A nonparametric lower bound for the number of species shared by multiple communities

In biological and ecological statistical inference, it is practically useful to provide a lower bound for species richness in a community. Chao (1984, 1989) derived a non-parametric lower bound for species richness in a single community. However, there have been no lower bounds proposed in the literature for the number of species shared by multiple communities. Based on sample species abundance or replicated incidence records from each of the N communities, we derive in this article a nonparametric approach to constructing a lower bound for the number of species shared by N (N≥2) communities. The approach is valid for all types of species abundance distributions (for abundance data) or species detection probabilities (for replicated incidence data). Variance estimators for the proposed lower bounds are obtained by using typical asymptotic theory. Simulation results are reported to examine the performance of the lower bounds. Replicated incidence data of ciliate species collected in three areas from Namibia, southwest Africa, are used for illustration. We also briefly discuss the application of the proposed method to estimate the size of a shared population (i.e., the number of individuals in the intersection of multiple populations) based on capture-recapture data from each population.     

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 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 conservation and fishery benefits of protecting large pike (Esox lucius L.) by harvest regulations in recreational fishing

Traditional fisheries management theory supports aggressive exploitation of old and large fish to maximize a stock’s biomass production and yield. Here we present an age-structured fish population model with multidimensional density-dependence to test the hypotheses that protection of large, fecund individuals is beneficial for the population and selected fisheries variables and that effects of maternal size on early survival rate change the resilience and fisheries productivity of a pike population (Esox lucius L.) exploited by recreational angling. We find that, compared to the traditional regulatory approach of management by small minimum-length limits (so that culling of large fish is encouraged), preservation of large and old individuals through harvestable-slot length limits promises considerable benefits for fisheries quality, without compromising the long-term conservation of the population. We also find that ignoring maternal effects on early survival of offspring might overestimate the equilibrium spawning stock abundance by up to 17% and the predicted harvest by up to 11%, potentially putting pike populations at risk from overharvest if size-dependent maternal effects are ignored in fisheries models. If the findings from our simulation study hold for empirical systems, they suggest altered harvest regulations in many of consumptive pike recreational fisheries are needed to protect large individuals to a greater extent that currently pursued.     

Capture-Recapture Smooth Estimation of Age-Specific Survival Probabilities in Animal Populations

Yielding sound estimates of survival according to age in wild populations where senescence or other age-related variations may occur is very important to management decision makers, and remains challenging. This paper proposes to use penalized maximum likelihood to obtain smooth estimates of annual survival probabilities across age in populations of wild animals followed by capture–recapture. We propose to use two different types of smoothing penalties, and we use ν-fold cross-validation to select the best value of the tuning parameter for the intensity of smoothing. We then assess the accuracy of the method by a simulation study with two different shapes of the relationship between age and survival, and we conclude that a careful use of this method provides reliable noise-free estimates of age-specific annual survival. We apply this procedure to the motivating data from a population of roe deer known to exhibit a marked decrease of survival with age, and we compare our results with those previously published on this population.     

Extension of landscape-based population viability models to ecoregional scales for conservation planning

Landscape-based population models are potentially valuable tools in facilitating conservation planning and actions at large scales. However, such models have rarely been applied at ecoregional scales. We extended landscape-based population models to ecoregional scales for three species of concern in the Central Hardwoods Bird Conservation Region and compared model projections against long-term trend data from the North American Breeding Bird Survey. We used a spatially-explicit demographic model and structured the regional population into ecological subsections on the basis of habitat, landscape patterns, and demographic rates to assess species viability. Our model projections were within 2% of the Breeding Bird Survey trends over the last 40 years for each species. Wood thrush (Hylocichla mustelina) populations remained relatively stable over the simulation and worm-eating warbler (Helmitheros vermivorus) abundance increased throughout most of the time period until reaching carrying capacity. In contrast, the prairie warbler (Dendroica discolor) population steadily declined by 0.59% annually. The combination of habitat and demographic modeling allowed us to create models that address processes driving these populations at all scales, which is critical to understanding how regional populations respond to landscape processes such as habitat loss and fragmentation. Therefore, because it is spatially explicit and directly addresses population growth and viability, this approach provides a valuable foundation to planning conservation strategies, offering the ability to identify the most salient risks to viability and explore ways to address them.     

