Publications of James S. Clark     :chronological  combined  bibtex listing:

Books

1. J.S. Clark. Models for Ecological Data. Princeton University Press, under contract.
2. J.S. Clark. Ecological data models with R. Princeton University Press, under contract.
3. Clark, J.S. and A. Gelfand (eds.). Applications of Computational Statistics in the Environmental Sciences: Hierarchical Bayes and MCMC Methods. Oxford University Press, under contract.
4. Clark, J.S., B.J. Stocks, H. Cachier, and J.G. Goldammer (eds.). Sediment Records of Biomass Burning and Global Change. Springer Verlag, Berlin, Germany, 1997.

Papers Published

1. J.S. Clark. "Why environmental scientists are becoming Bayesians." Ecology Letters 8 (2005): 2-14.
2. J.S. Clark. "Uncertainty in population growth rates calculated from demography: the hierarchical approach." Ecology 84 (2005): 1370-1381.
3. McLachlan, J.S., and J.S. Clark. "Reconstructing historical ranges with fossil data at continental scales." Forest Ecology and Management 197 (2004): 139-147.
4. Clark, J.S. and O. Bjornstad. "Population time series: Process variability, observation errors, missing values, lags, and hidden states." Ecology 85 (2004): 3140-3150.
5. Clark J.S., S. LaDeau, and I. Ibanez. "Fecundity of trees and the colonization-competition hypothesis." Ecological Monographs 74 (2004): 415-442.
6. J.S. Clark. "Neutral theory (communication arising): The stability of forest biodiversity." Nature 427 (2004): 696-697.
7. Mohan, J.E., J.S. Clark, and W.H. Schlesinger. "Genetic variation in germination, growth, and survivorship of red maple in response to subambient through elevated atmospheric CO2." Global Change Biology 10 (2004): 233-247.
8. Lynch, J.A., J.S. Clark, and B.J. Stocks. "Charcoal production, dispersal and deposition from the Fort Providence Experimental Fire: Interpreting fire regimes from charcoal records in boreal forests." Canadian Journal of Forest Research 34 (2004): 1642-1656.
9. J.S. Clark. "Reid’s Paradox: Tree migration capacity and rapid climate change." Conservation and Global Change (2004).
10. Clark, J.S. and J.S. McLachlan. "Stability of forest diversity." Nature 423 (2003): 635-638.
11. Higgins, S.I., J. S. Clark, R. Nathan, T. Hovestadt, F. Schurr, J. M. V. Fragoso, M. R. Aguiar, E. Ribbens, and S. Lavorel. "Forecasting plant migration rates: managing uncertainty for risk assessment." Journal of Ecology 91 (2003): 341-347.
12. Hille Ris Lambers, J. and J.S. Clark. "Effects of dispersal, shrubs, and density-dependent mortality on seed and seedling distributions in temperate forests." Canadian Journal of Forest Research 33 (2003): 783-795.
13. Beckage, B. and J.S. Clark. "Seedling survival and growth in Southern Appalachian forests: Does spatial heterogeneity maintain species diversity." Ecology 84 (2003): 1849-1861.
14. Clark, J.S., M. Lewis, J.S. McLachlan, J. Hille Ris Lambers. "Estimating population spread: what can we forecast and how well." Ecology 84 (2003): 1979-1988.
15. Calder, K. M. Lavine, P. Mueller, and J.S. Clark. "Incorporating multiple sources of stochasticity in population dynamic models." Ecology 84 (2003): 1395-1402.
16. Clark, J.S.. "Uncertainty in ecological inference and forecasting. (Special Feature)." Ecology 84 (2003): 1370-1381.
17. Clark, J.S.. "Uncertainty in population growth rates calculated from demography: the hierarchical approach." Ecology 84 (2003): 1349-1360.
18. Lynch, J.A., B. Bigelow, J.S. Clark, M. Edwards, and B. Finney. "Spatial and temporal variation in boreal fire." Journal of Geophysical Research 108 (2003): 8152-8169.
19. Clark, J. S., J. Mohan, M. Dietze, and I. Ibanez. "Coexistence: how to identify trophic tradeoffs." Ecology 84 (2003): 17-31.
