. To monitor their movements, stationary acoustic receivers were deployed at strategic locations throughout the Sound. Receivers located at the major entrances to the Gulf of Alaska were arranged in parallel arrays to determine the directional movements of the fish. Informative priors were used to incorporate the directional information recorded at the entrance arrays into the model. RESULTS: A seasonal migratory pattern was found at one of Prince William Sound's major entrances to the Gulf of Alaska. At this entrance, fish tended to enter the Gulf of Alaska during spring and summer after spawning and return to Prince William Sound during the fall and winter. Fish mortality was higher during spring and summer than fall and winter in both Prince William Sound and the Gulf of Alaska. CONCLUSIONS: An empirical Bayesian modeling approach can be used to extend the Arnason-Schwarz modeling framework to incorporate directional information from acoustic arrays to estimate survival and characterize the timing and direction of migratory movements of forage fish.

Estimation of bat colony size even with low recapture rates: an example based on the Cormack-Jolly-Seber model in Oaxaca, México / Estimación del tamaño de colonia en murciélagos incluso con bajas tasas de recaptura: un ejemplo basado en el modelo Cormack-Jolly-Seber en Oaxaca, México

Introduction: Group or colony size is an important variable that is related to biological, ecological, and conservation aspects of bats. However, estimating the size of each colony or group in roosts used by more than one species is particularly difficult, especially when recapture rates are very low (< 10 %). Objective: Estimate the colony size of 14 species of bats: one emballonurid, one natalid, four mormoopids, seven phyllostomids, and one vespertilionid, which roosted throughout one year (July 2016 to June 2017) in a mine and two caves -Cerro Huatulco and El Apanguito- in the Sierra Sur and Costa of the state of Oaxaca. Methods: We constructed capture-recapture histories per species and roost, and for species for which we obtained recaptures that represented at least 10 % of the captures, we used the probabilistic Cormack-Jolly-Seber model. In the case of species with no recaptures or with a recapture proportion lower than 10 %, we estimated the number of individuals per roost by applying the same proportion between the number of captured specimens and the estimated number for species with recaptures greater than 10 % and that they belonged to the same family or trophic guild. Results: The total estimated number of bats in the three studied roosts was 20 105. The highest colony size estimates were for the mormoopids Pteronotus fulvus and P. mesoamericanus from El Apanguito and P. fulvus from Cerro Huatulco, with 6 609, 4 092 and 2 212 individuals, respectively. Conclusions: The methodology used in this study allowed estimating the colony size for all registered species, even though only for 21.42 % the recapture rates were greater than 10 %. Therefore, we consider that this methodology represents a viable alternative to estimate colony size in other roosts. This information, together with the high species richness and importance for reproductive processes, allow us to propose these sites as Bat Protection and Conservation Areas in Mexico.

Introducción: El tamaño del grupo o colonia es una variable importante que está relacionada con los aspectos biológicos, ecológicos y de conservación de los murciélagos. Sin embargo, estimar el tamaño de cada colonia o grupo en refugios utilizados por más de una especie es particularmente difícil, especialmente cuando las tasas de recaptura son muy bajas (< 10 %). Objetivo: Estimar el tamaño de la colonia de 14 especies de murciélagos: un emballonúrido, un natálido, cuatro mormópidos, siete filostómidos y un vespertiliónido, que se refugiaron durante un año (Julio 2016 a Junio 2017) en una mina y dos cuevas -Cerro Huatulco y El Apanguito- en la Sierra Sur y Costa del estado de Oaxaca. Métodos: Construimos historias de captura-recaptura por especie y refugio, y para las especies que se obtuvieron recapturas que representaban al menos el 10 % de las capturas, utilizamos un modelo probabilístico de Cormack-Jolly-Seber para estimar el tamaño de sus colonias. En el caso de especies sin recapturas o con una proporción de recaptura inferior al 10 %, estimamos el número de individuos por refugio aplicando la misma proporción entre el número de individuos capturados y el número total estimado para las especies con recapturas mayores del 10 % y que pertenecieran a la misma familia o gremio trófico registradas con la mayor similitud ecológica y con suficientes recapturas para aplicar el modelo Cormack-Jolly-Seber. Resultados: El número total estimado de murciélagos en los tres refugios de estudio fue de 20 105. Las estimaciones de tamaño de colonia más altos fueron para los mormópidos Pteronotus fulvus y P. mesoamericanus de El Apanguito y P. fulvus en Cerro Huatulco, con 6 609, 4 092 and 2 212 individuos, respectivamente. Conclusiones: La metodología utilizada en este estudio permitió estimar el tamaño de la colonia para todas las especies registradas, a pesar de que solo para el 21.42 % las tasas de recaptura fueron superiores al 10 %. Por lo tanto, consideramos que esta metodología representa una alternativa viable para estimar el tamaño de colonia en otros refugios. Esta información, junto con los procesos de alta riqueza de especies y reproducción que tienen lugar en esta área, permiten proponer estos sitios como áreas de protección y conservación de murciélagos en México.

