Occupancy Modeling Framework Research Articles

Nest use dynamics of an undisturbed population of bald eagles.

Management or conservation targets based on demographic rates should be evaluated within the context of expected population dynamics of the species of interest. Wild populations can experience stable, cyclical, or complex dynamics, therefore undisturbed populations can provide background needed to evaluate programmatic success. Many raptor species have recovered from large declines caused by environmental contaminants, making them strong candidates for ongoing efforts to understand population dynamics and ecosystem processes in response to human‐caused stressors. Dynamic multistate occupancy models are a useful tool for analyzing species dynamics because they leverage the autocorrelation inherent in long‐term monitoring datasets to obtain useful information about the dynamic properties of population or reproductive states. We analyzed a 23‐year bald eagle monitoring dataset in a dynamic multistate occupancy modeling framework to assess long‐term nest occupancy and reproduction in Lake Clark National Park and Preserve, Alaska. We also used a hierarchical generalized linear model to understand changes in nest productivity in relation to environmental factors. Nests were most likely to remain in the same nesting state between years. Most notably, successful nests were likely to remain in use (either occupied or successful) and had a very low probability of transitioning to an unoccupied state in the following year. There was no apparent trend in the proportion of nests used by eagles through time, and the probability that nests transitioned into or out of the successful state was not influenced by temperature or salmon availability. Productivity was constant over the course of the study, although warm April minimum temperatures were associated with increased chick production. Overall our results demonstrate the expected nesting dynamics of a healthy bald eagle population that is largely free of human disturbance and can be used as a baseline for the expected dynamics for recovering bald eagle populations in the contiguous 48 states.

Ecological factors associated with site occupancy of an endemic chipmunk

ABSTRACTThe Oscura Mountains Colorado chipmunk (Neotamias quadrivittatus oscuraensis) is a rare subspecies of the Colorado chipmunk that is listed as threatened by the state of New Mexico, primarily because it is an endemic subspecies with a small, isolated habitat and the potential for continuing habitat loss. Knowledge about its ecology is limited, which has hindered the development of scientifically defensible management plans. Our goal was to better understand the ecological factors related to the distribution and habitat selection of this chipmunk. We deployed baited camera traps in the Oscura Mountains, New Mexico, USA, using an occupancy modeling framework to determine which ecological factors are associated with occupancy and detection probability. We collected microhabitat and landscape‐level data for use as covariates in the occupancy models. We detected the Oscura Mountains chipmunk at 26 of the 137 survey sites. Occupancy probability was not influenced by the microhabitat characteristics measured and the final model contained only landscape‐level covariates on occupancy. Probability of occupancy was positively associated with proximity to an escarpment, two‐needle pinyon (Pinus edulis) woodland vegetation community type, and elevation. Detection probability was positively associated with the presence of mature two‐needle pinyons at the site. Habitat loss is a major concern for this taxon, especially because climate change is expected to exacerbate threats to pinyon woodlands. Drought, wildfire, bark beetle (Ips confusus) outbreaks, and other diseases pose a large risk to conifer woodlands throughout the southwestern United States. Conserving the pinyon woodlands on the Oscura Mountains, particularly in areas near escarpments, will help maintain habitat that is important for the Oscura Mountains chipmunk. © 2018 The Wildlife Society.

Environmental DNA (eDNA) detects the pool frog (Pelophylax lessonae) at times when traditional monitoring methods are insensitive

Detection of endangered species is invaluable for conservation efforts, yet many traditional sampling techniques are ineffective at low population abundances or during certain periods of the year. Here, we compared results from a newly developed eDNA approach and the traditional observational method for the endangered pool frog (Pelophylax lessonae). Analysis using an occupancy-modeling framework indicated that the probability of pools being occupied using eDNA (0.93) was higher than for the traditional method of counting calling males and silent observed individuals (0.72). Detailed analysis revealed complementarity among the methods. That is, the traditional method gave a high rate of observation in June, whereas eDNA gave at least as many or more observations during other parts of the year. Discrepancies among the methods depended on the dominant lifecycle stage, and eDNA concentrations were higher when juveniles were present than at times when spawning occurred. eDNA concentrations were also positively related to P. lessonae observations. Our study demonstrates that an eDNA protocol for monitoring of endangered amphibian species can be particularly valuable during periods when individuals are hard to detect by observational methods, and provides guidance to sampling efforts for research and monitoring programs in other regions and systems.

