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Philosophical Transactions Of The Royal Society Of London. Series B, Biological Sciences[JOURNAL]
Philosophical Transactions Of The Royal Society Of London. Series B, Biological Sciences[JOURNAL]
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200 papers
The microlandscapes of tree trunks: the effect of lichen and tree-level characteristics on arthropod communities.
McGroarty J, Wiersma Y
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42343865 · Publisher ↗
Landscape ecologists frequently invoke a patch-mosaic analogy to describe patterns of different land covers across kilometres-extent landscapes. Patches of different species of lichen growing along a tree trunk can be vi...
Landscape ecologists frequently invoke a patch-mosaic analogy to describe patterns of different land covers across kilometres-extent landscapes. Patches of different species of lichen growing along a tree trunk can be viewed as a scaled-down version of this pattern. An advantage of working in these microlandscapes of tree trunks is that a stand of trees of the same species represents experimental replicate landscapes; something difficult to do for landscapes at the more traditional large extents. Here, we use such a microlandscape system to test how microlandscape patch patterns affect invertebrate community patterns within them. We hypothesized that trees with more diverse lichen communities would house more diverse arthropod fauna. We used a handheld vacuum to sample arthropods on lichen-covered balsam fir (Abies balsamea) boles on the Avalon Peninsula, Newfoundland, Canada and replicated this sampling with five trees per stand across nine stands growing in different mesoclimate conditions. Model selection showed arthropod abundance and diversity are affected by variation in lichen community composition and significantly so at the most pristine site. Total arthropod diversity was statistically positively correlated to total lichen cover. We further explore how a microlandscape such as this can be used to inform landscape ecology theory and applications across scales. This article is part of the theme issue 'Life in natural microcosms'.
Centimetre-scale landscapes to assess the motion behaviour and cognition of gastropods and bivalves.
Seuront L
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42343864 · Publisher ↗
Most ectotherms typically navigate topographically complex landscapes to find food and sexual partners while avoiding predation. However, it is still unclear how chemical, visual and contact cues interact and drive the b...
Most ectotherms typically navigate topographically complex landscapes to find food and sexual partners while avoiding predation. However, it is still unclear how chemical, visual and contact cues interact and drive the behavioural complexity observed in these organisms. This contribution illustrates how behavioural ecologists could take advantage of the unique modularity, chemical inertness, scalability, simplicity and affordability of LEGO® bricks and parts to create hypothesis-driven landscapes of various levels of complexity to unambiguously assess the behavioural responses of gastropods and bivalves and their ability to make choices in response to a range of chemical, visual and contact cues. The present work is based on terrestrial, freshwater and intertidal gastropods and two species of marine bivalves. I first demonstrate the chemical inertness of LEGO® bricks and parts towards gastropods and mussels. Then, purpose-built LEGO®-based experimental arenas are used to illustrate how they can be applied to address key issues and hypotheses related to the way gastropods and mussels perceive and react to a range of relevant chemical, visual and contact cues. In summary, this work provides a conceptual and technical framework to resolve to what extent motion behaviour is driven by a synergistic combination of chemotaxic, geotaxic, rheotaxic and thigmotaxic processes. This article is part of the theme issue 'Life in natural microcosms'.
Intertidal microcosms of wave-swept rocky shores: ecological and physiological insights from a uniquely stressful environment.
Denny M, Dowd WW
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42343863 · Publisher ↗
Owing to its unique combination of extreme physical severity and exceptional biological diversity, the intertidal zone of rocky shores has long served as a model system for development of ecological theories and experime...
Owing to its unique combination of extreme physical severity and exceptional biological diversity, the intertidal zone of rocky shores has long served as a model system for development of ecological theories and experimental tests of their predictions. This narrow interface between marine and terrestrial environments is a natural microcosm that presents organisms with rapid, extensive and often unpredictable variation in hydrodynamic forces, temperature, pH, oxygen availability and salinity. As ecologists struggle to predict the physical environment's effects on future community structure and function, it is essential to understand the physiological interactions among these factors and their role in ecology. Thus, the dynamic and heterogeneous nature of wave-swept rocky coasts provides an opportunity to exploit shoreline microcosms as a bellwether of climate change. Here, we review aspects of the intertidal environment that distinguish it from other microcosms and explore the nature of three smaller, embedded microcosms-tidepools, splashpools and the internal microcosms of individual organisms. Each of these systems comes with a distinct suite of physiological challenges and experimental potential. The variety of environmental interactions embodied by these microcosms positions rocky shores to continue serving as a model system for investigating environmental physiology, community ecology and the interplay between the two. This article is part of the theme issue 'Life in natural microcosms'.
