Comparison of size vs. life-state classification in demographic models for the terrestrial orchid Cleistes bifaria

Recent studies using capture-recapture modelling in terrestrial orchids have shown relationships among survival, life-state, climate and dormancy, but to date, there has been no rigorous study of the effects of size on demographic rates. Here we use multistate capture-recapture models to investigate the relationships between survival, ramet size, life-state, and propensity for extended dormancy of Cleistes bifaria in two populations in Florida and West Virginia. Using estimated leaf area as a measure of ramet size, we investigated relative fit to the data of models in which ramets were classified by life-state alone (dormant, vegetative, and flowering), size alone (dormant, small, and large), or by a combination of size and state (dormant, small vegetative, large vegetative, small flowering, and large flowering ramets). This scheme allowed us to compare the effects of a size versus state classification on survival and transition probabilities, including the propensity for dormancy. For survival rates, the size-classified model was preferable in terms of parsimony (AIC) to models classified either by state or by a combination of size and state. In C. bifaria, annual survival rate for large ramets was close to 1.0 and for small and dormant ramets, 0.91 and 0.76, respectively. This highlights the importance of protecting large plants. In contrast, a model combining life-state with ramet size was most parsimonious for explaining variation in transition rates. As the ‘size + state’ classification is convenient, holds more information, and seems more closely tied to fitness than classification by either size or life-state alone, it may be particularly useful in planning and assessing conservation management of orchids.     

Challenging conservation of migratory species: Sahelian rainfalls drive first-year survival of the vulnerable Lesser Kestrel Falco naumanni

In the context of attested global changes, accurate estimation of whether climatic fluctuations impact on population demographic parameters is needed for adequate management, especially for migratory species. We present a capture-recapture analysis linking survival rates of the vulnerable Lesser Kestrel (Falco naumanni) to annual rainfalls in the Sahel region, considered as a proxy of climatic conditions on wintering grounds. Recapture data were obtained from field observations of individuals ringed and sexed as juveniles over a 14-year monitoring period (1994-2007). We addressed a common but problematic situation in birds where: (i) sex is known with certainty for first-summer or older birds but only suspected for juveniles, and (ii) a large proportion of individuals never return to the study population (e.g. transient behavior). Transient behavior and unknown sexes were explicitly integrated considering a two age class in a multistate capture-recapture model. Survival was time-varying for juveniles (geometric mean: 0.499 ± 0.021) but constant - and higher - for adults (0.718 ± 0.013). Yearling survival probabilities were strongly correlated with rainfalls in the Sahel, suggesting a high dependence of juvenile upon the wintering conditions. While taking sex uncertainty into account, we detected no sex-dependence in survival. Incorporating the sensitivity of survival of wintering migratory birds to climatic variables such as precipitations in arid Sahelian ecosystem may allow to model conservation scenarios with a greater realism. Finally, we encourage the development of international management strategies for migratory species on wintering areas in addition to the existing conservation actions on summering Mediterranean grounds.     

Large-scale noninvasive genetic monitoring of wolverines using scats reveals density dependent adult survival

Noninvasive genetic monitoring has the potential to estimate vital rates essential for conservation and management of many species. In a long-term genetic capture-mark-recapture study using scats we evaluated temporal variation in adult survival in a wolverine (Gulo gulo) population in southern Norway. In contrast to most previous studies of large mammals we found evidence for negative density dependence in adult survival in this large carnivore. Both sexes showed the same pattern of density dependence, with higher annual survival rates in adult females than males. In addition, we also found an additive mortality effect of harvesting in the population, resulting in the lowest adult survival rates at a combination of high population density and high harvest rate. The additive effects of density and harvest on adult survival of wolverines have relevance to the conservation and management of solitary carnivores with strong intrasexual territoriality, especially for species where combats among conspecifics can cause serious injury or even mortality.     

