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Populations can adapt to novel selection pressures through dramatic frequency changes in a few genes of large effect or subtle shifts in many genes of small effect. The latter (polygenic adaptation) is expected to be the primary mode of evolution for many life-history traits but tends to be more difficult to detect than changes in genes of large effect. Atlantic cod (Gadus morhua) were subjected to intense fishing pressure over the twentieth century, leading to abundance crashes and a phenotypic shift toward earlier maturation across many populations. Here, we use spatially replicated temporal genomic data to test for a shared polygenic adaptive response to fishing using methods previously applied to evolve-and-resequence experiments. Cod populations on either side of the Atlantic show covariance in allele frequency change across the genome that are characteristic of recent polygenic adaptation. Using simulations, we demonstrate that the degree of covariance in allele frequency change observed in cod is unlikely to be explained by neutral processes or background selection. As human pressures on wild populations continue to increase, understanding and attributing modes of adaptation using methods similar to those demonstrated here will be important in identifying the capacity for adaptive responses and evolutionary rescue. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

The evolutionary shift from a single-element ear, multi-element jaw to a multi-element ear, single-element jaw during the transition to crown mammals marks one of the most dramatic structural transformations in vertebrates. Research on this transformation has focused on mammalian middle-ear evolution, but a mandible comprising only the dentary is equally emblematic of this evolutionary radiation. Here, we show that the remarkably diverse jaw shapes of crown mammals are coupled with surprisingly stereotyped jaw stiffness. This strength-based morphofunctional regime has a genetic basis and allowed mammalian jaws to effectively resist deformation as they radiated into highly disparate forms with markedly distinct diets. The main functional consequences for the mandible of decoupling hearing and mastication were a trade-off between higher jaw stiffness versus decreased mechanical efficiency and speed compared with non-mammals. This fundamental and consequential shift in jaw form-function underpins the ecological and taxonomic diversification of crown mammals. This article is part of the theme issue 'The mammalian skull: development, structure and function'.

The mammalian skull is an informative and versatile study system critical to research efforts across the broad spectrum of molecular, cellular, organismal and evolutionary sciences. The amount of knowledge concerning mammalian skull continues to grow exponentially, fuelled by the advent of new research methods and new material. Computed microtomography, including X-ray imaging using synchrotron radiation, proved to be an important tool for the descriptive and quantitative analysis of cranial anatomy. A major conceptual change, namely combining genetics and development with evolution into 'evo-devo' studies, also contributed to our knowledge of the mammalian skull enormously. These advances, coupled with novel techniques now allow researchers to integrate the process of cranial development with data from the fossil record, which is also augmented by seminal discoveries from Africa, Asia and both Americas. However, for decades, there has been no comprehensive source covering fundamental aspects of this vibrant field of evolutionary biology. To address this gap, we offer in this theme issue a balanced mix of research papers and reviews from leading experts in the field and a younger generation of scientists from five continents. This article is part of the theme issue 'The mammalian skull: development, structure and function'.

Collective behaviours, such as flocking in birds or decision making by bee colonies, are some of the most intriguing behavioural phenomena in the animal kingdom. The study of collective behaviour focuses on the interactions between individuals within groups, which typically occur over close ranges and short timescales, and how these interactions drive larger scale properties such as group size, information transfer within groups and group-level decision making. To date, however, most studies have focused on snapshots, typically studying collective behaviour over short timescales up to minutes or hours. However, being a biological trait, much longer timescales are important in animal collective behaviour, particularly how individuals change over their lifetime (the domain of developmental biology) and how individuals change from one generation to the next (the domain of evolutionary biology). Here, we give an overview of collective behaviour across timescales from the short to the long, illustrating how a full understanding of this behaviour in animals requires much more research attention on its developmental and evolutionary biology. Our review forms the prologue of this special issue, which addresses and pushes forward understanding the development and evolution of collective behaviour, encouraging a new direction for collective behaviour research. This article is part of a discussion meeting issue 'Collective behaviour through time'.

Navigation is one of the most heavily studied problems in robotics and is conventionally approached as a geometric mapping and planning problem. However, real-world navigation presents a complex set of physical challenges that defies simple geometric abstractions. Machine learning offers a promising way to go beyond geometry and conventional planning, allowing for navigational systems that make decisions based on actual prior experience. Such systems can reason about traversability in ways that go beyond geometry, accounting for the physical outcomes of their actions and exploiting patterns in real-world environments. They can also improve as more data is collected, potentially providing a powerful network effect. In this article, we present a general toolkit for experiential learning of robotic navigation skills that unifies several recent approaches, describe the underlying design principles, summarize experimental results from several of our recent papers, and discuss open problems and directions for future work. This article is part of the theme issue 'New approaches to 3D vision'.

Forest restoration is increasingly heralded as a global strategy to conserve biodiversity and mitigate climate change, yet long-term studies that compare the effects of different restoration strategies on tree recruit demographics are lacking. We measured tree recruit survival and growth annually in three restoration treatments-natural regeneration, applied nucleation and tree plantations-replicated at 13 sites in southern Costa Rica-and evaluated the changes over a decade. Early-successional seedlings had 14% higher survival probability in the applied nucleation than natural regeneration treatments. Early-successional sapling growth rates were initially 227% faster in natural regeneration and 127% faster in applied nucleation than plantation plots but converged across restoration treatments over time. Later-successional seedling and sapling survival were similar across treatments but later-successional sapling growth rates were 39% faster in applied nucleation than in plantation treatments. Results indicate that applied nucleation was equally or more effective in enhancing survival and growth of naturally recruited trees than the more resource-intensive plantation treatment, highlighting its promise as a restoration strategy. Finally, tree recruit dynamics changed quickly over the 10-year period, underscoring the importance of multi-year studies to compare restoration interventions and guide ambitious forest restoration efforts planned for the coming decades. This article is part of the theme issue 'Understanding forest landscape restoration: reinforcing scientific foundations for the UN Decade on Ecosystem Restoration'.

