Current Research

With my research colleagues we investigate questions concerning habitat relationships, demography, interspecific interactions, and the environmental and physical factors that determine the distribution and abundance of animal species and assemblages. This basic knowledge of natural history provides the ecological context for assessing the effects of anthropogenic influences, ranging from site-specific to ecoregional spatial scales. In turn this information contributes to ecoregional assessments and planning efforts requiring knowledge of management, conservation, and restoration priorities. In recent years I have focused on assessing vulnerability risk across the vertebrate species assemblage in the Sierra Nevada ecoregion, conducting studies of raptors (i.e., hawks, owls, falcons, eagles, vultures), both in the Sierra Nevada and across California, and on the development of ecoregional management and monitoring plans for the Sierra Nevada. Our research on Sierran vertebrate assemblages has focused on development of methods using information on population size, trend, distribution, range change, habitat associations, and other life history characteristics to assess the vulnerability of species to future population decline and extinction risk. The goal of this work is to provide objective and defensible methods for prioritizing species for conservation, research, and monitoring. Raptor studies are focused on the status, distribution, migration, habitat relationships, demography, population trends, monitoring, and response to management of species across California, with particular emphasis on California spotted owls and northern goshawks. In addition to basic and applied research in these topic areas, I am also interested in the development of integrative, multi-disciplinary ecoregional assessments and in the development and testing of monitoring designs to assess the effects of management.

Research Interests

My research interests are focused on the ecology, conservation, and management of species and systems.

Education

• University of California, Ph.D. Ecology 1999
• University of California, M.S. Wildland Resources Science 1991
• San Francisco State University, B.S. Zoology 1986

