A nonparametric method of estimation of the population size in capture–recapture experiments

A recent method for estimating a lower bound of the population size in capture–recapture samples is studied. Specifically, some asymptotic properties, such as strong consistency and asymptotic normality, are provided. The introduced estimator is based on the empirical probability generating function (pgf) of the observed data, and it is consistent for count distributions having a log-convex pgf (-class). This is a large family that includes mixed and compound Poisson distributions, and their independent sums and finite mixtures as well. The finite-sample performance of the lower bound estimator is assessed via simulation showing a better behavior than some close competitors. Several examples of application are also analyzed and discussed.     

No evidence for a negative effect of conspecific brood parasitism on annual survival of female Prothonotary Warblers

Species that provide intensive parental care could suffer fitness costs associated with conspecific brood parasitism. Here we evaluate the effect of conspecific brood parasitism on apparent annual survival probability of female Prothonotary Warblers Protonotaria citrea using a multistate model with imperfect state assignment analysed in a hierarchical Bayesian framework. We found no difference in annual survival probability between host and non‐host females. These findings agree with previous work in that there seems to be little apparent cost of conspecific brood parasitism to female Warblers in this system.     

Blood and cloacal swab sampling for avian influenza monitoring has no effect on survival rates of free‐ranging ducks

Concerns about the spread of avian influenza viruses (AIVs) have led to cloacal swab sampling of hundreds of thousands of birds worldwide as part of AIV surveillance schemes, but the effects of cloacal swabbing have not been adequately evaluated. We tested for differences between swabbed, swabbed and bled, and non‐sampled wild ducks in terms of live re‐encounter and dead recoveries for Common Pochard Aythya ferina and Tufted Duck Aythya fuligula, and also determined re‐encounter and recovery rates for Mallard Anas platyrhynchos and Common Teal Anas crecca. No effects of sampling methods were detected, except in Teal. Re‐encounter rates were lower in sampled Teal than in controls, with annual re‐encounter probabilities being 25% and 35% lower in males and females, respectively. Teal possibly left or avoided sampling sites, or sought sites where they were less detectable after sampling. In general, no deleterious effects were found, suggesting that cloacal swabbing and blood sampling are suitable methods for conducting AIV surveillance in ducks.     

A weighted partial likelihood approach for zero‐truncated models

Zero‐truncated data arises in various disciplines where counts are observed but the zero count category cannot be observed during sampling. Maximum likelihood estimation can be used to model these data; however, due to its nonstandard form it cannot be easily implemented using well‐known software packages, and additional programming is often required. Motivated by the Rao–Blackwell theorem, we develop a weighted partial likelihood approach to estimate model parameters for zero‐truncated binomial and Poisson data. The resulting estimating function is equivalent to a weighted score function for standard count data models, and allows for applying readily available software. We evaluate the efficiency for this new approach and show that it performs almost as well as maximum likelihood estimation. The weighted partial likelihood approach is then extended to regression modelling and variable selection. We examine the performance of the proposed methods through simulation and present two case studies using real data.     

A review of survival estimates for raptors and owls

This paper reviews the literature on survival estimates for different species of raptors and owls, examines the methods used to obtain the estimates, and draws out some general patterns arising. Estimating survival usually involves the marking of birds so that they can be recognized as individuals on subsequent encounters. Annual survival can then be estimated from: (1) birds ringed at known age (usually as nestlings) and subsequently reported by members of the public (usually as found dead), the ratio of recoveries at different ages being used to calculate annual survival; (2) marked breeding adults, trapped or re‐sighted in subsequent years in particular study areas, with the proportion re‐trapped (or re‐sighted) in each year being taken as the minimum annual survival; (3) live encounter (trapped or re‐sighted) of birds marked either as nestlings or breeding adults analysed using the capture–mark–recapture (or re‐sighting) methods to estimate annual survival; (4) a combination of reports of known‐age dead birds and re‐trapping/re‐sighting of live birds; (5) use of radio‐ or satellite‐tracking to follow the fates of individuals; and (6) the integration of these methods with other information, such as change in numbers between years, to derive estimates of survival and other demographic parameters. Studies confined to particular areas usually give estimates of ‘apparent annual survival’, because they take no account of birds that leave the area. However, radio‐ or satellite‐tracking makes it possible to estimate true survival, including survival of prebreeders that have low natal‐site fidelity (this usually requires satellite telemetry). As in other birds, the preferred method for estimating survival has changed over time, as new and more robust methods of estimation have been developed. Methods 1 and 2 were the first to be developed, but without statistical underpinning, while methods 3–6 were developed later on the basis of formal statistical models. This difference has to be borne in mind in comparing older with newer estimates for particular species. Published survival estimates were found for three species of Cathartidae, one of Pandionidae, 29 of Accipitridae, 12 of Falconidae, one of Tytonidae and nine of Strigidae, almost all from temperate Northern Hemisphere species. In most of these species more than one estimate was available, and in some separate estimates for different age or sex groups. The main patterns to emerge included: (1) a significant tendency for annual adult survival to increase with body weight, smaller species having annual survival rates mainly of 60–70%, medium‐sized species having rates mainly in the range 70–90% and the largest having rates of > 90%, in the absence of obvious human‐caused losses; (2) a lower survival in the first or prebreeding years of life than in subsequent years; (3) a lack of obvious or consistent differences in survival between the sexes, where these could be distinguished; and (4) in the few species for which enough data were available, a decline in annual survival rates in the later years of life.     

