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'.
Most larvae of phytophagous insects have little mobility, so they must complete their development on those plants 'chosen' by their mothers, even if this does not always increase the performance of her offspring. Here, we tested the hypothesis that the defence strategy expressed by host plants and the frequency at which they are represented within populations can condition both the preference of the female and the performance of her offspring. Using the plant Datura stramonium and its specialist insect Lema daturaphila, we conducted an experiment in which the frequency of resistant and tolerant genotypes within cages was manipulated, and the initial density of herbivorous adults was controlled. Results provide conclusive evidence of negative frequency-dependent oviposition preference for tolerant plants and differential density-dependent effect between resistant and tolerant plants on larval survival. Female oviposition preference also changed larval density, which in turn fed back to influence larval survival. Moreover, we found that oviposition preference for rare tolerant plants resulted, indeed, in lower plant fitness. Thus, the evolution of phytophagous insects' oviposition preference can be shaped by the frequency in which different plant defensive strategies are represented within the population and can create evolutionary feedback on their host plants. This article is part of the theme issue 'Exploring negative frequency dependent selection across levels: from genetics to ecology and back again'.
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'.
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'.
How non-neutral genetic variation is maintained in natural populations is a fundamental question in evolutionary biology. With environmental fluctuations, the effect of a mutant allele on fitness may also fluctuate between beneficial and deleterious relative to the wild-type allele. If this fitness fluctuation is specific to individuals of a certain stage or age in the life cycle, negative frequency-dependent selection arises, leading to high levels of polymorphism. This effect of within-population heterogeneity in fluctuating selection is an example of a diversity-promoting mechanism known as the storage effect. To obtain further insights on this effect and explore the conditions of polymorphism, models of age-structured populations with increasing complexity were investigated. How the geometric mean fitness of a rare allele is modified under the joint fluctuation of demography and selection was analysed, yielding the prediction that mutations whose average effects on fitness are deleterious can be maintained in polymorphism. It was also found that adding minimum iteroparity to the conventional model of discrete non-overlapping generations fully exerts the storage effect. These results suggest that the storage effect is expected under general within-population heterogeneity and they reinforce the conclusion that significant non-neutral genetic variation is highly plausible in natural populations under fluctuating environments. This article is part of the theme issue 'Exploring negative frequency dependent selection across levels: from genetics to ecology and back again'.
Recognition is critical for a wide range of biological interactions from the immune system at the cellular level to individual recognition mediating complex animal social structures. Identity signatures are common features of many animal traits and facilitate self/non-self and individual recognition across diverse taxa. Inherently, identity signatures show high levels of intra-population phenotypic diversity. While the existence of individually distinctive traits has attracted much attention, the developmental mechanisms and evolutionary pressures shaping identity signature diversity have been less well studied. Here, we review the evidence that selection shapes the phenotypic diversity of individual identity signals used in a range of social and sexual contexts. Evidence from comparative, developmental and behavioural studies shows that selection often shapes phenotypes to be signals rather than cues of identity. Population genomic evidence implicates negative frequency-dependent selection maintaining identity signalling diversity in humans and mice. Like the extreme diversity seen at allorecognition loci, such as major histocompatibility complex (MHC) in animals and self-incompatibility in plants, social processes in animals are drivers of phenotypic and genetic diversity. However, the quantitative traits contributing to identity signals in animals are more complex than allorecognition loci and thus the consequences of selection for individual identity signals probably differ in multiple ways in terms of the maintenance of allelic diversity. The role of cognition in shaping identity signalling traits and long-term patterns of phenotypic and allelic variation and divergence across populations and species is discussed. This article is part of the Theme Issue 'Exploring negative frequency dependent selection across levels: from genetics to ecology and back again'.
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'.
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'.
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'.
A generative model can be defined as a model of the latent causes of sensory input that can be used to generate new data samples. By examining empirical evidence and computational theory, we propose that the hippocampus can be characterized as a generative model. The hippocampus is a brain region important for memory. Recordings of neural activity from the hippocampus have led to the view that the hippocampus represents a cognitive map by abstracting a low-dimensional representation of the external world. We extend this view to suggest the hippocampus represents the latent, unobserved causes of sensory data by virtue of the position of the hippocampus within the deep cortical hierarchy. These representations of unobserved latent causes endow the hippocampus with capacity to generate new data samples that allow exploration of future hypotheticals and provide an internally generated training signal back to the generative model. We explore how perturbations to the hippocampal generative model may explain core symptoms of neuropsychiatric disorders such as those observed in psychosis. Together, this perspective provides a unified account of hippocampal function that explains how computations performed by the hippocampus support higher-order cognition and adaptive behaviour. This article is part of the theme issue 'The role of hippocampal predictions in cognition: bridging perception and memory'.
