Duke Forest Publications: Clark Lab

Duke Forest Publications: Clark Lab

  • Sharma, S., Y. Bergeron, M. Bogdziewicz, D.C. Bragg, D. Brockway, N.L. Cleavitt, B. Courbaud, A.J. Das, M. Dietze, T.J. Fahey, J.F. Franklin, G.S. Gilbert, C.H. Greenberg, Q. Guo, J. Hille Ris Lambers, I. Ibanez, J. Johnstone, C.L. Kilner, G. Kunstler, J.M. LaMontagne, D. Macias, J.A. Myers, R. Parmenter, C.L. Scher, W.H. Schlesinger, M. Steele, N.L. Stephenson, M. Swift, T.T. Veblen, A.V. Whipple, T.G. Whitham, A.P. Wion, K. Zhu, R. Zlotin, and J.S. Clark, 2022. North American tree migration paced by recruitment through contrasting east-west mechanisms. Proceedings of the National Academy of Sciences, . pdf: e2116691118.full
  • Qiu, T., S. Shubhi, C. W. Woodall, and J.S. Clark. 2021. Niche shifts from trees to fecundity to recruitment that determine species response to climate change. Frontiers in Ecology and Evolution 9, 863. https://www.frontiersin.org/article/10.3389/fevo.2021.719141, DOI10.3389/fevo.2021.719141.
  • Qiu, T., M.-C. Aravena, R. Andrus, D. Ascoli, Y. Bergeron, R. Berretti, M. Bogdziewicz, T. Boivin, R. Bonal, T. Caignard, R. Calama, J. J. Camarero, C.J. Clark, B. Courbaud, S. Delzon, S. Donoso Calderon, W. Farfan-Rios, C. A. Gehring, G. S. Gilbert, C. H. Greenberg, Q. Guo, J. Hille Ris Lambers, K. Hoshizaki, I. Ibanez, V. Journé, C. L. Kilner, R. K. Kobe, W. D. Koenig, G. Kunstler, J. M. LaMontagne, M. Ledwon, J. A. Lutz, R. Motta, J. A. Myers, T. A. Nagel, C. L. Nuñez, I. S. Pearse, Ł. Piechnik, J. R. Poulsen, R. Poulton-Kamakura, M. D. Redmond, C. D. Reid, K. C. Rodman, C. L. Scher, H. Schmidt Van Marle, B. Seget, S. Sharma, M. Silman, J. J. Swenson, M. Swift, M. Uriarte, G. Vacchiano, T. T. Veblen, A. V. Whipple, T. G. Whitham, A. P. Wion, S. J. Wright, K. Zhu, J. K. Zimmerman, M. Żywiec, and J. S. Clark. 2021. Is there tree senescence? The fecundity evidence. Proceedings of the National Academy of Sciences, 118, e2106130118; DOI: 10.1073/pnas.2106130118. e2106130118.full, pdf: qiuPNAS2021
  • Clark, J.S., R. Andrus, M. Aubry-Kientz, Y. Bergeron, M. Bogdziewicz, D.C. Bragg, D. Brockway, N.L. Cleavitt, S. Cohen, B. Courbaud, R. Daley, A.J. Das, M. Dietze, T.J. Fahey, I. Fer, J.F. Franklin, C.A. Gehring, G.S. Gilbert, C.H. Greenberg, Q. Guo, J. Hille Ris Lambers, I. Ibanez, J. Johnstone, C.L. Kilner, J. Knops, W.D. Koenig, G. Kunstler, J.M. Lamontagne, K.L. Legg, J. Luongo, J.A. Lutz, D. Macias, E.J. Mcintire, Y. Messaoud, C.M. Moore, E. Moran, J.A. Myers, O.B. Myers, C. Nunez, R. Parmenter, S. Pearson, R. Poulton-Kamakura, E. Ready, M.D. Redmond, C.D. Reid, K.C. Rodman, C.L. Scher, W.H. Schlesinger, A.M. Schwantes, E. Shanahan, S. Sharma, M. Steele, N.L. Stephenson, S. Sutton, J.J. Swenson, M. Swift, T.T. Veblen, A.V. Whipple, T.G. Whitham, A.P. Wion, K. Zhu, and R. Zlotin. 2021. Continent-wide tree fecundity driven by indirect climate effects. Nature Communications DOI: 10.1038/s41467-020-20836-3. pdf: s41467-020-20836-3
  • Qiu, T., C. Song, J. S. Clark, B. Seyednasrollah, and N. Rathnayaka. 2020. Understanding the continuous phenological development at daily time step with a Bayesian hierarchical space-time model: impacts of climate change and extreme weather events. Remote Sensing of Environment, in press.