Temporal and spatial variation in temperature and oxygen at the microscale: key niche axes for aquatic life.
Verberk WCEP, Bilton DT
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42343862 · Publisher ↗
To understand animal adaptations, we need accurate estimates of the ecological factors impacting organisms in nature. While temperature is a well-established driver of physiological performance, its effects in aquatic sy...
To understand animal adaptations, we need accurate estimates of the ecological factors impacting organisms in nature. While temperature is a well-established driver of physiological performance, its effects in aquatic systems are closely linked to water oxygenation. Oxygen levels are expected to differ spatially and fluctuate temporally much more strongly in water than on land, but our understanding of variation in temperature and oxygen levels in freshwaters remains limited. It is essential that environmental variation is recorded at spatial and temporal resolutions relevant to the organism. Here, we analyse spatial and temporal variation in water temperature and oxygenation across running and standing waters, using both microscale spot measurements and continuous loggers collecting data from the water column. Our results reaffirm that small-scale thermal gradients are much less pronounced in water than on land due to the high thermal conductivity and heat capacity of water. Regional weather conditions can therefore reliably predict water temperature across scales. By contrast, oxygen levels are much harder to predict from large-scale data as they can fluctuate sharply over very small spatial scales and within a single day, particularly in standing waters, exposing aquatic organisms to steep oxygen gradients. Our findings underscore the importance of incorporating fine-scale oxygen dynamics when studying aquatic species distributions and ecological strategies. This article is part of the theme issue 'Life in natural microcosms'.
Natural microcosms in ecology: fulfilling the promise of model systems?
Srivastava DS, Trzcinski MK, Petermann JS … +7 more , Céréghino R, Farjalla VF, Pires APF, Gonzalez AL, Kratina P, de Omena PM, Gotelli NJ
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42343861 · Publisher ↗
Natural microcosms (NMs) have been proposed as model systems for ecology based on their ubiquity, ease of study and natural context. We assess whether this potential has been met by examining 824 studies of six NMs (brom...
Natural microcosms (NMs) have been proposed as model systems for ecology based on their ubiquity, ease of study and natural context. We assess whether this potential has been met by examining 824 studies of six NMs (bromeliads, moss patches, nectar microbiomes, pitcher plants, rockpools, treeholes). Of these, we judged 314 studies to use NMs as model systems, testing a broad range of ecological theories. Although these theories spanned large biological, spatial and temporal scales, most studies concentrated on community-level niche processes occurring at local scales and within a generation-especially trophic control theories. However, metacommunity theory, which integrates over spatial and temporal scales, was also commonly studied. NMs were particularly effective in studying environmental stressors, often in combination with multitrophic effects or responses. While NMs have many advantages as model systems, there are limits to which theories can be tested due to specific life-histories of their inhabitants, uniqueness of certain ecosystem processes and frequency of disturbance. Particularly under-represented were tests of behavioural and ecosystem theory, long-term processes and impacts of invasive species. Greater use of molecular methods, community science and collaborative research networks could enable NMs to reach their full potential as model systems. This article is part of the theme issue 'Life in natural microcosms'.
Microbe-induced galls and plant defence: metabolite crosstalk in a co-evolutionary battle.
Miyata K, Yoshino-Kida M, Venkatesan R … +1 more , Sakakibara H
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42343860 · Publisher ↗
Plants and pathogens engage in complex biochemical communication, mediated by proteins, specialized metabolites, phytohormones and phytohormone-mimicking compounds. These interactions drive a dynamic 'co-evolutionary arm...
