Ecologie & Evolution

Abstract The metacommunity concept is an important way to think about linkages between different spatial scales in ecology. Here we review current understanding about this concept. We first investigate issues related to its definition as a set of local communities that are linked by dispersal of multiple potentially interacting species. We then identify four paradigms for metacommunities: the patch‐dynamic view, the species‐sorting view, the mass effects view and the neutral view, that each emphasizes different processes of potential importance in metacommunities. These have somewhat distinct intellectual histories and we discuss elements related to their potential future synthesis. We then use this framework to discuss why the concept is useful in modifying existing ecological thinking and illustrate this with a number of both theoretical and empirical examples. As ecologists strive to understand increasingly complex mechanisms and strive to work across multiple scales of spatio‐temporal organization, concepts like the metacommunity can provide important insights that frequently contrast with those that would be obtained with more conventional approaches based on local communities alone.

Boreal and subarctic peatlands comprise a carbon pool of 455 Pg that has accumulated during the postglacial period at an average net rate of 0.096 Pg/yr (1 Pg = 10 1 5 g). Using Clymo's (1984) model, the current rate is estimated at 0.076 Pg/yr. Longterm drainage of these peatlands is estimated to be causing the oxidation to CO 2 of a little more than 0.0085 Pg/yr, with conbustion of fuel peat adding °0.026 Pg/yr. Emissions of CH 4 are estimated to release ° 0.046 Pg of carbon annually. Uncertainties beset estimates of both stocks and fluxes, particularly with regard to Soviet peatlands. The influence of water table alterations upon fluxes of both CO 2 and CH 4 is in great need of investigation over a wide range of peatland environments, especially in regions where permafrost melting, thermokarst erosion, and the development of thaw lakes are likely results of climatic warming. The role of fire in the carbon cycle of peatlands also deserves increased attention. Finally, satellite—monitoring of the abundance of open water in the peatlands of the West Siberian Plain and the Hudson/James Bay Lowland is suggested as a likely method of detecting early effects of climatic warming upon boreal and subarctic peatlands.

Species distributional or trait data based on range map (extent‐of‐occurrence) or atlas survey data often display spatial autocorrelation, i.e. locations close to each other exhibit more similar values than those further apart. If this pattern remains present in the residuals of a statistical model based on such data, one of the key assumptions of standard statistical analyses, that residuals are independent and identically distributed (i.i.d), is violated. The violation of the assumption of i.i.d. residuals may bias parameter estimates and can increase type I error rates (falsely rejecting the null hypothesis of no effect). While this is increasingly recognised by researchers analysing species distribution data, there is, to our knowledge, no comprehensive overview of the many available spatial statistical methods to take spatial autocorrelation into account in tests of statistical significance. Here, we describe six different statistical approaches to infer correlates of species’ distributions, for both presence/absence (binary response) and species abundance data (poisson or normally distributed response), while accounting for spatial autocorrelation in model residuals: autocovariate regression; spatial eigenvector mapping; generalised least squares; (conditional and simultaneous) autoregressive models and generalised estimating equations. A comprehensive comparison of the relative merits of these methods is beyond the scope of this paper. To demonstrate each method's implementation, however, we undertook preliminary tests based on simulated data. These preliminary tests verified that most of the spatial modeling techniques we examined showed good type I error control and precise parameter estimates, at least when confronted with simplistic simulated data containing spatial autocorrelation in the errors. However, we found that for presence/absence data the results and conclusions were very variable between the different methods. This is likely due to the low information content of binary maps. Also, in contrast with previous studies, we found that autocovariate methods consistently underestimated the effects of environmental controls of species distributions. Given their widespread use, in particular for the modelling of species presence/absence data (e.g. climate envelope models), we argue that this warrants further study and caution in their use. To aid other ecologists in making use of the methods described, code to implement them in freely available software is provided in an electronic appendix.