A model-based solution for observational errors in laboratory studies.

Molecular techniques for detecting microorganisms, macroorganisms and infectious agents are susceptible to false-negative and false-positive errors. If left unaddressed, these observational errors may yield misleading inference concerning occurrence, prevalence, sensitivity, specificity and covariate relationships. Occupancy models are widely used to account for false-negative errors and more recently have even been used to address false-positive errors, too. Current modelling options assume false-positive errors only occur in truly negative samples, an assumption that yields biased inference concerning detection because a positive sample could be classified as such not because the target agent was successfully detected, but rather due to a false-positive test result. We present an extension to the occupancy modelling framework that allows false-positive errors in both negative and positive samples, thereby providing unbiased inference concerning occurrence and detection, as well as reliable conclusions about the efficacy of sampling designs, handling protocols and diagnostic tests. We apply the model to simulated data, showing that it recovers known parameters and outperforms other approaches that are commonly used when confronted with observation errors. We then apply the model to an experimental data set on Batrachochytrium dendrobatidis, a pathogenic fungus that is implicated in the global decline or extinction of hundreds of amphibian species. The model-based approach we present is not only useful for obtaining reliable inference when data are contaminated with observational errors, but also eliminates the need for establishing arbitrary thresholds or decision rules that have hidden and unintended consequences.

Environmental DNA detects a rare large river crayfish but with little relation to local abundance

Abstract Environmental DNA (eDNA) is DNA extracted from environmental samples (e.g. water) that can be used to infer presence or abundance of species, sometimes with greater sensitivity than conventional sampling methods. Previous eDNA applications to lotic ecosystems have shown promise in accurately inferring species presence, although studies attempting to estimate species abundance have had mixed results. This may be because eDNA applications in lotic environments are challenged by directional streamflow, which has the potential to transport detectable eDNA downstream from its source. Our study sought to evaluate whether results from eDNA corresponded well with the presence and abundance of the narrowly endemic, large river specialist crayfish Faxonius eupunctus obtained through a rigorous, well‐tested conventional sampling method, or instead, if downstream eDNA transport in this large river system might overwhelm the effect of local species abundance. We used a species‐specific quantitative PCR (qPCR) assay to amplify F. eupunctus eDNA collected in surface water samples from streams within the Eleven Point River drainage, Arkansas and Missouri, U.S.A. We estimated F. eupunctus eDNA detection probabilities and examined relationships between eDNA detection probability and site‐scale variables using a hierarchical occupancy and detection probability modelling framework. Results from eDNA sampling showed ˜90% agreement relative to our conventional sampling method in estimating F. eupunctus presence, although eDNA failed to detect F. eupunctus eDNA at two upstream sites where conventional sampling detected F. eupunctus individuals. We found a poor relationship between F. eupunctus eDNA detection probability and local F. eupunctus abundance, and a strong relationship between eDNA detection probability and upstream river distance, which we used as a proxy for the risk of downstream transport of eDNA from upstream F. eupunctus populations. Our results demonstrate eDNA is a largely reliable tool for estimating the presence of benthic organisms in large, freshwater rivers. However, the likelihood of detecting F. eupunctus eDNA presence in our study increased as we moved down the stream network, even though local species abundances were greatest at more upstream locations. Therefore, the ability of eDNA to accurately reflect species presence or abundance in some lotic environments may be hindered by the downstream transport of detectable eDNA.