The one‐inflated positive Poisson mixture model for use in population size estimation

The one‐inflated positive Poisson mixture model (OIPPMM) is presented, for use as the truncated count model in Horvitz–Thompson estimation of an unknown population size. The OIPPMM offers a way to address two important features of some capture–recapture data: one‐inflation and unobserved heterogeneity. The OIPPMM provides markedly different results than some other popular estimators, and these other estimators can appear to be quite biased, or utterly fail due to the boundary problem, when the OIPPMM is the true data‐generating process. In addition, the OIPPMM provides a solution to the boundary problem, by labelling any mixture components on the boundary instead as one‐inflation.     

Disentangling the effects of environmental conditions on wintering and breeding grounds on age‐specific survival rates in a trans‐Saharan migratory raptor

Migratory species are subject to environmental variability occurring on breeding and wintering grounds. Estimating the relative contribution of environmental factors experienced sequentially during breeding and wintering, and their potential interaction, to the variation of survival is crucial to predict population viability of migratory species. Here we investigated this issue for the Montagu's harrier Circus pygargus, a trans‐Saharan migrant. We analysed capture–recapture data from a 29‐year long monitoring of wing‐tagged offspring and adults at two study sites in France (Rochefort‐RO and Maine‐et‐Loire‐ML). The study period covers a climatic shift occurring in the Sahel with increasing rainfall following a period of droughts (Sahel greening). We found that harriers’ adult survival in RO (between 1988 and 2005) varied over time and was sensitive to the interaction between the amount of rainfall in the Sahel and the annual mean breeding success, two proxies of prey availability. The occurrence of adverse conditions on breeding and wintering grounds in the same year decreased survival from 0.70–0.77 to 0.48 ± 0.05. Juvenile survival in RO was slightly more sensitive to conditions in Europe than in the Sahel. Unexpectedly, lower survival rates were found in years with higher mean breeding success, suggesting compensatory density feedbacks may operate. By contrast, adult survival in ML, monitored between 1999 and 2017, was higher compared to RO (0.76 ± 0.03 versus 0.66 ± 0.02), remained constant and unaffected by any proxy of prey availability. This difference seems consistent with the fact that harriers in ML experienced better and especially less variable environmental conditions during breeding and wintering seasons compared to RO. Overall, we showed that survival of a migratory bird is sensitive to the level of variability in environmental conditions and that adverse conditions on wintering grounds can amplify the negative effects of conditions during the previous breeding season on birds’ survival.     

Hare's affairs: Lessons learnt from a noninvasive genetic monitoring for tracking mountain hare individuals

Systematic monitoring of individuals and their abundance over time has become an important tool to provide information for conservation. For genetic monitoring studies, noninvasive sampling has emerged as a valuable approach, particularly so for elusive or rare animals. Here, we present the 5‐year results of an ongoing noninvasive genetic monitoring of mountain hares (Lepus timidus) in a protected area in the Swiss Alps. We used nuclear microsatellites and a sex marker to identify individuals and assign species to noninvasively collected feces samples. Through including a marker for sex identification, we were able to assess sex ratio changes and sex‐specific demographic parameters over time. Male abundance in the area showed high fluctuations and apparent survival for males was lower than for females. Generally, males and females showed only little temporary migration into and out of the study area. Additionally, using genotyped tissue samples from mountain hares, European hares (Lepus europaeus) and their hybrids, we were able to provide evidence for the first occurrence of a European hare in the study area at an elevation of 2,300 m a.s.l. in spring 2016. For future monitoring studies, we suggest to include complementary analysis methods to reliably infer species identities of the individuals analyzed and, thus, not only monitor mountain hare individual abundance, but also assess the potential threats given through competitive exclusion by and hybridization with the European hare.     