Imagination is a biological function that is vital to human experience and advanced cognition. Despite this importance, it remains unknown how imagination is realized in the brain. Substantial research focusing on the hippocampus, a brain structure traditionally linked to memory, indicates that firing patterns in spatially tuned neurons can represent previous and upcoming paths in space. This work has generally been interpreted under standard views that the hippocampus implements cognitive abilities primarily related to actual experience, whether in the past (e.g. recollection, consolidation), present (e.g. spatial mapping) or future (e.g. planning). However, relatively recent findings in rodents identify robust patterns of hippocampal firing corresponding to a variety of alternatives to actual experience, in many cases without overt reference to the past, present or future. Given these findings, and others on hippocampal contributions to human imagination, we suggest that a fundamental function of the hippocampus is to generate a wealth of hypothetical experiences and thoughts. Under this view, traditional accounts of hippocampal function in episodic memory and spatial navigation can be understood as particular applications of a more general system for imagination. This view also suggests that the hippocampus contributes to a wider range of cognitive abilities than previously thought. This article is part of the theme issue 'Thinking about possibilities: mechanisms, ontogeny, functions and phylogeny'.

Mitochondrial dysfunction in cardiomyocytes is a hallmark of heart failure development. Although initial studies recognized the importance of different mitochondrial subpopulations, there is a striking lack of direct comparison of intrafibrillar (IF) versus perinuclear (PN) mitochondria during the development of HF. Here, we use multiple approaches to examine the morphology and functional properties of IF versus PN mitochondria in pressure overload-induced cardiac remodelling in mice, and in non-failing and failing human cardiomyocytes. We demonstrate that PN mitochondria from failing cardiomyocytes are more susceptible to depolarization of mitochondrial membrane potential, reactive oxygen species generation and impairment in Ca2+ uptake compared with IF mitochondria at baseline and under physiological stress protocol. We also demonstrate, for the first time to our knowledge, that under normal conditions PN mitochondrial Ca2+ uptake shapes nucleoplasmic Ca2+ transients (CaTs) and limits nucleoplasmic Ca2+ loading. The loss of PN mitochondrial Ca2+ buffering capacity translates into increased nucleoplasmic CaTs and may explain disproportionate rise in nucleoplasmic [Ca2+] in failing cardiomyocytes at increased stimulation frequencies. Therefore, a previously unidentified benefit of restoring the mitochondrial Ca2+ uptake may be normalization of nuclear Ca2+ signalling and alleviation of altered excitation-transcription, which could be an important therapeutic approach to prevent adverse cardiac remodelling. This article is part of the theme issue 'The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease'.

The visual pigments known as opsins are the primary molecular basis for colour vision in animals. Insects are among the most diverse of animal groups and their visual systems reflect a variety of life histories. The study of insect opsins in the fruit fly Drosophila melanogaster has led to major advances in the fields of neuroscience, development and evolution. In the last 25 years, research in D. melanogaster has improved our understanding of opsin genotype-phenotype relationships while comparative work in other insects has expanded our understanding of the evolution of insect eyes via gene duplication, coexpression and homologue switching. Even so, until recently, technology and sampling have limited our understanding of the fundamental mechanisms that evolution uses to shape the diversity of insect eyes. With the advent of genome editing and in vitro expression assays, the study of insect opsins is poised to reveal new frontiers in evolutionary biology, visual neuroscience, and animal behaviour. This article is part of the theme issue 'Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods'.

Recent advances in Bayesian phylogenetics offer substantial computational savings to accommodate increased genomic sampling that challenges traditional inference methods. In this review, we begin with a brief summary of the Bayesian phylogenetic framework, and then conceptualize a variety of methods to improve posterior approximations via Markov chain Monte Carlo (MCMC) sampling. Specifically, we discuss methods to improve the speed of likelihood calculations, reduce MCMC burn-in, and generate better MCMC proposals. We apply several of these techniques to study the evolution of HIV virulence along a 1536-tip phylogeny and estimate the internal node heights of a 1000-tip SARS-CoV-2 phylogenetic tree in order to illustrate the speed-up of such analyses using current state-of-the-art approaches. We conclude our review with a discussion of promising alternatives to MCMC that approximate the phylogenetic posterior. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.

Several scholars have long suggested that human language and remarkable communicative abilities originate from the need and motivation to cooperate and coordinate actions with others. Yet, little work has focused on when and how great apes communicate during joint action tasks, partly because of the widely held assumption that animal communication is mostly manipulative, but also because non-human great apes' default motivation seems to be competitive rather than cooperative. Here, we review experimental cooperative tasks and show how situational challenges and the degree of asymmetry in terms of knowledge relevant for the joint action task affect the likelihood of communication. We highlight how physical proximity and strength of social bond between the participants affect the occurrence and type of communication. Lastly, we highlight how, from a production point of view, communicators appear capable of calibrating their signalling and controlling their delivery, showing clear evidence of first-order intentionality. On the other hand, recipients appear to struggle in terms of making use of referential information received. We discuss different hypotheses accounting for this asymmetry and provide suggestions concerning how future work could help us unveil to what degree the need for cooperation has shaped our closest living relatives' communicative behaviour. This article is part of the theme issue 'Revisiting the human 'interaction engine': comparative approaches to social action coordination'.

