Predicting Patch Occupancy Research Articles

Predicting patch occupancy reveals the complexity of host range expansion.

Specialized plant-insect interactions are a defining feature of life on earth, yet we are only beginning to understand the factors that set limits on host ranges in herbivorous insects. To better understand the recent adoption of alfalfa as a host plant by the Melissa blue butterfly, we quantified arthropod assemblages and plant metabolites across a wide geographic region while controlling for climate and dispersal inferred from population genomic variation. The presence of the butterfly is successfully predicted by direct and indirect effects of plant traits and interactions with other species. Results are consistent with the predictions of a theoretical model of parasite host range in which specialization is an epiphenomenon of the many barriers to be overcome rather than a consequence of trade-offs in developmental physiology.

Functional connectivity as an indicator for patch occupancy in grassland specialists

Habitat specialists living in metapopulations are sensitive to habitat fragmentation. In most studies, the effects of fragmentation on such species are analyzed based on Euclidean inter-patch distances. This approach, however, ignores the role of the landscape matrix. Recently, therefore, functional distances that account for the composition of the landscape surrounding the habitat patches have been used more frequently as indicators for patch occupancy. However, the performance of functional and non-functional connectivity measures in predicting patch occupancy of such species has never been compared in a multi-species approach.Here we evaluate the effect of habitat connectivity on the patch occupancy of 13 habitat specialists from three different insect orders (Auchenorrhyncha, Lepidoptera, Orthoptera) in fragmented calcareous grasslands. In order to calculate functional distances we used four different sets of resistance values and rankings. We then modelled species’ occurrence using both Euclidean and functional (based on least-cost modelling) inter-patch distances as predictors.We found that functional connectivity measures provided better results than the non-functional approach. However, a functional connectivity measure that was based on very coarse land-cover data performed even better than connectivity measures that were based on much more detailed land-use data.In order to take into account possible effects of the landscape matrix on patch occupancy by habitat specialists, future metapopulation studies should use functional rather than Euclidean distances whenever possible. For practical applications, we recommend a ‘simple approach’ which requires only coarse land-cover data and in our study performed better than all other functional connectivity measures, even more complex ones.

Estimating breeding season abundance of golden‐cheeked warblers in Texas, USA

AbstractPopulation abundance estimates using predictive models are important for describing habitat use and responses to population‐level impacts, evaluating conservation status of a species, and for establishing monitoring programs. The golden‐cheeked warbler (Setophaga chrysoparia) is a neotropical migratory bird that was listed as federally endangered in 1990 because of threats related to loss and fragmentation of its woodland habitat. Since listing, abundance estimates for the species have mainly relied on localized population studies on public lands and qualitative‐based methods. Our goal was to estimate breeding population size of male warblers using a predictive model based on metrics for patches of woodland habitat throughout the species' breeding range. We first conducted occupancy surveys to determine range‐wide distribution. We then conducted standard point‐count surveys on a subset of the initial sampling locations to estimate density of males. Mean observed patch‐specific density was 0.23 males/ha (95% CI = 0.197–0.252, n = 301). We modeled the relationship between patch‐specific density of males and woodland patch characteristics (size and landscape composition) and predicted patch occupancy. The probability of patch occupancy, derived from a model that used patch size and landscape composition as predictor variables while addressing effects of spatial relatedness, best predicted patch‐specific density. We predicted patch‐specific densities as a function of occupancy probability and estimated abundance of male warblers across 63,616 woodland patches accounting for 1.678 million ha of potential warbler habitat. Using a Monte Carlo simulation, our approach yielded a range‐wide male warbler population estimate of 263,339 (95% CI: 223,927–302,620). Our results provide the first abundance estimate using habitat and count data from a sampling design focused on range‐wide inference. Managers can use the resulting model as a tool to support conservation planning and guide recovery efforts. © 2012 The Wildlife Society.

Predicting patch occupancy in fragmented landscapes at the rangewide scale for an endangered species: an example of an American warbler.

