A keystone gene underlies the persistence of an experimental food web

Keystone niche individuals: some are more unequal than others

Conspecific individuals often diverge in their foraging decisions. Indeed, across diverse taxa, generalist populations contain both generalist and specialist individuals. This intraspecific niche variation allows some individuals to contribute disproportionately to their population's niche. Here, we present the concept of keystone niche individuals and why it matters for ecologists.

From synthetic communities to synthetic ecosystems: exploring causalities in plant-microbe-environment interactions

The plant microbiota research field has rapidly shifted from efforts aimed at gaining a descriptive understanding of microbiota composition to a focus on acquiring mechanistic insights into microbiota functions and assembly rules. This evolution was driven by our ability to establish comprehensive collections of plant-associated microbes and to reconstruct meaningful microbial synthetic communities (SynComs). We argue that this powerful deconstruction-reconstruction strategy can be used to reconstitute increasingly complex synthetic ecosystems (SynEcos) and mechanistically understand high-level biological organization. The transitioning from simple to more advanced, fully tractable and programmable gnotobiotic SynEcos is ongoing and aims at rationally simplifying natural ecosystems by engineering them. Such reconstitution ecology approaches represent an untapped strategy for bridging the gap between ecology and functional biology and for unraveling plant-microbiota-environment mechanisms that modulate ecosystem health, assembly, and functioning.

Temporal Changes in the Role of Species Sorting and Evolution Determine Community Dynamics

Evolutionary change within community members and shifts in species composition via species sorting contribute to community and trait dynamics. However, we do not understand when and how both processes contribute to community dynamics. Here, we estimated the contributions of species sorting and evolution over time (60 days) in bacterial communities of 24 species under selection by a ciliate predator. We found that species sorting contributed to increased community carrying capacity, while evolution contributed to decreased anti-predator defences. The relative roles of both processes changed over time, and our analysis indicates that if initial trait variation was in the direction of selection, species sorting prevailed, otherwise evolution drove phenotypic change. Furthermore, community composition, population densities and genomic evolution were affected by phenotypic match-mismatch combinations of predator and prey evolutionary history. Overall, our findings help to integrate when and how ecological and evolutionary processes structure communities.

Defensive polyketides produced by an abundant gastropod are candidate keystone molecules in estuarine ecology

Secondary metabolites often function as antipredator defenses, but when bioactive at low concentrations, their off-target effects on other organisms may be overlooked. Candidate "keystone molecules" are proposed to affect community structure and ecosystem functions, generally originating as defenses of primary producers; the broader effects of animal chemistry remain largely unexplored, however. Here, we characterize five previously unreported polyketides (alderenes A to E) biosynthesized by sea slugs reaching exceptional densities (up to 9000 slugs per square meter) in Northern Hemisphere estuaries. Alderenes comprise only 0.1% of slug wet weight, yet rendered live slugs or dead flesh unpalatable to three co-occurring consumers, making a potential food resource unavailable and redirecting energy flow in critical nursery habitat. Alderenes also displaced infauna from the upper sediment of the mudflat but attracted ovipositing snails. By altering communities, such compounds may have unexpected cascading effects on processes ranging from bioturbation to reproduction of species not obviously connected to the producing organisms, warranting greater attention by ecologists.

Reducing herbivory in mixed planting by genomic prediction of neighbor effects in the field

Genetically diverse populations can increase plant resistance to natural enemies. Yet, beneficial genotype pairs remain elusive due to the occurrence of positive or negative effects of mixed planting on plant resistance, respectively called associational resistance or susceptibility. Here, we identify key genotype pairs responsible for associational resistance to herbivory using the genome-wide polymorphism data of the plant species Arabidopsis thaliana. To quantify neighbor interactions among 199 genotypes grown in a randomized block design, we employ a genome-wide association method named "Neighbor GWAS" and genomic prediction inspired by the Ising model of magnetics. These analyses predict that 823 of the 19,701 candidate pairs can reduce herbivory in mixed planting. We planted three pairs with the predicted effects in mixtures and monocultures, and detected 18-30% reductions in herbivore damage in the mixed planting treatment. Our study shows the power of genomic prediction to assemble genotype mixtures with positive biodiversity effects.