Potential biological removal of albatrosses and petrels with minimal demographic information

Seabirds such as albatrosses and petrels are frequently caught in longline and trawl fisheries, but limited demographic data for many species creates management challenges. A method for estimating the potential biological removal (the PBR method) for birds requires knowledge of adult survival, age at first breeding, a conservation goal, and the lower limit of a 60% confidence interval for the population size. For seabirds, usually only the number of breeding pairs is known, rather than the actual population size. This requires estimating the population size from the number of breeding pairs when important demographic variables, such as breeding success, juvenile survival, and the proportion of the adult population that engages in breeding, are unknown. In order to do this, a simple population model was built where some demographic parameters were known while others were constrained by considering plausible asymptotic estimates of the growth rate. While the median posterior population estimates are sensitive to the assumed population growth rate, the 20th percentile estimates are not. This allows the calculation of a modified PBR value that is based on the number of breeding pairs instead of the population size. For threatened albatross species, this suggests that human-caused mortalities should not exceed 1.5% of the number of breeding pairs, while for threatened petrel species, mortalities should be kept below 1.2% of the number of breeding pairs. The method is applied to 22 species and sub-species of albatrosses and petrels in New Zealand that are of management concern, of which at least 10 have suffered mortalities near or above these levels.     

The role of demographic compensation theory in incidental take assessments for endangered species

Many endangered species laws provide exceptions to legislated prohibitions through incidental take provisions as long as take is the result of unintended consequences of an otherwise legal activity. These allowances presumably invoke the theory of demographic compensation, commonly applied to harvested species, by allowing limited harm as long as the probability of the species’ survival or recovery is not reduced appreciably. Demographic compensation requires some density-dependent limits on survival or reproduction in a species’ annual cycle that can be alleviated through incidental take. Using a population model for piping plovers in the Great Plains, we found that when the population is in rapid decline or when there is no density dependence, the probability of quasi-extinction increased linearly with increasing take. However, when the population is near stability and subject to density-dependent survival, there was no relationship between quasi-extinction probability and take rates. We note however, that a brief examination of piping plover demography and annual cycles suggests little room for compensatory capacity. We argue that a population’s capacity for demographic compensation of incidental take should be evaluated when considering incidental allowances because compensation is the only mechanism whereby a population can absorb the negative effects of take without incurring a reduction in the probability of survival in the wild. With many endangered species there is probably little known about density dependence and compensatory capacity. Under these circumstances, using multiple system models (with and without compensation) to predict the population’s response to incidental take and implementing follow-up monitoring to assess species response may be valuable in increasing knowledge and improving future decision making.     

Predicting Life-History Traits for Female New Zealand Sea Lions, <Emphasis Type="Italic">Phocarctos hookeri</Emphasis>: Integrating Short-Term Mark-Recapture Data and Population Modeling

The trade-off between survival and reproduction by individuals is central to understanding life-history parameters of a species. Few mammal species have life-history information from long-term research. Instead, demographic models are commonly utilized to investigate an individual’s life-history strategy, species dynamics, and population trends. This research investigates age-related survival and reproductive performance of adult female New Zealand (NZ) sea lions (Phocarctos hookeri), using multi-state mark-recapture data from known-age branded individuals over five years. The mark-recapture analysis was integrated with a population model to predict the lifetime reproductive output of female NZ sea lions. The integration of an analysis of short-term datasets with population modeling allows for the prediction of life-history parameters of long lived animals when long-term information is not available. While such approaches involve some caveats, it provides a framework for investigating population dynamics and is preferential to unsubstantiated assumptions. This technique can lead to better design and implementation of conservation management for long lived species.     

