The Jolly-seber model: More than just abundance

Dynamics of Humoral Immunity to Myxoma and Rabbit Hemorrhagic Disease Viruses in Wild European Rabbits Assessed by Longitudinal Semiquantitative Serology

Myxoma virus (MYXV) and rabbit hemorrhagic disease virus (RHDV) are important drivers of the population decline of the European rabbit, an endangered keystone species. Both viruses elicit strong immune responses, but the long-term dynamics of humoral immunity are imperfectly known. This study aimed to assess the determinants of the long-term dynamics of antibodies to each virus based on a longitudinal capture-mark-recapture of wild European rabbits and semiquantitative serological data of MYXV and RHDV GI.2-specific IgG. The study included 611 indirect enzyme-linked immunosorbent assay (iELISA) normalized absorbance ratios for each MYXV and RHDV GI.2 from 505 rabbits from 2018 to 2022. Normalized absorbance ratios were analyzed using log-linear mixed models, showing a significant positive relationship with the time since the first capture of individual rabbits, with monthly increases of 4.1% for antibodies against MYXV and 2.0% against RHDV GI.2. Individual serological histories showed fluctuations over time, suggesting that reinfections boosted the immune response and likely resulted in lifelong immunity. Normalized absorbance ratios significantly increased with the seroprevalence in the population, probably because of recent outbreaks, and with body weight, highlighting the role of MYXV and RHDV GI.2 in determining survival to adulthood. Juvenile rabbits seropositive for both viruses were found, and the dynamics of RHDV GI.2 normalized absorbance ratios suggest the presence of maternal immunity up to 2 months of age. Semiquantitative longitudinal serological data provide epidemiological information, otherwise lost when considering only qualitative data, and support a lifelong acquired humoral immunity to RHDV GI.2 and MYXV upon natural infection. IMPORTANCE This study addresses the long-term dynamics of humoral immunity to two major viral pathogens of the European rabbit, an endangered keystone species of major ecological relevance. Such studies are particularly challenging in free-ranging species, and a combination of longitudinal capture-mark-recapture and semiquantitative serology was used to address this question. Over 600 normalized absorbance ratios of iELISA, obtained from 505 individual rabbits in 7 populations over 5 years, were analyzed using linear mixed models. The results support a lifelong acquired humoral immunity to myxoma virus and rabbit hemorrhagic disease virus upon natural infection and suggest the presence of maternal immunity to the latter in wild juvenile rabbits. These results contribute to understanding the epidemiology of two viral diseases threatening this keystone species and assist in developing conservation programs.

Migration and non-breeding ecology of the Yellow-breasted Chat Icteria virens

Detailed information spanning the full annual cycle is lacking for most songbird populations. We examined breeding, migration, and non-breeding sites for the Yellow-breasted Chat (Icteria virens, chat). We deployed archival GPS tags and light-level geolocators on breeding chats in British Columbia and light-level geolocators in California from 2013 to 2017 to determine migration routes and non-breeding sites. We examined whether chats overwintered in protected areas and characterized the percent of land cover within 1 km. We used a combination of genetics and stable hydrogen isotopes from feathers collected on non-breeding chats in Nayarit, Mexico (2017-2019) and migrating chats in Chiapas, Mexico (2018) and Veracruz, Mexico (2014-2015) to determine subspecies and infer breeding location. Endangered chats in British Columbia followed the Pacific Flyway and spent the non-breeding period in Sinaloa and Nayarit, Mexico. Two out of five chats spent the non-breeding period in protected areas, and the most common landcover type used was tropical or subtropical broadleaf deciduous forest. We found no mixing of eastern and western chats in our Mexico sites, suggesting strong migratory connectivity at the subspecies level. Western chats likely originating from multiple breeding latitudes spent the non-breeding period in Nayarit. Eastern Yellow-breasted Chats likely breeding across various latitudes migrated through Veracruz and Chiapas. Our results provide precise migration routes and non-breeding locations, and describe habitat cover types for chats, notably an endangered population in British Columbia, which may be valuable for habitat protection and conservation efforts.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10336-021-01931-8.

