Adam D. Miller

How frequency and intensity shape diversity–disturbance relationships

Understanding the relationship between disturbance regimes and species diversity has been of central interest to ecologists for decades. For example, the intermediate disturbance hypothesis proposes that diversity will be highest at intermediate levels of disturbance. Although peaked (hump-shaped) diversity–disturbance relationships (DDRs) have been documented in nature, many other DDRs have been reported as well. Here, we begin to theoretically unify these diverse empirical findings by showing how a single simple model can generate several different DDRs, depending on the aspect of disturbance that is considered. Additionally, we elucidate the competition-mediated mechanism underlying our results. Our findings have the potential to reconcile apparently conflicting empirical results on the effects of disturbance on diversity.

Altered dynamics of forest recovery under a changing climate

Forest regeneration following disturbance is a key ecological process, influencing forest structure and function, species assemblages, and ecosystem-climate interactions. Climate change may alter forest recovery dynamics or even prevent recovery, triggering feedbacks to the climate system, altering regional biodiversity, and affecting the ecosystem services provided by forests. Multiple lines of evidence - including global-scale patterns in forest recovery dynamics; forest responses to experimental manipulation of CO2 , temperature, and precipitation; forest responses to the climate change that has already occurred; ecological theory; and ecosystem and earth system models - all indicate that the dynamics of forest recovery are sensitive to climate. However, synthetic understanding of how atmospheric CO2 and climate shape trajectories of forest recovery is lacking. Here, we review these separate lines of evidence, which together demonstrate that the dynamics of forest recovery are being impacted by increasing atmospheric CO2 and changing climate. Rates of forest recovery generally increase with CO2 , temperature, and water availability. Drought reduces growth and live biomass in forests of all ages, having a particularly strong effect on seedling recruitment and survival. Responses of individual trees and whole-forest ecosystems to CO2 and climate manipulations often vary by age, implying that forests of different ages will respond differently to climate change. Furthermore, species within a community typically exhibit differential responses to CO2 and climate, and altered community dynamics can have important consequences for ecosystem function. Age- and species-dependent responses provide a mechanism by which climate change may push some forests past critical thresholds such that they fail to recover to their previous state following disturbance. Altered dynamics of forest recovery will result in positive and negative feedbacks to climate change. Future research on this topic and corresponding improvements to earth system models will be a key to understanding the future of forests and their feedbacks to the climate system.

The theoretical limit to plant productivity.

Human population and economic growth are accelerating the demand for plant biomass to provide food, fuel, and fiber. The annual increment of biomass to meet these needs is quantified as net primary production (NPP). Here we show that an underlying assumption in some current models may lead to underestimates of the potential production from managed landscapes, particularly of bioenergy crops that have low nitrogen requirements. Using a simple light-use efficiency model and the theoretical maximum efficiency with which plant canopies convert solar radiation to biomass, we provide an upper-envelope NPP unconstrained by resource limitations. This theoretical maximum NPP approached 200 tC ha(-1) yr(-1) at point locations, roughly 2 orders of magnitude higher than most current managed or natural ecosystems. Recalculating the upper envelope estimate of NPP limited by available water reduced it by half or more in 91% of the land area globally. While the high conversion efficiencies observed in some extant plants indicate great potential to increase crop yields without changes to the basic mechanism of photosynthesis, particularly for crops with low nitrogen requirements, realizing such high yields will require improvements in water use efficiency.

Diversity–disturbance relationships: frequency and intensity interact

An influential ecological theory, the intermediate disturbance hypothesis (IDH), predicts that intermediate levels of disturbance will maximize species diversity. Empirical studies, however, have described a wide variety of diversity–disturbance relationships (DDRs). Using experimental populations of microbes, we show that the form of the DDR depends on an interaction between disturbance frequency and intensity. We find that diversity shows a monotonically increasing, unimodal or flat relationship with disturbance, depending on the values of the disturbance aspects considered. These results confirm recent theoretical predictions, and potentially reconcile the conflicting body of empirical evidence on DDRs.