Negative environmental consequences of fossil fuels and concerns about petroleum supplies have spurred the search for renewable transportation biofuels. To be a viable alternative, a biofuel should provide a net energy gain, have environmental benefits, be economically competitive, and be producible in large quantities without reducing food supplies. We use these criteria to evaluate, through life-cycle accounting, ethanol from corn grain and biodiesel from soybeans. Ethanol yields 25% more energy than the energy invested in its production, whereas biodiesel yields 93% more. Compared with ethanol, biodiesel releases just 1.0%, 8.3%, and 13% of the agricultural nitrogen, phosphorus, and pesticide pollutants, respectively, per net energy gain. Relative to the fossil fuels they displace, greenhouse gas emissions are reduced 12% by the production and combustion of ethanol and 41% by biodiesel. Biodiesel also releases less air pollutants per net energy gain than ethanol. These advantages of biodiesel over ethanol come from lower agricultural inputs and more efficient conversion of feedstocks to fuel. Neither biofuel can replace much petroleum without impacting food supplies. Even dedicating all U.S. corn and soybean production to biofuels would meet only 12% of gasoline demand and 6% of diesel demand. Until recent increases in petroleum prices, high production costs made biofuels unprofitable without subsidies. Biodiesel provides sufficient environmental advantages to merit subsidy. Transportation biofuels such as synfuel hydrocarbons or cellulosic ethanol, if produced from low-input biomass grown on agriculturally marginal land or from waste biomass, could provide much greater supplies and environmental benefits than food-based biofuels.

All organisms, especially terrestrial plants and other sessile species, interact mainly with their neighbors, but neighborhoods can differ in composition because of dispersal and mortality. There is increasingly strong evidence that the spatial structure created by these forces profoundly influences the dynamics, composition, and biodiversity of communities. Nonspatial models predict that no more consumer species can coexist at equilibrium than there are limiting resources. In contrast, a similar model that includes neighborhood competition and random dispersal among sites predicts stable coexistence of a potentially unlimited number of species on a single resource. Coexistence occurs because species with sufficiently high dispersal rates persist in sites not occupied by superior competitors. Coexistence requires limiting similarity and two—way or three—way interspecific trade—offs among competitive ability, colonization ability, and longevity. This spatial competition hypothesis seems to explain the coexistence of the numerous plant species that compete for a single limiting resource in the grasslands of Cedar Creek Natural History Area. It provides a testable, alternative explanation for other high diversity communities, such as tropical forests. The model can be tested (1) by determining if coexisting species have the requisite trade—offs in colonization, competition, and longevity, (2) by addition of propagules of propagules to determine if local species abundances are limited by dispersal, and (3) by comparisons of the effects on biodiversity of high rates of propagule addition for species that differ in competitive ability.

(Uploaded by Plazi for the Bat Literature Project) No abstract provided.

Selection against deleterious alleles maintained by mutation may cause a reduction in the amount of genetic variability at linked neutral sites. This is because a new neutral variant can only remain in a large population for a long period of time if it is maintained in gametes that are free of deleterious alleles, and hence are not destined for rapid elimination from the population by selection. Approximate formulas are derived for the reduction below classical neutral values resulting from such background selection against deleterious mutations, for the mean times to fixation and loss of new mutations, nucleotide site diversity, and number of segregating sites. These formulas apply to random-mating populations with no genetic recombination, and to populations reproducing exclusively asexually or by self-fertilization. For a given selection regime and mating system, the reduction is an exponential function of the total mutation rate to deleterious mutations for the section of the genome involved. Simulations show that the effect decreases rapidly with increasing recombination frequency or rate of outcrossing. The mean time to loss of new neutral mutations and the total number of segregating neutral sites are less sensitive to background selection than the other statistics, unless the population size is of the order of a hundred thousand or more. The stationary distribution of allele frequencies at the neutral sites is correspondingly skewed in favor of rare alleles, compared with the classical neutral result. Observed reductions in molecular variation in low recombination genomic regions of sufficiently large size, for instance in the centromere-proximal regions of Drosophila autosomes or in highly selfing plant populations, may be partly due to background selection against deleterious mutations.