AIM: Our objective was to identify the distribution of the endangered golden-cheeked warbler (Setophaga chrysoparia) in fragmented oak-juniper woodlands by applying a geoadditive semiparametric occupancy model to better assist decision-makers in identifying suitable habitat across the species breeding range on which conservation or mitigation activities can be focused and thus prioritize management and conservation planning. LOCATION: Texas, USA. METHODS: We used repeated double-observer detection/non-detection surveys of randomly selected (n = 287) patches of potential habitat to evaluate warbler patch-scale presence across the species breeding range. We used a geoadditive semiparametric occupancy model with remotely sensed habitat metrics (patch size and landscape composition) to predict patch-scale occupancy of golden-cheeked warblers in the fragmented oak-juniper woodlands of central Texas, USA. RESULTS: Our spatially explicit model indicated that golden-cheeked warbler patch occupancy declined from south to north within the breeding range concomitant with reductions in the availability of large habitat patches. We found that 59% of woodland patches, primarily in the northern and central portions of the warbler's range, were predicted to have occupancy probabilities ≤0.10 with only 3% of patches predicted to have occupancy probabilities >0.90. Our model exhibited high prediction accuracy (area under curve = 0.91) when validated using independently collected warbler occurrence data. MAIN CONCLUSIONS: We have identified a distinct spatial occurrence gradient for golden-cheeked warblers as well as a relationship between two measurable landscape characteristics. Because habitat-occupancy relationships were key drivers of our model, our results can be used to identify potential areas where conservation actions supporting habitat mitigation can occur and identify areas where conservation of future potential habitat is possible. Additionally, our results can be used to focus resources on maintenance and creation of patches that are more likely to harbour viable local warbler populations.

Quantitative predictions for patch occupancy of capercaillie in fragmented habitats

A major conclusion of studying metapopulation biology is that species conservation should favor regional rather than local population persistence. Regional persistence is tightly linked to size, spatial configuration and quality of habitat patches. Hence it is important for the management of endangered species that priority patches can be identified. We developed a predictive model of patch occupancy by capercaillie, a threatened grouse species, based on a single snapshot of data. We used logistic regression to predict patch occupancy as a function of patch size, isolation, connectivity, relative altitude, and biogeographical area. The probability of a patch being occupied increased with patch size and increasing altitude, and decreased with increasing distance to the next occupied patch. Patch size was the most important predictor although occupied patches varied considerably in size. Our model only uses data on the number, size and spatial configuration of habitat patches. It is a useful tool to designate priority areas for conservation, i.e. large core patches with high resilience in habitat quality, smaller island-patches that still have high probability of being inhabited or becoming recolonised, and patches functioning as ‘‘stepping stones’’. If capercaillie is to be preserved, habitat suitability needs to be maintained in a functional network of patches that account for size and inter-patch distance thresholds as found in this study. We suggest that similar area-isolation relationships are valid for almost any region within the distribution range of capercaillie. The thresholds for occupancy are however likely to depend on characteristics of the respective landscape. The outcome of our study emphasises the need for future investigations that explore the relationship between patch occupancy, matrix quality and its resistance to dispersing individuals.

Viability and patch occupancy of a swamp rabbit metapopulation at the northern edge of its distribution

Swamp rabbits (Sylvilagus aquaticus) are state-endangered in Indiana, USA, and population decline has been attributed to habitat loss. We conducted pellet surveys as part of a long-term survey effort that has been conducted at approximate 10-year intervals over the last 40 years. We modeled patch occupancy and conducted a spatially-explicit population viability analysis (PVA). Although occupancy of individual patches varied over time, occupancy rate has been constant for the last 30 years, and Indiana swamp rabbits exist as a metapopulation that appears to be stable. Metapopulation dynamics were best characterized as being stationary, but area was an important factor in extinction rates; occupied patches (142±37ha) were significantly larger (P=0.01) than unoccupied patches (79±20ha). We did not find strong support for models with colonization rates as a function of distance to neighboring patches, nor was distance to contiguous patches of habitat significantly different (P=0.12) for occupied and unoccupied sites. Population viability analysis corroborated our findings based on occupancy modeling, and evaluation of the PVA model using occupancy data for the period 1985–2006 resulted in predictions that nearly matched our field observations (33% observed patch occupancy vs. 25% predicted patch occupancy). Population viability was most sensitive to reductions in survival and fecundity rates, but was otherwise robust to changes in parameters such as initial abundance and carrying capacity. Our findings provide novel insights into a poorly studied member of Sylvilagus and into species metapopulation dynamics at the edge of the range.

A Large-Scale Deforestation Experiment: Effects of Patch Area and Isolation on Amazon Birds

As compared with extensive contiguous areas, small isolated habitat patches lack many species. Some species disappear after isolation; others are rarely found in any small patch, regardless of isolation. We used a 13-year data set of bird captures from a large landscape-manipulation experiment in a Brazilian Amazon forest to model the extinction-colonization dynamics of 55 species and tested basic predictions of island biogeography and metapopulation theory. From our models, we derived two metrics of species vulnerability to changes in isolation and patch area. We found a strong effect of area and a variable effect of isolation on the predicted patch occupancy by birds.

