Publications

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

Limited capacity of habitat features to buffer grassland bird declines
N.A. Gilbert, P.J. Williams, D.J. Carlson, R.M. Dunlap, M. Worland, C.S. Jennelle, and E.F. Zipkin – Ecological Applications

Global impacts of anthropogenic threats on bird and mammal diet functional groups
S. Ayebare, P.J. Williams, S. Ceyzyk, and E.F. Zipkin – Global Ecology and Conservation

Estimating spatially varying occupancy trends for multi-scale conservation: An amphibian case study in the midwestern United States
J.W. Doser, M. Edwards, K.A. Larson, E.F. Zipkin, and C.S. Jennelle – Journal of Applied Ecology

Ontogenetic shifts in wood anatomy traits in tropical dry forests
P.J. Williams, E.F. Zipkin, A. González-Melo, B. Salgado-Negret, R. Gonzalez, N. Norden, J.P. Benavides-Tocarruncho, J.M. Cely, J. Abad, D. García-Villalobos, F. Garzón, Á. Idarraga, R. López Camacho, E. Moreno, J. Nieto, C. Pizano, J. Puentes, N. Pulido, K. Rivera, F. Rojas-Bautista, V. Salinas, J.F. Solorzano, and N.M. Umana – New Phytologist

Improving population analysis using indirect count data: A case study of chimpanzees and elephants
S. Ayebare, N.A. Gilbert, A.J. Plumptre, S. Nampindo, and E.F. Zipkin – Ecosphere

A case for assemblage-level conservation to address the biodiversity crisis
M.W. Belitz, C.J. Campbell, R.G. Drum, W. Leuenberger, T.L. Morelli, K. Nail, V. Shirey, W. Thogmartin, and E.F. Zipkin – Nature Reviews Biodiversity

Evaluating environmental drivers and synchrony of Arctic shorebird demographic rates to inform conservation management
K.L. Davis, R.B. Lanctot, S.T. Saalfeld, and E.F. Zipkin – Ecological Applications

Modeling complex species-environment relationships through spatially-varying coefficient occupancy models
J.W. Doser, A.O. Finley, S.P. Saunders, M. Kery, A.S. Weed, and E.F. Zipkin – Journal of Agricultural, Biological and Environmental Statistics

Rapid butterfly declines across the United States during the 21st century
C.B. Edwards, E.F. Zipkin, E.H. Henry, N.M. Haddad, M.L. Forister, K.J. Burls, S.P. Campbell, E.E. Crone, J. Diffendorfer, M.R. Douglas, R.G. Drum, C.E. Fallon, J. Glassberg, E.M. Grames, R. Hatfield, S. Hershcovich, S. Hoffman-Black, E.A. Larsen, W. Leuenberger, M. J. Linders, T. Longcore, C. Maffei, D.A. Marschalek, J. Michielini, N. Neupane, L. Ries, A. Shapiro, A. Swengel, S. Swengel, B. Van Deynze B, J. Wiedmann, W.E. Thogmartin, and C.B. Schultz – Science

Idiosyncratic spatial scaling of biodiversity–disease relationships
N.A. Gilbert, G.V. DiRenzo, and E.F. Zipkin – Ecography

Three decades of declines restructure butterfly communities in the Midwestern U.S.
W. Leuenberger, J.W. Doser, M.W. Belitz, L. Ries, N.M. Haddad, W. Thogmartin, and E.F. Zipkin – Proceedings of the National Academy of Sciences

Revealing species responses to environmental change through long-term data and mechanistic frameworks
E.F. Zipkin and P.J. Williams – Journal of Animal Ecology

spAbundance: An R package for single-species and multi-species spatially-explicit abundance models
J.W. Doser, A.O. Finley, M. Kery, and E.F. Zipkin – Methods in Ecology and Evolution

Guidelines for the use of spatially-varying coefficients in species distribution models
J.W. Doser, M. Kery, S.P. Saunders, A.O. Finley, B.L. Bateman, J. Grand, S. Reault, A.S. Weed, and E.F. Zipkin – Global Ecology and Biogeography