Assessing patterns of barn owl Tyto alba occupancy from call broadcast surveys

Owing to habitat loss, changes in farming practices, urbanization, and high mortality through vehicle collisions, barn owls Tyto alba are a species of conservation concern in portions of their range. This species can be secretive and difficult to survey, particularly away from breeding sites, so factors related to barn owl occurrence often remain unknown. We conducted nighttime broadcast surveys for barn owls during the early‐ and post‐breeding seasons and used an occupancy modeling framework to understand how factors related to landcover, landscape features, and human development related to occupancy in southern Idaho, USA. We also assessed the effectiveness of using broadcasts of conspecific vocalizations to improve owl detection. Barn owls were detected during 52 of 666 point counts and at 37 of 222 locations in the early‐breeding season and 50 of 198 point counts and 31 of 66 locations in the post‐breeding season. The probability of detecting barn owls was 0.32 ± 0.06 (SE) and 0.45 ± 0.07 (SE) during the early‐ and post‐breeding seasons, respectively. Based on analysis within 1‐km buffers surrounding point‐count locations, occupancy in the early‐breeding season increased with percentage of crop coverage and presence of trees and decreased with background noise. Post‐breeding season occupancy increased with stream length and decreased with area of development and distance from the Snake River, a major geologic feature that likely provided roost sites in its canyon walls and riparian woodlands and a dispersal corridor for juveniles. Broadcast of barn owl vocalizations increased detection probability as much as nine times. Thus, incorporating call broadcast into future barn owl surveys should help investigators reduce false conclusions of absence. Ultimately, understanding factors influencing occupancy of barn owls will facilitate effective conservation, especially in light of population pressures related to factors such as roadway mortality and loss of nesting sites with increased urbanization.

Animal movement affects interpretation of occupancy models from camera‐trap surveys of unmarked animals

AbstractOccupancy models are increasingly applied to data from wildlife camera‐trap (CT) surveys to estimate distribution, habitat use, or relative abundance of unmarked animals. Fundamental to the occupancy modeling framework is the temporal pattern of detections at camera stations, which is influenced by animal population density and the speed and scale of animal movement. How these factors interact withCTsampling designs to affect the interpretation of occupancy parameter estimates is unclear. We developed a simple yet ecologically relevant animal movement simulation to createCTdetections for animal populations varying in movement rate, home range area, and population density. We also variedCTsampling design by the duration of sampling and the density ofCTs in our simulated domain. A single‐species occupancy model was fitted to simulated detection histories, and model‐estimated probabilities of occupancy were compared to the asymptotic proportion of area occupied (PAO), calculated as the union of all simulated home ranges. Occupancy model parameter estimates were sensitive to simulated movement and sampling scenarios. Occupancy models overestimated asymptoticPAOwhen a low population density of simulated animals moved quickly over large home ranges and this positive bias was insensitive to sampling duration. Conversely, asymptoticPAOwas underestimated when simulated animals moved slowly in large‐ or intermediately sized home ranges. This negative bias decreased with increasing sampling duration and a lower density ofCTs. Our results emphasize that the interpretation of occupancy models depends on the underlying processes drivingCTdetections, specifically animal movement and population density, and that model estimates may not reliably reflect variation in these processes. We recommend carefully defining occupancy if it is applied toCTdata in order to better match sampling and analytical frameworks to the ecology of sampled wildlife species.

Improving mesocarnivore detectability with lures in camera-trapping studies

Context Camera trapping is commonly employed for studying carnivores because it provides better data than do other methods, and with lower costs. Increasing the probability of detecting the target species can reduce parameter uncertainty and survey effort required to estimate density and occurrence. Different methods, including attractants and baits, can be used to increase detectability. However, their efficacy has rarely been quantitatively assessed. Aims To quantify the efficacy of scent and bait attractants to increase the detection probability of mesocarnivores by camera trapping. Methods We tested two scent lures, valerian extract (Val) and lynx urine (LU), their combination (Val–LU), and a non-reward bait (i.e. not accessible to the animal), raw chicken, as carnivore attractants in two protected areas of central Spain. We used camera-trapping records under an occupancy-modelling framework to estimate attractant-specific detection probabilities for six mesocarnivore species, and quantified their effects by comparing these estimates with the baseline (i.e. no attractant) detectability. Key results The weekly detection probability of four mesocarnivore species (red fox, Vulpes vulpes, stone marten, Martes foina, common genet, Genetta genetta, and Eurasian badger, Meles meles) significantly increased when Val–LU (between 0.11 ± 0.07 and 0.67 ± 0.05) or chicken (between 0.31 ± 0.02 and 0.77 ± 0.22) were used as attractant, when compared with baseline detectability (between 0.01 ± 0.02 and 0.29 ± 0.05). Although rarely, wildcats (Felis silvestris) were mostly detected with Val–LU. The probability of detecting a species after k sampling occasions (7 days each) where it was present was highly improved with both Val–LU and chicken for all species (e.g. from 0.20 to 0.98 after four sampling occasions with chicken for the stone marten). Both attractants reduced the sampling time required to ascertain that a species was absent to between 42% and 15% of baseline values. Conclusions The tested attractants greatly improved the detectability of most Iberian mesocarnivores. Although chicken was preferable for some species such as stone marten, Val–LU is most efficient for detecting the whole mesocarnivore community, including rare species such as wildcats. Implications Attractant selection in studies using non-invasive detection methods must be supported by quantitative assessment of the detection probability associated to each attractant. Researchers must choose those attractants best fitting target species and study aims.