Planning entails running simulations forward to identify possible outcomes. It is useful for situations where outcomes are uncertain, costly or dangerous to pursue. A growing body of literature is finding that during theta states in the rodent hippocampus, sequences run forward along possible futures, enabling 'episodic future thinking' that can be used within a neural circuit for planning. Emerging data suggest that the prelimbic cortex initiates these simulations, an entorhinal-hippocampal interaction generates them and valuation systems in the ventral striatum (nucleus accumbens) and orbitofrontal cortex evaluate them, enabling downstream decision-making processes to take action. Within the hippocampus, each theta cycle carries activity representing the present followed by explorations of possible paths ahead of the animal. These representations occur serially and sequentially. These theta sweeps are not mere reflections of movement but dynamic cognitive simulations whose length, direction and content shift with learning, confidence and experience. Individual theta cycles change in length and representation from cycle to cycle, suggesting a cognitive role. In this review, we bring together that body of literature and identify open questions and controversies for future research, including questions regarding how sweeps are structured, how they shift between exploration and commitment, and how threat-related representations interface with avoidance circuits. This article is part of the theme issue 'The role of hippocampal predictions in cognition: bridging perception and memory'.
Sexual dimorphism evolves from sex-specific selective pressures and is often mediated by tissue-specific differential gene expression, although the mechanisms are not fully understood. Here, we investigate the role of DNA methylation as a potential regulator of tissue-specific sex-biased gene expression in the house sparrow (Passer domesticus). We found that both gene expression and DNA methylation show a strong tissue-specific pattern, and that samples clustered by tissue type, except in gonadal tissue, where there was a strong sex-specific clustering. Sex-biased gene expression and sex-biased DNA methylation patterns were more enriched on the Z-chromosome than on the autosomes, and most sex-biased genes were tissue-specific, with the majority of sex bias occurring in the gonads. As expected, we detected a strong negative correlation between DNA methylation levels and gene expression levels around the transcription start site (TSS). In gonads, sex-biased DNA methylation accounted for 14% of the sex differences in gene expression. These findings highlight heterogeneous methylation and expression patterns among tissues and thus the importance of choosing the correct tissue for studies aiming to gain insights into the evolution of sexually dimorphic traits. Understanding these genetic mechanisms is vital for comprehending the evolutionary potential of sexes, their ecological roles and for informing conservation efforts. This article is part of the theme issue 'Ecological epigenetics at the intersection of behaviour and life history variation in non-model animals'.
The early life environment can strongly influence behavioural development. However, little is known about the underlying neurogenomic mechanisms. Using a half-sib design, threespine stickleback fish were either raised by their fathers or hand-reared ('orphaned') for 10 days before living in a common-garden environment. As offspring developed, they were tested in one of three behavioural assays: an open field assay with a simulated predator attack, a social behaviour assay with a simulated predator attack, and a light-dark box assay. Offspring that received paternal care behaved in ways that we interpret as indicating increased boldness and sociability. Fish in the open field assay had their brains sampled one hour following the simulated attack; brains were sampled at the same time from full-sib controls. These brains were processed for gene expression (via 3'Tag-seq) and chromatin accessibility (via ATAC-seq). Paternal care treatment and the predator attack affected brain gene expression, but sex was also a major factor, despite fish being reproductively immature. Sex, and to a lesser extent, paternal care treatment, also influenced chromatin accessibility at a whole-genome scale. Our findings further our understanding of the mechanisms by which the early life environment-including the environment provided by parents-influences offspring behavioural development. This article is part of the theme issue 'Ecological epigenetics at the intersection of behaviour and life history variation in non-model animals'.
For sex-specific ornaments to be expressed only at a particular ontogenetic stage, genetic correlations between the sexes and between ontogenetic stages should be resolved. In vertebrates, sex-specific and ontogenetic stage-specific expression of sexual dimorphism is often mediated by sex steroid signalling. Here, we investigated the epigenetic mechanisms by which androgen induces sex-specific gene expression that may be involved in male-specific nuptial colouration in the three-spined stickleback (Gasterosteus aculeatus). First, we identified several androgen-responsive genes in skin tissues from the throat and ventral side of the body. The Tetratricopeptide repeat domain 39b (Ttc39b) gene, which is involved in the expression of red colouration in other vertebrates, was up-regulated in throat skin after androgen treatment. We also found that the Growth regulation by estrogen in breast cancer 1-like (Greb1l) gene, whose homologue is involved in the amplification of androgen signalling in human cancer cells, was up-regulated in both tissues after androgen treatment. Some gene-expression changes induced by the androgen treatment, including the change in Greb1l expression, were associated with changes in chromatin accessibility, as determined using assay for transposase-accessible chromatin using sequencing (ATAC-seq). These results suggest that at least some of the sex- and ontogenetic stage-specific gene expression may be achieved by epigenetic changes in chromatin accessibility. This article is part of the theme issue 'Ecological epigenetics at the intersection of behaviour and life history variation in non-model animals'.