20. Hille Ris Lambers, J.S. Clark, and J.B. Beckage. "Density Dependent Mortality and the Latitudinal Gradient in Species Diversity." Nature 417 (2002): 732-735.
21. Wyckoff, P.H. and J.S. Clark. "Growth and mortality for seven co-occurring tree species in the southern Appalachian Mountains: implications for future forest composition." Journal of Ecology 90 (2002): 604-615.
22. Clark, J.S., E.C. Grimm, J. J. Donovan, S.C. Fritz, D.R. Engstrom, and J.E. Almendinger. "Drought cycles and landscape responses to past aridity on prairies of the Northern Great Plains, USA." Ecology 83 (2002): 595-601.
23. Clark, J.S., B. Beckage, J. Hille Ris Lambers, I. Ibanez, S. LaDeau, J. MacLachlan, J. Mohan, and M. Rocca. "Dispersal and plant migration." Encyclopedia of Global Environmental Change 3 (2002): 81-93.
24. Clark, J.S., A. M. Gill, and A. P. Kershaw. "Spatial variability in fire regimes: its effects on recent and past vegetation." Flammable Austrailia: the Fire Regimes and Biodiversity of a Continent (2002): 125-144.
25. Kershaw, A. P., Clark, J.S., A. M. gill, and D. M. D'Costa. "A history of fire in Australia." Flammable Australia: the Fire Regimes and Biodiversity of a Continent (2002). (Pages 3-25)
26. Lavine, M., B. Beckage, and J.S. Clark. "Statistical modeling of seedling mortality." Journal of Agricultural, Biological, and Environmental Statistics 7 (2002): 21-41.
27. J.S. Clark, S.R. Carpenter, M. Barber, S. Collins, A. Dobson, J. Foley, D. Lodge, M. Pascual, R. Pielke, Jr., W. Pizer, C. Pringle, W. V. Reid, K.A. Rose, O. Sala, W.H. Schlesinger, D. Wall, and D. Wear.. "Ecological forecasts: an emerging imperative." Science 293 (2001): 657-660.
28. Camill, P., J.A Lynch, J.S. Clark, J.B. Adams and B. Jordan. "Changes in biomass, aboveground NPP, and peat accumulation following permafrost thaw in the boreal peatlands of Manitoba, Canada." Ecosystems 4 (2001): 461-478.
29. LaDeau, S. and J.S. Clark. "Rising CO2 and the fecundity of forest trees." Science 292 (2001): 95-98.
30. Clark, J.S., Lewis, M., and L. Horvath.. "Invasion by extremes: variation in dispersal and reproduction retards population spread." American Naturalist 157 (2001): 537-554.
31. Clark, J.S., L. Horvath, and M. Lewis. "On the estimation of spread for a biological population." Statistics and Probability Letters 51 (2001): 225-234.
32. Schlesinger, W.H., J.S. Clark, J.E. Mohan and C.D. Reid. "Global environmental change: effects on biodiversity." Research Priorities for Conservation Biology (2001): 175-224.
33. Clark, J.S., E.C. Grimm, J. Lynch, and P.J. Mueller. "Effects of Holocene climate change on the C4 grassland/woodland boundary in the Northern Central Plains." Ecology 82 (2001): 620-636.
34. Clark, J.S. and M. Lavine. "Bayesian statistics in ecology." Design and Analysis of Ecological Experiments (2001): 327–346.
35. Beckage, B., J.S. Clark, B.D. Clinton, and B.L. Haines. "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 (2000): 1617-1631.
36. Camill, P. and J.S. Clark. "Complex long-term climate responses of North American boreal forest and savanna." Ecosystems 3 (2000): 534-544.
37. Wyckoff, P.H. and J.S. Clark. "Predicting tree mortality from diameter growth: a comparison of maximum likelihood and Bayesian approaches." Canadian Journal of Forest Research 30 (2000): 156-167.
38. Knoepp, J.D., D.C. Coleman, D.A. Crossley, and J.S. Clark. "Biological indices of soil quality: an ecosystem case study of their use." Forest Ecology and Management 138 (2000): 357-368.