Publications

• Kramer, Anu ; Jones, Gavin M.; Whitmore, Sheila A.; Keane, John J.; Atuo, Fidelis A.; Dotters, Brian P.; Sawyer, Sarah C.; Stock, Sarah L.; Gutierrez, R.J. ; Peery, M. Zachariah. 2021. California spotted owl habitat selection in a fire-managed landscape suggests conservation benefit of restoring historical fire regimes.
• Wood, Connor M.; Kryshak, Nick ; Gustafson, Michaela ; Hofstadter, Daniel F.; Hobart, Brendan K.; Whitmore, Sheila A.; Dotters, Brian P.; Roberts, Kevin N.; Keane, John J.; Sawyer, Sarah C.; Gutiérrez, Rocky J.; Peery, M. Zachariah. 2021. Density dependence influences competition and hybridization at an invasion front.
• Kramer, H. Anu; Jones, Gavin M.; Kane, Van R.; Bartl-Geller, Bryce ; Kane, Jonathan T.; Whitmore, Sheila A.; Berigan, William J.; Dotters, Brian P.; Roberts, Kevin N.; Sawyer, Sarah C.; Keane, John J.; North, Malcolm P.; Gutierrez, R. J.; Peery, M. Zachariah. 2021. Elevational gradients strongly mediate habitat selection patterns in a nocturnal predator.
• Wood, Connor M.; Zulla, Ceeanna ; Whitmore, Sheila ; Reid, Dana ; Kramer, H. Anu; Keane, John J.; Sawyer, Sarah C.; Roberts, Kevin N.; Dotters, Brian P.; Klinck, Holger ; Berigan, William ; Gutiérrez, R. J.; Peery, M. Zachariah. 2021. Illuminating the nocturnal habits of owls with emerging tagging technologies.
• Hobart, Brendan K.; Kramer, H. Anu; Jones, Gavin M.; Dotters, Brian P.; Whitmore, Sheila A.; Keane, John J.; Peery, M. Zachariah. 2021. Stable isotopes reveal unexpected relationships between fire history and the diet of Spotted Owls.
• Wood, Connor ; Gutiérrez, R.J.; Keane, John ; Peery, M. Zachariah. 2020. Early detection of rapid Barred Owl population growth within the range of the California Spotted Owl advises the Precautionary Principle.
• Jones, Gavin M.; Gutierrez, R. J.; Block, William M.; Carlson, Peter C.; Comfort, Emily J.; Cushman, Samuel A.; Raymond J. Davis, ; Eyes, Stephanie A.; Franklin, Alan B.; Ganey, Joseph L.; Hedwall, Shaula ; Keane, John J.; Kelsey, Rodd ; Lesmeister, Damon B.; North, Malcolm P.; Roberts, Susan L.; Rockweit, Jeremy T.; Sanderlin, Jamie S.; Sawyer, Sarah C.; Solvesky, Ben ; Tempel, Douglas J.; Yiwan, Ho ; Westerling, A. Leroy; White, Gary C.; Peery, M. Zachariah. 2020. Spotted owls and forest fire: Comment.
• Wood, Connor M.; Klinck, Holger ; Gustafson, Michaela ; Keane, John J.; Sawyer, Sarah C.; Gutiérrez, R. J.; Peery, M. Zachariah. 2020. Using the ecological significance of animal vocalizations to improve inference in acoustic monitoring programs.
• Wood, Connor M.; Popescu, Viorel D.; Klinck, Holger ; Keane, John J.; Gutiérrez, R.J. ; Sawyer, Sarah C.; Peery, M. Zachariah. 2019. Detecting small changes in populations at landscape scales: a bioacoustic site-occupancy framework.
• Stephens, Scott ; Kobziar, Leda ; Collins, Brandon ; Davis, Raymond ; Fulé, Peter ; Gaines, William ; Ganey, Joseph ; Guldin, James ; Hessburg, Paul ; Hiers, Kevin ; Hoagland, Serra ; Keane, John ; Masters, Ronald ; McKellar, Ann ; Montague, Warren ; North, Malcolm ; Spies, Thomas A. 2019. Is fire for the birds How two rare species influence fire management across the US.
• Atuo, Fidelis A.; Roberts, Kevin ; Whitmore, Sheila ; Dotters, Brian P.; Raphael, Martin G.; Sawyer, Sarah C.; Keane, John J.; Gutiérrez, R.J. ; Zachariah Peery, M. . 2019. Resource selection by GPS-tagged California spotted owls in mixed-ownership forests.
• Hobart, Brendan K.; Roberts, Kevin N.; Dotters, Brian P.; Berigan, William J.; Whitmore, Sheila A.; Raphael, Martin G.; Keane, John J.; Gutiérrez, R.J. ; Peery, M. Zachariah. 2019. Site occupancy and reproductive dynamics of California spotted owls in a mixed-ownership landscape.
• Hobart, Brendan K.; Jones, Gavin M.; Roberts, Kevin N.; Dotters, Brian P.; Whitmore, Sheila A.; Berigan, William J.; Raphael, Martin G.; Keane, John J.; Gutiérrez, R.J. ; Peery, M. Zachariah. 2019. Trophic interactions mediate the response of predator populations to habitat change.
• Peery, Zach ; Wiens, David ; Bown, Robin ; Carlson, Peter C.; Dugger, Katie ; Dumbacher, Jack ; Franklin, Alan B.; Hamm, Keith A.; Higley, Mark ; Keane, John J. 2018. Barred owl research needs and prioritization in California.
• Jones, Gavin M.; Keane, John J.; Gutiérrez, R. J.; Peery, M. Zachariah. 2018. Declining old-forest species as a legacy of large trees lost.
• Gallagher, Claire V; Keane, John J.; Shaklee, Paula A.; Kramer, H. Anu; Gerrard, Ross . 2018. Spotted owl foraging patterns following fuels treatments, Sierra Nevada, California.
• Wood, Connor M.; Whitmore, Sheila A.; Gutiérrez, R.J. ; Sawyer, Sarah C.; Keane, John J.; Peery, M. Zachariah. 2018. Using metapopulation models to assess species conservation ecosystem restoration trade-offs.
