@article{goldstein_furnas_calhoun_larsen_karp_valpine_2024, title={Drought influences habitat associations and abundances of birds in California's Central Valley}, ISSN={["1472-4642"]}, DOI={10.1111/ddi.13827}, abstractNote={Abstract}, journal={DIVERSITY AND DISTRIBUTIONS}, author={Goldstein, Benjamin R. and Furnas, Brett J. and Calhoun, Kendall L. and Larsen, Ashley E. and Karp, Daniel S. and Valpine, Perry}, year={2024}, month={Mar} }
 @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} }