Peer Reviewed Publications

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Barnosky, A.D., Hadly, E.A., Gonzalez, P., Head, J., Polly, P.D., Lawing, A.M., Eronen, J.T., Ackerly, D.A., Alex, K., Biber, E., Blois, J., Brashares, J., Ceballos, G., David, E., Dietl, G.P., Dirzo, R., Doremus, H., Fortelius, M., Greene, H.W., Jellmann, J., Hickler, T., Jackson, S.T., Kemp, M., Koch, P.L., Kremem, C., Lindsey, E.L., Looy, C., Marshall, C.R., Mendenhall, C., Mulch, A., Mychajliw, A.M., Nowak, C., Ramakrishnan, U., Schnitzler, J., Shrestha, K.D., Solari, K., Stegner, L., Stegner, M.A., Stensth, N.C., Wake, M., and Z. Zhang. Merging paleobiology with conservation biology to guide the future of terrestrial ecosystems. Science. 355(594). DOI: 10.1126/science.aah4787. 

Cridland, J., Tustusui, N., and S.R. Ramirez. The complex demographic history and evolution of the western honey bee, Apis mellifera. Genome Biology and Evolution. 9(2):457-472.

Zeilinger, A.R., Rapacciulo. G., Turek, D., Oboyski, P.T., Aleida, R.P.P., and G.K. Roderick. Museum specimen data reveal emergence of a plant disease may be linked to increases in the insect vector population. Ecological Applicatons. 27(6):1827-1837. doi: 10.1002/eap.1569.


Davies, N., Field, D., Gavaghan, D., Holbrook, S.J., Planes, S., Toyer, M., Bosnall, M., Claudet, J., Roderick, G.R., Schmitt, R.J., Zettler, L.A., Berteaux, V., Bossin, H.C., Cabasse, C., Collin, A., Deck, J., Dell, T., Dunne, J., Gates, R., Harfoot., Hench, J.L., Hopuare, M., Kirch, P., Kotoulas, G., Kosenkov, A., Kusenko, A., Leichter, J.J., Lenihan, H., Magoulas, A., Martinez, N., Meyer, C., Stoll, B., Swalla, B., Tartakovsky, D.M., Murphy, H.T., Turyshev, S., Valdvinos, F., Williams, R., Wood, S. and IDEA Consortium. Simulating social-ecological systems: the Island Digitial Ecosystem Avatars (IDEA) consortium. Gigascience.

Kelly, M., Easterday, K.J., Rapacciuolo, Koo, M.S., McIntyre, P.J., and J.H. Thorne. Rescuing and Sharing historic vegetation data for ecological analysis: the California Vegetation Type Mapping Project. Biodiversity Informatics. 11(1).

Kelly, K.J., Mcintyre, P.J., Thorne, J.H., Santos, M.J. and M. Kelly. Assessing Threats and Conservation Status of Historical Centers of Oak Richness in California. Urban Planning. 1(4):65-78. DOI:10.17645/up.v1i4.726.

Kitzes, J. and M. Wilber. macroeco: reproducible ecological pattern analysis in Python. Ecography. 39(4):361-367. DOI: 10.1111/ecog.01905.

Walsh, R.E., Assis, A.P.A., Patton, J.L., Marroig, G., Dawson, T.E. and E.A. Lacey. Morphological and dietary responses of chipmunks to a century of climate change. Global Change Biology. 22(9):3233-3252. DOI: 10.1111/gcb.13216.


Batllori, E., D.D. Ackerly, and M.A. Moritz. A minimal model of fire-vegetation feedbacks and disturbance stochasticity generates alternative stable states in grassland-shrubland-woodland systems. Environ. Res. Let.  10(3): doi:10.1088/1748-9326/10/3/034018.

Chardon, N.I., W.K. Cornwell, Flint, L., Flint, A., and D.D. Ackerly. Topographic, latitudinal and climatic distribution of Pinus coulteri: geographic range limits are not at the edge of the climate envelope. 2015. Ecography 38(6):590-601.  doi:10.1111/ecog.00780.

Good, J.M.,  D. Vanderpool, S. Keeble, K. Bi. Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks. Evolution. 69(8): 1961-1972.

Harte, J., S. Saleska, and C. Levy. Convergent ecosystem responses to 23-year ambient and manipulated warming link advancing snowmelt and shrub encroachment to transient and long-term climate-soil carbon feedback.  Global Change Biology  21(6): 2349–2356. DOI: 10.1111/gcb.12831.

