Publications

In Press

Notes: Underlined authors are current or former members of the lab. See our Github archive for data and code to run models.

Grappling with uncertainty in ecological projections: a case study using the migratory monarch butterfly.

Neupane N., Zipkin E.F., Saunders S.P., and Ries L. In press. Ecosphere.

Changes in climate drive recent monarch butterfly dynamics.

Zylstra E.R., Ries L., Neupane N., Saunders S.P., Ramírez M.I., Rendón-Salinas E., Oberhauser K.S., Farr M.T., and Zipkin E.F. In press. Nature Ecology and Evolution.

Integrating automated acoustic vocalization data and point count surveys for estimation of bird abundance.

Doser J.W., Finley A.O., Weed A.S., and Zipkin E.F. 2021. Methods in Ecology and Evolution. 12: 1040-1049.

Trends in bird abundance differ among protected forests but not bird guilds.

Doser J.W., Weed A.S., Zipkin E.F., Miller K.M., and Finley A.O. 2021. Ecological Applications. 31: e02377.

Integrating distance sampling and presence-only data to estimate abundance.

Farr M.T., Green D.S., Holekamp K.E., and Zipkin E.F. 2021. Ecology. 102: e03204.

​Biotic and abiotic drivers of dispersion dynamics in a large-bodied tropical vertebrate, the Western Bornean orangutan.

Marshall A.J., Farr M.T., Beaudrot L., Zipkin E.F., Feilen K.L., Bell L.G., Setiawan E., Susanto T.W., Setia T.M, Leighton M., and Wittmer H.U. 2021. Oecologia. 196: 707-721.

Working across space and time: nonstationarity in ecological research and application.

Rollinson C.R., Finley A., Alexander M.R., Banerjee S., Hamil K.D., Koenig L.E., Locke D.H., Peterson M., Tingley M.W., Wheeler K., Youngflesh C., and Zipkin E.F. 2021. Frontiers in Ecology and the Environment. 19: 66-72.

Addressing data integration challenges to link ecological processes across scales.

Zipkin E.F., Zylstra E.R., Wright A.D., Saunders S.P., Finley A., Dietze M.C., Itter M., and Tingley M.W. 2021. Frontiers in Ecology and the Environment. 19: 30-38.

Accounting for sources of uncertainty when forecasting population responses to climate change.

Zylstra E.R. and Zipkin E.F. 2021. Journal of Animal Ecology. 90: 558-561.

The Dynamic Shift Detector: an algorithm to identify changes in parameter values governing populations.

Bahlai C.A. and Zipkin E.F. 2020.  PLOS Computational Biology. 16: e1007542.

Ecological dynamics: integrating empirical, statistical, and analytical methods.

Laubmeier A.N., Cazelles B., Cuddington K., Erickson K.D., Fortin M., Ogle K., Wikle C.K., Zhu K., and Zipkin E.F. 2020.  Trends in Ecology and Evolution. 35: 1090-1099.

Poor management in protected areas is associated with lowered tropical mammal diversity.

Oberosler V., Tenan S., Zipkin E.F., and Rovero F. 2020.  Animal Conservation. 23: 171-181.

When parks work: effect of anthropogenic disturbance on occupancy of tropical forest mammals.

Oberosler V., Tenan S., Zipkin E.F., and Rovero F. 2020.  Ecology and Evolution. 10: 3881-3894.

Moving from decision to action in conservation science.

Wright A.D., Bernard R.F., Mosher B.A., O’Donnell K.M., Braunagel T., DiRenzo G.V., Fleming J., Shafer C., Brand A.B., Zipkin E.F., and Grant E.H.C. 2020. Biological Conservation. 249: 108698.

A hierarchical analysis of habitat area, connectivity, and quality on amphibian diversity across scales.

Wright A.D., Grant E.H.C., and Zipkin E.F. 2020.  Landscape Ecology. 35: 529-544.
​

Tropical snake diversity collapses after widespread amphibian loss.

Zipkin E.F., DiRenzo G.V., Ray J.M., Rossman S., and Lips K.R. 2020.Science. 367: 814-816.

Disentangling herbivore impacts in early primary succession by refocusing the plant stress and plant vigor hypotheses on phenology.

Che-Castaldo C., Crisafulli C.M., Bishop J.G., Zipkin E.F., and Fagan W.F. 2019. Ecological Monographs. 89: e01389.

Disease structured N-mixture models: a practical guide to model disease dynamics using count data.

DiRenzo G.V., Che-Castaldo C., Saunders S.P., Grant E.H.C., and Zipkin E.F. 2019.  Ecology and Evolution. 9: 899-909.