The root of plant-plant interactions: Belowground special cocktails

Plants interact with each other via a multitude of processes among which belowground communication facilitated by specialized metabolites plays an important but overlooked role. Until now, the exact targets, modes of action, and resulting phenotypes that these metabolites induce in neighboring plants have remained largely unknown. Moreover, positive interactions driven by the release of root exudates are prevalent in both natural field conditions and controlled laboratory environments. In particular, intraspecific positive interactions suggest a genotypic recognition mechanism in addition to non-self perception in plant roots. This review concentrates on recent discoveries regarding how plants interact with one another through belowground signals in intra- and interspecific mixtures. Furthermore, we elaborate on how an enhanced understanding of these interactions can propel the field of agroecology forward.

Genetic underpinnings of arthropod community distributions in Populus trichocarpa

Community genetics seeks to understand the mechanisms by which natural genetic variation in heritable host phenotypes can encompass assemblages of organisms such as bacteria, fungi, and many animals including arthropods. Prior studies that focused on plant genotypes have been unable to identify genes controlling community composition, a necessary step to predict ecosystem structure and function as underlying genes shift within plant populations. We surveyed arthropods within an association population of Populus trichocarpa in three common gardens to discover plant genes that contributed to arthropod community composition. We analyzed our surveys with traditional single-trait genome-wide association analysis (GWAS), multitrait GWAS, and functional networks built from a diverse set of plant phenotypes. Plant genotype was influential in structuring arthropod community composition among several garden sites. Candidate genes important for higher level organization of arthropod communities had broadly applicable functions, such as terpenoid biosynthesis and production of dsRNA binding proteins and protein kinases, which may be capable of targeting multiple arthropod species. We have demonstrated the ability to detect, in an uncontrolled environment, individual genes that are associated with the community assemblage of arthropods on a host plant, further enhancing our understanding of genetic mechanisms that impact ecosystem structure.

Greenbeards in plants?

Greenbeards are selfish genetic elements that make their bearers behave either altruistically towards individuals bearing similar greenbeard copies or harmfully towards individuals bearing different copies. They were first proposed by W. D. Hamilton over 50 yr ago, to illustrate that kin selection may operate at the level of single genes. Examples of greenbeards have now been reported in a wide range of taxa, but they remain undocumented in plants. In this paper, we discuss the theoretical likelihood of greenbeard existence in plants. We then question why the greenbeard concept has never been applied to plants and speculate on how hypothetical greenbeards could affect plant-plant interactions. Finally, we point to different research directions to improve our knowledge of greenbeards in plants.

Dispersal stabilizes coupled ecological and evolutionary dynamics in a host-parasitoid system

When ecological and evolutionary dynamics occur on comparable timescales, persistence of the ensuing eco-evolutionary dynamics requires both ecological and evolutionary stability. This unites key questions in ecology and evolution: How do species coexist, and what maintains genetic variation in a population? In this work, we investigated a host-parasitoid system in which pea aphid hosts rapidly evolve resistance to Aphidius ervi parasitoids. Field data and mathematical simulations showed that heterogeneity in parasitoid dispersal can generate variation in parasitism-mediated selection on hosts through time and space. Experiments showed how evolutionary trade-offs plus moderate host dispersal across this selection mosaic cause host-parasitoid coexistence and maintenance of genetic variation in host resistance. Our results show how dispersal can stabilize both the ecological and evolutionary components of eco-evolutionary dynamics.