A spatially explicit capture–recapture estimator for single‐catch traps

Single‐catch traps are frequently used in live‐trapping studies of small mammals. Thus far, a likelihood for single‐catch traps has proven elusive and usually the likelihood for multicatch traps is used for spatially explicit capture–recapture (SECR) analyses of such data. Previous work found the multicatch likelihood to provide a robust estimator of average density. We build on a recently developed continuous‐time model for SECR to derive a likelihood for single‐catch traps. We use this to develop an estimator based on observed capture times and compare its performance by simulation to that of the multicatch estimator for various scenarios with nonconstant density surfaces. While the multicatch estimator is found to be a surprisingly robust estimator of average density, its performance deteriorates with high trap saturation and increasing density gradients. Moreover, it is found to be a poor estimator of the height of the detection function. By contrast, the single‐catch estimators of density, distribution, and detection function parameters are found to be unbiased or nearly unbiased in all scenarios considered. This gain comes at the cost of higher variance. If there is no interest in interpreting the detection function parameters themselves, and if density is expected to be fairly constant over the survey region, then the multicatch estimator performs well with single‐catch traps. However if accurate estimation of the detection function is of interest, or if density is expected to vary substantially in space, then there is merit in using the single‐catch estimator when trap saturation is above about 60%. The estimator's performance is improved if care is taken to place traps so as to span the range of variables that affect animal distribution. As a single‐catch likelihood with unknown capture times remains intractable for now, researchers using single‐catch traps should aim to incorporate timing devices with their traps.     

Seasonal variation of mortality,detectability, and body condition in a population of the adder (Vipera berus)

We analyzed seasonal variation in mortality rates in adult males and females of the European adder (Vipera berus), using data collected during a 13‐year capture–recapture study (2005–2017) in a large population. We concurrently obtained quantitative information on the seasonal variation in the detectability and body condition of adders. Our results show strong seasonality in body condition, encounter, and capture rates of adult adders, and these patterns differ markedly between sexes and between breeding and nonbreeding females. Seasonal variation in mortality rates was however virtually nonexistent in males and moderately low in both breeding and nonbreeding females. In addition, we found no evidence for among‐year differences in the seasonal mortality schedules of males and females. During periods of intensive basking, both males and pregnant females are highly visible for humans, but are not subject to strong natural mortality. This low susceptibility to predation is presumably induced by various factors, including the limitation of overt exposure to short periods of time and specific microhabitats, the dorsal coloration pattern that provides cryptic protection and possibly also an aposematic warning signal, and presumed seasonal differences in the foraging behavior and food requirements of natural predators. Our data provide some evidence that female adders, but not males, are relatively vulnerable to predation during the seasonal migrations between the hibernation and feeding habitats. Mortality in the females was not much elevated during their breeding years, but was notably highest in the spring of the ensuing nonbreeding year. After giving birth, reproductive females are extremely emaciated and have a weakened general condition. They then run the risk of dying from starvation either before, during, or after hibernation. The higher mortality after giving birth, that is sustained over a period of ca. 9 months, should be considered as an indirect and delayed survival cost of reproduction.     

A local evaluation of the individual state‐space to scale up Bayesian spatial capture–recapture

Spatial capture–recapture models (SCR) are used to estimate animal density and to investigate a range of problems in spatial ecology that cannot be addressed with traditional nonspatial methods. Bayesian approaches in particular offer tremendous flexibility for SCR modeling. Increasingly, SCR data are being collected over very large spatial extents making analysis computational intensive, sometimes prohibitively so. To mitigate the computational burden of large‐scale SCR models, we developed an improved formulation of the Bayesian SCR model that uses local evaluation of the individual state‐space (LESS). Based on prior knowledge about a species’ home range size, we created square evaluation windows that restrict the spatial domain in which an individual's detection probability (detector window) and activity center location (AC window) are estimated. We used simulations and empirical data analyses to assess the performance and bias of SCR with LESS. LESS produced unbiased estimates of SCR parameters when the AC window width was ≥5σ (σ: the scale parameter of the half‐normal detection function), and when the detector window extended beyond the edge of the AC window by 2σ. Importantly, LESS considerably decreased the computation time needed for fitting SCR models. In our simulations, LESS increased the computation speed of SCR models up to 57‐fold. We demonstrate the power of this new approach by mapping the density of an elusive large carnivore—the wolverine (Gulo gulo)—with an unprecedented resolution and across the species’ entire range in Norway (> 200,000 km²). Our approach helps overcome a major computational obstacle to population and landscape‐level SCR analyses. The LESS implementation in a Bayesian framework makes the customization and fitting of SCR accessible for practitioners working at scales that are relevant for conservation and management.     