It is predicted that climate change will cause species extinctions and distributional shifts in coming decades, but data to validate these predictions are relatively scarce. Here, we compare recent and historical surveys for 48 Mexican lizard species at 200 sites. Since 1975, 12% of local populations have gone extinct. We verified physiological models of extinction risk with observed local extinctions and extended projections worldwide. Since 1975, we estimate that 4% of local populations have gone extinct worldwide, but by 2080 local extinctions are projected to reach 39% worldwide, and species extinctions may reach 20%. Global extinction projections were validated with local extinctions observed from 1975 to 2009 for regional biotas on four other continents, suggesting that lizards have already crossed a threshold for extinctions caused by climate change.

Biodiversity lies at the core of ecosystem processes fueling our planet's vital life-support systems; its degradation--by us--is threatening our own well-being and will disproportionately impact the poor.

Abstract Recognition of the importance of land-use history and its legacies in most ecological systems has been a major factor driving the recent focus on human activity as a legitimate and essential subject of environmental science. Ecologists, conservationists, and natural resource policymakers now recognize that the legacies of land-use activities continue to influence ecosystem structure and function for decades or centuries—or even longer—after those activities have ceased. Consequently, recognition of these historical legacies adds explanatory power to our understanding of modern conditions at scales from organisms to the globe and reduces missteps in anticipating or managing for future conditions. As a result, environmental history emerges as an integral part of ecological science and conservation planning. By considering diverse ecological phenomena, ranging from biodiversity and biogeochemical cycles to ecosystem resilience to anthropogenic stress, and by examining terrestrial and aquatic ecosystems in temperate to tropical biomes, this article demonstrates the ubiquity and importance of land-use legacies to environmental science and management.

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In 1982, experimental nitrogen gradients were established on both existing and disturbed (disked) vegetation in three fields (abandoned 14, 25, and 48 yr) and on existing vegetation in native oak savannah. Each of these seven gradients contained five or six replicates of each of nine treatments that differed in the annual rate of nitrogen addition. In none of the fields did plant biomass, height, species richness, or light penetration respond to addition of P, K, Ca, Mg, S, and trace metals. In contrast, plant biomass and height increased significantly, and light penetration and species richness decreased significantly, with added nitrogen along all seven gradients. On average, >60% of the species had been displaced from high—nitrogen treatments by 1985. Nitrogen addition led to a period of transient dominance by certain species. Species that reached peak relative abundance in high—nitrogen treatments in 1982 tended to be rare in all but the low—nitrogen treatments by 1985. In contrast, the relative abundances of most species that dominated the high—nitrogen treatments in 1985 did not increase along the nitrogen gradients in 1982. The relative or absolute abundances of most common species changed significantly along the experimental gradients in at least 1 yr. By 1985, many common species were differentiated in their distributions along the seven gradients. In general, early successional annuals and short—lived perennials and plants of short stature at maturity reached their peak abundance in low—nitrogen plots, whereas plots, receiving high rates of nitrogen addition were dominated by long—lived herbaceous and woody species that are taller at maturity. A survey of 22 old fields at Cedar Creek, Minnesota, showed that total and available soil nitrogen increased during succession and that major species had individualistic, fairly Gaussian distributions along this temporal nitrogen gradient. The distributions along the experimental gradients of most of the common species were consistent with the pattern observed in the old—field survey, demonstrating that nitrogen influences the pattern of secondary succession at Cedar Creek. The major exception was Agropyron repens, and early successional grass that dominated high—nitrogen treatments on six of the seven gradients. Comparisons of species responses on the disturbed plots with those on plots of existing (undisturbed) vegetation showed that, by 1985, most species responded similarly to the nitrogen gradients despite great differences in their initial abundances. For instance, Agropyron repens, an initial dominant of Field A but rare in Fields B and C, was dominant in the high—nitrogen treatments in both the disturbed and undisturbed plots of these three fields. It invaded into and rapidly increased in abundance in numerous high—nitrogen plots from which it was initially absent. Schizachyrium scoparium declined along the nitrogen gradients both in undisked plots in which it was initially dominant and in disked plots in which it was initially rare. Such similarities suggest that the outcome of interspecific interactions among old—field plants is highly dependent on nitrogen supply rates, but fairly independent of initial plant abundances.