Oxytocin is an endogenous neuropeptide hormone that influences social behaviour and bonding in mammals. Variations in oxytocin receptor (OXTR) expression may play a role in the social deficits seen in autism spectrum disorder. Previous studies from our laboratory found a dense population of OXTR in the human substantia nigra (SN), a basal ganglia structure in the midbrain that is important in both movement and reward pathways. Here, we explore whether differences in OXTR can be identified in the dopaminergic SN pars compacta of individuals with autism. Postmortem human brain tissue specimens were processed for OXTR autoradiography from four groups: males with autism, females with autism, typically developing (TD) males and TD females. We found that females with autism had significantly lower levels of OXTR than the other groups. To examine potential gene expression differences, we performed in situ hybridization in adjacent slides to visualize and quantify OXTR mRNA as well as mRNA for tyrosine hydroxylase. We found no differences in mRNA levels for either gene across the four groups. These results suggest that a dysregulation in local OXTR protein translation or increased OXTR internalization/recycling may contribute to the differences in social symptoms seen in females with autism. This article is part of the theme issue 'Interplays between oxytocin and other neuromodulators in shaping complex social behaviours'.

Selective adult social attachments, or 'pair bonds', represent central relationships for individuals in a number of social species, including humans. Loss of a pair mate has emotional consequences that may or may not diminish over time, and that often translate into impaired psychological and physical health. In this paper, we review the literature on the neuroendocrine mechanisms for the emotional consequences of partner loss, with a special focus on hypothesized interactions between oxytocin, corticotropin-releasing hormone and the κ opioid system. This article is part of the theme issue 'Interplays between oxytocin and other neuromodulators in shaping complex social behaviours'.

Oxytocin (OT) and the OT receptor occupy essential roles in our current understanding of mammalian evolution, survival, sociality and reproduction. This narrative review examines the hypothesis that many functions attributed to OT can be traced back to conditions on early Earth, including challenges associated with managing life in the presence of oxygen and other basic elements, including sulfur. OT regulates oxidative stress and inflammation especially through effects on the mitochondria. A related nonapeptide, vasopressin, as well as molecules in the hypothalamic-pituitary-adrenal axis, including the corticotropin-releasing hormone family of molecules, have a broad set of functions that interact with OT. Interactions among these molecules have roles in the causes and consequence of social behaviour and the management of threat, fear and stress. Here, we discuss emerging evidence suggesting that unique properties of the OT system allowed vertebrates, and especially mammals, to manage over-reactivity to the 'side effects' of oxygen, including inflammation, oxidation and free radicals, while also supporting high levels of sociality and a perception of safety. This article is part of the theme issue 'Interplays between oxytocin and other neuromodulators in shaping complex social behaviours'.

Many species are shifting their ranges to keep pace with climate change, but habitat fragmentation and limited dispersal could impede these range shifts. In the case of climate-vulnerable foundation species such as tropical reef corals and temperate forest trees, such limitations might put entire communities at risk of extinction. Restoring connectivity through corridors, stepping-stones or enhanced quality of existing patches could prevent the extinction of several species, but dispersal-limited species might not benefit if other species block their dispersal. Alternatively, managers might relocate vulnerable species between habitats through assisted migration, but this is generally a species-by-species approach. To evaluate the relative efficacy of these strategies, we simulated the climate-tracking of species in randomized competitive metacommunities with alternative management interventions. We found that corridors and assisted migration were the most effective strategies at reducing extinction. Assisted migration was especially effective at reducing the extinction likelihood for short-dispersing species, but it often required moving several species repeatedly. Assisted migration was more effective at reducing extinction in environments with higher stochasticity, and corridors were more effective at reducing extinction in environments with lower stochasticity. We discuss the application of these approaches to an array of systems ranging from tropical corals to temperate forests. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'.

Given the many small-effect loci uncovered by genome-wide association studies (GWAS), polygenic scores have become central to genomic medicine, and have found application in diverse settings including evolutionary studies of adaptation. Despite their promise, polygenic scores have been found to suffer from limited portability across human populations. This at first seems in conflict with the observation that most common genetic variation is shared among populations. We investigate one potential cause of this discrepancy: stabilizing selection on complex traits. Counterintuitively, while stabilizing selection constrains phenotypic evolution, it accelerates the loss and fixation of alleles underlying trait variation within populations (GWAS loci). Thus even when populations share an optimum phenotype, stabilizing selection erodes the variance contributed by their shared GWAS loci, such that predictions from GWAS in one population explain less of the phenotypic variation in another. We develop theory to quantify how stabilizing selection is expected to reduce the prediction accuracy of polygenic scores in populations not represented in GWAS samples. In addition, we find that polygenic scores can substantially overstate average genetic differences of phenotypes among populations. We emphasize stabilizing selection around a common optimum as a useful null model to connect patterns of allele frequency and polygenic score differentiation. This article is part of the theme issue 'Celebrating 50 years since Lewontin's apportionment of human diversity'.

The multi-species coalescent (MSC) provides a theoretical foundation for modern phylogenetics and comparative population genetics. Its theoretical properties have been heavily studied but there are still aspects of the MSC that are largely unknown, including the covariances in pairwise coalescence times, which are fundamental for understanding the properties of statistics that combine data from multiple species, such as the fixation index (FST). The major contribution of this study is the derivation and implementation of exact expressions for the covariances of pairwise coalescence times under phylogenetic models with piecewise constant changes in population size, assuming no gene flow after species divergence. We use these expressions to derive the variance in average pairwise differences within and between populations. We then derive approximations for the expectation and bias of a sequence-based estimator of FST, a commonly used genetic measurement of population differentiation, when it is applied to a non-recombining region of the genome. We show that the estimator of FST is generally biased downward. A freely available software package is provided, STCov, to calculate the mean, variances and covariances in coalescence times presented here under user-defined piecewise-constant species trees. This article is part of the theme issue 'Celebrating 50 years since Lewontin's apportionment of human diversity'.