Persistence of a rare ancient cycad: Effects of environment and demography

Conservation of rare species is frequently complicated by their narrow niches and poor competitive abilities which limit their distribution to a few small populations. We studied how population size and structure of an endemic cycad of northwestern Mexico, Dioon sonorense, known to be threatened by widespread land conversion and plant extraction by humans, varied with 21 environmental variables. We also used matrix population models to show how population structure may affect its long-term persistence. Slope and soil exchangeable potassium explained a moderate proportion of the variance in the abundance of adult individuals, while abundance of adults and slope explained a large proportion of the variance in the abundance of seedlings. The strong non-linear relationships of seedling abundance with slope and adult abundance suggest threshold effects that may limit D. sonorense regeneration in less suitable environments. Modeling suggests that most of the study populations will not be viable in the long-term, except for the largest population. Modeling scenarios with large increments in fecundity and seedling survival produced modest gains in population growth. The long-term persistence of D. sonorense is shown in our study to be further threatened by: (a) small size of adult populations, (b) low-quality habitat in which most populations occur, and potentially, (c) the combined effect of low fecundity and recruitment.     

A conservation framework for the golden eagle in Scotland: Refining condition targets and assessment of constraint influences

Conservation strategies have three elements: species protection, site protection and, the most challenging component, conservation in the wider environment. Watson and Whitfield [Watson, J., Whitfield, P., 2002. A conservation framework for the golden eagle Aquila chrysaetos in Scotland. Journal of Raptor Research 36(1 Suppl.), 41-49.] proposed a conservation framework for the golden eagle in Scotland whose main innovation, taking a lead from EU conservation Directives, was to incorporate the concept of favourable condition and its maintenance by implementing conservation policies that are regionally targeted at known constraints in the wider environment. Three criteria were suggested to judge favourable condition: a national abundance target of breeding pairs, national and regional targets for breeding productivity, and regional targets for the extent of suitable habitat which is occupied by breeding pairs. Here we refine these criteria, first to take the national abundance target and use it to set regional targets. Distribution targets were implicitly incorporated by this process because abundance targets were set regionally, with regard to the proportion of known territories which should be occupied. This allowed us to dispense with the distribution criterion as originally proposed. Our next refinement was to base regional demographic targets not only on breeding productivity, but also on indirect measures of survival (which are likely to have more influence on population dynamics). Despite apparent overall population stability over the last 20 years, the national golden eagle population failed to meet the abundance target and only 3 of 16 regions where eagles have occupied territories since 1982 were considered to be in favourable condition. The key constraint preventing favourable condition being met was persecution, predominantly in some areas managed for grouse shooting. The advantages of a conservation framework over similar approaches, such as species action plans, are highlighted.     

Can supplemental food increase winter survival of a threatened cottontail rabbit?

Populations of New England cottontails (Sylvilagus transitionalis) have declined substantially in recent decades in response to habitat loss and fragmentation. Among some remnant populations, cottontails occupy small patches of thicket habitat where they experience high mortality rates as a consequence of limited food during winter. This limitation causes rabbits to forage away from cover where they are exposed to predators. Although conservation efforts are emerging to reverse the decline of New England cottontails, most are directed toward improving long-term viability by increasing the abundance of suitable habitats. Such efforts do little to improve the short-term survival of remaining cottontails. To address this immediate need, we evaluated the use of supplemental food as an approach to improve overwinter survival rates. We speculated that by positioning feeders in close proximity to escape cover, rabbits would be less vulnerable to predators. We evaluated this approach using eastern cottontails (Sylvilagus floridanus) as a research surrogate because this species is readily available and has similar habitat requirements to New England cottontails. Transmitter-equipped eastern cottontails were randomly assigned to either a fed or unfed group. Remotely-triggered cameras were also used to gauge use of feeders by cottontails and visits by other species. Winter survival rates were substantially greater for fed rabbits (70%) than for unfed rabbits (32%). Cameras revealed that rabbits were the most frequent consumer and that there was only limited carnivore activity near feeders. We conclude that supplemental feeding may improve survival of remaining New England cottontails as efforts to increase habitat availability continue to develop.     

