James H. Thorne

Contact Information

Dept. of Environmental Science and Policy University of California, Davis One Shields Avenue

Davis, CA 95616

Position: Research Scientist
Email: jhthorne@ucdavis.edu
Phone: (530) 752-4389
Office: Wickson 2120H


2006-2014 Research Scientist, Information Center for the Environment, University of California, Davis, CA.  

2005-2014 Adjunct faculty, Geography Graduate Group, University of California, Davis.

2003    Ph.D.   Ecology, University California, Davis

1997    M. A. Geography, University of California, Santa Barbara

1985    B.A.    Environmental Studies, University of California, Santa Cruz


Areas of Interest

Conservation Planning, Landscape Ecology, Climate Change, Informatics, Biogeography,     Historical Ecology, Species Distribution Modeling, Phenology, Environmental Policy, Urban Growth Modeling



English, French, Spanish



          To use my training in ecology, geography, and environmental science for landscape ecological research, teaching, and to develop effective conservation projects.



Current Projects


Resource Management Under Uncertainty, US National Parks. I am a landscape ecologist and GIS modeler for efforts to assess biological and ecosystem vulnerability to climate change in Sequoia and Kings Canyon, Death Valley, and Joshua Tree National Parks. Proactive vulnerability assessments, and development of conservation management strategies is a new area of research for the US National Parks, which is grappling with whether it is possible to increase biological resilience to climate change, and what management strategies might be required.

US Forest Service, International Projects. I developed the curriculum and teach an annual 3 week curriculum for selected 24 international mid-career forest and resource management professionals. Course locations include Washington, DC, UC Davis, and field locations throughout California. Participants are US AID, Embassy adjuncts and mangers in NGOs. I have several international collaborations developed through this program.

Jordan Protected Areas Climate Adaptation Plan Development. I am developed a Climate Change biodiversity adaptation plan for Jordan’s Royal Society for the Conservation, the national protected areas management entity in that country.

Climate Change Vulnerability Assessment for California.

I am a landscape ecologist, modeler and data coordinator for a multi-investigator effort to improve projections of vulnerability to California across multiple sectors including agriculture, water availability, fire, and biodiversity. My group produced downscaled historic and future climates, urban growth models, and a dynamic vegetation model.

Regional Advance Mitigation Planning (RAMP). I study human impacts on natural systems, with the objective of identifying sustainable designs and processes for human-environment interactions. We use an urban growth model to project patterns of new settlements according to various policy scenarios, and to evaluate how the footprint of future growth may impact habitats and wildlife. We also developed biologically relevant measures of landscape fragmentation for California (effective mesh size), and China. I direct a monitoring program assessing wildlife use of unimproved highway underpasses and wildlife road kill along highways on California’s central coast. This includes camera installations, track plates and tracking.

Strategic Highway Research Program (SHRP2B). I am lead PI on a project funded through the National Academy of Sciences and the Transportation Research Board to assist in development of a national environmental impact scoping tool for transportation projects. For this project we will assess transportation impacts from all programmed projects on Highway 101 from Santa Barbara to Mendocino counties using protocols we have developed during California RAMP projects. We will then work with the national tool developers (ICF, under SHRP2A) to test the tool and datasets they develop on the same stretch of highway.

San Joaquin Valley Greenprint Development.  I am lead PI on a project to develop a regional open space and sustainability design for eight counties in the San Joaquin Valley. The project is being conducted under the auspices of a coalition of 8 county governments and over 60 city governments, originally formed as part of the San Joaquin Blueprint planning process. This project will take special focus on incorporating agricultural interests into views of important open spaces to preserve. Funding comes through the Fresno Council of Governments and originates from the California Department of Conservation.

Korean Initiative. I advise faculty at Seoul National University and the National Inventory and Environmental Research Institute (the Korean equivalent of US EPA) to assess the vulnerability of their biodiversity to climate change; to quantify the impacts of roads on wildlife through landscape scale monitoring and experiment; and to develop studies from national inventory efforts.

Metropolitan Transportation Commission. I am working on a grant from the Moore Foundation to assess the impacts from planned transportation projects in the San Francisco Bay Area. Currently 699 planned projects over the next 30 years will require over 23 Billion in funding. Of these, we are analyzing a subset of 160 that will have impacts to natural resources. Findings will inform MTC and county CMAs of expected mitigation needs.

African Elephants. I advise a GIS analyst at Africa Wildlife Foundation on the development of spatial frameworks to assess movement and habitat preferences from 10 years of daily movement data, collected but not analyzed. From the movement data, regional connectivity models can be extended throughout east Africa.

Historical and Projected Landscape Ecology. I am interested in the impacts of climate change to human and biological communities, and use several tools to assess and predict change: historical and contemporary data, and modeled future projections. I led an effort to digitize ~200,000 km2 of historic California vegetation maps (1930s) and > 10,000 historic vegetation plots. When compared to over 20,000 contemporary vegetation plots and maps, shifts in species ranges and forest structure can be detected and modeled.

I also lead an initiative to bundle biological monitoring around weather stations. This involves development of standard monitoring protocols for plants and vertebrates. If this monitoring is installed near to weather stations, it adds great value to those data over time. I collaborate with multiple groups including the California Energy Commission and the US Forest Service.

Institute for Bird Populations. I am conducting a climate exposure analysis for 140 bird species of the Sierra Nevada Mountains, as part of a vulnerability assessment of those species under funding from the US FWS LCC initiative.

Butterfly Phenology 30 Year Study. http://butterfly.ucdavis.edu/. I oversaw development, analysis and online publication of a database of butterfly phenology, records recorded by Dr. Art Shapiro, UC Davis. I was author of a NSF grant ($217,000) obtained under the Informatics and Databases division, to register the 30+ year butterfly phenology study into a database and analyze the contents. We have over 85,000 species observation events from 10 sites forming a transect from San Francisco to Nevada.