Multispecies hierarchical modeling reveals variable responses of African carnivores to management alternatives.

Farr M. T., Green D.S., Holekamp K.E., Roloff G.J., and Zipkin E. F. 2019.  Ecological Applications. 29: e01845.

Can hyena behaviour provide information on abundances of sympatric carnivores?​

Green D.S., Farr M.T., Holekamp K.E., Strauss E.D., and Zipkin E.F. 2019.  Philosophical Transactions of the Royal Society B. 347: 20180052.

Long-term ecological changes influence herbivore diversity inside a protected area in the Mara-Serengeti ecosystem.

Green D.S., Zipkin E.F., Incorvaia D.C., and Holekamp K.E. 2019.  Global Ecology and Conservation. 20: e00697.

Tracking trends in monarch abundances over the 20th century is currently impossible using museum records.

Ries L., Zipkin E.F., and Guralnick R.P. 2019.  Proceedings of the National Academy of Sciences. 116: 13745-13748.

Disentangling data discrepancies with integrated population models.​

Saunders S.P., Farr M.T., Wright A.D., Bahlai C.A., Ribeiro Jr. J.W., Rossman S., Sussman A.L., Arnold T.W., and Zipkin E.F. 2019.  Ecology. 100: e02714.

Multiscale seasonal factors drive the size of winter monarch colonies.

Saunders S.P., Ries L., Nepuane N., Ramírez M.I., García-Serrano E., Rendón-Salinas E., and Zipkin E.F. 2019.  Proceedings of the National Academy of Sciences. 116: 8609-8614.

A comparative analysis of common methods to identify waterbird hotspots.

Sussman A.L., Gardner B., Adams E.M., Salas L., Kenow K.P., Luukkonen D.R., Monfils M.J., Mueller W.P., Williams K.A., Leduc-Lapierre M., and Zipkin E.F. 2019.  Methods in Ecology and Evolution. 10: 1454-1468.

From ecologically equivalent individuals to contrasting colonies: quantifying isotopic niche and individual foraging specialization in an endangered oceanic seabird.

Wiley A.E., Rossman S., Ostrom P.H., France C.A.M., Penniman J., Bailey C., Duvall F., Zipkin E.F., and James H.F. 2019.  Marine Biology. 166: 39.
​
Innovations in data integration for modeling populations.

Zipkin E.F., Inouye B.D., and Beissinger S.R. 2019.  Ecology. 100: e02713.

Models for assessing local-scale co-abundance of animal species while accounting for differential detectability and varied responses to the environment.

Brodie J.E., Helmy O., Mohd-Azlan J., Granados A., Bernard H., Giordano A., and Zipkin E.F. 2018. Biotropica. 50: 5-15.

Eco-evolutionary rescue promotes host-pathogen coexistence.

DiRenzo G.V., Zipkin E.F., Grant E.H.C., Royle J.A., Longo A.V., Zamudio K.R., and Lips K.R. 2018. Ecological Applications. 28: 1948-1962.

Evaluating population viability and efficacy of conservation management using integrated population models.

Saunders S.P., Cuthbert F.J., and Zipkin E.F. 2018.  Journal of Applied Ecology. 55: 1380-1392.
​
Local and cross-seasonal effects of climate and land-use on migratory monarch butterflies.

Saunders S.P., Ries L., Oberhauser K.S., Thogmartin W.E., and Zipkin E.F. 2018. Ecography. 41: 278-290.

Effects of agriculture and topography on tropical amphibian species and communities.

Ribeiro Jr. J.W., Siqueira T., Brejão G.L., and Zipkin E.F. 2018. Ecological Applications. 28: 1554-1564.

Flying through hurricane central: impacts of hurricanes on migrants with a focus on monarch butterflies​.

Ries L., Neupane N., Baum K., and Zipkin E.F. 2018.  Animal Migration. 5: 94-103.

Individual-level trait variation and negative density dependence affects growth in tropical tree seedlings.

Umana M.N., Zipkin E.F., Zhang C., Cao M., Lin L., and Swenson N.G. 2018. Journal of Ecology. 106: 2446-2455.

Synthesizing multiple data types for biological conservation using integrated populations models.

Zipkin E.F. and Saunders S.P. 2018.  Biological Conservation. 217: 240-250.

Differential matrix use by Neotropical birds based on species traits and landscape condition.

Kennedy C.M., Zipkin E.F., and Marra P.P. 2017.  Ecological Applications. 27: 619-631.

Broad-scale trophic shift in the pelagic North Pacific revealed by an oceanic seabird.

Ostrom P.H., Wiley A.E., James H.F., Rossman S., Walker W.A., Zipkin E.F., and Chikaraishi Y. 2017.  Proceedings of the Royal Society B. 284: 20162436.