  • Clark, J.S., C.L. Nuñez, and B. Tomasek. 2019. Foodwebs based on unreliable foundations: spatio-temporal masting merged with consumer movement, storage, and diet. Ecological Monographs89:e01381. 10.1002/ecm.1381 Appendix
  • Berdanier, A. and J. S. Clark. 2018. Tree water balance drives temperate forest responses to drought. Ecology, 99: 2506-2514ecologyBerdanier2018
  • Schliep, E.M., A. E. Gelfand, J. S Clark, and R. Kays. 2018. Joint Temporal Point Pattern Models for Proximate Species Occurrence in a Fixed Area Using Camera Trap Data. Journal of Agricultural, Biological, and Environmental Statistics, 23: 334–357.
  • Seyednasrollah, B. J. Swenson, J.-C. Domec, and J. S. Clark. 2018. Leaf phenology paradox: why warming matters most where it is already warm. Remote Sensing of Environment, 209, 446 – 455. 209: 446-455.
  • Kim, D., R. Oren, J. S. Clark, S. Palmroth1, A. C. Oishi, H. R. McCarthy, C. A. Maier, and K. Johnsen. 2017. Dynamics of soil CO2 efflux under varying atmospheric CO2 concentrations reveal dominance of slow processes. Global Change Biology, 23:3501 3512.
  • Berdanier, A., C. Miniat, and J.S. Clark. 2016. Predictive models for radial sap flux variation in coniferous, diffuse-porous, and ring-porous temperate trees. Tree Physiology, 36: 932-941berdanierTreePhys2016treePhys_berdanier2016Suppl
  • Berdanier, A. and J.S. Clark. 2016. Divergent reproductive allocation trade-offs with canopy exposure across tree species in temperate forests. Ecosphere, DOI:10.1002/ecs2.1313.
  • Berdanier, A. and J.S. Clark. 2016. Multi-year drought-induced morbidity preceding tree death in Southeastern US forests. Ecological Applications, 26:17-23. BerdanierEA2016
  • Bell, D.M. and J.S. Clark 2015. Seed predation and climate impacts on reproductive variation in temperate forests of the southeastern USA. Oecologia, 180, 1223–1234bell2016
  • Bell, D.M., E. J. Ward, C. Oishi, R. Oren, P. Flikkema, and J. S. Clark. 2015. A state-space modeling approach to estimating canopy conductance and associated uncertainties from sap flux density data. Tree Physiology,35: 792-802berdanierTreePhys2016
  • Clark, J.S., J. Melillo, J. Mohan, and C. Salk. 2014. The seasonal timing of warming that controls onset of the growing season. Global Change Biology20:1136-1145.
  • Clark, J.S., A.E. Gelfand, C.W. Woodall, and K. Zhu. 2014. More than the sum of the parts: forest climate response from joint species distribution models, Ecological Applications24:990–999.
  • 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.
  • Clark, J.S., J. Melillo, J. Mohan, and C. Salk. 2014. Tree phenology responses to winter chilling and spring warming, at north and south range limits. Functional Ecology, 28, 1344-1355. funcEcol2014funcEcol2014supplement
  • Ghosh, S., D.M. Bell, J.S. Clark, A.E. Gelfand, P.G. Flikkema. 2014. Process modeling for soil moisture using sensor network data.  Statistical Methodology 17, 99-112.
  • 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.
  • Benitez, S.B., M. Hersh, R. Vilgalys, and J.S. Clark. 2013. Pathogen regulation of plant diversity via effective specialization. Trends in Ecology and Evolution, 12: 705-711
  • Gelfand, A.E., S. Ghosh and J. S. Clark. 2013. Scaling integral projection models for analyzing size demography. Statistical Science, 28, 641-658. statSci2013
  • Bugalho, M.N., I. Ibánez, and J.S Clark. 2013. The effects of deer herbivory and forest type on tree recruitment vary with plant growth stage. Forest Ecology and Management, 308, 90–100. fem2013
  • Ghosh, S., D. M. Bell, J.S. Clark, A.E. Gelfand, and P. Flikkema.  2013. Process modeling for soil moisture using sensor network data. Statistical Methodology, in press. statMeth2013
  • Ward, E.J., D.M. Bell, J.S. Clark and R. Oren. 2012. Hydraulic time constants for transpiration of loblolly pine at Duke FACE. Tree Physiology, 33, 123-134. treePhys2012a,  treePhys2012aAppendix
  • Ward, E.J., R. Oren, D.M. Bell, J.S. Clark, H.R. McCarthy, H. Seok-Kim and J.-C. Domec. 2012. The effects of long-term elevated CO2 and nitrogen fertilization on stomatal conductance estimated from scaled sap flux measurements at Duke FACE.  Tree Physiology, 33, 135-151. treePhys2012a, treePhys2013bAppendix
  • Moran E.V. and J.S. Clark  2012. Between-site differences in the scale of dispersal and gene flow in red oak. PLoS ONE 7: e36492. doi:10.1371/journal.pone.0036492.
