Bibliography - J. Dushoff

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. 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.

3. Lichstein, J W., J. Dushoff, S. A. Levin, and Stephen W. Pacala, 2007: Intraspecific variation and species coexistence. American Naturalist, 170(6), doi:10.1086/522937 807-818
   [ Abstract ]

   We use a two-species model of plant competition to explore the effect of intraspecific variation on community dynamics. The competitive ability (“performance”) of each individual is assigned by an independent random draw from a species-specific probability distribution. If the density of individuals competing for open space is high (e.g., because fecundity is high), species with high maximum (or large variance in) performance are favored, while if density is low, species with high typical (e.g., mean) performance are favored. If there is an interspecific mean-variance performance trade-off, stable coexistence can occur across a limited range of intermediate densities, but the stabilizing effect of this trade-off appears to be weak. In the absence of this trade-off, one species is superior. In this case, intraspecific variation can blur interspecific differences (i.e., shift the dynamics toward what would be expected in the neutral case), but the strength of this effect diminishes as competitor density increases. If density is sufficiently high, the inferior species is driven to extinction just as rapidly as in the case where there is no overlap in performance between species. Intraspecific variation can facilitate coexistence, but this may be relatively unimportant in maintaining diversity in most real communities.

4. 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.

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