Temperature and precipitation at migratory grounds influence demographic trends of an Arctic-breeding bird.

Anthropogenic climate disruption, including temperature and precipitation regime shifts, has been linked to animal population declines since the mid-20th century. However, some species, such as Arctic-breeding geese, have thrived during this period. An increased understanding of how climate disruption might link to demographic rates in thriving species is an important perspective in quantifying the impact of anthropogenic climate disruption on the global state of nature. The Greenland barnacle goose (Branta leucopsis) population has increased tenfold in abundance since the mid-20th century. A concurrent weather regime shift towards warmer, wetter conditions occurred throughout its range in Greenland (breeding), Ireland and Scotland (wintering) and Iceland (spring and autumn staging). The aim of this study was to determine the relationship between weather and demographic rates of Greenland barnacle geese to discern the role of climate shifts in the population trend. We quantified the relationship between temperature and precipitation and Greenland barnacle goose survival and productivity over a 50 year period from 1968 to 2018. We detected significant positive relationships between warmer, wetter conditions on the Icelandic spring staging grounds and survival. We also detected contrasting relationships between warmer, wetter conditions during autumn staging and survival and productivity, with warm, dry conditions being the most favourable for productivity. Survival increased in the latter part of the study period, supporting the possibility that spring weather regime shifts contributed to the increasing population trend. This may be related to improved forage resources, as warming air temperatures have been shown to improve survival rates in several other Arctic and northern terrestrial herbivorous species through indirect bottom-up effects on forage availability.

Non-parallel changes in songbird migration timing are not explained by changes in stopover duration.

Shifts in the timing of animal migration are widespread and well-documented; however, the mechanism underlying these changes is largely unknown. In this study, we test the hypothesis that systematic changes in stopover duration-the time that individuals spend resting and refueling at a site-are driving shifts in songbird migration timing. Specifically, we predicted that increases in stopover duration at our study site could generate increases in passage duration-the number of days that a study site is occupied by a particular species-by changing the temporal breadth of observations and vise versa. We analyzed an uninterrupted 46-year bird banding dataset from Massachusetts, USA using quantile regression, which allowed us to detect changes in early-and late-arriving birds, as well as changes in passage duration. We found that median spring migration had advanced by 1.04 days per decade; that these advances had strengthened over the last 13 years; and that early-and late-arriving birds were advancing in parallel, leading to negligible changes in the duration of spring passage at our site (+0.07 days per decade). In contrast, changes in fall migration were less consistent. Across species, we found that median fall migration had delayed by 0.80 days per decade, and that changes were stronger in late-arriving birds, leading to an average increase in passage duration of 0.45 days per decade. Trends in stopover duration, however, were weak and negative and, as a result, could not explain any changes in passage duration. We discuss, and provide some evidence, that changes in population age-structure, cryptic geographic variation, or shifts in resource availability are consistent with increases in fall passage duration. Moreover, we demonstrate the importance of evaluating changes across the entire phenological distribution, rather than just the mean, and stress this as an important consideration for future studies.

