@article{sollmann_mohamed_niedballa_bender_ambu_lagan_mannan_ong_langner_gardner_et al._2017, title={Quantifying mammal biodiversity co-benefits in certified tropical forests}, volume={23}, ISSN={["1472-4642"]}, DOI={10.1111/ddi.12530}, abstractNote={Abstract}, number={3}, journal={DIVERSITY AND DISTRIBUTIONS}, author={Sollmann, Rahel and Mohamed, Azlan and Niedballa, Jurgen and Bender, Johannes and Ambu, Laurentius and Lagan, Peter and Mannan, Sam and Ong, Robert C. and Langner, Andreas and Gardner, Beth and et al.}, year={2017}, month={Mar}, pages={317–328} }
 @article{sollmann_gardner_williams_gilbert_veit_2016, title={A hierarchical distance sampling model to estimate abundance and covariate associations of species and communities}, volume={7}, ISSN={["2041-2096"]}, DOI={10.1111/2041-210x.12518}, abstractNote={Summary}, number={5}, journal={METHODS IN ECOLOGY AND EVOLUTION}, author={Sollmann, Rahel and Gardner, Beth and Williams, Kathryn A. and Gilbert, Andrew T. and Veit, Richard R.}, year={2016}, month={May}, pages={529–537} }
 @article{gardner_garner_cobb_moorman_2016, title={Factors Affecting Occupancy and Abundance of American Alligators at the Northern Extent of Their Range}, volume={50}, ISSN={["1937-2418"]}, DOI={10.1670/15-147}, abstractNote={Abstract Populations of American Alligators (Alligator mississippiensis) generally are considered more abundant at present than historically; however, little information exists to assess the population of alligators in North Carolina at the northern extent of the species' range. Investigation of the factors influencing the distribution and abundance of alligators in North Carolina could shed light on the species' response to rapid environmental change in the region. We conducted a two-phase study: 1) to assess the distribution of alligators in North Carolina using a site-occupancy design; and 2) to assess the patterns in abundance using a repeated sampling design for population estimation. Results showed that both occupancy and abundance decreased in more northern sites, in sites with higher salinity, and in sites that were generally more westward. Sites sampled later in June were more likely to be occupied than those sampled earlier in the month. Abundance also increased with greater shoreline vegetation complexity and varied between lakes, rivers, and estuaries. Compared with studies from 30 years prior, the population seems fairly stable in terms of abundance and distribution. Given the northern limits of the species and the negative association with salinity, continued monitoring is warranted to understand changes in distribution and abundance with respect to predicted rates of sea-level rise, salinization, and urbanization locally around coastal cities like Wilmington.}, number={4}, journal={JOURNAL OF HERPETOLOGY}, author={Gardner, Beth and Garner, Lindsey A. and Cobb, David T. and Moorman, Christopher E.}, year={2016}, month={Dec}, pages={541–547} }
 @article{goyert_gardner_sollmann_veit_gilbert_connelly_williams_2016, title={Predicting the offshore distribution and abundance of marine birds with a hierarchical community distance sampling model}, volume={26}, ISSN={["1939-5582"]}, DOI={10.1890/15-1955.1}, abstractNote={Abstract}, number={6}, journal={ECOLOGICAL APPLICATIONS}, author={Goyert, Holly F. and Gardner, Beth and Sollmann, Rahel and Veit, Richard R. and Gilbert, Andrew T. and Connelly, Emily E. and Williams, Kathryn A.}, year={2016}, month={Sep}, pages={1797–1815} }
 @article{sollmann_gardner_chandler_royle_sillett_2015, title={An open-population hierarchical distance sampling model}, volume={96}, ISSN={["1939-9170"]}, DOI={10.1890/14-1625.1}, abstractNote={Modeling population dynamics while accounting for imperfect detection is essential to monitoring programs. Distance sampling allows estimating population size while accounting for imperfect detection, but existing methods do not allow for estimation of demographic parameters. We develop a model that uses temporal correlation in abundance arising from underlying population dynamics to estimate demographic parameters from repeated distance sampling surveys. Using a simulation study motivated by designing a monitoring program for Island Scrub‐Jays (Aphelocoma insularis), we investigated the power of this model to detect population trends. We generated temporally autocorrelated abundance and distance sampling data over six surveys, using population rates of change of 0.95 and 0.90. We fit the data generating Markovian model and a mis‐specified model with a log‐linear time effect on abundance, and derived post hoc trend estimates from a model estimating abundance for each survey separately. We performed these analyses for varying numbers of survey points. Power to detect population changes was consistently greater under the Markov model than under the alternatives, particularly for reduced numbers of survey points. The model can readily be extended to more complex demographic processes than considered in our simulations. This novel framework can be widely adopted for wildlife population monitoring.}, number={2}, journal={ECOLOGY}, author={Sollmann, Rahel and Gardner, Beth and Chandler, Richard B. and Royle, J. Andrew and Sillett, T. Scott}, year={2015}, month={Feb}, pages={325–331} }