Quantifying interspecific and intraspecific diversity effects on ecosystem functioning

Rapid environmental changes result in massive biodiversity loss, with detrimental consequences for the functioning of ecosystems. Recent studies suggest that intraspecific diversity can contribute to ecosystem functioning to an extent comparable to contributions of interspecific diversity. Knowledge on the relative importance of these two sources of biodiversity is essential for predicting ecosystem consequences of biodiversity loss and will aid in the prioritization of conservation targets and implementation of management measures. However, our quantitative insights into how interspecific and intraspecific biodiversity loss affects ecosystem functioning and how the effects of these two sources of biodiversity loss on ecosystem functioning can be compared are still very limited. To facilitate such quantitative insights, we extend the interspecific Price partitioning method originally introduced by J. Fox in 2006, previously used to quantify species loss and gain effects on ecosystem functioning, to also account for the effects of intraspecific diversity loss and gain on ecosystem function. Using this extended version can yield the quantitative information required for answering research questions addressing correlations between interspecific and intraspecific diversity effects on ecosystem functioning, identifying interspecific and intraspecific groups with large effects, and assessing whether intraspecific diversity can compensate for losses in interspecific diversity. Applying this method to carefully designed experiments will provide additional insights into how biodiversity loss at different ecological levels contributes to and changes ecosystem functioning.

The Development of Plant Genome Sequencing Technology and Its Conservation and Application in Endangered Gymnosperms

Genome sequencing is widely recognized as a fundamental pillar in genetic research and legal studies of biological phenomena, providing essential insights for genetic investigations and legal analyses of biological events. The field of genome sequencing has experienced significant progress due to rapid improvements in scientific and technological developments. These advancements encompass not only significant improvements in the speed and quality of sequencing but also provide an unparalleled opportunity to explore the subtle complexities of genomes, particularly in the context of rare species. Such a wide range of possibilities has successfully supported the validation of plant gene functions and the refinement of precision breeding methodologies. This expanded scope now includes a comprehensive exploration of the current state and conservation efforts of gymnosperm gene sequencing, offering invaluable insights into their genomic landscapes. This comprehensive review elucidates the trajectory of development and the diverse applications of genome sequencing. It encompasses various domains, including crop breeding, responses to abiotic stress, species evolutionary dynamics, biodiversity, and the unique challenges faced in the conservation and utilization of gymnosperms. It highlights both ongoing challenges and the unveiling of forthcoming developmental trajectories.

Five fundamental ways in which complex food webs may spiral out of control

Theory suggests that increasingly long, negative feedback loops of many interacting species may destabilize food webs as complexity increases. Less attention has, however, been paid to the specific ways in which these 'delayed negative feedbacks' may affect the response of complex ecosystems to global environmental change. Here, we describe five fundamental ways in which these feedbacks might pave the way for abrupt, large-scale transitions and species losses. By combining topological and bioenergetic models, we then proceed by showing that the likelihood of such transitions increases with the number of interacting species and/or when the combined effects of stabilizing network patterns approach the minimum required for stable coexistence. Our findings thus shift the question from the classical question of what makes complex, unaltered ecosystems stable to whether the effects of, known and unknown, stabilizing food-web patterns are sufficient to prevent abrupt, large-scale transitions under global environmental change.

Eco-evolutionary dynamics: An experimental demonstration in nature

Ecological change drives rapid evolution, which then should feed back to influence ecological change. A new study uses experiments with Timema stick insects to demonstrate such feedbacks in nature, revealing that they can be very rapid, strong, and stabilizing.

Phylogenetically-conserved candidate genes unify biodiversity-ecosystem function relationships and eco-evolutionary dynamics across biological scales