Oak Restoration & Long-Term Field Experiment. I have run a restoration project that provides native Valley Oak (Quercus lobata) seedlings to restoration groups for 10 years. Last year 2 groups used >300 seedlings.

Publications coordinator, Information Center for the Environment (ICE), UC Davis. I coordinate GIS and model development undertaken by my lab for state and national agencies at ICE. In this capacity I identify the publishable elements of ongoing work, and support the development of peer-reviewed publications. This position requires the assembly of manuscript teams, identification of team members’ obligations for manuscripts, and preparation for meetings with local and regional government and private business.




ThorneJH & S McQuinn. Mapping Change in Sierra Nevada Forests. 2012. http://vimeo.com/41524838


Peer reviewed journal articles and book chapters:


Thorne, J.H., P.R. Huber, E. O’Donoghue, M. J. Santos. Regional Advanced Mitigation Planning (RAMP), a framework to unify infrastructure projects with sustainability goals Environmental Research Letters. In Press.

Casner, K.L., M.L. Forister, J. O’Brien, J.H. Thorne, D. Waetjan, A.M. Shaprio. 2014. Converging forces associated with the decline of an urban butterfly fauna. Conservation Biology. DOI: 10.1111/cobi.12241

McGrann, M. C., and J. H. Thorne. 2014. Elevation Ranges of Birds along California's Pacific Crest Trail.Western Birds 45(1):18-42.

Santos, MJ, JH Thorne, J Christensen, Z Frank. 2014. Assessing conservation success through reconstruction of the history of conservation land acquisitions and land-cover dynamics in a metropolitan area. Landscape and Urban Planning. 127:114-123.

Siegel, R.B, P. Pyle, J.H. Thorne, A. J. Holguin, C. A. Howell, S. Stock, M. W. Tingley. 2014. Vulnerability of birds to climate change in the Sierra Nevada Mountains of California. Avian Conservation and Ecology 9(1): 7. http://dx.doi.org/10.5751/ACE-00658-090107.

Zotano, J. G., F. R. Requena, J. H. Thorne. Attributes and roadblocks: a conservation assessment and policy review of the Sierra Bermeja, a Mediterranean serpentine landscape. Natural Areas Journal. In Press.



Thorne, JH, C. Seo, A. Basabose, M Gray, T Belfiore, RJ Hijmans. 2013. Spatial management options for mountain gorilla conservation under climate change: the effects of modeling alternative biological assumptions. Ecosphere. 4(9):108. http://dx.doi.org.10.1890/ES13-00123.1

Thorne, JH, MJ Santos, J Bjorkman. 2013. Historic and future conservation progress and urban growth impacts in the San Francisco Bay Area, California. PLoS ONE 8(6): e65258. doi:10.1371/journal.pone.0065258

Dolanc, C.R., B. Westfall, H.D. Safford, J.H. Thorne, M.W. Schwartz. 213. Growth-climate relationships for six subalpine tree species of the central Sierra Nevada, CA, USA. Canadian Journal of Forest Research. 43:1114-1126..

Dolanc, C. R., J.H. Thorne and H.D. Safford. 2013. Widespread shifts in the demographic structure of subalpine conifer forests over last 80 years in the central Sierra Nevada. Global Ecology and Biogeography. 22:264-276.

Dolanc, C. R., J.H. Thorne and H.D. Safford. 2013. Widespread shifts in the demographic structure of subalpine conifer forests over last 80 years in the central Sierra Nevada. Global Ecology and Biogeography. 22:264-276.

Dolanc, C. R., H. D. Safford, S. Z. Dobrowski, J. H. Thorne. 2013. Twentieth Century shifts in abundance and composition of vegetation types of the Sierra Nevada, CA, US. Journal of Applied Vegetation Science. Doi: 10.1111/avsc.1207.


Seo, C., J. H. Thorne, H. Kwon, C. H. Park, T. Choi. 2013. Disentangling roadkill, the influence of landscape, season and road type on cumulative vertebrate mortality. Landscape Ecology and Engineering. DOI 10.1007/s11355-013-0239-2.

Swanson, A.; Dobrowski, S.; Finley, A.; Thorne, J.; Schwartz, M. 2013. Spatially explicit methods capture prediction uncertainty in species distribution model forecasts through time. Global Ecology and Biogeography.22:242-251.


Huber, P.R., F. Shilling, J.H. Thorne,  S.E. Greco. 2012. Municipal and Regional Habitat Connectivity Planning. Landscape and Urban Planning. 105:15-26.

Roth, R. J. H.Thorne, R. Johnston, M. McCoy. 2012. Financial costs to agriculture and

municipal governments of urban growth in an agricultural valley. Journal of Agriculture, Food Systems, and Community Development.ISSN: 2152-0801 online www.AgDevJournal.com

Viers, J.H., A.K. Fermier, R.A. Hutchinson, J.F. Quinn, J.H. Thorne, M.G. Vaghti. 2012Multi-scale Patterns of Riparian Plant Diversity and Implications for Restoration. Restoration Ecology 20:160-169  doi: 10.1111/j.1526-100X.2011.00787.x


Dobrowski, S.Z., J.H. Thorne, J.A. Greenberg, H.D. Safford, A.R. Mynsberge, S.M. Crimmins, A.K. Swanson. 2011. Modeling plant distributions over 75 years of measured climate change in California, USA: Relating temporal transferability to species traits. Ecological Monographs 81:241-257.

Huber, R. P., J. H. Thorne, N. E. Roth, M McCoy. 2011. Assessing the ecological condition and vulnerability of a potential conservation network in a working landscape. Natural Areas Journal 31:234-245.

O’Brien, J. M., J. H. Thorne, and A. M. Shapiro. 2011. Once-Yearly Sampling for the Detection of Trends in Biodiversity: The Case of Willow Slough, California. Biological Conservation 144:2012-2019.


