A general approach to the analysis of habitat selection

The investigation of animal habitat selection aims at the detection of selective usage of habitat types and the identification of covariates influencing their selection. The results not only allow for a better understanding of the habitat selection process but are also intended to help improve the conservation of animals. Usually, habitat selection by larger animals is assessed by radio-tracking or visual observation studies, where the chosen habitat is determined for some animals at a set of specific points in time. Hence the resulting data often have the following structure: a categorical variable indicating the habitat type selected by an animal at a specific point in time is repeatedly observed and will be explained by covariates. These may either describe properties of the habitat types currently available and/or properties of the animal. In this paper, we present a general approach to the analysis of such data in a categorical regression setup. The proposed model generalizes and improves upon several of the approaches previously discussed in the literature. In particular, it accounts for changing habitat availability due to the movement of animals within the observation area. It incorporates both habitat- and animal-specific covariates, and includes individual-specific random effects to account for correlations introduced by the repeated measurements on single animals. Furthermore, the assumption that the effects are linear can be dropped by including the effects in nonparametric manner based on a penalized spline approach. The methodology is implemented in a freely available software package. We demonstrate the general applicability and the potential of the proposed approach in two case studies: The analysis of a songbird community in South-America and a study on brown bears in Central Europe.     

K-select analysis: a new method to analyse habitat selection in radio-tracking studies

Two kinds of wildlife habitat studies can be distinguished in the literature: hindcasting and forecasting studies. Hindcasting studies aim to emphasize among a large set of habitat variables those that are of interest for the focus species, whereas forecasting studies are intended to predict habitat selection according to a small number of habitat variables for a given area. We provide here a new analytical tool which relies on the concept of ecological niche, the K-select analysis, for hindcasting studies of habitat selection by animals using radio-tracking data. Each habitat variable defines one dimension in the ecological space. For each animal, the difference between the vector of average available habitat conditions and the vector of average used conditions defines the marginality vector. Its size is proportional to the importance of habitat selection, and its direction indicates which variables are selected. By performing a non-centered principal component analysis of the table containing the coordinates of the marginality vectors of each animal (row) on the habitat variables (column), the K-select analysis returns a linear combination of habitat variables for which the average marginality is greatest. It is a synthesis of variables which contributes the most to the habitat selection. As with principal component analysis, the biological significance of the factorial axes is deduced from the loading of variables. An example is provided: habitat selection by wild boar is studied in a Mediterranean habitat using the K-select analysis. The numerous advantages of the analysis (a large number of variables that can be included, individual variability in habitat selection taken into account, a lack of too strict underlying hypotheses) make it a powerful approach in radio-tracking studies designed to identify habitat variables that are selected by animals.     

A permutation-based combination of sign tests for assessing habitat selection

The analysis of habitat selection in radio-tagged animals is approached by comparing the portions of use against the portions of availability observed for each habitat type. Since data are linearly dependent with singular variance-covariance matrices, standard multivariate statistical tests cannot be applied. To bypass the problem, compositional data analysis is customarily performed via log-ratio transform of sample observations. The procedure is criticized in this paper, emphasizing the several drawbacks which may arise from the use of compositional analysis. An alternative nonparametric solution is proposed in the framework of multiple testing. The habitat use is assessed separately for each habitat type by means of the sign test performed on the original observations. The resulting p values are combined in an overall test statistic whose significance is determined permuting sample observations. The theoretical findings of the paper are checked by simulation studies. Applications to case studies previously considered in literature are discussed.     

Grizzly bear habitat selection is scale dependent.

