@article{teitsworth_humphries_archambault_pacifici_2024, title={Capital to Coast: Primary Drivers of Distribution in the Secretive and Data-Limited Neuse River Waterdog (Necturus lewisi)}, volume={112}, ISSN={["2766-1520"]}, DOI={10.1643/h2023036}, abstractNote={The lack of demographic data for many protected species often means that threats are poorly understood during recovery planning, and this results in difficulty defining sufficient metrics for assessing progress on recovery actions. The Neuse River Waterdog (Necturus lewisi) is a federally protected aquatic salamander endemic to the Neuse and Tar-Pamlico River basins of central and eastern North Carolina. It has quietly declined during four decades of intense urbanization, but the specific drivers of decline are unclear because there are no demographic data and only limited detection/non-detection information available. Our first objective was to clarify the drivers of decline by synthesizing the current knowledge of the hypothesized threats to N. lewisi. Because preexisting demographic data are lacking, we used prior natural history research and studies of ecologically similar species to develop hypotheses for the observed declines in occurrence. Our second objective was to update the knowledge of the species' current distribution throughout its historical range and then test our hypothesized threats using new occurrence data. We conducted detection/non-detection surveys across 116 locations throughout the species' historical range in two consecutive winter seasons (2018–2019 and 2019–2020) and modeled the effects of local and landscape variables representing three broad threat categories (pollution, flow suppression, and land use/land cover) using an occupancy modeling approach. We fit models representing all biologically relevant combinations of variables simultaneously, recognizing that threats are not independent in their effect. Dominant substrate type was the best predictor of occurrence and was negatively associated with the transition from cobble to silt (P < 0.05). Our analysis most supported the hypothesis that observed declines in the occurrence of N. lewisi are a delayed result of sedimentation-induced recruitment limitation. Uncertainty in the mechanism of decline remains because recruitment limitation could not be directly estimated with two years of occurrence data, yet this interpretation gained through an understanding of the species' underlying biology and current distribution contributes to the knowledge about present threats and will help guide and evaluate future recovery actions for this protected and narrowly endemic aquatic species.}, number={2}, journal={ICHTHYOLOGY AND HERPETOLOGY}, author={Teitsworth, Eric W. and Humphries, W. Jeffrey and Archambault, Jennifer M. and Pacifici, Krishna}, year={2024}, month={Jul}, pages={196–209} }
@article{cope_kwak_black_pacifici_archambault_cope_2024, title={Distribution, Occupancy, and Habitat of the Endangered Carolina Madtom: Implications for Recovery of an Endemic Stream Fish}, url={https://doi.org/10.3390/fishes9110454}, DOI={10.3390/fishes9110454}, journal={Fishes}, author={Cope, W. Robert and Kwak, Thomas J. and Black, Tyler R. and Pacifici, Krishna and Archambault, Jennifer M. and Cope, W. Gregory}, year={2024}, month={Nov} }
@article{jensen_cove_goldstein_kays_mcshea_pacifici_rooney_kierepka_2024, title={Geographic barriers but not life history traits shape the phylogeography of North American mammals}, volume={6}, ISSN={1466-822X 1466-8238}, url={http://dx.doi.org/10.1111/geb.13875}, DOI={10.1111/geb.13875}, abstractNote={Abstract Aim Synthesize literature on genetic structure within species to understand how geographic features and species traits influence past responses to climate change. Location North America. Time Period We synthesized phylogeographic studies from 1978 to 2023, which describe genetic lineages that diverged during the Pleistocene (≥11,700 years ago). Major Taxa Studied Mammals. Methods We conducted a literature review to map genetic breaks in species distributions, then tested a set of geographic hypotheses (e.g., mountains, rivers) to explain their position by comparing break locations to a grid within each species' sampled range using logistic regression. We then conducted a meta‐analysis using species‐specific model estimates to ask if life‐history traits explained variation in which barriers were most important in species' past response to climate change. Results Our findings reveal heterogeneity in both where North American mammal phylogeography has been studied and the density of genetic breaks across 229 species. We found relatively high concordance among carnivores, ungulates and lagomorphs, where breaks were associated with mountains, major water bodies and relatively even terrain. In contrast, we found high variability within rodents and shrews, and no evidence that intrinsic factors related to dispersal ability explained the importance of hypothesized barriers across all species. Main Conclusions Southern Mexico is a hotspot for genetic breaks that has yet to be integrated into the broader story of North American phylogeography. We show that mountains and major water bodies play particularly important roles as barriers, but substantial variation across species within orders suggests that there is more to the story besides shared climatic or phylogenetic histories. Thus, understanding the phylogeography of individual species will continue to be important given that our results suggest high variability in how species may respond to future global change.}, journal={Global Ecology and Biogeography}, publisher={Wiley}, author={Jensen, Alex J. and Cove, Michael V. and Goldstein, Benjamin R. and Kays, Roland and McShea, William and Pacifici, Krishna and Rooney, Brigit and Kierepka, Elizabeth}, year={2024}, month={Jun} }
@article{goldstein_jensen_kays_cove_mcshea_rooney_kierepka_pacifici_2024, title={Guidelines for estimating occupancy from autocorrelated camera trap detections}, volume={5}, ISSN={["2041-2096"]}, url={https://doi.org/10.1111/2041-210X.14359}, DOI={10.1111/2041-210X.14359}, abstractNote={Abstract Site occupancy models (SOMs) are a common tool for studying the spatial ecology of wildlife. When observational data are collected using passive monitoring field methods, including camera traps or autonomous recorders, detections of animals may be temporally autocorrelated, leading to biased estimates and incorrectly quantified uncertainty. We presently lack clear guidance for understanding and mitigating the consequences of temporal autocorrelation when estimating occupancy models with camera trap data. We use simulations to explore when and how autocorrelation gives rise to biased or overconfident estimates of occupancy. We explore the impact of sampling design and biological conditions on model performance in the presence of autocorrelation, investigate the usefulness of several techniques for identifying and mitigating bias and compare performance of the SOM to a model that explicitly estimates autocorrelation. We also conduct a case study using detections of 22 North American mammals. We show that a join count goodness‐of‐fit test previously proposed for identifying clustered detections is effective for detecting autocorrelation across a range of conditions. We find that strong bias occurs in the estimated occupancy intercept when survey durations are short and detection rates are low. We provide a reference table for assessing the degree of bias to be expected under all conditions. We further find that discretizing data with larger windows decreases the magnitude of bias introduced by autocorrelation. In our case study, we find that detections of most species are autocorrelated and demonstrate how larger detection windows might mitigate the resulting bias. Our findings suggest that autocorrelation is likely widespread in camera trap data and that many previous studies of occupancy based on camera trap data may have systematically underestimated occupancy probabilities. Moving forward, we recommend that ecologists estimating occupancy from camera trap data use the join count goodness‐of‐fit test to determine whether autocorrelation is present in their data. If it is, SOMs should use large detection windows to mitigate bias and more accurately quantify uncertainty in occupancy model parameters. Ecologists should not use gaps between detection periods, which are ineffective at mitigating temporal structure in data and discard useful data.}, journal={METHODS IN ECOLOGY AND EVOLUTION}, author={Goldstein, Benjamin R. and Jensen, Alex J. and Kays, Roland and Cove, Michael V. and Mcshea, William J. and Rooney, Brigit and Kierepka, Elizabeth M. and Pacifici, Krishna}, year={2024}, month={May} }
@article{bacheler_iii_tarnecki_shertzer_buckel_hostetter_pacifici_zulian_bubley_2025, title={Spatiotemporal dynamics and habitat use of red snapper (Lutjanus campechanus) on the southeastern United States Atlantic continental shelf}, volume={281}, ISSN={["1872-6763"]}, DOI={10.1016/j.fishres.2024.107200}, journal={FISHERIES RESEARCH}, author={Bacheler, Nathan M. and Iii, William F. Patterson and Tarnecki, Joseph H. and Shertzer, Kyle W. and Buckel, Jeffrey A. and Hostetter, Nathan J. and Pacifici, Krishna and Zulian, Viviane and Bubley, Walter J.}, year={2025}, month={Jan} }
@article{parsons_pacifici_shaw_cobb_boone_kays_2024, title={Urbanization and primary productivity mediate the predator-prey relationship between deer and coyotes}, volume={15}, ISSN={["2150-8925"]}, url={https://doi.org/10.1002/ecs2.4882}, DOI={10.1002/ecs2.4882}, abstractNote={Abstract Predator–prey interactions are important for regulating populations and structuring communities but are affected by many dynamic, complex factors across large scales, making them difficult to study. Integrated population models (IPMs) offer a potential solution to understanding predator–prey relationships by providing a framework for leveraging many different datasets and testing hypotheses about interactive factors. Here, we evaluate the coyote–deer ( Canis latrans – Odocoileus virginianus ) predator–prey relationship across the state of North Carolina (NC). Because both species have similar habitat requirements and may respond to human disturbance, we considered net primary productivity (NPP) and urbanization as key mediating factors. We estimated deer survival and fecundity by integrating camera trap, harvest, and biological and hunter observation datasets into a two‐stage, two‐sex Lefkovich population projection matrix. We allowed survival and fecundity to vary as functions of urbanization, NPP, and coyote density, and projected abundance forward to test eight hypothetical scenarios. We estimated initial average deer and coyote densities to be 11.83 (95% CI: 5.64, 20.80) and 0.46 (95% CI: 0.02, 1.45) individuals/km 2 , respectively. We found a negative, though highly uncertain, relationship between the current levels of coyote density and deer fecundity in most areas that became more negative under hypothetical conditions of lower NPP or higher urbanization, leading to lower projected deer abundances. Though not conclusive, our results indicate the possibility that coyotes could have stronger effects on deer populations in NC if their densities rise, but primarily in less productive and/or more suburban habitats. Our case study provides an example of how IPMs can be used to better understand the complex relationships between predator and prey under changing environmental conditions.}, number={6}, journal={ECOSPHERE}, author={Parsons, Arielle W. and Pacifici, Krishna and Shaw, Jonathan C. and Cobb, David and Boone, Hailey M. and Kays, Roland}, year={2024}, month={Jun} }
@article{casola_peterson_pacifici_sills_moorman_2023, title={Conservation motivations and willingness to pay for wildlife management areas among recreational user groups}, volume={132}, ISSN={0264-8377}, url={http://dx.doi.org/10.1016/j.landusepol.2023.106801}, DOI={10.1016/j.landusepol.2023.106801}, abstractNote={Conservation agencies routinely evaluate the costs and benefits of land management and land acquisition options for wildlife management areas (WMAs). Non-market values, for example visitors' consumer surplus, are often absent from these comparisons. Better estimates of willingness to pay (WTP) for WMAs will allow managers to quantify consumer surpluses for different user groups, identify opportunities to generate additional conservation funding, and improve communication with users. We used the contingent valuation method to estimate the WTP for conservation of WMAs by different user groups. We used interval censored regression to estimate WTP for each user group and modeled how WTP varied with visitation frequency, demographics, and type of use. Dual users, those who participated in both licensed (hunting, angling, or trapping) and non-licensed (all other) activities, had greater WTP ($200.07, 95% CI [$161.18, $238.95]) than users who exclusively participated in either a single non-licensed ($74.74, 95% CI [$50.45, $99.02]) or a single licensed activity ($68.21, 95% CI [$48.41, $88.00]). Willingness-to-pay increased with the number of visits to WMAs per year, college education, and income. The most popular donation motivations were that respondents cared about WMA conservation (72%), wanted WMAs to be around for future generations (70%) and personally benefited from the conservation of WMAs (64%). Similar to a scope test, this study demonstrated greater WTP by users who participate in more diverse recreation types on WMAs. Additionally, our findings show that WMA users, particularly users who engage in multiple activities including at least one that does not require a license, enjoy large consumer surpluses and thus could be drawn on for additional financial support for WMA conservation.}, journal={Land Use Policy}, publisher={Elsevier BV}, author={Casola, William R. and Peterson, M. Nils and Pacifici, Krishna and Sills, Erin O. and Moorman, Christopher E.}, year={2023}, month={Sep}, pages={106801} }
@article{kreh_pease_pacifici_2023, title={Efficacy of autonomous recording units to evaluate wild turkey gobbling chronology in North Carolina, USA}, volume={3}, ISSN={["2328-5540"]}, DOI={10.1002/wsb.1433}, abstractNote={AbstractWild turkey (Meleagris gallopavo) gobbling is a key component of hunter satisfaction, also providing insight into the underlying reproductive ecology of wild turkeys that can inform regulatory decisions. However, monitoring gobbling chronology over large geographic areas can be logistically challenging and identifying efficient monitoring schemes can help wildlife agencies better manage the species. We evaluated the efficacy and utility of autonomous recording units (ARUs) to detect wild turkey gobbles and deployed 51 ARUs to monitor gobbling chronology in North Carolina, USA. We conducted controlled field‐tests at 20 locations to compare how detection of gobbles differed by ARU software, manual review of ARUs, and in‐field human observers. Autonomous detections had the lowest probability, with detection probabilities approaching 0 at 300 m from the ARU. Autonomous detections of gobbles were affected by leaf‐on conditions and topographical interference while vegetation type surrounding ARUs had minimal and inconsistent effects on detection. We deployed ARUs on properties with little or no turkey hunting across North Carolina from March–May during 2016 through 2019 to explore annual and regional variation in gobbling chronology. We used ARUs to monitor gobbling chronology and recorded 53,943 hours of audio files from which we confirmed 113,737 gobbles out of a total of 602,053 possible sound events identified. We identified multimodal gobbling chronology across 3 primary physiographic regions in North Carolina. We also found comparable timing of gobbling chronology across the 3 regions, with 57–61% of gobbling occurring during the weeks in which hunting seasons occur. We recommend that researchers validate ARU performance to calibrate monitoring of gobbling chronology. Additionally, our gobbling chronology data suggest that a statewide framework, rather than a regionally split framework, is appropriate for wild turkey hunting in North Carolina.}, journal={WILDLIFE SOCIETY BULLETIN}, author={Kreh, Christopher D. and Pease, Brent S. and Pacifici, Krishna}, year={2023}, month={Mar} }
@article{boone_moorman_terando_moscicki_collier_chamberlain_pacifici_2023, title={Minimal shift of eastern wild turkey nesting phenology associated with projected climate change}, volume={6}, ISSN={2666-9005}, url={http://dx.doi.org/10.1016/j.ecochg.2023.100075}, DOI={10.1016/j.ecochg.2023.100075}, abstractNote={Climate change may induce mismatches between wildlife reproductive phenology and temporal occurrence of resources necessary for reproductive success. Verifying and elucidating the causal mechanisms behind potential mismatches requires large-scale, longer-duration data. We used eastern wild turkey (Meleagris gallopavo silvestris) nesting data collected across the southeastern U.S. over eight years to investigate potential climatic drivers of variation in nest initiation dates. We investigated climactic relationships with two datasets, one inclusive of successful and unsuccessful nests (full dataset) and another of just successful nests (successfully hatched dataset), to determine whether successfully hatched nests responded differently to weather changes than all nests did. In the full dataset, each 10 cm increase in January precipitation was associated with nesting occurring 0.46–0.66 days earlier, and each 10 cm increase in precipitation during the 30 days preceding nesting was associated with nesting occurring 0.17–0.21 days later. In the successfully hatched dataset, a 10 cm increase in March precipitation was associated with nesting occurring 0.67–0.74 days earlier, and an increase of one unit of variation in February maximum temperature was associated with nesting occurring 0.02 days later. We combined the results of these modeled relationships with multiple climate scenarios to understand potential implications of future climate change on wild turkey nesting phenology; results indicated that mean nest initiation date is projected to change by <0.1 day by 2040–2060. Wild turkey nesting phenology did not track changes in spring green-up timing, which could result in phenological mismatch between the timing of nesting and the availability of resources critical for successful reproduction.}, journal={Climate Change Ecology}, publisher={Elsevier BV}, author={Boone, Wesley W. and Moorman, Christopher E. and Terando, Adam J. and Moscicki, David J. and Collier, Bret A. and Chamberlain, Michael J. and Pacifici, Krishna}, year={2023}, month={Nov}, pages={100075} }