Predation by small mammalian carnivores in rural agro-ecosystems: An undervalued ecosystem service?

Africa is endowed with a diverse guild of small carnivores, which could benefit stakeholders by providing ecosystem services while fostering conservation tolerance for carnivores. To investigate the potential of small carnivores for the biological control of rodents within agro-ecosystems, we assessed both the ecological and social landscapes within two rural villages in the Vhembe Biosphere Reserve, South Africa. We employed a camera trapping survey underpinned by an occupancy modelling framework to distinguish between ecological and observation processes affecting small carnivore occupancy. We also used questionnaires to investigate perceptions of small carnivores and their role in pest control. We found the greatest diversity of small carnivores in land used for cropping in comparison to grazing or settlements. Probability of use by small carnivores was influenced negatively by the relative abundance of domestic dogs and positively by the relative abundance of livestock. Greater carnivore diversity and probability of use could be mediated through habitat heterogeneity, food abundance, or reduced competition from domestic carnivores. Village residents failed to appreciate the role of small carnivores in rodent control. Our results suggest that there is significant, although undervalued, potential for small carnivores to provide ecosystem services in agro-ecosystems.

Novel application of explicit dynamics occupancy models to ongoing aquatic invasions

Abstract Identification of suitable habitats, where invasive species can establish, is an important step towards controlling their spread. Accurate identification is difficult for new or slow invaders because unoccupied habitats may be suitable, given enough time for dispersal, while occupied habitats may prove to be unsuitable for establishment. To identify the suitable habitat of a recent invader, I used an explicit dynamics occupancy modelling framework to evaluate habitat covariates related to successful and failed establishments of American Bullfrogs (Lithobates catesbeianus) within the Yellowstone River floodplain of Montana, USA, from 2012 to 2016. During this 5‐year period, bullfrogs failed to establish at most sites they colonized. Bullfrog establishment was most likely to occur and least likely to fail at sites closest to human‐modified ponds and lakes and those with emergent vegetation. These habitat covariates were generally associated with the presence of permanent water. Suitable habitat for bullfrog establishment is abundant in the Yellowstone River floodplain, although many sites with suitable habitat remain uncolonized. Thus, the maximum distribution of bullfrogs is much greater than their current distribution. Synthesis and applications. Focused control efforts on habitats with or proximate to permanent waters are most likely to reduce the potential for invasive bullfrog establishment and spread in the Yellowstone River. The novel application of explicit dynamics occupancy models is a useful and widely applicable tool for guiding management efforts towards those habitats where new or slow invaders are most likely to establish and persist.

Fatal Attraction? Intraguild Facilitation and Suppression among Predators.

Competition and suppression are recognized as dominant forces that structure predator communities. Facilitation via carrion provisioning, however, is a ubiquitous interaction among predators that could offset the strength of suppression. Understanding the relative importance of these positive and negative interactions is necessary to anticipate community-wide responses to apex predator declines and recoveries worldwide. Using state-sponsored wolf (Canis lupus) control in Alaska as a quasi experiment, we conducted snow track surveys of apex, meso-, and small predators to test for evidence of carnivore cascades (e.g., mesopredator release). We analyzed survey data using an integrative occupancy and structural equation modeling framework to quantify the strengths of hypothesized interaction pathways, and we evaluated fine-scale spatiotemporal responses of nonapex predators to wolf activity clusters identified from radio-collar data. Contrary to the carnivore cascade hypothesis, both meso- and small predator occupancy patterns indicated guild-wide, negative responses of nonapex predators to wolf abundance variations at the landscape scale. At the local scale, however, we observed a near guild-wide, positive response of nonapex predators to localized wolf activity. Local-scale association with apex predators due to scavenging could lead to landscape patterns of mesopredator suppression, suggesting a key link between occupancy patterns and the structure of predator communities at different spatial scales.