Interspecific competition influences the composition of ecological communities. Species may differ in their needs for different resources, therefore resource availability may determine the outcome of interspecific interactions. Species often compete over food, shelter or both. When more than one resource is limited, different species may prioritize different resources. To determine the impact of resource availability on the competitive relationship between an invasive and a native species, we examined interactions between groups of the invasive Argentine ant (Linepithema humile) and the native odorous ant (Tapinoma sessile) over (1) food, (2) shelter or (3) both simultaneously. We further examined the mechanisms underlying the competitive relationship, asking whether aggressive interactions, exploratory behaviour or the order of arrival at a resource explained resource use. Shelter was preferred by both species when no competitors were present. In a competitive setting, L. humile groups controlled shelter through aggressive displacement but lost control over food due to investment of workers in the control of shelter. Thus, there are tradeoffs when competing over multiple resources and aggressive interactions allow invasive species to displace native species from a preferred resource. This article is part of the theme issue 'Intergroup conflict across taxa'.

The energetic costs and benefits of intergroup conflicts over feeding sites are widely hypothesized to be significant, but rarely quantified. In this study, we use short-term measures of energy gain and expenditure to test whether winning an intergroup encounter is associated with greater benefits, and losing with greater costs. We also test an alternative perspective, where groups fight for access to large food sources that are neither depletable nor consistently monopolizable: in this case, a group that has already fed on the resource and is willing to leave first (the loser) is supplanted by a newly arrived group (the winner). We evaluate energy balance and travel distance during and after encounters for six groups of red-tailed monkeys in Kibale National Park, Uganda. We find that winning groups experience substantial energetic benefits, but do so to recoup from earlier deficits. Losing groups, contrary to predictions, experience minimal energetic costs. Winners and losers are predictable based upon their use of the contested resource immediately before the encounter. The short-term payoffs associated with these stressful conflicts compensate for any associated costs and support the perception that between-group contests are an important feature of social life for species that engage in non-lethal conflicts. This article is part of the theme issue 'Intergroup conflict across taxa'.

The notion of dominance is ubiquitous across the animal kingdom, wherein some species/groups such relationships are strictly hierarchical and others are not. Modern approaches for measuring dominance have emerged in recent years taking advantage of increased computational power. One such technique, named Percolation and Conductance (Perc), uses both direct and indirect information about the flow of dominance relationships to generate hierarchical rank order that makes no assumptions about the linearity of these relationships. It also provides a new metric, known as 'dominance certainty', which is a complimentary measure to dominance rank that assesses the degree of ambiguity of rank relationships at the individual, dyadic and group levels. In this focused review, we will (i) describe how Perc measures dominance rank while accounting for both nonlinear hierarchical structure as well as sparsity in data-here we also provide a metric of dominance certainty estimated by Perc, which can be used to compliment the information dominance rank supplies; (ii) summarize a series of studies by our research team reflecting the importance of 'dominance certainty' on individual and societal health in large captive rhesus macaque breeding groups; and (iii) provide some concluding remarks and suggestions for future directions for dominance hierarchy research. This article is part of the theme issue 'The centennial of the pecking order: current state and future prospects for the study of dominance hierarchies'.

To make maps from airborne odours requires dynamic respiratory patterns. I propose that this constraint explains the modulation of memory by nasal respiration in mammals, including murine rodents (e.g. laboratory mouse, laboratory rat) and humans. My prior theories of limbic system evolution offer a framework to understand why this occurs. The answer begins with the evolution of nasal respiration in Devonian lobe-finned fishes. This evolutionary innovation led to adaptive radiations in chemosensory systems, including the emergence of the vomeronasal system and a specialization of the main olfactory system for spatial orientation. As mammals continued to radiate into environments hostile to spatial olfaction (air, water), there was a loss of hippocampal structure and function in lineages that evolved sensory modalities adapted to these new environments. Hence the independent evolution of echolocation in bats and toothed whales was accompanied by a loss of hippocampal structure (whales) and an absence of hippocampal theta oscillations during navigation (bats). In conclusion, models of hippocampal function that are divorced from considerations of ecology and evolution fall short of explaining hippocampal diversity across mammals and even hippocampal function in humans. This article is part of the theme issue 'Systems neuroscience through the lens of evolutionary theory'.

Recent well-documented cases of cultural evolution towards increasing efficiency in non-human animals have led some authors to propose that other animals are also capable of cumulative cultural evolution, where traits become more refined and/or complex over time. Yet few comparative examples exist of traits increasing in complexity, and experimental tests remain scarce. In a previous study, we introduced a foraging innovation into replicate subpopulations of great tits, the 'sliding-door puzzle'. Here, we track diffusion of a second 'dial puzzle', before introducing a two-step puzzle that combines both actions. We mapped social networks across two generations to ask if individuals could: (1) recombine socially-learned traits and (2) socially transmit a two-step trait. Our results show birds could recombine skills into more complex foraging behaviours, and naïve birds across both generations could learn the two-step trait. However, closer interrogation revealed that acquisition was not achieved entirely through social learning-rather, birds socially learned components before reconstructing full solutions asocially. As a consequence, singular cultural traditions failed to emerge, although subpopulations of birds shared preferences for a subset of behavioural variants. Our results show that while tits can socially learn complex foraging behaviours, these may need to be scaffolded by rewarding each component. This article is part of a discussion meeting issue 'The emergence of collective knowledge and cumulative culture in animals, humans and machines'.