EXTINCTION DEBT OF FOREST PLANTS PERSISTS FOR MORE THAN A CENTURY FOLLOWING HABITAT FRAGMENTATION

Following habitat fragmentation individual habitat patches may lose species over time as they pay off their "extinction debt." Species with relatively low rates of population extinction and colonization ("slow" species) may maintain extinction debts for particularly prolonged periods, but few data are available to test this prediction. We analyzed two unusually detailed data sets on forest plant distributions and land-use history from Lincolnshire, United Kingdom, and Vlaams-Brabant, Belgium, to test for an extinction debt in relation to species-specific extinction and colonization rates. Logistic regression models predicting the presence-absence of 36 plant species were first parameterized using data from Lincolnshire, where forest cover has been relatively low (approximately 5-8%) for the past 1000 years. Consistent with extinction debt theory, for relatively slow species (but not fast species) these models systematically underpredicted levels of patch occupancy in Vlaams-Brabant, where forest cover was reduced from approximately 25% to <10% between 1775 and 1900 (it is presently 6.5%). As a consequence, the ability of the Lincolnshire models to predict patch occupancy in Vlaams-Brabant was worse for slow than for fast species. Thus, more than a century after forest fragmentation reached its current level an extinction debt persists for species with low rates of population turnover.

DEVELOPING PROBABILISTIC MODELS TO PREDICT AMPHIBIAN SITE OCCUPANCY IN A PATCHY LANDSCAPE

Human-caused fragmentation of habitats is threatening an increasing number of animal and plant species, making an understanding of the factors influencing patch occupancy ever more important. The overall goal of the current study was to develop probabilistic models of patch occupancy for the mountain yellow-legged frog (Rana muscosa). This once-common species has declined dramatically, at least in part as a result of habitat fragmentation resulting from the introduction of predatory fish. We first describe a model of frog patch occupancy developed using semiparametric logistic regression that is based on habitat characteristics, fish presence/absence, and a spatial location term (the latter to account for spatial autocorrelation in the data). This model had several limitations including being constrained in its use to only the study area. We therefore developed a more general model that incorporated spatial autocorrelation through the use of an autocovariate term that describes the degree of isolation from neighboring frog populations (autologistic model). After accounting for spatial autocorrelation in patch occupancy, both models indicated that the probability of frog presence was strongly influenced by lake depth, elevation, fish presence/absence, substrate characteristics, and the degree of lake isolation. Based on cross-validation procedures, both models provided good fits to the data, but the autologistic model was more useful in predicting patch occupancy by frogs. We conclude by describing a possible application of this model in assessing the likelihood of persistence by frog populations.

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 (&lt;20%) for about 74% of all simulations, but 22% of the landscapes had differences openface&gt; 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.

A simple landscape‐scale test of a spatially explicit population model: patch occupancy in fragmented south‐eastern Australian forests

The results of a landscape‐scale test of ALEX, a widely used metapopulation model for Population Viability Analysis (PVA), are described. ALEX was used to predict patch occupancy by the laughing kookkaburra and the sacred kingfisher in patches of eucalypt forest in south‐eastern Australia. These predictions were compared to field surveys to determine the accuracy of the model. Predictions also were compared to a “naïve” null model assuming no fragmentation effects. The naïve null model significantly over‐predicted the number of eucalypt patches occupied by the sacred kingfisher, but the observed patch occupancy was not significantly different from that predicted using ALEX. ALEX produced a better fit to the field data than the naïve null model for the number of patches occupied by the laughing kookaburra. Nevertheless, ALEX still significantly over‐predicted the number of occupied patches, particularly remnants dominated by certain forest types – ribbon gum and narrow‐leaved peppermint. The predictions remained significantly different from observations, even when the habitat quality of these patches was reduced to zero. Changing the rate of dispersal improved overall predicted patch occupancy, but occupancy rates for the different forest types remained significantly different from the field observations. The lack of congruence between field data and model predictions could have arisen because the laughing kookaburra may move between an array of patches to access spatially separated food and nesting resources in response to fragmentation. Alternatively, inter‐specific competition may be heightened in a fragmented habitat. These types of responses to fragmentation are not incorporated as part of traditionally applied metapopulation models. Assessments of predictions from PVA models are rare but important because they can reveal the types of species for which forecasts are accurate and those for which they are not. This can assist the collection of additional empirical data to identify important factors affecting population dynamics.