  • 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(2): e30050. doi:10.1371/journal.pone.0030050.
  • 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,  93:1082-1094.
  • Clark, J.S. 2012. The coherence problem with the Unified Neutral Theory of Biodiversity.  Trends in Ecology and Evolution, 27:198-202 .
  • 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. ecologyHersh2012
  • Moran, E.V., J. Willis, and J.S. Clark. 2012. Genetic evidence for hybridization in red oaks. American Journal of Botany, 99, 92-100. ajb_moran2012
  • Clark, J.S., D. M. Bell, M. Kwit, 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, and J. S. Clark. 2012.  Inference for size demography from point pattern data using integral projection models. Journal of Agricultural, Biological and Environmental Statistics, 17, 641-677. jabes_ghosh2012
  • 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.
  • Agarwal, P., T. Mohave, H. Yu, and J. S. Clark. 2011. Exploiting temporal coherence in forest dynamics simulation. SCG ’11 Proceedings of the 27th Annual Symposium on Computational Geometry, Paris, France.
  • 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.
  • 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.
  • Moran, E.V. and J.S. Clark. 2010. Estimating seed and pollen movement in a monoecious plant: a hierarchical Bayesian approach integrating genetic and ecological data. Molecular Ecology, 20, 1248–1262. molEcol_moran2011
  • 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. EM2010, 80, 569–608. EM2010appendix-A, EM2010appendix-B
  • Clark, J.S. 2010. Individuals and the variation needed for high species diversity. Science 327, 1129-1132, science2010. scienceAppend2010
  • 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. Oecologia, in press.
  • Way, D.A., S. L. LaDeau, H. R. McCarthy, J. S. Clark, R. Oren, A. C. Finzi and R. B. Jackson. 2010. Greater seed production in elevated CO2 is not accompanied by reduced seed quality in Pinus taeda L.. Global Change Biology, 16, 1046-1056.
  • 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.
  • Clark, J.S. and M. H. Hersh. 2009. Inference when multiple pathogens affect multiple hosts: Bayesian model selection. Bayesian Analysis 4:337–366. bayesAnal2009
  • 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.
  • 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.
  • Vieilledent, G., B. Courbaud, G. Kunstler, J.-F. Dhote, 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.
  • Ibanez, I., Clark, J.S. and Dietze, M. 2009. Estimating performance of potential migrant species.  Global Change Biology, 15:1173-1188.
  • Ibanez, I., Clark, J.S. and Dietze, M. 2008. Evaluating the sources of potential migrant species: Implications under climate change. Ecological Applications, 18:1664-1678.
  • Dietze, M., M. Wolosin, J. S. Clark. 2008. Tree allometries: capturing diversity using a Hierarchical Bayes approach. Forest Ecology and Management 256:1939-1948.
  • Dietze, M., and J.S. Clark. 2008. Changing the gap-dynamics paradigm: vegetative regeneration control on forest response to disturbance.  Ecological Monographs 78:331­347.
  • Clark, J.S., M. Dietze, P. Agarwal, S. Chakraborty, I. Ibanez, S. LaDeau, and M. Wolosin. 2007. Resolving the biodiversity debate. Ecology Letters, 10: 647–662CR commentCA reply.
  • 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, 1942-1953.
  • 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, 77:163-177.
  • Govindarajan, S. M. Dietze, P. Agarwal, and J.S. Clark. 2007. A scalable algorithm for dispersing populations. Journal of Intelligent Information Systems, DOI 10.1007/s10844-006-0030-z.
  • Flikkema, P.G., P.J. K. Agarwal, J. S. Clark, C. Ellis, A. Gelfand, K. Munagala, and J. Yang. 2007. From data reverence to data relevance:  Model-mediated wireless sensing of the physical environment. Pages 988–994 in Y. Shi et al. (Eds.): ICCS 2007, Part I, LNCS 4487.