Overcoming data gaps using integrated models to estimate migratory species’ dynamics during cryptic periods of the annual cycle
M.T. Farr, E.R. Zylstra, L. Ries, and E.F. Zipkin – Methods in Ecology and Evolution

A century of statistical Ecology
N.A. Gilbert, B.R. Amaral, O.M. Smith, P.J. Williams, S. Ceyzyk, S. Ayebare, K.L. Davis, W. Leuenberger, J.W. Doser, and E.F. Zipkin – Ecology

A multispecies hierarchical model to integrate count and distance sampling data
N.A. Gilbert, C.M. Blommel, M.T. Farr, D.S. Green, K.E. Holekamp, and E.F. Zipkin – Ecology

Deep biogeographic barriers explain divergent global vertebrate communities
P.J. Williams, E.F. Zipkin, and J.F. Brodie – Nature Communications

Context matters in ecological forecasting: Lessons in predicting species distributions
E.F. Zipkin and J.W. Doser – Global Change Biology

An environmental habitat gradient and within-habitat segregation enable co-existence of ecologically similar bird species
S. Ayebare, J.W. Doser, A.J. Plumptre, I. Owiunji, H.Mugabe and E.F. Zipkin – Proceedings of the Royal Society B

Challenges and opportunities for using natural history collections to estimate insect population trends
C.L. Davis, R.P. Guralnick, and E.F. Zipkin – Journal of Animal Ecology

Breeding season management is unlikely to improve population viability of a data-deficient migratory species in decline
K.L. Davis, S.P. Saunders, S. Beilke, E.R. Ford, J. Fuller, A. Landgraf, and E.F. Zipkin – Biological Conservation

Integrated population models: Achieving their potential
F. Frost, R.S. McCrea, R. King, O. Gimenez, and E.F. Zipkin – Journal of Statistical Theory and Practice

Propagating uncertainty in ecological models to understand causation
N.A. Gilbert, H.N. Eyster, and E.F. Zipkin – Frontiers in Ecology and the Environment

Integrated community models: A framework combining multispecies data sources to estimate the status, trends and dynamics of biodiversity
E.F. Zipkin, J.W. Doser, C.L. Davis, W. Leuenberger, S. Ayebare, K.L. Davis – Journal of Animal Ecology

The implementation of irrigation leads to declines in farmland birds
X. Cabodevilla, A.D. Wright, D. Villanua, B. Arroyo, and E.F. Zipkin – Agriculture, Ecosystems and Environment

Errors in aerial survey count data: Identifying pitfalls and solutions
K.L. Davis, E.D. Silverman, A.L. Sussman, R. Wilson, and E.F. Zipkin – Ecology and Evolution

spOccupancy: An R package for single species, multispecies, and integrated spatial occupancy models
J.W. Doser, A.O. Finley, M. Kery, and E.F. Zipkin – Methods in Ecology and Evolution

Integrated community occupancy models: A framework to assess occurrence and biodiversity dynamics using multiple data sources
J.W. Doser, W. Leuenberger, T.S. Sillett, M.T. Hallworth, and E.F. Zipkin – Methods in Ecology and Evolution

Quantifying the conservation status and abundance trends of wildlife communities with detection-nondetection data
M.T. Farr, T. O’Brien, C.B. Yackulic, and E.F. Zipkin – Conservation Biology

Grappling with uncertainty in ecological projections: A case study using the migratory monarch butterfly
N. Neupane, E.F. Zipkin, S.P. Saunders, and L. Ries – Ecosphere

A comparison of monitoring designs to assess wildlife community parameters across spatial scales
A.D. Wright, E.H.C. Grant, and E.F. Zipkin – Ecological Applications

Biodiversity is decimated by the cascading effects of the amphibian-killing chytrid fungus
E.F. Zipkin and G.V. DiRenzo – PLOS Pathogens

Multi-season climate projections forecast declines in migratory monarch butterflies
E.R. Zylstra, N. Neupane, and E.F. Zipkin – Global Change Biology

