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.

At present, the disciplines of evolutionary biology and ecosystem science are weakly integrated. As a result, we have a poor understanding of how the ecological and evolutionary processes that create, maintain, and change biological diversity affect the flux of energy and materials in global biogeochemical cycles. The goal of this article was to review several research fields at the interfaces between ecosystem science, community ecology and evolutionary biology, and suggest new ways to integrate evolutionary biology and ecosystem science. In particular, we focus on how phenotypic evolution by natural selection can influence ecosystem functions by affecting processes at the environmental, population and community scale of ecosystem organization. We develop an eco-evolutionary model to illustrate linkages between evolutionary change (e.g. phenotypic evolution of producer), ecological interactions (e.g. consumer grazing) and ecosystem processes (e.g. nutrient cycling). We conclude by proposing experiments to test the ecosystem consequences of evolutionary changes.

Ecologists have increasingly focused on how rapid adaptive trait changes can affect population dynamics. Rapid adaptation can result from either rapid evolution or phenotypic plasticity, but their effects on population dynamics are seldom compared directly. Here we examine theoretically the effects of rapid evolution and phenotypic plasticity of antipredatory defense on predator-prey dynamics. Our analyses reveal that phenotypic plasticity tends to stabilize population dynamics more strongly than rapid evolution. It is therefore important to know the mechanism by which phenotypic variation is generated for predicting the dynamics of rapidly adapting populations. We next examine an advantage of a phenotypically plastic prey genotype over the polymorphism of specialist prey genotypes. Numerical analyses reveal that the plastic genotype, if there is a small cost for maintaining it, cannot coexist with the pairs of specialist counterparts unless the system has a limit cycle. Furthermore, for the plastic genotype to replace specialist genotypes, a forced environmental fluctuation is critical in a broad parameter range. When these results are combined, the plastic genotype enjoys an advantage with population oscillations, but plasticity tends to lose its advantage by stabilizing the oscillations. This dilemma leads to an interesting intermittent limit cycle with the changing frequency of phenotypic plasticity.

Understanding how ecological and evolutionary processes interdependently structure biosphere dynamics is a major challenge in the era of worldwide ecosystem degradation. However, our knowledge of 'eco-evolutionary feedbacks' depends largely on findings from simple systems representing limited spatial scales and involving few species. Here we review recent conceptual developments for the understanding of multispecies coevolutionary processes and then discuss how new lines of concepts and methods will accelerate the integration of ecology and evolutionary biology. To build a research workflow for integrating insights into spatiotemporal dynamics of species-rich systems, we focus on the roles of 'metacommunity hub' species, whose population size and/or genetic dynamics potentially control landscape- or regional-scale phenomena. As large amounts of network data are becoming available with high-throughput sequencing of various host-symbiont, prey-predator, and symbiont-symbiont interactions, we suggest it is now possible to develop bases for the integrated understanding and management of species-rich ecosystems.

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.

Evolution on a time scale similar to ecological dynamics has been increasingly recognized for the last three decades. Selection mediated by ecological interactions can change heritable phenotypic variation (i.e., evolution), and evolution of traits, in turn, can affect ecological interactions. Hence, ecological and evolutionary dynamics can be tightly linked and important to predict future dynamics, but our understanding of eco-evolutionary dynamics is still in its infancy and there is a significant gap between theoretical predictions and empirical tests. Empirical studies have demonstrated that the presence of genetic variation can dramatically change ecological dynamics, whereas theoretical studies predict that eco-evolutionary dynamics depend on the details of the genetic variation, such as the form of a tradeoff among genotypes, which can be more important than the presence or absence of the genetic variation. Using a predator-prey (rotifer-algal) experimental system in laboratory microcosms, we studied how different forms of a tradeoff between prey defense and growth affect eco-evolutionary dynamics. Our experimental results show for the first time to our knowledge that different forms of the tradeoff produce remarkably divergent ecoevolutionary dynamics, including near fixation, near extinction, and coexistence of algal genotypes, with quantitatively different population dynamics. A mathematical model, parameterized from completely independent experiments, explains the observed dynamics. The results suggest that knowing the details of heritable trait variation and covariation within a population is essential for understanding how evolution and ecology will interact and what form of eco-evolutionary dynamics will result.allele-specific quantitative PCR | Chlorella vulgaris | clonal models | grazing resistance | rapid evolution E volutionary dynamics, changes in intraspecific genotype frequency over generations, can have a time scale similar to that of ecological dynamics (1-3). Selection mediated by ecological interactions causes evolutionary dynamics, and evolution of traits, in turn, changes ecological interactions. Thus, understanding population dynamics needs to take account of the feedbacks between trait evolution and ecological interactions (i.e., eco-evolutionary feedbacks). These feedbacks have increasingly attracted ecologists' attention since Pimentel (4) proposed genetic feedback as a mechanism regulating animal populations (e.g., refs. 5-11). This integration of evolutionary biology and ecology has important implications in both basic and applied problems in biology (12)(13)(14)(15)(16)(17).Empirical studies have shown that rapid evolution can affect many ecological interactions, including predator-prey (18-20), host-parasite (21), herbivore-plant (22), competitive interactions (23), and interactions with abiotic environments (24-27). Previous empirical studies on eco-evolutionary feedbacks have usually compared the dynamics of populations with and without genetic variation, but recent theoretic...

Virulence of avian brood parasites can trigger a coevolutionary arms race, which favours rejection of parasitic eggs or chicks by host parents, and in turn leads to mimicry in parasite eggs or chicks [1-7]. The appearance of host offspring is critical to enable host parents to detect parasites. Thus, increasing accuracy of parasites' mimicry can favour a newly emerged host morph to escape parasites' mimicry. If parasites catch up with the hosts with a newly acquired mimetic morph, host polymorphism should be maintained through apostatic (negative frequency-dependent) selection, which favours hosts rarer morphs [1-3,7]. Among population-wide polymorphism, uniformity of respective host morphs in single host nests stochastically prevents parasites from targeting any specific morph of hosts and thus helps parents detect parasitism. Polymorphism in such a state is well-known in egg appearances of hosts of brood parasitic birds [2,3,7], which might also occur in chick appearances when arms races escalate. Here, we present evidence of polymorphism in chick skin coloration in a cuckoo-host system: the fan-tailed gerygone Gerygone flavolateralis and its specialist brood parasite, the shining bronze-cuckoo Chalcites lucidus in New Caledonia (Figure 1A-C).

Recent studies have increasingly recognized evolutionary rescue (adaptive evolution that prevents extinction following environmental change) as an important process in evolutionary biology and conservation science. Researchers have concentrated on single species living in isolation, but populations in nature exist within communities of interacting species, so evolutionary rescue should also be investigated in a multispecies context. We argue that the persistence or extinction of a focal species can be determined solely by evolutionary change in an interacting species. We demonstrate that prey adaptive evolution can prevent predator extinction in two-species predator–prey models, and we derive the conditions under which this indirect evolutionary interaction is essential to prevent extinction following environmental change. A nonevolving predator can be rescued from extinction by adaptive evolution of its prey due to a trade-off for the prey between defense against predation and population growth rate. As prey typically have larger populations and shorter generations than their predators, prey evolution can be rapid and have profound effects on predator population dynamics. We suggest that this process, which we term ‘indirect evolutionary rescue’, has the potential to be critically important to the ecological and evolutionary responses of populations and communities to dramatic environmental change.