 @article{mollet_kery_gardner_pasinelli_royle_2015, title={Estimating Population Size for Capercaillie (Tetrao urogallus L.) with Spatial Capture-Recapture Models Based on Genotypes from One Field Sample}, volume={10}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0129020}, abstractNote={We conducted a survey of an endangered and cryptic forest grouse, the capercaillie Tetrao urogallus, based on droppings collected on two sampling occasions in eight forest fragments in central Switzerland in early spring 2009. We used genetic analyses to sex and individually identify birds. We estimated sex-dependent detection probabilities and population size using a modern spatial capture-recapture (SCR) model for the data from pooled surveys. A total of 127 capercaillie genotypes were identified (77 males, 46 females, and 4 of unknown sex). The SCR model yielded atotal population size estimate (posterior mean) of 137.3 capercaillies (posterior sd 4.2, 95% CRI 130–147). The observed sex ratio was skewed towards males (0.63). The posterior mean of the sex ratio under the SCR model was 0.58 (posterior sd 0.02, 95% CRI 0.54–0.61), suggesting a male-biased sex ratio in our study area. A subsampling simulation study indicated that a reduced sampling effort representing 75% of the actual detections would still yield practically acceptable estimates of total size and sex ratio in our population. Hence, field work and financial effort could be reduced without compromising accuracy when the SCR model is used to estimate key population parameters of cryptic species.}, number={6}, journal={PLOS ONE}, author={Mollet, Pierre and Kery, Marc and Gardner, Beth and Pasinelli, Gilberto and Royle, J. Andrew}, year={2015}, month={Jun} }
 @article{sollmann_white_gardner_manley_2015, title={Investigating the effects of forest structure on the small mammal community in frequent-fire coniferous forests using capture-recapture models for stratified populations}, volume={80}, ISSN={["1618-1476"]}, DOI={10.1016/j.mambio.2015.03.002}, abstractNote={Small mammals comprise an important component of forest vertebrate communities. Our understanding of how small mammals use forested habitat has relied heavily on studies in forest systems not naturally prone to frequent disturbances. Small mammal populations that evolved in frequent-fire forests, however, may be less restricted to specific habitat conditions due to the instability of these resources in time and space. We investigate how canopy cover and the volume of coarse woody debris (CWD), covariates that are considered important for small mammals, impact abundance and body mass of eight small mammal species. Based on live-trapping data collected across 23 sites over three years in a frequent fire forest in the Sierra Nevada we apply capture-recapture models for stratified populations, a statistically rigorous, rarely used framework that allows joint modeling of detection, abundance and its response to covariates. Canopy cover had a strong negative association with the abundance of yellow-pine chipmunks and California ground squirrels, and a strong positive association with deer mice. CWD had a strong negative association with the abundance of golden-mantled ground squirrels, yellow-pine and long-eared chipmunks, and a strong positive association with deer mice. Whereas canopy cover influenced abundance and body mass similarly, CWD had a positive association with body mass and a negative association with abundance in some species. These patterns could arise if suitable habitat is monopolized by socially dominant individuals. Despite these habitat associations, the small mammal community in our study was dynamic and diverse, with spatial and temporal variation in dominant species suggesting that species were flexible in their use of habitat. This study suggests that it is important to understand the disturbance regimes when investigating habitat requirements, coexistence and evolutionary ecology of small mammal species.}, number={4}, journal={MAMMALIAN BIOLOGY}, author={Sollmann, Rahel and White, Angela M. and Gardner, Beth and Manley, Patricia N.}, year={2015}, month={Aug}, pages={247–254} }
 @article{flanders_gardner_winiarski_paton_allison_allan f. o'connell_2015, title={Key seabird areas in southern New England identified using a community occupancy model}, volume={533}, ISSN={["1616-1599"]}, DOI={10.3354/meps11316}, abstractNote={Seabirds are of conservation concern, and as new potential risks to seabirds are arising, the need to provide unbiased estimates of species’ distributions is growing. We applied community occupancy models to detection/non-detection data collected from repeated aerial striptransect surveys conducted in 2 large study plots off southern New England, USA; one off the coast of Rhode Island and the other in Nantucket Sound. A total of 17 seabird species were observed at least once in each study plot. We found that detection varied by survey date and effort for most species and the average detection probability across species was less than 0.4. We estimated the influence of water depth, sea surface temperature, and sea surface chl a concentration on species-specific occupancy. Diving species showed large differences between the 2 study plots in their predicted winter distributions, which were largely explained by water depth acting as a stronger predictor of occupancy in Rhode Island than in Nantucket Sound. Conversely, similarities between the 2 study plots in predicted winter distributions of surface-feeding species were explained by sea surface temperature or chlorophyll a concentration acting as predictors of these species’ occupancy in both study plots. We predicted the number of species at each site using the observed data in order to detect ‘hot-spots’ of seabird diversity and use in the 2 study plots. These results provide new information on detection of species, areas of use, and relationships with environmental variables that will be valuable for biologists and planners interested in seabird conservation in the region.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Flanders, Nicholas P. and Gardner, Beth and Winiarski, Kristopher J. and Paton, Peter W. C. and Allison, Taber and Allan F. O'Connell}, year={2015}, month={Aug}, pages={277–290} }
