Mathematica code for "A general framework for species-abundance distributions: linking traits and dispersal to explain commonness and rarity", Ecology Letters. Requires: Wolfram Mathematica (tested on v13.1) EcoEvo package (tested on v1.6.4) This research was supported by the Simons Foundation grant 343149, NSF grant DEB 17-54250 and NASA grant 80NSSC18K1084. Copyright: Creative Commons Attribution 4.0 International Open Access

Mathematica code for "A general framework for species-abundance distributions: linking traits and dispersal to explain commonness and rarity", Ecology Letters. Requires: Wolfram Mathematica (tested on v13.1) EcoEvo package (tested on v1.6.4) This research was supported by the Simons Foundation grant 343149, NSF grant DEB 17-54250 and NASA grant 80NSSC18K1084. Copyright: Creative Commons Attribution 4.0 International Open Access

Dental microwear consists of microscopic damage features on the occlusal surfaces of tooth enamel and reflects physical properties of the diet, as well as enamel structure and post- mortem history of the tooth. Microwear analysis has been used to infer the diets of extinct mammals through comparison of features on fossil teeth with those on teeth of living mammals with known diets. A method for documenting microwear of large mammals using a light microscope was developed as an alternative to approaches based on scanning electron microscopy. We adapted this method for investigating microwear features on squirrel teeth. Both modern and fossil squirrels occur in diverse terrestrial habitats and eat a range of herbivorous to omnivorous diets.

Dental microwear consists of microscopic damage features on the occlusal surfaces of tooth enamel and reflects physical properties of the diet, as well as enamel structure and post-mortem history of the tooth. Microwear analysis has been used to infer the diets of extinct mammals through comparison of features on fossil teeth with those on teeth of living mammals with known diets. A method for documenting microwear of large mammals using a light microscope was developed as an alternative to approaches based on scanning electron microscopy. We adapted this method for investigating microwear features on squirrel teeth. Both modern and fossil squirrels occur in diverse terrestrial habitats and eat a range of herbivorous to omnivorous diets. We compared microwear features from upper molars of several modern species of frugivorous tree squirrels and omnivorous ground squirrels. We also examined fossil sciurids from the Miocene Siwalik sequence of Pakistan and a Pliocene locality in the central plains of the United States. We found significant differences in microwear features among modern squirrels of different diets and habitats, suggesting that microwear features can be used to infer the diets or preferred habitats of extinct species. Microwear features were preserved on some of the fossil specimens. A comparison of Pliocene Spermophilus rexroadensis to modern Spermophilus suggests a diet similar to that of the modern species examined. Microwear of Miocene Eutamias differed from the pattern in any of the living squirrels examined. The approach presented here holds strong potential for illuminating the trophic ecomorphology of small-mammal fossils.

The principal objections to the proposition that organic agriculture can contribute significantly to the global food supply are low yields and insufficient quantities of organically acceptable fertilizers. We evaluated the universality of both claims. For the first claim, we compared yields of organic versus conventional or low-intensive food production for a global dataset of 293 examples and estimated the average yield ratio (organic: non-organic) of different food categories for the developed and the developing world. For most food categories, the average yield ratio was slightly < 1.0 for studies in the developed world and > 1.0 for studies in the developing world. With the average yield ratios, we modeled the global food supply that could be grown organically on the current agricultural land base. Model estimates indicate that organic methods could produce enough food on a global per capita basis to sustain the current human population, and potentially an even larger population, without increasing the agricultural land base. We also evaluated the amount of nitrogen potentially available from fixation by leguminous cover crops used as fertilizer. Data from temperate and tropical agroecosystems suggest that leguminous cover crops could fix enough nitrogen to replace the amount of synthetic fertilizer currently in use. These results indicate that organic agriculture has the potential to contribute quite substantially to the global food supply, while reducing the detrimental environmental impacts of conventional agriculture. Evaluation and review of this paper have raised important issues about crop rotations under organic versus conventional agriculture and the reliability of grey-literature sources. An ongoing dialogue on these subjects can be found in the Forum editorial of this issue.

When aerobic microbes deplete oxygen sufficiently, anaerobic metabolisms activate, driving losses of fixed nitrogen from marine oxygen minimum zones. Biogeochemical models commonly prescribe a 1-10 mu M critical oxygen concentration for this transition, a range consistent with previous empirical and recent theoretical work. However, the recently developed STOX sensor has revealed large regions with much lower oxygen concentrations, at or below its 1-10 nM detection limit. Here, we develop a simplified metabolic model of an aerobic microbe to provide a theoretical interpretation of this observed depletion. We frame the threshold as O*(2), the subsistence oxygen concentration of an aerobic microbial metabolism, at which anaerobic metabolisms can coexist with or outcompete aerobic growth. The framework predicts that this minimum oxygen concentration varies with environmental and physiological factors and is in the nanomolar range for most marine environments, consistent with observed concentrations. Using observed grazing rates to calibrate the model, we predict a minimum oxygen concentration of order 0.1-10 nM in the core of a coastal anoxic zone. We also present an argument for why anammox may be energetically favorable at a higher oxygen concentration than denitrification, as some observations suggest. The model generates hypotheses that could be tested in the field and provides a simple, mechanistic, and dynamic parameterization of oxygen depletion for biogeochemical models, without prescription of a fixed critical oxygen concentration.

Microorganisms oxidize organic nitrogen to nitrate in a series of steps. Nitrite, an intermediate product, accumulates at the base of the sunlit layer in the subtropical ocean, forming a primary nitrite maximum, but can accumulate throughout the sunlit layer at higher latitudes. We model nitrifying chemoautotrophs in a marine ecosystem and demonstrate that microbial community interactions can explain the nitrite distributions. Our theoretical framework proposes that nitrite can accumulate to a higher concentration than ammonium because of differences in underlying redox chemistry and cell size between ammonia- and nitrite-oxidizing chemoautotrophs. Using ocean circulation models, we demonstrate that nitrifying microorganisms are excluded in the sunlit layer when phytoplankton are nitrogen-limited, but thrive at depth when phytoplankton become light-limited, resulting in nitrite accumulation there. However, nitrifying microorganisms may coexist in the sunlit layer when phytoplankton are iron-or light-limited (often in higher latitudes). These results improve understanding of the controls on nitrification, and provide a framework for representing chemoautotrophs and their biogeochemical effects in ocean models.

Mechanistic description of the transition from aerobic to anaerobic metabolism is necessary for diagnostic and predictive modeling of fixed nitrogen loss in anoxic marine zones (AMZs). In a metabolic model where diverse oxygen- and nitrogen-cycling microbial metabolisms are described by underlying redox chemical reactions, we predict a transition from strictly aerobic to predominantly anaerobic regimes as the outcome of ecological interactions along an oxygen gradient, obviating the need for prescribed critical oxygen concentrations. Competing aerobic and anaerobic metabolisms can coexist in anoxic conditions whether these metabolisms represent obligate or facultative populations. In the coexistence regime, relative rates of aerobic and anaerobic activity are determined by the ratio of oxygen to electron donor supply. The model simulates key characteristics of AMZs, such as the accumulation of nitrite and the sustainability of anammox at higher oxygen concentrations than denitrification, and articulates how microbial biomass concentrations relate to associated water column transformation rates as a function of redox stoichiometry and energetics. Incorporating the metabolic model into an idealized two-dimensional ocean circulation results in a simulated AMZ, in which a secondary chlorophyll maximum emerges from oxygen-limited grazing, and where vertical mixing and dispersal in the oxycline also contribute to metabolic co-occurrence. The modeling approach is mechanistic yet computationally economical and suitable for global change applications.