Harte, J. and J. Kitzes. Inferring Regional-Scale Species Diversity from Small-Plot Censuses. PLOS ONE DOI:10.1371/journal.pone.0117527

Kéfi, S., E.L. Berlow, E.A. Wieters, S.A. Navarrete, S.A. Wood, L.N. Joppa, and U. Brose. Network structure beyond food webs: Mapping non-trophic and trophic interactions on Chilean rocky shores. Ecology 96: 291-303. DOI: 10.1890/13-1424.1.

Kitzes, J. and J. Harte.  Predicting extinction debt from community patterns. Ecology. 96(8):2127-2136.

McIntryre, P.J., Thorne, J.H. Dolanc, C.R., Flint, A.L., Flint, L.E., Kelly, N.M., and Ackerly, D.D. (2015). Twentieth-century shifts in forest structure in California: Denser forests, smaller trees, and increased dominance of oaks. PNAS 112(5): 1458-1463

Newman, E.A., L.Eisen, R. Eisen, N. Fedorova, J.M. Hasty, C.E. Vaughn, and R.S. Lane.  Borrelia burgdorferi sensu lato spirochetes in wild birds in northwestern California: Associations with ecological factors, bird behavior and tick infestation. PLOS ONE


Blumstein, D., K. Levy, E. Mayer, and J. Harte.  Gastrointestinal dysbiosis.  2014. Evolution, Medicine, and Public Health. 1(1):163.

Dralle, D.N., Boisrame, G.F.S. and Thompson, S.E.  Spatially variable groundwater recharge and the hillslope hydrologic response: Analytical solutions to the linearized hillslope Boussinesq equation. Water Resources Research 50(11):8515-8530. DOI: 10.1002/2013WR015144.

Ehinger, M., T.J. Mohr, J.B. Starcevich, J.L. Sachs, S.S. Porter and E.L. Simms. Specialization-generalization trade-off in a Bradyrhizobium symbiosis with wild legume hosts. BMC Ecology 14 (1):8.

Harte, J. Ecology must seek universal principles. 2014. Nature 508: 458.

Harte, J. and E.A. Newman. 2014. Maximum Information Entropy: A Foundation for Ecological Theory. Trends in Ecology and Evolution 29(7): 384–389

Iknayan, K.J., M.W. Tingley, B.J. Furnas, and S.R. Beissinger. 2014. Detecting diversity: emerging methods to estimate species diversity. Trends in Ecology and Evolution 29:2.

Kim, H. 2014. Water chemistry evolution through the critical zone. PhD dissertation, Department of Earth and Planetary Science, University of California, Berkeley. 162 pp.

Kim, H., J.K.B. Bishop, W. Dietrich and I.Y. Fung. 2014. Process dominance shift in solute chemistry as revealed by long-term high-frequency water chemistry observations of groundwater flowing through weathered argillite underlying a steep forested hillslope. Geochimica et Cosmochimica Acta (available online)

Muller, M.T., Dralle, D.N., and S.E. Thompson. 2014. Analytical model for flow duration curves in seasonally dry climates. Water Resources Research 50(7):5510-5531

Newman, E.A., M.E. Harte, N. Lowell, M. Wilber, and J. Harte. 2014. Empirical tests of within- and across-species energetics in a diverse plant community. Ecology 95(10): 2815-2825.

Porter, S.S. and E.L. Simms. 2014. Selection for cheating across disparate environments in the legume-rhizobium mutualism. Ecology Letters 17(9):1121-1129

Rapacciuolo, G., D.B. Roy, S. Gillings and A. Purvis. 2014. Temporal validation plots: quantifying
how well correlative species distribution models predict species’ range changes over time. Methods in Ecology and Evolution 5:407-420.

Rapacciuolo, G., S.P. Maher, A.C. Schneider, T.T. Hammond, M.D. Jabis, R.E. Walsh, K.J. Iknayan, G.K. Walden, M.F. Oldfather, D.D. Ackerly, S.R. Beissinger. 2014. Beyond a warming fingerprint: individualistic biogeographic responses to heterogeneous climate change in California. Global Change Biology 20:2841-2855 (DOI:10.1111/gcb.12638)

Rempe, D.M. and W.E. Dietrich. 2014. A bottom-up control on fresh-bedrock topography under landscapes. Proceedings of the National Academy of Sciences 111 (18): 6576-6581.

Tallis, H., et al.  incl. J. Harte. 2014. A call for inclusive conservation. Nature 515:27-28.

