Academic publishing requires linguistically inclusive policies.

Scientific knowledge is produced in multiple languages but is predominantly published in English. This practice creates a language barrier to generate and transfer scientific knowledge between communities with diverse linguistic backgrounds, hindering the ability of scholars and communities to address global challenges and achieve diversity and equity in science, technology, engineering and mathematics (STEM). To overcome those barriers, publishers and journals should provide a fair system that supports non-native English speakers and disseminates knowledge across the globe. We surveyed policies of 736 journals in biological sciences to assess their linguistic inclusivity, identify predictors of inclusivity, and propose actions to overcome language barriers in academic publishing. Our assessment revealed a grim landscape where most journals were making minimal efforts to overcome language barriers. The impact factor of journals was negatively associated with adopting a number of inclusive policies whereas ownership by a scientific society tended to have a positive association. Contrary to our expectations, the proportion of both open access articles and editors based in non-English speaking countries did not have a major positive association with the adoption of linguistically inclusive policies. We proposed a set of actions to overcome language barriers in academic publishing, including the renegotiation of power dynamics between publishers and editorial boards.

Different photoperiodic responses in diapause induction can promote the maintenance of genetic diversity via the storage effect in Daphnia pulex.

Understanding mechanisms that promote the maintenance of biodiversity (genetic and species diversity) has been a central topic in evolution and ecology. Previous studies have revealed that diapause can contribute to coexistence of competing genotypes or species in fluctuating environments via the storage effect. However, they tended to focus on differences in reproductive success (e.g. seed yield) and diapause termination (e.g. germination) timing. Here we tested whether different photoperiodic responses in diapause induction can promote coexistence of two parthenogenetic (asexual) genotypes of Daphnia pulex in Lake Fukami-ike, Japan. Through laboratory experiments, we confirmed that short day length and low food availability induced the production of diapausing eggs. Furthermore, we found that one genotype tended to produce diapausing eggs in broader environmental conditions than the other. Terminating parthenogenetic reproduction earlier decreases total clonal production, but the early diapausing genotype becomes advantageous by assuring reproduction in 'short' years where winter arrival is earlier than usual. Empirically parameterized theoretical analyses suggested that different photoperiodic responses can promote coexistence via the storage effect with fluctuations of the growing season length. Therefore, timing of diapause induction may be as important as diapause termination timing for promoting the maintenance of genetic diversity in fluctuating environments.

Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics.

Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in species-rich communities. Here, we examine whether community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was correlated with the magnitude of gene-repertoire overlaps among bacterial species, although the causation between the two variables deserves future extensive research. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).

Beyond simple adaptation: Incorporating other evolutionary processes and concepts into eco-evolutionary dynamics.

Studies of eco-evolutionary dynamics have integrated evolution with ecological processes at multiple scales (populations, communities and ecosystems) and with multiple interspecific interactions (antagonistic, mutualistic and competitive). However, evolution has often been conceptualised as a simple process: short-term directional adaptation that increases population growth. Here we argue that diverse other evolutionary processes, well studied in population genetics and evolutionary ecology, should also be considered to explore the full spectrum of feedback between ecological and evolutionary processes. Relevant but underappreciated processes include (1) drift and mutation, (2) disruptive selection causing lineage diversification or speciation reversal and (3) evolution driven by relative fitness differences that may decrease population growth. Because eco-evolutionary dynamics have often been studied by population and community ecologists, it will be important to incorporate a variety of concepts in population genetics and evolutionary ecology to better understand and predict eco-evolutionary dynamics in nature.

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.

Facilitative interaction networks in experimental microbial community dynamics.