Plants and pathogens engage in complex biochemical communication, mediated by proteins, specialized metabolites, phytohormones and phytohormone-mimicking compounds. These interactions drive a dynamic 'co-evolutionary arms race', as plants and microbes compete to gain an advantage, ultimately transforming the infection site into a distinct micro-ecosystem. Microbe-induced galls are abnormal plant organogenesis induced by specific pathogens, creating a niche where the pathogen manipulates the host plant machinery to ensure its own survival. Such galls adversely affect agricultural and horticultural productivity by stunting plant growth and causing deformities. However, the rapid cell proliferation in tumourigenesis, along with the mechanisms driving robust shoot and root re-differentiation, present exciting opportunities for innovative biotechnological applications. Therefore, elucidation of these mechanisms is crucial for advancing basic research with significant potential for agricultural applications. This review focuses on galls induced by Agrobacterium tumefaciens and Rhodococcus fascians-two phytopathogens that utilize phytohormones as tumour-inducing molecules-to highlight the mechanisms underlying plant-pathogen interactions within this specialized microenvironment. It also explores the evolutionary adaptations and strategies of these pathogens. Gaining insight into these biological processes is key to understanding the mechanisms driving biological diversity and evolution, with implications extending beyond plant pathology into the broader field of molecular plant physiology. This article is part of the theme issue 'Life in natural microcosms'.
Nutrient flows and trophic interactions in natural microcosms: typologies, boundaries and complexities.
Kulkarni M, Borges RM
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42343859 · Publisher ↗
Natural microcosms are small ecosystems with a range of nutrient sources and sinks. Natural microcosms vary in longevity and predictability, and have complex nutrient networks tractable to profiling. However, the boundar...
Natural microcosms are small ecosystems with a range of nutrient sources and sinks. Natural microcosms vary in longevity and predictability, and have complex nutrient networks tractable to profiling. However, the boundaries of microcosms are sometimes difficult to demarcate, making measurement of nutrient inflows (subsidies) challenging. Principal dichotomies in microcosm classification are whether they are open or closed to chance nutrient inputs, and whether they are biological or non-biological in origin. These dichotomies affect microcosm boundary demarcation and nutrient flows. We argue that there is strong yet unrealized potential for natural microcosms to advance theory in biogeochemistry and ecological stoichiometry owing to their amenability to experimentation and measurement of elemental sources and sinks for entire microcosms. Correspondingly, the understanding of natural microcosms would benefit from biogeochemical and ecological stoichiometry, which includes the characterization of the elemental phenotypes of organisms and their proximate or ultimate drivers. Considering widespread stoichiometric flexibility in organisms and mixotrophy in ecosystems, new nutrient network models are required to incorporate this trophic complexity. Microcosms harbour conglomerates of nutrients and organisms within which accurate nutrient book-keeping can be achieved. This Opinion piece provides ideas, outlines problems that need solutions and re-emphasizes the advantages of natural microcosms as model systems. This article is part of the theme issue 'Life in natural microcosms'.
Climate impacts on the multidiversity-multifunctionality relationship change with habitat type.
Antiqueira PAP, Srivastava DS, Velho LFM … +6 more , Rodrigues LC, Farjalla VF, Piccoli GCO, Santos VPD, Oliveira VM, Romero GQ
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42343858 · Publisher ↗
Extreme climatic events are expected to increase in frequency in the coming decades. However, it is largely unknown how these events will mediate the influence of multidiversity on ecosystem multifunctionality in differe...
Extreme climatic events are expected to increase in frequency in the coming decades. However, it is largely unknown how these events will mediate the influence of multidiversity on ecosystem multifunctionality in different habitats. Here, we conducted a manipulative field experiment to evaluate the impact of rainfall amount and frequency variation on freshwater multidiversity (macrofauna, microfauna, bacteria and algae) and ecosystem multifunctionality in contrasting environments. For this, we used natural microcosms (tank bromeliads) as model systems in forest environments that differed in structural environmental heterogeneity. Rainfall amount affected the bromeliad's multifunctionality, but the outcome depended on the type of environment, the biodiversity component and the dimension of the ecosystem multifunctionality (i.e. average, productivity or decomposition). Ecosystem functioning in the habitat with lower environmental heterogeneity was more sensitive to rainfall amount. Conversely, in the habitat with higher environmental heterogeneity, ecosystem functioning was more sensitive to biodiversity components. Our study brings new evidence of how climate change affects different dimensions of ecosystem functioning as mediated by multidiversity and its dependence on habitat properties. Our results improve the understanding of how global change can impact the multiple dimensions of biodiversity and ecosystem functioning in different habitat types. This article is part of the theme issue 'Life in natural microcosms'.