Cyclical fluctuations in reproductive output are widespread among perennial plants, from multi-year masting cycles in forest trees to alternate bearing in horticultural crops. In natural systems, ecological drivers such as climate and pollen limitation can result in synchrony among plants. Agricultural practices are generally assumed to outweigh ecological drivers that might synchronize alternate-bearing individuals, but this assumption has not been rigorously assessed and little is known about the role of pollen limitation as a driver of synchrony in alternate-bearing crops. We tested whether alternate-bearing perennial crops show signs of alternate bearing at a national scale and whether the magnitude of national-scale alternate bearing differs across pollination syndromes. We analysed the Food and Agriculture Organization of the United Nations time series (1961-2018) of national crop yields across the top-producing countries of 27 alternate-bearing taxa, 6 wind-pollinated and 21 insect-pollinated. Alternate bearing was common in these national data and more pronounced in wind-pollinated taxa, which exhibited a more negative lag-1 autocorrelation and a higher coefficient of variation (CV). We highlight the mutual benefits of integrating ecological theory and agricultural data for (i) advancing our understanding of perennial plant reproduction across time, space and taxa, and (ii) promoting stable farmer livelihoods and global food supply. This article is part of the theme issue 'The ecology and evolution of synchronized seed production in plants'.

Many plant species worldwide are dispersed by scatter-hoarding granivores: animals that hide seeds in numerous, small caches for future consumption. Yet, the evolution of scatter-hoarding is difficult to explain because undefended caches are at high risk of pilferage. Previous models have attempted to solve this problem by giving cache owners large advantages in cache recovery, by kin selection, or by introducing reciprocal pilferage of 'shared' seed resources. However, the role of environmental variability has been so far overlooked in this context. One important form of such variability is masting, which is displayed by many plant species dispersed by scatterhoarders. We use a mathematical model to investigate the influence of masting on the evolution of scatter-hoarding. The model accounts for periodically varying annual seed fall, caching and pilfering behaviour, and the demography of scatterhoarders. The parameter values are based mostly on research on European beech (Fagus sylvatica) and yellow-necked mice (Apodemus flavicollis). Starvation of scatterhoarders between mast years decreases the population density that enters masting events, which leads to reduced seed pilferage. Satiation of scatterhoarders during mast events lowers the reproductive cost of caching (i.e. the cost of caching for the future rather than using seeds for current reproduction). These reductions promote the evolution of scatter-hoarding behaviour especially when interannual variation in seed fall and the period between masting events are large. This article is part of the theme issue 'The ecology and evolution of synchronized seed production in plants'.

Soils play a critical role in the production of food and feed for a growing global population. Here, we review global patterns in soil characteristics, agricultural production and the fate of embedded soil nutrients. Nitrogen- and organic-rich soils supported the highest crop yields, yet the efficiency of nutrient utilization was concentrated in regions with lower crop productivity and lower rates of chemical fertilizer inputs. Globally, soil resources were concentrated in animal feed, resulting in large inefficiencies in nutrient utilization and losses from the food system. Intercontinental transport of soil-derived nutrients displaced millions of tonnes of nitrogen and phosphorus annually, much of which was ultimately concentrated in urban waste streams. Approximately 40% of the global agricultural land area was in small farms providing over 50% of the world's food and feed needs but yield gaps and economic constraints limit the ability to intensify production on these lands. To better use and protect soil resources in the global food system, policies and actions should encourage shifts to more nutrient-efficient diets, strategic intensification and technological improvement, restoration and maintenance of soil fertility and stability, and enhanced resilience in the face of global change. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.

Soil and soil biodiversity play critical roles in Nature's Contributions to People (NCP) # 10, defined as Nature's ability to regulate direct detrimental effects on humans, and on human-important plants and animals, through the control or regulation of particular organisms considered to be harmful. We provide an overview of pathogens in soil, focusing on human and crop pathogens, and discuss general strategies, and examples, of how soils' extraordinarily diverse microbial communities regulate soil-borne pathogens. We review the ecological principles underpinning the regulation of soil pathogens, as well as relationships between pathogen suppression and soil health. Mechanisms and specific examples are presented of how soil and soil biota are involved in regulating pathogens of humans and plants. We evaluate how specific agricultural management practices can either promote or interfere with soil's ability to regulate pathogens. Finally, we conclude with how integrating soil, plant, animal and human health through a 'One Health' framework could lead to more integrated, efficient and multifunctional strategies for regulating detrimental organisms and processes. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.

This theme issue provides an assessment of the contribution of soils to Nature's Contributions to People (NCP). The papers in this issue show that soils can contribute positively to the delivery of all NCP. These contributions can be maximized through careful soil management to provide healthy soils, but poorly managed, degraded or polluted soils may contribute negatively to the delivery of NCP. Soils are also shown to contribute positively to the UN Sustainable Development Goals. Papers in the theme issue emphasize the need for careful soil management. Priorities for soil management must include: (i) for healthy soils in natural ecosystems, protect them from conversion and degradation, (ii) for managed soils, manage in a way to protect and enhance soil biodiversity, health, productivity and sustainability and to prevent degradation, and (iii) for degraded soils, restore to full soil health. Our knowledge of what constitutes sustainable soil management is mature enough to implement best management practices, in order to maintain and improve soil health. The papers in this issue show the vast potential of soils to contribute to NCP. This is not only desirable, but essential to sustain a healthy planet and if we are to deliver sustainable development in the decades to come. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.

This special issue provides an assessment of the contribution of soils to Nature's Contributions to People (NCP). Here, we combine this assessment and previously published relationships between NCP and delivery on the UN Sustainable Development Goals (SDGs) to infer contributions of soils to the SDGs. We show that in addition to contributing positively to the delivery of all NCP, soils also have a role in underpinning all SDGs. While highlighting the great potential of soils to contribute to sustainable development, it is recognized that poorly managed, degraded or polluted soils may contribute negatively to both NCP and SDGs. The positive contribution, however, cannot be taken for granted, and soils must be managed carefully to keep them healthy and capable of playing this vital role. A priority for soil management must include: (i) for healthy soils in natural ecosystems, protect them from conversion and degradation; (ii) for managed soils, manage in a way to protect and enhance soil biodiversity, health and sustainability and to prevent degradation; and (iii) for degraded soils, restore to full soil health. We have enough knowledge now to move forward with the implementation of best management practices to maintain and improve soil health. This analysis shows that this is not just desirable, it is essential if we are to meet the SDG targets by 2030 and achieve sustainable development more broadly in the decades to come. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.