• North, Malcolm P.; Kane, Jonathan T.; Kane, Van R.; Asner, Gregory P.; Berigan, William; Churchill, Derek J.; Conway, Scott; Gutiérrez, R.J.; Jeronimo, Sean; Keane, John; Koltunov, Alexander; Mark, Tina; Moskal, Monika; Munton, Thomas; Peery, Zachary; Ramirez, Carlos; Sollmann, Rahel; White, Angela; Whitmore, Sheila. 2017. Cover of tall trees best predicts California spotted owl habitat.
• North, Malcolm P.; Schwartz, Mark W.; Collins, Brandon M.; Keane, John J. 2017. Current and projected condition of mid-elevation Sierra Nevada forests.
• Cade, Brian S.; Noon, Barry R.; Scherer, Rick D.; Keane, John J. 2017. Logistic quantile regression provides improved estimates for bounded avian counts: a case study of California Spotted Owl fledgling production.
• Keane, John J. 2017. Threats to the viability of California spotted owls.
• Kramer, Heather A.; Collins, Brandon M.; Gallagher, Claire V.; Keane, John; Stephens, Scott L.; Kelly, Maggi. 2016. Accessible light detection and ranging: estimating large tree density for habitat identification.
• Conner, Mary M.; Keane, John J.; Gallagher, Claire V.; Munton, Thomas E.; Shaklee, Paula A. 2016. Comparing estimates of population change from occupancy and mark-recapture models for a territorial species.
• Tempel, Douglas J.; Keane, John J.; Gutierrez, R. J.; Wolfe, Jared D.; Jones, Gavin M.; Koltunov, Alexander; Ramirez, Carlos M.; Berigan, William J.; Gallagher, Claire V.; Munton, Thomas E.; Shaklee, Paula A.; Whitmore, Sheila A.; Peery, M. Zachariah. 2016. Meta-analysis of California Spotted Owl (Strix occidentalis occidentalis) territory occupancy in the Sierra Nevada: habitat associations and their implications for forest management.
• Hessburg, Paul F.; Spies, Thomas A.; Perry, David A.; Skinner, Carl N.; Taylor, Alan H.; Brown, Peter M.; Stephens, Scott L.; Larson, Andrew J.; Churchill, Derek J.; Povak, Nicholas A.; Singleton, Peter H.; McComb, Brenda; Zielinski, William J.; Collins, Brandon M.; Salter, R. Brion; Keane, John J.; Franklin, Jerry F.; Riegel, Greg. 2016. Tamm Review: Management of mixed-severity fire regime forests in Oregon, Washington, and Northern California.
• Stephens, Scott L.; Miller, Jay D.; Collins, Brandon M.; North, Malcolm P.; Keane, John J.; Roberts, Susan L. 2016. Wildfire impacts on California spotted owl nesting habitat in the Sierra Nevada.
• Wu, Joanna X.; Siegel, Rodney B.; Loffland, Helen L.; Tingley, Morgan W.; Stock, Sarah L.; Roberts, Kevin N.; Keane, John J.; Medley, Joseph R.; Bridgman, Roy; Stermer, Chris. 2015. Diversity of great gray owl nest sites and nesting habitats in California.
• Carlson, Jennifer E.; Piirto, Douglas D.; Keane, John J.; Gill, Samantha J. 2015. Estimating site occupancy and detection probabilities for cooper's and sharp-shinned hawks in the Southern Sierra Nevada.
• Hull, Joshua; Englis , Andrew, Jr..; Medley, Joseph R.; Jepsen, Eric P.; Duncan, James R.; Ernest, Holly B.; Keane, John J. 2014. A new subspecies of great gray owl (Strix nebulosa) in the Sierra Nevada of California, U.S.A..
• Stephens, Scott L.; Bigelow, Seth W.; Burnett, Ryan D.; Collins, Brandon M.; Gallagher, Claire. V.; Keane, John; Kelt, Douglas A.; North, Malcolm P.; Roberts, Lance J.; Stine, Peter A.; Van Vuren, Dirk H. 2014. California spotted owl, songbird, and small mammal responses to landscape fuel treatments.
• Keane, John J. 2014. California spotted owl: scientific considerations for forest planning.
• North, Malcolm; Collins, Brandon; Keane, John; Long, Jonathan W.; Skinner, Carl; Zielinski, Bill. 2014. Synopsis of emergent approaches.
• Conner, Mary M.; Keane, John J.; Gallagher, Claire V.; Jehle, Gretchen; Munton, Thomas E.; Shaklee, Paula A.; Gerrard, Ross A. 2013. Realized population change for long-term monitoring: California spotted owl case study.
• Hull, J.M.; Fish, A.M.; Keane, J.J.; Mori, S.R.; Sacks, B.J; Hull, A.C. 2010. Estimation of Species Identification Error: Implications for Raptor Migration Counts and Trend Estimation.
• Blakesley, J.A.; Seamans, M.E.; Connor, M.M.; Franklin, A.B.; White, G.C.; Gutierrez, R.J.; Hines, J.E.; Nichols, J.D.; Munton, T.E.; Shaw, D.W.H.; Keane, J.J.; Steger, G.N.; McDonald, T.L. 2010. Population dynamics of the California spotted owl in the Sierra Nevada, California.
• Hull, J.M.; Keane, J.J.; Savage, W.K.; Godwin, S.A.; Shafer, J.; Jepsen, E.P.; Gerhardt, R.; Stermer, C.; Ernest, H.B. 2010. Range-wide genetic differentiation among North American great gray owls (Strix nebulosa) reveals a distinct lineage limited to the Sierra Nevada, California.
• Manley, P.N.; Zielinski, William J.; Stuart, C.M.; Keane, J.J.; Lind, A.J.; Brown, C.; Plymale, B.L.; Napper, C.O. 2000. Monitoring ecosystems in the Sierra Nevada: the conceptual model foundation.