Thorne, J.H., P.R. Huber, S. Harrison. 2010. Exploring tradeoffs among conservation goals in serpentine-rich landscapes. In. Harrison and Rajakaruna eds. Serpentine: A model for evolution and ecology. University of California Press.

Waetjen, D. P. J. H. Thorne, A. D. Hollander, A. M. Shapiro, and J. F. Quinn. 2010. The Butterfly Effect: An approach for web-based scientific data distribution and management with linkages to climate data and the semantic web. In: (Eds Anandarajan, M. & Anandarajan, A.) E-Research collaboration: Frameworks, Tools and Techniques. Springer-Verlag. Berlin.

G. F. Midgley, I. D. Davies, C. H. Albert, R. Altwegg, L. Hannah, G. O. Hughes, L. P. Ries, J. H. Thorne, C. Seo, W. Thuiller. 2010. BioMove – an integrated platform simulating the dynamic response of species to environmental change. Ecography. 33:612-616. doi: 10.1111/j.1600-0587.2009.06000.x

T. Li, F. Shilling, J. H. Thorne, F. Li, H. Schott, R. Boynton, A. M. Berry. 2010.  Fragmentation of China’s Landscape by Roads and Urban Areas. Landscape Ecology. 25:839-853. DOI 10.1007/s10980-010-9461-6

Huber, P. R., S. Greco, J. H. Thorne. 2010.Spatial scale and its effects on conservation network design: trade-offs and omissions in regional versus local scale planning. Landscape Ecology. 25: 683-695. http://www.springerlink.com/content/c3564585tt2uj64l/

Forister, M.L., A.C. McCall, N.J. Sander, J.A. Fordyce, J.H. Thorne, J. O’Brien, D.P. Waetjan, A.M. Shapiro. 2010. Compounded effects of climate change and habitat alternation shift patterns of butterfly diversity. Proceedings of the National Academy of Sciences. 107:1-5. http://www.pnas.org/content/early/2010/01/14/0909686107.full.pdf+html?sid=059e0402-a5e4-4ba2-bb34-ac4f73785d00

Santos, M.J. and J.H. Thorne. 2010. Contrasting culture and ecology: conservation planning of oak woodlands in Mediterranean landscapes of Portugal and California. Environmental Conservation 37:155-168.  doi:10.1017/S0376892910000238

Huber, P., J. H. Thorne, S. Greco. 2010. Boundaries make a difference: the effects of spatial and temporal parameters on conservation planning. Professional Geographer 62:1-17.

Schmidt, E., J. H. Thorne, P. Huber, N. Roth, E. Thompson, M McCoy. 2010.A new vision for prioritizing farmland preservation in the San Joaquin Valley, California. California Agriculture 64:129-134.


Thorne, J.H. 2009. Of refugia and colonization, an innovative use of biogeography for climate studies. Frontiers of biogeography 1.2:5-6.

Beardsley, K., J. H.Thorne, N. E. Roth, M. McCoy. 2009. Impact of Rapid Human Population Growth on Biological Resources in the San Joaquin Valley of California. Landscape and Urban Planning 9:172-183.doi:10.1016/j.landurbplan.2009.07.003  

Thorne, J. H., J.H. Viers, J. Price, D. M. Stoms. 2009. Spatial patterns of endemic plants in California. Natural Areas Journal 29:137-148.

Thorne, J. H., P. Huber, E. Girvetz, J. F. Quinn, M. McCoy. 2009. Integration of regional mitigation assessment and conservation planning.  Ecology and Society 14:47 [online] http://www.ecologyandsociety.org/vol14/iss1/art47/.

Williams, C. Seo, J. H. Thorne, J. N., J. K. Nelson, S. Erwin, J. M. O’Brien, M. W. Schwartz. 2009. Using species distribution models to predict new occurrences for rare plants.  Diversity and Distributions. 15: 565-576. DOI: 10.1111/j.1472-4642.2009.00567.x

Thorne, J. H., E. H. Girvetz, and M. McCoy. 2009. Evaluating aggregate terrestrial impacts of road construction projects for advanced regional mitigation. Environmental Management 43: 936-948. DOI: 10.1007/s00267-008-9246-8

Seo, C., J. H. Thorne, L. Hannah, W. Thuiller. 2009. Scale effects in species distribution models; implications for planning under climate change. Biology Letters 5:39-43.http://journals.royalsociety.org/content/x08310826r318131/?p=4f7483d92f474fef8c5b5d3ece83f86e&pi=0

Thorne, J. H., B. J. Morgan, and J. A, Kennedy. 2008. Vegetation Change over 60 Years in the Central Sierra Nevada. Madroño55:223-237.

Harrison, S., J. H. Viers, J. H. Thorne, J. B. Grace. 2008. Favorable Environments and the Persistence of Naturally Rare Species. Conservation Letters1: 65-74.


Girvetz, E. H, J. H. Thorne, A. M Berry, and J. A.G. Jaeger. 2008. Integration of Landscape fragmentation analysis into regional planning: a state-wide multiscale case study for California. Landscape and Urban Planning 86: 205-218. http://www.sciencedirect.com/science/journal/01692046

Girvetz, E. H., J. A. G. Jaeger, J. H. Thorne. 2007. Comment on „Roadless Space of the Conterminous United States“. Science- Technical Comment 1240b.

Thorne, J. H., J. M. O’Brien, M. L. Forister, and A. M. Shapiro. 2006. Building Phenological Models from Presence/Absence Data for a Butterfly Fauna.Ecological Applications 16(5) 1730-1743.

Thorne, J.H., S. Gao, A. D. Hollander, J. A.  Kennedy, M. McCoy, R. A. Johnston, J. F. Quinn. 2006. Modeling potential species richness and urban buildout to identify mitigation sites along a California highway. Journal of Transportation Research D11(4) 233-314.