Occupancy and Detection of Clinch Dace Using Two Gear Types

Abstract The Clinch Dace Chrosomus sp. cf. saylori, discovered in 1999, is an undescribed headwater fish species of global conservation concern with a limited distribution in two counties in southwest Virginia. Highly efficient sampling gears are key to monitoring headwater fish assemblages in Appalachia, including those containing Clinch Dace. Additional information is needed regarding the habitat requirements of the species to understand responses to future mining and logging activities in the region. An occupancy modeling framework is useful to account for incomplete detection, with multiple sampling gears in presence–absence surveys for cryptic or rare species. We detected Clinch Dace at 13 of 70 sites. Occupancy corrected for imperfect detection probability did not differ from naïve occupancy estimates and was 0.19. Clinch Dace occurred in streams with higher substrate embeddedness and catchment forest cover. Backpack electrofishing had a 55% higher probability of detecting Clinch Dace in a 50-m subreach than minnow traps. Appropriate management actions for this species may focus on preserving forested cover in occupied watersheds and monitoring the future impact of surface mining activities that increase total dissolved solids. Sampling protocols for the imperiled Clinch Dace can incorporate both gears and adjust sampling effort to maximize species detection in specific habitats and with specific research goals.

Development and field validation of a regional, management-scale habitat model: A koala Phascolarctos cinereus case study.

Species distribution models have great potential to efficiently guide management for threatened species, especially for those that are rare or cryptic. We used MaxEnt to develop a regional‐scale model for the koala Phascolarctos cinereus at a resolution (250 m) that could be used to guide management. To ensure the model was fit for purpose, we placed emphasis on validating the model using independently‐collected field data. We reduced substantial spatial clustering of records in coastal urban areas using a 2‐km spatial filter and by modeling separately two subregions separated by the 500‐m elevational contour. A bias file was prepared that accounted for variable survey effort. Frequency of wildfire, soil type, floristics and elevation had the highest relative contribution to the model, while a number of other variables made minor contributions. The model was effective in discriminating different habitat suitability classes when compared with koala records not used in modeling. We validated the MaxEnt model at 65 ground‐truth sites using independent data on koala occupancy (acoustic sampling) and habitat quality (browse tree availability). Koala bellows (n = 276) were analyzed in an occupancy modeling framework, while site habitat quality was indexed based on browse trees. Field validation demonstrated a linear increase in koala occupancy with higher modeled habitat suitability at ground‐truth sites. Similarly, a site habitat quality index at ground‐truth sites was correlated positively with modeled habitat suitability. The MaxEnt model provided a better fit to estimated koala occupancy than the site‐based habitat quality index, probably because many variables were considered simultaneously by the model rather than just browse species. The positive relationship of the model with both site occupancy and habitat quality indicates that the model is fit for application at relevant management scales. Field‐validated models of similar resolution would assist in guiding management of conservation‐dependent species.

Detecting long-term occupancy changes in Californian odonates from natural history and citizen science records

In a world of rapid environmental change, effective biodiversity conservation and management relies on our ability to detect changes in species occurrence. While long-term, standardized monitoring is ideal for detecting change, such monitoring is costly and rare. An alternative approach is to use historical records from natural history collections as a baseline to compare with recent observations. Here, we combine natural history collection data with citizen science observations within a hierarchical Bayesian occupancy modeling framework to identify changes in the occupancy of Californian dragonflies and damselflies (Odonata) over the past century. We model changes in the probability of occupancy of 34 odonate species across years and as a function of climate, after correcting for likely variation in detection probability using proxies for recorder effort and seasonal variation. We then examine whether biological traits can help explain variation in temporal trends. Models built using only opportunistic records identify significant changes in occupancy across years for 14 species, with eight of those showing significant declines and six showing significant increases in occupancy in the period 1900–2013. These changes are consistent with estimates obtained using more standardized resurvey data, regardless of whether resurvey data are used individually or in conjunction with the opportunistic dataset. We find that species increasing in occupancy over time are also those whose occupancy tends to increase with higher minimum temperatures, which suggests that these species may be benefiting from increasing temperatures across California. Furthermore, these species are also mostly habitat generalists, whilst a number of habitat specialists display some of the largest declines in occupancy across years. Our approach enables more robust estimates of temporal trends from opportunistic specimen and observation data, thus facilitating the use of these data in biodiversity conservation and management.