Integrating count and detection-nondetection data to model population dynamics.

Zipkin E.F., Rossman S., Yackulic C., Wiens J.D., Thorson J.T., Davis R.J., and Grant E.H.C. 2017. Ecology. 98: 1640-1650.

Incorporating imperfect detection into joint models of communities: a response to Warton et al.

Beissinger S.R., Iknayan K.J., Guillera-Arroita G., Zipkin E.F., Dorazio R.M., Royle J.A., and Kéry M. 2016.  Trends in Ecology and Evolution. 31: 736-737.

Hierarchical analysis of taxonomic variation in intraspecific competition across fish species.

Foss-Grant A.P., Zipkin E.F., Thorson J.T., Jensen O., and Fagan W.F. 2016.  Ecology. 97: 1724-1734.

Beyond carbon and nitrogen: guidelines for estimating three dimensional isotopic niche space.

Rossman S., Ostrom P., Gordon F., Zipkin E.F. 2016. Ecology and Evolution. 6: 2405-2413.

Dynamic N-occupancy models: estimating demographic rates and local abundances from detection-nondetection data.

Rossman S., Yackulic C., Saunders S.P., Reid J., Davis R., and Zipkin E.F. 2016. Ecology. 97: 3300-3307.

Evaluating confidence in climate-based predictions of population change in a migratory species.

Saunders S.P., Ries L., Oberhauser K.S., and Zipkin E.F. 2016. Global Ecology and Biogeography. 25: 1000-1012.

Joint dynamic species distribution models: a tool for community ordination and spatiotemporal monitoring.

Thorson J.T., Ianelli J., Larsen E., Scheuerell M. Szuwalski C., and Zipkin E.F. 2016. Global Ecology and Biogeography. 25: 1144-1158.

Brodie J.F., Giordano A.J., Zipkin E.F., Bernard H., Azad M.A.J., and Ambu, L. 2015. Correlation and persistence of hunting and logging impacts on tropical rainforest mammals. Conservation Biology. 29: 110-121.

Kanno Y., Letcher B.H., Hitt N.P., Boughton D.A., Wofford J.E.B., and Zipkin E.F. 2015. Seasonal weather patterns drive population vital rates and persistence in a stream fish. Global Change Biology. 21: 1856-1870.

Karatayev V.A., Kraft C.E., and Zipkin E.F. 2015. Racing through life: maturation rate plasticity regulates overcompensation and increases persistence. Ecosphere. 6: art203. doi:10.1890/ES14-00513.1.

​Yue S., Brodie J.F., Zipkin E.F., and Bernard H. 2015. Oil palm plantations fail to support mammal diversity. Ecological Applications. 25: 2285-2292.

Zipkin E.F. 2015. Book review: Case studies in Bayesian statistical modeling and analysis. The Quarterly Review of Biology. 3: 319-320.

Zipkin E.F., Kinlan B.P., Sussman A.L., Rypkema D., Wimer M., and O’Connell A.F. 2015. Statistical guidelines for assessing marine avian hotspots and coldspots: a case study on wind energy development in the U.S. Atlantic Ocean. Biological Conservation. 191: 216-223.

Kanno Y., Letcher B.H., Vokoun J.C., and Zipkin E.F. 2014. Spatial variability in survival of adult brook trout within two intensively surveyed headwater stream networks. Canadian Journal of Fisheries and Aquatic Sciences. 71: 1010-1019.

Pacifici K., Zipkin E.F., Collazo J., Irizarry R., and DeWan A. 2014. Guidelines for a priori grouping of species in hierarchical community models. Ecology and Evolution. 4: 877-888.

Thorson J.T., Jensen O., and Zipkin E.F. 2014. How variable is recruitment for marine fishes? A hierarchical model for testing life history theory. Canadian Journal of Fisheries and Aquatic Sciences. 71: 973-983.

Zipkin E.F., Leirness J.B., Kinlan B.P., O’Connell A.F., and Silverman E.D. 2014. Fitting statistical distributions to sea duck count data: implications for survey design and abundance estimation. Statistical Methodology. 17: 67-81.

Zipkin E.F., Sillett T.S., Grant E.H.C., Chandler R.B., and Royle J.A. 2014. Inferences from count data using multi-state population models: a comparison to capture-recapture approaches. Ecology and Evolution. 4: 417-426.

Zipkin E.F., Thorson J.T., See K., Lynch H.J., Grant E.H.C., Kanno Y., Chandler R.B., Letcher B.H., and Royle J.A. 2014. Modeling structured population dynamics using data from unmarked individuals. Ecology. 95: 22-29.