Thorne, J.H., D. Cameron, and J.F. Quinn. 2006. A conservation design for the central coast of California and the evaluation of mountain lion as an umbrella species.Natural Areas Journal 26:137-148.

Schwartz, M. W., J. Thorne, and  J.H. Viers. 2006 Biotic homogenization of the California flora in urban and urbanizing regions. Biological Conservation 127(3): 282-291.

Viers, J. H., J. H. Thorne, and J. F. Quinn. 2006. CalJep: A spatial distribution database of CalFlora and Jepson plant species. San FranciscoEstuary and Watershed Science. Vol. 4, Issue 1 (February 2006), Article 1. http://repositories.cdlib.org/jmie/sfews/vol4/iss1/art1

Stubblefield, A., S. Chandra, S. Eagan, T. Dampil, G. Davaadorzh, D. Gilroy, J. Sampson, R. Allen, J. Thorne, Z. Hogan. 2005. Impacts of gold mining and land use alterations on the water quality of central Mongolian rivers. Integrated Environmental Assessment and Management1(3) 1-7.

Thorne, J.H., J. A. Kennedy,  T.  Keeler-Wolf J. F. Quinn, M. McCoy, J. Menke.2004.

A new vegetation map of Napa County using the Manual of California Vegetation Classification and its comparison to other digital vegetation maps.Madroño 51(4) 343-363.

Vander Zanden, J., J.D. Olden, J.H. Thorne, N.E. Mandrake. 2004. Predicting occurrences and impacts of smallmouth bass introductions in north temperate lakes. Ecological Applications 14(1) 132-148.

Thorne, J.H. 2003. Development and Interpretation of Ecological Datasets for Conservation Planning and Natural Resources Management. PhD Dissertation, UC, Davis.




Peer Reviewed Technical & Government Reports:

Thorne, J. H. Forest Vegetation Patterns. 2013. In: Indicators of Climate Change in California. Editors: T. Kadir, L. Mazur, C Milanes, K. Randles, California Environmental Protection Agency, Office of Environmental Health Hazard Assessment. California Department of Environmental Health Hazard Assessment, Sacramento, CA.

Thorne, J.H. and H. Mussein. Climate Change Exposure and Adaptation Models for Four Protected Areas of the Jordan Rift Valley. Technical Report to the Royal Society for Conservation of Nature, Jordan. In Revision.

Siegel, R., P. Pyle, A.J. Holguin, J.H. Thorne. Climate ChangeVulnerability Assessment for 117 Species of Sierra Nevada Birds. US Fish and Wildlife Landscape Conservation Cooperative Report.  In Review.

Thorne, James, Ryan Boynton, Lorraine Flint, Alan Flint, and Thuy-N’goc Le (University of California, Davis and U.S. Geological Survey). 2012. Development and Application of Downscaled Hydroclimatic Predictor Variables for Use in Climate Vulnerability and Assessment Studies. California Energy Commission. Publication number: CEC-500-2012‑010.

Thorne, James, Bjorkman, Jacquelyn, Roth, Nathaniel. (University of California, Davis). 2012.Urban Growth in California: Projecting growth in California (2000-2050) under six alternative policy scenarios and assessing impacts to future dispersal corridors, fire threats and climate-sensitive agriculture.California Energy Commission. Publication number: CEC-500-2012-009.

Cornwell, W. K., S.A. Stuart, A. Ramirez, C.R. Dolanc, J.H. Thorne, D.D. Ackerly. 2012.

Climate Change Impacts on California Vegetation: Physiology, Life History, and

Ecosystem Change. California Energy Commission. Publication number: CEC-500


Hannah, Lee, M. Rebecca Shaw, Makihiko Ikegami, Patrick R. Roehrdanz, Oliver Soong, and

James Thorne. 2012. Consequences of Climate Change for Native Plants and

Conservation.California Energy Commission. Publication number: CEC-500-2012-024.

Santos, Maria J., Craig Moritz, and James H. Thorne. 2012. Identifying Vulnerable Species and

Adaptation Strategies in the Southern Sierra of California Using Historical Resurveys.California Energy Commission. Publication number: CEC‐500‐2012‐025.

Hiatt, S., Owen, P., Pallin, A., Davis, J., Slaton, MR, Thorne, J. In Review. Los Padres National Forest: Firescape Monterey, Landtype Association Ecological Unit Inventory. San Francisco State University, SF, CA.

Schwartz, M.W.J.Thorne, A. Holguin. Biodiversity. In: Panek, J & J. Battles eds. Natural Resource Condition Assessment for Sequoia and Kings Canyon National Parks. In Press.

Thorne, J.H., W.B. Monahan, A. Holguin, and M.W. Schwartz. Landscape Ecology. In: Pannek, J & J. Battles eds. Natural Resource Condition Assessment for Sequoia and Kings Canyon National Parks. In Press.

Thorne, J.H., C. Seo. 2011. Modeling Species Distribution under Several Climate Change Scenarios for Mountain Gorillas.  In: The Implications of Global Climate Change for Mountain Gorilla Conservation in the Albertine Rift. Africa Wildlife Foundation. Washington, D.C.

Huber, P.R., F.M. Shilling, J.H. Thorne, S.E. Greco, and N.E. Roth. 2010. Safe Passages and the City of Riverbank: Wildlife Connectivity in the San Joaquin Valley, California. University of California, Davis.

T. Diamond, C. McFarland, J. Keller, J.H. Thorne. 2010. The Central Coast Connectivity Project: Northern Monterey Linkage Report. Connectivity for Wildlife LLC and Big Sur Land Trust, Monterey, CA. 33pg.

Thorne, J. H. 2009 Impacts on biological systems: Vegetation- Forest Vegetation Patterns. pp. 136-142. In: Indicators of Climate Change in California. Ed: L. Mazur. California Environmental Protection Agency, Sacramento. http://oehha.ca.gov/multimedia/epic/pdf/ClimateChangeIndicatorsApril2009.pdf

Thorne, J. H., E. Girvetz, M.C. McCoy. 2008. Report on California state-wide mitigation needs forecasting database. Technical Report to the California Department of Transportation, UC Davis, CA.