A temporally stratified extension of space-for-time Cormack-Jolly-Seber for migratory animals.

Understanding drivers of temporal variation in demographic parameters is a central goal of mark-recapture analysis. To estimate the survival of migrating animal populations in migration corridors, space-for-time mark-recapture models employ discrete sampling locations in space to monitor marked populations as they move past monitoring sites, rather than the standard practice of using fixed sampling points in time. Because these models focus on estimating survival over discrete spatial segments, model parameters are implicitly integrated over the temporal dimension. Furthermore, modeling the effect of time-varying covariates on model parameters is complicated by unknown passage times for individuals that are not detected at monitoring sites. To overcome these limitations, we extended the Cormack-Jolly-Seber (CJS) framework to estimate temporally stratified survival and capture probabilities by including a discretized arrival time process in a Bayesian framework. We allow for flexibility in the model form by including temporally stratified covariates and hierarchical structures. In addition, we provide tools for assessing model fit and comparing among alternative structural models for the parameters. We demonstrate our framework by fitting three competing models to estimate daily survival, capture, and arrival probabilities at four hydroelectric dams for over 200 000 individually tagged migratory juvenile salmon released into the Snake River, USA.

Estimability of migration survival rates from integrated breeding and winter capture-recapture data.

Long-distance migration is a common phenomenon across the animal kingdom but the scale of annual migratory movements has made it difficult for researchers to estimate survival rates during these periods of the annual cycle. Estimating migration survival is particularly challenging for small-bodied species that cannot carry satellite tags, a group that includes the vast majority of migratory species. When capture-recapture data are available for linked breeding and non-breeding populations, estimation of overall migration survival is possible but current methods do not allow separate estimation of spring and autumn survival rates. Recent development of a Bayesian integrated survival model has provided a method to separately estimate the latent spring and autumn survival rates using capture-recapture data, though the accuracy and precision of these estimates has not been formally tested. Here, I used simulated data to explore the estimability of migration survival rates using this model. Under a variety of biologically realistic scenarios, I demonstrate that spring and autumn migration survival can be estimated from the integrated survival model, though estimates are biased toward the overall migration survival probability. The direction and magnitude of this bias are influenced by the relative difference in spring and autumn survival rates as well as the degree of annual variation in these rates. The inclusion of covariates can improve the model's performance, especially when annual variation in migration survival rates is low. Migration survival rates can be estimated from relatively short time series (4-5 years), but bias and precision of estimates are improved when longer time series (10-12 years) are available. The ability to estimate seasonal survival rates of small, migratory organisms opens the door to advancing our understanding of the ecology and conservation of these species. Application of this method will enable researchers to better understand when mortality occurs across the annual cycle and how the migratory periods contribute to population dynamics. Integrating summer and winter capture data requires knowledge of the migratory connectivity of sampled populations and therefore efforts to simultaneously collect both survival and tracking data should be a high priority, especially for species of conservation concern.

Annual Abundance and Population Structure of Two Dung Beetle Species in a Human-Modified Landscape.

Population studies are essential for understanding different aspects of species' biology, estimating extinction probability, and determining evolutionary and life history. Using the mark-recapture method, we studied the abundance and population structure of dung beetle species (Deltochilum mexicanum and Dichotomius satanas) over one year in a human-modified landscape in Mexico. We captured 1960 individuals with a net recapture rate of 11%. Deltochilum mexicanum had a higher rate of recapture (14%) than Dichotomius satanas (5%). Annual variation in abundance was similar for both species, with maximum abundance occurring in summer and a marked reduction during winter. Deltochilum mexicanum was dominant inside the forest, and its abundance was influenced by vegetation cover, temperature, and humidity. Dichotomius satanas was more frequent outside the forest, and none of the considered environmental variables affected its abundance. The adult sex ratio of Deltochilum mexicanum was female-biased, whereas that of Dichotomius satanas was male-biased. The maximum estimated population size was similar for both species, but Deltochilum mexicanum had a higher number of new individuals and survival rate. Since species with different biological attributes presented a similar pattern of abundance and population structure, we conclude that environmental conditions are the main regulator of dung beetle populations in the human-modified landscape.