Assessing the effectiveness of conservation measures: Resolving the “wicked” problem of the Steller sea lion

“Wicked” problems are those that are complex and that change when solutions are applied. Many conflicts in conservation fall into this category. The study approached the problem of how to constrain the apparent wickedness of a problem in the conservation management of a species by using simple empirical indicators to carry out iterative assessment of the risk to a population and to document how this risk evolves in relation to the addition of new data and the implementation of management actions. Effects of high levels of uncertainty within data and also concerning population structure were examined through stochastic simulation and by exploration of scenarios. Historical trends in the example used, the Steller sea lion, showed rapid declines in abundance in some regions during the 1980s. The current total population is 130,000-150,000 Steller sea lions through Alaska and British Columbia and this number has been stable since about 1990 in spite of regional differences in population dynamics. Regional differences in the sequence of changes in the number of pups and non-pups, suggested that an internal re-distribution of juveniles could have happened between 1980 and 1990. Current productivity also appears close to the long-term mean. Stochastic population projection using various scenarios showed that, based upon this history, the risk of extinction for the population has declined and is below reasonable thresholds for considering the population to be endangered. The trends in risk suggest that management actions taken since 1990 have probably been effective. Consequently, the conservation management objectives for the Steller sea lion are probably being met. The approach provides a mechanism, based upon experience and scenario analysis, for exploring future policy options and may help to constrain the debate amongst stakeholders about the cost-benefit trade-offs associated with different options.     

Differences in the reproductive success and survival of the rufous treecreeper (Climacteris rufa) between a fragmented and unfragmented landscape

The rufous treecreeper (Climacteris rufa) has declined in abundance in the agricultural regions of southwestern Australia. The patterns of decline are well documented, but the processes that threaten population persistence are poorly understood. I compared the reproductive success and survival of the treecreeper between three sites in an unfragmented landscape and four remnant categories (large, small, grazed and ungrazed) in a fragmented, agricultural landscape. Nest success and annual productivity were significantly higher in the unfragmented landscape, but varied between sites and remnant categories within landscapes. Nest success was lowest in grazed remnants and annual productivity was positively associated with territory size in the fragmented landscape. Fledgling survival rates did not differ between landscapes, but there was a trend for juvenile survival rates to be higher in the unfragmented landscape. I used artificial nests to compare relative predation rates between landscapes, and provisioning rates and prey biomass brought to nestlings to assess differences in food availability. There were no landscape differences in predation rates, but provisioning rates to nestlings and total prey biomass were significantly lower in the fragmented landscape. Mean habitat quality was also lower in the fragmented landscape, although it differed between remnant categories. Reduced reproductive success, juvenile survival, food availability and habitat quality may threaten the viability of the rufous treecreeper population living in the fragmented landscape. Limiting the modification of remaining habitat (e.g. removing stock grazing) and improving habitat quality are required to assist in the conservation of this species.     

Changes in the Abundance of Vascular Plants under the Impact of Industrial Air Pollution: A Meta-analysis

We applied a meta-analytic approach to improve an understanding of the effects of pollution on the primary productivity of terrestrial ecosystems. We identified 73 data sources reporting changes in the abundance of vascular plants (measured as the percentage of ground cover, biomass per unit area, canopy closure and stem basal area) around 75 polluters located in 18 countries (137 effect sizes). The overall effect was negative but varied among the vegetation layers and types of polluters. The strongest detrimental impact on productivity was due to non-ferrous smelters. The abundance of trees was decreased around both acidifying and alkalifying polluters, whereas the abundance of shrubs and field-layer vegetation decreased only near acidifying polluters. Overall, a decline of vegetation was observed in boreal and temperate forests but not in treeless biomes (deserts, tundra or grasslands). The magnitude of the detrimental effects on trees increased with the duration of the polluters?? impact around acidifying polluters but decreased around alkalifying polluters. Adverse effects on the field layer became more severe with increasing community productivity; in combination with the conclusions of previous meta-analyses, this result indicates that diverse and highly productive communities are likely to be the most susceptible to pollution impacts. In general, the pollution effects on the abundance of vascular plants were less detrimental than the effects on their growth and diversity, indicating that primary productivity in polluted ecosystems is maintained by the preferential growth of several pollution-tolerant species.     