The intra- and interspecific facets of biodiversity have traditionally been analysed separately, limiting our understanding of how evolution has shaped biodiversity, how biodiversity (as a whole) alters ecological dynamics and hence eco-evolutionary feedbacks at the community scale. Here, we propose using candidate genes phylogenetically-conserved across species and sustaining functional traits as an inclusive biodiversity unit transcending the intra- and interspecific boundaries. This framework merges knowledge from functional genomics and functional ecology, and we first provide guidelines and a concrete example for identifying phylogenetically-conserved candidate genes (PCCGs) within communities and for measuring biodiversity from PCCGs. We then explain how biodiversity measured at PCCGs can be linked to ecosystem functions, which unifies recent observations that both intra- and interspecific biodiversity are important for ecosystem functions. We then highlight the eco-evolutionary processes shaping PCCG diversity patterns and argue that their respective role can be inferred from concepts derived from population genetics. Finally, we explain how PCCGs may shift the field of eco-evolutionary dynamics from a focal-species approach to a more realistic focal-community approach. This framework provides a novel perspective to investigate the global ecosystem consequences of diversity loss across biological scales, and how these ecological changes further alter biodiversity evolution.

Genome-wide association study of aphid abundance highlights a locus affecting plant growth and flowering in Arabidopsis thaliana

Plant life-history traits, such as size and flowering, contribute to shaping variation in herbivore abundance. Although plant genes involved in physical and chemical traits have been well studied, less is known about the loci linking plant life-history traits and herbivore abundance. Here, we conducted a genome-wide association study (GWAS) of aphid abundance in a field population of Arabidopsis thaliana. This GWAS of aphid abundance detected a relatively rare but significant variant on the third chromosome of A. thaliana, which was also suggestively but non-significantly associated with the presence or absence of inflorescence. Out of candidate genes near this significant variant, a mutant of a ribosomal gene (AT3G13882) exhibited slower growth and later flowering than a wild type under laboratory conditions. A no-choice assay with the turnip aphid, Lipaphis erysimi, found that aphids were unable to successfully establish on the mutant. Our GWAS of aphid abundance unexpectedly found a locus affecting plant growth and flowering.

Statistical methods to identify mechanisms in studies of eco-evolutionary dynamics

While the reciprocal effects of ecological and evolutionary dynamics are increasingly recognized as an important driver for biodiversity, detection of such eco-evolutionary feedbacks, their underlying mechanisms, and their consequences remains challenging. Eco-evolutionary dynamics occur at different spatial and temporal scales and can leave signatures at different levels of organization (e.g., gene, protein, trait, community) that are often difficult to detect. Recent advances in statistical methods combined with alternative hypothesis testing provides a promising approach to identify potential eco-evolutionary drivers for observed data even in non-model systems that are not amenable to experimental manipulation. We discuss recent advances in eco-evolutionary modeling and statistical methods and discuss challenges for fitting mechanistic models to eco-evolutionary data.

Single-gene resolution of diversity-driven overyielding in plant genotype mixtures

In plant communities, diversity often increases productivity and functioning, but the specific underlying drivers are difficult to identify. Most ecological theories attribute positive diversity effects to complementary niches occupied by different species or genotypes. However, the specific nature of niche complementarity often remains unclear, including how it is expressed in terms of trait differences between plants. Here, we use a gene-centred approach to study positive diversity effects in mixtures of natural Arabidopsis thaliana genotypes. Using two orthogonal genetic mapping approaches, we find that between-plant allelic differences at the AtSUC8 locus are strongly associated with mixture overyielding. AtSUC8 encodes a proton-sucrose symporter and is expressed in root tissues. Genetic variation in AtSUC8 affects the biochemical activities of protein variants and natural variation at this locus is associated with different sensitivities of root growth to changes in substrate pH. We thus speculate that - in the particular case studied here - evolutionary divergence along an edaphic gradient resulted in the niche complementarity between genotypes that now drives overyielding in mixtures. Identifying genes important for ecosystem functioning may ultimately allow linking ecological processes to evolutionary drivers, help identify traits underlying positive diversity effects, and facilitate the development of high-performance crop variety mixtures.