39. Clark, J.S., B. Beckage, P. Camill, B. Cleveland, J. Hille Ris Lambers, J. Lichter, J. MacLachlan, J. Mohan, and P. Wyckoff. "Interpreting recruitment limitation in forests." American Journal of Botany 86 (1999): 1-16.
40. Clark, J.S., M. Silman, R. Kern, E. Macklin, and J. Hille Ris Lambers. "Seed dispersal near and far: generalized patterns across temperate and tropical forests." Ecology 80 (1999): 1475-1494.
41. Clark, J. S., C. Fastie, G. Hurtt, S. T. Jackson, C. Johnson, G. King, M. Lewis, J. Lynch, S. Pacala, I.C. Prentice, E. W. Schupp, T. Webb III, and P. Wyckoff. "Reid’s Paradox of rapid plant migration." BioScience 48 (1998): 13-24.
42. Clark, J. S., J. Lynch, and B. J. Stocks. "Relationships between charcoal particles in air and sediments in west-central Siberia." The Holocene 8 (1998): 19-30.
43. Clark, J. S., E. Macklin, and L. Wood. "Stages and spatial scales of recruitment limitation in southern Appalachian forests." Ecological Monographs 68 (1998): 213-235.
44. Camill, P. and J.S. Clark. "Climate change disequilibrium of boreal permafrost peatlands caused by local processes." American Naturalist 151 (1998): 207-222.
45. Collatz, G.J., J.A. Berry, and J. S. Clark. "Effects of climate and atmospheric CO2 partial pressure on the global distribution of C4 plants: past, present, and future." 114 (1998): 441-454.
46. J.S. Clark. "Why trees migrate so fast: Confronting theory with dispersal biology and the paleo record." American Naturalist 152 (1998): 204-224.
47. J.S. Clark. "Introduction to sediment records of biomass burning and global change." Sediment Records of Biomass Burning and Global Change (1997): 1-9.
48. J.S. Clark and W. A. Patterson. "Background and local charcoal in sediments: scales of fire evidence in the paleorecord.." Sediment Records of Biomass Burning and Global Change (1997): 23-48.
49. J.S. Clark. "Facing short-term extrapoloation with long-term evidence: Holocene fire in the north-eastern US forests." Journal of Ecology 85 (1997): 377-380.
50. Pitelka, L. F., J. Ash, S. Berry, R.H.W. Bradshaw, L. Brubaker, J.S. Clark, M.B. Davis, J.M. Dyer, R.H. Gardner, H. Gitay, G. Hope R. Hengeveld, B. Huntley, G.A. King, S. Lavorel, R.N. Mack, G.P. Malanson, M. McGlone, I.R. Noble, I.C. Prentice, M. Rejmane. "Plant migration and climate change." American Scientist 85 (1997): 464-473.
51. J.S. Clark and T. C. Hussey. "Estimating the mass flux of charcoal from sediment records: the effect of particle size, morphology, and orientation." The Holocene 6 (1996): 129-144.
52. J.S. Clark. "Baseline biomass burning emissions of eastern North America." Biomass Burning and Global Change (1996): 750-757.
53. J.S. Clark and P. J. H. Richard. "The role of paleofire in boreal and other cool-coniferous forests." Fire in Ecosystem of Boreal Eurasia (1996): 65-89.
54. Clark, J. S., T. C. Hussey, and P. D. Royall. "Presettlement analogs for Quaternary fire regimes in eastern North America." Journal of Paleolimnology 16 (1996): 79-96.  [abs]
55. J.S. Clark and P. D. Royall. "Local and regional sediment charcoal evidence for fire regimes in presettlement northeastern North America." Journal of Ecology 84 (1996): 365-382.
56. Clark, J. S., P. D. Royall, and C. Chumbley. "The role of fire during climate change in an eastern North American forest at Devil’s Bathtub, New York." Ecology 77 (1996): 2148-2166.
57. Clark, J.S., B.J. Stocks, and P. J.H. Richard. "Climate implications of biomass burning since the 19th century in eastern North America." Global Change Biology 2 (1996): 433-458.