Age-structured Jolly-Seber model expands inference and improves parameter estimation from capture-recapture data

Understanding the influence of individual attributes on demographic processes is a key objective of wildlife population studies. Capture-recapture and age data are commonly collected to investigate hypotheses about survival, reproduction, and viability. We present a novel age-structured Jolly-Seber model that incorporates age and capture-recapture data to provide comprehensive information on population dynamics, including abundance, age-dependent survival, recruitment, age structure, and population growth rates. We applied our model to a multi-year capture-recapture study of polar bears (Ursus maritimus) in western Hudson Bay, Canada (2012–2018), where management and conservation require a detailed understanding of how polar bears respond to climate change and other factors. In simulation studies, the age-structured Jolly-Seber model improved precision of survival, recruitment, and annual abundance estimates relative to standard Jolly-Seber models that omit age information. Furthermore, incorporating age information improved precision of population growth rates, increased power to detect trends in abundance, and allowed direct estimation of age-dependent survival and changes in annual age structure. Our case study provided detailed evidence for senescence in polar bear survival. Median survival estimates were lower (<0.95) for individuals aged <5 years, remained high (>0.95) for individuals aged 7–22 years, and subsequently declined to near zero for individuals >30 years. We also detected cascading effects of large recruitment classes on population age structure, which created major shifts in age structure when these classes entered the population and then again when they reached prime breeding ages (10–15 years old). Overall, age-structured Jolly-Seber models provide a flexible means to investigate ecological and evolutionary processes that shape populations (e.g., via senescence, life expectancy, and lifetime reproductive success) while improving our ability to investigate population dynamics and forecast population changes from capture-recapture data.

Migration ecology of western gray catbirds

BACKGROUND

For many songbirds in North America, we lack movement details about the full annual cycle, notably outside the breeding season. Understanding how populations are linked spatially between breeding and overwintering periods (migratory connectivity) is crucial to songbird conservation and management. We assessed migratory connectivity for 2 breeding populations of Gray Catbirds (Dumetella carolinensis) west of and within the Rocky Mountains by determining migration routes, stopover sites, and overwintering locations. Additionally, we compared apparent annual survivorship for both populations.

METHODS

We deployed 39 archival light-level geolocators and 21 Global Positioning System (GPS) tags on catbirds in the South Okanagan Valley, British Columbia, Canada, and 32 geolocators and 52 GPS tags in the Bitterroot River Valley, Montana, USA. These devices allowed us to determine migration routes, stopover sites, overwintering locations, and migratory connectivity. Migratory connectivity was quantified using Mantel's correlation. We used mark-recapture of colour banded catbirds in both sites to estimate apparent annual survivorship.

RESULTS

We retrieved 6 geolocators and 19 GPS tags with usable data. Gray Catbirds from both populations passed through the Rocky Mountains eastward before heading south towards their overwintering locations in northeastern Mexico and Texas. Stopover sites during fall migration occurred primarily in Montana, Kansas, Oklahoma, and Arkansas. Overwintering locations spanned Texas and 5 states in northeastern Mexico. Individual catbirds used up to 4 distinct sites during the overwintering period. Catbirds separated by almost 500 km during the breeding season overlapped during the non-breeding season, suggesting weak migratory connectivity among western populations (Mantel's correlation = 0.013, P-value = 0.41). Catbird apparent annual survivorship estimates were higher in British Columbia (0.61 ± 0.06 females; 0.64 ± 0.05 males) than in Montana (0.34 ± 0.05 females; 0.43 ± 0.04 males), though the main driver of these differences remain unclear.

