Dynamics of Hybridization and Introgression in Red Wolves and Coyotes

Abstract:  Hybridization and introgression are significant causes of endangerment in many taxa and are considered the greatest biological threats to the reintroduced population of red wolves ( Canis rufus ) in North Carolina (U.S.A.). Little is known, however, about these processes in red wolves and coyotes ( C. latrans ). We used individual-based simulations to examine the process of hybridization and introgression between these species. Under the range of circumstances we considered, red wolves in colonizing and established populations were quickly extirpated, persisted near the carrying capacity, or had intermediate outcomes. Sensitivity analyses suggested that the probabilities of quasi extinction and persistence of red wolves near the carrying capacity were most affected by the strength of two reproductive barriers: red wolf challenges and assortative mating between red wolves and coyotes. Because model parameters for these barriers may be difficult to estimate, we also sought to identify other predictors of red wolf population fate. The proportion of pure red wolves in the population was a strong predictor of the future probabilities of red wolf quasi extinction and persistence. Finally, we examined whether sterilization can be effective in minimizing introgression while allowing the reintroduced red wolf population to grow. Our results suggest sterilization can be an effective short-term strategy to reduce the likelihood of extirpation in colonizing populations of red wolves. Whether red wolf numbers are increased by sterilization depends on the level of sterilization effort and the acting reproductive barriers. Our results provide an outline of the conditions likely required for successful reestablishment and long-term maintenance of populations of wild red wolves in the presence of coyotes. Our modeling approach may prove generally useful in providing insight into situations involving complex species interactions when data are few.     

Demographic Viability of a Relict Population of the Critically Endangered Plant Borderea chouardii

Abstract:   In addition to human-caused changes in the environment, natural stochasticity may threaten species persistence, and its impact must be taken into account when priorities are established and management plans are designed. Borderea chouardii is a Tertiary relict at risk of extinction that occurs in only one location in the world, where the probability of human disturbance is low. Its persistence, therefore, is mainly linked to its response to natural threats such as stochasticity. Over 8 years I monitored up to 25% of this rupicolous small geophyte. The population had an unbalanced size structure and 90% failure in seed arrival at appropriate microhabitats, which suggests a problem with recruitment. I used matrix models to describe its population dynamics, conducted hand sowings, and performed stochastic simulations to investigate the effect of environmental stochasticity on population trend and viability. I modeled several scenarios to represent a variety of ecological situations, such as population reduction, episodic or persistent disease, and enhancement or decrease of recruitment. Population growth rate (λ) was never significantly different from unity over the study period. The risk of extinction was null over the next five centuries under current conditions. Increase of mortality and decrease of recruitment reduced stochastic population growth rate, but no factor except a persistent increase of 10% mortality resulted in extinction. These results are the consequence of the plant's extremely long life span (over 300 years) and low temporal variability of key vital rates. Even though hand sowing significantly increased the stochastic population growth rate, other approaches may be more important for the persistence of this species. The extremely slow capacity for recovery following disturbances renders habitat preservation essential. In addition, the founding of new populations would reduce the risk associated with habitat destruction.     

Catastrophic Reproductive Failure, Terrestrial Survival, and Persistence of the Marbled Salamander

Abstract:  Wide variation in reproductive success is common among amphibians that breed in seasonal ponds, but persistence of adults can buffer against these fluctuations, particularly for long-lived species. We hypothesized that the frequent episodes of catastrophic failure of the marbled salamander ( Ambystoma opacum ) enhance the importance of high terrestrial survival. At Rainbow Bay in South Carolina reproductive success was poor (<1 metamorph/breeding female) in nearly half of the 22 years that the species bred. Complete failure occurred in 6 of 22 years. To study catastrophic failure, we adapted an age-structured, individual-based model with density-dependent growth and survival of larvae. The model was based on extensive data from local field studies and experiments. With consistently good survival in the pond stages, the simulated population required survival probabilities in the upland stages (juveniles and adults) near 0.5/year to persist and near 0.8/year to achieve the increases observed. Catastrophic failure, occurring randomly with probability 0.5/year, created additional fluctuations in the population, raised the thresholds of survival required for persistence, and caused extinction under conditions that were otherwise favorable. The marbled salamander at Rainbow Bay is not at great risk of extinction because of catastrophic failure, but the risk increases dramatically if life span is decreased or frequency of failure is increased. Any reduction in terrestrial survival will have deleterious consequences by reducing the breeding populations at equilibrium, even if it does not jeopardize persistence. Our model provides assessments of risk that can be applied to poorly studied species with similar life histories, such as the endangered flatwoods salamander ( A. cingulatum ).     

