Eco-evolutionary maintenance of diversity in fluctuating environments.

Growing evidence suggests that temporally fluctuating environments are important in maintaining variation both within and between species. To date, however, studies of genetic variation within a population have been largely conducted by evolutionary biologists (particularly population geneticists), while population and community ecologists have concentrated more on diversity at the species level. Despite considerable conceptual overlap, the commonalities and differences of these two alternative paradigms have yet to come under close scrutiny. Here, we review theoretical and empirical studies in population genetics and community ecology focusing on the 'temporal storage effect' and synthesise theories of diversity maintenance across different levels of biological organisation. Drawing on Chesson's coexistence theory, we explain how temporally fluctuating environments promote the maintenance of genetic variation and species diversity. We propose a further synthesis of the two disciplines by comparing models employing traditional frequency-dependent dynamics and those adopting density-dependent dynamics. We then address how temporal fluctuations promote genetic and species diversity simultaneously via rapid evolution and eco-evolutionary dynamics. Comparing and synthesising ecological and evolutionary approaches will accelerate our understanding of diversity maintenance in nature.

Frequent, infinitesimal bottlenecks maximize the rate of microbial adaptation.

Serial passaging is a fundamental technique in experimental evolution. The choice of bottleneck severity and frequency poses a dilemma: longer growth periods allow beneficial mutants to arise and grow over more generations, but simultaneously necessitate more severe bottlenecks with a higher risk of those same mutations being lost. Short growth periods require less severe bottlenecks, but come at the cost of less time between transfers for beneficial mutations to establish. The standard laboratory protocol of 24-h growth cycles with severe bottlenecking has logistical advantages for the experimenter but limited theoretical justification. Here we demonstrate that contrary to standard practice, the rate of adaptive evolution is maximized when bottlenecks are frequent and small, indeed infinitesimally so in the limit of continuous culture. This result derives from revising key assumptions underpinning previous theoretical work, notably changing the metric of optimization from adaptation per serial transfer to per experiment runtime. We also show that adding resource constraints and clonal interference to the model leaves the qualitative results unchanged. Implementing these findings will require liquid-handling robots to perform frequent bottlenecks, or chemostats for continuous culture. Further innovation in and adoption of these technologies has the potential to accelerate the rate of discovery in experimental evolution.

Pulsed, continuous or somewhere in between? Resource dynamics matter in the optimisation of microbial communities.

The optimisation of synthetic and natural microbial communities has vast potential for emerging applications in medicine, agriculture and industry. Realising this goal is contingent on a close correlation between theory, experiments, and the real world. Although the temporal pattern of resource supply can play a major role in microbial community assembly, resource dynamics are commonly treated inconsistently in theoretical and experimental research. Here we explore how the composition of communities varies under continuous resource supply, typical of theoretical approaches, versus pulsed resource supply, typical of experiments. Using simulations of classical resource competition models, we show that community composition diverges rapidly between the two regimes, with almost zero overlap in composition once the pulsing interval stretches beyond just four hours. The implication for the rapidly growing field of microbial community optimisation is that the resource supply regime must be tailored to the community being optimised. As such, we argue that resource supply dynamics should be considered both a constraint in the design of novel microbial communities and as a tuning mechanism for the optimisation of pre-existing communities like those found in the human gut.

Extending the gleaner-opportunist trade-off.

Species exhibit various trade-offs that can result in stable coexistence of competitors. The gleaner-opportunist trade-off to fluctuations in resource abundance is one of the most intuitive, yet also misunderstood, coexistence-promoting trade-offs. Here, we review its history as an ecological concept, discuss extensions to the classical theory and outline opportunities to advance its understanding. The mechanism of coexistence between species that grow relatively faster than their competitors in a low-resource environment (i.e. a gleaner) versus a high-resource environment (i.e. an opportunist) was first proposed in the 1970s. Stable coexistence could emerge between gleaners and opportunists if the opportunist species (dominant in unstable environments) dampens resource fluctuations via relatively convex functional responses, while the gleaner species (dominant in stable environments) promotes fluctuations, or diminishes them less than the opportunist does, via relatively saturating functional responses. This fluctuation-dependent coexistence mechanism has since been referred to by various names, including the Armstrong-McGehee mechanism and relative nonlinearity of competition. Several researchers have argued this mechanism likely plays a relatively minor role in species coexistence owing in part to the restricted range of conditions that allow it to operate. More recent theoretical research, however, suggests that relative nonlinearity can operate over wider conditions than previously thought. Here, we identify several novel, or little explored, extensions to the gleaner-opportunist trade-off that can yield species coexistence under phenomena as diverse as fluctuations in predation/pathogen pressure, multiple resources, phenotypic plasticity and rapid evolution, amongst other phenomena. While the original definition of the gleaner-opportunist trade-off may be imperfect as a collective for these extensions, we argue that a subtle reframing of the trade-off focusing on species' performance in equilibrium versus fluctuating conditions (irrespective of preferences for high or low resources, predation pressure or other competitive factors) reveals their fundamental commonality in stable coexistence via relative nonlinearity. An extended framing shines a light on the potential ubiquity of this canonical trade-off in nature and on the breadth of theoretical and empirical terrain that remains to be trodden.