 @article{henry_haddad_wilson_hughes_gardner_2015, title={Point-count methods to monitor butterfly populations when traditional methods fail: a case study with Miami blue butterfly}, volume={19}, ISSN={["1572-9753"]}, DOI={10.1007/s10841-015-9773-6}, number={3}, journal={JOURNAL OF INSECT CONSERVATION}, author={Henry, Erica H. and Haddad, Nick M. and Wilson, John and Hughes, Phillip and Gardner, Beth}, year={2015}, month={Jun}, pages={519–529} }
 @article{hostetter_gardner_schweitzer_boettcher_wilke_addison_swilling_pollock_simons_2015, title={Repeated count surveys help standardize multi-agency estimates of American Oystercatcher (Haematopus palliatus) abundance}, volume={117}, ISSN={0010-5422 1938-5129}, url={http://dx.doi.org/10.1650/CONDOR-14-185.1}, DOI={10.1650/condor-14-185.1}, abstractNote={ABSTRACT The extensive breeding range of many shorebird species can make integration of survey data problematic at regional spatial scales. We evaluated the effectiveness of standardized repeated count surveys coordinated across 8 agencies to estimate the abundance of American Oystercatcher (Haematopus palliatus) breeding pairs in the southeastern United States. Breeding season surveys were conducted across coastal North Carolina (90 plots) and the Eastern Shore of Virginia (3 plots). Plots were visited on 1–5 occasions during April–June 2013. N-mixture models were used to estimate abundance and detection probability in relation to survey date, tide stage, plot size, and plot location (coastal bay vs. barrier island). The estimated abundance of oystercatchers in the surveyed area was 1,048 individuals (95% credible interval: 851–1,408) and 470 pairs (384–637), substantially higher than estimates that did not account for detection probability (maximum counts of 674 individuals and 316 pairs). Detection probability was influenced by a quadratic function of survey date, and increased from mid-April (~0.60) to mid-May (~0.80), then remained relatively constant through June. Detection probability was also higher during high tide than during low, rising, or falling tides. Abundance estimates from N-mixture models were validated at 13 plots by exhaustive productivity studies (2–5 surveys wk−1). Intensive productivity studies identified 78 breeding pairs across 13 productivity plots while the N-mixture model abundance estimate was 74 pairs (62–119) using only 1–5 replicated surveys season−1. Our results indicate that standardized replicated count surveys coordinated across multiple agencies and conducted during a relatively short time window (closure assumption) provide tremendous potential to meet both agency-level (e.g., state) and regional-level (e.g., flyway) objectives in large-scale shorebird monitoring programs.}, number={3}, journal={The Condor}, publisher={Oxford University Press (OUP)}, author={Hostetter, Nathan J. and Gardner, Beth and Schweitzer, Sara H. and Boettcher, Ruth and Wilke, Alexandra L. and Addison, Lindsay and Swilling, William R. and Pollock, Kenneth H. and Simons, Theodore R.}, year={2015}, month={Aug}, pages={354–363} }
 @article{bozarth_gardner_rockwood_maldonado_2015, title={Using Fecal DNA and Spatial Capture-Recapture to Characterize a Recent Coyote Colonization}, volume={22}, ISSN={["1938-5307"]}, DOI={10.1656/045.022.0124}, abstractNote={Abstract 
 The arrival of a novel predator in an ecosystem necessitates many wildlife-management decisions that should be based on sound demographic data. Canis latrans (Coyote) has experienced a dramatic range expansion across North America since the early 19th century, completing its colonization of the continental US in the mid-Atlantic region over the past 20 years. Their arrival in the suburbs of Washington, DC, has generated much public attention, and demonstrated a need for demographic information about this species. To address the challenges of surveying an elusive animal, we used fecal DNA to describe the population genetics and demographics of a newly colonized Coyote population at Marine Corps Base Quantico (MCBQ) in northern Virginia. We collected 331 scats over a period of 2 years at MCBQ, resulting in identification of 23 unique individual Coyotes and 41 total Coyote captures that were analyzed using spatial capture—recapture models. We found evidence of colonization by multiple genetic lineages and a low population density of 0.047 individuals/km2. Importantly, this study incorporates a new class of models on individual animals identified by genotype data derived from fecal DNA and demonstrates the utility of these models in surveying elusive animals.}, number={1}, journal={NORTHEASTERN NATURALIST}, author={Bozarth, Christine A. and Gardner, Beth and Rockwood, Larry L. and Maldonado, Jesus E.}, year={2015}, month={Mar}, pages={144–162} }