The purpose of our study is to show how ecologists' interpretation of habitat selection by grizzly bears (Ursus arctos) is altered by the scale of observation and also how management questions would be best addressed using predetermined scales of analysis. Using resource selection functions (RSF) we examined how variation in the spatial extent of availability affected our interpretation of habitat selection by grizzly bears inhabiting mountain and plateau landscapes. We estimated separate models for females and males using three spatial extents: within the study area, within the home range, and within predetermined movement buffers. We employed two methods for evaluating the effects of scale on our RSF designs. First, we chose a priori six candidate models, estimated at each scale, and ranked them using Akaike Information Criteria. Using this method, results changed among scales for males but not for females. For female bears, models that included the full suite of covariates predicted habitat use best at each scale. For male bears that resided in the mountains, models based on forest successional stages ranked highest at the study-wide and home range extents, whereas models containing covariates based on terrain features ranked highest at the buffer extent. For male bears on the plateau, each scale estimated a different highest-ranked model. Second, we examined differences among model coefficients across the three scales for one candidate model. We found that both the magnitude and direction of coefficients were dependent upon the scale examined; results varied between landscapes, scales, and sexes. Greenness, reflecting lush green vegetation, was a strong predictor of the presence of female bears in both landscapes and males that resided in the mountains. Male bears on the plateau were the only animals to select areas that exposed them to a high risk of mortality by humans. Our results show that grizzly bear habitat selection is scale dependent. Further, the selection of resources can be dependent upon the availability of a particular vegetation type on the landscape. From a management perspective, decisions should be based on a hierarchical process of habitat selection, recognizing that selection patterns vary across scales.     

Different habitats, different habits? Response to foraging information in the parasitic wasp Venturia canescens

The parasitic wasp, Venturia canescens (Gravenhorst) (Hymenoptera: Ichneumonidae), has two reproductive modes, namely, thelytoky or arrhenotoky, and occurs in habitats with highly variable or relatively stable host abundances, respectively. Since information processing is costly, we expected that information indicating resource availability would be mainly used by the thelytokous wasps and less so by the arrhenotokous type. This idea was explored by two different approaches. In a study on patch-time allocation, we used females from ten populations and measured patch-residence times of individuals that visited multiple patches at different encounter rates. In a more detailed approach, thelytokous and arrhenotokous females from a single location were observed continuously while foraging, and all behaviors were recorded. Wasps of both reproductive modes (i.e., both habitat types) used information for the assessment of habitat quality. However, the way that the information was used differed between them. Whereas thelytokous females used foraging information to maximize their efficiency at high patch-encounter rates, arrhenotokous females merely reduced the number of offspring produced without changing patch times. The behavior of the arrhenotokous females should result in a spreading of offspring across the habitat and, thus, reduced sib-mating. The foraging strategy of these wasps might therefore be an adaptation to reduce costs associated with inbreeding.     

Generalized functional responses for species distributions

Researchers employing resource selection functions (RSFs) and other related methods aim to detect correlates of space-use and mitigate against detrimental environmental change. However, an empirical model fit to data from one place or time is unlikely to capture species responses under different conditions because organisms respond nonlinearly to changes in habitat availability. This phenomenon, known as a functional response in resource selection, has been debated extensively in the RSF literature but continues to be ignored by practitioners for lack of a practical treatment. We therefore extend the RSF approach to enable it to estimate generalized functional responses (GFRs) from spatial data. GFRs employ data from several sampling instances characterized by diverse profiles of habitat availability. By modeling the regression coefficients of the underlying RSF as functions of availability, GFRs can account for environmental change and thus predict population distributions in new environments. We formulate the approach as a mixed-effects model so that it is estimable by readily available statistical software. We illustrate its application using (1) simulation and (2) wolf home-range telemetry. Our results indicate that GFRs can offer considerable improvements in estimation speed and predictive ability over existing mixed-effects approaches.     

Kernel-based home range method for data with irregular sampling intervals

Studies of habitat selection and movements often use radio-tracking data for defining animal home ranges. Home ranges (HR) can be approximated by a utilization density distribution (UD) that instead of assuming uniform use of areas within HR boundary provides a probabilistic measure of animal space use. In reality, radio-tracking data contain periods of frequent autocorrelated observations interspersed with temporally more independent observations. Using such temporally irregular data directly may result in biased UD estimates, because areas that have been sampled intensively receive too much weight. The problem of autocorrelation has been tackled by resampling data with an appropriate time interval. However, resampling may cause a large reduction in the data set size along with a loss of information. Evidently, biased UD estimates or reduction in data may prejudice the results on animal habitat selection and movement. We introduce a new method for estimating UDs with temporally irregular data. The proposed method, called the time kernel, accounts for temporal aggregation of observations and gives less weight to temporally autocorrelated observations. A further extension of the method accounts also for spatially aggregated observations with relatively low weights given to observations that are both temporally and spatially aggregated. We test the behaviour of the time kernel method and its spatiotemporal version using simulated data. In addition, the method is applied to a data set of brown bear locations.     