Estimating the hidden number of scrapie affected holdings in Great Britain using a simple,truncated count model allowing for heterogeneity

None of the current surveillance streams monitoring the presence of scrapie in Great Britain provide a comprehensive and unbiased estimate of the prevalence of the disease at the holding level. Previous work to estimate the under-ascertainment adjusted prevalence of scrapie in Great Britain applied multiple-list capture-recapture methods. The enforcement of new control measures on scrapie-affected holdings in 2004 has stopped the overlapping between surveillance sources and, hence, the application of multiple-list capture-recapture models. Alternative methods, still under the capture-recapture methodology, relying on repeated entries in one single list have been suggested in these situations. In this article, we apply one-list capture-recapture approaches to data held on the Scrapie Notifications Database to estimate the undetected population of scrapie-affected holdings with clinical disease in Great Britain for the years 2002, 2003, and 2004. For doing so, we develop a new diagnostic tool for indication of heterogeneity as well as a new understanding of the Zelterman and Chao’s lower bound estimators to account for potential unobserved heterogeneity. We demonstrate that the Zelterman estimator can be viewed as a maximum likelihood estimator for a special, locally truncated Poisson likelihood equivalent to a binomial likelihood. This understanding allows the extension of the Zelterman approach by means of logistic regression to include observed heterogeneity in the form of covariates—in case studied here, the holding size and country of origin. Our results confirm the presence of substantial unobserved heterogeneity supporting the application of our two estimators. The total scrapie-affected holding population in Great Britain is around 300 holdings per year. None of the covariates appear to inform the model significantly.     

Full Open Population Capture–Recapture Models With Individual Covariates

Traditional analyses of capture–recapture data are based on likelihood functions that explicitly integrate out all missing data. We use a complete data likelihood (CDL) to show how a wide range of capture–recapture models can be easily fitted using readily available software JAGS/BUGS even when there are individual-specific time-varying covariates. The models we describe extend those that condition on first capture to include abundance parameters, or parameters related to abundance, such as population size, birth rates or lifetime. The use of a CDL means that any missing data, including uncertain individual covariates, can be included in models without the need for customized likelihood functions. This approach also facilitates modeling processes of demographic interest rather than the complexities caused by non-ignorable missing data. We illustrate using two examples, (i) open population modeling in the presence of a censored time-varying individual covariate in a full robust design, and (ii) full open population multi-state modeling in the presence of a partially observed categorical variable. Supplemental materials for this article are available online.     

Genetic and demographic responses of fragmented Acacia dealbata (Mimosaceae) populations in southeastern Australia

Genetic and demographic studies of fragmented populations of common plant species often reveal negative impacts that are likely to constrain persistence. Examining species that are broadly representative of functional groups within fragmented landscapes is one approach to providing a better understanding of how these processes will influence vegetation persistence. Acacias are a significant component of the Australian flora, with Acacia dealbata being a common and representative species of fragmented landscapes across New South Wales. Previous reproductive assessments of fragmented A. dealbata populations indicated significant constraints for small populations through low reproductive output mediated by fertilisation success. This study examined genetic diversity, mating system, and progeny growth parameters of the seed crops produced by these populations to assess whether further constraints to persistence could be detected. Spatially explicit simulation studies were also conducted to assess the persistence likelihood of fragmented populations. Landscape parameters such as population size and plant density were useful predictors for some of the genetic and demographic responses, but a poor response signal was generally observed. Strong evidence for a self-incompatibility mechanism was observed in A. dealbata and is likely to be the major driver of population persistence. Self-incompatibility in small populations limits mate availability and eliminates inbred progeny early in the reproductive cycle leading to poor reproductive output. The simulation data provides further evidence that mate limitation in smaller populations (<200 plants and 40 S alleles) constrains reproductive output and persistence. These data indicate that introducing new germplasm to smaller populations can dramatically improve their persistence likelihood.     

Modelling demography and extinction risk in the endangered Balearic shearwater

Several demographic parameters of Balearic shearwater (Puffinus mauretanicus) were estimated and used to model extinction probabilities for the species, which is an endemic seabird confined to a Mediterranean archipelago. Adult survival was analyzed through capture-recapture models at two colonies free of adult predators during 1997-2002. Extinction probabilities for the world breeding population were modelled using Monte Carlo simulations of population trajectories, introducing stochasticity both demographic and environmental. Adult survival estimate (0.780, SE=0.020, 95% Confidence Intervals: 0.739-0.816) was unusually low for a Procellariiform, suggesting that sources of mortality other than predators (e.g. fishing gears) also occur. A deterministic model showed a declining trend for the world breeding population (λ=0.952), and significantly less than 1. Population viability analysis showed that in the presence of environmental and demographic stochasticities, mean extinction time for the world population was estimated at 40.4 years (SE=0.2), and mean growth rate showed a 7.4% decrease per year. Demographic stochasticity played a more important role than environmental stochasticity in population growth rate.     