Genome mining-guided activation of two silenced tandem genes in Raoultella ornithinolytica XF201 for complete biodegradation of phthalate acid esters

Phthalates (PAEs) are ubiquitous in soils and food products and thus pose a high risk to human health. Herein, genome mining revealed a great diversity of bacteria with PAEs-degrading potential. Mining of the genome of Raoultella ornithinolytica XF201, a novel strain isolated from Dongxiang wild rice rhizosphere, revealed the presence of two silenced tandem genes pcdGH (encoding protocatechuate 3,4-dioxygenase, 3,4-PCD), key aromatic ring-cleaving genes in PAEs biodegradation. Ribosome engineering was successfully utilized to activate the expression of pcdGH genes to produce 3,4-PCD in the mutant XF201-G2U5. The mutant XF201-G2U5 showed high 3,4-PCD activity and could remove 94.5 % of di-n butyl phthalate (DBP) in 72 h. The degradation kinetics obeyed the first-order kinetic model. Strain XF201-G2U5 could also degrade the other PAEs and the main intermediate metabolites, ultimately leading to tricarboxylic acid cycle. Therefore, this strategy facilitates novel bacterial resources discovery for bioremediation of PAEs and other emerging contaminants.

The Resilience of Plant-Pollinator Networks

There is growing awareness of pollinator declines worldwide. Conservation efforts have mainly focused on finding the direct causes, while paying less attention to building a systemic understanding of the fragility of these communities of pollinators. To fill this gap, we need operational measures of network resilience that integrate two different approaches in theoretical ecology. First, we should consider the range of conditions compatible with the stable coexistence of all of the species in a community. Second, we should address the rate and shape of network collapse once this safe operational space is exited. In this review, we describe this integrative approach and consider several mechanisms that may enhance the resilience of pollinator communities, chiefly rewiring the network of interactions, increasing heterogeneity, allowing variance, and enhancing coevolution. The most pressing need is to develop ways to reduce the gap between these theoretical recommendations and practical applications. This perspective shifts the emphasis from traditional approaches focusing on the equilibrium states to strategies that allow pollination networks to cope with global environmental change.

Functional diversity and metabolic engineering of plant-specialized metabolites

Plants are talented biochemists that produce a broad diversity of small molecules. These so-called specialized metabolites (SMs) play critical roles in the adaptive evolution of plants to defend against biotic and abiotic stresses, attract pollinators, and modulate soil microbiota for their own benefits. Many plant SMs have been used as nutrition and flavor compounds in our daily food, as well as drugs for treatment of human diseases. Current multi-omics tools have significantly accelerated the process of biosynthetic pathway elucidation in plants through correlation analyses, genetic mapping, and de novo biosynthetic gene cluster predictions. Understanding the biosynthesis of plant SMs has enabled reconstitution of naturally occurring specialized metabolic pathways in microbial hosts, providing a sustainable supply of these high-value molecules. In this review, we illustrate the general functions of several typical plant SMs in natural ecosystems and for human societies. We then provide an overview of current methods elucidating the biosynthetic pathways of plant SMs, and synthetic biology strategies that optimize the efficiency of heterologous biosynthetic pathways in microbial hosts. Moving forward, dissection of the functions and application of plant SMs by using current multidiscipline approaches would be greatly benefit to the scientific community and human societies.

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.

Genetic basis of speciation and adaptation: from loci to causative mutations

Does evolution proceed in small steps or large leaps? How repeatable is evolution? How constrained is the evolutionary process? Answering these long-standing questions in evolutionary biology is indispensable for both understanding how extant biodiversity has evolved and predicting how organisms and ecosystems will respond to changing environments in the future. Understanding the genetic basis of phenotypic diversification and speciation in natural populations is key to properly answering these questions. The leap forward in genome sequencing technologies has made it increasingly easier to not only investigate the genetic architecture but also identify the variant sites underlying adaptation and speciation in natural populations. Furthermore, recent advances in genome editing technologies are making it possible to investigate the functions of each candidate gene in organisms from natural populations. In this article, we discuss how these recent technological advances enable the analysis of causative genes and mutations and how such analysis can help answer long-standing evolutionary biology questions.

This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.

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’.

Eco-evolutionary effects of keystone genes

The rapid evolution of specific genes within species can drive ecological changes.