Girvetz, E.H., J.H. Thorne, J.F. Quinn, M.C. McCoy. 2008. Early Biological Mitigation Needs Assessment: Elkhorn Slough Pilot Project. Technical Report to the California Department of Transportation, UC Davis, CA.

Huber, P., E.H. Girvetz, J.H. Thorne, A. Hollander, J.F. Quinn, M.C. McCoy. 2008. Early biological mitigation needs assessment: Pleasant Grove pilot project. Technical Report to the California Department of Transportation, UC Davis, CA.

L. Hannah, G. Midgley, I Davies, F Davis, L Ries, W Thuiller, J Thorne, C Seo, D Stoms, N Snider. 2007.  BioMove – Improvement and Parameterization of a Hybrid Model for the Assessment of  Climate Change Impacts on the Vegetation of California. Technical Report for California Energy Commission, Public Interest Energy Research, Sacramento, CA. 96 p.

Thorne, J., J. Bjorkman, S. Thrasher, R. Kelsey, and B. J. Morgan. 2007. 1930s extent of oak species in the central Sierra Nevada. USForest Service General Technical Report. http://www.fs.fed.us/psw/publications/documents/psw_gtr217/psw_gtr217_569.pdf

Beardsley, K., J.H. Thorne, M.C. McCoy. 2007. Policy Implications of Growth Modeling and Environmental Assessment in the San Joaquin Valley.Technical Report published by John Muir Institute for the Environment, UC Davis, CA.

Thorne, J. H. 2006. The development of 70-year old Wieslander Vegetation maps and an assessment of landscape change in the central Sierra Nevada. Technical Report for California Energy Commission, Public Interest Energy Research, Sacramento, CA. 115 p.

Thorne, J.H., B. J. Morgan, T. R. Kelsey, and J. A. Kennedy. 2006. Wieslander Vegetation Type Maps: A Digitizing Process Manual. Technical Report prepared for the Pacific Northwest Research Station, US Forest Service. University of California, Davis.

Thorne, James, M. McCoy, A. Hollander, N. Roth, and J. Quinn. 2005.Regional Analysis for Transportation Corridor Planning. Proceedings of the International Conference on Environment and Transportation, San Diego, CA. 

Thorne, J.H., D. Cameron, V. Jigour. 2002. A Guide to Wildlands Conservation in the Central Coast Region of California. CaliforniaWilderness Coalition, Davis CA. http://cain.ice.ucdavis.edu/repository/CC.pdf

Davis F. W., D. M Stoms, A. D. Hollander, K.A. Thomas, P.A. Stine, D. Odion, M. I. Borchert, J. H. Thorne, M. V. Gray, K. Warner, and J. Graae. 1998. The California Gap Analysis Project – Final Report. June 30, 1998. Universityof California, Santa Barbara. http://www.biogeog.ucsb.edu/projects/gap/gap_home.html

Thorne, J.H. 1997. GAP Analysis: the vegetation of northwest California. Master’s thesis. University of California, Santa Barbara.




Published Conference Proceedings and Presentations

Thorne, JH, J. Bjorkman, MJ Santos. Which produces less-impacting patterns of urban growth, targeted or general public policies. Ecological Society of American, Annual Meeting, Sacramento, CA. Accepted

Choe, H., JH Thorne, C Seo. 2014. Plant biodiversity and conservation assessment in South Korea using rarely recorded data and a multi-response species distribution model. Ecological Society of America Annual Meeting, Sacramento, CA. Accepted

Thorne, JH, J Bjorkman, PR Huber, E O’Donoghue. 2013. Cross-testing transferability of national mitigation planning tools with California’s Regional Advance Mitigation Planning (RAMP) framework on a new pilot region (450 miles of US 101). International Conference on Environment and Transportation, Scottsdale, AZ.

Huber, PR, JH Thorne, NR Siepel. 2013. Convergence of Green- and Blueprints: Integrating Long Range Transportation Planning and Landscape Connectivity. International Conference on Environment and Transportation, Scottsdale, AZ.

Santos, M.J., J.H. Thorne, Z. Frank & J. Christensen. 2012. Reconstructing the conservation history of California over the last 80 years. Ecological Society of America. Portland, OR USA.

Santos, M.J., J.H. Thorne, Z. Frank & J. Christensen. 2012. Reconstructing the conservation history of the San Francisco Bay Area over the last 80 years. North American Conference on Conservation Biology, Oakland, CA USA.

Santos, MJ, JH Thorne, C Moritz. 2011. Do changes in habitat predict observed changes in small mammals in Yosemite National Park? Ecological Society of America, Austin, Texas, USA

Santos, M.J., J. H. Thorne & C. Moritz. 2011. Do changes in habitat predict observed changes in small mammals in Yosemite National Park? Ecological Society of America, Austin, Texas, USA.

Thorne, J.H. & M.J. Santos. 2011. Historic and contemporary landcover, urban areas and protected areas as a framework for regional conservation planning. Ecological Society of America, Austin, Texas, USA.

Santos, M.J., J. Bjorkman, R. Branciforte, L. Orman, J. Christensen & J.H. Thorne. 2011. Conservation history of the Bay Area: when and what was conserved over the last 80 years. Bay Area Conservation Symposium. UC Berkeley

Thorne, JH, MJ Santos, J MacKenzie. 2011. Conservation in metropolitan regions: assessing trends and threats of development and climate change. Ecological Society of America, Austin, TX.

Thorne, JT, E. O’Donoghue, PR Huber, M McCoy. 2011. Moving forward, a review of California’s approaches to the challenges and solutions for successful regional advance mitigation planning. International Conference on Ecology and Transportation, Seattle, WA.