The use of camera traps for estimating tiger and leopard populations in the high altitude mountains of Bhutan

We used camera traps in combination with capture-recapture data analysis to provide the first reliable density estimates for tigers and leopards from the high altitude and rugged terrain in Bhutan’s Jigme Singye Wangchuck National Park. Fifty days of camera trapping in each of five study zones collapsed into two trapping blocks, resulted in a sampling effort of 4050 trap days. Camera trapping yielded 17 tiger photos (14 left flanked and 3 right flanked) and 48 leopard photos (25 left flanked and 23 right flanked). Using photos of these left flank, the closed heterogeneous Jackknife Model M_h was the best fit for the capture history data. A capture probability () of 0.04 was obtained for both tigers and leopards, thus generating population size (N) of 8 tigers (SE = 2.12) and 16 leopards (SE = 2.91) with densities of 0.52 tiger 100 km⁻² and 1.04 leopard 100 km⁻². Photographic evidence indicated that tigers and leopards did not overlap in their spatial use of space. Tigers preferred less disturbed areas located further away from settlements, while leopards appeared to be more resilient to disturbances in so far as they were found nearer to human settlements. Camera trapping using a capture-recapture framework was an effective tool for assessing population sizes for tiger and leopard in low density areas such as Bhutan.     

Viability of mountain caribou in British Columbia, Canada: Effects of habitat change and population density

Population viability analyses (PVA) are frequently employed to develop recovery plans and inform management of endangered species. Translating results from PVA into meaningful management recommendations often depends on an understanding of how population parameters change with environmental conditions as well as population density. The decline of mountain caribou (Rangifer tarandus caribou) in British Columbia, Canada, is believed to be caused by apparent competition with alternative prey species following changes to the forest age structure from timber harvest and wildfire. In addition, populations have been shown to decline at faster rates at low population density. To evaluate the potential effects of habitat change and population density on population persistence, we used stochastic projection models for 10 distinct populations varying in initial size from <10 to approximately 150 females. In an initial model, we used estimates of vital rates based on information sampled from >350 radiocollared caribou between 1984 and 2004. We then compared the results of the initial model to a set of models that evaluated the effects of habitat conditions and population density via their expected relationships to female adult survival. Assuming that vital rates remain constant over a 200-year time frame, only three populations have high probabilities (>0.95) of extinction. When models incorporate the declines in adult female survival know to occur with increasing proportions of young forest and declining population densities, all 10 populations are predicted to decline to extinction within <200 years. Based on our results, we suggest that PVA models that fail to incorporate the effects of changes in vital rates with habitat and population density may lead to overly optimistic assessments of the probability of population persistence in endangered species.     

Metapopulation dynamics and conservation of the marsh fritillary butterfly: Population viability analysis and management options for a critically endangered species in Western Europe

This study investigates the dynamics and viability of a marsh fritillary butterfly Euphydryas aurinia metapopulation in a Belgian successional landscape. Based on capture-mark-recapture and winter nest census data, we first estimated demography (survival and recruitment rates, population size, density dependence) and dispersal parameters (emigration rate, effect of patch connectivity on dispersal, mortality during dispersal). Then using RAMAS/GIS platform, we parameterised a population viability analysis (PVA) model with these parameters to simulate the future of this metapopulation under different scenarios.The metapopulation does not seem viable even if natural reforestation is controlled by adequate management. In its present state, the patch system is not able to sustain enough individuals: due to the large temporal fluctuations in demographic parameters, a carrying capacity far higher than currently would be necessary to limit extinction risk to 1%, suggesting the existence of an extinction debt for the species in Belgium. The situation of E. aurinia appears much worse compared to two other fritillary species threatened in Belgium, for which similar PVA are available. It is therefore urgent to increase the carrying capacity of the patch system. How and where it is achieved are of secondary importance for the gain in viability: improvement of habitat quality through restoration, or increase of habitat quantity via enlargement of existing patches and/or creation of new habitat in the matrix. A regime of management based on regular re-opening and maintenance of habitat patches may be the only guarantee of long-term persistence for this critically endangered species in Belgium.     

