Bibliography - D. W. Purves

1. Lichstein, J W., J. Dushoff, Kiona Ogle, Anping Chen, D. W. Purves, J. P. Caspersen, and Stephen W. Pacala, 2010: Unlocking the forest inventory data: relating individual tree performance to unmeasured environmental factors. Ecological Applications, (20(3)), doi:10.1890/08-2334.1 684-699
   [ Abstract ]

   Geographically extensive forest inventories, such as the USDA Forest Service's Forest Inventory and Analysis (FIA) program, contain millions of individual tree growth and mortality records that could be used to develop broad-scale models of forest dynamics. A limitation of inventory data, however, is that individual-level measurements of light (L) and other environmental factors are typically absent. Thus, inventory data alone cannot be used to parameterize mechanistic models of forest dynamics in which individual performance depends on light, water, nutrients, etc. To overcome this limitation, we developed methods to estimate species-specific parameters (θ_G) relating sapling growth (G) to L using data sets in which G, but not L, is observed for each sapling. Our approach involves: (1) using calibration data that we collected in both eastern and western North America to quantify the probability that saplings receive different amounts of light, conditional on covariates x that can be obtained from inventory data (e.g., sapling crown class and neighborhood crowding); and (2) combining these probability distributions with observed G and x to estimate θ_G using Bayesian computational methods. Here, we present a test case using a data set in which G, L, and x were observed for saplings of nine species. This test data set allowed us to compare estimates of θ_G obtained from the standard approach (where G and L are observed for each sapling) to our method (where G and x, but not L, are observed). For all species, estimates of θ_G obtained from analyses with and without observed L were similar. This suggests that our approach should be useful for estimating light-dependent growth functions from inventory data that lack direct measurements of L. Our approach could be extended to estimate parameters relating sapling mortality to L from inventory data, as well as to deal with uncertainty in other resources (e.g., water or nutrients) or environmental factors (e.g., temperature).

2. Purves, D. W., J W. Lichstein, N. Strigul, and Stephen W. Pacala, August 2008: Predicting and understanding forest dynamics using a simple tractable model. Proceedings of the National Academy of Sciences of the United States of America, www.pnas.org cgi doi 10.1073 pnas.0807754105, 105(44), 17018-17022,
   [ Abstract ]

   The perfect-plasticity approximation (PPA) is an analytically tractable model of forest dynamics, defined in terms of parameters for individual trees, including allometry, growth, and mortality. We estimated these parameters for the eight most common species on each of four soil types in the US Lake states (Michigan, Wisconsin, and Minnesota) by using short-term (<15-year) inventory data from individual trees. We implemented 100-year PPA simulations given these parameters and compared these predictions to chronosequences of stand development. Predictions for the timing and magnitude of basal area dynamics and ecological succession on each soil were accurate, and predictions for the diameter distribution of 100-year-old stands were correct in form and slope. For a given species, the PPA provides analytical metrics for early-successional performance (H₂₀, height of a 20-year-old open-grown tree) and late-successional performance (Z^*, equilibrium canopy height in monoculture). These metrics predicted which species were early or late successional on each soil type. Decomposing Z^*, showed that (i) succession is driven both by superior understory performance and superior canopy performance of late-successional species, and (ii) performance differences primarily reflect differences in mortality rather than growth. The predicted late-successional dominants matched chronosequences on xeromesic (Quercus rubra) and mesic (codominance by Acer rubrum and Acer saccharum) soil. On hydromesic and hydric soils, the literature reports that the current dominant species in old stands (Thuja occidentalis) is now failing to regenerate. Consistent with this, the PPA predicted that, on these soils, stands are now succeeding to dominance by other latesuccessional species (e.g., Fraxinus nigra, A. rubrum).

3. Purves, D. W., and Stephen W. Pacala, 2008: Predictive Models of Forest Dynamics. Science, Vol. 320(no. 5882), doi:10.1126/science.1155359 1452 - 1453
   [ Abstract ]

   Dynamic global vegetation models (DGVMs) have shown that forest dynamics could dramatically alter the response of the global climate system to increased atmospheric carbon dioxide over the next century. But there is little agreement between different DGVMs, making forest dynamics one of the greatest sources of uncertainty in predicting future climate. DGVM predictions could be strengthened by integrating the ecological realities of biodiversity and height-structured competition for light, facilitated by recent advances in the mathematics of forest modeling, ecological understanding of diverse forest communities, and the availability of forest inventory data.

4. Strigul, N., D. Pristinski, D. W. Purves, J. Dushoff, and Stephen W. Pacala, 2008: Scaling from Trees to Forests: Tractable Macroscopic Equations for Forest Dynamics. Ecological Monographs, 78(4), doi:10.1890/08-0082.1 523-525
   [ Abstract ]

   Individual-based forest simulators, such as TASS and SORTIE, are spatial stochastic processes that predict properties of populations and communities by simulating the fate of every plant throughout its life cycle. Although they are used for forest management and are able to predict dynamics of real forests, they are also analytically intractable, which limits their usefulness to basic scientists. We have developed a new spatial individual-based forest model that includes a perfect plasticity formulation for crown shape. Its structure allows us to derive an accurate approximation for the individual-based model that predicts mean densities and size structures using the same parameter values and functional forms, and also it is analytically tractable. The approximation is represented by a system of von Foerster partial differential equations coupled with an integral equation that we call the perfect plasticity approximation (PPA). We have derived a series of analytical results including equilibrium abundances for trees of different crown shapes, stability conditions, transient behaviors, such as the constant yield law and self-thinning exponents, and two species coexistence conditions.