CONCLUSIONS

Our results provide high precision geographic details during the breeding, migration, and overwintering phases of the annual cycle for western Gray Catbirds. Notably, we found that western catbirds followed the Central Flyway as opposed to the Pacific Flyway. We document that catbirds used multiple sites over winter, contrary to the popular belief that this phase of the annual cycle is stationary for most songbirds.

Metapopulation dynamics over 25 years of a beetle, Osmoderma eremita, inhabiting hollow oaks

Osmoderma eremita is a species of beetle that inhabits hollows in ancient trees, which is a habitat that has decreased significantly during the last century. In southeastern Sweden, we studied the metapopulation dynamics of this beetle over a 25 year period, using capture-mark-recapture. The metapopulation size had been rather stable over time, but in most of the individual trees there had been a positive or negative trend in population development. The probability of colonisation was higher in well-connected trees with characteristics reflecting earlier successional stages, and the probability of extinction higher in trees with larger diameter (i.e. in later successional stages), which is expected from a habitat-tracking metapopulation. The annual tree mortality and fall rates (1.1% and 0.4%, respectively) are lower than the colonisation and extinction rates (5-7%), indicating that some of the metapopulation dynamics are due to the habitat dynamics, but many colonisations and extinctions take place for other reasons, such as stochastic events in small populations. The studied metapopulation occurs in an area with a high density of hollow oaks and where the oak pastures are still managed by grazing. In stands with fewer than ten suitable trees, the long-term extinction risk may be considerable, since only a small proportion of all hollow trees harbours large populations, and the population size in trees may change considerably during a decade.

Demographic benefits of early season resources for bumble bee (B. vosnesenskii) colonies

The temporal distribution of resources is an important aspect of habitat quality that can substantially impact population success. Although it is widely accepted that floral resources directly influence wild bee population sizes, we lack experimental data evaluating how resource availability affects colony growth via demographic mechanisms. To achieve this, we tracked marked individuals in bumble bee (Bombus vosnesenskii) colonies to evaluate whether worker survival and reproduction responded to experimentally elevated forage early in colony development. Specifically, we assessed the effect of early resource environment on worker and sexual offspring production, and the survival and body size of individual workers. We also assessed whether responses of colonies differed when exposed to higher or lower resource environments at a relatively smaller (~ 10 workers) or larger (~ 20 workers) size. Resource supplementation always resulted in greater total offspring and male production; however, the influence of supplementation on worker production and quality depended on colony size at the start of supplementation. Among colonies that were initially smaller, colonies that were supplemented produced fewer but larger bodied and longer lived workers compared to control counterparts. Among colonies that were initially larger, colonies that were supplemented produced more workers than corresponding controls, but without changes to worker quality. Collectively, these results provide clear experimental evidence that greater resource availability early in colony development increases overall productivity, and indicate that colonies may pursue different allocation strategies in response to the resource environment, investing in more or better workers.

Assessing the effect of density on population growth when modeling individual encounter data

The relative role of density-dependent and density-independent variation in vital rates and population size remains largely unsolved. Despite its importance to the theory and application of population ecology, and to conservation biology, quantifying the role and strength of density dependence is particularly challenging. We present a hierarchical formulation of the temporal symmetry approach, also known as the Pradel model, that permits estimation of the strength of density dependence from capture-mark-reencounter data. A measure of relative population size is built in the model and serves to detect density dependence directly on population growth rate. The model is also extended to account for temporal random variability in demographic rates, allowing estimation of the temporal variance of population growth rate unexplained by density dependence. We thus present a model-based approach that enable to test and quantify the effect of density-dependent and density-independent factors affecting population fluctuations in a single modeling framework. More generally, we use this modeling framework along with simulated and empirical data to show the value of including density dependence when modeling individual encounter data without the need for auxiliary data.