Human-associated microbiota suppress invading bacteria even under disruption by antibiotics.

In light of their adverse impacts on resident microbial communities, it is widely predicted that broad-spectrum antibiotics can promote the spread of resistance by releasing resistant strains from competition with other strains and species. We investigated the competitive suppression of a resistant strain of Escherichia coli inoculated into human-associated communities in the presence and absence of the broad and narrow spectrum antibiotics rifampicin and polymyxin B, respectively. We found strong evidence of community-level suppression of the resistant strain in the absence of antibiotics and, despite large changes in community composition and abundance following rifampicin exposure, suppression of the invading resistant strain was maintained in both antibiotic treatments. Instead, the strength of competitive suppression was more strongly associated with the source community (stool sample from individual human donor). This suggests microbiome composition strongly influences the competitive suppression of antibiotic-resistant strains, but at least some antibiotic-associated disruption can be tolerated before competitive release is observed. A deeper understanding of this association will aid the development of ecologically-aware strategies for managing antibiotic resistance.

Using ecological coexistence theory to understand antibiotic resistance and microbial competition.

Tackling antibiotic resistance necessitates deep understanding of how resource competition within and between species modulates the fitness of resistant microbes. Recent advances in ecological coexistence theory offer a powerful framework to probe the mechanisms regulating intra- and interspecific competition, but the significance of this body of theory to the problem of antibiotic resistance has been largely overlooked. In this Perspective, we draw on emerging ecological theory to illustrate how changes in resource niche overlap can be equally important as changes in competitive ability for understanding costs of resistance and the persistence of resistant pathogens in microbial communities. We then show how different temporal patterns of resource and antibiotic supply, alongside trade-offs in competitive ability at high and low resource concentrations, can have diametrically opposing consequences for the coexistence and exclusion of resistant and susceptible strains. These insights highlight numerous opportunities for innovative experimental and theoretical research into the ecological dimensions of antibiotic resistance.

Rapid evolution promotes fluctuation-dependent species coexistence.

Recent studies have demonstrated that rapid contemporary evolution can play a significant role in regulating population dynamics on ecological timescales. Here we identify a previously unrecognised mode by which rapid evolution can promote species coexistence via temporal fluctuations and a trade-off between competitive ability and the speed of adaptive evolution. We show that this interaction between rapid evolution and temporal fluctuations not only increases the range of coexistence conditions under a gleaner-opportunist trade-off (i.e. low minimum resource requirement [R* ] vs. high maximum growth rate) but also yields stable coexistence in the absence of a classical gleaner-opportunist trade-off. Given the propensity for both oscillatory dynamics and different rates of adaptation between species (including rapid evolution and phenotypic plasticity) in the real world, we argue that this expansion of fluctuation-dependent coexistence theory provides an important overlooked solution to the so-called 'paradox of the plankton'.

Publisher Correction: Intensive farming drives long-term shifts in avian community composition.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Intensive farming drives long-term shifts in avian community composition.

Agricultural practices constitute both the greatest cause of biodiversity loss and the greatest opportunity for conservation1,2, given the shrinking scope of protected areas in many regions. Recent studies have documented the high levels of biodiversity-across many taxa and biomes-that agricultural landscapes can support over the short term1,3,4. However, little is known about the long-term effects of alternative agricultural practices on ecological communities4,5 Here we document changes in bird communities in intensive-agriculture, diversified-agriculture and natural-forest habitats in 4 regions of Costa Rica over a period of 18 years. Long-term directional shifts in bird communities were evident in intensive- and diversified-agricultural habitats, but were strongest in intensive-agricultural habitats, where the number of endemic and International Union for Conservation of Nature (IUCN) Red List species fell over time. All major guilds, including those involved in pest control, pollination and seed dispersal, were affected. Bird communities in intensive-agricultural habitats proved more susceptible to changes in climate, with hotter and drier periods associated with greater changes in community composition in these settings. These findings demonstrate that diversified agriculture can help to alleviate the long-term loss of biodiversity outside natural protected areas1.