Bolker B., Gardner B., Maunder M., Berg C.W., Brooks M., Comita L., Crone E., Cubaynes S., Davies T., de Valpine P., Ford J., Gimenez O., Kery M., Kim E.J., Lennert-Cody C., Magnusson A., Martell S., Nash J., Nielsen A., Regetz J., Skaug H., and Zipkin E.F. 2013. Strategies for fitting nonlinear ecological models in R, AD Model Builder, and BUGS. Methods in Ecology and Evolution. 4: 501-512.

Grant E.H.C., Zipkin E.F., Nichols J.D., and Campbell J.P. 2013. A strategy for monitoring and managing declines in an amphibian community. Conservation Biology. 27: 1245-1253.

Mattsson B.J., Zipkin E.F., Blank P.J., Gardner B., Sauer J.R., and Royle J.A. 2013. Explaining local-scale species distributions: relative contributions of spatial autocorrelation and landscape heterogeneity for an avian assemblage. PLoS ONE. 8(2): e55097.

Sauer J.R., Blank P.J., Zipkin E.F., Fallon J.E., and Fallon F.W. 2013. Using multi-species occupancy models in structured decision making on managed lands. Journal of Wildlife Management. 77: 117-127.

White A.M., Zipkin E.F., Manley P.N., and Schlesinger, M.D. 2013. Conservation of avian diversity in the Sierra Nevada: moving beyond a single-species management focus. PLoS ONE. 8(5): e63088.

White A.M., Zipkin E.F., Manley P.N., and Schlesinger, M.D. 2013. Simulating avian species and foraging group responses to fuel reduction treatments in coniferous forests. Forest Ecology and Management. 304: 261-274.

Yackulic C., Chandler R., Zipkin E.F., Royle J.A., Nichols J.D., Grant E.H.C., and Veran S. 2013. Presence-only modelling using Maxent: when can we trust the inferences? Methods in Ecology and Evolution. 4: 236-243.

Zipkin E.F., Grant E.H.C., and Fagan W.F. 2012. Evaluating the predictive abilities of community occupancy models using AUC while accounting for imperfect detection. Ecological Applications. 22: 1962-1972.

Zipkin E.F., Ries L., Reeves R., Regetz J., and Oberhauser K. 2012. Tracking climate impacts on the migratory monarch butterfly. Global Change Biology. 18: 3039-3049.

Ruiz-Gutiérrez V. and Zipkin E.F. 2011. Detection biases yield misleading patterns of species persistence and colonization in fragmented landscapes. Ecosphere. 2: art61.

DeWan A. and Zipkin E.F. 2010. An integrated sampling and analysis approach for improved biodiversity monitoring. Environmental Management. 45: 1223-1230.

Martin J., O’Connell A.F., Kendall W.L., Runge M.C., Simons T.R., Waldstein A.H., Schulte S.A., Converse S.J., Smith G.W., Pinion T., Rikard M., and Zipkin E.F. 2010. Optimal control of native predators. Biological Conservation. 143: 1751-1758.

Ruiz-Gutiérrez V., Zipkin E.F., and Dhondt A.A. 2010. Occupancy dynamics in a tropical bird community: unexpectedly high forest use by birds classified as non-forest species. Journal of Applied Ecology. 47: 621-630.

Zipkin E.F., Gardner B., Gilbert A.T., O’Connell A.F., Royle J.A., and Silverman E.D. 2010. Distribution patterns of wintering sea ducks in relation to the North Atlantic Oscillation and local environmental characteristics. Oecologia. 163: 893-902.

Zipkin E.F., Jennelle C.S., and Cooch E.G. 2010. A primer on the application of Markov chains to the study of wildlife disease dynamics. Methods in Ecology and Evolution. 1: 192-198.

Zipkin E.F., Royle J.A., Dawson D.K., and Bates S. 2010. Multi-species occurrence models to evaluate the effects of conservation and management actions. Biological Conservation. 143: 479-484.

Zipkin E.F., DeWan A., and Royle J.A. 2009. Impacts of forest fragmentation on species richness: a hierarchical approach to community modelling. Journal of Applied Ecology. 46: 815-822.

Zipkin E.F., Kraft C.E., Cooch E.G., and Sullivan P.J. 2009. When can efforts to control nuisance and invasive species backfire? Ecological Applications. 19: 1585-1595.

Zipkin E.F., Sullivan P.J., Cooch E.G., Kraft C.E., Shuter B.J., and Weidel B.C. 2008. Overcompensatory response of a smallmouth bass population to harvest: release from competition? Canadian Journal of Fisheries and Aquatic Sciences. 65: 2279-2292.