Integrating automated acoustic vocalization data and point count surveys for estimation of bird abundance
J.W. Doser, A.O. Finley, A.S. Weed, and E.F. Zipkin – Methods in Ecology and Evolution

Trends in bird abundance differ among protected forests but not bird guilds
J.W. Doser, A.S. Weed, E.F. Zipkin, K.M. Miller, and A.O. Finley – Ecological Applications

Integrating distance sampling and presence-only data to estimate abundance
M.T. Farr, D.S. Green, K.E. Holekamp, and E.F. Zipkin – Ecology

​Biotic and abiotic drivers of dispersion dynamics in a large-bodied tropical vertebrate, the Western Bornean orangutan
A.J. Marshall, M.T. Farr, L. Beaudrot, E.F. Zipkin, K.L. Feilen, L.G. Bell, E. Setiawan, T.W. Susanto, T.M. Setia, M. Leighton, and H.U. Wittmer – Oecologia

Working across space and time: Nonstationarity in ecological research and application
C.R. Rollinson, A.O. Finley, M.R. Alexander, S. Banerjee, K.D. Hamil, L.E. Koenig, D.H. Locke, M. Peterson, M.W. Tingley, K. Wheeler, C. Youngflesh, and E.F. Zipkin – Frontiers in Ecology and the Environment

Addressing data integration challenges to link ecological processes across scales
E.F. Zipkin, E.R. Zylstra, A.D. Wright, S.P. Saunders, A. Finley, M.C. Dietze, M. Itter, and M.W. Tingley – Frontiers in Ecology and the Environment

Changes in climate drive recent monarch butterfly dynamics
E.R. Zylstra, L. Ries, N. Neupane, S.P. Saunders, M.I. Ramírez, E. Rendón-Salinas, K.S. Oberhauser, M.T. Farr, and E.F. Zipkin – Nature Ecology and Evolution

Accounting for sources of uncertainty when forecasting population responses to climate change
E.R. Zylstra and E.F. Zipkin – Journal of Animal Ecology

Ecological dynamics: Integrating empirical, statistical, and analytical methods
A.N. Laubmeier, B. Cazelles, K. Cuddington, K.D. Erickson, M. Fortin, K. Ogle, C.K. Wikle, K. Zhu, and E.F. Zipkin – Trends in Ecology and Evolution

Poor management in protected areas is associated with lowered tropical mammal diversity
V. Oberosler, S. Tenan, E.F. Zipkin, and F. Rovero – Animal Conservation

When parks work: Effect of anthropogenic disturbance on occupancy of tropical forest mammals
V. Oberosler, S. Tenan, E.F. Zipkin, and F. Rovero – Ecology and Evolution

Moving from decision to action in conservation science
A.D. Wright, R.F. Bernard, B.A. Mosher, K.M. O’Donnell, T. Braunagel, G.V. DiRenzo, J. Fleming, C. Shafer, A.B. Brand, E.F. Zipkin, and E.H.C. Grant – Biological Conservation

A hierarchical analysis of habitat area, connectivity, and quality on amphibian diversity across scales
A.D. Wright, E.H.C. Grant, and E.F. Zipkin – Landscape Ecology

Tropical snake diversity collapses after widespread amphibian loss
E.F. Zipkin, G.V. DiRenzo, J.M. Ray, S. Rossman, and K.R. Lips – Science

Disentangling herbivore impacts in early primary succession by refocusing the plant stress and plant vigor hypotheses on phenology
C. Che-Castaldo, C.M. Crisafulli, J.G. Bishop, E.F. Zipkin, and W.F. Fagan – Ecological Monographs

Disease structured N-mixture models: A practical guide to model disease dynamics using count data
G.V. DiRenzo, C. Che-Castaldo, S.P. Saunders, E.H.C. Grant, and E.F. Zipkin – Ecology and Evolution