  • Mohan, J.E., J. S. Clark, and W. H. Schlesinger. 2007. Long-term CO2 enrichment of an intact forest ecosystem: implications for temperate forest regeneration and succession.  Ecological Applications, 17:1198-1212.
  • Flikkema, P.G., P.K. Agarwal, J.S. Clark, C. Ellis, A. Gelfand, K. Munagala, and J. Yang.  2006. Model-driven dynamic control of embedded wireless sensor networks.  Proc. 6th International Conference on Computational Science, Workshop on Dynamic Data Driven Application Systems, Reading, UK.
  • LaDeau, S.L. and J.S. Clark. 2006. Elevated CO2 and tree fecundity: the role of tree size, interannual variability, and population heterogeneity.  Global Change Biology, 12:822-833.
  • Mohan, J. E., L. H. Ziska, R. B. Thomas, R. C. Sicher, K. George, J. S. Clark, W. H. Schlesinger. 2006.  Biomass and toxicity responses of poison ivy (Toxicodendron radicans) to elevated atmospheric CO2.  Proceedings of the National Academy of Sciences.  103 (24): 9086.
  • LaDeau, S. and J.S. Clark. 2006. Pollen production by Pinus taeda L.(Pinaceae) growing in elevated atmospheric CO2Functional Ecology, 20:541-547.
  • Ibanez, I., J. S. Clark, M. C. Dietze, K. Feeley, M. Hersh, S. LaDeau, A. McBride, N. E. Welch, and M. S. Wolosin. 2006. Predicting biodiversity change: Outside the climate envelope, beyond the species-area curve.  Ecology, 87:1896-1906.
  • Clark, J.S. and S.L. LaDeau. 2006. Synthesizing ecological experiments and observational data with Hierarchical Bayes. Pages 41 – 58 in J.S. Clark and A. Gelfand (eds). Hierarchical Models of the Environment. Oxford University Press.
  • Beckage, B., M. Lavine, and J.S. Clark. 2005. Estimating variability in seedling survival from count data. Journal of Ecology, 93: 1177-1184.
  • HilleRisLambers, J. and J.S. Clark. 2005. The benefits of seed banking for Acer rubrum: maximizing seedling recruitment.  Canadian Journal of Forest Research 35: 806-813.
  • Beckage, B. and J.S. Clark. 2005. Do seed and seedling predation contribute to the coexistence of three co-occuring tree species? Oecologia, 143:458-469.
  • Hille Ris Lambers, J., J.S. Clark., and M. Lavine. 2005. Seed banking in temperate forests: Implications for recruitment limitation. Ecology, 86:85-95.
  • Govindarajan, S., M. Dietze, P. Agarwal, and J.S. Clark. 2004. A scalable model of forest dynamics. Proceedings of the 20th Symposium on Computational Geometry SCG, 106-115.
  • Wyckoff, P. and J.S. Clark. 2005. Comparing predictors of tree growth: the case for exposed canopy 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, 74:415-442.
  • 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
  • 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 of Forest Research 33: 783-795.
  • Clark, J. S., J. Mohan, M. Dietze, and I. Ibanez. 2003. Coexistence: how to identify trophic tradeoffs. Ecology, 84:17-31.  Appendix.
  • Hille Ris Lambers, J. S. Clark, and J., B. Beckage.  2002. Density dependent mortality and the latitudinal gradient in species diversity.  Nature, 417:732–735.
  • Wyckoff, P.H. and J.S. Clark. 2002. Growth and mortality for seven co-occurring tree species in the southern Appalachian Mountains: implications for future forest composition.  Journal of Ecology, 90:604–615.
  • Lavine, M., B. Beckage, and J.S. Clark. 2002.  Statistical modeling of seedling mortalityJournal of Agricultural, Biological, and Environmental Statistics, 7: 21-41.
  • LaDeau, S. and J.S. Clark. 2001. Rising CO2 and the fecundity of forest trees, Science 292:95-98.
  • 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 understories. Canadian Journal of Forest Research 30: 1617-1631.
  • 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. MacLachlan, J. Mohan, and P. Wyckoff. 1999. Interpreting recruitment limitation in forests.  American Journal of Botany, 86:1-16.
  • Clark, J.S., M. Silman, R. Kern, E. Macklin, and J. Hille Ris Lambers. 1999. Seed dispersal near and far: generalized patterns across temperate and tropical forests.  Ecology 80:1475-1494.
  • Clark, J. S., E. Macklin, and L. Wood.  1998. Stages and spatial scales of recruitment limitation in southern Appalachian forests.  Ecological Monographs 68:213-235.