Winter Habitat Associations for Spotted Skunks (Spilogale spp) in South-Central Wyoming

Abstract Long-term trends suggest the eastern spotted skunk (Spilogale putorius) experienced a significant decrease in populations throughout the distribution of the species, necessitating development of range-wide management and conservation strategies. However, information on the basic ecology for both S. putorius and the western spotted skunk (S. gracilis) is lacking especially in regions where the distribution of these two species is predicted to converge. We evaluated habitat associations for spotted skunks in an occupancy modeling framework within the foothill transitional habitat of south-central Wyoming during–December 2014. We found occurrence of spotted skunks was positively associated with rocky outcroppings (β = 2.51, se = 1.11, 95% ci = 0.34–4.68, P-value = 0.02). During late-fall and winter, rocky outcropping may represent an important habitat requirement of spotted skunks in this region.

Habitat Patch Use by Fishers in the Deciduous Forest-Dominated Landscape of the Central Appalachian Mountains, USA

Abstract Fishers (Pekania pennanti) are often associated with the coniferous and mixed forests of the northern United States and central Canada, and their ecology has been studied extensively in portions of their distributional range. Recently, natural range expansion and reintroductions have led to recolonization by fishers to portions of the central Appalachian Mountains, where deciduous forest is the dominant vegetation type. We used noninvasive hair-snare surveys and microsatellite genetic analysis to detect fishers in the central Appalachian Mountains of Pennsylvania. We used these detections within an occupancy modeling framework to explore habitat patch use by fishers and the forest characteristics and land use features that influenced it. We found that the likelihood of patch use by fishers was related to forests with higher proportions of low-density residential areas. Our results also suggested that lower road densities might be related to higher likelihood of fisher patch use. Fishers in Pennsylvania tolerated some forms of land development. Patch use was not driven by forest type or canopy cover, at least within our deciduous forest-dominated study areas. Future research identifying threshold values at which forest cover and land development affect patch use by fishers in the central Appalachian Mountains will better inform management decisions with respect to sites for future reintroduction of fishers.

Extending utility of hierarchical models to multi‐scale habitat selection

AbstractAimCharacterizing animal habitat selection is central to ecology and conservation, and understanding selection across multiple spatial scales is a particular priority for research. However, the ability of selection models to capture multi‐scale response has been limited by the dual analytical hurdles of cross‐scale collinearity and overlapping landscapes. The aim of this study was to overcome these limitations using a novel, spatially hierarchical approach.LocationNorth America's northern Great Plains (U.S.A. and Canada).MethodsWe developed a novel adaptation of the occupancy modelling framework that integrates animal response conditionally across scales. We then compared outcomes to those from a traditional multi‐scale model. We illustrated our approach using the breeding distribution of two North American grassland songbirds of conservation concern, Sprague's Pipit Anthus spragueii and Chestnut‐collared Longspur Calcarius ornatus.ResultsOur model successfully captured bird response to local habitat within a broader landscape context, even when habitat associations occurred in opposite directions across scale. Probabilities of occupancy were more strongly affected by local conditions when landscape context was favourable than when it was unfavourable. The traditional multi‐scale approach extended problems of scale into spatial predictions by over‐estimating occurrence where conditions were locally favourable but regionally unsuitable.Main conclusionsThe spatially hierarchical approach provides an integrated model of habitat selection across scales by allowing broader landscape context to shape local response to conditions. For grassland songbirds, our application enabled targeting that could enhance the expected benefits of conservation when compared to the traditional approach.

Subdivision design and stewardship affect bird and mammal use of conservation developments.