A Test of Positive Association for Detecting Heterogeneity in Capture for Capture-Recapture Data.

The Cormack-Jolly-Seber (CJS) model assumes that all marked animals have equal recapture probabilities at each sampling occasion, but heterogeneity in capture often occurs and should be taken into account to avoid biases in parameter estimates. Although diagnostic tests are generally used to detect trap-dependence or transience and assess the overall fit of the model, heterogeneity in capture is not routinely tested for. In order to detect and identify this phenomenon in a CJS framework, we propose a test of positive association between previous and future encounters using Goodman-Kruskal's gamma. This test is based solely on the raw capture histories and makes no assumption on model structure. The development of the test is motivated by a dataset of Sandwich terns (Thalasseus sandvicensis), and we use the test to formally show that they exhibit heterogeneity in capture. We use simulation to assess the performance of the test in the detection of heterogeneity in capture, compared to existing and corrected diagnostic goodness-of-fit tests, Leslie's test of equal catchability and Carothers' extension of the Leslie test. The test of positive association is easy to use and produces good results, demonstrating high power to detect heterogeneity in capture. We recommend using this new test prior to model fitting as the outcome will guide the model-building process and help draw more accurate biological conclusions. Supplementary materials accompanying this paper appear online. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary materials for this article are available at 10.1007/s13253-017-0315-4.

Cryptic disease-induced mortality may cause host extinction in an apparently stable host-parasite system.

The decline of wildlife populations due to emerging infectious disease often shows a common pattern: the parasite invades a naive host population, producing epidemic disease and a population decline, sometimes with extirpation. Some susceptible host populations can survive the epidemic phase and persist with endemic parasitic infection. Understanding host-parasite dynamics leading to persistence of the system is imperative to adequately inform conservation practice. Here we combine field data, statistical and mathematical modelling to explore the dynamics of the apparently stable Rhinoderma darwinii-Batrachochytrium dendrobatidis (Bd) system. Our results indicate that Bd-induced population extirpation may occur even in the absence of epidemics and where parasite prevalence is relatively low. These empirical findings are consistent with previous theoretical predictions showing that highly pathogenic parasites are able to regulate host populations even at extremely low prevalence, highlighting that disease threats should be investigated as a cause of population declines even in the absence of an overt increase in mortality.

The fishing and natural mortality of large, piscivorous Bull Trout and Rainbow Trout in Kootenay Lake, British Columbia (2008-2013).

BACKGROUND: Estimates of fishing and natural mortality are important for understanding, and ultimately managing, commercial and recreational fisheries. High reward tags with fixed station acoustic telemetry provides a promising approach to monitoring mortality rates in large lake recreational fisheries. Kootenay Lake is a large lake which supports an important recreational fishery for large Bull Trout and Rainbow Trout. METHODS: Between 2008 and 2013, 88 large (≥500 mm) Bull Trout and 149 large (≥500 mm) Rainbow Trout were marked with an acoustic transmitter and/or high reward ($100) anchor tags in Kootenay Lake. The subsequent detections and angler recaptures were analysed using a Bayesian individual state-space Cormack-Jolly-Seber (CJS) survival model with indicator variable selection. RESULTS: The final CJS survival model estimated that the annual interval probability of being recaptured by an angler was 0.17 (95% CRI [0.11-0.23]) for Bull Trout and 0.14 (95% CRI [0.09-0.19]) for Rainbow Trout. The annual interval survival probability for Bull Trout was estimated to have declined from 0.91 (95% CRI [0.76-0.97]) in 2009 to just 0.46 (95% CRI [0.24-0.76]) in 2013. Rainbow Trout survival was most strongly affected by spawning. The annual interval survival probability was 0.77 (95% CRI [0.68-0.85]) for a non-spawning Rainbow Trout compared to 0.41 (95% CRI [0.30-0.53]) for a spawner. The probability of spawning increased with the fork length for both species and decreased over the course of the study for Rainbow Trout. DISCUSSION: Fishing mortality was relatively low and constant while natural mortality was relatively high and variable. The results indicate that angler effort is not the primary driver of short-term population fluctations in the Rainbow Trout abundance. Variation in the probability of Rainbow Trout spawning suggests that the spring escapement at the outflow of Trout Lake may be a less reliable index of abundance than previously assumed. Multi-species stock assessment models need to account for the fact that large Bull Trout are more abundant than large Rainbow Trout in Kootenay Lake.