An overview of closed capture-recapture models

This article reviews various models for both discrete-time and continuous-time closed capture-recapture experiments. The traditional discrete-time models assume that the samples are independent. Dependence may be caused by local dependence (list dependence) within each animal or by heterogeneity among animals. Three different approaches that can incorporate dependence into models are reviewed, i.e., ecological models, log-linear models, and the sample-coverage approach. The statistical tools involved in population size estimation in these three approaches cover a wide range of methodologies. There has been relatively little published research for the continuous-time counterparts. The counting process approach, which is the framework for most existing estimation procedures for continuous-time models, is reviewed. The connection of continuous-time models to recurrent event analysis in the context of failure time inferences is discussed. The applications of capture-recapture models to other disciplines are briefly presented. Remarks about the limitations of the models are made and some future research directions are also suggested.     

Genetic Introgression and the Survival of Florida Panther Kittens

Estimates of survival for the young of a species are critical for population models. These models can often be improved by determining the effects of management actions and population abundance on this demographic parameter. We used multiple sources of data collected during 1982-2008 and a live-recapture dead-recovery modeling framework to estimate and model survival of Florida panther (Puma concolor coryi) kittens (age 0-1 year). Overall, annual survival of Florida panther kittens was 0.323 ± 0.071 (SE), which was lower than estimates used in previous population models. In 1995, female pumas from Texas (P. c. stanleyana) were released into occupied panther range as part of an intentional introgression program to restore genetic variability. We found that kitten survival generally increased with degree of admixture: F₁ admixed and backcrossed to Texas kittens survived better than canonical Florida panther and backcrossed to canonical kittens. Average heterozygosity positively influenced kitten and older panther survival, whereas index of panther abundance negatively influenced kitten survival. Our results provide strong evidence for the positive population-level impact of genetic introgression on Florida panthers. Our approach to integrate data from multiple sources was effective at improving robustness as well as precision of estimates of Florida panther kitten survival, and can be useful in estimating vital rates for other elusive species with sparse data.     

The Jolly-seber model: More than just abundance

The Jolly-Seber model provides estimates of abundance, survival, and capture rates from capture-recapture experiments. This article will describe recent extensions to the following cases: (a) multiple-cohort studies where recruitment rates are compared among cohorts, (b) age-specific breeding proportions, and (c) population growth rates. Finally, new areas of research needed for this model are proposed.     

Pattern-oriented modelling for estimating unknown pre-breeding survival rates: The case of the Lesser Spotted Woodpecker (Picoides minor)

In population viability analysis we are often faced with a lack of knowledge of survival rates in animal populations. In particular, survival of recruits is usually hard to assess. However, data on population structure might be considered as patterns that contain valuable information to estimate missing parameters indirectly. As an example for this pattern-oriented modelling and parameterization, pre-breeding survival rate of the endangered Lesser Spotted Woodpecker (Picoides minor) was determined here using data on population structure (e.g. sex ratio) and reproductive success at the population level (e.g. nesting success). Therefore, an individual-based model was developed simulating the population dynamics for two different populations that had been empirically studied at Lake Möckeln, Sweden, and Taunus, Germany. For both populations, a small range for pre-breeding survival rates could be identified wherein all simulated patterns corresponded best to the empirical values. Pre-breeding survival rate was found to be higher in the German scenario than in the Swedish and geographical variation in life-history traits is discussed as a possible reason. It is concluded that the pattern-oriented approach is a valuable method for estimating missing demographic parameters, even when using weak patterns from empirical investigations. Furthermore, it was shown that the use of multiple patterns is necessary for this purpose.     