Variable contribution of inquilines to prey digestion in Nepenthes pitcher plants: the role of pitcher traits.
Bazile V, Lamonica D, Le Moguédec G … +2 more , Marshall D, Gaume L
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42343857 · Publisher ↗
While prey capture has been extensively studied in pitcher plants, prey digestion, particularly the role of pitcher inhabitants in prey decomposition, has received little attention. We tested and compared prey decomposit...
While prey capture has been extensively studied in pitcher plants, prey digestion, particularly the role of pitcher inhabitants in prey decomposition, has received little attention. We tested and compared prey decomposition among four Nepenthes species, which vary in pitcher traits and associated inquiline guilds. In a field experiment, 15 prey items were introduced into the digestive fluid of 120 newly opened pitcher tanks of four Nepenthes species and 30 water-filled artificial tanks. Half of the tanks of each type were bagged with insect-screening net and after 1 month prey count and degradation were compared between treatments. Whereas prey was recovered from all bagged tanks, a significant part was missing from the unbagged lidless artificial and N. ampullaria tanks. The probability of prey recovery also increased with tank height but did not decrease with the abundance of any inquiline guild, suggesting that missing prey was removed by external visitors. Prey degradation was greater in unbagged tanks, varied across species and increased significantly with the abundance of saprophages and plant detritus. These results highlight the involvement of inquilines and falling debris in prey breakdown in these carnivorous plants, with species-specific relative contributions, and they suggest a role of pitcher shape in protecting against kleptoparasitism. This article is part of the theme issue 'Life in natural microcosms'.
Small ecosystems, big insights: tank bromeliads as model systems to investigate human-induced global changes.
Antiqueira PAP, Romero GQ
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42343856 · Publisher ↗
The impacts of global change on biodiversity and ecosystems have become a pressing concern for researchers, necessitating the selection of suitable model systems for empirical investigation. For decades, natural microcos...
The impacts of global change on biodiversity and ecosystems have become a pressing concern for researchers, necessitating the selection of suitable model systems for empirical investigation. For decades, natural microcosms, particularly tank bromeliads, have proven invaluable in addressing fundamental questions in ecology and evolution. Their natural environmental conditions, high multitrophic diversity and small size facilitate both realistic and highly replicable controlled experiments across the Neotropics. Tank bromeliads have thus emerged as effective model systems for studying various anthropogenic impacts. This review synthesizes studies employing bromeliads in space-for-time substitution approaches and experiments simulating human-induced changes in temperature, precipitation, habitat and biodiversity loss, detritus quality, ecological interactions and ecosystem processes. These studies consistently reveal the profound effects of human drivers on organismal vulnerability, ecological dynamics, food webs and ecosystem functioning. By enabling the investigation of multiple ecological questions across scales and levels of biological organization, these 'big answers from small worlds' provide critical insights into the impacts of global changes on complex systems. These findings from bromeliad microecosystems can be used as guiding strategies to preserve and manage natural freshwater ecosystems amidst ongoing global change. This article is part of the theme issue 'Life in natural microcosms'.
Symbiotic organs in insects: diversity, functional implications, and terminology.
Baños-Quintana AP, de Carvalho ASP, Kaltenpoth M
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42343855 · Publisher ↗
With over a million described species, insects represent the most successful group of animals on Earth. One of the drivers of insect diversity is their ability to engage in multifold beneficial symbioses with microorgani...