Using visible implant elastomer to study ammocoete populations with Cormack-Jolly-Seber models

This study examined the efficacy of marking wild populations of lampreys with visible implant elastomer (VIE) for 6-18 months to examine ammocoete movements using Cormack-Jolly-Seber (CJS) open-population models. These methods were tested on two lamprey populations in different river systems. American brook lamprey Lethenteron appendix at Dyke Creek apparent survival (φ) was high in the summer and winter (c. 0·7), but declined after flow events in the spring and autumn. Sea lamprey Petromyzon marinus at Oquaga Creek φ in the top-ranked models varied with stream location and time. Estimates of φ were similar to Dyke Creek during the summer (c. 0·7), but declined after flow events and remained low (c. 0·1) in winter. Open-population models support current understanding of ammocoete movement, i.e. dispersal is driven by high-flow events at certain times of the year. The present study provides a framework to study ammocoetes with VIE.

Estimating the size of an open population using sparse capture-recapture data

Sparse capture-recapture data from open populations are difficult to analyze using currently available frequentist statistical methods. However, in closed capture-recapture experiments, the Chao sparse estimator (Chao, 1989, Biometrics 45, 427-438) may be used to estimate population sizes when there are few recaptures. Here, we extend the Chao (1989) closed population size estimator to the open population setting by using linear regression and extrapolation techniques. We conduct a small simulation study and apply the models to several sparse capture-recapture data sets.

Population Estimation Methods for Free-Ranging Dogs: A Systematic Review

The understanding of the structure of free-roaming dog populations is of extreme importance for the planning and monitoring of populational control strategies and animal welfare. The methods used to estimate the abundance of this group of dogs are more complex than the ones used with domiciled owned dogs. In this systematic review, we analyze the techniques and the results obtained in studies that seek to estimate the size of free-ranging dog populations. Twenty-six studies were reviewed regarding the quality of execution and their capacity to generate valid estimates. Seven of the eight publications that take a simple count of the animal population did not consider the different probabilities of animal detection; only one study used methods based on distances; twelve relied on capture-recapture models for closed populations without considering heterogeneities in capture probabilities; six studies applied their own methods with different potential and limitations. Potential sources of bias in the studies were related to the inadequate description or implementation of animal capturing or viewing procedures and to inadequacies in the identification and registration of dogs. Thus, there was a predominance of estimates with low validity. Abundance and density estimates carried high variability, and all studies identified a greater number of male dogs. We point to enhancements necessary for the implementation of future studies and to potential updates and revisions to the recommendations of the World Health Organization with respect to the estimation of free-ranging dog populations.

Spatial heterogeneity in response of male greater sage-grouse lek attendance to energy development

Landscape modification due to rapidly expanding energy development, in particular oil and gas, in the westernUSA, have prompted concerns over how such developments may impact wildlife. One species of conservation concern across much of the Intermountain West is the greater sage-grouse (Centrocercusurophasianus). Sage-grouse have been petitioned for listing under provisions of the Endangered Species Act 7 times and the state of Wyoming alone represents 64% of the extant sage-grouse population in the eastern portion of their range. Consequently, the relationship between sage-grouse populations and oil and gas development in Wyoming is an important component to managing the long-term viability of this species. We used 814 leks from the Wyoming Game and Fish Department's lek survey database and well pad data from the Wyoming Oil and Gas Conservation Commission to evaluate changes in sage-grouse lek counts as a function of oil and gas development since 1991.From 1991-2011 we found that oil and gas well-pad density increased 3.6-fold across the state and was associated with a 24% decline in the number of male sage-grouse. Using a spatial and temporally structured analysis via Geographically Weighted Regression, we found a 1-to-4 year time lag between development density and lek decline. Sage-grouse also responded to development densities at multiple spatial neighborhoods surrounding leks, including broad scales of 10 km. However, sage-grouse lek counts do not always decline as a result of oil and gas development. We found similar development densities resulting in different sage-grouse lek count responses, suggesting that development density alone is insufficient to predict the impacts that oil and gas development have on sage-grouse. Finally, our analysis suggests a maximum development density of 1 well-pad within 2 km of leks to avoid measurable impacts within 1 year, and <6 well-pads within 10 km of leks to avoid delayed impacts.