@article{torres-molinari_engman_pacifici_dolloff_myers_kwak_2023, title={Patterns in longitudinal distribution of American Eel (Anguilla rostrata) population characteristics in rivers of Puerto Rico}, volume={7}, ISSN={["1365-2400"]}, DOI={10.1111/fme.12645}, abstractNote={AbstractAmerican Eel (Anguilla rostrata) population characteristics and distribution remain drastically understudied in the Caribbean region. We conducted the first island‐wide study to evaluate the distribution of density, length, and sex in relation to distance from the mouth of 23 stream reaches in five rivers in Puerto Rico. We found 287 American Eel at a mean density of 156.7 fish/ha. Sex ratios favored females (52:3) but most of the eel sampled were undifferentiated or undetermined. Generalized linear modeling indicated that upstream habitats with low eel density were optimal environments for production of large and female eel. Our findings indicate that Puerto Rico could significantly contribute to the spawning population and strengthen knowledge of American Eel in the Caribbean. Our findings could be used to guide local and range‐wide conservation efforts to ensure stream connectivity and access to optimal upstream habitat for survival of the population.}, journal={FISHERIES MANAGEMENT AND ECOLOGY}, author={Torres-Molinari, A. and Engman, A. C. and Pacifici, K. and Dolloff, C. A. and Myers, B. J. E. and Kwak, T. J.}, year={2023}, month={Jul} }
@article{boone_moorman_moscicki_collier_chamberlain_terando_pacifici_2023, title={Robust assessment of associations between weather and eastern wild turkey nest success}, volume={88}, ISSN={0022-541X 1937-2817}, url={http://dx.doi.org/10.1002/jwmg.22524}, DOI={10.1002/jwmg.22524}, abstractNote={AbstractTemperature and precipitation have been identified as factors that potentially influence eastern wild turkey (Meleagris gallopavo silvestris) reproduction, but robust analyses testing the relationship between weather parameters and turkey nest success are lacking. Therefore, we assessed how weather influenced turkey daily nest survival using 8 years of data collected from 715 nests across the southeastern United States. We also conducted exploratory analyses investigating if weather conditions during or prior to nesting best predicted nest success. We then assessed the possible implications of climate change through 2041–2060 for future eastern wild turkey daily nest survival and nest success for variables determined significant in analyses. During incubation, positive anomalies of minimum daily temperature were associated with greater daily nest survival. Precipitation during nesting was not a good predictor of daily nest survival. Exploratory analyses unexpectedly indicated that weather conditions in January prior to incubation were more important to nest success than weather conditions during incubation. In January, negative anomalies of minimum temperature and greater average daily precipitation were associated with greater nest success. Projections of future nest success or daily nest survival based on these relationships with the predictive covariates, and informed by climate models, suggest that nest success may increase as January precipitation increases and that daily nest survival may increase as temperature during incubation increases. These positive associations could be offset by a negative association between nest success and the expected increases in January minimum average temperature. Additional research is needed to investigate causes of these relationships and assess the implications of climate change for eastern wild turkey poult survival.}, number={2}, journal={The Journal of Wildlife Management}, publisher={Wiley}, author={Boone, Wesley W. and Moorman, Christopher E. and Moscicki, David J. and Collier, Bret A. and Chamberlain, Michael J. and Terando, Adam J. and Pacifici, Krishna}, year={2023}, month={Nov} }
@article{wightman_ulrey_bakner_cantrell_ruth_rushton_cedotal_kilgo_moscicki_pacifici_et al._2023, title={Survival and cause-specific mortality of male wild turkeys across the southeastern United States}, volume={12}, ISSN={["1937-2817"]}, DOI={10.1002/jwmg.22531}, abstractNote={AbstractEstimating survival and cause‐specific mortality of male eastern wild turkeys (Meleagris gallopavo silvestris) is important for understanding population dynamics and implementing appropriate harvest management. To better understand age‐specific estimates of annual survival and harvest rates, we captured and marked male wild turkeys with leg bands (n = 311) or bands and transmitters (n = 549) in Georgia, Louisiana, North Carolina, and South Carolina, USA, during 2014–2022. We fitted time to event models to data from radio‐marked birds to estimate cause‐specific mortality and annual survival. We used band recovery models incorporating both band recovery and telemetry data to further investigate harvest rates and survival. Annual survival from known‐fate models in hunted populations was 0.54 (95% CI = 0.49–0.59) for adults and 0.86 (95% CI = 0.81–0.92) for juveniles. Cause‐specific mortality analysis produced an annual harvest estimate of 0.29 (95% CI = 0.24–0.33) for adults and 0.02 (95% CI = 0.01–0.03) for juveniles, whereas predation was 0.15 (95% CI = 0.10–0.20) and 0.12 (95% CI = 0.08–0.17), respectively. Annual survival for adult males in a non‐hunted population was 0.83 (95% CI = 0.72–0.97). Survival rate was negatively correlated with harvest rate, indicating harvest was an additive mortality source. Annual survival from band recovery models was 0.40 (95% CI = 0.37–0.44) for adults and 0.88 (95% CI = 0.81– 0.93) for juveniles, whereas annual harvest estimates were 0.24 (95% CI = 0.23–0.25) for adults and 0.04 (95% CI = 0.03–0.05) for juveniles. Both models suggested no differences in annual survival across years or among study areas, which included privately owned and public properties. Harvest was an additive mortality source for male wild turkeys, suggesting that managers interested in increasing annual survival of adult males could consider ways of reducing harvest rates.}, journal={JOURNAL OF WILDLIFE MANAGEMENT}, author={Wightman, Patrick H. and Ulrey, Erin E. and Bakner, Nicholas W. and Cantrell, Jay R. and Ruth, Charles R. and Rushton, Emily and Cedotal, Cody A. and Kilgo, John C. and Moscicki, David J. and Pacifici, Krishna and et al.}, year={2023}, month={Dec} }
@article{vanvuuren_vanvuuren_silverberg_manning_pacifici_dorgeloh_campbell_2023, title={Ungulate responses and habituation to unmanned aerial vehicles in Africa's savanna}, volume={18}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0288975}, abstractNote={This article tests the hypothesis that “the likelihood that the species will react and level at which they do to the unmanned aerial vehicle (UAV) is related to the altitude, number of passes, sound intensity, type of UAV, takeoff distance, and species.” This paper examined the behavioral responses of a group of free ranging ungulate species (Oryx, Kudu, Springbok, Giraffe, Eland, Hartebeest, and Impala) found in an animal reserve in Namibia to the presence of different in-flight UAV models. The study included 397 passes (trials) over 99 flights at altitudes ranging from 15 to 55 meters in three categories of response level: No response, Alert, and Movement. The ungulates were unhabituated to the UAVs and the study was conducted in the presence of stress-inducing events that occur naturally in the environment. Certain species were found to be more reactive than others, in addition to several displaying different response levels in single or mixed herd environments. Zebras were found to be less responsive in mixed herd environments while Oryx were present, as compared to when the Oryx were not; suggesting that some species may respond based on other species perception of threat or their relative fitness levels. The UAVs also produced inconsistent response rates between movement and alert behavior. The reference vehicle, Phantom 3 was much more likely than the Mavic to induce an alert response, while both having similar probabilities of inducing a movement response. Furthermore, the Custom X8 showed significantly more alert and movement responses than the other UAVs. This shows there may be several aspects to the UAVs that affect the responses of the ungulates. For instance, the sound intensity may alert the species more often, but close proximity may induce a movement response. More generally, the data shows that when the UAV is flying above 50 meters and has a measured sound intensity below 50 dB, the likelihood of inducing a movement response on an ungulate species is below 6% regardless of the vehicle on the first pass over the animals. Additionally, with each subsequent pass the likelihood of response dropped by approximately 20 percent. The results suggest a stronger correlation between flight altitude and response across the different ungulates, and the evidence suggests rapid habituation to the UAVs.}, number={7}, journal={PLOS ONE}, author={vanVuuren, Marlice and vanVuuren, Rudie and Silverberg, Larry M. and Manning, Joe and Pacifici, Krishna and Dorgeloh, Werner and Campbell, Jennifer}, year={2023}, month={Jul} }
@article{boone_pacifici_moorman_kays_2023, title={Using decoys and camera traps to estimate depredation rates and neonate survival}, volume={18}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0293328}, DOI={10.1371/journal.pone.0293328}, abstractNote={Ungulate neonates—individuals less than four weeks old—typically experience the greatest predation rates, and variation in their survival can influence ungulate population dynamics. Typical methods to measure neonate survival involve capture and radio-tracking of adults and neonates to discover mortality events. This type of fieldwork is invasive and expensive, can bias results if it leads to neonate abandonment, and may still have high uncertainty about the predator species involved. Here we explore the potential for a non-invasive approach to estimate an index for neonate survival using camera traps paired with decoys that mimic white-tailed deer (Odocoileus virginianus) neonates in the first month of life. We monitored sites with camera traps for two weeks before and after the placement of the neonate decoy and urine scent lure. Predator response to the decoy was classified into three categories: did not approach, approached within 2.5 m but did not touch the decoy, or physically touched the decoy; when conducting survival analyses, we considered these second two categories as dead neonates. The majority (76.3%) of the predators approached the decoy, with 51.1% initiating physical contact. Decoy probability of survival was 0.31 (95% CI = 0.22, 0.35) for a 30-day period. Decoys within the geographic range of American black bear (Ursus americanus) were primarily (75%) attacked by bears. Overall, neonate survival probability decreased as predator abundance increased. The camera-decoy protocol required about ½ the effort and 1/3 the budget of traditional capture-track approaches. We conclude that the camera-decoy approach is a cost-effective method to estimate a neonate survival probability index based on depredation probability and identify which predators are most important.}, number={10}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Boone, Hailey M. and Pacifici, Krishna and Moorman, Christopher E. and Kays, Roland}, editor={Corti, PauloEditor}, year={2023}, month={Oct}, pages={e0293328} }
@article{sanders_stewart_pacifici_hess_olfenbuttel_deperno_2023, title={Variations in reproduction and age structure in the North American river otter in North Carolina, USA}, volume={87}, ISSN={0022-541X 1937-2817}, url={http://dx.doi.org/10.1002/jwmg.22361}, DOI={10.1002/jwmg.22361}, abstractNote={AbstractHistorically, the North American river otter (Lontra canadensis; otter) was distributed across North Carolina, USA, but populations were decimated by the early 1900s. Otter trapping was prohibited in 1938, reopened in 1947, and gradually expanded until it was opened statewide in 2005. Between 1986 and 1992, the North Carolina Wildlife Resources Commission and Great Smoky Mountains National Park released 404 otters to restore populations in western North Carolina. Our objective was to determine if the age structure and reproductive rates of otters throughout North Carolina shifted from 1978 to 2018 between remnant and reintroduced populations. During the 1978–1980 (period 1; Coastal Plain) and the 2009–2013 and 2014–2016 (period 2; statewide) trapping seasons, we collected 1,439 otter carcasses from licensed trappers, fur buyers, and wildlife damage control agents throughout the 3 Furbearer Management Units (FMUs) and 14 river basins in North Carolina. We conducted necropsies, used cementum annuli of the lower canine for age analysis, and counted corpora lutea and fetuses for fecundity estimates. Age distributions for all otters were skewed toward the younger age classes and did not differ between collection periods. During period 1, adults in the Coastal Plain had higher corpora lutea counts than during period 2, whereas Coastal Plain yearlings and juveniles had higher numbers of corpora lutea during period 2. During period 2, corpora lutea counts differed among FMUs; counts in the Mountain FMU (x̄ = 2.56) were higher than in the Coastal Plain FMU (x̄ = 1.62) or the Piedmont FMU (x̄ = 1.91). Within the Coastal Plain FMU and pooling all age classes, fecundity increased by 45% from period 1 to period 2. Adult fecundity in the Coastal Plain FMU declined 16% from period 1 to period 2, while juveniles and yearlings began reproducing between the periods, indicating that reproduction has shifted to younger age classes between 1978 and 2018.}, number={3}, journal={The Journal of Wildlife Management}, publisher={Wiley}, author={Sanders, Charles W., II and Stewart, Dennis L. and Pacifici, Krishna and Hess, George R. and Olfenbuttel, Colleen and DePerno, Christopher S.}, year={2023}, month={Jan} }
@article{casola_peterson_sills_pacifici_moorman_2022, title={Economic contributions of wildlife management areas in North Carolina}, volume={140}, ISSN={1389-9341}, url={http://dx.doi.org/10.1016/j.forpol.2022.102747}, DOI={10.1016/j.forpol.2022.102747}, abstractNote={Wildlife management areas (WMAs) provide a wide range of ecosystem services. Among these services, hunting and fishing often make the most obvious contribution to local and state economies through the expenditures of the hunters and anglers. However, the total economic contributions of WMAs also include other forms of recreation that are generally less visible, unlicensed, and less well understood. Quantifying the size of the economic contribution from all recreationists can inform decisions about investment in and management of public lands. To this end, we estimated the direct, indirect, and induced economic contributions of recreation on protected land managed by the state of North Carolina (NC) primarily for hunting, fishing, and wildlife conservation (hereafter WMAs). We collected data on visitation and conducted in-person intercept surveys at 9 WMAs to estimate the number of visits and expenditures per visit for people engaged in activities that required licenses (e.g., hunting) and activities that did not (e.g., hiking and bird watching). We estimated annual visitation on the 9 study WMAs, accounting for differences in location, hunting season, day of the week, and weather. We then predicted annual visitation at all 94 WMAs in NC using a predictive regression model. Most visitors did not engage in any licensed activities, and those visitors spent more per trip on average ($119.83) and had greater variability in expenses than visitors engaged in licensed activities ($84.19). We used the estimates of total annual visits, expenditures per visit, and the distribution of those expenditures across sectors to calculate the economic contribution of recreation on each of the 9 study WMAs and on the entire WMA system in NC. Recreation was responsible for approximately 2200 jobs, $84 million USD in annual labor income, and $140 million USD in value added annually in NC. The majority of this contribution was due to visits made by users not engage in licensed uses of WMAs, as those users were more numerous, spent more per trip, and were more likely to visit WMAs in peri-urban areas with more economic linkages than rural areas.}, journal={Forest Policy and Economics}, publisher={Elsevier BV}, author={Casola, William R. and Peterson, M. Nils and Sills, Erin O. and Pacifici, Krishna and Moorman, Christopher E.}, year={2022}, month={Jul}, pages={102747} }
@article{pease_pacifici_kays_2022, title={Exploring spatial nonstationarity for four mammal species reveals regional variation in environmental relationships}, volume={13}, ISSN={["2150-8925"]}, url={https://doi.org/10.1002/ecs2.4166}, DOI={10.1002/ecs2.4166}, abstractNote={AbstractBroad‐scale ecological research on species distributions commonly presumes that the correlative relationships discovered are stationary over space. This is an assumption of most species distribution models (SDMs) that combine observations of species occurrence with environmental characteristics to understand current ecological correlates and to predict distributions based on those relationships. However, ecological relationships may vary spatially because of changes in the environment (i.e., resource availability) or the organism itself (i.e., local adaptation). Discovering this within‐species variation typically requires dense datasets over large geographic areas, which are now being provided by the recent proliferation of open‐access biodiversity occurrence records. Using nearly 4000 sampling locations from an open‐access, state‐wide camera‐trapping project, we explore the space‐varying effects of covariates on the distribution of four mammal species at two scales: region‐specific and fine resolution, with the latter estimated using spatially varying coefficients (SVC) models, to understand the scale of spatial variation in ecological relationships. Among the four species tested, the ecological relationships for two were best explained with the regional models, equivocal results for one species, while the SVC model had superior fit and predictive performance for the final species (white‐tailed deer, Odocoileus virginianus). Spatial nonstationarity was more common in relationships with landscape composition characteristics, such as housing density, than in landscape configuration metrics, such as patch richness density. One of the most appealing results of an SVC approach is not only the improved predictions across large landscapes but also understanding how animals are responding to the environment differently at the management unit level. For example, we found that deer's spatially varying relationship with forest cover was best explained by an interactive effect of deer management units (i.e., differences in deer populations) and predator pressure. These findings lead to a new hypothesis about how deer may be differentially using forested environments across space and could be a promising area of future research. Given sufficient data, accounting for nonstationarity in SDMs can show large‐scale ecological patterns while also detecting local level changes in animal ecology in areas small enough that management or protection can be readily implemented.}, number={8}, journal={ECOSPHERE}, publisher={Wiley}, author={Pease, Brent S. and Pacifici, Krishna and Kays, Roland}, year={2022}, month={Aug} }