Effects of Social Structure and Prey Dynamics on Extinction Risk in Gray Wolves

Extinction models based on diffusion theory generally fail to incorporate two important aspects of population biology—social structure and prey dynamics. We include these aspects in an individual-based extinction model for small, isolated populations of the gray wolf (Canis lupus). Our model predicts mean times to extinction significantly longer than those predicted by more general (diffusion) models. According to our model, an isolated population of 50 wolves has a 95% chance of surviving just 9 years and only a 30% chance of surviving beyond 100 years. Reflecting the influence of social structure, a wolf population initially comprising 50 individuals is expected to persist only a few years longer, on average (71 years), than is a population initially comprising just a single reproductive pair (62 years). In contrast, substantially greater average prey abundance leads to dramatically longer expected persistence times. Autocorrelated prey dynamics result in a more complex distribution of extinction times than predicted by many extinction models. We contend that demographic stochasticity may pose the greatest threat to small, isolated wolf populations, although environmental stochasticity and genetic effects may compound this threat. Our work highlights the importance of considering social structure and resource dynamics in the development of population viability analyses.     

Erosion of Heterozygosity in Fluctuating Populations

Abstract: Demographic, environmental, and genetic stochasticity threaten the persistence of isolated populations. The relative importance of these intertwining factors remains unresolved, but a common view is that random demographic and environmental events will usually drive small populations to the brink of extinction before genetic deterioration poses a serious threat. To evaluate the potential importance of genetic factors, we analyzed a model linking demographic and environmental conditions to the loss of genetic diversity in isolated populations undergoing natural levels of fluctuation. Nongenetic processes—environmental stochasticity and population demography—were modeled according to a bounded diffusion process. Genetic processes were modeled by quantifying the rate of drift according to the effective population size, which was predicted from the same parameters used to describe the nongenetic processes. We combined these models to predict the heterozygosity remaining at the time of extinction, as predicted by the nongenetic portion of the model. Our model predicts that many populations will lose most or all of their neutral genetic diversity before nongenetic random events lead to extinction. Given the abundant evidence for inbreeding depression and recent evidence for elevated extinction rates of inbred populations, our findings suggest that inbreeding may be a greater general threat to population persistence than is generally recognized. Therefore, conservation biologists should not ignore the genetic component of extinction risk when assessing species endangerment and developing recovery plans.     

Design and validation of a spatially explicit simulation model for bottomland hardwood forests

Species composition in forests depends on the interaction of species traits and species availability. Yet many forest simulation models focus only on interactions of adult trees and saplings, ignoring how species become members of the community. We modify a published forest model for bottomland hardwood forests (program SWAMP [Phipps, R.L., 1979. Simulation of wetlands forest vegetation dynamics. Ecol. Modell. 7, 257–288]) to make it spatially explicit and incorporate explicit seed production and dispersal algorithms. The resulting individual-based, spatially explicit forest simulator (YAFSIM) combines mechanistic seed dispersal with growth and mortality of trees to track forest dynamics over time. We describe the structure of the model and test its validity for dynamics in small bottomland hardwood patches in the Mississippi Alluvial Valley. Dynamics of species composition and basal areas of trees predicted by Yazoo Forest Simulator (YAFSIM) were similar to those of natural second- and old-growth bottomland forests. However, diversity of simulated forest patches declined over time largely because of random dynamics acting on small, isolated populations.     