A Threshold Model for Heron Productivity

We demonstrate the potential of conditionally Gaussian state-space models in integrated population modeling, when certain model parameters may be functions of previous observations. The approach is applied to a heron census, and the data are best described by a model with three population-size thresholds which determine the population productivity. The model provides an explanation of how the population rebounds rapidly after major falls in size, which are characteristic of the data. By contrast, a simple logarithmic regression of productivity on population size was not significant. The results are of ecological interest, and suggest hypotheses for further investigation. Supplementary figures are available online.     

Effects of organic matter removal, soil compaction, and vegetation control on Collembolan populations

Collembola can be among the most numerous meso-invertebrates in the forest floor and, through their interaction with primary decomposers in the decomposition food web, may affect litter decomposition and consequently site productivity. This study was conducted to determine whether Collembolan abundance could be impacted by organic matter removal, compaction, and vegetation control on a loblolly pine (Pinus taeda L.) plantation. Monthly soil and litter samples were taken over 2 years and the fauna extracted from them using modified Tulgren funnels. Organic matter removal and vegetation control generally caused a significant decrease in Collembolan populations, while compaction did not significantly affect Collembolan populations. These results indicate that habitat was the primary influence on population abundance in this experiment, possibly via its influence on desiccation. Sensitivity of collembolan populations to habitat changes caused by organic matter removal indicates a potential effect on long-term site productivity.     

Population Estimates From Aerial Photographic Surveys of Naturally and Variably Marked Bowhead Whales

Abundance, mortality, and population growth of bowhead whales (Balaena mysticetus) are estimated from captures of 4,894 putatively different individuals obtained from 10 years of systematic photographic surveys conducted during the spring migration when most of the Bering–Chukchi–Beaufort population of bowheads migrates past Point Barrow, Alaska. A stringent matching protocol designed to prevent false positive matches of the naturally, but variably marked individuals, led to 42 resightings between years. The flip side of this stringency is a presence of false negatives, i.e., some true recaptures are not recognized as such. The problem of false negatives is addressed by modeling the capture process and the matching process. The captures of an individual are assumed to follow a Poisson process with intensity depending stochastically on the individual whale and on the year. The probability of successfully matching a capture to a previous capture is estimated by logistic regression on the degree of marking and image quality. Individuals are recruited by the Pella–Tomlinson population model, and their mortality rate is assumed to be constant. The point estimate of yearly growth rate is 3.2%, and bowhead abundance in 2001 is estimated to be 8,250, similar to previous estimates.     

Confidence intervals for expected abundance of rare species

In many ecological research studies, abundance data are skewed and contain more zeros than might be expected. Often, the aim is to model abundance in terms of covariates, and to estimate expected abundance for a given set of covariate values. An approach that has been advocated recently involves the use of a conditional model. This allows one to separately model presence and abundance given presence, which should lead to a more complete understanding as to how the covariates influence abundance. The focus of this article is on the calculation of confidence intervals for expected abundance given particular values of the covariates. The standard Wald confidence interval is symmetric, and therefore unlikely to be of much use for skewed data, where reliable confidence intervals for abundance will generally be asymmetric. The purpose of this article is to show how to calculate a profile likelihood confidence interval for expected abundance using a conditional model.     