@article{patton_pacifici_collazo_2022, title={Modeling and estimating co-occurrence between the invasive Shiny Cowbird and its Puerto Rican hosts}, volume={5}, ISSN={["1573-1464"]}, DOI={10.1007/s10530-022-02825-3}, journal={BIOLOGICAL INVASIONS}, author={Patton, Philip T. and Pacifici, Krishna and Collazo, Jaime A.}, year={2022}, month={May} }
@article{parsons_dawrs_nelson_norton_virdi_hasan_epperson_holst_chan_leos-barajas_et al._2022, title={Soil Properties and Moisture Synergistically Influence Nontuberculous Mycobacterial Prevalence in Natural Environments of Hawai'i}, volume={4}, ISSN={["1098-5336"]}, DOI={10.1128/aem.00018-22}, abstractNote={Nontuberculous mycobacteria (NTM) are ubiquitous in the environment, being found commonly in soils and natural bodies of freshwater. However, little is known about the environmental niches of NTM and how they relate to NTM prevalence in homes and other human-dominated areas.}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Parsons, Arielle W. and Dawrs, Stephanie N. and Nelson, Stephen T. and Norton, Grant J. and Virdi, Ravleen and Hasan, Nabeeh A. and Epperson, L. Elaine and Holst, Brady and Chan, Edward D. and Leos-Barajas, Vianey and et al.}, year={2022}, month={Apr} }
@article{pease_pacifici_kays_reich_2022, title={What drives spatially varying ecological relationships in a wide-ranging species?}, volume={7}, ISSN={["1472-4642"]}, url={https://doi.org/10.1111/ddi.13594}, DOI={10.1111/ddi.13594}, abstractNote={AbstractAimDecades of research on species distributions has revealed geographic variation in species‐environment relationships for a given species. That is, the way a species uses the local environment varies across geographic space. However, the drivers underlying this variation are contested and still largely unexplored. Niche traits that are conserved should reflect the evolutionary history of a species whereas more flexible ecological traits could vary at finer scales, reflecting local adaptation.LocationNorth America.MethodsWe used mammal observations during a 5‐year period from the iNaturalist biodiversity database and a local ensemble modelling approach to explore spatial variation in American black bear (Ursus americanus) relationships with eight ecological correlates. We tested four biologically driven hypotheses to explain the patterns of local adaptation. We evaluated non‐stationarity in ecological relationships using a Stationarity Index and tested predictive performance using an independent, national‐level animal occurrence data set.ResultsWe documented considerable spatial non‐stationarity in all eight environmental relationships, with the greatest spatial variation occurring in bear's relationship to climatic factors. Notably, the greatest variation in environmental relationships tended to occur along the current boundaries of the species' range, potentially representing the ecological limits to the species geographic range. We additionally documented that spatial variation in relationships with land cover and anthropogenic factors were best explained by niche conservatism at the subspecies level, whereas climatic relationships were better explained by local adaptation.Main ConclusionsBased on these results, we propose that the current distribution of American black bear is determined by an evolutionary legacy of habitat relationships unique to each subspecies combined with more fine‐scale local adaptation to climatic conditions. This result suggests that black bears should be adaptable to climatic changes over the 21st century and that management of habitat and human‐bear relationships could be considered at the subspecies level.}, journal={DIVERSITY AND DISTRIBUTIONS}, publisher={Wiley}, author={Pease, Brent S. and Pacifici, Krishna and Kays, Roland and Reich, Brian}, year={2022}, month={Jul} }
@article{rosche_moorman_kroeger_pacifici_jones_deperno_2021, title={Effects of Prescribed Fire on Northern Bobwhite Nesting Ecology}, volume={45}, ISSN={2328-5540 2328-5540}, url={http://dx.doi.org/10.1002/wsb.1183}, DOI={10.1002/wsb.1183}, abstractNote={ABSTRACTRepeated prescribed fire can create and maintain areas with sparse overstory tree cover and a dense grass‐forb‐shrub understory, providing habitat for northern bobwhite (Colinus virginianus; hereafter, bobwhite). Despite potential benefits of prescribed fires for conserving bobwhite habitat, burning during the nesting season may destroy bobwhite nests and reduce available nesting cover. We monitored radio‐transmittered bobwhite (n = 104) from 2016 to 2018 to describe nest‐site selection and determine the risk of nest destruction on a 17,000‐ha North Carolina military installation, Fort Bragg, managed with rotational growing‐season and dormant‐season prescribed fires on an approximate 3‐year return interval. We located 48 nests, of which 8 (16%) were in areas burned the same year, 9 (19%) were in one‐year post fire, 25 (52%) were in 2‐years post fire, and 6 (13%) were in ≥3‐years post fire areas. We compared vegetation composition and structure at nests to nearby random locations and determined bobwhite selected nest sites with greater woody understory and wiregrass cover, lower basal areas of pines and hardwoods, and less distance to the nearest road. Two nests (6.7%) were destroyed during prescribed fires, but success of incubated nests was high (67%). We calculated the overall risk of nest destruction by prescribed fire as the proportion of active nests in areas with ≥3 years since last fire multiplied by the proportion of the study area burned each week. Overall, 11% (weekly = 0.75%, range = 0–3%) of the study area was burned during the 2016 nesting season (3 June to 3 September), 4% (weekly = 0.31%, range 0–2%) of the study area was burned during the 2017 nesting season (5 June to 2 September), and 7.5% (weekly = 0.58%, range 0–5%) of the study area was burned during the 2018 nesting season (3 June to 31 August). We estimated that no more than 0.75% of bobwhite nests across the study site were exposed to fire annually. Most growing‐season fires occurred before the bobwhite nesting season, which limited direct effects of prescribed fire on bobwhite nest survival. However, shifting prescribed fires to later in the growing season to better match the historical lightning season (i.e., after 1 June) would increase the risk of nest destruction. Because bobwhite used older roughs (i.e. areas 2 years since fire) for nesting, shortening the fire return interval to less than 3 years would increase the proportion of nests exposed to fire. Additionally, a shortened fire return interval would decrease available nesting cover, especially in regions with low soil fertility where vegetation change following fire is less rapid than on more productive soils. © 2021 The Wildlife Society.}, number={2}, journal={Wildlife Society Bulletin}, publisher={Wiley}, author={Rosche, Sarah B. and Moorman, Christopher E. and Kroeger, Anthony J. and Pacifici, Krishna and Jones, Jeffrey G. and DePerno, Christopher S.}, year={2021}, month={Jun}, pages={249–257} }
@article{cope_kwak_black_pacifici_harris_miller_raley_hallerman_2021, title={Genetic Structure and Diversity of the Endemic Carolina Madtom and Conservation Implications}, volume={41}, ISSN={["1548-8675"]}, url={https://doi.org/10.1002/nafm.10589}, DOI={10.1002/nafm.10589}, abstractNote={AbstractIdentification and conservation of genetic diversity within and among freshwater fish populations are important to better manage and conserve imperiled species. The Carolina Madtom Noturus furiosus is a small, nongame catfish that is endemic to the Tar and Neuse River basins of North Carolina. Genetic structure has not been studied in the species, and given recent population declines in both basins, identification of remaining genetic diversity within the species is vital for informing conservation efforts. To assess the status and trends of Carolina Madtom genetic structure, we analyzed genetic markers from 173 individuals to (1) define population genetic structure, (2) assess intra‐ and interbasin genetic differentiation in the Tar and Neuse River basins, and (3) present management implications to guide conservation efforts. Using 10 microsatellite primers developed for the related Yellowfin Madtom N. flavipinnis, we observed low genetic diversity in Carolina Madtoms. Genotype frequencies within samples were not in Hardy–Weinberg equilibrium, with a deficit of heterozygotes that could be due to family structure, inbreeding, or segregation of null alleles. Mean (±SD) M‐ratios for the Tar River (0.414 ± 0.117) and Neuse River (0.117 ± 0.102) basin collections indicated that both populations have experienced recent demographic bottlenecks, with that in the Neuse River basin population being more severe. Effective population size estimates for the respective populations were small, on the order of tens of individuals, driving low genetic diversity within populations. However, the multilocus population differentiation metrics (mean ± SE = 0.135 ± 0.031) and DEST (0.125 ± 0.029) were significantly different from zero (P < 0.001), indicating significant genetic differentiation between the Tar and Neuse River basin populations. Our findings will inform managers on the status of genetic variation in the Carolina Madtom and will guide conservation toward protective listing and management decisions to maintain the viability of this important endemic species.}, number={S1}, journal={NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT}, publisher={Wiley}, author={Cope, W. Robert and Kwak, Thomas J. and Black, Tyler R. and Pacifici, Krishna and Harris, Sheila C. and Miller, Caitlin M. and Raley, Morgan E. and Hallerman, Eric M.}, year={2021}, month={Oct}, pages={S27–S41} }
@article{rivera-burgos_collazo_terando_pacifici_2021, title={Linking demographic rates to local environmental conditions: Empirical data to support climate adaptation strategies for Eleutherodactylus frogs}, volume={28}, ISSN={["2351-9894"]}, url={https://doi.org/10.1016/j.gecco.2021.e01624}, DOI={10.1016/j.gecco.2021.e01624}, abstractNote={Conducting managed species translocations and establishing climate change refugia are adaptation strategies to cope with projected consequences of global warming, but successful implementation requires on-the-ground validation of demographic responses to transient climate conditions. Here we estimated the effect of nine abiotic and biotic factors on local occupancy and an index of abundance (few or chorus) for four amphibian species (Eleutherodactylus wightmanae, E. brittoni, E. antillensis, and E. coqui) in Puerto Rico, USA. We also assessed how the same factors influenced reproductive activity of E. coqui and how species responded to hurricane María (20 September 2017). As predicted, occupancy and abundance of E. wightmanae, E. brittoni and E. coqui were positively and strongly influenced by abiotic covariates (e.g., relative humidity) that characterize high elevation, mesic habitats. E. antillensis exhibited the opposite pattern, with highest probabilities (≥0.6) recorded at ≤300 m and with average relative humidity<75%. Biotic covariates (e.g., canopy cover) had a weak influence on both parameters, regardless of species. High probabilities (≥0.9) of detecting an E. coqui chorus and active nests occurred at sites experiencing average relative humidity of>80% and temperature of ≤26 °C. Moderate to high probabilities of detecting a chorus (0.4–0.7) were recorded at sites with average temperatures>26 °C, but no reproductive activity was detected, implying that monitoring abundance alone could misrepresent the capacity of a local population to sustain itself. The possibility underscores the importance of understanding the interplay between local demographic and environmental parameters in the advent of global warming to help guide monitoring and management decisions, especially for high elevation specialists. Hurricanes can inflict marked reductions in population numbers, but impacts vary by location and species. We found that the abundance (chorus) of E. antillensis and E. brittoni increased after the hurricane, but the abundance of the other two species did not differ between years. Lack of impacts was probably mediated by low structural damage to forest tracts (e.g., 9% canopy loss). Our findings help assess habitat suitability in terms of parameters that foster local population growth, which provides a basis for testing spatio-temporal predictions about demographic rates in potential climate refugia and for designing criteria to help guide managed translocations.}, journal={GLOBAL ECOLOGY AND CONSERVATION}, publisher={Elsevier BV}, author={Rivera-Burgos, Ana C. and Collazo, Jaime A. and Terando, Adam J. and Pacifici, Krishna}, year={2021}, month={Aug} }
@article{casola_peterson_wu_sills_pease_pacifici_2021, title={Measuring the value of public hunting land using a hedonic approach}, volume={8}, ISSN={["1533-158X"]}, DOI={10.1080/10871209.2021.1953196}, abstractNote={ABSTRACT Acquisition of public land is critical for wildlife conservation and can impact local tax bases and property values. Those impacts reflect the capitalized value of benefits (e.g., recreational opportunities) and costs (e.g., nuisance wildlife) of living near protected areas. We employed the hedonic price framework to determine how proximity and adjacency to public hunting land in North Carolina were capitalized into housing prices. We modeled sale price as the composite value of structural, neighborhood, and environmental characteristics. Proximity to public hunting land had positive effects on sale price in some locations, whereas adjacency had negative effects in some locations. These relationships were dependent on the sociocultural context of the public hunting land, including proximity to other forms of public land. This research may help facilitate negotiations among stakeholders impacted by protected areas, including land dedicated to wildlife-based recreation.}, journal={HUMAN DIMENSIONS OF WILDLIFE}, author={Casola, William R. and Peterson, M. Nils and Wu, Yu and Sills, Erin O. and Pease, Brent S. and Pacifici, Krishna}, year={2021}, month={Aug} }
@article{pease_pacifici_collazo_2021, title={Survey design optimization for monitoring wildlife communities in areas managed for federally endangered species}, volume={24}, ISSN={["1469-1795"]}, DOI={10.1111/acv.12681}, abstractNote={AbstractIn wildlife communities composed of federally endangered species, there are often several species of conservation concern that have not yet warranted federally mandated protection. These species often need continued monitoring to inform the direction of future management. While recovering endangered species is an important conservation goal, practitioners are challenged by balancing federally mandated protocols with actions that promote non‐listed priority species. Practitioners need an understanding of how focused, single‐species management actions may affect non‐listed priority species, but developing a monitoring protocol that can detect such effects with limited resources is a challenge. Here we use constrained optimization as a path to identifying a sampling scheme that overcomes these logistical challenges and then illustrate its potential in the Sandhills region of North Carolina, USA. Using empirical results from multi‐year avian community monitoring, we parameterized simulations to understand how varying the number of sampling locations and site visits affected the optimal monitoring protocol across three different avian community composition scenarios: a community with (1) 10 percent, (2) 25 percent, or (3) 50 percent non‐listed priority species. We found the greatest rate of change in precision of community‐level metrics, such as species richness, by increasing sampling replicates when surveying up to 50 sites. Importantly, this trend was apparent across all three community scenarios, indicating relatively predictable changes in uncertainty regardless of community composition. In contrast, increasing the sampling frequency did not consistently reduce uncertainty in species‐level parameters such as occupancy probability. Concerningly, we saw the greatest variation when communities were comprised of 50 percent non‐listed species suggesting increasingly complex monitoring protocols may be required if the number of non‐listed priority species continues to increase. Practitioners could consider reducing detection error of priority species through increasing sampling frequency, as this can strongly affect optimization study designs.}, number={5}, journal={ANIMAL CONSERVATION}, author={Pease, B. S. and Pacifici, K. and Collazo, J. A.}, year={2021}, month={Oct}, pages={756–769} }
@article{kays_arbogast_baker‐whatton_beirne_boone_bowler_burneo_cove_ding_espinosa_et al._2020, title={An empirical evaluation of camera trap study design: How many, how long and when?}, volume={11}, ISSN={2041-210X 2041-210X}, url={http://dx.doi.org/10.1111/2041-210X.13370}, DOI={10.1111/2041-210X.13370}, abstractNote={Abstract
Camera traps deployed in grids or stratified random designs are a well‐established survey tool for wildlife but there has been little evaluation of study design parameters.