Modeling resource selection using polytomous logistic regression and kernel density estimates

Wildlife resource selection studies typically compare used to available resources; selection or avoidance occurs when use is disproportionately greater or less than availability. Comparing used to available resources is problematic because results are often greatly influenced by what is considered available to the animal. Moreover, placing relocation points within resource units is often difficult due to radiotelemetry and mapping errors. Given these problems, we suggest that an animal’s resource use be summarized at the scale of the home range (i.e., the spatial distribution of all point locations of an animal) rather than by individual points that are considered used or available. To account for differences in use-intensity throughout an animal’s home range, we model resource selection using kernel density estimates and polytomous logistic regression. We present a case study of elk (Cervus elaphus) resource selection in South Dakota to illustrate the procedure. There are several advantages of our proposed approach. First, resource availability goes undefined by the investigator, which is a difficult and often arbitrary decision. Instead, the technique compares the intensity of animal use throughout the home range. This technique also avoids problems with classifying locations rigidly as used or unused. Second, location coordinates do not need to be placed within mapped resource units, which is problematic given mapping and telemetry error. Finally, resource use is considered at an appropriate scale for management because most wildlife resource decisions are made at the level of the patch. Despite the advantages of this use-intensity procedure, future research should address spatial autocorrelation and develop spatial models for ordered categorical variables.     

Space use in lions, <Emphasis Type="Italic">Panthera leo</Emphasis>, in the Selous Game Reserve: social and ecological factors

Habitat qualities, such as food supply or access to refuges, often influence home-range size. Furthermore, such qualitative differences usually lead to conspecific competition over space, which can be an important factor in determining the distribution of individuals within populations. In carnivores, patterns of resource dispersion are hypothesized to determine home range-size and group size. But in contests over space (or other resources), larger groups usually dominate smaller ones, and group size should therefore also affect home-range size. Here I describe the space use of lions, Panthera leo, in the Selous Game Reserve, Tanzania, and ask whether space use is related to pride size, habitat, or relatedness. Home ranges varied in size, but size showed no correlation to number of adult females in the pride or to habitat type. Lions exhibited a significant preference for riverine and short-grass habitat, and a significant avoidance of acacia woodland. Habitat preference ratios largely reflected prey availability in each habitat. Outer areas, as well as core areas of home ranges, were often used by two or more prides. Overlaps showed no correlation to relatedness among prides or habitat type. Thus, whereas home-range sizes and overlaps were determined by factors that could not be revealed by demographic factors or analyses of habitat composition or genetic structure, lion space use within each home range seemed driven mostly by prey availability, which mainly varies with habitat type.     

Iberian Lynx in a Fragmented Landscape: Predispersal, Dispersal, and Postdispersal Habitats

Abstract: Applied conservation biology must provide solutions for the conservation of species in modern landscapes, where prime habitats are being continuously fragmented and altered and animals are restricted to small, nonviable populations. We studied habitat selection in a fragmented population of endangered Iberian lynx (   Lynx pardinus ) by examining 14 years of radiotracking data obtained from lynx trapped in two different source areas. Habitat selection was studied independently for predispersal lynx in the source areas, for dispersing individuals through the region, and for postdispersing animals, most of which settled far from their point of origin. A multivariate analysis of variance showed that habitat use differed significantly among these phases and between area of origin, but not between sexes. The habitat type most used, and best represented within home ranges, was the mediterranean scrubland. Pine plantations were also important during and after dispersal. The rest of the habitats were either avoided (open habitats) or used according to availability ( pine and eucalyptus plantations) by dispersing lynx. Differences due to lynx origin were detected only during predispersal and dispersal and were observed because animals from each area had different habitat availability. Lynx with established territories did not use areas at random. They occupied patches of mediterranean scrubland more often than would be expected from scrubland availability during predispersal; the rest of the habitats were included within home ranges less than would be expected from their availability in the landscape. Results indicate that dispersing animals may use habitats of lower quality than habitats used by resident individuals, which suggests that conservation strategies applied across regions might be a viable objective.     

