Jim Clark, Professor of Global Environmental Change and Statistical Science

Jim Clark

Research Emphasis:

Consequences of climate, CO2, and disturbance on dynamics of forests.

CWT Committees:

CWT Science Advisory Committee

Contact Information:

Primary Organization:  Duke University

Mailing Address:

Dr. James S. Clark
Nicholas School of the Environment
Department of Statistical Science
Durham, NC 27706

Office Phone:  919.613.8036

E-Mail:  jimclark@duke.edu

Web Page:  https://sites.nicholas.duke.edu/clarklab/people/

CWT Data Sets:

1047 (Climate Vulnerability of Southern Appalachian Forests)

1300 (Microclimate data from stations within the Great Smoky Mountains National Park, NC)

1046 (Tree census, demography, and exposed canopy area data at the Coweeta LTER Terrestrial Gradient Sites, Coweeta Hydrological Laboratory, Otto, NC from 1993 to 2014)

1113 (Manual soil moisture measurements from ten artificial forest gaps at the Coweeta Hydrologic Laboratory, North Carolina , 2000-2014)

1114 (Continuous microclimate measurements from Forest Site J, Coweeta Hydrologic Laboratory, North Carolina, 2007-2016.)

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CWT Publications and Presentations: (custom bibliography)

Journal Articles

Aaron B. Berdanier, Chelcy F. Miniat, and James S. Clark, (2016) Predictive models for radial sap flux variation in coniferous, diffuse-porous and ring-porous temperate trees Tree Physiol. 36 (8): 932-941 doi:10.1093/treephys/tpw027

Bell, D.M. & Clark, J.S. (2016), Seed predation and climate impacts on reproductive variation in temperate forests of the southeastern USA, Oecologia 180: 1223. doi:10.1007/s00442-015-3537-6

Berdanier, A. and J.S. Clark. 2016. Multi-year drought-induced morbidity preceding tree death in Southeastern US forests. Ecological Applications 26(1):17-23. doi: 10.1890/15-0274.1

Berdanier, A. B., and J. S. Clark. 2016. Divergent reproductive allocation trade-offs with canopy exposure across tree species in temperate forests. Ecosphere 7(6):e01313. 10.1002/ecs2.1313

Clark, J. S. (2016), Why species tell more about traits than traits about species: predictive analysis. Ecology, 97: 1979–1993. doi:10.1002/ecy.1453

Schliep, Erin M., Alan E. Gelfand, James S, Clark and Kai Zhu, 2015, Modeling change in forest biomass across the eastern US, Environmental and Ecological Statistics, pp 1-19,10.1007/s10651-015-0321-z

Zhu, K., C. Woodall, and J.S. Clark. 2015. Prevalence and strength of density-dependent tree recruitment, Ecology 96(9):2319-2327.

Clark, J.S., D.M. Bell, M.C. Kwit, and K. Zhu. 2014. Competition-interaction landscapes for the joint response of forests to climate change. Global Change Biology, 20, 1979-1991.

James S. Clark, Alan E. Gelfand, Christopher W. Woodall, and Kai Zhu 2014. More than the sum of the parts: forest climate response from joint species distribution models. Ecological Applications 24:990 - 999. http://dx.doi.org/10.1890/13-1015.1

Wu, W., Clark, J.S., and J. Vose. 2014. Response of hydrology to climate change in the southern Appalachian Mountains using Bayesian inference. Hydrologic Processes, 28, 1616-1626.

Zhu, K, C. W. Woodall, S. Ghosh, A. E. Gelfand, and J. S. Clark. 2014. Dual impacts of climate change: forest migration and turnover through life history. Global Change Biology, 20:251-264.

Clark, J.S., D. M Bell, M. Kwit, A. Powell, And K. Zhu. 2013. Dynamic inverse prediction and sensitivity analysis with high-dimensional responses: application to climate-change vulnerability of biodiversity. Journal of Biological, Environmental, and Agricultural Statistics, 18:376-404.

