Education
2003-2005 Post-Doctoral Position, Center for Applied Biodiversity Studies, Conservation International. Advisor: Lee Hannah.
2003 Ph.D. Ecology, University California, Davis Advisors: Drs. James F. Quinn and Michael G. Barbour
1997 M. A. Geography, University of California, Santa Barbara Advisor: Dr. Frank Davis
1985 B.A. Environmental Studies, University of California, Santa Cruz 1986
Professional Interests
My professional interests include Landscape Ecology, Conservation Planning, Biogeography, Climate Change, Historical Ecology, Species Distribution Modeling, Phenology, Environmental Policy, Informatics, Urban Growth Modeling. Regions of experience include California, the US West, British Columbia, Alaska, Ecuador, Chile, Argentina. I speak English, French, and Spanish.
Current Projects
Publications coordinator, Information Center for the Environment (ICE), UC Davis I coordinate much of the GIS and model development undertaken 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. Since beginning this effort 8 months ago, seven manuscripts have been developed and are either published or submitted. This position also requires the assembly of manuscript teams, and identification of team members’ obligations for manuscript production.
California Department of Transportation (CalTrans), Regional Mitigation Assessment Methods Development & Urban Growth Modeling I am Lead Ecologist on a project assisting CalTrans to develop state-wide, regional, and local biological and ecological assessment capabilities. I coordinate scientific efforts of 6 team members on this project. We have assembled state-wide, district, county, and site specific data, and compiled them into a GIS. GIS outputs were converted to a database allowing the user to query the projected biological impacts for single or multiple projects, or for any of 6 levels of nested watersheds, counties or transportation planning districts. The multiple scales of GIS information provide the information to explore various trends relating to planned growth of the transportation infrastructure, and whether there are efficiencies to be gained by identifying species requiring mitigation at multiple sites. This permits either the most effective mitigation of all, avoidance, or permits regional planning for those species, which benefits both the projects and the species. We also developed Effective Mesh Size statistics for California watersheds, a calculation of landscape fragmentation that can be tied to biological movement requirements of different terrestrial vertebrates. These studies are being used to inform a group of agency regulators who are considering a historic permitting of advanced mitigation acquisition in the Elkhorn Slough watershed.
Wieslander Historical Vegetation Studies. I run a program with a staff of 6 to digitize 80-year old vegetation maps in California (the Wieslander Vegetation Type Maps). These 80-year old maps cover about 1/3 of California. My group has digitized maps covering ~80,000 km2 of the Sierra Nevada. We have developed landcover change detection techniques, and found large shifts related to climate change in conifer forest along the western lower edge of the Sierra Nevada. This forest trailing edge has shifted uphill 180 meters since the 1930s, and 500m since 1850. I have raised funds from a wide variety of agencies as both grants and competitive contracts, and have established a wide range of contacts throughout the state on this project. Funding sources include: the California Energy Commission, 7 US Forest Service units (Klamath, Lassen, Plumas, Tahoe, El Dorado, Tahoe Basin, & Regional) and two US National Parks (Lassen and Sequoia). We are examining relative differences in landcover change between private lands and lands managed by the US Forest Service and National Parks, and have a number of papers in press and in review.
Conservation International, Climate Change Studies. I collaborate with the Center for Applied Biodiversity Science, Conservation International (CABS, CI). We have modeled California plant response to climate change, for which we assembled climate surfaces and vegetation plot data (some 25,000) to parameterize species range models, which were projected for 400 California plant species for current and future climate conditions. These modeled species ranges will be used to run a spatially explicit, stage-based demographic model of dispersal called BioMove under climate change scenarios. The goal is to evaluate the chances different species have of keeping up with their shifting suitable environments under rapid climate change.
Landscape Fragmentation and Connectivity Planning. I am science advisor to a group of 8 studying what species are able to traverse highways around San Jose, CA, including bobcat, coyote and badger. Field crews set camera and video monitoring stations, and are assembling a GIS to examine impacts of proposed future urban growth on the species in the region. My involvement came about because of a conservation network design I did for mountain lion on the central coast of California, which indicated a corridor need in the area between the Santa Cruz Mountains and the inner coast range. We recently presented at a San Jose city council meeting, at which plans for development of 20,000 housing units in Coyote Valley were tabled pending further review of the biological data we presented, which invalidated the city’s Environmental Impact Report.
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 his 30 year study of butterfly phenology into a database and analyze the contents. We have over 80,000 species observation events from 10 sites forming a transect from San Francisco to the east side of the Sierra Nevada. I developed daily probability values for observing butterfly species at each site. These are used for comparative phenology, to examine potential daily species richness, and as a way to measure species decline. We have one paper published and several in review or development.