58. J.S. Clark. "Testing disturbance theory with long-term data: alternative life history solutions to the distribution of events." American Naturalist 148 (1996): 976-996.
59. J.S. Clark. "Terrestrial biotic responses to environmental change and feedbacks to climate." Climate Change 1995: The Science of Climate Change (1996): 445-482.
60. J.S. Clark. "Fire in ecosystems of boreal Eurasia: the Bor Forest Island Fire Experiment Fire Research Campaign Asia - North (FIRESCAN)." Biomass Burning and Global Change (1996): 848-873.
61. Weiss, K. F., J. G. Goldammer, J. S. Clark, D. A. Livingstone, and M. O. Andreae. "Reconstruction of prehistoric fire regimes in East Africa by lake sediment analysis." Biomass Burning and Global Change (1996).
62. Clark, J. S., and Y. Ji.. "Fecundity and dispersal in plant populations: implications for structure and diversity." The American Naturalist 146 (1995): 72-111.
63. Clark, J. S., and P. D. Royall. "Transformation of a northern hardwood forest by aboriginal (Iroquois) fire: charcoal evidence from Crawford Lake, Ontario, Canada." The Holocene 5 (1995): 1-9.
64. J.S. Clark and P. D. Royall. "Particle-size evidence for source areas of charcoal accumulation in Late Holocene sediments of eastern North American lakes." Quaternary Research 43 (1995): 80-89.
65. Wright, H. E., and J. S. Clark. "Charcoal analysis of varved lake sediments." Laminated Sediments and Archaeology, Journal of the European Study Group on Physical, Chemical, Mathematical and Biological Techniques Applied to Archaeology (1995): 125-130.
66. J.S. Clark. "Climate and Indian effects on southern Ontario forests: forum." 5 (1995): 371-379.
67. J.S. Clark. "Fire in boreal ecosystems of Eurasia: first results of the Bor Forest Island Fire Experiment, Fire Research Campaign Asia-North (FIRESCAN)." Journal of World Resources Review (1994): 499-519.
68. J.S. Clark and P. D. Royall. "Pre-industrial particulate emissions and carbon sequestration from biomass burning in North America." Biogeochemistry 23 (1994): 1-17.
69. J.S. Clark. "Sensitivity of forest communities to global climate change." Biotic Interactions and Global Change (1993): 315-332.
70. J.S. Clark. "Functional groups and ecological consistencies: population perspectives on regional forest dynamics." Scaling Processes between Leaf and Landscape Levels (1993): 255-286.
71. J.S. Clark and J. Robinson. "Paleoecology of Fire." Fire in the Environment: its Ecological, Climatic, and Atmospheric Chemical Importance (1993): 193-214.
72. J.S. Clark. "Fire, climate, and forest processes during the last 2000 years." Ecology and Paleoecology of Elk Lake (1993): 295-308.
73. J.S. Clark. "Shifting mosaic population dynamics." Patch Dynamics S. Levin, T.M. Powell, and J.H. Steele (1993).
74. Binkley, D., P. Becker-Heidman, J.S. Clark, P.J. Crutzen, P. Frost, A.M. Gill, A. Granström, F. Mack, J.–C. Menaut, R.W. Wein, and B. van Wilgren. "Impacts of fires on ecosystems." Fire in the Environment: its Ecological, Climatic, and Atmospheric Chemical importance (1993): 359-374.
75. J.S. Clark. "Scale relationships in boreal forest." Trends in Ecology and Evolution 8 (1993): 220.
76. J.S. Clark and Reid, C.D.. "Sensitivity of unmanaged ecosystems to global change." Non-linear Responses to Global Change, Resources for the Future (1993): 53-89.
77. J.S. Clark. "Disturbance, climate change, and forest rehabilitation." Ecosystem Rehabilitation: Preamble to Sustained Development (1992): 165-186.
78. J.S. Clark. "Implications of individual plant growth for landscape patterns of age structure, net primary production, and resource availabilities." Populations, Communities, and Ecosystems: an Individual Perspective (1992): 421-454.
