Sex-specific population dynamics and demography of capercaillie (Tetrao urogallus L.) in a patchy environment

Modeling the population dynamics of patchily distributed species is a challenge, particularly when inference must be based on incomplete and small data sets such as those from most species of conservation concern. Here, we develop an open population spatial capture–recapture (SCR) model with sex-specific detection and population dynamics parameters to investigate population trend and sex-specific population dynamics of a capercaillie (Tetrao urogallus) population in Switzerland living in eight distinct forest patches totaling 22 km² within a region of 908 km² and sampled via scat collection. Our model accounts for the patchy distribution of habitat and the uncertainty introduced by collecting data only every third year, while producing sex by patch population trajectories. The estimated population trajectory was a decline of 2% per year; however, the sex specificity of the model revealed a decline in the male population only, with no evidence of decline in the female population. The decline observed in males was explained by the demography of just two of the eight patches. Our study highlights the flexibility of open population SCR models for assessing population trajectories through time and across space and emphasizes the desirability of estimating sex-stratified population trends especially in species of conservation concern.     

Open population maximum likelihood spatial capture‐recapture

Open population capture‐recapture models are widely used to estimate population demographics and abundance over time. Bayesian methods exist to incorporate open population modeling with spatial capture‐recapture (SCR), allowing for estimation of the effective area sampled and population density. Here, open population SCR is formulated as a hidden Markov model (HMM), allowing inference by maximum likelihood for both Cormack‐Jolly‐Seber and Jolly‐Seber models, with and without activity center movement. The method is applied to a 12‐year survey of male jaguars (Panthera onca) in the Cockscomb Basin Wildlife Sanctuary, Belize, to estimate survival probability and population abundance over time. For this application, inference is shown to be biased when assuming activity centers are fixed over time, while including a model for activity center movement provides negligible bias and nominal confidence interval coverage, as demonstrated by a simulation study. The HMM approach is compared with Bayesian data augmentation and closed population models for this application. The method is substantially more computationally efficient than the Bayesian approach and provides a lower root‐mean‐square error in predicting population density compared to closed population models.     

Big cats at large: Density,structure, and spatio-temporal patterns of a leopard population free of anthropogenic mortality

Human impact is near pervasive across the planet and studies of wildlife populations free of anthropogenic mortality are increasingly scarce. This is particularly true for large carnivores that often compete with and, in turn, are killed by humans. Accordingly, the densities at which carnivore populations occur naturally, and their role in shaping and/or being shaped by natural processes, are frequently unknown. We undertook a camera-trap survey in the Sabi Sand Game Reserve (SSGR), South Africa, to examine the density, structure and spatio-temporal patterns of a leopard Panthera pardus population largely unaffected by anthropogenic mortality. Estimated population density based on spatial capture–recapture models was 11.8 ± 2.6 leopards/100 km². This is likely close to the upper density limit attainable by leopards, and can be attributed to high levels of protection (particularly, an absence of detrimental edge effects) and optimal habitat (in terms of prey availability and cover for hunting) within the SSGR. Although our spatio-temporal analyses indicated that leopard space use was modulated primarily by “bottom-up” forces, the population appeared to be self-regulating and at a threshold that is unlikely to change, irrespective of increases in prey abundance. Our study provides unique insight into a naturally-functioning carnivore population at its ecological carrying capacity. Such insight can potentially be used to assess the health of other leopard populations, inform conservation targets, and anticipate the outcomes of population recovery attempts.     

Density estimation in a wolverine population using spatial capture–recapture models

Classical closed-population capture–recapture models do not accommodate the spatial information inherent in encounter history data obtained from camera-trapping studies. As a result, individual heterogeneity in encounter probability is induced, and it is not possible to estimate density objectively because trap arrays do not have a well-defined sample area. We applied newly-developed, capture–recapture models that accommodate the spatial attribute inherent in capture–recapture data to a population of wolverines (Gulo gulo) in Southeast Alaska in 2008. We used camera-trapping data collected from 37 cameras in a 2,140-km² area of forested and open habitats largely enclosed by ocean and glacial icefields. We detected 21 unique individuals 115 times. Wolverines exhibited a strong positive trap response, with an increased tendency to revisit previously visited traps. Under the trap-response model, we estimated wolverine density at 9.7 individuals/1,000 km² (95% Bayesian CI: 5.9–15.0). Our model provides a formal statistical framework for estimating density from wolverine camera-trapping studies that accounts for a behavioral response due to baited traps. Further, our model-based estimator does not have strict requirements about the spatial configuration of traps or length of trapping sessions, providing considerable operational flexibility in the development of field studies. © 2011 The Wildlife Society.     