From an ecological perspective, many animals, particularly birdstext, are exposed to increasing stress levels in the context of the current climate crisis. Therefore, the development of tools that can reliably measure long-term stress exposure in animals is fundamental. Epigenetic mechanisms offer a promising approach, as stress during early development can alter DNA methylation in peripheral cells, such as avian red blood cells (RBCs). Here, we investigated whether distinct early-life environments leave specific epigenetic marks in RBCs, as well as the persistence of these marks. Male chickens were exposed from day 4 to 3.5 weeks of age to either social isolation stress (SIS), environmental enrichment or control barren conditions. RBCs were collected immediately after exposure and after six months. We found that, with age, SIS increased the number of hypermethylated regions, while enrichment induced mostly hypomethylated regions and fewer overall methylation changes. The control group showed a balanced mix of hyper- and hypomethylated regions. Pathway analysis revealed that differentially methylated region (DMR)-associated genes in SIS were enriched for immune-metabolic pathways, while those in the enrichment group were linked to microRNA regulation and nuclear receptor signalling. Therefore, we show that differing early-life environmental conditions leave persistent and distinct epigenetic signatures in RBCs, with potentially different functional consequences. This article is part of the theme issue 'Ecological epigenetics at the intersection of behaviour and life history variation in non-model animals'.
How does the brain generate meaning from the continuous flow of sensory input? We propose that meaning is not the product of isolated regions or circuits but an emergent property of large-scale recurrently connected networks in which the hippocampus plays a pivotal role. Drawing from cognitive science, developmental studies and systems neuroscience, we outline five key principles by which the brain constructs meaning. (i) Network-level emergence: meaning arises from the coordinated activity of distributed hubs, with the hippocampus serving as a central node that binds activity across modalities and timescales. (ii) Reentrant processing: bidirectional hippocampal-cortical loops allow prior experience to continuously inform new perception, enabling prediction, disambiguation and context-sensitive interpretation. (iii) Dynamic stability: hippocampal computations help maintain attractor-like network states that stabilize semantic representations while retaining flexibility to incorporate novelty. (iv) Grounding and multi-level integration: by linking embodied sensorimotor experiences with abstract symbolic relations, meanings remain anchored in real-world invariants yet extend to higher-order concepts. (v) Context-dependency: through its role in relational binding, the hippocampus dynamically modulates meaning as a function of task demands, prior knowledge and emotional states. By integrating microcircuit dynamics with global network organization, we argue that meaning reflects the brain's capacity to stabilize and flexibly reconfigure distributed states in response to ongoing input and goals. This synthesis highlights the hippocampus as indispensable for transforming sensory input into coherent, context-rich meaning across the lifespan. This article is part of the theme issue 'The role of hippocampal predictions in cognition: bridging perception and memory'.
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'.
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'.
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'.
There is a growing interest in the genomic and developmental basis of discrete or multimodal phenotypes governed by genetic polymorphisms. Recent research has uncovered the genomic basis of such polymorphisms and their maintenance through balancing selection such as negative frequency-dependent selection (NFDS). Such polymorphisms often originate through structural genomic changes or through mutations in regulatory genes. Historically, researchers focused on male-limited polymorphisms and intrasexual competition as drivers of NFDS. However, an increasing number of female-limited polymorphisms are being discovered, with sexual conflict, social selection or natural selection maintaining such polymorphisms. Still, significant gaps in our understanding of female-limited polymorphisms linger, partly as a historical legacy of a male-centric research focus on conspicuous male phenotypes. We review and synthesize female-limited polymorphisms, their maintenance, genetic architecture, genomic basis, developmental origin, microevolutionary dynamics and macroevolutionary diversification. Animals with female-limited polymorphisms include invertebrates (e.g. bedbugs, butterflies, damselflies and fruit flies) but also vertebrates (e.g. birds, mammals and reptiles). By highlighting female-limited polymorphisms, we draw attention to the unique sex-specific selection pressures on females distinguishing them from male-limited polymorphisms. Finally, wee present a conceptual model aimed to explain the origin and evolution of female-limited polymorphisms and outline future research avenues in this emerging field. This article is part of the theme issue 'Exploring negative frequency dependent selection across levels: from genetics to ecology and back again'.