79. J.S. Clark. "Validating model predictions of climate and vegetation change." Earth System Modeling (1992): 423-440.
80. J.S. Clark. "Density-independent mortality, density compensation, and gap formation in plant populations." Theoretical Population Biology 42 (1992): 172-198.
81. Morris, L.A., P.B. Bush, and J.S. Clark. "Ecological impacts and risks associated with forest management." Predicting Ecosystem Risk (1992): 153-214.
82. J.S. Clark. "Ecosystem sensitivity to climate change and complex responses." Global Change and Life on Earth (1991): 65-98.
83. J.S. Clark. "Forest-tree growth rates and probability of gap origin–a comment." Ecology 72 (1991): 1166-1169.
84. J.S. Clark. "Disturbance and tree life history on the shifting mosaic landscape." 72 (1991): 1102-1118.
85. J.S. Clark. "Disturbance and population structure on the shifting mosaic landscape." Ecology 72 (1991): 1119-1137.
86. J.S. Clark. "Fire and climate change during the last 750 years in northwestern Minnesota." Ecological Monographs 60 (1990): 135-159.
87. J.S. Clark. "Integration of ecological levels: individual plant growth, population mortality, and ecosystem dynamics." Journal of Ecology 78 (1990): 275-299.
88. J.S. Clark. "Effects of 20th century climate change and fire suppression on forest production and decomposition in northwestern Minnesota." Canadian Journal of Forest Research 20 (1990): 219-232.
89. J.S. Clark. "Population and evolutionary consequences of being a coastal plant: long-term evidence from the North Atlantic coasts." Aquatic Science Reviews 2 (1990): 509-533.
90. J.S. Clark. "Landscape interactions among nitrogen mineralization, species composition, and long-term disturbance." Biogeochemisty 11 (1990): 1-22.
91. J.S. Clark. "Water balance and fire occurrence during the last 160 years in northwestern Minnesota." Journal of Ecology 77 (1989): 989-1004.
92. J.S. Clark. "Clark, J.S. 1989. Forests are for burning." Natural History 1 (1989): 50-53.
93. J.S. Clark, J. Merkt, and H. Müller. "Post Glacial fire, vegetation, and cultural history of the northern Alpine forelands, southwest Germany." Journal of Ecology 77 (1989): 897-925.
94. J.S. Clark. "Ecological disturbance as a renewal process: theory and application to fire history." Oikos 56 (1989): 17-30.
95. J.S. Clark. "Effects of climate change on fire regime in northwestern Minnesota." Nature 334 (1988): 233-235.
96. J.S. Clark. "Stratigraphic charcoal analysis on petrographic thin sections: recent fire history in northwestern Minnesota." Quaternary Research 30 (1988): 81-91.
97. J.S. Clark. "Particle motion and the theory of charcoal analysis: source area, transport, deposition, and sampling." Quaternary Research 30 (1988): 67-80.
98. J.S. Clark and Patterson, W.A.. "Dating of the organic deposits." Geomorphic Development of Long Island’s South Shore Barriers (1987).
99. J.S. Clark. "Dynamism in the barrier-beach vegetation of Great South Beach, New York." Ecological Monographs 56 (1986): 97-126.
100. J.S. Clark. "Late Holocene vegetation and coastal processes at a Long Island tidal marsh." 74 (1986): 561-578.
101. J.S. Clark. "Coastal forest tree populations in a changing environment, southeastern Long Island, New York." Ecological Monographs 56 (1986): 259-277.
102. J.S. Clark, Overpeck, J., Webb, T., and Patterson, W.A.. "Pollen stratigraphic correlation and dating of barrier-beach peat sections." Review of Palaeobotany and Palynology 47 (1986): 145-168.
103. J.S. Clark. "Vegetation and land-use history of the William Floyd Estate, Fire Island National Seashore, New York." (1986). (National Park Service, Office of Scientific Studies Technical Report OSS 86-3, Boston, Massachusetts)
104. J.S. Clark and W.A. Patterson. "The development of a tidal marsh: upland and oceanic influences." Ecological Monographs 55 (1985): 189-217.