Life history of the endangered Japanese striped loach,Cobitis kaibarai (Cypriniformes: Cobitidae), with special reference to its reproductive ecology and the influence of creek reshapings on its population density

In recent years, the biodiversity of freshwater fishes has been markedly decreasing worldwide because of anthropogenic activities. The Japanese striped loach, Cobitis kaibarai (Cypriniformes: Cobitidae), is a primary freshwater fish endemic to northern Kyushu, Japan. This species is designated as endangered IB class in the Red List by the Japan Ministry of the Environment. Its population is decreasing, possibly because of habitat loss and degradation. To conserve C. kaibarai populations, information on its basic ecology is necessary; nonetheless, its detailed life history and reproductive ecology have yet to be clarified. In this study, the authors conducted monthly capture–mark–recapture surveys and periodical observations to investigate the life history, spawning sites and season of C. kaibarai. They also evaluated the influence of creek reshaping (concrete revetment) on the C. kaibarai population in Saga Plain, northern Kyushu. Between 2015 and 2018, more individuals were captured during winter than summer. The average body width of females peaked in early June and small immatures were confirmed from July. Some individuals were captured across 15 or more months after their initial marking. In the survey of reproductive sites, eggs and larvae of C. kaibarai were found in shallow areas in mid-June; these were temporarily submerged following the increase in water level from early June. Therefore, C. kaibarai spawns in shallow areas during this season. Based on the capture–mark–recapture surveys, the estimated population density of C. kaibarai significantly decreased in a census site that had undergone creek reshaping, which contrasted with the results in a control site, where no significant difference was detected. The standard length of C. kaibarai increased following creek reshaping, suggesting that the proportion of C. kaibarai postponing spawning had increased, possibly because of degradation of spawning environments. The results of this study provide important ecological knowledge for the conservation of C. kaibarai and emphasize the importance of shallow waters for floodplain spawners.     

A likelihood ratio test for completed sampling in population size estimation studies

We propose a likelihood ratio test to assess that sampling has been completed in closed population size estimation studies. More precisely, we assess if the expected number of subjects that have never been sampled is below a user-specified threshold. The likelihood ratio test statistic has a nonstandard distribution under the null hypothesis. Critical values can be easily approximated and tabulated, and they do not depend on model specification. We illustrate in a simulation study and three real data examples, one of which involves ascertainment bias of amyotrophic lateral sclerosis in Gulf War veterans.     

An open spatial capture–recapture model for estimating density,movement, and population dynamics from line‐transect surveys

The purpose of many wildlife population studies is to estimate density, movement, or demographic parameters. Linking these parameters to covariates, such as habitat features, provides additional ecological insight and can be used to make predictions for management purposes. Line‐transect surveys, combined with distance sampling methods, are often used to estimate density at discrete points in time, whereas capture–recapture methods are used to estimate movement and other demographic parameters. Recently, open population spatial capture–recapture models have been developed, which simultaneously estimate density and demographic parameters, but have been made available only for data collected from a fixed array of detectors and have not incorporated the effects of habitat covariates. We developed a spatial capture–recapture model that can be applied to line‐transect survey data by modeling detection probability in a manner analogous to distance sampling. We extend this model to a) estimate demographic parameters using an open population framework and b) model variation in density and space use as a function of habitat covariates. The model is illustrated using simulated data and aerial line‐transect survey data for North Atlantic right whales in the southeastern United States, which also demonstrates the ability to integrate data from multiple survey platforms and accommodate differences between strata or demographic groups. When individuals detected from line‐transect surveys can be uniquely identified, our model can be used to simultaneously make inference on factors that influence spatial and temporal variation in density, movement, and population dynamics.     