5. Purves, D. W., J W. Lichstein, and Stephen W. Pacala, 2007: Crown Plasticity and Competition for Canopy Space: A New Spatially Implicit Model Parameterized for 250 North American Tree Species. PLOS one, (9), doi:10.1371/journal.pone.0000870
   [ Abstract ]

   Background. Canopy structure, which can be defined as the sum of the sizes, shapes and relative placements of the tree crowns in a forest stand, is central to all aspects of forest ecology. But there is no accepted method for deriving canopy structure from the sizes, species and biomechanical properties of the individual trees in a stand. Any such method must capture the fact that trees are highly plastic in their growth, forming tessellating crown shapes that fill all or most of the canopy space. Methodology/Principal Findings. We introduce a new, simple and rapidly-implemented model–the Ideal Tree Distribution, ITD–with tree form (height allometry and crown shape), growth plasticity, and space-filling, at its core. The ITD predicts the canopy status (in or out of canopy), crown depth, and total and exposed crown area of the trees in a stand, given their species, sizes and potential crown shapes. We use maximum likelihood methods, in conjunction with data from over 100,000 trees taken from forests across the coterminous US, to estimate ITD model parameters for 250 North American tree species. With only two free parameters per species–one aggregate parameter to describe crown shape, and one parameter to set the so-called depth bias–the model captures between-species patterns in average canopy status, crown radius, and crown depth, and within-species means of these metrics vs stem diameter. The model also predicts much of the variation in these metrics for a tree of a given species and size, resulting solely from deterministic responses to variation in stand structure. Conclusions/Significance. This new model, with parameters for US tree species, opens up new possibilities for understanding and modeling forest dynamics at local and regional scales, and may provide a new way to interpret remote sensing data of forest canopies, including LIDAR and aerial photography.

6. Fiore, A. M., L. W. Horowitz, D. W. Purves, H. Levy II, M. J. Evans, Y. Wang, Y. Li, and R. M. Yantosca, 2005: Evaluating the contribution of changes in isoprene emissions to surface ozone trends over the eastern United States. Journal of Geophysical Research, 110(D12303), doi:10.1029/2004JD005485
   [ Abstract ]

   Reducing surface ozone (O₃) to concentrations in compliance with the national air quality standard has proven to be challenging, despite tighter controls on O₃ precursor emissions over the past few decades. New evidence indicates that isoprene emissions changed considerably from the mid-1980s to the mid-1990s owing to land-use changes in the eastern United States (Purves et al., 2004). Over this period, U.S. anthropogenic VOC (AVOC) emissions decreased substantially. Here we apply two chemical transport models (GEOS-CHEM and MOZART-2) to test the hypothesis, put forth by Purves et al. (2004), that the absence of decreasing O₃ trends over much of the eastern United States may reflect a balance between increases in isoprene emissions and decreases in AVOC emissions. We find little evidence for this hypothesis; over most of the domain, mean July afternoon (1300–1700 local time) surface O₃ is more responsive (ranging from -9 to +7 ppbv) to the reported changes in anthropogenic NO_x emissions than to the concurrent isoprene (-2 to +2 ppbv) or AVOC (-2 to 0 ppbv) emission changes. The estimated magnitude of the O₃ response to anthropogenic NO_x emission changes, however, depends on the base isoprene emission inventory used in the model. The combined effect of the reported changes in eastern U.S. anthropogenic plus biogenic emissions is insufficient to explain observed changes in mean July afternoon surface O₃ concentrations, suggesting a possible role for decadal changes in meteorology, hemispheric background O₃, or subgrid-scale chemistry. We demonstrate that two major uncertainties, the base isoprene emission inventory and the fate of isoprene nitrates (which influence surface O₃ in the model by -15 to +4 and +4 to +12 ppbv, respectively), preclude a well-constrained quantification of the present-day contribution of biogenic or anthropogenic emissions to surface O₃ concentrations, particularly in the high-isopreneemitting southeastern United States. Better constraints on isoprene emissions and chemistry are needed to quantitatively address the role of isoprene in eastern U.S. air quality.