105. J.S. Clark. "Chronologies for recent sediments in coastal environments." Proceedings of the 12th Nordic Symposium on Sediments 12 (1984): 76-81.
106. J.S. Clark and Patterson, W.A.. "Pollen, 210Pb, and opaque spherules: an integrated approach to dating and sedimentation in the intertidal environment." Journal of Sedimentary Petrology 54 (1984): 1249-1263.

Papers Accepted

1. Govindarajan, S. M. Dietze, P. Agarwal, and J.S. Clark. "A scalable algorithm for dispersing populations." Journal of Intelligent Information Systems  (2005). in press
2. Hille Ris Lambers, J., J.S. Clark., and M. Lavine. "Seed banking in temperate forests: Implications for recruitment limitation." Ecology  (2005). in press
3. Wyckoff, P. and J.S. Clark. "Comparing predictors of tree growth: the case for exposed canopy area." Canadian Journal of Forest Research  (2005). in press
4. Govindarajan, S., M. Dietze, P. Agarwal, and J.S. Clark. "A scalable model of forest dynamics." Proceedings of the ACM Symposium on Computational Geometry  (2005). in press
5. Brown K.J., Clark J.S., Grimm E.C., Donovan J.J., and Mueller PG. "Fire cycles in North American interior grasslands and their relation to prairie droughts." Proceedings of the National Academy of Sciences  (2005). in press
6. HilleRisLambers, J. and J.S. Clark. "The benefits of seed banking for Acer rubrum: maximizing seedling recruitment." Canadian Journal of Forest Research  (2005). in press
7. Gelfand, A., J.S. Clark, and B. Carin. "Elements of Bayesian Inference." Applications of Computational Statistics in the Environmental Sciences: Hierarchical Bayes and MCMC Methods  (2005 under contract). in press
8. Beckage, B. and J.S. Clark. "Do seed and seedling predation contribute to the coexistence of three co-occuring tree species?." Oecologia  (2005). in press
9. McLachlan, J.S., J.S. Clark, and P.S. Manos. "Molecular indicators of tree migration capacity under rapid climate change." Ecology  (2005). in press
10. Lewis, M.A., Neubert, M.G., Caswell, H., Clark, J.S., and Shea, K.. "A guide to calculating discrete-time invasion rates from data." Conceptual ecology and invasions biology: Reciprocal approaches to nature  (2005). in press
11. J.S. Clark and S.L. LaDeau. "Synthesizing ecological experiments and observational data with Hierarchical Bayes." Applications of Computational Statistics in  (2005). in press
12. Clark,J.S., G. Ferraz, N. Oguge, H. Hays, and J. DiCostanzo. "Hierarchical Bayes for structured and variable populations: from capture-recapture data to life-history prediction." Ecology  (2005). in press
13. Clark, J.S. and O. Bjornstad. "Population inference from messy data: Errors, missing and hidden states, and lagged responses." Ecology  (2003).

Papers Submitted

1. LaDeau, S.L. and J.S. Clark. "Elevated CO2 and tree fecundity: the role of tree size, interannual variability, and population heterogeneity."   (in review).
2. Ibáñez, I., J. S. Clark, M. C. Dietze, K. Feeley, M. Hersh, S. LaDeau, A. McBride, N. E. Welch, and M. S. Wolosin. "Predicting biodiversity change: Outside the climate envelope, beyond the species-area curve."   (in review).
3. Mohan, J.E., J. S. Clark, and W. H. Schlesinger. "Long-term CO2 enrichment of an intact forest ecosystem: implications for temperate forest regeneration and succession."   (in review).
4. Clark, J.S. "Data to ecosystem prediction: complexity, variability, and uncertainty with hierarchical Bayes."   (2003).
5. Beckage, B. and J.S. Clark. "Do seed and seedling predation contribute to the coexistence of three co-occuring tree species."   (2003).
6. Hille Ris Lambers, J., J.S. Clark., and M. Lavine. "Seed banking in temperate forests: Implications for recruitment limitation."   (2003).
7. Clark, J.S., G. Ferraz, and N. Oguge. "Population inference from messy data: Structured, variable, and uncertain demographic change."   (2003).  [abs]