Vico, G., Thompson, S.E., Manzoni S., Molini, A., Albertson,m J.D., Almeida-Cortez, J.S., Fay,P.A., Feng, X., Guswa, A.J., Liu, H., Wilson, T.G. and A.Porporato. 2014. Climatic, ecophysiological and phenological controls on plant ecohydrological strategies in seasonally dry ecosystems. Ecohydrology (doi:10.1002/eco.1533, 2014).


Bi, K., Linderoth, T., Vanderpool, D., Good, J., Nielsen, R., Moritz, C. 2013. Unlocking the Vault: Next Generation Museum Population Genomics. Molecular Ecology (DOI: 10.1111/mec.12516)

Cowart, A., and R. Byrne. 2013. A Paleolimnological Record of Late Holocene Vegetation Change from the Central California Coast. California Archaeology 5(2):337-352.

Cuthrell, R.Q., M.G. Hylkema, and L. Collins. 2013. Natural Resources, Geomorphology, and Archaeology of Site CA-SMA-113 in Quiroste Valley Cultural Preserve, California. California Archaeology 5(2):247-264.

Cuthrell, R.Q. 2013. Archaeobotanical Evidence on Landscape Management Practices and Foodways at CA-SMA-113. California Archaeology 5(2):265-290.

Evett, R.R., and Rob Q. Cuthrell. 2013. Phytolith Evidence for a Grass-Dominated Prairie Landscape at Quiroste Valley on the Central Coast of California. California Archaeology 5(2):319-335.

Fine, P.V.A.,T.M. Misiewicz, A.S. Chavez, and R.Q. Cuthrell. 2013. Population Genetic Structure of California Hazelnut, An Important Food Source for People in Quiroste Valley in the Late Holocene. California Archaeology 5(2):353-370.

Gifford-Gonzalez, D., C.M. Boone, and R.E.B. Reid. 2013. The Fauna from Quiroste: Insights into Indigenous Foodways, Culture, and Land Management. California Archaeology. 5(2):291-317.

Harte, J., J. Kitzes, E. Newman, and A. Rominger. 2013. Taxon Categories and the Universal Species-Area RelationshipAmerican Naturalist 181: 282-287.

Hylkema, M. G., and R.Q. Cuthrell. 2013. An Archaeological and Historical View of Quiroste Tribal Genesis. California Archaeology 5(2):225-245.

Lightfoot, K.G., and V. Lopez. 2013. The Study of Indigenous Landscape Management Practices in California: An Introduction. California Archaeology 5(2):209-219.

Lightfoot, K.G., R.Q. Cuthrell, C.M. Boone, R. Byrne, A.S. Chavez, L. Collins, A. Cowart, R.R. Evett, P.V.A. Fine, D. Gifford-Gonzalez, M.G. Hylkema, V. Lopez ,T.M. Misiewicz, and R.E.B. Reid. 2013.  Anthropogenic Burning on the Central California Coast in Late Holocene and Early Historical Times: Findings, Implications, and Future Directions. California Archaeology 5(2):371-390.

Lightfoot, K.G, R. Q. Cuthrell, C. J. Striplen, and M. G. Hylkema. 2013. Rethinking the Study of Landscape Management Practices Among Hunter-Gatherers in North America. American Antiquity 78: 285-301.

Lopez, A. 2013. The Amah Mutsun Tribal Band: Reflections on Collaborative Archaeology. California Archaeology 5(2):221-223.

Lyons, A., W. Turner, and W. Getz. 2013. Home range plus: a space-time characterization of movement over real landscapes. Movement Ecology 1:2.


Illustration by Lily Li

Barnosky, Anthony D., Elizabeth A. Hadly, Jordi Bascompte, Eric L. Berlow, James H. Brown, Mikael Fortelius, Wayne M. Getz, John Harte, Alan Hastings, Pablo A. Marquet, Neo D. Martinez, Arne Mooers, Peter Roopnarine, Geerat Vermeij, John W. Williams, Rosemary Gillespie, Justin Kitzes, Charles Marshall, Nicholas Matzke, David P. Mindell, Eloy Revilla, and Adam B. Smith. 2012. Approaching a state shift in Earth’s biosphere. Nature 486: 52-58.


Illustration by Lily Li

Bi, K., D. Vanderpool, S. Singhal, T. Linderoth, C. Moritz, J.M. Good. 2012. Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales. BMC Genomics 13: 403.