 @article{reich_gardner_2014, title={A spatial capture-recapture model for territorial species}, volume={25}, DOI={10.1002/env.2317}, abstractNote={Advances in field techniques have lead to an increase in spatially referenced capture–recapture data to estimate a species' population size as well as other demographic parameters and patterns of space usage. Statistical models for these data have assumed that the number of individuals in the population and their spatial locations follow a homogeneous Poisson point process model, which implies that the individuals are uniformly and independently distributed over the spatial domain of interest. In many applications, there is reason to question independence, for example, when species display territorial behavior. In this paper, we propose a new statistical model, which allows for dependence between locations to account for avoidance or territorial behavior. We show via a simulation study that accounting for this can improve population size estimates. The method is illustrated using a case study of small mammal trapping data to estimate avoidance and population density of adult female field voles (Microtus agrestis) in Northern England. Copyright © 2014 John Wiley & Sons, Ltd.}, number={8}, journal={Environmetrics}, author={Reich, Brian and Gardner, B.}, year={2014}, pages={630–637} }
 @article{raabe_gardner_hightower_2014, title={A spatial capture-recapture model to estimate fish survival and location from linear continuous monitoring arrays}, volume={71}, ISSN={["1205-7533"]}, DOI={10.1139/cjfas-2013-0198}, abstractNote={ We developed a spatial capture–recapture model to evaluate survival and activity centres (i.e., mean locations) of tagged individuals detected along a linear array. Our spatially explicit version of the Cormack–Jolly–Seber model, analyzed using a Bayesian framework, correlates movement between periods and can incorporate environmental or other covariates. We demonstrate the model using 2010 data for anadromous American shad (Alosa sapidissima) tagged with passive integrated transponders (PIT) at a weir near the mouth of a North Carolina river and passively monitored with an upstream array of PIT antennas. The river channel constrained migrations, resulting in linear, one-dimensional encounter histories that included both weir captures and antenna detections. Individual activity centres in a given time period were a function of the individual’s previous estimated location and the river conditions (i.e., gage height). Model results indicate high within-river spawning mortality (mean weekly survival = 0.80) and more extensive movements during elevated river conditions. This model is applicable for any linear array (e.g., rivers, shorelines, and corridors), opening new opportunities to study demographic parameters, movement or migration, and habitat use. }, number={1}, journal={CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES}, author={Raabe, Joshua K. and Gardner, Beth and Hightower, Joseph E.}, year={2014}, month={Jan}, pages={120–130} }
 @article{dunn_boustany_roberts_brazer_sanderson_gardner_halpin_2014, title={Empirical move-on rules to inform fishing strategies: a New England case study}, volume={15}, ISSN={["1467-2979"]}, DOI={10.1111/faf.12019}, abstractNote={Abstract}, number={3}, journal={FISH AND FISHERIES}, author={Dunn, Daniel C. and Boustany, Andre M. and Roberts, Jason J. and Brazer, Eric and Sanderson, Melissa and Gardner, Beth and Halpin, Patrick N.}, year={2014}, month={Sep}, pages={359–375} }
 @article{martin_edwards_bled_fonnesbeck_dupuis_gardner_koslovsky_aven_ward-geiger_carmichael_et al._2014, title={Estimating Upper Bounds for Occupancy and Number of Manatees in Areas Potentially Affected by Oil from the Deepwater Horizon Oil Spill}, volume={9}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0091683}, abstractNote={The explosion of the Deepwater Horizon drilling platform created the largest marine oil spill in U.S. history. As part of the Natural Resource Damage Assessment process, we applied an innovative modeling approach to obtain upper estimates for occupancy and for number of manatees in areas potentially affected by the oil spill. Our data consisted of aerial survey counts in waters of the Florida Panhandle, Alabama and Mississippi. Our method, which uses a Bayesian approach, allows for the propagation of uncertainty associated with estimates from empirical data and from the published literature. We illustrate that it is possible to derive estimates of occupancy rate and upper estimates of the number of manatees present at the time of sampling, even when no manatees were observed in our sampled plots during surveys. We estimated that fewer than 2.4% of potentially affected manatee habitat in our Florida study area may have been occupied by manatees. The upper estimate for the number of manatees present in potentially impacted areas (within our study area) was estimated with our model to be 74 (95%CI 46 to 107). This upper estimate for the number of manatees was conditioned on the upper 95%CI value of the occupancy rate. In other words, based on our estimates, it is highly probable that there were 107 or fewer manatees in our study area during the time of our surveys. Because our analyses apply to habitats considered likely manatee habitats, our inference is restricted to these sites and to the time frame of our surveys. Given that manatees may be hard to see during aerial surveys, it was important to account for imperfect detection. The approach that we described can be useful for determining the best allocation of resources for monitoring and conservation.}, number={3}, journal={PLOS ONE}, author={Martin, Julien and Edwards, Holly H. and Bled, Florent and Fonnesbeck, Christopher J. and Dupuis, Jerome A. and Gardner, Beth and Koslovsky, Stacie M. and Aven, Allen M. and Ward-Geiger, Leslie I. and Carmichael, Ruth H. and et al.}, year={2014}, month={Mar} }
 @article{bowling_moorman_deperno_gardner_2014, title={Influence of Landscape Composition on Northern Bobwhite Population Response to Field Border Establishment}, volume={78}, ISSN={["1937-2817"]}, DOI={10.1002/jwmg.639}, abstractNote={ABSTRACT}, number={1}, journal={JOURNAL OF WILDLIFE MANAGEMENT}, author={Bowling, Shannon A. and Moorman, Christopher E. and Deperno, Christopher S. and Gardner, Beth}, year={2014}, month={Jan}, pages={93–100} }