Modest dietary restriction (DR) prolongs life in a wide range of organisms, spanning single-celled yeast to mammals. Here, we report the use of recent techniques in nutrition research to quantify the detailed relationship between diet, nutrient intake, lifespan, and reproduction in Drosophila melanogaster. Caloric restriction (CR) was not responsible for extending lifespan in our experimental flies. Response surfaces for lifespan and fecundity were maximized at different protein-carbohydrate intakes, with longevity highest at a protein-to-carbohydrate ratio of 1:16 and egg-laying rate maximized at 1:2. Lifetime egg production, the measure closest to fitness, was maximized at an intermediate P:C ratio of 1:4. Flies offered a choice of complementary foods regulated intake to maximize lifetime egg production. The results indicate a role for both direct costs of reproduction and other deleterious consequences of ingesting high levels of protein. We unite a body of apparently conflicting work within a common framework and provide a platform for studying aging in all organisms.

Several estimators of population differentiation have been proposed in the recent past to deal with various types of genetic markers (i.e., allozymes, nucleotide sequences, restriction fragment length polymorphisms, or microsatellites). We discuss the relationships among these estimators and show how a single analysis of variance framework can accomodate these qualitatively different data types.

We implement a Bayesian Markov chain Monte Carlo algorithm for estimating species divergence times that uses heterogeneous data from multiple gene loci and accommodates multiple fossil calibration nodes. A birth-death process with species sampling is used to specify a prior for divergence times, which allows easy assessment of the effects of that prior on posterior time estimates. We propose a new approach for specifying calibration points on the phylogeny, which allows the use of arbitrary and flexible statistical distributions to describe uncertainties in fossil dates. In particular, we use soft bounds, so that the probability that the true divergence time is outside the bounds is small but nonzero. A strict molecular clock is assumed in the current implementation, although this assumption may be relaxed. We apply our new algorithm to two data sets concerning divergences of several primate species, to examine the effects of the substitution model and of the prior for divergence times on Bayesian time estimation. We also conduct computer simulation to examine the differences between soft and hard bounds. We demonstrate that divergence time estimation is intrinsically hampered by uncertainties in fossil calibrations, and the error in Bayesian time estimates will not go to zero with increased amounts of sequence data. Our analyses of both real and simulated data demonstrate potentially large differences between divergence time estimates obtained using soft versus hard bounds and a general superiority of soft bounds. Our main findings are as follows. (1) When the fossils are consistent with each other and with the molecular data, and the posterior time estimates are well within the prior bounds, soft and hard bounds produce similar results. (2) When the fossils are in conflict with each other or with the molecules, soft and hard bounds behave very differently; soft bounds allow sequence data to correct poor calibrations, while poor hard bounds are impossible to overcome by any amount of data. (3) Soft bounds eliminate the need for "safe" but unrealistically high upper bounds, which may bias posterior time estimates. (4) Soft bounds allow more reliable assessment of estimation errors, while hard bounds generate misleadingly high precisions when fossils and molecules are in conflict.

BACKGROUND: Forest, grass, and peat fires release approximately 2 petagrams of carbon into the atmosphere each year, influencing weather, climate, and air quality. OBJECTIVE: We estimated the annual global mortality attributable to landscape fire smoke (LFS). METHODS: Daily and annual exposure to particulate matter ≤ 2.5 μm in aerodynamic diameter (PM(2.5)) from fire emissions was estimated globally for 1997 through 2006 by combining outputs from a chemical transport model with satellite-based observations of aerosol optical depth. In World Health Organization (WHO) subregions classified as sporadically affected, the daily burden of mortality was estimated using previously published concentration-response coefficients for the association between short-term elevations in PM(2.5) from LFS (contrasted with 0 μg/m3 from LFS) and all-cause mortality. In subregions classified as chronically affected, the annual burden of mortality was estimated using the American Cancer Society study coefficient for the association between long-term PM(2.5) exposure and all-cause mortality. The annual average PM(2.5) estimates were contrasted with theoretical minimum (counterfactual) concentrations in each chronically affected subregion. Sensitivity of mortality estimates to different exposure assessments, counterfactual estimates, and concentration-response functions was evaluated. Strong La Niña and El Niño years were compared to assess the influence of interannual climatic variability. RESULTS: Our principal estimate for the average mortality attributable to LFS exposure was 339,000 deaths annually. In sensitivity analyses the interquartile range of all tested estimates was 260,000-600,000. The regions most affected were sub-Saharan Africa (157,000) and Southeast Asia (110,000). Estimated annual mortality during La Niña was 262,000, compared with 532,000 during El Niño. CONCLUSIONS: Fire emissions are an important contributor to global mortality. Adverse health outcomes associated with LFS could be substantially reduced by curtailing burning of tropical rainforests, which rarely burn naturally. The large estimated influence of El Niño suggests a relationship between climate and the burden of mortality attributable to LFS.