Facilitative interactions between microbial species are ubiquitous in various types of ecosystems on the Earth. Therefore, inferring how entangled webs of interspecific interactions shift through time in microbial ecosystems is an essential step for understanding ecological processes driving microbiome dynamics. By compiling shotgun metagenomic sequencing data of an experimental microbial community, we examined how the architectural features of facilitative interaction networks could change through time. A metabolic modeling approach for estimating dependence between microbial genomes (species) allowed us to infer the network structure of potential facilitative interactions at 13 time points through the 110-day monitoring of experimental microbiomes. We then found that positive feedback loops, which were theoretically predicted to promote cascade breakdown of ecological communities, existed within the inferred networks of metabolic interactions prior to the drastic community-compositional shift observed in the microbiome time-series. We further applied "directed-graph" analyses to pinpoint potential keystone species located at the "upper stream" positions of such feedback loops. These analyses on facilitative interactions will help us understand key mechanisms causing catastrophic shifts in microbial community structure.

Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics.

BACKGROUND: Microbiome dynamics are both crucial indicators and potential drivers of human health, agricultural output, and industrial bio-applications. However, predicting microbiome dynamics is notoriously difficult because communities often show abrupt structural changes, such as "dysbiosis" in human microbiomes. METHODS: We integrated theoretical frameworks and empirical analyses with the aim of anticipating drastic shifts of microbial communities. We monitored 48 experimental microbiomes for 110 days and observed that various community-level events, including collapse and gradual compositional changes, occurred according to a defined set of environmental conditions. We analyzed the time-series data based on statistical physics and non-linear mechanics to describe the characteristics of the microbiome dynamics and to examine the predictability of major shifts in microbial community structure. RESULTS: We confirmed that the abrupt community changes observed through the time-series could be described as shifts between "alternative stable states" or dynamics around complex attractors. Furthermore, collapses of microbiome structure were successfully anticipated by means of the diagnostic threshold defined with the "energy landscape" analysis of statistical physics or that of a stability index of nonlinear mechanics. CONCLUSIONS: The results indicate that abrupt microbiome events in complex microbial communities can be forecasted by extending classic ecological concepts to the scale of species-rich microbial systems. Video Abstract.

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.

Integrating eco-evolutionary dynamics and modern coexistence theory.

Community ecology typically assumes that competitive exclusion and species coexistence are unaffected by evolution on the time scale of ecological dynamics. However, recent studies suggest that rapid evolution operating concurrently with competition may enable species coexistence. Such findings necessitate general theory that incorporates the coexistence contributions of eco-evolutionary processes in parallel with purely ecological mechanisms and provides metrics for quantifying the role of evolution in shaping competitive outcomes in both modelling and empirical contexts. To foster the development of such theory, here we extend the interpretation of the two principal metrics of modern coexistence theory-niche and competitive ability differences-to systems where competitors evolve. We define eco-evolutionary versions of these metrics by considering how invading and resident species adapt to conspecific and heterospecific competitors. We show that the eco-evolutionary niche and competitive ability differences are sums of ecological and evolutionary processes, and that they accurately predict the potential for stable coexistence in previous theoretical studies of eco-evolutionary dynamics. Finally, we show how this theory frames recent empirical assessments of rapid evolution effects on species coexistence, and how empirical work and theory on species coexistence and eco-evolutionary dynamics can be further integrated.

How does genetic architecture affect eco-evolutionary dynamics? A theoretical perspective.

Recent studies have revealed the importance of feedbacks between contemporary rapid evolution (i.e. evolution that occurs through changes in allele frequencies) and ecological dynamics. Despite its inherent interdisciplinary nature, however, studies on eco-evolutionary feedbacks have been mostly ecological and tended to focus on adaptation at the phenotypic level without considering the genetic architecture of evolutionary processes. In empirical studies, researchers have often compared ecological dynamics when the focal species under selection has a single genotype with dynamics when it has multiple genotypes. In theoretical studies, common approaches are models of quantitative traits where mean trait values change adaptively along the fitness gradient and Mendelian traits with two alleles at a single locus. On the other hand, it is well known that genetic architecture can affect short-term evolutionary dynamics in population genetics. Indeed, recent theoretical studies have demonstrated that genetic architecture (e.g. the number of loci, linkage disequilibrium and ploidy) matters in eco-evolutionary dynamics (e.g. evolutionary rescue where rapid evolution prevents extinction and population cycles driven by (co)evolution). I propose that theoretical approaches will promote the synthesis of functional genomics and eco-evolutionary dynamics through models that combine population genetics and ecology as well as nonlinear time-series analyses using emerging big data. This article is part of the theme issue 'Genetic basis of adaptation and speciation: from loci to causative mutations'.