Innovation-the combination of invention and social learning-can empower species to invade new niches via cultural adaptation. Social learning has typically been regarded as the fundamental driver for the emergence of traditions and thus culture. Consequently, invention has been relatively understudied outside the human lineage-despite being the source of new traditions. This neglect leaves basic questions unanswered: what factors promote the creation of new ideas and practices? What affects their spread or loss? We critically review the existing literature, focusing on four levels of investigation: traits (what sorts of behaviours are easiest to invent?), individuals (what factors make some individuals more likely to be inventors?), ecological contexts (what aspects of the environment make invention or transmission more likely?), and populations (what features of relationships and societies promote the rise and spread of new inventions?). We aim to inspire new research by highlighting theoretical and empirical gaps in the study of innovation, focusing primarily on inventions in non-humans. Understanding the role of invention and innovation in the history of life requires a well-developed theoretical framework (which embraces cognitive processes) and a taxonomically broad, cross-species dataset that explicitly investigates inventions and their transmission. We outline such an agenda here. This article is part of the theme issue 'Foundations of cultural evolution'.

Phylogenetic analyses increasingly take centre-stage in our understanding of the processes shaping patterns of cultural diversity and cultural evolution over time. Just as biologists explain the origins and maintenance of trait differences among organisms using phylogenetic methods, so anthropologists studying cultural macroevolutionary processes use phylogenetic methods to uncover the history of human populations and the dynamics of culturally transmitted traits. In this paper, we revisit concerns with the validity of these methods. Specifically, we use simulations to reveal how properties of the sample (size, missing data), properties of the tree (shape) and properties of the traits (rate of change, number of variants, transmission mode) might influence the inferences that can be drawn about trait distributions across a given phylogeny and the power to discern alternative histories. Our approach shows that in two example datasets specific combinations of properties of the sample, of the tree and of the trait can lead to potentially high rates of Type I and Type II errors. We offer this simulation tool to help assess the potential impact of this list of persistent perils in future cultural macroevolutionary work. This article is part of the theme issue 'Foundations of cultural evolution'.

Studies in natural populations are essential to understand the evolutionary ecology of senescence and terminal allocation. While there are an increasing number of studies investigating late-life variation in different life-history traits of wild populations, little is known about these patterns in social behaviour. We used long-term individual based data on yellow-bellied marmots (Marmota flaviventer) to quantify how affiliative social behaviours and different life-history traits vary with age and in the last year of life, and how patterns compare between the two. We found that some social behaviours and all life-history traits varied with age, whereas terminal last year of life effects were only observed in life-history traits. Our results imply that affiliative social behaviours do not act as a mechanism to adjust allocation among traits when close to death, and highlight the importance of adopting an integrative approach, studying late-life variation and senescence across multiple different traits, to allow the identification of potential trade-offs. This article is part of the theme issue 'Ageing and sociality: why, when and how does sociality change ageing patterns?'

We advance an account that grounds cognition, specifically decision-making, in an activity all organisms as autonomous systems must perform to keep themselves viable-controlling their production mechanisms. Production mechanisms, as we characterize them, perform activities such as procuring resources from their environment, putting these resources to use to construct and repair the organism's body and moving through the environment. Given the variable nature of the environment and the continual degradation of the organism, these production mechanisms must be regulated by control mechanisms that select when a production is required and how it should be carried out. To operate on production mechanisms, control mechanisms need to procure information through measurement processes and evaluate possible actions. They are making decisions. In all organisms, these decisions are made by multiple different control mechanisms that are organized not hierarchically but heterarchically. In many cases, they employ internal models of features of the environment with which the organism must deal. Cognition, in the form of decision-making, is thus fundamental to living systems which must control their production mechanisms. This article is part of the theme issue 'Basal cognition: conceptual tools and the view from the single cell'.

Perception is not the passive registration of incoming sensory data. Rather, it involves some analysis by synthesis, based on past experiences and context. One adaptive consequence of this arrangement is imagination-the ability to richly simulate sensory experiences, interrogate and manipulate those simulations, in service of action and decision making. In this paper, we will discuss one possible cost of this adaptation, namely hallucinations-perceptions without sensory stimulation, which characterize serious mental illnesses like schizophrenia, but which also occur in neurological illnesses, and-crucially for the present piece-are common also in the non-treatment-seeking population. We will draw upon a framework for imagination that distinguishes voluntary from non-voluntary experiences and explore the extent to which the varieties and features of hallucinations map onto this distinction, with a focus on auditory-verbal hallucinations (AVHs)-colloquially, hearing voices. We will propose that sense of agency for the act of imagining is key to meaningfully dissecting different forms and features of AVHs, and we will outline the neural, cognitive and phenomenological sequelae of this sense. We will conclude that a compelling unifying framework for action, perception and belief-predictive processing-can incorporate observations regarding sense of agency, imagination and hallucination. This article is part of the theme issue 'Offline perception: voluntary and spontaneous perceptual experiences without matching external stimulation'.