With over a million described species, insects represent the most successful group of animals on Earth. One of the drivers of insect diversity is their ability to engage in multifold beneficial symbioses with microorganisms, often involving specialized host organs to accommodate intra- or extracellular symbionts. The existence of such organs and their importance for sustaining and transmitting beneficial symbionts has been known for over a century, and specific terms have been established for categorizing organs harbouring intracellular bacteria (bacteriomes) or fungi (mycetomes), or cuticular crypts containing extracellular fungi (mycetangia). For others, however, general terms are lacking, e.g. organs containing extracellular bacteria associated with the cuticle or with the digestive tract. Furthermore, previously established terms have been misused in other contexts. Notably, 'bacteriome' has been increasingly employed in the microbiome field to refer to bacterial communities, instead of the term's original meaning of specialized organs housing intracellular bacterial symbionts. Here, we review and categorize the diversity of symbiotic organs in insects and propose a unified terminology. Our hope is that this common language will facilitate communication and thereby support the field of symbiosis research in unravelling commonalities and differences in the evolution, ecology, development, physiology and molecular basis across symbiotic interactions. This article is part of the theme issue 'Life in natural microcosms'.
Trapped in a hot microcosm: how flower microclimate contributes to pollination syndrome in a thermogenic system.
Leclerc MAJ, Gibernau M, Villain T … +1 more , Pincebourde S
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42343854 · Publisher ↗
Microclimates within microcosms are often stated to shelter occupants from adverse conditions, yet our limited knowledge narrows our ability to estimate the vulnerability to warming of species exploiting them. We charact...
Microclimates within microcosms are often stated to shelter occupants from adverse conditions, yet our limited knowledge narrows our ability to estimate the vulnerability to warming of species exploiting them. We characterized the microclimate temperature of the floral chamber of a thermogenic plant that produces heat in the context of pollination syndrome. Pollinators (Psychoda moth flies) of Arum italicum are trapped within the floral chamber for 24 h, thereby potentially exposing insects to dangerous temperatures. We report a strong temperature gradient across the floral chamber. We propose two hypotheses for the role of this temperature gradient in the pollination syndrome depending on environmental context. Under moderate conditions, the system relies on the exact position of the thermogenic organ to discourage insects from escaping the chamber, while temperature at the bottom of the chamber corresponds to the moth fly's preferred temperature, motivating the insect to remain there long enough to get covered by pollen. Under extreme conditions, the floral chamber may provide a thermal reward to avoid the Psychoda fly from reaching its thermal limits. Our comprehensive mechanistic analysis of the microclimate in a thermogenic flower highlights the importance of coevolutionary trajectories between temperature regulation by plants and their pollinators' thermal biology. This article is part of the theme issue 'Life in natural microcosms'.
On the consequences of collapsing introductions and range expansions under a single framework: A Comment on 'The concept of biological invasions in the Anthropocene: introductions and range expansions' (2026), by Carlton and Schwindt.
Griffen BD, Marlow BN
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42272396 · Publisher ↗
Abstract loading — click title to view on PubMed.
Invited reply: On the striking benefits of merging introductions and range expansions under a single invasions framework:a reply to Griffen & Marlow (2026).
Carlton JT, Schwindt E
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42272395 · Publisher ↗
Abstract loading — click title to view on PubMed.
Negative frequency-dependent selection: a positive outlook with deep learning.
Santander CG, Campelo Dos Santos AL, Arnab SP … +2 more , Fumagalli M, DeGiorgio M
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42272394 · Publisher ↗
Balancing selection is a mode of natural selection that maintains genetic diversity through various mechanisms, including negative frequency-dependent selection (NFDS). However, distinguishing the genomic signature of NF...
Balancing selection is a mode of natural selection that maintains genetic diversity through various mechanisms, including negative frequency-dependent selection (NFDS). However, distinguishing the genomic signature of NFDS from those of other balancing selection modes, such as overdominance, remains a significant challenge. In this perspective, we outline strategies to improve the modelling of genomic patterns expected under NFDS, with the goal of better differentiating them from signals of neutrality and alternative selection processes. We demonstrate how resource-efficient deep transfer learning, combined with novel data preprocessing and the modelling of genomic autocovariation, can effectively detect and characterize NFDS using either phased or unphased genotypes, and with or without temporal data from ancient DNA. Finally, we offer practical recommendations for both empiricists and method developers on advancing the detection of NFDS in genomic data. This article is part of the theme issue 'Exploring negative frequency dependent selection across levels: from genetics to ecology and back again'.