Huber, PR, DR Cameron,  JH Thorne, TM Frink. 2011. Regional advance mitigation planning: a pilot study integrating multi-agency mitigation needs and actions within a comprehensive ecological framework. International Conference on Ecology and Transportation, Seattle, WA.

Santos, M.J., J. Bjorkman, R. Branciforte, L. Orman, J. Christensen & J.H. Thorne. 2011. Conservation history of the Bay Area: when and what was conserved over the last 80 years. Bay Area Conservation Symposium. UC Berkeley.

Crimmins, SM, S. Dobrowski, AR Mynsberge, JH Thorne. 2010. 20th century shifts in optimum elevations of California plants: the importance of spatial scale. Ecological Society of America Meeting, Pittsburgh, PA.

Thorne, JH, S Dobrowski, HD Safford. 2010. Hardwood expansion along a conifer-oak ecotone. Ecological Society of America Meeting, Pittsburgh, PA.

Dobrowski, S, JH Thorne, J Greenberg, HD Safford, AR Mysenbridge, SM Crimmins. 2010. Predicting the present from the past: Modeling plant species distributions over 75 years of measured climate change in California, USA. Ecological Society of America Meeting, Pittsburgh, PA.

Yacoub, R., T Keeler-Wolf, JH Thorne. 2010. Using legacy datasets to analyze changes in vegetation distribution: examples and considerations. Ecological Society of America Meeting, Pittsburgh, PA.

Matthew L. Forister (1), Andrew C. McCall (2), Nathan J. Sanders (3), James A. Fordyce (4), James H. Thorne (5), Joshua O'Brien (6), David P. Waetjen (7), and Arthur M. Shapiro (8). 2010. Patterns of richness and decline: 35 years of butterflies along an altitudinal transect in Northern California. 6th International Conference on the Biology of Butterflies, University of Alberta

Huber, P.R., F.M. Shilling, J.H. Thorne, S.E. Greco, J.F. Quinn, N.E. Roth, J.D. Hightower, L. Podolsky. 2010. Incorporating landscape connectivity principles into planning at multiple spatial scales in an intensive agricultural region.  International Association for Landscape Ecology. Athens, Georgia.

Boynton, R.,J.H.Thorne et al. 2010Measuring the Fragmentation of China's Landscape Using Effective Mesh Size. ESRI Users conference, Riverside CA. Accepted.

Thorne, J.H. 2010. 70 Years of Vegetation Dynamics and climate change in the Sierra Nevada. The Wildlife Society, Visalia, CA. Plenary talk.


Beardsley, K. J.H. Thorne, J. F. Quinn. 2009. Estimating Greenhouse Gas (GHG) Emissions in 2050 from New Buildings in California. American Geophysical Union Fall Meeting, San Francisco.

T. Diamond, C. McFarland, J. Thorne, J. Keller, D. Myers, and J. Devers. 2009. California Central Coast Wildlife Connectivity Project: Identifying and implementing connectivity for wildlife movement throughout the Central Coast of California. The Wildlife Society, Western Chapter, Monterey CA.

Thorne, J. H. 2009. Vegetation Shifts in the Sierra Nevada over the past 100 years. California Energy Commission’s Climate Change Conference, Sacramento, CA.

Thorne, J.H. 2009. Stories from California: using vegetation plot data for biodiversity studies, mapping, landcover change and climate studies. Workshop of Biodiversity and Protection Areas – About Habitat Modelling. Graduate School of Environmental Studies, Seoul National University, Seoul North Korea. Invited Keynote.

Bjorkman, J., J. H. Thorne. 2009. Landscape Change in the Bay Area. ESRI User Conference.

P. R. Huber, D. Cameron, J. H. Thorne, T. M. Frink. 2009. Regional Advance Mitigation Planning: a Pilot Study Integrating Multi-agency Mitigation Needs and Actions Within a Comprehensive Ecological Framework. International Conference on Ecology and Transportation. Duluth, MN.

Thorne, J. H., S. E. Cameron. 2008. Three scales of vegetation response to climate change and fire over the past 70 years. Yosemite National Park Hydroclimatology Conference, CA.

Thorne, J. H. 2008. Use of Oaks in Urban and Rural Restoration Settings. Annual Oak Restoration Symposium, Sierra Foothills Research Station, University of California.

Thorne, J. H., J. Bjorkman, R. Boynton, S. Thrasher. 2008. Observed Changes in Vegetation Patterns in California. California Energy Commission’s Second Annual Climate Change Conference, Sacramento, CA.

Thorne, J.H., S. Dobrowski, R. Boynton, S. Thrasher, J. Bjorkman, H. Safford. 2008. Ecotones and Vegetation Bands – 70 years of vegetation dynamics in the Sierra Nevada. California Society for Ecological Restoration, Santa Rosa, CA. Invited talk.

Thorne, J.H., S. Dobrowski, H. Safford. 2008. Comparing 70 year old vegetation maps in California: lessons from the Sierra Nevada and Bay Area. Ecological Society of America Meetings, Milwaukee, WI. Invited talk.

Seo Changwan, J. H. Thorne, L. Hannah, W. Thuiller. 2008. "Scale Sensitivity of Species Distribution Models for Conservation Planning", 28th Annual Conference International Association for Impact Assessment, 4-10 May 2008, Perth, Western Australia 2008

Bjorkman, J., J.H. Thorne, S. Thrasher, R. Boynton. 2008. Landscape change in the Bay Area: using historic maps to show vegetation change.  10th Annual Bay Area Conservation Biology Symposium, Davis, CA.

Girvetz, E. H., J.A.G. Jaeger, J. H. Thorne, A.M. Berry. 2007. Integrating habitat fragmentation analysis into transportation planning using the effective mesh size landscape metric.

Paper to the International Conference on Ecology and Transportation.

Thorne, J. H., E. H. Girvetz, and M. McCoy. 2007. A multi-scale and context sensitive state-wide environmental mitigation planning tool for transportation projects in California. Paper to the International Conference on Ecology and Transportation.