Functional neuroimaging using MRI relies on measurements of blood oxygen level-dependent (BOLD) signals from which inferences are made about the underlying neuronal activity. This is possible because neuronal activity elicits increases in blood flow via neurovascular coupling, which gives rise to the BOLD signal. Hence, an accurate interpretation of what BOLD signals mean in terms of neural activity depends on a full understanding of the mechanisms that underlie the measured signal, including neurovascular and neurometabolic coupling, the contribution of different cell types to local signalling, and regional differences in these mechanisms. Furthermore, the contributions of systemic functions to cerebral blood flow may vary with ageing, disease and arousal states, with regard to both neuronal and vascular function. In addition, recent developments in non-invasive imaging technology, such as high-field fMRI, and comparative inter-species analysis, allow connections between non-invasive data and mechanistic knowledge gained from invasive cellular-level studies. Considered together, these factors have immense potential to improve BOLD signal interpretation and bring us closer to the ultimate purpose of decoding the mechanisms of human cognition. This theme issue covers a range of recent advances in these topics, providing a multidisciplinary scientific and technical framework for future work in the neurovascular and cognitive sciences. This article is part of the theme issue 'Key relationships between non-invasive functional neuroimaging and the underlying neuronal activity'.

Bone loss and heightened fracture risk are common conditions associated with ageing in modern human populations and have been attributed to both hormonal and other metabolic and behavioural changes. To what extent these age-related trends are specific to modern humans or generally characteristic of natural populations of other taxa is not clear. In this study, we use computed tomography to examine age changes in long bone and vertebral structural properties of 34 wild-adult Virunga mountain gorillas (Gorilla beringei beringei) whose skeletons were recovered from natural accumulations. Chronological ages were known or estimated from sample-specific dental wear formulae and ranged between 11 and 43 years. Gorillas show some of the same characteristics of skeletal ageing as modern humans, including endosteal and some periosteal expansion. However, unlike in humans, there is no decline in cortical or trabecular bone density, or in combined geometric-density measures of strength, nor do females show accelerated bone loss later in life. We attribute these differences to the lack of an extended post-reproductive period in gorillas, which provides protection against bone resorption. Increases in age-related fractures (osteoporosis) in modern humans may be a combined effect of an extended lifespan and lower activity levels earlier in life. This article is part of the theme issue 'Evolution of the primate ageing process'.

Humans have the longest post-reproductive lifespans and lowest rates of actuarial ageing among primates. Understanding the links between slow actuarial ageing and physiological change is critical for improving the human 'healthspan'. Physiological dysregulation may be a key feature of ageing in industrialized populations with high burdens of chronic 'diseases of civilization', but little is known about age trajectories of physiological condition in subsistence populations with limited access to public health infrastructure. To better characterize human physiological dysregulation, we examined age trajectories of 40 biomarkers spanning the immune (n = 13 biomarkers), cardiometabolic (n = 14), musculoskeletal (n = 6) and other (n = 7) systems among Tsimane forager-horticulturalists of the Bolivian Amazon using mixed cross-sectional and longitudinal data (n = 22 115 observations). We characterized age-related changes using a multi-system statistical index of physiological dysregulation (Mahalanobis distance; Dm) that increases with age in both humans and other primates. Although individual biomarkers showed varied age profiles, we found a robust increase in age-related dysregulation for Tsimane (β = 0.17-0.18) that was marginally faster than that reported for an industrialized Western sample (β = 0.14-0.16), but slower than that of other non-human primates. We found minimal sex differences in the pace or average level of dysregulation for Tsimane. Our findings highlight some conserved patterns of physiological dysregulation in humans, consistent with the notion that somatic ageing exhibits species-typical patterns, despite cross-cultural variation in environmental exposures, lifestyles and mortality. This article is part of the theme issue 'Evolution of the primate ageing process'.

Microorganismal diversity can be explained in large part by selection imposed from both the abiotic and biotic environments, including-in the case of host-associated microbiomes-interactions with eukaryotes. As such, the diversity of host-associated microbiomes can be usefully studied across a variety of scales: within a single host over time, among host genotypes within a population, between populations and among host species. A plethora of recent studies across these scales and across diverse systems are: (i) exemplifying the importance of the host genetics in shaping microbiome composition; (ii) uncovering the role of the microbiome in shaping key host phenotypes; and (iii) highlighting the dynamic nature of the microbiome. They have also raised a critical question: do these complex associations fit within our existing understanding of evolution and coevolution, or do these often intimate and seemingly cross-generational interactions follow novel evolutionary rules from those previously identified? Herein, we describe the known importance of (co)evolution in host-microbiome systems, placing the existing data within extant frameworks that have been developed over decades of study, and ask whether there are unique properties of host-microbiome systems that require a paradigm shift. By examining when and how selection can act on the host and its microbiome as a unit (termed, the holobiont), we find that the existing conceptual framework, which focuses on individuals, as well as interactions among individuals and groups, is generally well suited for understanding (co)evolutionary change in these intimate assemblages. This article is part of the theme issue 'The role of the microbiome in host evolution'.

Many white-faced capuchin monkey dyads in Lomas Barbudal, Costa Rica, practise idiosyncratic interaction sequences that are not part of the species-typical behavioural repertoire. These interactions often include uncomfortable or risky elements. These interactions exhibit the following characteristics commonly featured in definitions of rituals in humans: (i) they involve an unusual intensity of focus on the partner, (ii) the behaviours have no immediate utilitarian purpose, (iii) they sometimes involve 'sacred objects', (iv) the distribution of these behaviours suggests that they are invented and spread via social learning, and (v) many behaviours in these rituals are repurposed from other behavioural domains (e.g. extractive foraging). However, in contrast with some definitions of ritual, capuchin rituals are not overly rigid in their form, nor do the sequences have specific opening and closing actions. In our 9260 h of observation, ritual performance rate was uncorrelated with amount of time dyads spent in proximity but (modestly) associated with higher relationship quality and rate of coalition formation across dyads. Our results suggest that capuchin rituals serve a bond-testing rather than a bond-strengthening function. Ritual interactions are exclusively dyadic, and between-dyad consistency in form is low, casting doubt on the alternative hypothesis that they enhance group-wide solidarity. This article is part of the theme issue 'Ritual renaissance: new insights into the most human of behaviours'.