Releasing Adults versus Young in Reintroductions: Interactions between Demography and Genetics

Abstract:  We integrated genetics and demography into population modeling in the context of species restorations, in which both the origin of released individuals and the management strategy may influence the success of introduction. Through an explicit individual-based simulation approach, we investigated the effects of the age of released individuals by exploring the relative merits of releasing juveniles or adults to establish populations. We included the effect of genetic variability responsible for inbreeding depression and mutational meltdown. Our general analysis uncovered an interaction between the age of founders and the extent of intrapopulation fitness variability, which substantially influenced the efficiency of selection in populations founded by juveniles and had subsequent positive consequences for long-term persistence compared with the case in which adults were released. We then applied the model to the case of the reintroduction of the Griffon Vulture ( Gyps fulvus fulvus ) to southern France, for which post-release data were available. The demographic aspects of this reintroduction were already analyzed and published, suggesting that it is more efficient to release adults than juveniles, despite an observed reduction of demographic parameters following the release of adults. In that context, the inclusion of genetic considerations qualitatively changes the conclusion, predicting reduced long-term extinction risk if juveniles rather than adults are released.     

Forecasting extinction risk with nonstationary matrix models.

Matrix population growth models are standard tools for forecasting population change and for managing rare species, but they are less useful for predicting extinction risk in the face of changing environmental conditions. Deterministic models provide point estimates of lambda, the finite rate of increase, as well as measures of matrix sensitivity and elasticity. Stationary matrix models can be used to estimate extinction risk in a variable environment, but they assume that the matrix elements are randomly sampled from a stationary (i.e., non-changing) distribution. Here we outline a method for using nonstationary matrix models to construct realistic forecasts of population fluctuation in changing environments. Our method requires three pieces of data: (1) field estimates of transition matrix elements, (2) experimental data on the demographic responses of populations to altered environmental conditions, and (3) forecasting data on environmental drivers. These three pieces of data are combined to generate a series of sequential transition matrices that emulate a pattern of long-term change in environmental drivers. Realistic estimates of population persistence and extinction risk can be derived from stochastic permutations of such a model. We illustrate the steps of this analysis with data from two populations of Sarracenia purpurea growing in northern New England. Sarracenia purpurea is a perennial carnivorous plant that is potentially at risk of local extinction because of increased nitrogen deposition. Long-term monitoring records or models of environmental change can be used to generate time series of driver variables under different scenarios of changing environments. Both manipulative and natural experiments can be used to construct a linking function that describes how matrix parameters change as a function of the environmental driver. This synthetic modeling approach provides quantitative estimates of extinction probability that have an explicit mechanistic basis.     

Analysis of neighborhood dynamics of forest ecosystems using likelihood methods and modeling.

Advances in computing power in the past 20 years have led to a proliferation of spatially explicit, individual-based models of population and ecosystem dynamics. In forest ecosystems, the individual-based models encapsulate an emerging theory of "neighborhood" dynamics, in which fine-scale spatial interactions regulate the demography of component tree species. The spatial distribution of component species, in turn, regulates spatial variation in a whole host of community and ecosystem properties, with subsequent feedbacks on component species. The development of these models has been facilitated by development of new methods of analysis of field data, in which critical demographic rates and ecosystem processes are analyzed in terms of the spatial distributions of neighboring trees and physical environmental factors. The analyses are based on likelihood methods and information theory, and they allow a tight linkage between the models and explicit parameterization of the models from field data. Maximum likelihood methods have a long history of use for point and interval estimation in statistics. In contrast, likelihood principles have only more gradually emerged in ecology as the foundation for an alternative to traditional hypothesis testing. The alternative framework stresses the process of identifying and selecting among competing models, or in the simplest case, among competing point estimates of a parameter of a model. There are four general steps involved in a likelihood analysis: (1) model specification, (2) parameter estimation using maximum likelihood methods, (3) model comparison, and (4) model evaluation. Our goal in this paper is to review recent developments in the use of likelihood methods and modeling for the analysis of neighborhood processes in forest ecosystems. We will focus on a single class of processes, seed dispersal and seedling dispersion, because recent papers provide compelling evidence of the potential power of the approach, and illustrate some of the statistical challenges in applying the methods.     