Female and male Eurasian lynx have distinct spatial tactics at different life‐history stages in a high‐density population

Knowledge regarding the spatial behavior of the Eurasian lynx is mainly inferred from populations in Europe. We used GPS telemetry to record the spatial behavior of nine individuals in northwestern Anatolia obtaining eleven home ranges (HRs). Analyses revealed the smallest mean HR sizes (n_{HR ♀}  = 4) at 57 km² (95% kernel utilization distribution, KUD) and 56 km² (95% minimum convex polygon, MCP), ever reported for adult female Eurasian lynx. Adult males either occupied small permanent territories (n_HR♂._T = 2), with a mean of 176 km² (95% KUD) and 150 km² (95% MCP), or were residents without territories (floaters, n_HR♂. _F  = 2) roaming across large, stable HRs with a mean size of 2,419 km² (95% KUD) and 1,888 km² (95% MCP), comparable to HR sizes of Scandinavian lynx populations. Three disperser subadult males did not hold stable HRs (mean 95% KUD = 203 km², mean 95% MCP = 272 km²). At 4.9 individuals per 100 km², population density was one of the highest recorded, suggesting that the presence of adult male floaters was a consequence of a landscape fully occupied by territorials and revealing a flexibility of spatial behavior of Eurasian lynx not previously recognized. Such a high population density, small HRs, and behavioral flexibility may have been aided by the legal protection from and apparent low levels of poaching of this population. The observed spatial tactics are unlikely to be seen in most of the previously studied Eurasian lynx populations, as they either suffer medium to high levels of human‐caused mortality or were unlikely to be at carrying capacity. For effective and appropriate conservation planning, data from felid populations in a reasonably natural state such as ours, where space, density, prey, and pathogens are likely to be the key drivers of spatial dynamics, are therefore essential.     

In a rough spot: Declines in Arthroleptella rugosa calling densities are explained by invasive pine trees

Basing conservation interventions on evidence is important for justifying their associated cost and gauging their effectiveness. For amphibians, the number of studies available to support conservation action plans is limited. Here, we sought to determine the effect of invasive pine trees on the calling densities of a Critically Endangered frog species, endemic to the Western Cape province in South Africa. The Rough Moss frog, Arthroleptella rugosa, is an anuran restricted to a small patch of fire-driven fynbos habitat prone to invasion by Cluster Pines, Pinus pinaster. We use acoustic spatially explicit capture–recapture methods to estimate frog densities at multiple sites (n = 12) over ten years. Sites were classified as invaded or uninvaded by P. pinaster, and this information, along with the time since the last fire, were used as explanatory variables for frog density in a generalized linear mixed model. Frog densities were found to be significantly affected by P. pinaster invasion status. At invaded sites, there was a negative relationship between call densities and time since fire, while at uninvaded sites the same relationship was positive. These results confirm previous suggestions that invasive pine trees cause population declines in A. rugosa. Our findings can be used to support conservation interventions for A. rugosa, specifically the use of fire in an adaptive management context to control pine invasion across its range.     

Estimating elephant density using motion-sensitive cameras: challenges,opportunities, and parameters for consideration

With extinction rates far exceeding the natural background rate, reliable monitoring of wildlife populations has become crucial for adaptive management and conservation. Robust monitoring is often labor intensive with high economic costs, particularly in the case of those species that are subject to illegal poaching, such as elephants, which require frequent and accurate population estimates over large spatial scales. Dung counting methods are commonly employed to estimate the density of elephants; however, in the absence of a full survey calibration, these can be unreliable in heterogeneous habitats where dung decay rates may be highly variable. We explored whether motion-sensitive cameras offer a simple, lower cost, and reliable alternative for monitoring in challenging forest environments. We estimated the density of African savanna elephants (Loxodanta africana) in a montane forest using the random encounter model and assessed the importance of surveying parameters for future survey design. We deployed motion-sensitive cameras in 65 locations in the Aberdare Conservation Area in Kenya during June to August in 2015 to 2017, for a survey effort of 967 days, and a mean encounter rate of 0.09 ± 0.29 (SD) images/day. Elephants were captured in 16 locations. Density estimates varied between vegetation types, with estimates ranging from 6.27/km² in shrub, 1.1/km² in forest, 0.53/km² in bamboo (Yushania alpine), and 0.44/km² in the moorlands. The average speed of animal movement and the camera detection zone had the strongest linear associations with density estimates (R = −0.97). The random encounter model has the potential to offer an alternative, or complementary method within the active management framework for monitoring elephant populations in forests at a relatively low cost.     

oSCR: a spatial capture–recapture R package for inference about spatial ecological processes