We used an empirical subsampling approach involving 2,225 camera deployments run at 41 study areas around the world to evaluate three aspects of camera trap study design (number of sites, duration and season of sampling) and their influence on the estimation of three ecological metrics (species richness, occupancy and detection rate) for mammals.
We found that 25–35 camera sites were needed for precise estimates of species richness, depending on scale of the study. The precision of species‐level estimates of occupancy (ψ) was highly sensitive to occupancy level, with <20 camera sites needed for precise estimates of common (ψ > 0.75) species, but more than 150 camera sites likely needed for rare (ψ < 0.25) species. Species detection rates were more difficult to estimate precisely at the grid level due to spatial heterogeneity, presumably driven by unaccounted habitat variability factors within the study area. Running a camera at a site for 2 weeks was most efficient for detecting new species, but 3–4 weeks were needed for precise estimates of local detection rate, with no gains in precision observed after 1 month. Metrics for all mammal communities were sensitive to seasonality, with 37%–50% of the species at the sites we examined fluctuating significantly in their occupancy or detection rates over the year. This effect was more pronounced in temperate sites, where seasonally sensitive species varied in relative abundance by an average factor of 4–5, and some species were completely absent in one season due to hibernation or migration.
We recommend the following guidelines to efficiently obtain precise estimates of species richness, occupancy and detection rates with camera trap arrays: run each camera for 3–5 weeks across 40–60 sites per array. We recommend comparisons of detection rates be model based and include local covariates to help account for small‐scale variation. Furthermore, comparisons across study areas or times must account for seasonality, which could have strong impacts on mammal communities in both tropical and temperate sites.
}, number={6}, journal={Methods in Ecology and Evolution}, publisher={Wiley}, author={Kays, Roland and Arbogast, Brian S. and Baker‐Whatton, Megan and Beirne, Chris and Boone, Hailey M. and Bowler, Mark and Burneo, Santiago F. and Cove, Michael V. and Ding, Ping and Espinosa, Santiago and et al.}, editor={Fisher, DianaEditor}, year={2020}, month={Apr}, pages={700–713} }
@article{huberman_reich_pacifici_collazo_2020, title={Estimating the drivers of species distributions with opportunistic data using mediation analysis}, volume={11}, ISSN={["2150-8925"]}, url={https://doi.org/10.1002/ecs2.3165}, DOI={10.1002/ecs2.3165}, abstractNote={AbstractEcological occupancy modeling has historically relied on high‐quality, low‐quantity designed‐survey data for estimation and prediction. In recent years, there has been a large increase in the amount of high‐quantity, unknown‐quality opportunistic data. This has motivated research on how best to combine these two data sources in order to optimize inference. Existing methods can be infeasible for large datasets or require opportunistic data to be located where designed‐survey data exist. These methods map species occupancies, motivating a need to properly evaluate covariate effects (e.g., land cover proportion) on their distributions. We describe a spatial estimation method for supplementarily including additional opportunistic data using mediation analysis concepts. The opportunistic data mediate the effect of the covariate on the designed‐survey data response, decomposing it into a direct and indirect effect. A component of the indirect effect can then be quickly estimated via regressing the mediator on the covariate, while the other components are estimated through a spatial occupancy model. The regression step allows for use of large quantities of opportunistic data that can be collected in locations with no designed‐survey data available. Simulation results suggest that the mediated method produces an improvement in relative MSE when the data are of reasonable quality. However, when the simulated opportunistic data are poorly correlated with the true spatial process, the standard, unmediated method is still preferable. A spatiotemporal extension of the method is also developed for analyzing the effect of deciduous forest land cover on red‐eyed vireo distribution in the southeastern United States and find that including the opportunistic data do not lead to a substantial improvement. Opportunistic data quality remains an important consideration when employing this method, as with other data integration methods.}, number={6}, journal={ECOSPHERE}, publisher={Wiley}, author={Huberman, David B. and Reich, Brian J. and Pacifici, Krishna and Collazo, Jaime A.}, year={2020}, month={Jun} }
@article{grantham_reich_laber_pacifici_dunn_fierer_gebert_allwood_faith_2020, title={Global forensic geolocation with deep neural networks}, volume={69}, ISSN={["1467-9876"]}, DOI={10.1111/rssc.12427}, abstractNote={SummaryAn important problem in modern forensic analyses is identifying the provenance of materials at a crime scene, such as biological material on a piece of clothing. This procedure, which is known as geolocation, is conventionally guided by expert knowledge of the biological evidence and therefore tends to be application specific, labour intensive and often subjective. Purely data-driven methods have yet to be fully realized in this domain, because in part of the lack of a sufficiently rich source of data. However, high throughput sequencing technologies can identify tens of thousands of fungi and bacteria taxa by using DNA recovered from a single swab collected from nearly any object or surface. This microbial community, or microbiome, may be highly informative of the provenance of the sample, but data on the spatial variation of microbiomes are sparse and high dimensional and have a complex dependence structure that render them difficult to model with standard statistical tools. Deep learning algorithms have generated a tremendous amount of interest within the machine learning community for their predictive performance in high dimensional problems. We present DeepSpace: a new algorithm for geolocation that aggregates over an ensemble of deep neural network classifiers trained on randomly generated Voronoi partitions of a spatial domain. The DeepSpace algorithm makes remarkably good point predictions; for example, when applied to the microbiomes of over 1300 dust samples collected across continental USA, more than half of geolocation predictions produced by this model fall less than 100 km from their true origin, which is a 60% reduction in error from competing geolocation methods. Moreover, we apply DeepSpace to a novel data set of global dust samples collected from nearly 30 countries, finding that dust-associated fungi alone predict a sample's country of origin with nearly 90% accuracy.}, number={4}, journal={JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS}, author={Grantham, Neal S. and Reich, Brian J. and Laber, Eric B. and Pacifici, Krishna and Dunn, Robert R. and Fierer, Noah and Gebert, Matthew and Allwood, Julia S. and Faith, Seth A.}, year={2020}, month={Aug}, pages={909–929} }
@article{sanders_olfenbuttel_pacifici_hess_livingston_deperno_2020, title={LEPTOSPIRA, PARVOVIRUS, AND TOXOPLASMA IN THE NORTH AMERICAN RIVER OTTER (LONTRA CANADENSIS) IN NORTH CAROLINA, USA}, volume={56}, ISSN={["1943-3700"]}, DOI={10.7589/2019-05-129}, abstractNote={Abstract: The North American river otter (Lontra canadensis) is the largest mustelid in North Carolina, US, and was once extirpated from the central and western portions of the state. Over time and after a successful reintroduction project, otters are now abundant and occur throughout North Carolina. However, there is a concern that diseases may have an impact on the otter population, as well as on other aquatic mammals, either through exposure to emerging diseases, contact with domestic animals such as domestic cats (Felis catus), or less robust condition of individuals through declines in water quality. We tested brain and kidney tissue from harvested otters for the pathogens that cause leptospirosis, parvovirus, and toxoplasmosis. Leptospirosis and toxoplasmosis are priority zoonoses and are maintained by domestic and wild mammals. Although parvovirus is not zoonotic, it does affect pets, causing mild to fatal symptoms. Across the 2014–15 and 2015–16 trapping seasons, we tested 220 otters (76 females, 144 males) using real-time PCR for Leptospira interrogans, parvovirus, and Toxoplasma gondii. Of the otters tested, 1% (3/220) were positive for L. interrogans, 19% (41/220) were positive for parvovirus, and 24% (53/220) were positive for T. gondii. Although the pathogens for parvovirus and toxoplasmosis are relatively common in North Carolina otters, the otter harvest has remained steady and the population appears to be abundant and self-sustaining. Therefore, parvovirus and toxoplasmosis do not currently appear to be negatively impacting the population. However, subsequent research should examine transmission parameters between domestic and wild species and the sublethal effects of infection.}, number={4}, journal={JOURNAL OF WILDLIFE DISEASES}, author={Sanders, Charles W., II and Olfenbuttel, Colleen and Pacifici, Krishna and Hess, George R. and Livingston, Robert S. and DePerno, Christopher S.}, year={2020}, month={Oct}, pages={791–802} }
@article{sanders_pacifici_hess_olfenbuttel_deperno_2020, title={Metal contamination of river otters in North Carolina}, volume={192}, ISBN={1573-2959}, ISSN={0167-6369 1573-2959}, url={http://dx.doi.org/10.1007/s10661-020-8106-8}, DOI={10.1007/s10661-020-8106-8}, abstractNote={Aquatic apex predators are vulnerable to environmental contaminants due to biomagnification. North American river otter (Lontra canadensis) populations should be closely monitored across their range due to point and nonpoint pollution sources. Nonetheless, no information exists on environmental contaminants in the North Carolina otter population. Metals and metalloids occur naturally across the landscape, are essential for cellular function, and become toxic when concentrated unnaturally. We conducted our study across the three Furbearer Management Units (FMU) and 14 river basins of North Carolina. We determined the concentrations of arsenic, cadmium, calcium, cobalt, copper, iron, lead, magnesium, manganese, mercury, molybdenum, selenium, thallium, and zinc in liver and kidney samples from 317 otters harvested from 2009 to 2016. Arsenic, lead, and thallium samples were tested at levels below the limit of detection. With the exception of cadmium, we detected all other elements at higher levels in the liver compared with the kidney. Specifically, cadmium, cobalt, copper, iron, magnesium, manganese, mercury, molybdenum, and zinc levels differed by tissue type analyzed. Most element concentrations remained stable or increased with otter age. We detected higher levels of mercury and selenium in the Lower Pee Dee and Cape Fear river basins. River basins within the Mountain FMU were higher in cadmium, copper, iron, lead, and zinc, whereas the Coastal Plain FMU was lower in cobalt and manganese. None of the elements occurred at toxic levels. Our research establishes baseline concentration levels for North Carolina, which will benefit future monitoring efforts and provide insight into future changes in the otter population.}, number={2}, journal={Environmental Monitoring and Assessment}, publisher={Springer Science and Business Media LLC}, author={Sanders, Charles W., II and Pacifici, Krishna and Hess, George R. and Olfenbuttel, Colleen and DePerno, Christopher S.}, year={2020}, month={Jan} }
@article{casola_peterson_pacifici_moorman_2020, title={Public support and visitation impacts of Sunday hunting on public hunting lands}, volume={26}, ISSN={1087-1209 1533-158X}, url={http://dx.doi.org/10.1080/10871209.2020.1811923}, DOI={10.1080/10871209.2020.1811923}, abstractNote={Sunday hunting legislation is complex, and often controversial, resulting in recreation impacts for both traditional (hunters, anglers, trappers) and non-traditional (e.g., hikers, birders, bikers,...}, number={1}, journal={Human Dimensions of Wildlife}, publisher={Informa UK Limited}, author={Casola, William R. and Peterson, M. Nils and Pacifici, Krishna and Moorman, Christopher E.}, year={2020}, month={Aug}, pages={94–97} }
@article{foley_pacifici_baird_webster_swaim_read_2021, title={Residency and movement patterns of Cuvier's beaked whales Ziphius cavirostris off Cape Hatteras, North Carolina, USA}, volume={660}, ISSN={["1616-1599"]}, DOI={10.3354/meps13593}, abstractNote={Cuvier’s beaked whalesZiphius cavirostrisare wide-ranging, deep-diving cetaceans that are particularly sensitive to anthropogenic noise. Current stock assessments assume a single population in the western North Atlantic Ocean, but knowledge of the residency patterns and distribution of the species is currently lacking in the region. Here we describe the spatial ecology of 20 Cuvier’s beaked whales equipped with satellite-linked tags off Cape Hatteras, North Carolina, USA, between 2014 and 2017. We applied a hierarchical switching state-space model to filter location estimates and define behavioral states of area-restricted search (ARS) and transit. We used kernel density estimation to identify high use areas, and net squared displacement analyses to assess residency. The vast majority (96%) of locations were classified as ARS behavior, suggesting that tagged whales allocated much of their time to foraging. Maximum net displacement had a sample median of 50 km, and 81% of individual whales were classified as demonstrating a resident, or ‘home range,’ movement pattern. Overall, our research indicates a localized population of Cuvier’s beaked whales occupying the area off Cape Hatteras. The tagged animals demonstrated a small, defined core use area and exhibited little displacement from the region. These patterns of movement and spatial use can inform future conservation and management of this species, which is vulnerable to anthropogenic disturbances caused by several sources, including mid-frequency active sonar and seismic exploration.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Foley, Heather J. and Pacifici, Krishna and Baird, Robin W. and Webster, Daniel L. and Swaim, Zachary T. and Read, Andrew J.}, year={2021}, month={Feb}, pages={203–216} }
@article{burke_peterson_sawyer_moorman_serenari_pacifici_2019, title={A method for mapping hunting occurrence using publicly available, geographic variables}, volume={43}, ISSN={["1938-5463"]}, DOI={10.1002/wsb.994}, abstractNote={ABSTRACTThe spatial distribution of land available for hunting has received scant attention in the literature, but it fundamentally affects the feasibility of wildlife management. Modeling the distribution of hunting lands can be logistically difficult because of data requirements and the dynamic nature of landscapes and landowner preferences. We describe one approach to address this challenge using spatially explicit logistic regression models that accurately predict whether each parcel of land in North Carolina, USA, was hunted using free and publicly available geographic predictors. We collected data to develop and validate models from surveys of nonindustrial (n = 1,936) and industrial (n = 670) private landowners conducted during 2016 in North Carolina. Property size and housing and road density predicted whether hunting occurred correctly on 96% of nonindustrial parcels. Property size, housing and road density, and distance to the nearest city correctly predicted whether hunting occurred for 94% of industrial parcels. These results suggest wildlife managers may be able to accurately map and quantify where hunting occurs using relatively few publicly available geographic predictors. Future refinement of the methodology and model parameters is likely needed in different regions, with independent data sets, before adopting widespread implementation of underlying methods. This mapping method will facilitate assessing the efficacy of hunting as a wildlife management tool for overabundant species. Similarly the mapping approach would improve wildlife population estimates based on hunter harvest data by providing a more rigorous estimate of land that is huntable per harvested animal reported. © 2019 The Wildlife Society.}, number={3}, journal={WILDLIFE SOCIETY BULLETIN}, author={Burke, Conner R. and Peterson, M. Nils and Sawyer, David T. and Moorman, Christopher E. and Serenari, Christopher and Pacifici, Krishna}, year={2019}, month={Sep}, pages={537–545} }