Author Correction: A global test of ecoregions.

The original paper was published without unique DOIs for GBIF occurrence downloads. These have now been inserted as references 70-76, and the error has been corrected in the PDF and HTML versions of the article.

Applying modern coexistence theory to priority effects.

Modern coexistence theory is increasingly used to explain how differences between competing species lead to coexistence versus competitive exclusion. Although research testing this theory has focused on deterministic cases of competitive exclusion, in which the same species always wins, mounting evidence suggests that competitive exclusion is often historically contingent, such that whichever species happens to arrive first excludes the other. Coexistence theory predicts that historically contingent exclusion, known as priority effects, will occur when large destabilizing differences (positive frequency-dependent growth rates of competitors), combined with small fitness differences (differences in competitors' intrinsic growth rates and sensitivity to competition), create conditions under which neither species can invade an established population of its competitor. Here we extend the empirical application of modern coexistence theory to determine the conditions that promote priority effects. We conducted pairwise invasion tests with four strains of nectar-colonizing yeasts to determine how the destabilizing and fitness differences that drive priority effects are altered by two abiotic factors characterizing the nectar environment: sugar concentration and pH. We found that higher sugar concentrations increased the likelihood of priority effects by reducing fitness differences between competing species. In contrast, higher pH did not change the likelihood of priority effects, but instead made competition more neutral by bringing both fitness differences and destabilizing differences closer to zero. This study demonstrates how the empirical partitioning of priority effects into fitness and destabilizing components can elucidate the pathways through which environmental conditions shape competitive interactions.

The mechanistic basis for higher-order interactions and non-additivity in competitive communities.

Motivated by both analytical tractability and empirical practicality, community ecologists have long treated the species pair as the fundamental unit of study. This notwithstanding, the challenge of understanding more complex systems has repeatedly generated interest in the role of so-called higher-order interactions (HOIs) imposed by species beyond the focal pair. Here we argue that HOIs - defined as non-additive effects of density on per capita growth - are best interpreted as emergent properties of phenomenological models (e.g. Lotka-Volterra competition) rather than as distinct 'ecological processes' in their own right. Using simulations of consumer-resource models, we explore the mechanisms and system properties that give rise to HOIs in observational data. We demonstrate that HOIs emerge under all but the most restrictive of assumptions, and that incorporating non-additivity into phenomenological models improves the quantitative and qualitative accuracy of model predictions. Notably, we also observe that HOIs derive primarily from mechanisms and system properties that apply equally to single-species or pairwise systems as they do to more diverse communities. Consequently, there exists a strong mandate for further recognition of non-additive effects in both theoretical and empirical research.

A global test of ecoregions.

A foundational paradigm in biological and Earth sciences is that our planet is divided into distinct ecoregions and biomes demarking unique assemblages of species. This notion has profoundly influenced scientific research and environmental policy. Given recent advances in technology and data availability, however, we are now poised to ask whether ecoregions meaningfully delimit biological communities. Using over 200 million observations of plants, animals and fungi we show compelling evidence that ecoregions delineate terrestrial biodiversity patterns. We achieve this by testing two competing hypotheses: the sharp-transition hypothesis, positing that ecoregion borders divide differentiated biotic communities; and the gradual-transition hypothesis, proposing instead that species turnover is continuous and largely independent of ecoregion borders. We find strong support for the sharp-transition hypothesis across all taxa, although adherence to ecoregion boundaries varies across taxa. Although plant and vertebrate species are tightly linked to sharp ecoregion boundaries, arthropods and fungi show weaker affiliations to this set of ecoregion borders. Our results highlight the essential value of ecological data for setting conservation priorities and reinforce the importance of protecting habitats across as many ecoregions as possible. Specifically, we conclude that ecoregion-based conservation planning can guide investments that simultaneously protect species-, community- and ecosystem-level biodiversity, key for securing Earth's life support systems into the future.

Coexistence theory and the frequency-dependence of priority effects.

Priority effects are commonly used to describe a broad suite of phenomena capturing the influence of species arrival order on the diversity, composition and function of ecological communities. Several studies have suggested reframing priority effects around the stabilizing and equalizing concepts of coexistence theory. We show that the only compatible priority effects are those characterized by positive frequency-dependence, irrespective of whether they emerge in equilibrium or non-equilibrium systems.