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'.

A unified framework for herbivore-to-producer biomass ratio reveals the relative influence of four ecological factors.

The biomass ratio of herbivores to primary producers reflects the structure of a community. Four primary factors have been proposed to affect this ratio, including production rate, defense traits and nutrient contents of producers, and predation by carnivores. However, identifying the joint effects of these factors across natural communities has been elusive, in part because of the lack of a framework for examining their effects simultaneously. Here, we develop a framework based on Lotka-Volterra equations for examining the effects of these factors on the biomass ratio. We then utilize it to test if these factors simultaneously affect the biomass ratio of freshwater plankton communities. We found that all four factors contributed significantly to the biomass ratio, with carnivore abundance having the greatest effect, followed by producer stoichiometric nutrient content. Thus, the present framework should be useful for examining the multiple factors shaping various types of communities, both aquatic and terrestrial.

Intraspecific Adaptation Load: A Mechanism for Species Coexistence.

Evolutionary ecological theory suggests that selection arising from interactions with conspecifics, such as sexual and kin selection, may result in evolution of intraspecific conflicts and evolutionary 'tragedy of the commons'. Here, we propose that such an evolution of conspecific conflicts may affect population dynamics in a way that enhances species coexistence. Empirical evidence and theoretical models suggest that more abundant species is more susceptible to invasion of 'selfish' individuals that increase their own reproductive success at the expense of population growth (intraspecific adaptation load). The density-dependent intraspecific adaptation load gives rise to a self-regulation mechanism at the population level, and stabilizes species coexistence at the community level by negative frequency-dependence.

How (co)evolution alters predator responses to increased mortality: extinction thresholds and hydra effects.

Population responses to environmental change depend on both the ecological interactions between species and the evolutionary responses of all species. In this study, we explore how evolution in prey, predators, or both species affect the responses of predator populations to a sustained increase in mortality. We use an eco-evolutionary predator-prey model to explore how evolution alters the predator extinction threshold (defined as the minimum mortality rate that prevents population growth at low predator densities) and predator hydra effects (increased predator abundance in response to increased mortality). Our analysis identifies how evolutionary responses of prey and predators individually affect the predator extinction threshold and hydra effects, and how those effects are altered by interactions between the evolutionary responses. Based on our theoretical results, we predict that it is common in natural systems for evolutionary responses in one or both species to allow predators to persist at higher mortality rates than would be possible in the absence of evolution (i.e., evolution increases the predator mortality extinction threshold). We also predict that evolution-driven hydra effects occur in a minority of natural systems, but are not rare. We revisited published eco-evolutionary models and found that evolution causes hydra effects and increases the predator extinction threshold in many studies, but those effects have been overlooked. We discuss the implications of these results for species conservation, predicting population responses to environmental change, and the possibility of evolutionary rescue.

When rarity has costs: coexistence under positive frequency-dependence and environmental stochasticity.