Spatial capture–recapture (SCR) methods have become widely applied in ecology. The immediate adoption of SCR is due to the fact that it resolves some major criticisms of traditional capture–recapture methods related to heterogeneity in detectabililty, and the emergence of new technologies (e.g. camera traps, non‐invasive genetics) that have vastly improved our ability to collection spatially explicit observation data on individuals. However, the utility of SCR methods reaches far beyond simply convenience and data availability. SCR presents a formal statistical framework that can be used to test explicit hypotheses about core elements of population and landscape ecology, and has profound implications for how we study animal populations. In this software note, we describe the technical basis and analytical workflow of oSCR, an R package for analyzing spatial encounter history data using a multi‐session sex‐structured likelihood. The impetus for developing oSCR was to create an accessible and transparent analysis tool that allows users to conveniently and intuitively formulate statistical models that map directly to fundamental processes of interest in spatial population ecology (e.g. space use, resource selection, density and connectivity). We have placed an emphasis on creating a transparent and accessible code base that is coupled with a logical workflow that we hope stimulates active participation in further technical developments.     

A trans‐national monarch butterfly population model and implications for regional conservation priorities

1. The monarch has undergone considerable population declines over the past decade, and the governments of Mexico, Canada, and the United States have agreed to work together to conserve the species. 2. Given limited resources, understanding where to focus conservation action is key for widespread species like monarchs. To support planning for continental‐scale monarch habitat restoration, we address the question of where restoration efforts are likely to have the largest impacts on monarch butterfly (Danaus plexippus Linn.) population growth rates. 3. We present a spatially explicit demographic model simulating the multi‐generational annual cycle of the eastern monarch population, and use the model to examine management scenarios, some of which focus on particular regions of North America. 4. Improving the monarch habitat in the north central or southern parts of the monarch range yields a slightly greater increase in the population growth rate than restoration in other regions. However, combining restoration efforts across multiple regions yields population growth rates above 1 with smaller simulated improvements in habitat per region than single‐region strategies. 5. S ynthesis and applications: These findings suggest that conservation investment in projects across the full monarch range will be more effective than focusing on one or a few regions, and will require international cooperation across many land use categories.     

Current distribution,breeding population and habitat use of the globally threatened Grey-necked Picathartes Picathartes oreas in south-eastern Nigeria: a call for conservation action

The Grey-necked Picathartes Picathartes oreas is a globally threatened bird species in Africa with a wild population of less than 10,000 individuals. The Nigerian population, which has been poorly studied, is restricted to the forest of Cross River. This study re-assessed the distribution, breeding population, habitat use and current threats of the Grey-necked Picathartes by revisiting the 91 breeding sites identified during the first and only survey of the species in 1987. We estimated a breeding population of 164 individuals across 82 breeding sites. Only 72 breeding sites were found in the localities where 91 had been registered in 1987. Thirteen (18%) of these 72 sites were no longer active and showed evidence of human disturbance. The occurrence of Grey-necked Picathartes’ nest sites was positively predicted by higher number of emergent trees, larger rocks and negatively related to disturbance matrices. Similarly, larger colony sizes were associated with high canopy cover and rock height. Also, the probability of finding an active nest within a breeding colony was significantly predicted by increased canopy, tree density and ground cover. Human threats included farming, wire snares, egg and juvenile removal, bush burning, and hunter’s camps. These threats, though specific to the Grey-necked Picathartes, threaten the integrity of the Cross River forest habitats.     

Extremely low effective population sizes, genetic structuring and reduced genetic diversity in a threatened bumblebee species, Bombus sylvarum (Hymenoptera: Apidae)

Habitat fragmentation may severely affect survival of social insect populations as the number of nests per population, not the number of individuals, represents population size, hence they may be particularly prone to loss of genetic diversity. Erosion of genetic diversity may be particularly significant among social Hymenoptera such as bumblebees (Bombus spp.), as this group may be susceptible to diploid male production, a suggested direct cost of inbreeding. Here, for the first time, we assess genetic diversity and population structuring of a threatened bumblebee species (Bombus sylvarum) which exists in highly fragmented habitat (rather than oceanic) islands. Effective population sizes, estimated from identified sisterhoods, were very low (range 21-72) suggesting that isolated populations will be vulnerable to loss of genetic variation through drift. Evidence of significant genetic structuring between populations (theta = 0.084) was found, but evidence of a bottleneck was detected in only one population. Comparison across highly fragmented UK populations and a continental population (where this species is more widespread) revealed significant differences in allelic richness attributable to a high degree of genetic diversity in the continental population. While not directly related to population size, this is perhaps explained by the high degree of isolation between UK populations relative to continental populations. We suggest that populations now existing on isolated habitat islands were probably linked by stepping-stone populations prior to recent habitat loss.