@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{preckler-quisquater_kierepka_reding_piaggio_sacks_2023, title={Can demographic histories explain long-term isolation and recent pulses of asymmetric gene flow between highly divergent grey fox lineages?}, volume={32}, ISSN={["1365-294X"]}, DOI={10.1111/mec.17105}, abstractNote={Abstract}, number={19}, journal={MOLECULAR ECOLOGY}, author={Preckler-Quisquater, Sophie and Kierepka, Elizabeth M. and Reding, Dawn M. and Piaggio, Antoinette J. and Sacks, Benjamin N.}, year={2023}, month={Oct}, pages={5323–5337} }
 @article{statham_aylward_barthman-thompson_kierepka_sacks_2022, title={Landscape genetics of an endangered salt marsh endemic: Identifying population continuity and barriers to dispersal}, volume={6}, ISSN={["1572-9737"]}, DOI={10.1007/s10592-022-01446-6}, abstractNote={Abstract}, journal={CONSERVATION GENETICS}, author={Statham, Mark J. and Aylward, Cody M. and Barthman-Thompson, Laureen and Kierepka, Elizabeth M. and Sacks, Benjamin N.}, year={2022}, month={Jun} }
 @article{watt_kierepka_ferreira_koen_row_bowman_wilson_murray_2021, title={Canada lynx (Lynx canadensis) gene flow across a mountain transition zone in western North America}, volume={99}, ISSN={["1480-3283"]}, DOI={10.1139/cjz-2019-0247}, abstractNote={Mountain ecotones have the potential to cause multiple patterns in divergence, from simple barrier effects to more fundamental ecological divergence. Most work in mountain ecotones in North America has focused on reinforcement between refugial populations, making prediction of how mountains impact species that are not restricted to separate glacial refugia remains difficult. This study focused on the Canada lynx (Lynx canadensis Kerr, 1792), a highly mobile felid considered to be a habitat and dietary specialist. Specifically, we used 14 microsatellite loci and landscape genetic tools to investigate if the Rocky Mountains and associated climatic transitions influence lynx genetic differentiation in western North America. Although lynx exhibited high gene flow across the region, analyses detected structuring of neutral genetic variation across our study area. Gene flow for lynx most strongly related to temperature and elevation compared with other landscape variables (terrain roughness, percent forest cover, and habitat suitability index) and geographic distance alone. Overall, genetic structure in lynx is most consistent with barrier effects created by the Rocky Mountains rather than ecological divergence. Furthermore, warmer temperatures had a measurable impact on gene flow, which suggests connectivity may further decrease in peripheral or fragmented populations as climate warms.}, number={2}, journal={CANADIAN JOURNAL OF ZOOLOGY}, author={Watt, C. M. and Kierepka, E. M. and Ferreira, C. C. and Koen, E. L. and Row, J. R. and Bowman, J. and Wilson, P. J. and Murray, D. L.}, year={2021}, month={Feb}, pages={131–140} }
 @article{davis_keiter_kierepka_slootmaker_piaggio_beasley_pepin_2020, title={A comparison of cost and quality of three methods for estimating density for wild pig (Sus scrofa)}, volume={10}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-020-58937-0}, DOI={10.1038/s41598-020-58937-0}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Davis, Amy J. and Keiter, David A. and Kierepka, Elizabeth M. and Slootmaker, Chris and Piaggio, Antoinette J. and Beasley, James C. and Pepin, Kim M.}, year={2020}, month={Feb} }
 @article{kierepka_anderson_swihart_rhodes_2020, title={Differing, multiscale landscape effects on genetic diversity and differentiation in eastern chipmunks}, volume={124}, ISSN={0018-067X 1365-2540}, url={http://dx.doi.org/10.1038/s41437-020-0293-0}, DOI={10.1038/s41437-020-0293-0}, abstractNote={Understanding how habitat loss and fragmentation impact genetic variation is a major goal in landscape genetics, but to date, most studies have focused solely on the correlation between intervening matrix and genetic differentiation at a single spatial scale. Several caveats exist in these study designs, among them is the inability to include measures of genetic diversity in addition to differentiation. Both genetic metrics help predict population persistence, but are expected to function at differing spatial scales, which requires a multiscale investigation. In this study, we sampled two distinct spatial scales in 31 independent landscapes along a gradient of landscape context (i.e., forest amount, configuration, and types of intervening matrix) to investigate how landscape heterogeneity influences genetic diversity and differentiation in the forest-associated eastern chipmunk (Tamias striatus). Overall, quality of intervening matrix was correlated with genetic differentiation at multiple spatial scales, whereas only configuration was associated with regional scale genetic diversity. Habitat amount, in contrast, did not influence genetic differentiation or diversity at either spatial scale. Based on our findings, landscape effects on genetic variation appears to differ based on spatial scale, the type of genetic response variable, and random variation among landscapes, making extrapolation of results from single scale, unreplicated studies difficult. We encourage landscape geneticists to utilize multiscale, replicated landscapes with both genetic diversity, and differentiation to gain a more comprehensive understanding of how habitat loss and fragmentation influence genetic variation.