Comparison of Two Types of Metapopulation Models in Real and Artificial Landscapes

Abstract: Application of metapopulation models is becoming increasingly widespread in the conservation of species in fragmented landscapes. We provide one of the first detailed comparisons of two of the most common modeling techniques, incidence function models and stage-based matrix models, and test their accuracy in predicting patch occupancy for a real metapopulation. We measured patch occupancies and demographic rates for regional populations of the Florida scrub lizard (   Sceloporus woodi ) and compared the observed occupancies with those predicted by each model. Both modeling strategies predicted patch occupancies with good accuracy ( 77–80%) and gave similar results when we compared hypothetical management scenarios involving removal of key habitat patches and degradation of habitat quality. To compare the two modeling approaches over a broader set of conditions, we simulated metapopulation dynamics for 150 artificial landscapes composed of equal-sized patches (2–1024 ha) spaced at equal distances (50–750 m). Differences in predicted patch occupancy were small to moderate (<20%) for about 74% of all simulations, but 22% of the landscapes had differences openface> 50%. Incidence function models and stage-based matrix models differ in their approaches, assumptions, and requirements for empirical data, and our findings provide evidence that the two models can produce different results. We encourage researchers to use both techniques and further examine potential differences in model output. The feasibility of obtaining data for population modeling varies widely among species and limits the modeling approaches appropriate for each species. Understanding different modeling approaches will become increasingly important as conservation programs undertake the challenge of managing for multiple species in a landscape context.     

Local extinction of grassland plants: the landscape matrix is more important than patch attributes

Past studies of local extinctions in fragmented habitats most often tested the influence of fragment size and isolation while ignoring how differences in the surrounding landscape matrix may govern extinction. We assessed how both the spatial attributes of remnant patches (area and isolation) and landscape factors (extent of urbanization and maximum inter-fire interval) influence the persistence of native plant species in grasslands in western Victoria, Australia. Persistence was determined in 2001 by resurveying 30 remnants first surveyed in the 1980s, and correlates of extinction were assessed using Bayesian logistic regression models. On average, 26% of populations of native species became locally extinct over two decades. Area and isolation had little effect on the probability of local extinction, but urbanization and longer maximum inter-fire intervals increased extinction risk. These findings suggest that the native grasslands studied are relatively insensitive to area- and isolation-based fragmentation effects and that short-term persistence of plant populations requires the maintenance of habitat quality. The latter is strongly influenced by the landscape matrix surrounding remnant patches through changes in fire regimes and increased exogenous disturbance.     

The control of emigration and its consequences for the survival of populations

Dispersal is the key process enhancing the long-term persistence of metapopulations in heterogeneous and dynamic landscapes. However, any individual emigrating from a occupied patch also increases the risk of local population extinction. The consequences of this increase for metapopulation persistence likely depend on the control of emigration. In this paper, we present results of individual-based simulations to compare the consequences of density-independent (DIE) and density-dependent (DDE) emigration on the extinction risk of local populations and a two-patch metapopulation. (1) For completely isolated patches extinction risk increases linearly with realised emigration rates in the DIE scenario. (2) For the DDE scenario extinction risk is nearly insensitive to emigration as longs as emigration probabilities remain below ≈0.2. Survival chances are up to half an order of magnitude larger than for populations with DIE. (3) For low dispersal mortality both modes of emigration increase survival of a metapopulation by ca. one order of magnitude. (4) For high dispersal mortality only DDE can improve the global survival chances of the metapopulation. (5) With DDE individuals are only removed from a population at high population density and the risk of extinction due to demographic stochasticity is thus much smaller compared to the DIE scenario.With density-dependent emigration prospects of metapopulations survival may thus be much higher compared to a system with density-independent emigration. Consequently, the knowledge about the factors driving emigration may significantly affect our conclusions concerning the conservation status of species.     

Inferring Metapopulation Dynamics from Patch-Level Incidence of Florida Scrub Plants

Spatial structure and dynamics of multiple populations may explain species distribution patterns in patchy communities with heterogeneous disturbance regimes, especially when species have poor dispersal. The endemic-rich Florida (U.S.A.) rosemary scrub occupies about 4% of the west portion of Archbold Biological Station and occurs scattered within a matrix of less xeric vegetation. Longer fire-return times and higher frequency of open patches in rosemary scrub provide favorable habitat for many plant species. Occupancy of 123 species of vascular plants and ground lichens in 89 patches was determined by repeated site surveys. About two-thirds of the species occurring at more than 14 patches had a significant logistic regression of presence on time-since-fire, patch size, patch isolation, or their interactions. Species with presence related to the interaction between patch isolation and patch size were primarily herbs and small shrubs specializing in rosemary scrub. These results suggest the importance of spatial characteristics of the landscape for population turnover of these species. An incidence-based metapopulation model was used to predict extinction and colonization probabilities of those species with presence in rosemary scrub patches related to the studied spatial variables. This is the first attempt to apply incidence-based metapopulation models to plants. The results showed stronger effects of patch size and patch isolation on extinction probabilities of herbs than on those of woody species. Because of their effect on spatial heterogeneity and habitat availability, fire suppression and habitat destruction may decrease persistence probabilities for these rosemary scrub specialists, many of which are endangered species.     