Multispecies hierarchical modeling reveals variable responses of African carnivores to management alternatives
M. T. Farr, D.S. Green, K.E. Holekamp, G.J. Roloff, and E. F. Zipkin – Ecological Applications

Can hyena behaviour provide information on abundances of sympatric carnivores?​
D.S. Green, M.T. Farr, K.E. Holekamp, E.D. Strauss, and E.F. Zipkin – Philosophical Transactions of the Royal Society B

Long-term ecological changes influence herbivore diversity inside a protected area in the Mara-Serengeti ecosystem
D.S. Green, E.F. Zipkin, D.C. Incorvaia, and K.E. Holekamp – Global Ecology and Conservation

Tracking trends in monarch abundances over the 20th century is currently impossible using museum records
L. Ries, E.F. Zipkin, and R.P. Guralnick – Proceedings of the National Academy of Sciences

Disentangling data discrepancies with integrated population models​
S.P. Saunders, M.T. Farr, A.D. Wright, C.A. Bahlai, J.W. Ribeiro Jr., S. Rossman, A.L. Sussman, T.W. Arnold, and E.F. Zipkin – Ecology

Multiscale seasonal factors drive the size of winter monarch colonies
S.P. Saunders, L. Ries, N. Nepuane, M.I. Ramírez, E. García-Serrano, E. Rendón-Salinas, and E.F. Zipkin – Proceedings of the National Academy of Sciences

A comparative analysis of common methods to identify waterbird hotspots
A.L. Sussman, B. Gardner, E.M. Adams, L. Salas, K.P. Kenow, D.R. Luukkonen, M.J. Monfils, W.P.Mueller, K.A. Williams, M. Leduc-Lapierre, and E.F. Zipkin – Methods in Ecology and Evolution

From ecologically equivalent individuals to contrasting colonies: Quantifying isotopic niche and individual foraging specialization in an endangered oceanic seabird
A.E. Wiley, S. Rossman, P.H. Ostrom, C.A.M. France, J. Penniman, J. Bailey, F. Duvall, E.F. Zipkin, and H.F. James – Marine Biology

Innovations in data integration for modeling populations
E.F. Zipkin, B.D. Inouye, and S.R. Beissinger – Ecology

Models for assessing local-scale co-abundance of animal species while accounting for differential detectability and varied responses to the environment
J.E. Brodie, O. Helmy, J. Mohd-Azlan, A. Granados, H. Bernard, A. Giordano, and E.F. Zipkin – Biotropica

Eco-evolutionary rescue promotes host-pathogen coexistence
G.V. DiRenzo, E.F. Zipkin, E.H.C. Grant, J.A. Royle, A.V. Longo, K.R. Zamudio, and K.R. Lips – Ecological Applications

Evaluating population viability and efficacy of conservation management using integrated population models
S.P. Saunders, F.J. Cuthbert, and E.F. Zipkin – Journal of Applied Ecology

Local and cross-seasonal effects of climate and land-use on migratory monarch butterflies
S.P. Saunders, L. Ries, K.S. Oberhauser, W.E. Thogmartin, and E.F. Zipkin – Ecography

Effects of agriculture and topography on tropical amphibian species and communities
J.W. Ribeiro Jr., T. Siqueira, G.L. Brejão, and E.F. Zipkin – Ecological Applications

Flying through hurricane central: Impacts of hurricanes on migrants with a focus on monarch butterflies​
L. Ries, N. Neupane, K. Baum, and E.F. Zipkin – Animal Migration

Individual-level trait variation and negative density dependence affects growth in tropical tree seedlings
M.N. Umana, E.F. Zipkin, C. Zhang, M. Cao, L. Lin, and N.G. Swenson – Journal of Ecology

Synthesizing multiple data types for biological conservation using integrated populations models
E.F. Zipkin and S.P. Saunders – Biological Conservation

Differential matrix use by Neotropical birds based on species traits and landscape condition
C.M. Kennedy, E.F. Zipkin, and P.P. Marra – Ecological Applications