}, number={3}, journal={Heredity}, publisher={Springer Science and Business Media LLC}, author={Kierepka, Elizabeth M. and Anderson, Sara J. and Swihart, Robert K. and Rhodes, Olin E., Jr}, year={2020}, month={Jan}, pages={457–468} }
 @article{engeman_byrd_dozier_mcalister_edens_kierepka_smyser_myers_2019, title={Feral swine harming insular sea turtle reproduction: The origin, impacts, behavior and elimination of an invasive species}, volume={99}, ISSN={1146-609X}, url={http://dx.doi.org/10.1016/j.actao.2019.103442}, DOI={10.1016/j.actao.2019.103442}, abstractNote={Feral swine are among the world's most destructive invasive species wherever they are found, with translocations figuring prominently in their range expansions. In contrast, sea turtles are beloved species that are listed as threatened or endangered throughout the world and are the focus of intense conservation efforts. Nest predation by feral swine severely harms sea turtle reproduction in many locations around the world. Here we quantify and economically assess feral swine nest predation at North Island, South Carolina, an important loggerhead sea turtle nesting beach. Feral swine depredation of North Island sea turtle nests was first detected in 2005, with annual nest monitoring initiated in 2010 documenting nearly total losses to feral swine in 2010 and 2011. The cumulative valuation of annual losses for North Island from 2010 to 2016 ranged as high as $1,166,500. To improve nesting success, an integrated approach for eliminating feral swine was implemented in 2010 and greatly intensified in 2013 by adding federal experts. Removal efforts were challenging due to the island's remoteness and impenetrable habitats, weather, hazards in accessing the island, and wariness of the animals, especially as their population diminished. Removal of the final 11 swine required efforts from 2014 to 2016. Nest predation was highly variable and provided another example of the significance of conditioning by feral swine to sea turtle nests on the consequent severity of nest predation. Even the final individual inflicted heavy losses before his removal. Genetic analyses of feral swine removed from North Island and the adjacent mainland revealed that the island's population did not originate from the nearby mainland, meaning they were (illegally) introduced to the island.}, journal={Acta Oecologica}, publisher={Elsevier BV}, author={Engeman, Richard M. and Byrd, Robert W. and Dozier, Jamie and McAlister, Mark A. and Edens, James O. and Kierepka, Elizabeth M. and Smyser, Timothy J. and Myers, Noel}, year={2019}, month={Aug}, pages={103442} }
 @article{kierepka_juarez_turner_smith_hamilton_lyons_hall_beasley_rhodes_2019, title={Population Genetics of Invasive Brown Tree Snakes (Boiga irregularis) on Guam, USA}, volume={75}, ISSN={0018-0831}, url={http://dx.doi.org/10.1655/d-18-00057}, DOI={10.1655/d-18-00057}, abstractNote={Abstract: The introduction of Brown Tree Snakes (BTS; Boiga irregularis) on Guam has had devastating impacts on native wildlife and human infrastructure, resulting in concerted efforts to control p...}, number={3}, journal={Herpetologica}, publisher={Herpetologists League}, author={Kierepka, Elizabeth M. and Juarez, Rebeca and Turner, Kelsey and Smith, Joshua and Hamilton, Matthew and Lyons, Phillip and Hall, Marc A. and Beasley, James C. and Rhodes, Olin E.}, year={2019}, month={Sep}, pages={208} }
 @article{milligan_archer_ferchaud_hand_kierepka_waples_2018, title={Disentangling genetic structure for genetic monitoring of complex populations}, volume={11}, ISSN={1752-4571}, url={http://dx.doi.org/10.1111/eva.12622}, DOI={10.1111/eva.12622}, abstractNote={Abstract}, number={7}, journal={Evolutionary Applications}, publisher={Wiley}, author={Milligan, Brook G. and Archer, Frederick I. and Ferchaud, Anne-Laure and Hand, Brian K. and Kierepka, Elizabeth M. and Waples, Robin S.}, year={2018}, month={Mar}, pages={1149–1161} }