Oak Restoration & Long-Term Field Experiment I run a restoration project that provides seedling Valley Oak (Quercus lobata) to a wide range of restoration groups. Last year 6 different groups used our services. I also serve as lead ecologist on a 5 year grant from to study oak restoration practices in degraded California woodlands and savannahs. We installed two, 5-year planting experiments aimed at determining effective and cost effective restoration techniques for private land owners (predominantly ranchers) interested in restoration of Coast Live Oak (Quercus agrifolia), Blue Oak (Quercus douglasii), and Valley Oak on their properties. Planting locations are in the Coast Range in Solano and Yolo Counties. This program involves over 30 volunteers, agency and NGO groups.
National Biological Information Infrastructure, California Node. http://cain.nbii.org/portal/server.pt I co-directed the National Biological Information Infrastructure’s California Information Node, a website. The site, based at the UC Davis, Information Center for the Environment, is tasked with delivering biological information on-line. I participate the group’s vegetation mapping and data components, and have assisted the group in web publication of much of the material on the website. We recently posted digital range maps for 7887 California vascular plant taxa, derived from a plant geo-database I developed by crossing the plant names and spatial extents from the two major California Flora.
Manuscripts in Review
Thorne, J. H., J.H. Viers, J. Price, D. M. Stoms. Spatial patterns of endemic plants in California. Natural Areas Journal
Thorne, J. H., P. Huber, E. Girvetz, M. McCoy. Integration of regional mitigation assessment and conservation planning. Ecology and Society.
Huber, R. P., J. H. Thorne, N. E. Roth, M McCoy. Assessing the ecological condition and vulnerability of a potential conservation network in a working landscape. Ecology and Society.
Roth, R. J. H. Thorne, M. McCoy. Financial costs to agriculture and municipal governments of urban growth in an agricultural valley. Journal of the American Planning Association. In Revision
Beardsley, K., J. H. Thorne, N. E. Roth, M. McCoy. Impact of Rapid Human Population Growth on Biological Resources in the San Joaquin Valley of California. Landscape and Urban Planning. In Revision.
Selected Publications
Williams, J. N., J. K. Nelson, S. Erwin, C. Seo, J. M. O’Brien, J. H. Thorne, M. W. Schwartz. Predicting occurrences of six narrowly endemic serpentine-associated plants of the northern California Coast Range. Diversity and Distributions. Accepted
Thorne, J. H., E. H. Girvetz, and M. McCoy. Evaluating aggregate terrestrial impacts of road construction projects for advanced regional mitigation. Environmental Management. Accepted.
Seo, C., J. H. Thorne, L. Hannah, W. Thuiller. Scale effects in species distribution models; implications for planning under climate change. Biology Letters. In Press
Thorne, J. H., B. J. Morgan, and J. A, Kennedy. Vegetation Change over 60 Years in the Central Sierra Nevada. Madroño. In Press.
Harrison, S., J. H. Viers, J. H. Thorne, J. B. Grace. 2008. Favorable Environments and the Persistence of Naturally Rare Species. Conservation Letters 1: 65-74. http://www3.interscience.wiley.com/journal/118902559/home
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 D 11(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 Francisco Estuary 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 Management 1(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.
Davis F. W., et al. 1999. Gap Analysis of Mainland California: An Interactive Atlas of Terrestrial Biodiversity and Land Management. An Interactive CD copyright Environmental Systems Research Institute, Inc.
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. University of California, Santa Barbara.
Thorne, Jim, David Stoms, and Frank Davis. 1996. The Northwestern Region. In: Geographic Information Systems Analysis of the Biodiversity of California. Report to the National Fish and Wildlife Foundation, 132-141.
Peer Reviewed Technical Reports
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.
Thorne, J., J. Bjorkman, S. Thrasher, R. Kelsey, and B. J. Morgan. 2007. 1930s extent of oak species in the central Sierra Nevada. US Forest Service General Technical Report. In Press
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. California Wilderness Coalition, Davis CA.
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. University of California, Santa Barbara.
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, 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.
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.
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.
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. Model selection for predictive species range mapping. IAEA, Korea 2007.
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.
California-Based Experience
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 Mountains Preserve & 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.
Other Experience
Domincan Republic: assisting The Nature Conservancy in global training of Karst Inventory and Conservation.
Have worked extensively in the national parks in Alaska.
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.
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.