Consumer-resource body-size relationships in natural food webs

It has been suggested that differences in body size between consumer and resource species may have important implications for interaction strengths, population dynamics, and eventually food web structure, function, and evolution. Still, the general distribution of consumer-'resource body-size ratios in real ecosystems, and whether they vary systematically among habitats or broad taxonomic groups, is poorly understood. Using a unique global database on consumer and resource body sizes, we show that the mean body-size ratios of aquatic herbivorous and detritivorous consumers are several orders of magnitude larger than those of carnivorous predators. Carnivorous predator-prey body-size ratios vary across different habitats and predator and prey types (invertebrates, ectotherm, and endotherm vertebrates). Predator-prey body-size ratios are on average significantly higher (1) in freshwater habitats than in marine or terrestrial habitats, (2) for vertebrate than for invertebrate predators, and (3) for invertebrate than for ectotherm vertebrate prey. If recent studies that relate body-size ratios to interaction strengths are general, our results suggest that mean consumer-resource interaction strengths may vary systematically across different habitat categories and consumer types.     

Individual and combined effects of Ca/Mg ratio and water on trait expression in Mimulus guttatus

Low Ca/Mg ratios (a defining component of serpentine soils) and low water environmental conditions often co-occur in nature and are thought to exert strong selection pressures on natural populations. However, few studies test the individual and combined effects of these environmental factors. We investigated the effects of low Ca/Mg ratio and low water availability on plant leaf, stem, stolon, and floral traits of Mimulus guttatus, a bodenvag species, i.e., a species that occurs in serpentine and non-serpentine areas. We quantified genetic variation and genetic variation for plasticity for these leaf, stem, stolon, and floral traits at three hierarchical levels: field-habitat type, population, and family, and we evaluated the relative importance of local adaptation and plasticity. We chose two populations and 10 families per population from four distinct field "habitat types" in northern California: high Ca/Mg ratio (non-serpentine) and season-long water availability, high Ca/Mg ratio and seasonally drying, low Ca/Mg ratio (serpentine) and season-long water availability, and low Ca/Mg ratio and seasonally drying. Seedlings were planted into greenhouse treatments that mimicked the four field conditions. We only detected genetic variation for stem diameter and length of longest leaf at the field-habitat level, but we detected genetic variation at the family level for nearly all traits. Soil chemistry and water availability had strong phenotypic effects, alone and in combination. Our hypothesis of an association between responses to low water levels and low Ca/Mg ratio was upheld for length of longest leaf, stem diameter, corolla width, and total number of reproductive units, whereas for other traits, responses to Ca/Mg ratio and low water were clearly independent. Our results suggest that traits may evolve independently from Ca/Mg ratios and water availability and that our focal traits were not simple alternative measures of vigor. We found genetic variation for plasticity both at the field-habitat type and family levels for half of the traits studied. Phenotypic plasticity and genetic variation for plasticity appear to be more important than local adaptation in the success of these M. guttatus populations found across a heterogeneous landscape in northern California. Phenotypic plasticity is an important mechanism maintaining the broad ecological breadth of native populations of M. guttatus.     

A dynamic host selection model for mountain pine beetle,Dendroctonus ponderosae Hopkins

The link between individual habitat selection decisions (i.e., mechanism) and the resulting population distributions of dispersing organisms (i.e., outcome) has been little-studied in behavioural ecology. Here we consider density-dependent habitat (i.e., host) selection for an energy- and time-limited forager: the mountain pine beetle (Dendroctonus ponderosae Hopkins). We present a dynamic state variable model of individual beetle host selection behaviour, based on an individual’s energy state. Field data are incorporated into model parameterization which allows us to determine the effects of host availability (with respect to host size, quality, and vigour) on individuals’ decisions. Beetles choose larger trees with thicker phloem across a larger proportion of the state-space than smaller trees with thinner phloem, but accept lower quality trees more readily at low energy- and time-states. In addition, beetles make habitat selection decisions based on host availability, conspecific attack densities, and beetle distributions within a forest stand. This model provides a framework for the development of a spatial game model to examine the implications of these results for attack dynamics of beetle populations.     