Clark, James S., David M. Bell, Matthew Kwit, A., Anne Stine, Ben Vierra, and Kai Zhu. 2012. Individual scale inference to anticipate climate change vulnerability of biodiversity. Philosophical Transactions of the Royal Society B 367:236-246.

Clark, J.S. 2012. The coherence problem with the Unified Neutral Theory of Biodiversity. Trends in Ecology and Evolution, 27:198-202.

Clark, J.S., B.D. Soltoff, A.S. Powell, and Q.D. Read. 2012. Evidence from individual inference for high-dimensional coexistence: long term experiments on recruitment response. PLoS One, 7 e30050. doi:10.1371/journal.pone.0030050.

Clark, J.S., D. M. Bell, M. Kwit, A. Powell, R. Roper, A. Stine, B. Vierra, and K. Zhu. 2012. Individual-scale inference to anticipate climate-change vulnerability of biodiversity. Philosophical Transactions of the Royal Society B, 367, 236-246.

Ghosh, S., A.E. Gelfand, K. Zhu, and J.S. Clark. 2012. The k-ZIG: flexible modeling for zero-inflated counts. Biometrics, on-line edition.

Ghosh, S., Gelfand, A. and Clark, J.S. 2012. Inference for size demography from point pattern data using integral projection models. Journal of Agricultural, Biological and Environmental Statistics. (DOI: 10.1007/s13253-012-0121-y)

Hersh, M.H., J.S. Clark, and R. Vilgalys. 2012. Evaluating the impacts of fungal seedling pathogens on temperate forest seedling survival. Ecology, 93: 511-520.

Moran, E. and Clark, J.S. 2012. Between-Site Differences in the Scale of Dispersal and Gene Flow in Red Oak. PLoS ONE. 7(5):e36492. (DOI: 10.1371/journal.pone.0036492)

Moran, E.V. and J.S. Clark. 2012. Causes and consequences of unequal seed production in forest trees: a case study in red oaks. Ecology. 93(5):1082-1094.

Moran, E.V., J. Willis, and J.S. Clark. 2012. Genetic evidence for hybridization in red oaks. American Journal of Botany. 99(1):92-100.

Uriarte M., J. S. Clark, J. K. Zimmerman, L. S. Comita, J. Forero-Montaña, and J. Thompson. 2012. Multi-dimensional tradeoffs in species responses to disturbance: Implications for diversity in a subtropical forest. Ecology. 93(1):191-205

Wu, W., Clark, J.S. and Vose, J.M. 2012. Application of a full hierarchical Bayesian model in assessing streamflow response to a climate change scenario at the Coweeta Basin, NC, USA. Journal of Resources and Ecology. 3(2):118-128. (DOI: http://dx.doi.org/10.5814/j.issn.1674-764x.2012.02.003)

Zhu, K., C.W. Woodall, and J.S. Clark. 2012. Failure to migrate: lack of tree range expansion in response to climate change. Global Change Biology, DOI: 10.1111/j.1365-2486.2011.02571.x

Clark, J.S., D.M. Bell, M.H. Hersh, and L. Nichols. 2011. Climate change vulnerability of forest biodiversity: climate and resource tracking of demographic rates. Global Change Biology, 17, 1834-1849.

Clark, J.S., D.M. Bell, M.H. Hersh, M. Kwit, E. Moran, C. Salk, A. Stine, D. Valle, and K. Zhu. 2011. Individual-scale variation, species-scale differences: inference needed to understand diversity. Ecology Letters 14, 1273-1287.

Clark, J.S., P. Agarwal , D.M. Bell , P. Flikkema , A. Gelfand , X. Nguyen , E. Ward , and J. Yang. 2011. Inferential ecosystem models, from network data to prediction. Ecological Applications, 21,1523-1536.

Luo,Y. K. Ogle, C. Tucker, S. Fei, C, Gao, S. Ladeau, J. S. Clark, and D. S. Schimel. 2011. Ecological forecasting and data assimilation in a data-rich era. Ecological Applications 21, 1429–1442.

Moran, Emily V. and James S. Clark. 2011. Estimating seed and pollen movement in a monoecious plant: a hierarchical Bayesian approach integrating genetic and ecological data. Molecular Ecology 20:1248-1262.