Stable coexistence relies on negative frequency-dependence, in which rarer species invading a patch benefit from a lack of conspecific competition experienced by residents. In nature, however, rarity can have costs, resulting in positive frequency-dependence (PFD) particularly when species are rare. Many processes can cause positive frequency-dependence, including a lack of mates, mutualist interactions, and reproductive interference from heterospecifics. When species become rare in the community, positive frequency-dependence creates vulnerability to extinction, if frequencies drop below certain thresholds. For example, environmental fluctuations can drive species to low frequencies where they are then vulnerable to PFD. Here, we analyze deterministic and stochastic mathematical models of two species interacting through both PFD and resource competition in a Chessonian framework. Reproductive success of individuals in these models is reduced by a product of two terms: the reduction in fecundity due to PFD, and the reduction in fecundity due to competition. Consistent with classical coexistence theory, the effect of competition on individual reproductive success exhibits negative frequency-dependence when individuals experience greater intraspecific competition than interspecific competition, i.e., niche overlap is less than one. In the absence of environmental fluctuations, our analysis reveals that (1) a synergistic effect of PFD and niche overlap that hastens exclusion, (2) trade-offs between susceptibility to PFD and maximal fecundity can mediate coexistence, and (3) coexistence, when it occurs, requires that neither species is initially rare. Analysis of the stochastic model highlights that environmental fluctuations, unless perfectly correlated, coupled with PFD ultimately drive one species extinct. Over any given time frame, this extinction risk decreases with the correlation of the demographic responses of the two species to the environmental fluctuations, and increases with the temporal autocorrelation of these fluctuations. For species with overlapping generations, these trends in extinction risk persist despite the strength of the storage effect decreasing with correlated demographic responses and increasing with temporal autocorrelations. These results highlight how the presence of PFD may alter the outcomes predicted by modern coexistence mechanisms.

Modelling inducible defences in predator-prey interactions: assumptions and dynamical consequences of three distinct approaches.

Inducible defences against predation are widespread in the natural world, allowing prey to economise on the costs of defence when predation risk varies over time or is spatially structured. Through interspecific interactions, inducible defences have major impacts on ecological dynamics, particularly predator-prey stability and phase lag. Researchers have developed multiple distinct approaches, each reflecting assumptions appropriate for particular ecological communities. Yet, the impact of inducible defences on ecological dynamics can be highly sensitive to the modelling approach used, making the choice of model a critical decision that affects interpretation of the dynamical consequences of inducible defences. Here, we review three existing approaches to modelling inducible defences: Switching Function, Fitness Gradient and Optimal Trait. We assess when and how the dynamical outcomes of these approaches differ from each other, from classic predator-prey dynamics and from commonly observed eco-evolutionary dynamics with evolving, but non-inducible, prey defences. We point out that the Switching Function models tend to stabilise population dynamics, and the Fitness Gradient models should be carefully used, as the difference with evolutionary dynamics is important. We discuss advantages of each approach for applications to ecological systems with particular features, with the goal of providing guidelines for future researchers to build on.

Publisher Correction: Core microbiomes for sustainable agroecosystems.

Owing to a technical error, this Perspective was originally published without its received and accepted dates; the dates "Received: 31 December 2017; Accepted: 23 March 2018" have now been included in all versions.

A shady phytoplankton paradox: when phytoplankton increases under low light.

Light is a fundamental driver of ecosystem dynamics, affecting the rate of photosynthesis and primary production. In spite of its importance, less is known about its community-scale effects on aquatic ecosystems compared with those of nutrient loading. Understanding light limitation is also important for ecosystem management, as human activities have been rapidly altering light availability to aquatic ecosystems. Here we show that decreasing light can paradoxically increase phytoplankton abundance in shallow lakes. Our results, based on field manipulation experiments, field observations and models, suggest that, under competition for light and nutrients between phytoplankton and submersed macrophytes, alternative stable states are possible under high-light supply. In a macrophyte-dominated state, as light decreases phytoplankton density increases, because macrophytes (which effectively compete for nutrients released from the sediment) are more severely affected by light reduction. Our results demonstrate how species interactions with spatial heterogeneity can cause an unexpected outcome in complex ecosystems. An implication of our findings is that partial surface shading for controlling harmful algal bloom may, counterintuitively, increase phytoplankton abundance by decreasing macrophytes. Therefore, to predict how shallow lake ecosystems respond to environmental perturbations, it is essential to consider effects of light on the interactions between pelagic and benthic producers.

Core microbiomes for sustainable agroecosystems.

In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary research strategies to optimize microbiome functions in agroecosystems. Informatics now allows us to identify members and characteristics of 'core microbiomes', which may be deployed to organize otherwise uncontrollable dynamics of resident microbiomes. Integration of microfluidics, robotics and machine learning provides novel ways to capitalize on core microbiomes for increasing resource-efficiency and stress-resistance of agroecosystems.