 @article{ergon_gardner_2014, title={Separating mortality and emigration: modelling space use, dispersal and survival with robust-design spatial capture-recapture data}, volume={5}, ISSN={["2041-2096"]}, DOI={10.1111/2041-210x.12133}, abstractNote={Summary}, number={12}, journal={METHODS IN ECOLOGY AND EVOLUTION}, author={Ergon, Torbjorn and Gardner, Beth}, year={2014}, month={Dec}, pages={1327–1336} }
 @article{wilton_puckett_beringer_gardner_eggert_belant_2014, title={Trap Array Configuration Influences Estimates and Precision of Black Bear Density and Abundance}, volume={9}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0111257}, abstractNote={Spatial capture-recapture (SCR) models have advanced our ability to estimate population density for wide ranging animals by explicitly incorporating individual movement. Though these models are more robust to various spatial sampling designs, few studies have empirically tested different large-scale trap configurations using SCR models. We investigated how extent of trap coverage and trap spacing affects precision and accuracy of SCR parameters, implementing models using the R package secr. We tested two trapping scenarios, one spatially extensive and one intensive, using black bear (Ursus americanus) DNA data from hair snare arrays in south-central Missouri, USA. We also examined the influence that adding a second, lower barbed-wire strand to snares had on quantity and spatial distribution of detections. We simulated trapping data to test bias in density estimates of each configuration under a range of density and detection parameter values. Field data showed that using multiple arrays with intensive snare coverage produced more detections of more individuals than extensive coverage. Consequently, density and detection parameters were more precise for the intensive design. Density was estimated as 1.7 bears per 100 km2 and was 5.5 times greater than that under extensive sampling. Abundance was 279 (95% CI = 193–406) bears in the 16,812 km2 study area. Excluding detections from the lower strand resulted in the loss of 35 detections, 14 unique bears, and the largest recorded movement between snares. All simulations showed low bias for density under both configurations. Results demonstrated that in low density populations with non-uniform distribution of population density, optimizing the tradeoff among snare spacing, coverage, and sample size is of critical importance to estimating parameters with high precision and accuracy. With limited resources, allocating available traps to multiple arrays with intensive trap spacing increased the amount of information needed to inform parameters with high precision.}, number={10}, journal={PLOS ONE}, author={Wilton, Clay M. and Puckett, Emily E. and Beringer, Jeff and Gardner, Beth and Eggert, Lori S. and Belant, Jerrold L.}, year={2014}, month={Oct} }
 @article{carrillo-rubio_kery_morreale_sullivan_gardner_cooch_lassoie_2014, title={Use of Multispecies Occupancy Models to Evaluate the Response of Bird Communities to Forest Degradation Associated with Logging}, volume={28}, ISSN={["1523-1739"]}, DOI={10.1111/cobi.12261}, abstractNote={Abstract}, number={4}, journal={CONSERVATION BIOLOGY}, author={Carrillo-Rubio, Eduardo and Kery, Marc and Morreale, Stephen J. and Sullivan, Patrick J. and Gardner, Beth and Cooch, Evan G. and Lassoie, James P.}, year={2014}, month={Aug}, pages={1034–1044} }
 @article{sollmann_gardner_parsons_stocking_mcclintock_simons_pollock_allan f. o'connell_2013, title={A spatial mark-resight model augmented with telemetry data}, volume={94}, ISSN={["1939-9170"]}, DOI={10.1890/12-1256.1}, abstractNote={Abundance and population density are fundamental pieces of information for population ecology and species conservation, but they are difficult to estimate for rare and elusive species. Mark–resight models are popular for estimating population abundance because they are less invasive and expensive than traditional mark–recapture. However, density estimation using mark–resight is difficult because the area sampled must be explicitly defined, historically using ad hoc approaches. We developed a spatial mark–resight model for estimating population density that combines spatial resighting data and telemetry data. Incorporating telemetry data allows us to inform model parameters related to movement and individual location. Our model also allows <100% individual identification of marked individuals. We implemented the model in a Bayesian framework, using a custom‐made Metropolis‐within‐Gibbs Markov chain Monte Carlo algorithm. As an example, we applied this model to a mark–resight study of raccoons (Procyon lotor) on South Core Banks, a barrier island in Cape Lookout National Seashore, North Carolina, USA. We estimated a population of 186.71 ± 14.81 individuals, which translated to a density of 8.29 ± 0.66 individuals/km2 (mean ± SD). The model presented here will have widespread utility in future applications, especially for species that are not naturally marked.}, number={3}, journal={ECOLOGY}, author={Sollmann, Rahel and Gardner, Beth and Parsons, Arielle W. and Stocking, Jessica J. and McClintock, Brett T. and Simons, Theodore R. and Pollock, Kenneth H. and Allan F. O'Connell}, year={2013}, month={Mar}, pages={553–559} }
 @article{mcgowan_gardner_2013, title={Evaluating Methodological Assumptions of Catch-Curve Survival Estimation for Unmarked Precocial Shorebird Chicks}, volume={36}, ISSN={["1938-5390"]}, DOI={10.1675/063.036.0112}, abstractNote={Abstract. 