Wu, W., J.S. Clark, and J. Vose. 2011. Assimilating multi-source uncertainties of a parsimonious conceptual hydrological model using hierarchical Bayesian modeling. Journal of Hydrology, 394, 436-446.

Clark, J.S., D. Bell, C. Chu, B. Courbaud, M. Dietze, M. Hersh, J. HilleRisLambers, I. Ibanez, S. L. LaDeau, S. M. McMahon, C.J.E. Metcalf, J. Mohan, E. Moran, L. Pangle, S. Pearson, C. Salk, Z. Shen, D. Valle, and P. Wyckoff. 2010. High dimensional coexistence based on individual variation: a synthesis of evidence. Ecological Monographs, 80:569-608

Clark, James S. 2010. Individuals and the Variation Needed for High Species Diversity in Forest Trees. Science, 327: 1129-1132.

Luo, Y., S. Niu, J. Melillo, C. Beier, J.S. Clark, A. Classen, E. Davidson, J. S. Dukes, D. Evans, C. Field, C. I. Czimczik, M. Keller, L. Kueppers, R. Norby, S. L. Pelini, E. Pendall, E. Rastetter, J. Six, M. Smith, M. Tjoelker, M. Torn. 2010. Coordinated approaches to quantify Long-Term Ecosystem dynamics in response to global change. Global Change Biology, in press.

Vieilledent, G., B. Courbaud, G. Kunstler, J.-F. Dhote, and J.S. Clark. 2010. Individual variability in tree allometry determines light resource allocation in forest ecosystems: a hierarchical Bayesian approach. Oecolgia, in press.

Clark, J.S. and M. H. Hersh. 2009. Inference when multiple pathogens affect multiple hosts: Bayesian model selection. Bayesian Analysis 4:337 - 366

Colchero, F., R. A. Medellin, J. S. Clark, R. Lee, and G. G. Katul. 2009. Predicting population survival under future climate change: density dependence, drought and extraction in an insular bighorn sheep. Journal of Animal Ecology, 78:666-673.

Cressie, N., C. A. Calder, J. S. Clark, J. M. Ver Hoef, and C. K. Wikle. 2009. Accounting for uncertainty in ecological analysis: the strengths and limitations of hierarchical statistical modeling. Ecological Applications, 19:553-570.

Ibanez, I., Clark, J.S., Dietze, M.C. 2009. Estimating colonization potential of migrant tree species. Global Change Biology. 15: 1173-1188

James S. Clark. 2009. Beyond Neutral Science. Trends in Ecology and Evolution, 24 (1): 8-15

McMahon, S. M., M. C. Dietze, M. H. Hersh, E. V. Moran, and J. S. Clark. 2009. A predictive framework to understand forest responses to global change. Pages 221-236 in R. Ostfeld and W.H. Schlesinger (eds) Year in Ecology and Conservation Biology 2009.

Metcalf, C.J.E., J. S. Clark, and D. A. Clark. 2009. Tree growth inference and prediction when the point of measurement changes: modelling around buttresses in tropical forests. Journal of Tropical Ecology, 25:1-12.

Metcalf, C.J.E., J. S. Clark, and S. M. McMahon. 2009. Overcoming data sparseness and parametric constraints in modeling of tree mortality: a new non-parametric Bayesian model. Canadian Journal of Forest Research, 39, 1677-1687.

Noel, C., Calder, C., Clark, J., Ver Hoef, J., Wikle, C. 2009. Accounting for uncertainty in ecological analysis: the strengths and limitations of hierarchical statistic modeling. Ecological Applications, 19(3): 553-570

Vieilledent, G., B. Courbaud, G. Kunstler, J.-F. Dhôte, and J. S. Clark. 2009. Biases in the estimation of size dependent mortality models: advantages of a semi-parametric approach. Canadian Journal of Forest Research, 39, 1430-1443.

Dietze, M.C., Clark, J.S. 2008. Changing the Gap Dynamics Paradigm: Vegetative Regeneration Control on Forest Response to Disturbance. Ecological Monographs 78(3) 331-347.