Intersections of evolution and ecology of polymorphisms from the viewpoint of demographic performance.
Takahashi Y, Noriyuki S, Ueno T
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42272393 · Publisher ↗
Genetic polymorphisms in a population may enhance demographic performance, as ecological niche partitioning among phenotypes can reduce negative interactions such as resource competition and predation risk. However, an i...
Genetic polymorphisms in a population may enhance demographic performance, as ecological niche partitioning among phenotypes can reduce negative interactions such as resource competition and predation risk. However, an increase in maladaptive or harmful phenotypes can reduce population performance, causing confusion among researchers about the ecological consequences of genetic polymorphism. Here, we propose a general framework for understanding the population-level ecological effects of genetic polymorphisms arising from adaptive evolution (balanced polymorphism) and stochastic processes (temporal polymorphism). To this end, we use the yardstick effect of diversity, which isolates the ecological effect of genetic diversity itself on population performance (e.g. growth rate and carrying capacity). In a population with balanced polymorphisms maintained by selection, genetic polymorphisms tend to have a positive diversity effect on its performance. By contrast, the diversity effect of temporal polymorphisms, which are maintained by gene flow, mutation and similar processes, is predicted to be zero, although such polymorphisms may increase genetic load and thereby reduce population performance. A negative diversity effect is only predicted when temporal polymorphisms are subject to positive frequency-dependent selection. This simple, systematic framework integrates the evolutionary mechanisms that establish genetic polymorphisms and their demographic functions, thereby enabling predictions of their ecological consequences. This article is part of the theme issue 'Exploring negative frequency dependent selection across levels: from genetics to ecology and back again'.
Can ancient DNA and other forms of time-sampled data aid in the inference of negative frequency-dependent selection?
Soni V
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42272392 · Publisher ↗
Negative frequency-dependent selection (NFDS) is commonly viewed as the most efficacious form of balancing selection. Despite this, inferring NFDS remains challenging, and questions remain as to its relative importance i...
Negative frequency-dependent selection (NFDS) is commonly viewed as the most efficacious form of balancing selection. Despite this, inferring NFDS remains challenging, and questions remain as to its relative importance in maintaining genetic variation in populations. Recent advances in both sequencing and genotyping technologies have resulted in a considerable increase in the number of publicly available human ancient DNA datasets, creating new opportunities for development of methods for the inference of NFDS from time-sampled data. In this perspective, I present three brief simulation studies to show how time-sampled data can help improve inference power. First, I show how multiple time points can help us distinguish between recent NFDS and partial selective sweeps, as well as other forms of balancing selection, based on allele frequency trajectories. I then demonstrate how selective effects can be distinguished from population history based on changes in genetic variation and the site frequency spectrum over time. Finally, I apply an approximate Bayesian computation approach to compare the power of multiple and single time point datasets in estimating the time for which NFDS has been shaping variation. Thus, I argue that data from multiple timepoints can facilitate the generation of new methodological approaches for better inference of NFDS. This article is part of the theme issue 'Exploring negative frequency dependent selection across levels: from genetics to ecology and back again'.
Negative frequency-dependent selection underlies overyielding through neighbour genotypic effects in Arabidopsis thaliana.
Sato Y
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42272391 · Publisher ↗
Negative frequency-dependent selection (FDS) can increase both genetic diversity and population-level mean fitness. While the dual consequence of negative FDS has been theoretically recognized, its genomic basis remains...