Photo‐identification as a simple tool for studying invasive lionfish Pterois volitans populations

Photo‐tagging, i.e. using a specific software to match colour patterns on photographs, was tested as a means to identify individual Indo‐Pacific Pterois volitans to assist with population and movement studies of this invasive species. The stripe pattern on the flank of adult P. volitans (n = 48) was the most individually distinctive of three body regions tested, leading to correct individual identification on 68 and 82% of tests with a single and two images of the reference individual, respectively. Photo‐tagging is inexpensive, logistically simple and can involve citizen scientists, making it a viable alternative to traditional tagging to provide information on P. volitans distribution, movement patterns and recolonization rates after removals.     

Genetic sampling for estimating density of common species

Understanding population dynamics requires reliable estimates of population density, yet this basic information is often surprisingly difficult to obtain. With rare or difficult‐to‐capture species, genetic surveys from noninvasive collection of hair or scat has proved cost‐efficient for estimating densities. Here, we explored whether noninvasive genetic sampling (NGS) also offers promise for sampling a relatively common species, the snowshoe hare (Lepus americanus Erxleben, 1777), in comparison with traditional live trapping. We optimized a protocol for single‐session NGS sampling of hares. We compared spatial capture–recapture population estimates from live trapping to estimates derived from NGS, and assessed NGS costs. NGS provided population estimates similar to those derived from live trapping, but a higher density of sampling plots was required for NGS. The optimal NGS protocol for our study entailed deploying 160 sampling plots for 4 days and genotyping one pellet per plot. NGS laboratory costs ranged from approximately $670 to $3000 USD per field site. While live trapping does not incur laboratory costs, its field costs can be considerably higher than for NGS, especially when study sites are difficult to access. We conclude that NGS can work for common species, but that it will require field and laboratory pilot testing to develop cost‐effective sampling protocols.     

Experimental evidence of long‐term reproductive costs in a colonial nesting seabird

Trade‐offs between current and future reproduction are central to the evolution of life histories. Experiments that manipulate brood size provide an effective approach to investigating future costs of current reproduction. Most manipulative studies to date, however, have addressed only the short‐term effects of brood size manipulation. Our goal was to determine whether survival or breeding costs of reproduction in a long‐lived species manifest beyond the subsequent breeding season. To this end, we investigated long‐term survival and breeding effects of a multi‐year reproductive cost experiment conducted on black‐legged kittiwakes Rissa tridactyla, a long‐lived colonial nesting seabird. We used multi‐state capture–recapture modeling to assess hypotheses regarding the role of experimentally reduced breeding effort and other factors, including climate phase and colony size and productivity, on future survival and breeding probabilities during the 16‐yr period following the experiment. We found that forced nest failures had a positive effect on breeding probability over time, but had no effect on long‐term survival. This apparent canalization of survival suggests that adult survival is the most important parameter influencing fitness in this long‐lived species, and that adults should pay reproductive costs in ways that do not compromise this critical life history parameter. When declines in adult survival rate are observed, they may indicate populations of conservation concern.     

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.     

Seasonal climate effects on the survival of a hibernating mammal

Global climate change and associated regional climate variability is impacting the phenology of many species, ultimately altering individual fitness and population dynamics. Yet, few studies have considered the effects of pertinent seasonal climate variability on phenology and fitness. Hibernators may be particularly susceptible to changes in seasonal climate since they have a relatively short active season in which to reproduce and gain enough mass to survive the following winter. To understand whether and how seasonal climate variability may be affecting hibernator fitness, we estimated survival from historical (1964–1968) and contemporary (2014–2017) mark–recapture data collected from the same population of Uinta ground squirrels (UGS, Urocitellus armatus), a hibernator endemic to the western United States. Despite a locally warming climate, the phenology of UGS did not change over time, yet season‐specific climate variables were important in regulating survival rates. Specifically, older age classes experienced lower survival when winters or the following springs were warm, while juveniles benefited from warmer winter temperatures. Although metabolic costs decrease with decreasing temperature in the hibernacula, arousal costs increase with decreasing temperature. Our results suggest that this trade‐off is experienced differently by immature and mature individuals. We also observed an increase in population density during that time period, suggesting resources are less limited today than they used to be. Cheatgrass is now dominating the study site and may provide a better food source to UGS than native plants did historically.