Atomic-level functional model of dengue virus Envelope protein infectivity

Significance Dengue virus (DENV) infects nearly 400 million people annually, and approximately 40% of the world’s population lives at risk for infection. Without a therapeutic or vaccine available, DENV remains a major public health burden. Our studies provide a comprehensive structure–function analysis of the DENV Envelope protein, integrating information from numerous Envelope structures with our functional data into a cohesive mechanistic model. This model describes the dynamic processes by which specific residue interactions within Envelope mediate infectivity—from fusion-loop triggering to hinge movement to membrane fusion—and may also apply to related class II viral fusion proteins. Because of the importance of the specific amino acids identified, our results also identify new functional residue targets for DENV vaccines and therapeutics. A number of structures have been solved for the Envelope (E) protein from dengue virus and closely related flaviviruses, providing detailed pictures of the conformational states of the protein at different stages of infectivity. However, the key functional residues responsible for mediating the dynamic changes between these structures remain largely unknown. Using a comprehensive library of functional point mutations covering all 390 residues of the dengue virus E protein ectodomain, we identified residues that are critical for virus infectivity, but that do not affect E protein expression, folding, virion assembly, or budding. The locations and atomic interactions of these critical residues within different structures representing distinct fusogenic conformations help to explain how E protein (i) regulates fusion-loop exposure by shielding, tethering, and triggering its release; (ii) enables hinge movements between E domain interfaces during triggered structural transformations; and (iii) drives membrane fusion through late-stage zipper contacts with stem. These results provide structural targets for drug and vaccine development and integrate the findings from structural studies and isolated mutagenesis efforts into a cohesive model that explains how specific residues in this class II viral fusion protein enable virus infectivity.

Stacked Crop Rotations Exploit Weed-Weed Competition for Sustainable Weed Management

Abstract Crop rotation has long been considered one of the simplest and most effective tools for managing weeds. In this paper, we demonstrate how crop rotations can be strategically arranged to harness a novel mechanism of weed suppression: weed-weed competition. Specifically, we consider how crop stacking, or increasing the number of consecutive plantings of a single crop within a rotation, can decrease the size of the weed seed bank, by forcing weeds to compete with each other in similar environments for longer periods of time, while still reaping the traditional benefits of crop rotation. Using an annual plant model, we investigate the theoretical effects of stacked crop rotations on weeds that have different life-history strategies and phenology. Our results show that when weeds compete within a season, stacking can reduce the weed seed bank compared to rotations without stacked crops. Although more research is needed to fully understand the effects of crop stacking on other aspects of the system, such as insect pests and diseases, our research suggests that crop stacking has the potential to improve weed suppression without additional inputs, and their associated costs and externalities. More generally, improving management by changing the temporal arrangement of disturbances is a novel, process-based approach that could likely be applied to other weed management practices, such as mowing and herbicide application, and which could involve mechanisms other than weed-weed competition. Leveraging this new application of existing ecological theory to improve weed management strategies holds great promise.

Interactions between frequency and size of disturbance affect competitive outcomes

Disturbance has many effects on ecological communities, and it is often suggested that disturbance can affect species diversity by altering competitive outcomes. However, disturbance regimes have many distinct aspects that may act, and interact, to influence species diversity. While there are many theoretical models of disturbance-prone communities, few have specifically documented how interactions between different aspects of a disturbance regime change competitive outcomes. Here, we present a model of two plant species subject to disturbance which we then use to examine species coexistence over varying levels of two aspects of disturbance: frequency, and spatial extent (i.e., area disturbed). We show that the competitive outcome is affected differently by changes in each aspect and that the effect of disturbance frequency on species coexistence depends strongly on the spatial extent of the disturbance, and vice versa. We classify the nature of these interactions between disturbance frequency and extent on the basis of the shape of the resulting coexistence regions in a frequency–extent parameter plane. Our results illustrate that different types of interaction can result from differences in life-history traits that control species-specific sensitivity to frequency and extent of disturbance. Thus, our analysis shows that the various aspects of disturbance must be carefully considered in concert with the life-history traits of the community members in order to assess the consequences of disturbance.