@article{taillie_moorman_smart_pacifici_2019, title={Bird community shifts associated with saltwater exposure in coastal forests at the leading edge of rising sea level}, volume={14}, ISSN={["1932-6203"]}, url={https://doi.org/10.1371/journal.pone.0216540}, DOI={10.1371/journal.pone.0216540}, abstractNote={Rising sea levels dramatically alter the vegetation composition and structure of coastal ecosystems. However, the implications of these changes for coastal wildlife are poorly understood. We aimed to quantify responses of avian communities to forest change (i.e., ghost forests) in a low-lying coastal region highly vulnerable to rising sea level. We conducted point counts to sample avian communities at 156 forested points in eastern North Carolina, USA in 2013–2015. We modelled avian community composition using a multi-species hierarchical occupancy model and used metrics of vegetation structure derived from Light Detection and Ranging (LiDAR) data as covariates related to variation in bird responses. We used this model to predict occupancy for each bird species in 2001 (using an analogous 2001 LiDAR dataset) and 2014 and used the change in occupancy probability to estimate habitat losses and gains at 3 spatial extents: 1) the entire study area, 2) burned forests only, and 3) unburned, low-lying coastal forests only. Of the 56 bird species we investigated, we observed parameter estimates corresponding to a higher likelihood of occurring in ghost forest for 34 species, but only 9 of those had 95% posterior intervals that did not overlap 0, thus having strong support. Despite the high vulnerability of forests in the region to sea level rise, habitat losses and gains associated with rising sea level were small relative to those resulting from wildfire. Though the extent of habitat changes associated with the development of ghost forest was limited, these changes likely are more permanent and may compound over time as sea level rises at an increasing rate. As such, the proliferation of ghost forests from rising sea level has potential to become an important driver of forest bird habitat change in coastal regions.}, number={5}, journal={PLOS ONE}, author={Taillie, Paul J. and Moorman, Christopher E. and Smart, Lindsey S. and Pacifici, Krishna}, year={2019}, month={May} }
@article{hody_moreno_meyer_pacifici_kays_2019, title={Canid collision-expanding populations of coyotes (Canis latrans) and crab-eating foxes (Cerdocyon thous) meet up in Panama}, volume={100}, ISSN={["1545-1542"]}, DOI={10.1093/jmammal/gyz158}, abstractNote={Abstract
The rise of the Panamanian Isthmus 3–4 million years ago enabled the first dispersal of mammals between North and South America in what is known as the Great American Biotic Interchange. Modern deforestation threatens the historic forest connectivity and creates new habitat for open-country species, as documented by recent expansions of North American coyotes (Canis latrans) and South American crab-eating foxes (Cerdocyon thous) into Central America. We used camera traps to map the expansions of these species into eastern Panama and found that, by 2015, coyote populations had colonized most agricultural area west of Lago Bayano. Most of our camera arrays east of this point documented crab-eating foxes, and evidence from roadkills showed some foxes had advanced farther west, but we never documented both species at the same camera-trap array, suggesting the possibility of fine-scale spatial avoidance. We used a data fusion approach to build species distribution models combining our camera surveys with records from the literature and roadkill. While the auxiliary data improved the predictive accuracy for both species, few clear habitat patterns emerged, which might reflect the generalist tendencies of these canids, or the fact that both are in the early stages of colonizing the region. Camera-trap photos showed that both species were nocturnal and revealed some dog-like morphology in coyotes, which could indicate their recent hybridization with dogs (Canis familiaris). Our continued monitoring of the Darién documented single coyotes moving through the western edge of the area in 2016 and 2018. This leaves only the great Darién forests between coyotes and South America. If deforestation continues in the region, these two invasive canids could represent the first of a new, Not-So-Great American Biotic Interchange, where generalist species adapted to human disturbance cross continents and threaten native biota.}, number={6}, journal={JOURNAL OF MAMMALOGY}, author={Hody, Allison W. and Moreno, Ricardo and Meyer, Ninon F. V. and Pacifici, Krishna and Kays, Roland}, year={2019}, month={Dec}, pages={1819–1830} }
@article{cope_kwak_black_pacifici_2019, title={Evaluation of Artificial Cover Units as a Sampling Technique and Habitat Enhancement for Madtoms in Rivers}, volume={39}, ISSN={["1548-8675"]}, url={https://doi.org/10.1002/nafm.10317}, DOI={10.1002/nafm.10317}, abstractNote={AbstractInstream habitat degradation and loss are major threats to freshwater fishes and critical conservation issues among nongame species due to a lack of research and knowledge concerning their habitat requirements. Instream physical cover is an important component of fish habitat, especially for benthic species that require cover for reproduction and shelter from predators. One such species is the Carolina Madtom Noturus furiosus, a small, imperiled, nongame catfish that is endemic to the Neuse and Tar River basins of North Carolina. To enhance understanding of instream cover dynamics, we constructed artificial cover units from terra cotta materials and deployed them in rivers to (1) evaluate whether they could be an effective passive‐sampling technique to estimate detection and occupancy of the Carolina Madtom and (2) determine their potential to enhance habitat in systems where instream cover has been lost. Artificial cover units were deployed at eight sites in the Neuse and Tar River basins, and the units collected 30 Carolina Madtoms at two sites in the Tar River basin. Occupancy modeling estimated a Carolina Madtom detection probability of 0.92 using artificial cover units. Compared to other standardized sampling methods, artificial cover units were an efficient passive‐sampling technique for detecting Carolina Madtoms. Observations also revealed that artificial cover units were occupied by Carolina Madtoms for reproduction. These findings provide an additional means by which natural resource managers can assess the status of this imperiled species via an inexpensive passive‐sampling device that can provide spawning habitat and protection from predators as well as helping to mitigate the effects of instream habitat degradation.}, number={4}, journal={NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT}, publisher={Wiley}, author={Cope, W. Robert and Kwak, Thomas J. and Black, Tyler R. and Pacifici, Krishna}, year={2019}, month={Aug}, pages={778–787} }
@book{grantham_reich_laber_pacifici_dunn_fierer_gebert_allwood_faith_2019, title={Global forensic geolocation with deep neural networks}, url={https://arxiv.org/abs/1905.11765}, number={1905.11765}, author={Grantham, Neal S. and Reich, Brian J. and Laber, Eric B. and Pacifici, Krishna and Dunn, Robert R. and Fierer, Noah and Gebert, Matthew and Allwood, Julia S. and Faith, Seth A.}, year={2019} }
@inproceedings{casola_peterson_wu_sills_pease_pacifici_leung_birckhead_mcrae_2019, title={Measuring the Value of Public Hunting Land Using a Hedonic Approach}, author={Casola, William R. and Peterson, M.Nils and Wu, Yu and Sills, Erin O. and Pease, Brent S. and Pacifici, Krishna and Leung, Yu-Fai and Birckhead, Jessie and McRae, Brian}, year={2019} }
@inproceedings{sanders_pacifici_olfenbuttel_deperno_2019, title={Metals Contamination of Otters in North Carolina}, author={Sanders, Charles W. and Pacifici, Krishna and Olfenbuttel, Colleen and DePerno, Chris S.}, year={2019} }
@article{rosche_moorman_pacifici_jones_deperno_2019, title={Northern bobwhite breeding season habitat selection in fire‐maintained pine woodland}, volume={83}, ISSN={0022-541X 1937-2817}, url={http://dx.doi.org/10.1002/jwmg.21683}, DOI={10.1002/jwmg.21683}, abstractNote={ABSTRACTDespite the acknowledged importance of prescribed fire in creating northern bobwhite (Colinus virginianus) breeding cover, little research has investigated bobwhite breeding season habitat selection relative to time since fire. In 2016 and 2017, we monitored radio‐tagged bobwhite on a 17,000‐ha portion of a military installation managed with frequent (every ~3 years) prescribed fires, applied during the growing and dormant seasons. We monitored bobwhite to determine which vegetation characteristics associated with prescribed burning were important to bobwhite breeding season habitat selection at the microsite (i.e., telemetry location compared to nearby random location) and the macrosite scale (i.e., the burn‐unit containing the location compared to study area availability). During 2 breeding seasons, we collected 2,315 bobwhite locations and compared percent cover of vegetation, days since burn, basal area, and distance to key landscape features (e.g., stream, wildlife opening) at a subset of microsite locations (301 locations during 2016 and 890 locations during 2017) to paired random locations. At the microsite scale, bobwhite selected lower basal area of hardwoods, greater woody understory cover, greater other (not wiregrass [Aristida stricta]) grass cover, and greater forb cover than at random points. At the macrosite scale, bobwhite selected units with <4.6 m2/ha basal area (combined hardwoods and pines) in 2016 and units with <9.2 m2/ha basal area in 2017. At the macrosite scale, bobwhite selected for areas burned in the dormant season of the same year, avoided areas burned in the growing season of the same year, and used other times since last burn categories proportionate to their availability. The selection for a low basal area at both scales indicates prescribed fire effects would be limited by shading from dense overstory, and the shrubs, grasses, and forbs that provide essential cover for bobwhite during the breeding season will not develop. In lower productivity soil regions similar to our study area, we advise that thinning operations set target basal areas below 10 m2/ha to create and maintain breeding season habitat for northern bobwhite. © 2019 The Wildlife Society}, number={5}, journal={The Journal of Wildlife Management}, publisher={Wiley}, author={Rosche, Sarah B. and Moorman, ChristopheR E. and Pacifici, Krishna and Jones, Jeffrey G. and DePerno, Christopher S.}, year={2019}, month={May}, pages={1226–1236} }
@book{hu_laber_li_meyer_pacifici_2019, title={Note on Thompson sampling for large decision problems}, url={https://arxiv.org/abs/1905.04735}, number={1905.04735}, journal={ArXiv}, author={Hu, Tao and Laber, Eric B. and Li, Zhen and Meyer, Nick J. and Pacifici, Krishna}, year={2019} }
@article{boggs_moorman_hazel_greenberg_pacifici_2020, title={Relationships between white-footed mice and logging residue: Informing the sustainability of potential wood bioenergy harvests}, volume={457}, ISSN={0378-1127}, url={http://dx.doi.org/10.1016/j.foreco.2019.117706}, DOI={10.1016/j.foreco.2019.117706}, abstractNote={We examined local and site-scale relationships between white-footed mice (Peromyscus leucopus) and logging residue after timber harvests to assess potential effects of expanding bioenergy markets in the southern Appalachian region of the United States. We sampled mice in 10 recent (2013–2015) clearcut or shelterwood harvests dominated either by white pine or hardwoods prior to harvest. We captured mice May–August, 2016 and 2017 using 10 grids of 60 Sherman traps spaced 15 m apart and set twice for five consecutive nights in each year. We categorized traps as either near (≤5 m) or far (>5 m) from coarse woody debris (CWD; woody debris ≥10 cm in diameter). We estimated site-level woody debris volumes using modified prism sweep sampling and determined vegetation, woody debris, and ground cover composition at each trap location. White-footed mouse occupancy increased with greater trap-level CWD cover in all stands, and greater site-level woody debris volume in white pine stands. Mouse abundance increased with greater site-level woody debris volume, and abundance was greater at white pine sites than hardwood sites. These results demonstrate that residual logging debris is important to white-footed mice, both at the local- and site-scale. Reductions in residual logging debris following harvests, including via removal of low value stems for wood bioenergy, likely will result in decreased white-footed mouse occupancy and abundance. We recommend developing proactive strategies to retain scattered logging residues following even-aged timber harvests, especially in cases where bioenergy harvests occur in the southern Appalachian region.}, journal={Forest Ecology and Management}, publisher={Elsevier BV}, author={Boggs, April D. and Moorman, Christopher E. and Hazel, Dennis W. and Greenberg, Cathryn H. and Pacifici, Krishna}, year={2020}, month={Feb}, pages={117706} }
@article{pacifici_reich_miller_pease_2019, title={Resolving misaligned spatial data with integrated species distribution models}, volume={100}, ISSN={["1939-9170"]}, DOI={10.1002/ecy.2709}, abstractNote={AbstractAdvances in species distribution modeling continue to be driven by a need to predict species responses to environmental change coupled with increasing data availability. Recent work has focused on development of methods that integrate multiple streams of data to model species distributions. Combining sources of information increases spatial coverage and can improve accuracy in estimates of species distributions. However, when fusing multiple streams of data, the temporal and spatial resolutions of data sources may be mismatched. This occurs when data sources have fluctuating geographic coverage, varying spatial scales and resolutions, and differing sources of bias and sparsity. It is well documented in the spatial statistics literature that ignoring the misalignment of different data sources will result in bias in both the point estimates and uncertainty. This will ultimately lead to inaccurate predictions of species distributions. Here, we examine the issue of misaligned data as it relates specifically to integrated species distribution models. We then provide a general solution that builds off work in the statistical literature for the change‐of‐support problem. Specifically, we leverage spatial correlation and repeat observations at multiple scales to make statistically valid predictions at the ecologically relevant scale of inference. An added feature of the approach is that addressing differences in spatial resolution between data sets can allow for the evaluation and calibration of lesser‐quality sources in many instances. Using both simulations and data examples, we highlight the utility of this modeling approach and the consequences of not reconciling misaligned spatial data. We conclude with a brief discussion of the upcoming challenges and obstacles for species distribution modeling via data fusion.}, number={6}, journal={ECOLOGY}, author={Pacifici, Krishna and Reich, Brian J. and Miller, David A. W. and Pease, Brent S.}, year={2019}, month={Jun} }
@inproceedings{kays_boone_pacifici_pease_shaw_smith_may_2019, title={State-Wide Citizen Science Mammal Survey As Science, Conservation, and Public Engagement: North Carolina’s Candid Critters}, author={Kays, Roland and Boone, Hailey and Pacifici, Krishna and Pease, Brent S. and Shaw, Jon and Smith, Chris and May, Ann M.}, year={2019} }
@article{miller_pacifici_sanderlin_reich_2019, title={The recent past and promising future for data integration methods to estimate species' distributions}, volume={10}, ISSN={["2041-2096"]}, DOI={10.1111/2041-210X.13110}, abstractNote={Abstract
With the advance of methods for estimating species distribution models has come an interest in how to best combine datasets to improve estimates of species distributions. This has spurred the development of data integration methods that simultaneously harness information from multiple datasets while dealing with the specific strengths and weaknesses of each dataset.
We outline the general principles that have guided data integration methods and review recent developments in the field. We then outline key areas that allow for a more general framework for integrating data and provide suggestions for improving sampling design and validation for integrated models.
Key to recent advances has been using point‐process thinking to combine estimators developed for different data types. Extending this framework to new data types will further improve our inferences, as well as relaxing assumptions about how parameters are jointly estimated. These along with the better use of information regarding sampling effort and spatial autocorrelation will further improve our inferences.
Recent developments form a strong foundation for implementation of data integration models. Wider adoption can improve our inferences about species distributions and the dynamic processes that lead to distributional shifts.