Developing effective tools for conservation on private lands is increasingly important for global biodiversity conservation; private lands are located in more productive and biologically diverse areas, and they face accelerated rates of land conversion. One strategy is conservation development (CD) subdivisions, which cluster houses in a small portion of a property and preserve the remaining land as protected open space. Despite widespread use, the characteristics that make CD more or less effective at achieving biodiversity conservation are not well understood. We investigated CD's ability to successfully protect animal populations by examining bird and mammal occurrences in 14 CD subdivisions and four undeveloped areas (range: 14-432ha) in northern Colorado, USA. Using point count and camera trap data in an occupancy modeling framework, we evaluated the relative importance of nine subdivision design factors (e.g., housing density, proportion of CD protected) and 14 stewardship factors (e.g., presence of livestock, percent native vegetation cover) in influencing the overall community composition and the probability of use by 16 birds and six mammals. We found that habitat use by 75% of birds and 83% of mammals was associated with design characteristics that maximized the natural or undisturbed land area both within and near the development (e.g., proportion of CD protected, total area of protected open space, proportion of natural land cover in the surrounding landscape). These factors were also associated with an increasing dominance of human-sensitive bird species, larger-bodied mammals, and mammals with larger home ranges. Habitat use by birds was also influenced by local land use composition and quality, and use by several bird and mammal species decreased with increased localized disturbances. We found few differences in habitat use between sampling sites in undeveloped areas and in CD subdivisions. These similarities indicate that, if CDs are large enough or located within a matrix of undeveloped land, they can provide habitat that supports similar use patterns as protected areas without housing development. By incorporating characteristics that promote the persistence of sensitive birds and mammals on private lands, CDs have potential to preserve native biodiversity in areas threatened by expanding residential development.

Using landscape habitat associations to prioritize areas of conservation action for terrestrial birds.

Predicting species distributions has long been a valuable tool to plan and focus efforts for biodiversity conservation, particularly because such an approach allows researchers and managers to evaluate species distribution changes in response to various threats. Utilizing data from a long-term monitoring program and land cover data sets, we modeled the probability of occupancy and colonization for 38 bird Species of Greatest Conservation Need (SGCN) in the robust design occupancy modeling framework, and used results from the best models to predict occupancy and colonization on the Iowa landscape. Bird surveys were conducted at 292 properties from April to October, 2006–2014. We calculated landscape habitat characteristics at multiple spatial scales surrounding each of our surveyed properties to be used in our models and then used kriging in ArcGIS to create predictive maps of species distributions. We validated models with data from 2013 using the area under the receiver operating characteristic curve (AUC). Probability of occupancy ranged from 0.001 (SE < 0.001) to 0.995 (SE = 0.004) for all species and probability of colonization ranged from 0.001 (SE < 0.001) to 0.999 (SE < 0.001) for all species. AUC values for predictive models ranged from 0.525–0.924 for all species, with 17 species having predictive models considered useful (AUC > 0.70). The most important predictor for occupancy of grassland birds was percentage of the landscape in grassland habitat, and the most important predictor for woodland birds was percentage of the landscape in woodland habitat. This emphasizes the need for managers to restore specific habitats on the landscape. In an era during which funding continues to decrease for conservation agencies, our approach aids in determining where to focus limited resources to best conserve bird species of conservation concern.

Land cover dynamics influence distribution of breeding birds in the Great Plains, USA

Grasslands are one of the most endangered ecosystems globally. Large tracts of grassland in the Great Plains, USA have been converted to cropland since the early 1900s, and woodlands are rapidly encroaching into many grasslands of the region due to changes in land management practices. Changes in the arrangement and proportion of different land cover types can affect biodiversity. We used bird survey data to identify the effect of land cover change on breeding bird ranges within the Great Plains over a 10-year period. Each species was categorized into one of the following habitat guilds: grassland, shrubland, woodland, wetland and generalist. We calculated the proportion of each land cover (including cropland, grassland, woodland, developed, barren, water bodies and wetlands) within a 1.6km radius of each bird survey starting point. Within an occupancy modeling framework, we estimated colonization and extinction rates for each species and averaged them to the guild level. We also quantified changes in land cover from grassland to other cover types. Results show that grasslands were mostly converted to cropland and woodland, which were accompanied by positive extinction rates for certain grassland species. Extinction rates at the guild level were unrelated to increases in any land cover type, and observed land cover changes largely favored the shrubland guild. Overall, habitat-guild responses show little influence of woodland or cropland expansion at regional scales, although certain species ranges are predicted to decrease with increases in woodland. Future research should consider a finer scaled approach focusing on species-level responses when short-term land cover changes are considered.