 @article{kanine_kierepka_castleberry_mengak_nibbelink_glenn_2018, title={Influence of landscape heterogeneity on the functional connectivity of Allegheny woodrats (Neotoma magister) in Virginia}, volume={19}, ISSN={1566-0621 1572-9737}, url={http://dx.doi.org/10.1007/s10592-018-1093-4}, DOI={10.1007/s10592-018-1093-4}, number={5}, journal={Conservation Genetics}, publisher={Springer Science and Business Media LLC}, author={Kanine, Jennifer M. and Kierepka, Elizabeth M. and Castleberry, Steven B. and Mengak, Michael T. and Nibbelink, Nathan P. and Glenn, Travis C.}, year={2018}, month={Aug}, pages={1259–1268} }
 @article{kierepka_kilgo_rhodes_2017, title={Effect of compensatory immigration on the genetic structure of coyotes}, volume={81}, ISSN={0022-541X}, url={http://dx.doi.org/10.1002/jwmg.21320}, DOI={10.1002/jwmg.21320}, abstractNote={ABSTRACT}, number={8}, journal={The Journal of Wildlife Management}, publisher={Wiley}, author={Kierepka, Elizabeth M. and Kilgo, John C. and Rhodes, Olin E., Jr}, year={2017}, month={Jul}, pages={1394–1407} }
 @article{kierepka_anderson_swihart_rhodes_2016, title={Evaluating the influence of life-history characteristics on genetic structure: a comparison of small mammals inhabiting complex agricultural landscapes}, volume={6}, ISSN={2045-7758}, url={http://dx.doi.org/10.1002/ece3.2269}, DOI={10.1002/ece3.2269}, abstractNote={Abstract}, number={17}, journal={Ecology and Evolution}, publisher={Wiley}, author={Kierepka, Elizabeth M. and Anderson, Sara J. and Swihart, Robert K. and Rhodes, Olin E., Jr}, year={2016}, month={Aug}, pages={6376–6396} }
 @article{kierepka_latch_2016, title={High gene flow in the American badger overrides habitat preferences and limits broadscale genetic structure}, volume={25}, ISSN={0962-1083 1365-294X}, url={http://dx.doi.org/10.1111/mec.13915}, DOI={10.1111/mec.13915}, abstractNote={Abstract}, number={24}, journal={Molecular Ecology}, publisher={Wiley}, author={Kierepka, E. M. and Latch, E. K.}, year={2016}, month={Nov}, pages={6055–6076} }
 @article{kierepka_unger_keiter_beasley_rhodes_cunningham_piaggio_2016, title={Identification of robust microsatellite markers for wild pig fecal DNA}, volume={80}, ISSN={0022-541X}, url={http://dx.doi.org/10.1002/jwmg.21102}, DOI={10.1002/jwmg.21102}, abstractNote={ABSTRACT}, number={6}, journal={The Journal of Wildlife Management}, publisher={Wiley}, author={Kierepka, Elizabeth M. and Unger, Shem D. and Keiter, David A. and Beasley, James C. and Rhodes, Olin E., Jr and Cunningham, Fred L. and Piaggio, Antoinette J.}, year={2016}, month={Jun}, pages={1120–1128} }
 @article{anderson_kierepka_swihart_latch_rhodes_2015, title={Assessing the Permeability of Landscape Features to Animal Movement: Using Genetic Structure to Infer Functional Connectivity}, volume={10}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0117500}, DOI={10.1371/journal.pone.0117500}, abstractNote={Human-altered environments often challenge native species with a complex spatial distribution of resources. Hostile landscape features can inhibit animal movement (i.e., genetic exchange), while other landscape attributes facilitate gene flow. The genetic attributes of organisms inhabiting such complex environments can reveal the legacy of their movements through the landscape. Thus, by evaluating landscape attributes within the context of genetic connectivity of organisms within the landscape, we can elucidate how a species has coped with the enhanced complexity of human altered environments. In this research, we utilized genetic data from eastern chipmunks (Tamias striatus) in conjunction with spatially explicit habitat attribute data to evaluate the realized permeability of various landscape elements in a fragmented agricultural ecosystem. To accomplish this we 1) used logistic regression to evaluate whether land cover attributes were most often associated with the matrix between or habitat within genetically identified populations across the landscape, and 2) utilized spatially explicit habitat attribute data to predict genetically-derived Bayesian probabilities of population membership of individual chipmunks in an agricultural ecosystem. Consistency between the results of the two approaches with regard to facilitators and inhibitors of gene flow in the landscape indicate that this is a promising new way to utilize both landscape and genetic data to gain a deeper understanding of human-altered ecosystems.}, number={2}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Anderson, Sara J. and Kierepka, Elizabeth M. and Swihart, Robert K. and Latch, Emily K. and Rhodes, Olin E.}, editor={Slotow, RobEditor}, year={2015}, month={Feb}, pages={e0117500} }