Broad-scale trophic shift in the pelagic North Pacific revealed by an oceanic seabird
P.H. Ostrom, A.E. Wiley, H.F. James, S. Rossman, W.A. Walker, E.F. Zipkin, and Y. Chikaraishi – Proceedings of the Royal Society B

Integrating count and detection-nondetection data to model population dynamics
E.F. Zipkin, S. Rossman, C. Yackulic, J.D. Wiens, J.D. Thorson, R.J. Davis, and E.H.C. Grant – Ecology

Incorporating imperfect detection into joint models of communities: A response to Warton et al
S.R. Beissinger, S.R. Iknayan, G. Guillera-Arroita, E.F. Zipkin, R.M. Dorazio, J.A. Royle, and J.A. Kéry – Trends in Ecology and Evolution

Hierarchical analysis of taxonomic variation in intraspecific competition across fish species
A.P. Foss-Grant, E.F. Zipkin, J.T. Thorson, O. Jensen, and W.F. Fagan – Ecology

Beyond carbon and nitrogen: Guidelines for estimating three dimensional isotopic niche space
S. Rossman, S. Ostrom, F. Gordon, E.F. Zipkin – Ecology and Evolution

Dynamic N-occupancy models: Estimating demographic rates and local abundances from detection-nondetection data
S. Rossman, S. Yackulic, S.P. Saunders, J. Reid, R. Davis, and E.F. Zipkin – Ecology

Evaluating confidence in climate-based predictions of population change in a migratory species
S.P. Saunders, L. Ries, K.S. Oberhauser, and E.F. Zipkin – Global Ecology and Biogeography

Joint dynamic species distribution models: A tool for community ordination and spatiotemporal monitoring
J.T. Thorson, J.T. Ianelli, E. Larsen, M. Scheuerell, M. Szuwalski, and E.F. Zipkin – Global Ecology and Biogeography

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

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

Racing through life: Maturation rate plasticity regulates overcompensation and increases persistence
V.A. Karatayev, V.A. Kraft, and E.F. Zipkin – Ecosphere

​Oil palm plantations fail to support mammal diversity
S. Yue, J.F. Brodie, E.F. Zipkin, and H. Bernard – Ecological Applications

Book review: Case studies in Bayesian statistical modeling and analysis
E.F. Zipkin – The Quarterly Review of Biology

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

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

Guidelines for a priori grouping of species in hierarchical community models
K. Pacifici, E.F. Zipkin, J. Collazo, R. Irizarry, and R. DeWan – Ecology and Evolution

How variable is recruitment for marine fishes? A hierarchical model for testing life history theory
J.T. Thorson, J.T. Jensen, and E.F. Zipkin – Canadian Journal of Fisheries and Aquatic Sciences

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

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

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

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

A strategy for monitoring and managing declines in an amphibian community
E.H.C. Grant, E.F. Zipkin, J.D. Nichols, and J.P. Campbell – Conservation Biology

Explaining local-scale species distributions: Relative contributions of spatial autocorrelation and landscape heterogeneity for an avian assemblage
B.J. Mattsson, E.F. Zipkin, P.J. Blank, B. Gardner, J.R. Sauer, and J.R. Royle – PLOS ONE

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

Conservation of avian diversity in the Sierra Nevada: Moving beyond a single-species management focus
A.M. White, E.F. Zipkin, P.N. Manley, and M.D. Schlesinger – PLOS ONE

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

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

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

Tracking climate impacts on the migratory monarch butterfly
E.F. Zipkin, L. Ries, R. Reeves, J. Regetz, and K. Oberhauser – Global Change Biology

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

An integrated sampling and analysis approach for improved biodiversity monitoring
A. DeWan and E.F. Zipkin – Environmental Management

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

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

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

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

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

Impacts of forest fragmentation on species richness: A hierarchical approach to community modelling
E.F. Zipkin, A. DeWan, and J.A. Royle – Journal of Applied Ecology

When can efforts to control nuisance and invasive species backfire?
E.F. Zipkin, C.E. Kraft, E.G. Cooch, and P.J. Sullivan – Ecological Applications

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