A recipe for postfledging survival in great tits Parus major: be large and be early (but not too much).

Survival of juveniles during the postfledging period can be markedly low, which may have major consequences on avian population dynamics. Knowing which factors operating during the nesting phase affect postfledging survival is crucial to understand avian breeding strategies. We aimed to obtain a robust set of predictors of postfledging local survival using the great tit (Parus major) as a model species. We used mark-recapture models to analyze the effect of hatching date, temperatures experienced during the nestling period, fledging size and body mass on first-year postfledging survival probability of great tit juveniles. We used data from 5192 nestlings of first clutches ringed between 1993 and 2010. Mean first-year postfledging survival probability was 15.2%, and it was lower for smaller individuals, as well as for those born in either very early or late broods. Our results stress the importance of choosing an optimum hatching period, and raising large chicks to increase first-year local survival probability in the studied population.

Maximum penalized likelihood estimation in semiparametric mark-recapture-recovery models.

We discuss the semiparametric modeling of mark-recapture-recovery data where the temporal and/or individual variation of model parameters is explained via covariates. Typically, in such analyses a fixed (or mixed) effects parametric model is specified for the relationship between the model parameters and the covariates of interest. In this paper, we discuss the modeling of the relationship via the use of penalized splines, to allow for considerably more flexible functional forms. Corresponding models can be fitted via numerical maximum penalized likelihood estimation, employing cross-validation to choose the smoothing parameters in a data-driven way. Our contribution builds on and extends the existing literature, providing a unified inferential framework for semiparametric mark-recapture-recovery models for open populations, where the interest typically lies in the estimation of survival probabilities. The approach is applied to two real datasets, corresponding to gray herons (Ardea cinerea), where we model the survival probability as a function of environmental condition (a time-varying global covariate), and Soay sheep (Ovis aries), where we model the survival probability as a function of individual weight (a time-varying individual-specific covariate). The proposed semiparametric approach is compared to a standard parametric (logistic) regression and new interesting underlying dynamics are observed in both cases.

multimark: an R package for analysis of capture-recapture data consisting of multiple "noninvasive" marks.