Timing of disturbance alters competitive outcomes and mechanisms of coexistence in an annual plant model

Ecological disturbance is inherently a multi-faceted phenomenon; disturbance events can differ in distinct quantifiable aspects, such as intensity, duration, spatial extent, and time since last disturbance. Though effects of disturbance timing (specifically, time within a season) have been investigated empirically, theoretical work is lacking, in part because effects of disturbance may depend on the timing relative to the life cycle of the species in question. To demonstrate a theoretical basis for the effects of timing, we develop a model of annual plants subject to soil disturbance. We show that timing of disturbance can have significant effects on community composition. In addition, we quantify the mechanisms of coexistence acting under different timing regimes and show that differences in timing lead to different coexistence mechanisms. Specifically, we find that early disturbance (which enhances germination from the seed bank) generates the storage effect, whereas coexistence under late disturbance (which reduces adult fecundity and contributions to the soil seed bank) depends more on relative nonlinearity of competition. We discuss these two distinct mechanisms within the context of the underlying ecological processes, and we also briefly consider the broader implications of our analyses for disturbance timing in real communities. Our findings extend ecological disturbance theory by linking timing to specific competitive outcomes and can be applied to a wide range of disturbance-prone communities. Because we identify the underlying mechanisms resulting from different disturbance timings, our results can potentially inform theory for conservation and invasive species management practice.

Alteration of forest succession and carbon cycling under elevated CO2

Regenerating forests influence the global carbon (C) cycle, and understanding how climate change will affect patterns of regeneration and C storage is necessary to predict the rate of atmospheric carbon dioxide (CO2 ) increase in future decades. While experimental elevation of CO2 has revealed that young forests respond with increased productivity, there remains considerable uncertainty as to how the long-term dynamics of forest regrowth are shaped by elevated CO2 (eCO2 ). Here, we use the mechanistic size- and age- structured Ecosystem Demography model to investigate the effects of CO2 enrichment on forest regeneration, using data from the Duke Forest Free-Air Carbon dioxide Enrichment (FACE) experiment, a forest chronosequence, and an eddy-covariance tower for model parameterization and evaluation. We find that the dynamics of forest regeneration are accelerated, and stands consistently hit a variety of developmental benchmarks earlier under eCO2 . Because responses to eCO2 varied by plant functional type, successional pathways, and mature forest composition differed under eCO2 , with mid- and late-successional hardwood functional types experiencing greater increases in biomass compared to early-successional functional types and the pine canopy. Over the simulation period, eCO2 led to an increase in total ecosystem C storage of 9.7 Mg C ha(-1) . Model predictions of mature forest biomass and ecosystem-atmosphere exchange of CO2 and H2 O were sensitive to assumptions about nitrogen limitation; both the magnitude and persistence of the ecosystem response to eCO2 were reduced under N limitation. In summary, our simulations demonstrate that eCO2 can result in a general acceleration of forest regeneration while altering the course of successional change and having a lasting impact on forest ecosystems.

Coexistence of species with different dispersal across landscapes: a critical role of spatial correlation in disturbance

Disturbance is key to maintaining species diversity in plant communities. Although the effects of disturbance frequency and extent on species diversity have been studied, we do not yet have a mechanistic understanding of how these aspects of disturbance interact with spatial structure of disturbance to influence species diversity. Here we derive a novel pair approximation model to explore competitive outcomes in a two-species system subject to spatially correlated disturbance. Generally, spatial correlation in disturbance favoured long-range dispersers, while distance-limited dispersers were greatly suppressed. Interestingly, high levels of spatial aggregation of disturbance promoted long-term species coexistence that is not possible in the absence of disturbance, but only when the local disperser was intrinsically competitively superior. However, spatial correlation in disturbance led to different competitive outcomes, depending on the disturbed area. Concerning ecological conservation and management, we theoretically demonstrate that introducing a spatially correlated disturbance to the system or altering an existing disturbance regime can be a useful strategy either to control species invasion or to promote species coexistence. Disturbance pattern analysis may therefore provide new insights into biodiversity conservation.