Dietze, M.C., Wolosin, M.S., Clark, J.S. 2008. Capturing diversity and interspecific variability in allometries: A hierarchical approach. Forest Ecology and Management 256: 1939-1948

Ibanez, I., Clark, J.S., Dietze, M.C. 2008. Evaluating the Sources of Potential Migrant Species: Implications Under Climate Change. Ecological Applications, 18(7): 1664-1678.

Clark, J.S., M. Dietze, S. Chakraborty, P.K. Agarwal, I. Ibanez, S. LaDeau, and M. Wolosin. 2007. Resolving the biodiversity paradox. Ecology. 10: 647-662.

Clark, J.S., M. Wolosin, M. Dietze, I. Ibanez, S. LaDeau, M. Welsh, and B. Kloeppel. 2007. Tree growth inference and prediction from diameter censuses and ring widths. Ecological Applications 17(7): 1942-1953.

Dietze, M. and J. S. Clark. 2007. Rethinking gap dynamics: the impact of damaged trees and sprouts. Ecological Monographs 78:331-347.

Ibanez, I., J.S. Clark, S. LaDeau, and J. Hille Ris Lambers. 2007. Exploiting temporal variability to understand tree recruitment response to climate change. Ecological Monographs. 77(2): 163-177.

Beckage, B., and J. Clark. 2005. Does predation contribute to tree diversity? Oecologia. 143: 458-469.

Beckage, B., M. Lavine, and J. Clark. 2005. Survival of tree seedlings across space and time: estimates from long-term count data. Journal of Ecology. 93: 1177-1184.

Clark, J.S. 2005. Why environmental scientists are becoming Bayesians. Ecology Letters. 8: 2-14.

Hille Ris Lambers, J., and J.S. Clark. 2005. The benefits of seed banking for red maple (Acer rubrum): maximizing seedling recruitment. Canadian Journal Forestry Research. 35: 806-813.

Hille Ris Lambers, J., J.S. Clark, and M. Lavine. 2005. Implications of seed banking for recruitment of southern Appalachian woody species. Ecology. 86(1): 85-95.

Wyckoff, P.H., and J.S. Clark. 2005. Tree growth prediction using size and exposed crown area. Canadian Journal of Forest Research. 35: 13-20.

Clark, J.S., S. LaDeau, and I. Ibanez. 2004. Fecundity of trees and the colonization-competition hypothesis. Ecological Monographs. 74(3): 415-442.

Mohan, J.E., J.S. Clark, and W.H. Schlesinger. 2004. Genetic variation in germination, growth, and survivorship of red maple in response to subambient through elevated atmospheric CO2. Global Change Biology. 10: 233-247.

Beckage, B., and J.S. Clark. 2003. Seedling survival and growth of three forest tree species: the role of spatial heterogeneity. Ecology: 84(7): 1849-1861.

Clark, J.S., J. Mohan, M. Dietze, I. Ibanez. 2003. Coexistence: How to identify trophic trade-offs. Ecology. 84(1): 17-31.

Hille Ris Lambers, J., and J.S. Clark. 2003. Effects of dispersal, shrubs, and density-dependent mortality on seed and seedling distributions in temperate forests. Canadian Journal Forestry Research. 33: 783-795.

Hille Ris Lambers, J., J.S. Clark, and B. Beckage. 2002. Density-dependent mortality and the latitudinal gradient in species diversity. Nature. 417: 732-735.

Hille Ris Lambers,J, JS Clark, and B Beckage. 2002. Density dependent mortality and the latitudinal gradient in species diversity. Nature 417:732-735.

Lavine, M., B. Beckage, and J.S. Clark. 2002. Statistical modeling of seedling mortality. Journal of Agricultrual, Biological, and Environmental Statistics. 7(1): 21-41.

Wyckoff, P.H., and J.S. Clark. 2002. The relationship between growth and mortality for seven co-occurring tree species in the southern Appalachian Mountains. Journal of Ecology. 90: 604-615.