 @article{kierepka_latch_2015, title={Fine-scale landscape genetics of the American badger (Taxidea taxus): disentangling landscape effects and sampling artifacts in a poorly understood species}, volume={116}, ISSN={0018-067X 1365-2540}, url={http://dx.doi.org/10.1038/hdy.2015.67}, DOI={10.1038/hdy.2015.67}, abstractNote={Landscape genetics is a powerful tool for conservation because it identifies landscape features that are important for maintaining genetic connectivity between populations within heterogeneous landscapes. However, using landscape genetics in poorly understood species presents a number of challenges, namely, limited life history information for the focal population and spatially biased sampling. Both obstacles can reduce power in statistics, particularly in individual-based studies. In this study, we genotyped 233 American badgers in Wisconsin at 12 microsatellite loci to identify alternative statistical approaches that can be applied to poorly understood species in an individual-based framework. Badgers are protected in Wisconsin owing to an overall lack in life history information, so our study utilized partial redundancy analysis (RDA) and spatially lagged regressions to quantify how three landscape factors (Wisconsin River, Ecoregions and land cover) impacted gene flow. We also performed simulations to quantify errors created by spatially biased sampling. Statistical analyses first found that geographic distance was an important influence on gene flow, mainly driven by fine-scale positive spatial autocorrelations. After controlling for geographic distance, both RDA and regressions found that Wisconsin River and Agriculture were correlated with genetic differentiation. However, only Agriculture had an acceptable type I error rate (3–5%) to be considered biologically relevant. Collectively, this study highlights the benefits of combining robust statistics and error assessment via simulations and provides a method for hypothesis testing in individual-based landscape genetics.}, number={1}, journal={Heredity}, publisher={Springer Science and Business Media LLC}, author={Kierepka, E M and Latch, E K}, year={2015}, month={Aug}, pages={33–43} }
 @article{kierepka_latch_2014, title={Performance of partial statistics in individual-based landscape genetics}, volume={15}, ISSN={1755-098X}, url={http://dx.doi.org/10.1111/1755-0998.12332}, DOI={10.1111/1755-0998.12332}, abstractNote={Abstract}, number={3}, journal={Molecular Ecology Resources}, publisher={Wiley}, author={Kierepka, E. M. and Latch, E. K.}, year={2014}, month={Sep}, pages={512–525} }
 @article{kierepka_latch_swanson_2012, title={Influence of sampling scheme on the inference of sex-biased gene flow in the American badger (Taxidea taxus)}, volume={90}, ISSN={0008-4301 1480-3283}, url={http://dx.doi.org/10.1139/z2012-094}, DOI={10.1139/z2012-094}, abstractNote={Population genetics has fueled a substantial growth in studies of dispersal, a life-history trait that has important applications in ecology and evolution. Mammals typically exhibit male-biased gene flow, so this pattern often serves as a null hypothesis in empirical studies. Estimation of dispersal using population genetics is not without biases, so we utilized a combination of population genetic methods and simulations to evaluate gene flow within the American badger ( Taxidea taxus (Schreber, 1777)), a highly elusive and poorly understood mustelid. A total of 132 badgers captured between 2001 and 2002 were genotyped at nine microsatellite loci to investigate fine-scale genetic structure consistent with philopatry in females and dispersal in males. Resultant genetic patterns were largely consistent with a panmictic population with little evidence for sex-biased dispersal, and simulations confirmed that our sampling scheme did not substantially impact our statistics. An overall deficiency of heterozygotes was observed across the Lower Peninsula, which indicates either a Wahlund effect, mixing of separate populations, or inbreeding. Our study emphasizes the importance in deciphering between actual behavioral mechanisms and sampling effects when interpreting genetic data to understand other factors that influence dispersal like population density and territoriality.}, number={10}, journal={Canadian Journal of Zoology}, publisher={Canadian Science Publishing}, author={Kierepka, E.M. and Latch, E.K. and Swanson, B.J.}, year={2012}, month={Oct}, pages={1231–1242} }
 @article{latch_kierepka_heffelfinger_rhodes_2011, title={Hybrid swarm between divergent lineages of mule deer (Odocoileus hemionus)}, volume={20}, ISSN={0962-1083}, url={http://dx.doi.org/10.1111/j.1365-294x.2011.05349.x}, DOI={10.1111/j.1365-294x.2011.05349.x}, abstractNote={Abstract}, number={24}, journal={Molecular Ecology}, publisher={Wiley}, author={Latch, Emily K. and Kierepka, Elizabeth M. and Heffelfinger, James R. and Rhodes, Olin E.}, year={2011}, month={Nov}, pages={5265–5279} }