Habitat Patch Arrangement and Metapopulation Persistence of Predators and Prey

This study tests whether spatial dynamics can stabilize metapopulations with a small number of patches and tests the influence of patch arrangement. I measured persistence of predator and prey protists in replicated microcosms with two to four patches. Predators persisted for 85–437 generations (26–130 d). As predicted by single‐species and/or predator‐prey metapopulation models, substantial variation in predator metapopulation persistence was accounted for by the amount of patches or habitat, number of dispersal corridors, maximum interpatch distance, and proportion of patches providing colonists (which depends on the explicit spatial arrangement of patches). Contrary to expectation, persistence was not influenced by loops of patches or patch similarity. Persistence was also shorter in four‐patch loops than three‐patch loops, indicating an interaction between patch number and arrangement, which is not predicted by published models. Spatial synchrony of density fluctuations was central to predator persistence but had complex effects on extinction‐colonization dynamics, rescue effects, and predator‐prey interaction strength. Levins’s model, containing only extinction‐colonization dynamics, predicted patch occupancy for prey but not predators. Predators did, however, show rescue effects and changes in interaction strength. This work illustrates the need to combine experimentation with modeling to understand the mechanisms of spatial dynamics.

Connectivity in fragmented populations: Abax parallelepipedus in a hedgerow network landscape

Landscape heterogeneity, i.e. the diversity in patch quality affects the movements of many species. The forest carabid Abax parallelepipedus survives as fragmented populations in hedgerow networks where linear wooded elements are used as corridors for movement between local populations. Mean distances covered by individuals per unit of time differ according to the quality of the woody habitat. In this paper, we examine how the individual behaviour in various habitat types translates into the distribution of the species at the landscape level. Our results indicate that the euclidian distance to the nearest site occupied by the species is a highly significant descriptor of the functional connectivity of the hedgerow network. Integrating the structure and the quality of the hedgerow network in the estimation of connectivity slightly improves the correlation between connectivity and the distribution of A. parallelepipedus but does not appear necessary to predict patch occupancy in the network studied.

Stochastic Spatial Models: From Simulations to Mean Field and Local Structure Approximations

A discrete stochastic spatial model for a single species is examined. First, detailed spatial simulations are performed using stochastic cellular automata. Then, several analytic approximations are made. First, two versions of mean field theory are presented: the infinite-dispersal mean field approximation, which is a metapopulation-like model, and the local-dispersal mean field approximation, which incorporates the locality of the cellular automaton model but assumes that no spatial correlations develop in the lattice. Next, the local-dispersal mean field theory is generalised into several varieties of local structure theory, in which one assumes that groups of nearby sites in the lattice are correlated, and tracks such correlations under the action of the cellular automaton rule. Assuming such local correlations allows one to predict patch occupancy as well as the degree of clustering in the cellular automaton model much more accurately than mean field theory, especially in parameter regimes where mean field theory does poorly. Simulation and mean field theory are seen to be two opposite extremes of an entire spectrum of methods that may be used to investigate discrete spatial models.

The Quantitative Incidence Function Model and Persistence of an Endangered Butterfly Metapopulation

The incidence function model is derived from a linear first‐order Markov chain of the presence or absence of a species in a habitat patch. The model can be parameterized with “snapshot” presence/absence data from a patch network. Using the estimated parameter values the Markov chain can be iterated in the same or in some other patch network to generate quantitative predictions about transient metapopulation dynamics and the stochastic steady state. We tested the ability of the incidence function model to predict patch occupancy using extensive data on an endangered butterfly, the Glanville fritillary (Melitaea cinxia) Parameter values were estimated with data collected from a 50‐patch network in 1991. In 1993 we surveyed the entire geographic range of the species in Finland, within an area of 50 × 70 km2, with 1502 habitat patches (dry meadows) of which 536 were occupied. Model predictions were generated for the 1502 patches and were compared with the observed pattern of occupancy in 1993. The model predicted patch occupancy well in more than half of the study area, but prediction was poor for one quarter of the area, probably because of regional variation in habitat quality and because metapopulations may have been perturbed away from the steady state. The incidence function model provides a practical tool for making quantitative predictions about metapopulation dynamics of species living in fragmented landscapes.