Predicting how defaunation-induced changes in seed predation and dispersal will affect tropical tree populations

The loss of large animals due to overhunting and habitat loss potentially affects tropical tree populations and carbon cycling. Trees reliant on large-bodied seed dispersers are thought to be particularly negatively affected by defaunation. But besides seed dispersal, defaunation can also increase or decrease seed predation. It remains unclear how these different defaunation effects on early life stages ultimately affect tree population dynamics. We reviewed the literature on how tropical animal loss affects different plant life stages, and we conducted a meta-analysis of how defaunation affects seed predation. We used this information to parameterize models that altered matrix projection models from a suite of tree species to simulate defaunation-caused changes in seed dispersal and predation. We assessed how applying these defaunation effects affected population growth rates. On average, population-level effects of defaunation were negligible, suggesting that defaunation may not cause the massive reductions in forest carbon storage that have been predicted. In contrast to previous hypotheses, we did not detect an effect of seed size on changes in seed predation rates. The change in seed predation did not differ significantly between exclosure experiments and observational studies, although the results of observational studies were far more variable. Although defaunation surely affects certain tree taxa, species that benefit or are harmed by it and net changes in forest carbon storage cannot currently be predicted based on available data. Further research on how factors such as seed predation vary across tree species and defaunation scenarios is necessary for understanding cascading changes in species composition and diversity.     

On the elasticity of range limits during periods of expansion

Dispersal is known to play a crucial role in the formation of species' ranges. Recent studies demonstrate that dispersiveness increases rapidly during the range expansion of species due to a fitness increase for dispersers at the expanding front. R. D. Holt concluded, however, that emigration should decline after the period of invasion and hence predicted some range contraction following the initial expansion phase. In this study, we evaluate this hypothesis using a spatially explicit individual-based model of populations distributed along environmental gradients. In our experiments we allow the species to spread along a gradient of declining conditions. Results show that range contraction did emerge in a gradient of dispersal mortality, caused by the rapid increase in emigration probability during invasion and selection disfavoring dispersal, once a stable range is formed. However, gradients in growth rate, local extinction rate, and patch capacity did not lead to a noticeable contraction of the range. We conclude, that the phenomenon of range contraction may emerge, but only under conditions that select for a reduction in dispersal at the range edge in comparison to the core region once the expansion period is over.     

Fitting probability models to population dynamics data

Methods for modeling population dynamics in probability using the generalized point process approach are developed. The life history of these populations is such that seasonal reproduction occurs during a short time. Several models are developed and analyzed. Data about two species: colonial spiders (Stegodyphus dumicola) and a migratory bird (wood thrush, Hylocichla mustelina) are used to estimate model parameters with appropriate log maximum likelihood functions. For the spiders, the model is fitted to provide evolutionary feasible colony size based on maximum likelihood estimates of fecundity and survival data. For the migratory bird species, a maximum likelihood estimates are derived for the fecundity and survival rates of young and adult birds and immigration rate. The presented approach allows computation of quantities of interest such as probability of extinction and average time to extinction.     

Colonization and extinction in dynamic habitats: an occupancy approach for a Great Plains stream fish assemblage