Ries, L. P., L. Hannah, C. Seo, J. H. Thorne, F. Davis, 2007, A dynamic species modeling approach to assess climate change impacts on California tree species, American Geophysical Union Annual Meeting; Dec 10-14, S. F, CA

Seo, C., J. H. Thorne, L. Hannah, W. Thuiller 2007, Climate Change and Biodiversity Conservation Planning : Species Distribution Models Applications, Vietnam-Korea EIA Workshop,   December 6-8, 2007, Hanoi, Vietnam.

Hannah, L., C. Seo, G. Midgley, J. H. Thorne, D. Stoms, I. Davies, W. Thuiller, N. Snider, F. W. Davis, 2006, Dynamic Modeling of Climate Change Impacts on California Endemic Tree Species, Third  Annual Climate Change Research Conference, September 13-15, 2006, Sacramento, California.

Ries,  L., Lee Hannah, C. Seo, J. H. Thorne, Frank W. Davis, David Stoms, 2007, Dynamic species modeling; Predicting CA vegetation niches under climate change, Fourth Annual California Climate Change Conference, September 10-13, 2007, Sacramento, California.

Thorne, J. H., S. Dobrowski, H. Safford. 2007. A 70 year review of landscape change across the Sierra Nevada. Ecological Society of America, San Jose, CA. 

Cameron, S. E., J. H. Thorne. 2007. Influence of fire and climate change on vegetation in a mountainous national park. Ecological Society of America, San Jose, CA.

Huber, P., N. E. Roth, K. Beardsley, J. H. Thorne, M. McCoy, R. Meade. 2007. Potential impacts of urban growth on an ecological network in the San Joaquin Valley, California. American Association of Geographers, San Francisco, CA.

Seo C., J. H. Thorne, D. Stoms, W. Thullier, F. Davis, and L. Hannah. 2007. Model selection for predictive species range mapping. IAEA, Korea.

Thorne, J. H. 2007. Retreat of the trailing edge of ponderosa pine forests in the Sierra Nevada over 140 years. The Wildlife Society Meetings, Monterey. Invited Talk.

Thorne, J. H. and T.R. Kelsey. 2006. 140 Dynamics of a Forest Ecotone under climate and environmental change. American Geophysical Union Meeting, San Francisco. Invited talk.

Thorne, James. 2006. Forest Change over 140 Years in the Central Sierra Nevada. Ecological Society of America Meeting. Memphis, TN.

Hannah, L., J.H. Thorne, C. Seo, D. Stoms, I. Davies, G. Midgley, W. Thullier and F. Davis. 2005. Modeling climate change impacts on biodiversity.  California Energy Commission’s Second Annual Climate Change Conference, Sacramento, CA.

Thorne, J.H. and B.J. Morgan. 2005. Developing historical vegetation maps to support modeling in California. California Energy Commission’s Second Annual Climate Change Conference, Sacramento, CA.

Thorne, James, Joshua Obrien, Mathew Forister, Arthur Shapiro. 2005. Butterfly community phenology across an altitudinal transect. Ecological Society of America Meeting.

O'Brien, Joshua, Forister, Matthew, Thorne, J., Shapiro, Arthur. 2005. Detection of long-term changes in an alpine butterfly community using non-parametric bootstrap methods. Ecological Society of America Meeting.

Quinn, James, Hollander, Allan, Thorne, James, Viers, Joshua. 2005. SPIRE: Semantic Web applications for biodiversity and invasive species. Ecological Society of America Meeting

Anderson, Kayce, Forister, Matthew, Shapiro, Arthur, O'Brien, J, Thorne, J. 2005. Urban boundaries in a biodiversity hotspot: Declining butterfly diversity in California's modified Central Valley. Ecological Society of America Meeting.

Viers, Joshua, Thorne, James, Vaghti, Mehrey, Quinn, James. 2005. Patterns of regional and local diversity in the California Bay-Delta ecoregion and its watersheds: Lessons for riparian restoration and monitoring. Ecological Society of America Meeting.

Thorne, James. 2004. A Conservation Design for the Central Coast of California using modeled cores and corridors for mountain lion (Felis concolor). Society for Conservation Biology, UC Davis.


Review and Editorial Activities

Reviewer for International Scientific Journals

            Global Change Biology (2007)

  Ecology (since 2006)

            Biogeography (since 2005)

            Oikos (since 2006)

            Landscape and Urban Planning (2007)


Professional Activities

2005-present    Advisor to ecosystem connectivity initiatives in the Santa Cruz Mountains area.

2004-present    Advisor to oak conservation program in Yolo County


California State Legislature & University of California, Davis- Outstanding Staff Award. 2007. For most dedicated Community Service staff member from the University of California, Davis.


Dissertations and Theses Supervised


Ph. D. Dissertations: Committee member (4)

Masters Theses: Committee member (2)

Graduate Students Advised

Melissa Whitaker- MA studying butterfly populations

Michael McGrann- PhD studying plants of the Sierra Nevada

Nate Roth - PhD studying economic impacts of urban growth.

Karen Willet-PhD Completed 2009. Use of Urban Growth Models to simulate policy and assess impacts of future growth on biotic resources.

Patrick Huber- PhD Geography, UCD 2009. Now a post-doc working with me on conservation assessment and network design.

Ethan Inlander, MA Geography, UCSB. 2004. Now GIS specialist for TNC, Arkansas.