Evaluation of the extinction risk and of conservation alternatives for a very small insular population: the bearded vulture Gypaetus barbatus in Corsica

The bearded vulture Gypaetus barbatus is a large, long-lived osteophagus vulture whose abundance and breeding range have drastically declined during the last century, making it one of the most endangered European bird species. We evaluated the extinction risk of the bearded vulture population in Corsica (a small, isolated breeding population of 8-10 pairs), one of the last extant populations in Western Europe, and estimated its probability of extinction to be 0.165 over the next 50 years. A sensitivity analysis to assess the influence of uncertain demographic rates showed that it is critical to estimate precisely the values of pre-adult survival. Neither the type nor the parameters of density dependence acting on fecundity and survival rates influenced much the extinction risk of the Corsican population. We evaluated the effect of four realistic conservation actions that could be implemented on the Corsican bearded vulture population and rank them in terms of their respective decrease of the current extinction risk faced by this population. We found that the release of two juveniles every other year for 12 years and the increase of fecundity due to selective food provisioning would reduce by more than one-half the current extinction risk of Corsican bearded vulture population. In contrast, even substantial increases in the carrying capacity through large supplemental feeding produced very modest decreases in the extinction risk, thus calling into question the efficacy of one of the main pan-European conservation strategies for this species. Re-establishing a population network within the Mediterranean could be a potentially better strategy, though its efficacy depends on natal dispersal among populations that is currently unknown.     

Assessing the risks of extinction for local populations of roan antelope Hippotragus equinus

We estimated the minimum size of the roan antelope Hippotragus equinus population in the Parc National de l'Akagera in Rwanda to be at least 144 animals, based on a two and a half year study of individually recognized stable social groups. Data from the same study were used to estimate the annual birth rate, and the survival rate of male calves, female calves, adult females and juvenile females; and to identify factors which would result in year-to-year variations in survival. The results of this analysis were incorporated into an age-structured model of the population's dynamics which took account of demographic and environmental stochasticity. This model was then used to determine the viability of the roan population in the park and to identify demographic characteristics whose occurrence could be used to predict when the population was most at risk of extinction.The risk of extinction could be predicted if the number of stable groups within the park was monitored in September of each year. This risk could be greatly reduced if a reciprocal arrangement was established with other protected areas such that the population in the park could be reinforced with new stable groups when the number of stable groups fell below three. However, the risks—particularly of disease transfer—associated with such reinforcement programmes should be clearly recognized.     

Evaluating effects of deforestation, hunting, and El Niño events on a threatened lemur

Madagascar ranks as one of the world’s top extinction hotspots because of its high endemism and high rate of habitat degradation. Global climate phenomena such as El Niño Southern Oscillations may have confounding impacts on the island’s threatened biota but these effects are less well known. We performed a demographic study of Propithecus edwardsi, a lemur inhabiting the eastern rainforest of Madagascar, to evaluate the impact of deforestation, hunting, and El Niño on its population and to re-evaluate present endangerment categorization under the IUCN. Over 18 years of demographic data, including survival and fecundity rates were used to parameterize a stochastic population model structured with three stage classes (yearlings, juveniles, and adults). Results demonstrate that hunting and deforestation are the most significant threats to the population. Analysis of several plausible scenarios and combinations of threat revealed that a 50% population decline within three generations was very likely, supporting current IUCN classification. However, the analysis also suggested that changing global cycles may pose further threat. The average fecundity of lemurs was over 65% lower during El Niño years. While not as severe as deforestation or hunting, if El Niño events remain at the current high frequency there may be negative consequences for the population. We suggest that it is most critical for this species continued survival to create more protected areas, not only to thwart hunting and deforestation, but also to give this endangered lemur a better chance to recover from and adapt to altered climate cycles in the future.