Predators, prey, and transient states in the assembly of spatially structured communities

Ecological theory suggests that both dispersal limitation and resource limitation can exert strong effects on community assembly. However, empirical studies of community assembly have focused almost exclusively on communities with a single trophic level. Thus, little is known about the combined effects of dispersal and resource limitation on assembly of communities with multiple trophic levels. We performed a landscape-scale experiment using spatially arranged mesocosms to study effects of dispersal and resource limitation on the assembly dynamics of aquatic invertebrate communities with two trophic levels. We found that interplay between dispersal and resource limitation regulated the assembly of predator and prey trophic levels in these pond communities. Early in assembly, predators and prey were strongly dispersal limited, and resource (i.e., prey) availability did not influence predator colonization. Later in assembly, after predators colonized, resource limitation was the strongest driver of predator abundance, and dispersal limitation played a negligible role. Thus, habitat isolation affected predators directly by reducing predator colonization rate, and indirectly through the effect of distance on prey availability. Dispersal and resource limitation of predators resulted in a transient period in which predators were absent or rare in isolated habitats. This period may be important for understanding population dynamics of vulnerable prey species. Our findings demonstrate that dispersal and resource limitation can jointly regulate assembly dynamics in multi-trophic systems. They also highlight the need to develop a temporal picture of the assembly process in multi-trophic communities because the availability and spatial distribution of limiting resources (i.e., prey) and the distribution of predators can shift radically over time.     

Fine-scale habitat modeling of a top marine predator: do prey data improve predictive capacity?

Predators and prey assort themselves relative to each other, the availability of resources and refuges, and the temporal and spatial scale of their interaction. Predictive models of predator distributions often rely on these relationships by incorporating data on environmental variability and prey availability to determine predator habitat selection patterns. This approach to predictive modeling holds true in marine systems where observations of predators are logistically difficult, emphasizing the need for accurate models. In this paper, we ask whether including prey distribution data in fine-scale predictive models of bottlenose dolphin (Tursiops truncatus) habitat selection in Florida Bay, Florida, U.S.A., improves predictive capacity. Environmental characteristics are often used as predictor variables in habitat models of top marine predators with the assumption that they act as proxies of prey distribution. We examine the validity of this assumption by comparing the response of dolphin distribution and fish catch rates to the same environmental variables. Next, the predictive capacities of four models, with and without prey distribution data, are tested to determine whether dolphin habitat selection can be predicted without recourse to describing the distribution of their prey. The final analysis determines the accuracy of predictive maps of dolphin distribution produced by modeling areas of high fish catch based on significant environmental characteristics. We use spatial analysis and independent data sets to train and test the models. Our results indicate that, due to high habitat heterogeneity and the spatial variability of prey patches, fine-scale models of dolphin habitat selection in coastal habitats will be more successful if environmental variables are used as predictor variables of predator distributions rather than relying on prey data as explanatory variables. However, predictive modeling of prey distribution as the response variable based on environmental variability did produce high predictive performance of dolphin habitat selection, particularly foraging habitat.     