}, number={1}, journal={METHODS IN ECOLOGY AND EVOLUTION}, author={Miller, David A. W. and Pacifici, Krishna and Sanderlin, Jamie S. and Reich, Brian J.}, year={2019}, month={Jan}, pages={22–37} }
@article{irizarry_collazo_pacifici_reich_battle_2018, title={Avian response to shade-layer restoration in coffee plantations in Puerto Rico}, volume={26}, ISSN={["1526-100X"]}, url={https://doi.org/10.1111/rec.12697}, DOI={10.1111/rec.12697}, abstractNote={Documenting the evolving processes associated with habitat restoration and how long it takes to detect avian demographic responses is crucial to evaluate the success of restoration initiatives and to identify ways to improve their effectiveness. The importance of this endeavor prompted the U.S. Fish and Wildlife Service and the USDA Natural Resources Conservation Service to evaluate their sun‐to‐shade coffee restoration program in Puerto Rico initiated in 2003. We quantified the responses of 12 resident avian species using estimates of local occupancy and extinction probabilities based on surveys conducted in 2015–2017 at 65 restored farms grouped according to time‐since‐initial‐restoration (TSIR): new (2011–2014), intermediate (2007–2010), and old (2003–2006). We also surveyed 40 forest sites, which served as reference sites. Vegetation complexity increased with TSIR, ranging between 35 and 40% forest cover in farms 6–9 years TSIR. Forest specialists (e.g. Loxigilla portoricencis) exhibited highest average occupancy in farms initially classified as intermediate (6–9 years) and old (>10 years), paralleling occupancy in secondary forests. Occupancy of open‐habitat specialists (e.g. Tiaris olivaceus) was more variable, but higher in recently restored farms. Restoring the shade layer has the potential to heighten ecological services derived from forest specialists (e.g. frugivores) without losing the services of many open‐habitat specialists (e.g. insectivores). Annual local extinction probability for forest specialists decreased with increasing habitat complexity, strengthening the potential value of shade restoration as a tool to enhance habitat for avifauna that evolved in forested landscapes.}, number={6}, journal={RESTORATION ECOLOGY}, publisher={Wiley}, author={Irizarry, Amarilys D. and Collazo, Jaime A. and Pacifici, Krishna and Reich, Brian J. and Battle, Kathryn E.}, year={2018}, month={Nov}, pages={1212–1220} }
@article{reich_pacifici_stallings_2018, title={Integrating auxiliary data in optimal spatial design for species distribution modelling}, volume={9}, ISSN={["2041-2096"]}, DOI={10.1111/2041-210x.13002}, abstractNote={Abstract
Traditional surveys used to create species distribution maps and estimate ecological relationships are expensive and time consuming. Citizen science offers a way to collect a massive amount of data at negligible cost and has been shown to be a useful supplement to traditional analyses. However, there remains a need to conduct formal surveys to firmly establish ecological relationships and trends.
In this paper, we investigate the use of auxiliary (e.g. citizen science) data as a guide to designing more efficient ecological surveys. Our aim is to explore the use of opportunistic data to inform spatial survey design through a novel objective function that minimizes misclassificaton rate (i.e. false positives and false negatives) of the estimated occupancy maps. We use an initial occupancy estimate from auxiliary data as the prior in a Bayesian spatial occupancy model, and an efficient posterior approximation that accounts for spatial dependence, covariate effects, and imperfect detection in an exchange algorithm to search for the optimal set of sampling locations to minimize misclassification rate.
We examine the optimal design as a function of the detection rate and quality of the citizen‐science data, and compare this optimal design with several common ad hoc designs via an extensive simulation study. We then apply our method to eBird data for the brown‐headed nuthatch in the Southeast US.
We argue that planning a survey with the use of auxiliary data improves estimation accuracy and may significantly reduce the costs of sampling.
}, number={6}, journal={METHODS IN ECOLOGY AND EVOLUTION}, author={Reich, Brian J. and Pacifici, Krishna and Stallings, Jonathan W.}, year={2018}, month={Jun}, pages={1626–1637} }
@article{waples_kays_fredrickson_pacifici_mills_2018, title={Is the Red Wolf a Listable Unit Under the US Endangered Species Act?}, volume={109}, ISSN={0022-1503 1465-7333}, url={http://dx.doi.org/10.1093/jhered/esy020}, DOI={10.1093/jhered/esy020}, abstractNote={Abstract Defining units that can be afforded legal protection is a crucial, albeit challenging, step in conservation planning. As we illustrate with a case study of the red wolf (Canis rufus) from the southeastern United States, this step is especially complex when the evolutionary history of the focal taxon is uncertain. The US Endangered Species Act (ESA) allows listing of species, subspecies, or Distinct Population Segments (DPSs) of vertebrates. Red wolves were listed as an endangered species in 1973, and their status remains precarious. However, some recent genetic studies suggest that red wolves are part of a small wolf species (C. lycaon) specialized for heavily forested habitats of eastern North America, whereas other authors suggest that red wolves arose, perhaps within the last ~400 years, through hybridization between gray wolves (C. lupus) and coyotes (C. latrans). Using published genetic, morphological, behavioral, and ecological data, we evaluated whether each evolutionary hypothesis would lead to a listable unit for red wolves. Although the potential hybrid origin of red wolves, combined with abundant evidence for recent hybridization with coyotes, raises questions about status as a separate species or subspecies, we conclude that under any proposed evolutionary scenario red wolves meet both criteria to be considered a DPS: they are Discrete compared with other conspecific populations, and they are Significant to the taxon to which they belong. As population-level units can qualify for legal protection under endangered-species legislation in many countries throughout the world, this general approach could potentially be applied more broadly.}, number={5}, journal={Journal of Heredity}, publisher={Oxford University Press (OUP)}, author={Waples, Robin S and Kays, Roland and Fredrickson, Richard J and Pacifici, Krishna and Mills, L Scott}, year={2018}, month={Jun}, pages={585–597} }
@article{laber_meyer_reich_pacifici_collazo_drake_2018, title={Optimal treatment allocations in space and time for on‐line control of an emerging infectious disease}, volume={67}, ISSN={0035-9254 1467-9876}, url={http://dx.doi.org/10.1111/rssc.12266}, DOI={10.1111/rssc.12266}, abstractNote={SummaryA key component in controlling the spread of an epidemic is deciding where, when and to whom to apply an intervention. We develop a framework for using data to inform these decisions in realtime. We formalize a treatment allocation strategy as a sequence of functions, one per treatment period, that map up-to-date information on the spread of an infectious disease to a subset of locations where treatment should be allocated. An optimal allocation strategy optimizes some cumulative outcome, e.g. the number of uninfected locations, the geographic footprint of the disease or the cost of the epidemic. Estimation of an optimal allocation strategy for an emerging infectious disease is challenging because spatial proximity induces interference between locations, the number of possible allocations is exponential in the number of locations, and because disease dynamics and intervention effectiveness are unknown at outbreak. We derive a Bayesian on-line estimator of the optimal allocation strategy that combines simulation–optimization with Thompson sampling. The estimator proposed performs favourably in simulation experiments. This work is motivated by and illustrated using data on the spread of white nose syndrome, which is a highly fatal infectious disease devastating bat populations in North America.}, number={4}, journal={Journal of the Royal Statistical Society: Series C (Applied Statistics)}, publisher={Wiley}, author={Laber, Eric B. and Meyer, Nick J. and Reich, Brian J. and Pacifici, Krishna and Collazo, Jaime A. and Drake, John M.}, year={2018}, month={Jul}, pages={743–789} }
@inproceedings{cope_kwak_black_pacifici_hallerman_harris_miller_raley_2018, title={Status, Habitat, and Genetics of the Endemic Carolina Madtom}, author={Cope, William R. and Kwak, Thomas J. and Black, Tyler R. and Pacifici, Krishna and Hallerman, Eric M. and Harris, Sheila C. and Miller, Caitlin and Raley, Morgan E.}, year={2018} }
@article{morris_reich_pacifici_lei_2017, title={A spatial model for rare binary events}, volume={24}, ISSN={["1573-3009"]}, DOI={10.1007/s10651-017-0385-z}, number={4}, journal={ENVIRONMENTAL AND ECOLOGICAL STATISTICS}, author={Morris, Samuel A. and Reich, Brian J. and Pacifici, Krishna and Lei, Yuancai}, year={2017}, month={Dec}, pages={485–504} }
@article{pandolfo_kwak_cope_heise_nichols_pacifici_2017, title={Declining Occurrence and Low Colonization Probability in Freshwater Mussel Assemblages: A Dynamic Occurrence Modeling Approach}, volume={20}, ISSN={2472-2944}, url={http://dx.doi.org/10.31931/fmbc.v20i1.2017.13-19}, DOI={10.31931/fmbc.v20i1.2017.13-19}, abstractNote={ABSTRACT Mussel monitoring data are abundant, but methods for analyzing long-term trends in these data are often uninformative or have low power to detect changes. We used a dynamic occurrence model, which accounted for imperfect species detection in surveys, to assess changes in species occurrence in a long-term data set (1986–2011) for the Tar River basin of North Carolina, USA. Occurrence of all species decreased steadily over the time period studied. Occurrence in 1986 ranged from 0.19 for Utterbackia imbecillis to 0.60 for Fusconaia masoni. Occurrence in 2010–2011 ranged from 0.10 for Lampsilis radiata to 0.40 for F. masoni. The maximum difference between occurrence in 1986 and 2011 was a decline of 0.30 for Alasmidonta undulata. Mean persistence for all species was high (0.97, 95% CI = 0.95–0.99); however, mean colonization probability was very low (<0.01, 95% CI = <0.01–0.01). These results indicate that mussels persisted at sites already occupied but that they have not colonized sites where they had not occurred previously. Our findings highlight the importance of modeling approaches that incorporate imperfect detection in estimating species occurrence and revealing temporal trends to inform conservation planning.}, number={1}, journal={Freshwater Mollusk Biology and Conservation}, publisher={BioOne}, author={Pandolfo, Tamara J. and Kwak, Thomas J. and Cope, W. Gregory and Heise, Ryan J. and Nichols, Robert B. and Pacifici, Krishna}, year={2017}, month={Mar}, pages={13} }
@article{monroe_collazo_pacifici_reich_puente-rolón_terando_2017, title={Occupancy and Abundance of Eleutherodactylus Frogs in Coffee Plantations in Puerto Rico}, volume={73}, ISSN={0018-0831}, url={http://dx.doi.org/10.1655/herpetologica-d-16-00089}, DOI={10.1655/herpetologica-d-16-00089}, abstractNote={Shaded coffee plantations are of conservation value for many taxa, particularly for resident avifauna in the face of extensive landscape changes. Yet, little is known about the value of coffee plantations for amphibians because there are scant demographic data to index their value among species with different habitat preferences. We estimated the probability of occupancy of three frog species: Eleutherodactylus wightmanae, a forest species; E. brittoni, a grassland species; and E. antillensis, an open habitat species. Occupancy was estimated in sun and shaded plantations, and in secondary forest, in the west-central mountains of Puerto Rico. We also estimated the probability that a survey station was occupied by no individuals, one, or >1 individual, as a proxy of abundance. The aforementioned parameters, and local colonization and extinction probability, were modeled as a function of weather conditions (temperature, humidity) and vegetation cover at the sampling station (5 m) and contextual (100 m) scales. Encounter histories were obtained with passive acoustic recorders between February and July in 2015. Consistent with known habitat preferences, the highest occupancies were associated with secondary forests for E. wightmanae and sun plantations for E. brittoni. Occupancy probability for E. antillensis was similar across habitat types, indicating no aversion to shaded–forested habitats. Shaded plantations harbored moderate levels of occupancy for all species, indicating their potential value for multispecies conservation. Local colonization rates increased with forest cover for E. wightmanae, and with open habitats for E. brittoni and E. antillensis. Open habitats harbored a higher abundance of E. brittoni and E antillensis, but lower values for E. wightmanae. Sun and shaded plantations could provide quality habitat for Eleutherodactylus spp. if managed for features that promote local colonization and abundance.}, number={4}, journal={Herpetologica}, publisher={Herpetologists League}, author={Monroe, Kelen D. and Collazo, Jaime A. and Pacifici, Krishna and Reich, Brian J. and Puente-Rolón, Alberto R. and Terando, Adam J.}, year={2017}, month={Dec}, pages={297} }
@article{monroe_collazo_pacifici_reich_puente-rolón_terando_2017, title={Occupancy and abundance of Eleutherodactylus wightmanae and E. brittoni along elevational gradients in west-central Puerto Rico}, volume={40}, journal={Caribbean Naturalist}, author={Monroe, Kelen D. and Collazo, Jaime A. and Pacifici, Krishna and Reich, Brian J. and Puente-Rolón, Alberto R. and Terando, Adam J.}, year={2017}, pages={1–18} }
@book{gaydos_pacifici_meentemeyer_rizzo_2017, place={Albany, CA}, title={Resilience of diversity-disease risk interactions following wildfire disturbance}, url={https://www.fs.usda.gov/treesearch/pubs/53990}, journal={Proceedings of the Sudden Oak Death Sixth Science Symposium}, institution={Gen}, author={Gaydos, Devon A. and Pacifici, Krishna and Meentemeyer, Ross K. and Rizzo, David M.}, year={2017} }
@book{patton_pacifici_collazo_2016, title={Inferring habitat quality and habitat selection using static site occupancy models}, url={https://arxiv.org/abs/1607.05175}, author={Patton, Philip T. and Pacifici, Krishna and Collazo, Jaime}, year={2016} }
@article{pacifici_reich_miller_gardner_stauffer_singh_mckerrow_collazo_2017, title={Integrating multiple data sources in species distribution modeling: a framework for data fusion}, volume={98}, ISSN={["1939-9170"]}, DOI={10.1002/ecy.1710}, abstractNote={AbstractThe last decade has seen a dramatic increase in the use of species distribution models (SDMs) to characterize patterns of species’ occurrence and abundance. Efforts to parameterize SDMs often create a tension between the quality and quantity of data available to fit models. Estimation methods that integrate both standardized and non‐standardized data types offer a potential solution to the tradeoff between data quality and quantity. Recently several authors have developed approaches for jointly modeling two sources of data (one of high quality and one of lesser quality). We extend their work by allowing for explicit spatial autocorrelation in occurrence and detection error using a Multivariate Conditional Autoregressive (MVCAR) model and develop three models that share information in a less direct manner resulting in more robust performance when the auxiliary data is of lesser quality. We describe these three new approaches (“Shared,” “Correlation,” “Covariates”) for combining data sources and show their use in a case study of the Brown‐headed Nuthatch in the Southeastern U.S. and through simulations. All three of the approaches which used the second data source improved out‐of‐sample predictions relative to a single data source (“Single”). When information in the second data source is of high quality, the Shared model performs the best, but the Correlation and Covariates model also perform well. When the information quality in the second data source is of lesser quality, the Correlation and Covariates model performed better suggesting they are robust alternatives when little is known about auxiliary data collected opportunistically or through citizen scientists. Methods that allow for both data types to be used will maximize the useful information available for estimating species distributions.}, number={3}, journal={ECOLOGY}, author={Pacifici, Krishna and Reich, Brian J. and Miller, David A. W. and Gardner, Beth and Stauffer, Glenn and Singh, Susheela and McKerrow, Alexa and Collazo, Jaime A.}, year={2017}, month={Mar}, pages={840–850} }
@article{pandolfo_kwak_cope_heise_nichols_pacifici_2016, title={Species traits and catchment-scale habitat factors influence the occurrence of freshwater mussel populations and assemblages}, volume={61}, ISSN={0046-5070}, url={http://dx.doi.org/10.1111/fwb.12807}, DOI={10.1111/fwb.12807}, abstractNote={Summary
Conservation of freshwater unionid mussels presents unique challenges due to their distinctive life cycle, cryptic occurrence and imperilled status. Relevant ecological information is urgently needed to guide their management and conservation.
We adopted a modelling approach, which is a novel application to freshwater mussels to enhance inference on rare species, by borrowing data among species in a hierarchical framework to conduct the most comprehensive occurrence analysis for freshwater mussels to date. We incorporated imperfect detection to more accurately examine effects of biotic and abiotic factors at multiple scales on the occurrence of 14 mussel species and the entire assemblage of the Tar River Basin of North Carolina, U.S.A.