A simulation study of how simple mark-recapture methods can be combined with destructive subsampling to facilitate surveys of flying insects

Mark-recapture techniques are used for studies of animal populations. With only three sampling occasions, both Bailey's triple-catch (BTC) and Jolly-Seber's (J-S) stochastic method can be applied. As marking and handling of fragile organisms may harm them, and thereby affect their chances of being recaptured, handling should be minimized. This can be achieved by taking a subsample before the main sample at the second sampling occasion. Individuals in the main sample are marked and released, whereas those in the subsample are only used for identifying recaptures. Monte-Carlo simulation was used to compare the subsampling method with the ordinary mark-recapture methods. Model-generated populations were sampled with and without subsampling to provide estimates of population size, loss, and dilution rates. The estimated parameters were compared with their true values to identify biases associated with the sampling methods, using 81 different combinations of population size, dilution rate, loss rate, and sampling effort. Each combination was replicated 1,000 times. In no cases did subsampling perform more poorly than the ordinary methods. J-S was slightly more accurate than BTC to estimate the population size, but only when sampling effort was high. The relative biases associated with estimates of dilution and loss rates were substantial, but declined with increasing population size and sampling effort. Confidence limits for the population parameters generally were reliable and tended to be conservative. We therefore conclude that ordinary mark-recapture methods can be supplemented with subsampling without sacrificing accuracy. Subsampling is especially advantageous in cases where marks are difficult to observe under field conditions.

Modeling association among demographic parameters in analysis of open population capture-recapture data

We present a hierarchical extension of the Cormack-Jolly-Seber (CJS) model for open population capture-recapture data. In addition to recaptures of marked animals, we model first captures of animals and losses on capture. The parameter set includes capture probabilities, survival rates, and birth rates. The survival rates and birth rates are treated as a random sample from a bivariate distribution, thus the model explicitly incorporates correlation in these demographic rates. A key feature of the model is that the likelihood function, which includes a CJS model factor, is expressed entirely in terms of identifiable parameters; losses on capture can be factored out of the model. Since the computational complexity of classical likelihood methods is prohibitive, we use Markov chain Monte Carlo in a Bayesian analysis. We describe an efficient candidate-generation scheme for Metropolis-Hastings sampling of CJS models and extensions. The procedure is illustrated using mark-recapture data for the moth Gonodontis bidentata.

Survival of bowhead whales, Balaena mysticetus, estimated from 1981-1998 photoidentification data

Annual survival probability of bowhead whales, Balaena mysticetus, was estimated using both Bayesian and maximum likelihood implementations of Cormack and Jolly-Seber (JS) models for capture-recapture estimation in open populations and reduced-parameter generalizations of these models. Aerial photographs of naturally marked bowheads collected between 1981 and 1998 provided the data. The marked whales first photographed in a particular year provided the initial 'capture' and 'release' of those marked whales and photographs in subsequent years the 'recaptures'. The Cormack model, often called the Cormack-Jolly-Seber (CJS) model, and the program MARK were used to identify the model with a single survival and time-varying capture probabilities as the most appropriate for these data. When survival was constrained to be one or less, the maximum likelihood estimate computed by MARK was one, invalidating confidence interval computations based on the asymptotic standard error or profile likelihood. A Bayesian Markov chain Monte Carlo (MCMC) implementation of the model was used to produce a posterior distribution for annual survival. The corresponding reduced-parameter JS model was also fit via MCMC because it is the more appropriate of the two models for these photoidentification data. Because the CJS model ignores much of the information on capture probabilities provided by the data, its results are less precise and more sensitive to the prior distributions used than results from the JS model. With priors for annual survival and capture probabilities uniform from 0 to 1, the posterior mean for bowhead survival rate from the JS model is 0.984, and 95% of the posterior probability lies between 0.948 and 1. This high estimated survival rate is consistent with other bowhead life history data.