 Estimating productivity for precocial species can be difficult because young birds leave their nest within hours or days of hatching and detectability thereafter can be very low. Recently, a method for using a modified catch-curve to estimate precocial chick daily survival for age based count data was presented using Piping Plover (Charadrius melodus) data from the Missouri River. However, many of the assumptions of the catch-curve approach were not fully evaluated for precocial chicks. We developed a simulation model to mimic Piping Plovers, a fairly representative shorebird, and age-based count-data collection. Using the simulated data, we calculated daily survival estimates and compared them with the known daily survival rates from the simulation model. We conducted these comparisons under different sampling scenarios where the ecological and statistical assumptions had been violated. Overall, the daily survival estimates calculated from the simulated data corresponded well with true survival rates of the simulation. Violating the accurate aging and the independence assumptions did not result in biased daily survival estimates, whereas unequal detection for younger or older birds and violating the birth death equilibrium did result in estimator bias. Assuring that all ages are equally detectable and timing data collection to approximately meet the birth death equilibrium are key to the successful use of this method for precocial shorebirds.}, number={1}, journal={WATERBIRDS}, author={McGowan, Conor P. and Gardner, Beth}, year={2013}, month={Mar}, pages={82–87} }
 @article{mattsson_zipkin_gardner_blank_sauer_royle_2013, title={Explaining Local-Scale Species Distributions: Relative Contributions of Spatial Autocorrelation and Landscape Heterogeneity for an Avian Assemblage}, volume={8}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0055097}, abstractNote={Understanding interactions between mobile species distributions and landcover characteristics remains an outstanding challenge in ecology. Multiple factors could explain species distributions including endogenous evolutionary traits leading to conspecific clustering and endogenous habitat features that support life history requirements. Birds are a useful taxon for examining hypotheses about the relative importance of these factors among species in a community. We developed a hierarchical Bayes approach to model the relationships between bird species occupancy and local landcover variables accounting for spatial autocorrelation, species similarities, and partial observability. We fit alternative occupancy models to detections of 90 bird species observed during repeat visits to 316 point-counts forming a 400-m grid throughout the Patuxent Wildlife Research Refuge in Maryland, USA. Models with landcover variables performed significantly better than our autologistic and null models, supporting the hypothesis that local landcover heterogeneity is important as an exogenous driver for species distributions. Conspecific clustering alone was a comparatively poor descriptor of local community composition, but there was evidence for spatial autocorrelation in all species. Considerable uncertainty remains whether landcover combined with spatial autocorrelation is most parsimonious for describing bird species distributions at a local scale. Spatial structuring may be weaker at intermediate scales within which dispersal is less frequent, information flows are localized, and landcover types become spatially diversified and therefore exhibit little aggregation. Examining such hypotheses across species assemblages contributes to our understanding of community-level associations with conspecifics and landscape composition.}, number={2}, journal={PLOS ONE}, author={Mattsson, Brady J. and Zipkin, Elise F. and Gardner, Beth and Blank, Peter J. and Sauer, John R. and Royle, J. Andrew}, year={2013}, month={Feb} }
 @article{chen_kery_plattner_ma_gardner_2013, title={Imperfect detection is the rule rather than the exception in plant distribution studies}, volume={101}, ISSN={["1365-2745"]}, DOI={10.1111/1365-2745.12021}, abstractNote={Summary}, number={1}, journal={JOURNAL OF ECOLOGY}, author={Chen, Guoke and Kery, Marc and Plattner, Matthias and Ma, Keping and Gardner, Beth}, year={2013}, month={Jan}, pages={183–191} }
 @article{sollmann_gardner_chandler_shindle_onorato_royle_allan f. o'connell_2013, title={Using multiple data sources provides density estimates for endangered Florida panther}, volume={50}, ISSN={["1365-2664"]}, DOI={10.1111/1365-2664.12098}, abstractNote={Summary}, number={4}, journal={JOURNAL OF APPLIED ECOLOGY}, author={Sollmann, Rahel and Gardner, Beth and Chandler, Richard B. and Shindle, David B. and Onorato, David P. and Royle, Jeffrey Andrew and Allan F. O'Connell}, year={2013}, month={Aug}, pages={961–968} }
 @article{noss_gardner_maffei_cuellar_montano_romero-munoz_sollman_o'connell_2012, title={Comparison of density estimation methods for mammal populations with camera traps in the Kaa-Iya del Gran Chaco landscape}, volume={15}, ISSN={["1469-1795"]}, DOI={10.1111/j.1469-1795.2012.00545.x}, abstractNote={Abstract}, number={5}, journal={ANIMAL CONSERVATION}, author={Noss, A. J. and Gardner, B. and Maffei, L. and Cuellar, E. and Montano, R. and Romero-Munoz, A. and Sollman, R. and O'Connell, A. F.}, year={2012}, month={Oct}, pages={527–535} }