The single assemblage estimate of detection probability for all species was 0.42 (95% CI, 0.36–0.47) with no species‐ or site‐specific detection effects identified. We empirically observed 15 mussel species in the basin but estimated total species richness at 21 (95% CI, 16–24) when accounting for imperfect detection.
Mean occurrence probability among species ranged from 0.04 (95% CI, 0.01–0.16) for Alasmidonta undulata, an undescribed Lampsilis sp., and Strophitus undulatus to 0.67 (95% CI, 0.42–0.86) for Elliptio icterina. Median occurrence probability among sites was <0.30 for all species with the exception of E. icterina. Site occurrence probability generally related to mussel conservation status, with reduced occurrence for endangered and threatened species.
Catchment‐scale abiotic variables (stream power, agricultural land use) and species traits (brood time, host specificity, tribe) influenced the occurrence of mussel assemblages more than reach‐ or microhabitat‐scale features.
Our findings reflect the complexity of mussel ecology and indicate that habitat restoration alone may not be adequate for mussel conservation. Catchment‐scale management can benefit an entire assemblage, but species‐specific strategies may be necessary for successful conservation. The hierarchical multispecies modelling approach revealed findings that could not be elucidated by other means, and the approach may be applied more broadly to other river basins and regions. Accurate measures of assemblage dynamics, such as occurrence and species richness, are required to create management plans for effective conservation.
}, number={10}, journal={Freshwater Biology}, publisher={Wiley}, author={Pandolfo, Tamara J. and Kwak, Thomas J. and Cope, W. Gregory and Heise, Ryan J. and Nichols, Robert B. and Pacifici, Krishna}, year={2016}, month={Aug}, pages={1671–1684} }
@inbook{terando_reich_pacifici_costanza_mckerrow_collazo_2017, title={Uncertainty Quantification and Propagation for Projections of Extremes in Monthly Area Burned Under Climate Change: A Case Study in the Coastal Plain of Georgia, USA}, volume={223}, ISBN={0}, ISSN={2328-8779}, url={http://dx.doi.org/10.1002/9781119028116.ch16}, DOI={10.1002/9781119028116.ch16}, abstractNote={Human-caused climate change is predicted to affect the frequency of hazard-linked extremes. Unusually large wildfires are a type of extreme event that is constrained by climate and can be a hazard to society but also an important ecological disturbance. This chapter focuses on changes in the frequency of extreme monthly area burned by wildfires for the end of the 21st century for a wildfire-prone region in the southeast United States. Predicting changes in area burned is complicated by the large and varied uncertainties in how the climate will change and in the models used to predict those changes. The chapter characterizes and quantifies multiple sources of uncertainty and propagate the expanded prediction intervals of future area burned. It illustrates that while accounting for multiple sources of uncertainty in global change science problems is a difficult task, it will be necessary in order to properly assess the risk of increased exposure to these society-relevant events.}, booktitle={NATURAL HAZARD UNCERTAINTY ASSESSMENT: MODELING AND DECISION SUPPORT}, publisher={John Wiley & Sons, Inc.}, author={Terando, Adam J. and Reich, Brian and Pacifici, Krishna and Costanza, Jennifer and McKerrow, Alexa and Collazo, Jaime A.}, year={2017}, pages={245–256} }
@article{grantham_reich_pacifici_laber_menninger_henley_barberán_leff_fierer_dunn_2015, title={Fungi Identify the Geographic Origin of Dust Samples}, volume={10}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0122605}, DOI={10.1371/journal.pone.0122605}, abstractNote={There is a long history of archaeologists and forensic scientists using pollen found in a dust sample to identify its geographic origin or history. Such palynological approaches have important limitations as they require time-consuming identification of pollen grains, a priori knowledge of plant species distributions, and a sufficient diversity of pollen types to permit spatial or temporal identification. We demonstrate an alternative approach based on DNA sequencing analyses of the fungal diversity found in dust samples. Using nearly 1,000 dust samples collected from across the continental U.S., our analyses identify up to 40,000 fungal taxa from these samples, many of which exhibit a high degree of geographic endemism. We develop a statistical learning algorithm via discriminant analysis that exploits this geographic endemicity in the fungal diversity to correctly identify samples to within a few hundred kilometers of their geographic origin with high probability. In addition, our statistical approach provides a measure of certainty for each prediction, in contrast with current palynology methods that are almost always based on expert opinion and devoid of statistical inference. Fungal taxa found in dust samples can therefore be used to identify the origin of that dust and, more importantly, we can quantify our degree of certainty that a sample originated in a particular place. This work opens up a new approach to forensic biology that could be used by scientists to identify the origin of dust or soil samples found on objects, clothing, or archaeological artifacts.}, number={4}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Grantham, Neal S. and Reich, Brian J. and Pacifici, Krishna and Laber, Eric B. and Menninger, Holly L. and Henley, Jessica B. and Barberán, Albert and Leff, Jonathan W. and Fierer, Noah and Dunn, Robert R.}, editor={Rokas, AntonisEditor}, year={2015}, month={Apr}, pages={e0122605} }
@article{pacifici_reich_dorazio_conroy_2016, title={Occupancy estimation for rare species using a spatially-adaptive sampling design}, volume={7}, ISSN={["2041-2096"]}, DOI={10.1111/2041-210x.12499}, abstractNote={Summary
Spatially clustered populations create unique challenges for conservation monitoring programmes. Advances in methodology typically are focused on either the design or the modelling stage of the study but do not involve integration of both.
We integrate adaptive cluster sampling and spatial occupancy modelling by developing two models to handle the dependence induced by cluster sampling. We compare these models to scenarios using simple random sampling and traditional occupancy models via simulation and data collected on a rare plant species, Tamarix ramosissima, found in China.
Our simulations show a marked improvement in confidence interval coverage for the new models combined with cluster sampling compared to simple random sampling and traditional occupancy models, with greatest improvement in the presence of low detection probability and spatial correlation in occupancy.
Accounting for the design using the simple cluster random‐effects model reduces bias considerably, and full spatial modelling reduces bias further, especially for large n when the spatial covariance parameters can be estimated reliably. Both new models build on the strength of occupancy modelling and adaptive sampling and perform at least as well, and often better, than occupancy modelling alone.
We believe our approach is unique and potentially useful for a variety of studies directed at patchily distributed, clustered or rare species exhibiting spatial variation.
}, number={3}, journal={METHODS IN ECOLOGY AND EVOLUTION}, author={Pacifici, Krishna and Reich, Brian J. and Dorazio, Robert M. and Conroy, Michael J.}, year={2016}, month={Mar}, pages={285–293} }
@article{barberán_dunn_reich_pacifici_laber_menninger_morton_henley_leff_miller_et al._2015, title={The ecology of microscopic life in household dust}, volume={282}, ISSN={0962-8452 1471-2954}, url={http://dx.doi.org/10.1098/rspb.2015.1139}, DOI={10.1098/rspb.2015.1139}, abstractNote={We spend the majority of our lives indoors; yet, we currently lack a comprehensive understanding of how the microbial communities found in homes vary across broad geographical regions and what factors are most important in shaping the types of microorganisms found inside homes. Here, we investigated the fungal and bacterial communities found in settled dust collected from inside and outside approximately 1200 homes located across the continental US, homes that represent a broad range of home designs and span many climatic zones. Indoor and outdoor dust samples harboured distinct microbial communities, but these differences were larger for bacteria than for fungi with most indoor fungi originating outside the home. Indoor fungal communities and the distribution of potential allergens varied predictably across climate and geographical regions; where you live determines what fungi live with you inside your home. By contrast, bacterial communities in indoor dust were more strongly influenced by the number and types of occupants living in the homes. In particular, the female : male ratio and whether a house had pets had a significant influence on the types of bacteria found inside our homes highlighting that who you live with determines what bacteria are found inside your home.}, number={1814}, journal={Proceedings of the Royal Society B: Biological Sciences}, publisher={The Royal Society}, author={Barberán, Albert and Dunn, Robert R. and Reich, Brian J. and Pacifici, Krishna and Laber, Eric B. and Menninger, Holly L. and Morton, James M. and Henley, Jessica B. and Leff, Jonathan W. and Miller, Shelly L. and et al.}, year={2015}, month={Sep}, pages={20151139} }
@inproceedings{meyer_laber_pacifici_reich_drake_2014, title={An adaptive control strategy for the West Africa Ebola outbreak}, url={http://daphnia.ecology.uga.edu/drakelab/wp-content/uploads/2016/01/meyer-et-al-geogia-tech-ebola-jan-22-2015.pdf}, author={Meyer, Nicholas J. and Laber, Eric B. and Pacifici, Krishna and Reich, Brian J. and Drake, John}, year={2014} }
@article{fackler_pacifici_martin_mcintyre_2014, title={Efficient Use of Information in Adaptive Management with an Application to Managing Recreation near Golden Eagle Nesting Sites}, volume={9}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0102434}, DOI={10.1371/journal.pone.0102434}, abstractNote={It is generally the case that a significant degree of uncertainty exists concerning the behavior of ecological systems. Adaptive management has been developed to address such structural uncertainty, while recognizing that decisions must be made without full knowledge of how a system behaves. This paradigm attempts to use new information that develops during the course of management to learn how the system works. To date, however, adaptive management has used a very limited information set to characterize the learning that is possible. This paper uses an extension of the Partial Observable Markov Decision Process (POMDP) framework to expand the information set used to update belief in competing models. This feature can potentially increase the speed of learning through adaptive management, and lead to better management in the future. We apply this framework to a case study wherein interest lies in managing recreational restrictions around golden eagle (Aquila chrysaetos) nesting sites. The ultimate management objective is to maintain an abundant eagle population in Denali National Park while minimizing the regulatory burden on park visitors. In order to capture this objective, we developed a utility function that trades off expected breeding success with hiker access. Our work is relevant to the management of human activities in protected areas, but more generally demonstrates some of the benefits of POMDP in the context of adaptive management.}, number={8}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Fackler, Paul L. and Pacifici, Krishna and Martin, Julien and McIntyre, Carol}, editor={Margalida, AntoniEditor}, year={2014}, month={Aug}, pages={e102434} }
@article{pacifici_zipkin_collazo_irizarry_dewan_2014, title={Guidelines for a priori grouping of species in hierarchical community models}, volume={4}, ISSN={["2045-7758"]}, DOI={10.1002/ece3.976}, abstractNote={AbstractRecent methodological advances permit the estimation of species richness and occurrences for rare species by linking species‐level occurrence models at the community level. The value of such methods is underscored by the ability to examine the influence of landscape heterogeneity on species assemblages at large spatial scales. A salient advantage of community‐level approaches is that parameter estimates for data‐poor species are more precise as the estimation process “borrows” from data‐rich species. However, this analytical benefit raises a question about the degree to which inferences are dependent on the implicit assumption of relatedness among species. Here, we assess the sensitivity of community/group‐level metrics, and individual‐level species inferences given various classification schemes for grouping species assemblages using multispecies occurrence models. We explore the implications of these groupings on parameter estimates for avian communities in two ecosystems: tropical forests in Puerto Rico and temperate forests in northeastern United States. We report on the classification performance and extent of variability in occurrence probabilities and species richness estimates that can be observed depending on the classification scheme used. We found estimates of species richness to be most precise and to have the best predictive performance when all of the data were grouped at a single community level. Community/group‐level parameters appear to be heavily influenced by the grouping criteria, but were not driven strictly by total number of detections for species. We found different grouping schemes can provide an opportunity to identify unique assemblage responses that would not have been found if all of the species were analyzed together. We suggest three guidelines: (1) classification schemes should be determined based on study objectives; (2) model selection should be used to quantitatively compare different classification approaches; and (3) sensitivity of results to different classification approaches should be assessed. These guidelines should help researchers apply hierarchical community models in the most effective manner.}, number={7}, journal={ECOLOGY AND EVOLUTION}, author={Pacifici, Krishna and Zipkin, Elise F. and Collazo, Jaime A. and Irizarry, Julissa I. and DeWan, Amielle}, year={2014}, month={Apr}, pages={877–888} }
@article{nichols_fackler_pacifici_murphy_nichols_2014, title={Reducing fatigue damage for ships in transit through structured decision making}, volume={38}, ISSN={0951-8339}, url={http://dx.doi.org/10.1016/j.marstruc.2014.04.002}, DOI={10.1016/j.marstruc.2014.04.002}, abstractNote={Research in structural monitoring has focused primarily on drawing inference about the health of a structure from the structure's response to ambient or applied excitation. Knowledge of the current state can then be used to predict structural integrity at a future time and, in principle, allows one to take action to improve safety, minimize ownership costs, and/or increase the operating envelope. While much time and effort has been devoted toward data collection and system identification, research to-date has largely avoided the question of how to choose an optimal maintenance plan. This work describes a structured decision making (SDM) process for taking available information (loading data, model output, etc.) and producing a plan of action for maintaining the structure. SDM allows the practitioner to specify his/her objectives and then solves for the decision that is optimal in the sense that it maximizes those objectives. To demonstrate, we consider the problem of a Naval vessel transiting a fixed distance in varying sea-state conditions. The physics of this problem are such that minimizing transit time increases the probability of fatigue failure in the structural supports. It is shown how SDM produces the optimal trip plan in the sense that it minimizes both transit time and probability of failure in the manner of our choosing (i.e., through a user-defined cost function). The example illustrates the benefit of SDM over heuristic approaches to maintaining the vessel.}, journal={Marine Structures}, publisher={Elsevier BV}, author={Nichols, J.M. and Fackler, P.L. and Pacifici, K. and Murphy, K.D. and Nichols, J.D.}, year={2014}, month={Oct}, pages={18–43} }
@article{fackler_pacifici_2014, title={Addressing structural and observational uncertainty in resource management}, volume={133}, ISSN={["1095-8630"]}, DOI={10.1016/j.jenvman.2013.11.004}, abstractNote={Most natural resource management and conservation problems are plagued with high levels of uncertainties, which make good decision making difficult. Although some kinds of uncertainties are easily incorporated into decision making, two types of uncertainty present more formidable difficulties. The first, structural uncertainty, represents our imperfect knowledge about how a managed system behaves. The second, observational uncertainty, arises because the state of the system must be inferred from imperfect monitoring systems. The former type of uncertainty has been addressed in ecology using Adaptive Management (AM) and the latter using the Partially Observable Markov Decision Processes (POMDP) framework. Here we present a unifying framework that extends standard POMDPs and encompasses both standard POMDPs and AM. The approach allows any system variable to be observed or not observed and uses any relevant observed variable to update beliefs about unknown variables and parameters. This extends standard AM, which only uses realizations of the state variable to update beliefs and extends standard POMDP by allowing more general stochastic dependence among the observable variables and the state variables. This framework enables both structural and observational uncertainty to be simultaneously modeled. We illustrate the features of the extended POMDP framework with an example.}, journal={JOURNAL OF ENVIRONMENTAL MANAGEMENT}, author={Fackler, Paul and Pacifici, Krishna}, year={2014}, month={Jan}, pages={27–36} }