7. Purves, D. W., and Stephen W. Pacala, 2005: Ecological drift in niche-structured communities: neutral pattern does not imply neutral process. Biotic Interactions in the Tropics, Chapter 5, 107-138
   [ Abstract ]

   We can define a neutral community as one in which all species, and so all individuals, are equivalent, in the sense that they are interchangeable at all times and under all conditions. In contrast, we can define a structured community as one in which species are not equivalent, and species-specified differences affect the population dynamics, and therefore the behaviour of the community. This distinction is an important one, because in a neutral community the biodiversity, as measured by species richness and abundance patterns, has nothing to do with the biogeochemical functioning of the community (e.g. carbon fixation and nutrient-cycling). In fact, in a truly neutral community one could eliminate all but one species without affecting the biogeochemical functioning of the community at all. In contrast, much of the species-specific variation in biological traits observed in reality has direct relevance for the functioning of the community. For example, the short-term carbon uptake of a forest depends on the growth rates of the individual trees, and the long-term carbon storage depends on adult life-span and wood density, and there is wide species-specific variation in these traits. In niche-structured communities, the biodiversity and functioning are intimately linked, and some combination of at least some species is required to maintain the functioning of the community. In the most highly structured community possible there is no equivalence between any of the species, which is the so-called “one species one niche” idea so prevalent in the history of ecology: in such a community, removing just one species has a significant impact on the dynamics and functioning of the community. Which of these two pictures of communities – neutral or structured – is nearer to the truth? Is it “one species one niche” or “all species one niche”? This is the neutral vs structure debate, and it continues apace because there is good evidence for both sides of the argument.

8. Purves, D. W., and J. Dushoff, 2005: Directed seed dispersal and metapopulation response to habitat loss and disturbance: application to Eichhornia paniculata. Journal of Ecology, 93(4), doi:10.1111/j.1365-2745.2005.00988.x 658-669
   [ Abstract ]

   1. Seed dispersal is often directed towards locations with particular characteristics, particularly where seeds are dispersed by animals. The potential importance of directed seed dispersal for the response of plant metapopulations to habitat loss and changes in disturbance rate is assessed, and illustrated with a case study of a metapopulation of an aquatic plant. 2. The Levins model is extended to include preferential dispersal towards suitable habitat and towards unoccupied patches. Both increase patch occupancy, decrease the minimum habitat cover required for persistence and increase the maximum allowable disturbance rate, while preferential dispersal towards unoccupied patches also makes reductions in abundance due to increased disturbance rates more threshold-like. 3. Applying classical metapopulation approaches, which assume random dispersal, to a species that features directed dispersal, is expected to give systematic errors in prediction. For example, where dispersal is directed towards suitable habitat regardless of occupancy, the Levins model will tend to overestimate the response to habitat loss, and where dispersal is directed towards unoccupied patches, the Levins model will tend to underestimate the response to changes in disturbance rate. 4. Eichhornia paniculata is an aquatic plant restricted to ephemeral pools. Seed dispersal is by waterfowl, and so is directed towards suitable habitat. Data on habitat cover and patch occupancy from Husband and Barrett in 1998 fit well with our model but deviate significantly from the predictions of the Levins model. The parameter estimates imply dispersal very strongly directed towards suitable habitat, and that without this the minimum density of pools required for persistence would be at least 10 times greater than the highest densities observed, implying that the species would go locally extinct. 5. To our knowledge, this is the first quantitative demonstration that the nature and strength of directed dispersal affects the robustness of fragmented plant populations to anthropogenic disturbance. This calls for increased attention to be paid to the behaviour of seed-dispersing animals, and how this behaviour varies between different plant communities.

9. Purves, D. W., J. P. Caspersen, P. R. Moorcroft, G. C. Hurtt, and Stephen W. Pacala, 2004: Human-induced Changes in U.S. Biogenic Volatile Organic Compound Emissions: evidence from long-term forest inventory data. Global Change Biology, 10(10), doi:10.1111/j.1365-2486.2004.00844.x 1737-1755
   [ Abstract ]

   Volatile organic compounds (VOCs) emitted by woody vegetation influence global climate forcing and the formation of tropospheric ozone. We use data from over 250 000 re-surveyed forest plots in the eastern US to estimate emission rates for the two most important biogenic VOCs (isoprene and monoterpenes) in the 1980s and 1990s, and then compare these estimates to give a decadal change in emission rate. Over much of the region, particularly the southeast, we estimate that there were large changes in biogenic VOC emissions: half of the grid cells (1° X 1°) had decadal changes in emission rate outside the range -2.3% to +16.8% for isoprene, and outside the range 0.2–17.1% for monoterpenes. For an average grid cell the estimated decadal change in heatwave biogenic VOC emissions (usually an increase) was three times greater than the decadal change in heatwave anthropogenic VOC emissions (usually a decrease, caused by legislation). Leaf-area increases in forests, caused by anthropogenic disturbance, were the most important process increasing biogenic VOC emissions. However, in the southeast, which had the largest estimated changes, there were substantial effects of ecological succession (which decreased monoterpene emissions and had location-specific effects on isoprene emissions), harvesting (which decreased monoterpene emissions and increased isoprene emissions) and plantation management (which increased isoprene emissions, and decreased monoterpene emissions in some states but increased monoterpene emissions in others). In any given region, changes in a very few tree species caused most of the changes in emissions: the rapid changes in the southeast were caused almost entirely by increases in sweetgum (Liquidambar styraciflua) and a few pine species. Therefore, in these regions, a more detailed ecological understanding of just a few species could greatly improve our understanding of the relationship between natural ecological processes, forest management, and biogenic VOC emissions.

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