Clark, J, L. Horvath, and M. Lewis. 2001. On the estimation of spread rate for a biological population. Statistics & Probability Letters. 51: 225-234

Clark, J.S., M. Lewis, and L. Horvath. 2001. Invasion by extremes: Population spread with variation in dispersal and reproduction. The American Naturalist. 157(5): 537-554.

Clark, J.S., S.R. Carpenter, M. Barber, S. Collins, A. Dobson, J.A. Foley, D.M. Lodge, M. Pascual, R. Pielke Jr., W. Pizer, C. Pringle, and W. Reid. 2001. Ecological Forecasts: An Emerging Imperative. Science. 293: 657-660.

Beckage, B., J.S. Clark, B.D. Clinton, and B.L. Haines. 2000. A long-term study of tree seedling recruitment in southern Appalachian forests: the effects of canopy gaps and shrub understudies. Canadian Journal Forestry Research. 30: 1617-1631.

Knoepp, J.D., D.C. Coleman, D.A. Crossley Jr., and J.S. Clark. 2000. Biological indices of soil quality; an ecosystem case study of their use. Forest Ecology and Management. 138: 357-368.

Wyckoff, P.H. and J.S. Clark. 2000. Predicting tree mortality from diameter growth: a comparison of maximum likelihood and Bayesian approaches. Canadian Journal of Forest Research. 30:156-167.

Clark, J.S., B. Beckage, P. Camill, B. Cleveland,J. Hille Ris Lambers, J. Lichter, J. McLachlan, J. Mohan, and P. Wyckoff. 1999. Interpreting Recruitment Limitation In Forests. American Journal of Botany. 86(1): 1-16.

Clark, J.S., M. Silman, R. Kern, E. Macklin, and J. Hille Ris Lambers. 1999. Seed Dispersal Near And Far: Patterns Across Temperate And Tropical Forests. Ecology. 80(5): 1475-1494.

Clark, J.S. 1998. Why Trees Migrate So Fast: Confronting Theory with Dispersal Biology and the Paleorecord. The American Naturalist. 152(2): 204-224.

Clark, J.S., C. Fastie, G. Hurtt, S.T. Jackson, C. Johnson, G.A. King, M. Lewis, J. Lynch, S. Pacala, C. Prentics, E.W. Schupp, T. Webb III, and P. Wyckoff. 1998. Reid's paradox of rapid plant migration: dispersal theory and interpretation of paleoecological records. Bioscience 48(1): 13-24.

Clark, J.S., E. Macklin, and L. Wood. 1998. Stages and spatial scales of recruitment limitation in Southern Appalachian forests. Ecological Monographs. 68(2): 213-235.

Pitelka, L.F., R.H. Gardner, J. Ash, S. Berry, H. Gitay, I.R. Noble, A. Saunders, R.H.W. Bradshaw, L. Brubaker, J.S. Clark, M.B. Davis, S. Sugita, J.M. Dyer, R. Hengeveld, G. Hope, B. Huntley, G.A. King, S. Lavorel, R.N. Mack, G.P. Malanson, and M. McGlon. Plant Migration and Climate Change. American Scientist 85: 464-473.

Clark, J.S., B.J. Stocks., and P.J.H. Richard. 1996. Climate implications of biomass burning since the 19th century in eastern North America. Global Change Biology 2: 433-442.

Clark, J.S., and Y. Ji. 1995. Fecundity and dispersal in plant populations: implications for structure and diversity. The American Naturalist. 146(1): 72-111.

Books and Book Sections

Clark, J.S., D. Bell, M. Dietze, M. Hersh, I. Ibanez, S. LaDeau, S. M. McMahon, C.J.E. Metcalf, E. Moran, L. Pangle, and M. Wolosin. 2010. Models for demography of plant populations. Pages 431 - 481 in T. O'Hagan and M. West (eds) Handbook of Bayesian Analysis, Oxford University Press.

Conference Posters and Presentations

Agarwal, P., T. Mohave, H. Yu, and J. S. Clark. 2011. Exploiting temporal coherence in forest dynamics simulation. SCoG 2011 Symposium on Computational Geometry, June 13–15, 2011, Paris, France.