Classes Taught at Graduate and Undergraduate Level


As Instructor:

  1. Week long training course in Karst cave conservation in Spanish for The Nature Conservancy in the Dominican Republic. 2008
  2. Training Courses (5) in English and French for Park Rangers from 15 countries in Africa. Dec. 2003-  Dec. 2004. Instruction in how to set up the computational data entry for the MIKE (Monitoring Illegal Killing of Elephants) program.  I helped design, then teach two levels of computer orientation, database use and GIS orientation. Courses were taught in Kenya, Cameroon and Niger. Contact Karen Beardsley– University of California, Davis coordinator for education component of the MIKE program. 530-752-5678
  3. Conservation and GIS. I taught an upper division course on the uses of GIS in conservation projects at UC Santa Barbara. Contact Ethan Inlander 479-973-9110, co-presenter.
  4. Ran an internship program at UCSB for students to help register 25 years of bird observation records stored at the Vertebrate Natural History Museum. Contact John Gallo gallo@geog.ucsb.edu.


Co-taught, or as Teaching Assistant

  1. Ecological Field Methods – Dr. Jim Quinn, UC Davis 2002, 2003
  2. Vegetation of California- Dr. Michael Barbour, UC Davis 2002
  3. Biogeography, upper division, undergraduate- Dr. Frank Davis, UCSB 1996
  4. Physical Geography- Dr. Jeff Dozier UCSB 1996
  5. Introduction to Environmental Studies- Social Systems- Dr. Robert Hatherill, UCSB 1995, 1996
  6. Introduction to Environmental Studies- Physical Systems- UCSB 1995.


Countries & States worked in

Have worked extensively in the national parks in Alaska.

South Korea: am advising the National Institute of Environmental Research (NIER) on their biological survey protocols, and co-authoring papers on Asiatic black bear reintroductions and road kill monitoring.

Cameroon, Kenya, Niger: Trained Park Wardens in database use and GPS as part of ‘Monitoring Illegal Killing of Elephants.

Mongolia: field studies of impacts of Gold Mining on rivers containing world’s largest salmon, Hucho taimen taimen.

Chile, Argentina: 3 month field examination of conservation conditions in the southern temperate rainforests.

Ecuador, Costa Rica, Guatemala: Studied what makes conservation projects successful.

Domican Republic, training of cave conservation biologists.

Canada: studied old growth coastal forests on mid-coast of British Columbia, involved in campaign to create the Tatshinshini Provincial Park.

Mexico: Extensive expedition experience in the Copper Canyon region & Baja, California; served as translator for Lumi Indians (from Washington State) who were doing a trans-tribal training with the Lacandon Maya in southern Mexico. Translated from English to Spanish. Another translator then translated to Mayan.

California-Based Projects 

Have worked in all terrestrial ecoregions of California, including:

1) Survey of potential UC reserve sites in Modoc Plateau;

2) Vegetation mapping and plot surveys in Klamath & Shasta/Trinity National Forests;

3) Field surveys of vegetation for the California GAP Analysis Program- Sierra Nevada, East Side, North Coast, Central Coast;

4) National Park Service studies of effects of acid rain and forest monitoring – Sequoia National Park;

5) Supervised surveying of over 1100 vegetation plots in the Mojave & Sonoran Desert regions, included coordinating surveys on 3 national parks (Death Valley, Joshua Tree and Mojave National Preserve), 4 military bases (Naval Air Warfare Center Weapons Division China Lake, Edwards Air Force Base, Fort Irwin, and the Marine Corps Air Ground Combat Center), 2 nature reserves (Granite MountainsPreserve & Desert Research Center), and the BLM lands;

6) Field surveys of mountain lion suitable habitat (core and corridors) in the Central Coast of California;

7) Herpetological field work in central and southern coastal California;

8) Teaching (TA) of field ecology and vegetation courses in central and southern California, and the north coast;

9) Oak restoration and long term studies in the Central Valley of California;

10) First state-wide existing vegetation & conservation lands (GAP Analysis Project);

11) Development of CalJep, a geodatabase of the distributions of 7887 California plants;

12) Assembly of over 25,000 vegetation plots surveyed by various researchers & agencies;

13) Co-developed models of over 400 California plant ranges under current and future Climate;

            14) Oversight of development of county-by-county urban growth models projecting future urban growth in California under business as usual assumptions (ongoing);

            15) Development of the Wieslander Vegetation maps, originally surveyed in the 1930s covering 1/3 of the state (ongoing, Sierra Nevada and Bay Area completed);

            16) Created MCV 1 ha mmu vegetation map of Napa County

17) Development of a state-wide mitigation needs assessment database for Caltrans;

18) Development of 2 pilot projects assessing potential contributions of multi-project road mitigation efforts to regional conservation designs, for Caltrans.

 Professional Memberships

            Ecological Society of America

            American Geophysical Union

            Society for Conservation Biology, UC Davis Chapter

Selected Extra Curricular

Survey of old-growth forest plots, Mid-Coast, British Columbia, Canada. Summer 2003. I installed over 20 vegetation plots in remote locations accessed through the fjords near Bella Coola, British Columbia. Access was by boat, with targeted areas those slated for future logging.

Head of restoration committee of the UC Davis chapter of the Society for Conservation Biology, 2002-2006.

Participant- TNC workshops to identify conservation priorities on Central Coast of California.

President, UC Davis Chapter of Society of Conservation Biology, 2002-2003.

Co-founded the Conception Coast Project 1994-1996. This is a successful non-profit organization that provides GIS support and analysis for conservation projects in the Santa Barbara region. http://conceptioncoast.org/Conception_Coast_Project.html.

Mandolin Player in local bluegrass band, Ghost Pine Ramblers.

2003-2005  Post-Doctoral Position, Center for Applied Biodiversity Studies, Conservation International. Advisor: Lee Hannah.




Resources (Contributor)


Dataset: Monitoring

  • A collection of about 35 plot databases queried for presence of 340 California invasive plant species.
  • This dataset contains butterfly presence/absence data as well as abundance data from 11 sites ranging from the Sacramento River delta, through the Sacramento Valley and Sierra Nevada mountains, to the high desert of the western Great Basin. The data has been collected by Dr. Arthur Shapiro, regularly (approximately two-week intervals) since as early as 1972.