Three markedly different models of multispecies competition-one mechanistic, one phenomenological, and one statistical-all predict that greater diversity increases the temporal stability of the entire community, decreases the temporal stability of individual populations, and increases community productivity. We define temporal stability as the ratio of mean abundance to its standard deviation. Interestingly, the temporal stability of entire communities is predicted to increase fairly linearly, without clear saturation, as diversity increases. Species composition is predicted to be as important as diversity in affecting community stability and productivity. The greater temporal stability of more diverse communities is caused by higher productivity at higher diversity (the "overyielding" effect), competitive interactions (the "covariance" effect), and statistical averaging (the "portfolio" effect). The relative contribution of each cause of temporal stability changes as diversity increases, but the net effect is that greater diversity stabilizes the community even though it destabilizes individual populations. This theory agrees with recent experiments and provides a degree of resolution to the diversity-stability debate: both sides of the longstanding debate were correct, but one addressed population stability and the other addressed community stability.

Abstract Many museums and academic institutions maintain first-rate collections of biological materials, ranging from preserved whole organisms to DNA libraries and cell lines. These biological collections make innumerable contributions to science and society in areas as divergent as homeland security, public health and safety, monitoring of environmental change, and traditional taxonomy and systematics. Moreover, these collections save governments and taxpayers many millions of dollars each year by effectively guiding government spending, preventing catastrophic events in public health and safety, eliminating redundancy, and securing natural and agricultural resources. However, these contributions are widely underappreciated by the public and by policymakers, resulting in insufficient financial support for maintenance and improvement of biological collections.

The development of mechanistic, predictive ecological theory will entail the explicit inclusion of organismal tradeoffs, of environmental constraints, and of the basic mechanisms of interspecific interaction. This approach was used to address the causes of species dominance and successional dynamics in sandplain vegetation in Minnesota. A series of field experiments performed over the last eight years have shown that the major constraints on plants were soil nitrogen and disturbance, with nitrogen competition being a major force. Nutrients other than nitrogen (P, K, Ca, Mg, S and trace metals), herbivory, and light were of minor importance. As predicted by theory, the superior nitrogen competitors were the species that, when growing in long-term monocultures in the field, lowered soil extractable N the most. These species had high root biomass and low tissue N levels. Seven alternative hypotheses of succession, each named after its underlying tradeoff, were proposed and tested. The colonization - nutrient competition hypothesis provided the best explanation for the initial dominance (years 0 to 40) of herbs, whereas the nutrient versus light competition hypothesis best explained the long-term dominance by woody plants. Hypotheses involving transient dynamics caused by differences in maximal growth rates were rejected. In total, the results demonstrate that the inclusion of simple mechanisms of interspecific interactions, and of allocationbased tradeoffs, can allow models to predict the composition and successional dynamics of vegetation.

The interaction of climate and the timing of low tides along the West Coast of the United States creates a complex mosaic of thermal environments, in which northern sites can be more thermally stressful than southern sites. Thus, climate change may not lead to a poleward shift in the distribution of intertidal organisms, as has been proposed, but instead will likely cause localized extinctions at a series of "hot spots." Patterns of exposure to extreme climatic conditions are temporally variable, and tidal predictions suggest that in the next 3 to 5 years "hot spots" are likely to appear at several northern sites.