@article{farrae_albeke_pacifici_nibbelink_peterson_2013, title={Assessing the influence of habitat quality on movements of the endangered shortnose sturgeon}, volume={97}, ISSN={0378-1909 1573-5133}, url={http://dx.doi.org/10.1007/S10641-013-0170-2}, DOI={10.1007/S10641-013-0170-2}, number={6}, journal={Environmental Biology of Fishes}, publisher={Springer Science and Business Media LLC}, author={Farrae, Daniel J. and Albeke, Shannon E. and Pacifici, Krishna and Nibbelink, Nathan P. and Peterson, Douglas L.}, year={2013}, month={Aug}, pages={691–699} }
@article{collazo_fackler_pacifici_white_llerandi-roman_dinsmore_2013, title={Optimal allocation of captive-reared Puerto Rican parrots: Decisions when divergent dynamics characterize managed populations}, volume={77}, ISSN={0022-541X}, url={http://dx.doi.org/10.1002/JWMG.569}, DOI={10.1002/JWMG.569}, abstractNote={Reintroduction programs often face the challenge of sustaining multiple populations, each with unique demographic rates. Decision makers must determine how to allocate afinite number of captive-reared animals among these populations to achieve the fundamental objective of the program. We explored the optimal allocation of captive-reared Puerto Rican parrots (Amazona vittata) to 3 distinct populations: a struggling relict (population 1), a successfully reintroduced population (population 2), and a potential (new) population (population 3). We illustrate decision tradeoffs using 4 hypothetical scenarios of demographic performance created using the parrot literature and expert opinion and find the optimal decision by formulating the problem as a Markov decision process. Across all scenarios, our analysis favored releasing parrots into population 2 first when population sizes were small, followed by releases into population 3, and subsequently to population 1. The point in the decision space at which these transitions occurred was a function of location demographic rates. Releasing parrots in a location harboring an extant population versus a location that does not is advisable if differences in environmental conditions that promote population growth between locations are small. If management actions cannot ameliorate limiting factors in a location, decisions will favor translocations from such locations and allocations to locations where growth is more likely. When the cost of conducting a release is considered, managers should occasionally postpone releases to avoid these costs. This is optimal whenever the weighted contribution of the additional parrots to the sum of the discounted additional expected future population levels is less than the size of the fixed costs. This was most often the case for population 1 as costs increased. 2013 The Wildlife Society.}, number={6}, journal={The Journal of Wildlife Management}, publisher={Wiley}, author={Collazo, Jaime A. and Fackler, Paul L. and Pacifici, Krishna and White, Thomas H., Jr. and Llerandi-Roman, Ivan and Dinsmore, Stephen J.}, year={2013}, month={Jun}, pages={1124–1134} }
@article{collazo_fackler_pacifici_white_llerandi-roman_dinsmore_2013, title={Sophia title}, volume={77}, number={6}, journal={Journal of Wildlife Management}, author={Collazo, J. A. and Fackler, P. L. and Pacifici, K. and White, T. H. and Llerandi-Roman, I. and Dinsmore, S. J.}, year={2013}, pages={1124–1134} }
@inproceedings{terando_reich_pacifici_2013, title={Uncertainty quantification and propagation in a complex human-environment system driven by fire and climate}, author={Terando, A.J. and Reich, B.J. and Pacifici, K.}, year={2013} }
@phdthesis{pacifici_2012, place={Athens, Georgia}, title={A Bayesian Hierarchical Spatial Model for West Nile Virus in New York City: Evaluating an Approach to Handle Large Spatial Data Sets}, school={University of Georgia}, author={Pacifici, Jamian Krishna}, year={2012} }
@article{pacifici_dorazio_conroy_2012, title={A two-phase sampling design for increasing detections of rare species in occupancy surveys}, volume={3}, ISSN={["2041-2096"]}, DOI={10.1111/j.2041-210x.2012.00201.x}, abstractNote={Summary1. Occupancy estimation is a commonly used tool in ecological studies owing to the ease at which data can be collected and the large spatial extent that can be covered. One major obstacle to using an occupancy‐based approach is the complications associated with designing and implementing an efficient survey. These logistical challenges become magnified when working with rare species when effort can be wasted in areas with none or very few individuals.2. Here, we develop a two‐phase sampling approach that mitigates these problems by using a design that places more effort in areas with higher predicted probability of occurrence. We compare our new sampling design to traditional single‐season occupancy estimation under a range of conditions and population characteristics. We develop an intuitive measure of predictive error to compare the two approaches and use simulations to assess the relative accuracy of each approach.3. Our two‐phase approach exhibited lower predictive error rates compared to the traditional single‐season approach in highly spatially correlated environments. The difference was greatest when detection probability was high (0·75) regardless of the habitat or sample size. When the true occupancy rate was below 0·4 (0·05–0·4), we found that allocating 25% of the sample to the first phase resulted in the lowest error rates.4. In the majority of scenarios, the two‐phase approach showed lower error rates compared to the traditional single‐season approach suggesting our new approach is fairly robust to a broad range of conditions and design factors and merits use under a wide variety of settings.5. Synthesis and applications. Conservation and management of rare species are a challenging task facing natural resource managers. It is critical for studies involving rare species to efficiently allocate effort and resources as they are usually of a finite nature. We believe our approach provides a framework for optimal allocation of effort while maximizing the information content of the data in an attempt to provide the highest conservation value per unit of effort.}, number={4}, journal={METHODS IN ECOLOGY AND EVOLUTION}, author={Pacifici, Krishna and Dorazio, Robert M. and Conroy, Michael J.}, year={2012}, month={Aug}, pages={721–730} }
@phdthesis{pacifici_2011, place={Athens, Georgia}, title={Conservation and Management of Rare Species: The Development of Adaptive Models to Reduce Uncertainty Influencing Decision Making}, school={University of Georgia}, author={Pacifici, Jamian Krishna}, year={2011} }
@article{alldredge_pacifici_simons_pollock_2008, title={A novel field evaluation of the effectiveness of distance and independent observer sampling to estimate aural avian detection probabilities}, volume={45}, ISSN={0021-8901 1365-2664}, url={http://dx.doi.org/10.1111/j.1365-2664.2008.01517.x}, DOI={10.1111/j.1365-2664.2008.01517.x}, abstractNote={Summary 1. The validation of field sampling techniques is a concern for applied ecologists due to the strong model assumptions implicit in all methods. Computer simulations make replication easy, but they do not give insights into how much bias occurs in real populations. Testing sampling methods on populations of known size can establish directly how well estimators perform, but such populations are very hard to find, and replicate, and they may have unusual attributes. 2. We present a field validation of distance and double-observer methods of estimating detection probabilities on aural avian point counts. Our research is relevant to conservation agencies worldwide who design thousands of avian monitoring programmes based primarily on auditory point counts. The programmes are a critical component in the management of many avian species. 3. Our validation used a simulation system which mimics birds calling in a field environment. The system allowed us to vary singing rate, species, distance, the complexity of points, and other factors. 4. Distance methods performed poorly, primarily due to large localization errors, and estimates did not improve for simplified points. 5. For the double-observer method, two pairs of observers tended to underestimate true population size, while the third pair tended to double-count birds which overestimated the population. Detection probabilities were always higher and population estimates lower when observers subjectively matched birds compared to an objective rule and showed a slight negative bias and good precision. A simplified 45-degree matching rule did not improve the performance of double-observer estimates which had a slight positive bias and much lower precision. Double-observer estimates did improve on the simplified points. 6. Synthesis and applications . We encourage ecologists working with sampling methods to develop similar methods of working with simulated populations through use of technology. Our simulated field evaluation has demonstrated the difficulty of accurately estimating population size when limited to aural detections. Problems are related to limitations in the ability of observers to localize sound, estimate distance, and accurately identify birds during a count. Other sources of error identified are the effects of observers, singing rate, singing orientation and background noise.}, number={5}, journal={Journal of Applied Ecology}, publisher={Wiley}, author={Alldredge, Mathew W. and Pacifici, Krishna and Simons, Theodore R. and Pollock, Kenneth H.}, year={2008}, month={Oct}, pages={1349–1356} }
@book{moore_mattsson_mordecai_pacifici_conroy_peterson_cooper_2008, title={An Adaptive Sample Survey Design for the Ivory-billed Woodpecker}, url={http://usgs-cru-individual-data.s3.amazonaws.com/cmoore/tech_publications/Conroy%20et%20al%20(2008)%20IBWO%20Final%20Report-1.pdf}, number={1434-02HQRU1551}, author={Moore, Clinton T. and Mattsson, Brady J. and Mordecai, Rua S. and Pacifici, Krishna and Conroy, Michael J. and Peterson, James T. and Cooper, Robert J.}, year={2008}, month={Mar} }
@inproceedings{cooper_mordecai_mattsson_conroy_pacifici_peterson_moore_2008, title={Design for a region-wide adaptive search for the ivorybilled woodpecker with the objective of estimating occupancy and related parameters}, booktitle={Tundra to Tropics: Connecting Birds, Habitats and People: 4th International Partners in Flight Conference, 13-16 February 2008, McAllen, Texas: Abstracts}, author={Cooper, R.J. and Mordecai, Rua S. and Mattsson, B.G. and Conroy, M.J. and Pacifici, K. and Peterson, J.T. and Moore, C.T.}, year={2008} }
@article{pacifici_simons_pollock_2008, title={EFFECTS OF VEGETATION AND BACKGROUND NOISE ON THE DETECTION PROCESS IN AUDITORY AVIAN POINT-COUNT SURVEYS}, volume={125}, ISSN={0004-8038 1938-4254}, url={http://dx.doi.org/10.1525/auk.2008.07078}, DOI={10.1525/auk.2008.07078}, abstractNote={Abstract We used a bird-song simulation system to experimentally assess the effects of habitat, vegetation structure, and background noise on detection probability in aural avian point counts. We simulated bird songs of seven species in two habitats (mixed pine–hardwood forest and deciduous forest) and two leaf conditions (leaves on and leaves off) with two levels of background noise (~40 dB and ~50 dB). Estimated detection probabilities varied greatly among species, and complex interactions among all the factors existed. Background noise and the presence of leaves on trees decreased detection probabilities, and estimated detection probabilities were higher in mixed pine–hardwood forest than in deciduous forest. At 100 m, average estimated detection probabilities ranged from 0 to 1 and were lowest for the Black-and-white Warbler (Mniotilta varia) and highest for the Brown Thrasher (Toxostoma rufum). Simulations of expected counts, based on the best logistic model, indicated that observers detect between 3% (for the worst observer, least detectable species, with leaves on the trees and added background noise in the deciduous forest) and 99% (for the best observer, most detectable species, with no leaves on the trees and no added background noise in the mixed forest) of the total count. The large variation in expected counts illustrates the importance of estimating detection probabilities directly. The large differences in detection probabilities among species suggest that tailoring monitoring protocols to specific species of interest may produce better estimates than a single protocol applied to a wide range of species.}, number={3}, journal={The Auk}, publisher={Oxford University Press (OUP)}, author={Pacifici, Krishna and Simons, Theodore R. and Pollock, Kenneth H.}, year={2008}, month={Jul}, pages={600–607} }
@inbook{simons_pollock_wettroth_alldredge_pacifici_brewster_2009, title={Sources of Measurement Error, Misclassification Error, and Bias in Auditory Avian Point Count Data}, ISBN={9780387781501 9780387781518}, url={http://dx.doi.org/10.1007/978-0-387-78151-8_10}, DOI={10.1007/978-0-387-78151-8_10}, booktitle={Modeling Demographic Processes In Marked Populations}, publisher={Springer US}, author={Simons, Theodore R. and Pollock, Kenneth H. and Wettroth, John M. and Alldredge, Mathew W. and Pacifici, Krishna and Brewster, Jerome}, year={2009}, pages={237–254} }
@article{alldredge_simons_pollock_pacifici_2007, title={A Field Evaluation of the Time-of-Detection Method to Estimate Population Size and Density for Aural Avian Point Counts}, volume={2}, ISSN={1712-6568}, url={http://dx.doi.org/10.5751/ace-00205-020213}, DOI={10.5751/ace-00205-020213}, abstractNote={The time-of-detection method for aural avian point counts is a new method of estimating abundance, allowing for uncertain probability of detection. The method has been specifically designed to allow for variation in singing rates of birds. It involves dividing the time interval of the point count into several subintervals and recording the detection history of the subintervals when each bird sings. The method can be viewed as generating data equivalent to closed capture–recapture information. The method is different from the distance and multiple-observer methods in that it is not required that all the birds sing during the point count. As this method is new and there is some concern as to how well individual birds can be followed, we carried out a field test of the method using simulated known populations of singing birds, using a laptop computer to send signals to audio stations distributed around a point. The system mimics actual aural avian point counts, but also allows us to know the size and spatial distribution of the populations we are sampling. Fifty 8-min point counts (broken into four 2-min intervals) using eight species of birds were simulated. Singing rate of an individual bird of a species was simulated following a Markovian process (singing bouts followed by periods of silence), which we felt was more realistic than a truly random process. The main emphasis of our paper is to compare results from species singing at (high and low) homogenous rates per interval with those singing at (high and low) heterogeneous rates. Population size was estimated accurately for the species simulated, with a high homogeneous probability of singing. Populations of simulated species with lower but homogeneous singing probabilities were somewhat underestimated. Populations of species simulated with heterogeneous singing probabilities were substantially underestimated. Underestimation was caused by both the very low detection probabilities of all distant individuals and by individuals with low singing rates also having very low detection probabilities. RESUME. La methode fondee sur le temps de detection utilisee dans le contexte des points d’ecoute represente une nouvelle approche pour estimer l’abondance des oiseaux en tenant compte de la probabilite incertaine de detection. Cette methode a ete specialement concue pour tenir compte du taux variable de chant observe chez les oiseaux. Elle consiste a diviser l’intervalle de temps passe a un point d’ecoute en sous-intervalles et de noter l’historique de detection des sous-intervalles ou chaque individu est detecte. Les donnees obtenues par cette methode peuvent etre considerees comme etant equivalentes a celles obtenues par la capture-recapture dans une population fermee. La methode differe des approches fondees sur la distance et les observateurs multiples du fait qu’elle n’exige pas que tous les individus chantent durant le point d’ecoute. Puisque cette methode est nouvelle et qu’il existe une incertitude quant a la capacite de suivre les individus, nous avons effectue une evaluation sur le terrain de sa precision en utilisant des simulations sur des populations connues d’oiseaux chanteurs a l’aide d’un ordinateur portatif qui envoyait des signaux a des stations audio distribuees autour du point d’ecoute. Ce systeme imite un veritable point Colorado Division of Wildlife, Cooperative Fish and Wildlife Research Unit, Dept of Zoology, North Carolina State University Avian Conservation and Ecology Ecologie et conservation des oiseaux 2(2): 13 http://www.ace-eco.org/vol2/iss2/art13/ d’ecoute tout en permettant de connaitre l’effectif et la distribution des populations echantillonnees. Cinquante points d’ecoute de 8 min (separes en intervalles de 2 min) ont ete simules pour huit especes d’oiseaux. Le taux de vocalisation de chaque individu a ete simule a l’aide d’une chaine de Markov (periodes de chant suivies de periodes de silence), ce qui nous semblait plus realiste qu’un processus purement aleatoire. L’objectif principal de notre article etait de comparer les resultats pour des especes chantant a une frequence homogene (elevee ou faible) par intervalle avec d’autres especes chantant a des frequences heterogenes (elevees ou faibles). L’effectif de la population a ete estime precisement pour les especes simulees ayant une frequence de vocalisation homogene et elevee. L’effectif des populations des especes simulees presentant une frequence de vocalisation faible mais homogene a ete legerement sous-estime. Dans les cas des especes chantant a des frequences heterogenes, les populations etaient fortement sousestimees. La sous-estimation etait causee a la fois par la faible probabilite de detection de tous les individus eloignes et des individus chantant a des frequences faibles.}, number={2}, journal={Avian Conservation and Ecology}, publisher={Resilience Alliance, Inc.}, author={Alldredge, Mathew W. and Simons, Theodore R. and Pollock, Kenneth H. and Pacifici, Krishna}, year={2007}, pages={13} }