I describe an open-source R package, multimark, for estimation of survival and abundance from capture-mark-recapture data consisting of multiple "noninvasive" marks. Noninvasive marks include natural pelt or skin patterns, scars, and genetic markers that enable individual identification in lieu of physical capture. multimark provides a means for combining and jointly analyzing encounter histories from multiple noninvasive sources that otherwise cannot be reliably matched (e.g., left- and right-sided photographs of bilaterally asymmetrical individuals). The package is currently capable of fitting open population Cormack-Jolly-Seber (CJS) and closed population abundance models with up to two mark types using Bayesian Markov chain Monte Carlo (MCMC) methods. multimark can also be used for Bayesian analyses of conventional capture-recapture data consisting of a single-mark type. Some package features include (1) general model specification using formulas already familiar to most R users, (2) ability to include temporal, behavioral, age, cohort, and individual heterogeneity effects in detection and survival probabilities, (3) improved MCMC algorithm that is computationally faster and more efficient than previously proposed methods, (4) Bayesian multimodel inference using reversible jump MCMC, and (5) data simulation capabilities for power analyses and assessing model performance. I demonstrate use of multimark using left- and right-sided encounter histories for bobcats (Lynx rufus) collected from remote single-camera stations in southern California. In this example, there is evidence of a behavioral effect (i.e., trap "happy" response) that is otherwise indiscernible using conventional single-sided analyses. The package will be most useful to ecologists seeking stronger inferences by combining different sources of mark-recapture data that are difficult (or impossible) to reliably reconcile, particularly with the sparse datasets typical of rare or elusive species for which noninvasive sampling techniques are most commonly employed. Addressing deficiencies in currently available software, multimark also provides a user-friendly interface for performing Bayesian multimodel inference using capture-recapture data consisting of a single conventional mark or multiple noninvasive marks.

Evaluation of abundance indexes in open population studies: a comparison in populations of small mammals in southern Brazil / Avaliação de índices de abundância em estudos de populações abertas: uma comparação em populações de pequenos mamíferos do sul do Brasil

Many manuscripts comparing populations and/or analysing the structure of animal communities use indexes of captures as synonymous of abundance. However, the basic methods more suitable to this assumption - probabilistic estimates based on equal capture probability - have not been considered. In this study, the deviations caused by different types of capture indexes are compared with a common probabilistic population estimator (Cormack-Jolly-Seber). The analyses showed that Minimum Number Known Alive (MNKA) and the number of individuals showed greater association with the population estimator than with non-probabilistic indexes based on recaptures. Therefore, none of the indexes presented the same performance to estimate population size estimation which can lead to ecological misinterpretation. Some recommendations were also described.

Muitos estudos comparam populações e/ou analisam a estrutura de comunidades animais usando índices de captura como se fossem sinônimos de abundância. No entanto, os métodos mais adequados considerando o pressuposto - estimativas probabilísticas baseadas na igualdade da probabilidade de capturas - não têm sido considerados. Neste estudo, os desvios causados por diferentes tipos de índices de captura são comparados com um dos mais comuns estimadores populacionais probabilísticos (Cormack-Jolly-Seber). As análises mostraram que o número mínimo de animais conhecidos vivos (MNKA) e o número de indivíduos apresentaram maior associação com o estimador populacional do que com os índices não probabilísticos baseados em recapturas. Entretanto, nenhum dos índices apresentou o mesmo desempenho do estimador populacional o que pode levar a interpretações equivocadas. Algumas recomendações foram também descritas.

Top-down and bottom-up influences on demographic rates of Antarctic fur seals Arctocephalus gazella.

Two major drivers in population dynamics are bottom-up processes, such as environmental factors that affect foraging success, and the top-down impacts of predation. Many populations of marine mammal and seabird species appear to be declining in response to reductions in prey associated with the bottom-up effects of climate change. However, predation, which usually occurs at sea and is difficult to observe, may also play a key role. We analysed drivers of population dynamics of Antarctic fur seals Arctocephalus gazella at Cape Shirreff from 1997 to 2009, including a predator that targets pre-weaned pups and bottom-up environmental effects in an ecosystem particularly sensitive to small changes in temperature. We use Bayesian mark-recapture analysis to demonstrate that although large-scale environmental variability affects annual adult survival and reproduction, first year survival appears to be driving the current decline in this population (as defined by a decline in the annual number of pups born). Although the number of pups increased during the first third of the study, first year survival and recruitment of those pups in later years was very low. Such low survival may be driven by leopard seal Hydrurga leptonyx predation, particularly prior to weaning. Our results suggest that without leopard seal predation, this population would most likely increase in size, despite the observed bottom-up effects of climate changes on adult vital rates. More broadly, our results show how age-targeted predation could be a major factor in population decline of K-selected colonial breeders.