 @article{oppel_meirinho_ramirez_gardner_allan f. o'connell_miller_louzao_2012, title={Comparison of five modelling techniques to predict the spatial distribution and abundance of seabirds}, volume={156}, ISSN={["1873-2917"]}, DOI={10.1016/j.biocon.2011.11.013}, abstractNote={Knowledge about the spatial distribution of seabirds at sea is important for conservation. During marine conservation planning, logistical constraints preclude seabird surveys covering the complete area of interest and spatial distribution of seabirds is frequently inferred from predictive statistical models. Increasingly complex models are available to relate the distribution and abundance of pelagic seabirds to environmental variables, but a comparison of their usefulness for delineating protected areas for seabirds is lacking. Here we compare the performance of five modelling techniques (generalised linear models, generalised additive models, Random Forest, boosted regression trees, and maximum entropy) to predict the distribution of Balearic Shearwaters (Puffinus mauretanicus) along the coast of the western Iberian Peninsula. We used ship transect data from 2004 to 2009 and 13 environmental variables to predict occurrence and density, and evaluated predictive performance of all models using spatially segregated test data. Predicted distribution varied among the different models, although predictive performance varied little. An ensemble prediction that combined results from all five techniques was robust and confirmed the existence of marine important bird areas for Balearic Shearwaters in Portugal and Spain. Our predictions suggested additional areas that would be of high priority for conservation and could be proposed as protected areas. Abundance data were extremely difficult to predict, and none of five modelling techniques provided a reliable prediction of spatial patterns. We advocate the use of ensemble modelling that combines the output of several methods to predict the spatial distribution of seabirds, and use these predictions to target separate surveys assessing the abundance of seabirds in areas of regular use.}, journal={BIOLOGICAL CONSERVATION}, author={Oppel, Steffen and Meirinho, Ana and Ramirez, Ivan and Gardner, Beth and Allan F. O'Connell and Miller, Peter I. and Louzao, Maite}, year={2012}, pages={94–104} }
 @article{martin_edwards_burgess_percival_fagan_gardner_ortega-ortiz_ifju_evers_rambo_2012, title={Estimating Distribution of Hidden Objects with Drones: From Tennis Balls to Manatees}, volume={7}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0038882}, abstractNote={Unmanned aerial vehicles (UAV), or drones, have been used widely in military applications, but more recently civilian applications have emerged (e.g., wildlife population monitoring, traffic monitoring, law enforcement, oil and gas pipeline threat detection). UAV can have several advantages over manned aircraft for wildlife surveys, including reduced ecological footprint, increased safety, and the ability to collect high-resolution geo-referenced imagery that can document the presence of species without the use of a human observer. We illustrate how geo-referenced data collected with UAV technology in combination with recently developed statistical models can improve our ability to estimate the distribution of organisms. To demonstrate the efficacy of this methodology, we conducted an experiment in which tennis balls were used as surrogates of organisms to be surveyed. We used a UAV to collect images of an experimental field with a known number of tennis balls, each of which had a certain probability of being hidden. We then applied spatially explicit occupancy models to estimate the number of balls and created precise distribution maps. We conducted three consecutive surveys over the experimental field and estimated the total number of balls to be 328 (95%CI: 312, 348). The true number was 329 balls, but simple counts based on the UAV pictures would have led to a total maximum count of 284. The distribution of the balls in the field followed a simulated environmental gradient. We also were able to accurately estimate the relationship between the gradient and the distribution of balls. Our experiment demonstrates how this technology can be used to create precise distribution maps in which discrete regions of the study area are assigned a probability of presence of an object. Finally, we discuss the applicability and relevance of this experimental study to the case study of Florida manatee distribution at power plants.}, number={6}, journal={PLOS ONE}, author={Martin, Julien and Edwards, Holly H. and Burgess, Matthew A. and Percival, H. Franklin and Fagan, Daniel E. and Gardner, Beth E. and Ortega-Ortiz, Joel G. and Ifju, Peter G. and Evers, Brandon S. and Rambo, Thomas J.}, year={2012}, month={Jun} }
 @article{sollmann_gardner_belant_2012, title={How Does Spatial Study Design Influence Density Estimates from Spatial Capture-Recapture Models?