Negative frequency-dependent selection (FDS) can increase both genetic diversity and population-level mean fitness. While the dual consequence of negative FDS has been theoretically recognized, its genomic basis remains unknown. To explore a genetic link between negative FDS and overyielding, I conducted a genome-wide association study (GWAS) of neighbour genotypic effects on the growth of 98 Arabidopsis thaliana genotypes. By incorporating neighbour genotypic similarity, this GWAS analysis detected the most significant single-nucleotide polymorphism (SNP) on the fifth chromosome of A. thaliana, which was 6 kbp from a known locus responsible for indirect genetic effects. I found negative FDS on the most significant SNP, where individual plants increased their biomass in the presence of neighbours with a dissimilar allele. I also observed overyielding in which a biallelic mixture of the most significant SNP showed a 3% increase in biomass compared with monoallelic conditions. Furthermore, I focused on the genomic region near the most significant SNP and found a signature of balancing selection near a negative regulator of ethylene responses, SIRTUIN 2. The present analysis uncovered a quantitative trait locus linking balanced polymorphisms and overyielding in A. thaliana, providing a proof of principle to understand the maintenance of polymorphism and its positive impact on population productivity. This article is part of the theme issue 'Exploring negative frequency-dependent selection across levels: from genetics to ecology and back again'.
Repeated signatures of balancing selection in small and large populations of guppies (Poecilia reticulata).
Paris JR, Whiting JR, Ferrer Obiol J … +2 more , Hughes KA, Fraser BA
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42272390 · Publisher ↗
Balancing selection is a powerful evolutionary force that maintains adaptive genetic and phenotypic diversity. Although methods to detect the footprints of balancing selection in genomic data have advanced, we still lack...
Balancing selection is a powerful evolutionary force that maintains adaptive genetic and phenotypic diversity. Although methods to detect the footprints of balancing selection in genomic data have advanced, we still lack a clear understanding of how repeatable these signatures appear in wild populations, and how this repeatability is shaped by demographic history and existing genetic variation. The Trinidadian guppy (Poecilia reticulata) provides an ideal model to test the repeatability of balancing selection in the wild as there is strong evidence that negative frequency-dependent selection (NFDS) maintains colour polymorphism. We define repeatability as the same genomic window showing evidence of balancing selection across populations, regardless of origin (i.e. independence versus ancestral maintenance). Analysing whole-genome sequencing data from 11 guppy populations (n = 195) with contrasting demographic contexts, we apply scans of balancing selection to explore which genomic regions show evidence of repeatability. We find that populations with small Ne show less genetic repeatability but still exhibit population-specific regions of elevated diversity, implicating independent balancing selection or other evolutionary mechanisms. We identify 23 regions with repeated signatures of balancing selection, including a region on LG22 containing genes involved in colour, vision, mate choice and social behaviour. Investigating the repeatability of balancing selection in small and large populations improves our knowledge of how demographic factors interact with selective processes to shape natural variation. This article is part of the theme issue 'Exploring negative frequency dependent selection across levels: from genetics to ecology and back again'.
The geographic structure of pathogen resistance phenotypes under balancing selection.
Ebert D, Krebs M
Philos Trans R Soc Lond B Biol Sci · 2026 Jun · PMID 42272389 · Publisher ↗
The Red Queen model of host-parasite coevolution is based on time-lagged negative frequency-dependent selection resulting from highly specific interactions of the antagonists within populations. This model has been the p...
The Red Queen model of host-parasite coevolution is based on time-lagged negative frequency-dependent selection resulting from highly specific interactions of the antagonists within populations. This model has been the preferred theory for explaining the elevated levels of genetic diversity and even trans-species polymorphisms found in the disease genes of many organisms, including humans. Several genomic analyses with plants and animals revealed reduced spatial differentiation and balancing selection at disease genes; however, the geographic distribution of disease-related phenotypes has not been studied. Filling this gap is important, as balancing selection acts on phenotypes, expected to create an even distribution of phenotypes across space. Daphnia magna, a host with strong evidence of Red Queen coevolution, shows a strong pattern of isolation by distance and phylogeographic population structure. Here, we analyse the distribution of resistance phenotypes from 236 populations across 4 continents in response to 14 isolates of the coevolving pathogen Pasteuria ramosa. Polymorphisms for resistance phenotypes show a rather even geographic distribution without isolation by distance and little difference among phylogeographic host clades, coinciding with patterns expected for traits under balancing selection. This finding strongly supports the Red Queen model of antagonistic coevolution by negative frequency-dependent selection. This article is part of the theme issue 'Exploring negative frequency dependent selection across levels: from genetics to ecology and back again'.
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