Complementary habitat use by wild bees in agro-natural landscapes

Human activity causes abrupt changes in resource availability across the landscape. In order to persist in human-altered landscapes organisms need to shift their habitat use accordingly. Little is known about the mechanisms by which whole communities persist in human-altered landscapes, including the role of complementary habitat use. We define complementary habitat use as the use of different habitats at different times by the same group of species during the course of their activity period. We hypothesize that complementary habitat use is a mechanism through which native bee species persist in human-altered landscapes. To test this idea, we studied wild bee communities in agro-natural landscapes and explored their community-level patterns of habitat and resource use over space and time. The study was conducted in six agro-natural landscapes in the eastern United States, each containing three main bee habitat types (natural habitat, agricultural fields, and old fields). Each of the three habitats exhibited a unique seasonal pattern in amount, diversity, and composition of floral resources, and together they created phenological complementarity in foraging resources for bees. Individual bee species as well as the bee community responded to these spatiotemporal patterns in floral availability and exhibited a parallel pattern of complementary habitat use. The majority of wild bee species, including all the main crop visitors, used fallow areas within crops early in the season, shifted to crops in mid-season, and used old-field habitats later in the season. The natural-forest habitat supported very limited number of bees, mostly visitors of non-crop plants. Old fields are thus an important feature in these arable landscapes for maintaining crop pollination services. Our study provides a detailed examination of how shifts in habitat and resource use may enable bees to persist in highly dynamic agro-natural landscapes, and points to the need for a broad cross-habitat perspective in managing these landscapes.     

Territorial resource valuation deviates from habitat quality in an ecologically trapped,long-distance migratory bird

Preference measures are widely used in habitat selection studies to test an animal’s choice relative to particular habitat features, but most measures are subject to criticism as they fail to indicate the underlying behavioral motivation. Order of settlement on breeding sites has been proposed as an effective measure in migratory organisms, as it conceptually approaches a choice experiment. We tested the assumption that early red-backed shrikes (Lanius collurio) are more willing to defend their territorial resource than individuals arriving later. We earlier showed that shrikes arriving first settled in forest plantations that resulted in lower reproductive success compared to territories on farmland, suggesting an ecological trap. Therefore, individuals are expected to place higher value on the lower quality sites in forests. Within the context of resource valuation theory in animal contests, we used a simulated territorial intrusion experiment to measure territorial defense and to evaluate the perceived value of the territory during the settlement phase in both habitat types. Males arriving early were much more motivated to defend their territory than late birds. After correction for the disparity in the timing of arrival between habitat types, shrikes also more vigorously defended their territories in the forest habitat associated with the lowest reproductive returns. Although some resource valuation mechanisms remain unclear, our results show that early and late-arriving individuals strongly differ in behavioral motivation to hold their territorial resources. This study also demonstrates for the first time that organisms may exhibit a higher degree of territorial aggressiveness in a lower quality habitat.     

Terrestrial habitat selection and strong density-dependent mortality in recently metamorphosed amphibians

To predict the effects of terrestrial habitat change on amphibian populations, we need to know how amphibians respond to habitat heterogeneity, and whether habitat choice remains consistent throughout the life-history cycle. We conducted four experiments to evaluate how the spatial distribution of juvenile wood frogs, Rana sylvatica (including both overall abundance and localized density), was influenced by habitat choice and habitat structure, and how this relationship changed with spatial scale and behavioral phase. The four experiments included (1) habitat manipulation on replicated 10-ha landscapes surrounding breeding pools; (2) short-term experiments with individual frogs emigrating through a manipulated landscape of 1 m wide hexagonal patches; and habitat manipulations in (3) small (4-m2); and (4) large (100-m2) enclosures with multiple individuals to compare behavior both during and following emigration. The spatial distribution of juvenile wood frogs following emigration resulted from differences in the scale at which juvenile amphibians responded to habitat heterogeneity during active vs. settled behavioral phases. During emigration, juvenile wood frogs responded to coarse-scale variation in habitat (selection between 2.2-ha forest treatments) but not to fine-scale variation. After settling, however, animals showed habitat selection at much smaller scales (2-4 m2). This resulted in high densities of animals in small patches of suitable habitat where they experienced rapid mortality. No evidence of density-dependent habitat selection was seen, with juveniles typically choosing to remain at extremely high densities in high-quality habitat, rather than occupying low-quality habitat. These experiments demonstrate how prediction of the terrestrial distribution of juvenile amphibians requires understanding of the complex behavioral responses to habitat heterogeneity. Understanding these patterns is important, given that human alterations to amphibian habitats may generate extremely high densities of animals, resulting in high density-dependent mortality.