Analyzing designed experiments in distance sampling

Distance sampling is a survey technique for estimating the abundance or density of wild animal populations. Detection probabilities of animals inherently differ by species, age class, habitats, or sex. By incorporating the change in an observer’s ability to detect a particular class of animals as a function of distance, distance sampling leads to density estimates that are comparable across different species, ages, habitats, sexes, and so on. Increasing interest in evaluating the effects of management practices on animal populations in an experimental context has led to a need for suitable methods of analyzing distance sampling data. We outline a two-stage approach for analyzing distance sampling data from designed experiments, in which a two-step bootstrap is used to quantify precision and identify treatment effects. We illustrate this approach using data from a before—after control-impact experiment designed to assess the effects of large-scale prescribed fire treatments on bird densities in ponderosa pine forests of the southwestern United States.     

Climate change is linked to long-term decline in a stream salamander

Amphibian declines have been documented worldwide and several have been linked to climate change, but the long-term data needed to detect declines are largely restricted to pond-breeding species. This limits our knowledge of population trends in other major groups of amphibians, including stream salamanders, which have their greatest diversity in North America. I hypothesized that increasing air temperature and precipitation in northeastern North America caused abundance of the stream salamander Gyrinophilus porphyriticus in a New Hampshire population to decline between 1999 and 2010. I found a significant decline in abundance of G. porphyriticus adults over this 12-year period, and no trend in larval abundance. Adult abundance was negatively related to annual precipitation, which is predicted to increase further in the Northeast due to climate change. Analysis of a 6-year capture–mark–recapture data set for the same population showed no temporal variation in larval and adult detectability, validating the abundance data, and no variation in larval and adult survival. However, survival during metamorphosis from the larval to adult stage declined dramatically. These results suggest that increasing precipitation is causing a decline in adult recruitment, which, if it persists, will lead to local extinction. A likely mechanism for the decline in adult recruitment is mortality of metamorphosing individuals during spring and fall floods, which have increased in volume and frequency with the increase in precipitation. More broadly, this study presents strong evidence that the amphibian decline crisis extends to North America’s stream salamanders, and shows the critical need to collect population data on these species.     

Increase of a Caribbean leatherback turtle Dermochelys coriacea nesting population linked to long-term nest protection

The leatherback turtle Dermochelys coriacea is considered to be at serious risk of global extinction, despite ongoing conservation efforts. Intensive long-term monitoring of a leatherback nesting population on Sandy Point (St. Croix, US Virgin Islands) offers a unique opportunity to quantify basic population parameters and evaluate effectiveness of nesting beach conservation practices. We report a significant increase in the number of females nesting annually from ca. 18-30 in the 1980s to 186 in 2001, with a corresponding increase in annual hatchling production from ca. 2000 to over 49,000. We then analyzed resighting data from 1991 to 2001 with an open robust-design capture-mark-recapture model to estimate annual nester survival and adult abundance for this population. The expected annual survival probability was estimated at ca. 0.893 (95% CI: 0.87-0.92) and the population was estimated to be increasing ca. 13% pa since the early 1990s. Taken together with DNA fingerprinting that identify mother-daughter relations, our findings suggest that the increase in the size of the nesting population since 1991 was probably due to an aggressive program of beach protection and egg relocation initiated more than 20 years ago. Beach protection and egg relocation provide a simple and effective conservation strategy for this Northern Caribbean nesting population as long as adult survival at sea remains relatively high.     

Modelling the population dynamics of the Mt. Graham red squirrel: Can we predict its future in a changing environment with multiple threats?

The Mt. Graham red squirrel (Tamiasciurus hudsonicus grahamensis; MGRS) is among the most critically endangered mammals in the United States and is isolated on the periphery of the species’ range, potentially increasing its conservation priority. To investigate potential threats to the population and provide a tool for land managers, we developed a spatially explicit population dynamics model. We tested model predictions using available range-wide data from the literature and field work specific to the MGRS. A general model input data set using mean life history values overpredicted MGRS abundance. However, we found significant correlation with known squirrel abundance using a general data set with curtailed fecundity and survival. A model with MGRS-specific data provided the best fit to observed population size. We investigated potential impacts of two major threats to the MGRS: competition from introduced Abert’s squirrels (Sciurus aberti) and increased levels of predation. Predation and particularly competition could have significant effects on the future population of the MGRS. Careful attention must be used to model the viability of fringe populations as peripheral populations can have a different life history than populations found in the range core.