Despite the importance of habitat in determining species distribution and persistence, habitat dynamics are rarely modeled in studies of metapopulations. We used an integrated habitat-occupancy model to simultaneously quantify habitat change, site fidelity, and local colonization and extinction rates for larvae of a suite of Great Plains stream fishes in the Arikaree River, eastern Colorado, USA, across three years. Sites were located along a gradient of flow intermittency and groundwater connectivity. Hydrology varied across years: the first and third being relatively wet and the second dry. Despite hydrologic variation, our results indicated that site suitability was random from one year to the next. Occupancy probabilities were also independent of previous habitat and occupancy state for most species, indicating little site fidelity. Climate and groundwater connectivity were important drivers of local extinction and colonization, but the importance of groundwater differed between periods. Across species, site extinction probabilities were highest during the transition from wet to dry conditions (range: 0.52-0.98), and the effect of groundwater was apparent with higher extinction probabilities for sites not fed by groundwater. Colonization probabilities during this period were relatively low for both previously dry sites (range: 0.02-0.38) and previously wet sites (range: 0.02-0.43). In contrast, no sites dried or remained dry during the transition from dry to wet conditions, yielding lower but still substantial extinction probabilities (range: 0.16-0.63) and higher colonization probabilities (range: 0.06-0.86), with little difference among sites with and without groundwater. This approach of jointly modeling both habitat change and species occupancy will likely be useful to incorporate effects of dynamic habitat on metapopulation processes and to better inform appropriate conservation actions.     

What stops the ‘diploid male vortex’?—A simulation study for species with single locus complementary sex determination

The survival of hymenopteran populations especially that of ecologically and economically important pollinators and parasitoids, has become a major topic for empirical and theoretical studies. Complementary sex determination (CSD) in Hymenoptera may impose a substantial genetic load through the production of inviable or sterile diploid males. Modelling and laboratory studies have indicated that this genetic load may trigger a ‘diploid male vortex’ leading to rapid extinction of populations.Here we take a broader theoretical approach to analyze why populations exhibiting CSD persist in nature, even if they contain large proportions of homozygous diploid individuals. Using an individual-based model of spatially structured hymenopteran populations, we show that (i) inviability or reduced fertility of homozygous individuals, (ii) female-biased sex ratio, and (iii) strong intra-specific competition can mitigate the negative influence of CSD on population persistence and that (iv) already extremely low dispersal rates will result in long term survival. These findings underline the importance of life history traits for population survival and demonstrate that rather specific conditions must be met to initiate the ‘diploid male vortex’.     

Correlations among Extinction Risks Assessed by Different Systems of Threatened Species Categorization

Abstract:  Many different systems are used to assess levels of threat faced by species. Prominent ones are those used by the World Conservation Union, NatureServe, and the Florida Game and Freshwater Fish Commission (now the Florida Fish and Wildlife Conservation Commission). These systems assign taxa a threat ranking by assessing their demographic and ecological characteristics. These threat rankings support the legislative protection of species and guide the placement of conservation programs in order of priority. It is not known, however, whether these assessment systems rank species in a similar order. To resolve this issue, we assessed 55 mainly vertebrate taxa with widely differing life histories under each of these systems and determined the rank correlations among them. Moderate, significant positive correlations were seen among the threat rankings provided by the three systems (correlations 0.58–0.69). Further, the threat rankings for taxa obtained using these systems were significantly correlated to their rankings based on predicted probability of extinction within 100 years as determined by population viability analysis (correlations 0.28–0.37). The different categorization systems, then, yield related but not identical threat rankings, and these rankings are associated with predicted extinction risk.     

Utility of Measuring Abundance versus Consistent Occupancy in Predicting Biodiversity Persistence

Abstract:  The primary goals of reserve selection are to represent all chosen units of biodiversity and to ensure their long-term persistence while minimizing costs. We considered two simple proxies of species persistence: a time series of point-count data to calculate abundance and a time series of presence–absence data to calculate permanence (a measure of consistent occupancy over time). Using two 10-year intervals of data from the North American Breeding Bird Survey, we compared the performance of each measure at predicting persistence 18 years later. For nonrare species, abundance and permanence predicted persistence similarly well. We performed complementarity-based reserve selections with data on species abundance and permanence (from 1970 to 1979) and then evaluated the effectiveness of the reserve networks at maintaining species populations and efficiency in land use (data from 1997 to 2006). Abundance proved a better predictor of future local persistence than permanence, which justifies the relatively larger financial and temporal costs of collecting a time series of point-count data to estimate abundance. If future extinction events were used as a measure of reserve-network effectiveness, the performance of abundance and permanence did not differ markedly. Nevertheless, when future abundance, which is a more sensitive measure of network effectiveness, was used, abundance was significantly better than permanence at selecting longer-term, high-quality, species-specific habitat but required larger reserves to do so .