}, volume={7}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0034575}, abstractNote={When estimating population density from data collected on non-invasive detector arrays, recently developed spatial capture-recapture (SCR) models present an advance over non-spatial models by accounting for individual movement. While these models should be more robust to changes in trapping designs, they have not been well tested. Here we investigate how the spatial arrangement and size of the trapping array influence parameter estimates for SCR models. We analysed black bear data collected with 123 hair snares with an SCR model accounting for differences in detection and movement between sexes and across the trapping occasions. To see how the size of the trap array and trap dispersion influence parameter estimates, we repeated analysis for data from subsets of traps: 50% chosen at random, 50% in the centre of the array and 20% in the South of the array. Additionally, we simulated and analysed data under a suite of trap designs and home range sizes. In the black bear study, we found that results were similar across trap arrays, except when only 20% of the array was used. Black bear density was approximately 10 individuals per 100 km2. Our simulation study showed that SCR models performed well as long as the extent of the trap array was similar to or larger than the extent of individual movement during the study period, and movement was at least half the distance between traps. SCR models performed well across a range of spatial trap setups and animal movements. Contrary to non-spatial capture-recapture models, they do not require the trapping grid to cover an area several times the average home range of the studied species. This renders SCR models more appropriate for the study of wide-ranging mammals and more flexible to design studies targeting multiple species.}, number={4}, journal={PLOS ONE}, author={Sollmann, Rahel and Gardner, Beth and Belant, Jerrold L.}, year={2012}, month={Apr} }
 @article{wegan_curtis_rainbolt_gardner_2012, title={Temporal sampling frame selection in DNA-based capture-mark-recapture investigations}, volume={23}, DOI={10.2192/ursus-d-11-00013.1}, abstractNote={Abstract Capture–mark–recapture (CMR) population parameter estimation utilizing DNA analysis from remotely-collected hair samples to identify individuals and generate encounter histories has become the standard methodology for estimating abundance of American black (Ursus americanus) and grizzly bear (U. arctos) populations. However, few published studies have examined the time frame for efficiently collecting high-quality hair samples. Our objectives were to examine several measures of hair trapping success and sample quality, such as DNA amplification rates and the mean number of black bear hair samples collected per trap visit, from hair-snare samples collected in 2 non-overlapping, multi-interval sampling frames conducted during 2005 and 2006 at Fort Drum Military Installation in northern New York. Through our data analyses and a review of 12 other bear CMR studies using remote hair sampling, we emphasize that temporal sampling frame is a crucial consideration in study design. To avoid biased population estimates and to use financial, personnel, and temporal resources effectively, hair sampling should be conducted during late spring and early summer.}, number={1}, journal={URSUS}, author={Wegan, M. T. and Curtis, P. D. and Rainbolt, R. E. and Gardner, B.}, year={2012}, pages={42–51} }
 @article{martin_royle_mackenzie_edwards_kery_gardner_2011, title={Accounting for non-independent detection when estimating abundance of organisms with a Bayesian approach}, volume={2}, ISSN={["2041-2096"]}, DOI={10.1111/j.2041-210x.2011.00113.x}, abstractNote={Summary}, number={6}, journal={METHODS IN ECOLOGY AND EVOLUTION}, author={Martin, Julien and Royle, J. Andrew and Mackenzie, Darryl I. and Edwards, Holly H. and Kery, Marc and Gardner, Beth}, year={2011}, month={Dec}, pages={595–601} }
 @article{sollmann_furtado_gardner_hofer_jacomo_torres_silveira_2011, title={Improving density estimates for elusive carnivores: Accounting for sex-specific detection and movements using spatial capture-recapture models for jaguars in central Brazil}, volume={144}, ISSN={["1873-2917"]}, DOI={10.1016/j.biocon.2010.12.011}, abstractNote={Owing to habitat conversion and conflict with humans, many carnivores are of conservation concern. Because of their elusive nature, camera trapping is a standard tool for studying carnivores. In many vertebrates, sex-specific differences in movements – and therefore detection by cameras – are likely. We used camera trapping data and spatially explicit sex-specific capture–recapture models to estimate jaguar density in Emas National Park in the central Brazilian Cerrado grassland, an ecological hotspot of international importance. Our spatially explicit model considered differences in movements and trap encounter rate between genders and the location of camera traps (on/off road). We compared results with estimates from a sex-specific non-spatial capture–recapture model. The spatial model estimated a density of 0.29 jaguars 100 km−2 and showed that males moved larger distances and had higher trap encounter rates than females. Encounter rates with off-road traps were one tenth of those for on-road traps. In the non-spatial model, males had a higher capture probability than females; density was estimated at 0.62 individuals 100 km−2. The non-spatial model likely overestimated density because it did not adequately account for animal movements. The spatial model probably underestimated density because it assumed a uniform distribution of jaguars within and outside the reserve. Overall, the spatial model is preferable because it explicitly considers animal movements and allows incorporating site-specific and individual covariates. With both methods, jaguar density was lower than reported from most other study sites. For rare species such as grassland jaguars, spatially explicit capture–recapture models present an important advance for informed conservation planning.}, number={3}, journal={BIOLOGICAL CONSERVATION}, author={Sollmann, Rahel and Furtado, Mariana Malzoni and Gardner, Beth and Hofer, Heribert and Jacomo, Anah T. A. and Torres, Natalia Mundim and Silveira, Leandro}, year={2011}, month={Mar}, pages={1017–1024} }