Species coexistence through simultaneous fluctuation-dependent mechanisms.

Understanding the origins and maintenance of biodiversity remains one of biology's grand challenges. From theory and observational evidence, we know that variability in environmental conditions through time is likely critical to the coexistence of competing species. Nevertheless, experimental tests of fluctuation-driven coexistence are rare and have typically focused on just one of two potential mechanisms, the temporal storage effect, to the neglect of the theoretically equally plausible mechanism known as relative nonlinearity of competition. We combined experiments and simulations in a system of nectar yeasts to quantify the relative contribution of the two mechanisms to coexistence. Resource competition models parameterized from single-species assays predicted the outcomes of mixed-culture competition experiments with 83% accuracy. Model simulations revealed that both mechanisms have measurable effects on coexistence and that relative nonlinearity can be equal or greater in magnitude to the temporal storage effect. In addition, we show that their effect on coexistence can be both antagonistic and complementary. These results falsify the common assumption that relative nonlinearity is of negligible importance, and in doing so reveal the importance of testing coexistence mechanisms in combination.

Genomic diversity of a nectar yeast clusters into metabolically, but not geographically, distinct lineages.

Both dispersal limitation and environmental sorting can affect genetic variation in populations, but their contribution remains unclear, particularly in microbes. We sought to determine the contribution of geographic distance (as a proxy for dispersal limitation) and phenotypic traits (as a proxy for environmental sorting), including morphology, metabolic ability and interspecific competitiveness, to the genotypic diversity in a nectar yeast species, Metschnikowia reukaufii. To measure genotypic diversity, we sequenced the genomes of 102 strains of M. reukaufii isolated from the floral nectar of hummingbird-pollinated shrub, Mimulus aurantiacus, along a 200-km coastline in California. Intraspecific genetic variation showed no detectable relationship with geographic distance, but could be grouped into three distinct lineages that correlated with metabolic ability and interspecific competitiveness. Despite ample evidence for strong competitive interactions within and among nectar yeasts, a full spectrum of the genotypic and phenotypic diversity observed across the 200-km coastline was represented even at a scale as small as 200 m. Further, more competitive strains were not necessarily more abundant. These results suggest that dispersal limitation and environmental sorting might not fully explain intraspecific diversity in this microbe and highlight the need to also consider other ecological factors such as trade-offs, source-sink dynamics and niche modification.

Can dispersal investment explain why tall plant species achieve longer dispersal distances than short plant species?

Tall plant species disperse further distances than do short species, within and across dispersal syndromes, yet the driver underpinning this relationship is unclear. The ability of taller plants to invest more in dispersal structures may explain the positive relationship between plant height and dispersal distance. Here, we quantify the cross-species relationships between presence of dispersal structures, dispersal investment plant height and dispersal distance. Plant height, dispersal syndrome and dispersal investment data were collated for 1613 species from the literature, with dispersal distance data collated for 114 species. We find that species with high dispersal investment disperse further than do species with low dispersal investment. Tall species have a greater probability of having dispersal structures on their seeds compared with short species. For species with dispersal structures on their seeds, plant height is very weakly related to dispersal investment. Our results provide the first global confirmation of the dispersal investment-distance hypothesis, and show dispersal investment can be used for predicting species dispersal distances. However, our results and those of previous studies indicate plant height is still the best proxy for estimating species dispersal distances due to it being such a readily available plant trait.

Phylogenetic and functional dissimilarity does not increase during temporal heathland succession.

Succession has been a focal point of ecological research for over a century, but thus far has been poorly explored through the lens of modern phylogenetic and trait-based approaches to community assembly. The vast majority of studies conducted to date have comprised static analyses where communities are observed at a single snapshot in time. Long-term datasets present a vantage point to compare established and emerging theoretical predictions on the phylogenetic and functional trajectory of communities through succession. We investigated within, and between, community measures of phylogenetic and functional diversity in a fire-prone heathland along a 21 year time series. Contrary to widely held expectations that increased competition through succession should inhibit the coexistence of species with high niche overlap, plots became more phylogenetically and functionally clustered with time since fire. There were significant directional shifts in individual traits through time indicating deterministic successional processes associated with changing abiotic and/or biotic conditions. However, relative to the observed temporal rate of taxonomic turnover, both phylogenetic and functional turnover were comparatively low, suggesting a degree of functional redundancy among close relatives. These results contribute to an emerging body of evidence indicating that limits to the similarity of coexisting species are rarely observed at fine spatial scales.