We apply a new quantitative method for investigating how children's exploration changes across age in order to gain insight into how exploration unfolds over the course of a human life from a life-history perspective. In this study, different facets of exploratory play were quantified using a novel touchscreen environment across a large sample and wide age range of children in the USA (n = 105, ages = 1 year and 10 months to 12 years and 2 months). In contrast with previous theories that have suggested humans transition from more exploratory to less throughout maturation, we see children transition from less broadly exploratory as toddlers to more efficient and broad as adolescents. Our data cast doubt on the picture of human life history as involving a linear transition from more curious in early childhood to less curious with age. Instead, exploration appears to become more elaborate throughout human childhood. This article is part of the theme issue 'Life history and learning: how childhood, caregiving and old age shape cognition and culture in humans and other animals'.

The evolutionary biologist W. D. Hamilton (Hamilton 1966 J. Theor. Biol.12, 12-45. (doi:10.1016/0022-5193(66)90184-6)) famously showed that the force of natural selection declines with age, and reaches zero by the age of reproductive cessation. However, in social species, the transfer of fitness-enhancing resources by postreproductive adults increases the value of survival to late ages. While most research has focused on intergenerational food transfers in social animals, here we consider the potential fitness benefits of information transfer, and investigate the ecological contexts where pedagogy is likely to occur. Although the evolution of teaching is an important topic in behavioural biology and in studies of human cultural evolution, few formal models of teaching exist. Here, we present a modelling framework for predicting the timing of both information transfer and learning across the life course, and find that under a broad range of conditions, optimal patterns of information transfer in a skills-intensive ecology often involve postreproductive aged teachers. We explore several implications among human subsistence populations, evaluating the cost of hunting pedagogy and the relationship between activity skill complexity and the timing of pedagogy for several subsistence activities. Long lifespan and extended juvenility that characterize the human life history likely evolved in the context of a skills-intensive ecological niche with multi-stage pedagogy and multigenerational cooperation. This article is part of the theme issue 'Life history and learning: how childhood, caregiving and old age shape cognition and culture in humans and other animals'.

Natural selection has evidently mediated many species characteristics relevant to the evolution of learning, including longevity, length of the juvenile period, social organization, timing of cognitive and motor development, and age-related shifts in behavioural propensities such as activity level, flexibility in problem-solving and motivation to seek new information. Longitudinal studies of wild populations can document such changes in behavioural propensities, providing critical information about the contexts in which learning strategies develop, in environments similar to those in which learning strategies evolved. The Lomas Barbudal Monkey Project provides developmental data for the white-faced capuchin, Cebus capucinus, a species that has converged with humans regarding many life-history and behavioural characteristics. In this dataset, focused primarily on learned aspects of foraging behaviour, younger capuchins are more active overall, more curious and opportunistic, and more prone to inventing new investigative and foraging-related behaviours. Younger individuals more often seek social information by watching other foragers (especially older foragers). Younger individuals are more creative, playful and inventive, and less neophobic, exhibiting a wider range of behaviours when engaged in extractive foraging. Whereas adults more often stick with old solutions, younger individuals often incorporate recently acquired experience (both social and asocial) when foraging. This article is part of the theme issue 'Life history and learning: how childhood, caregiving and old age shape cognition and culture in humans and other animals'.

The evolution of pre-zygotic reproductive isolation is a key step in the process of speciation. In many organisms, particularly insects, chemical labels are used as pheromones for species-specific mate recognition. Although an enormous body of knowledge exists regarding the patterns of pheromone chemical ecology, much less is known about the evolutionary processes that underlie the origin of new mating pheromones. Here, we examine case studies that have illuminated the origins of species-specific mating pheromones and suggest future directions for productive research. This article is part of the theme issue 'Signal detection theory in recognition systems: from evolving models to experimental tests'.

During a two-day Royal Society meeting entitled 'Memory reactivation: replaying events past, present and future' held at Chicheley Hall in May, 2019, we discussed and defined a set of terms for investigating and reporting in memory reactivations to facilitate a common language and thus simplifying comparison of results. Here, we present the results of the discussion and supply a set of terms such as reactivation and replay, for which the authors have reached a common consensus. This article is part of the Theo Murphy meeting issue 'Memory reactivation: replaying events past, present and future'.

According to complementary learning systems theory, integrating new memories into the neocortex of the brain without interfering with what is already known depends on a gradual learning process, interleaving new items with previously learned items. However, empirical studies show that information consistent with prior knowledge can sometimes be integrated very quickly. We use artificial neural networks with properties like those we attribute to the neocortex to develop an understanding of the role of consistency with prior knowledge in putatively neocortex-like learning systems, providing new insights into when integration will be fast or slow and how integration might be made more efficient when the items to be learned are hierarchically structured. The work relies on deep linear networks that capture the qualitative aspects of the learning dynamics of the more complex nonlinear networks used in previous work. The time course of learning in these networks can be linked to the hierarchical structure in the training data, captured mathematically as a set of dimensions that correspond to the branches in the hierarchy. In this context, a new item to be learned can be characterized as having aspects that project onto previously known dimensions, and others that require adding a new branch/dimension. The projection onto the known dimensions can be learned rapidly without interleaving, but learning the new dimension requires gradual interleaved learning. When a new item only overlaps with items within one branch of a hierarchy, interleaving can focus on the previously known items within this branch, resulting in faster integration with less interleaving overall. The discussion considers how the brain might exploit these facts to make learning more efficient and highlights predictions about what aspects of new information might be hard or easy to learn. This article is part of the Theo Murphy meeting issue 'Memory reactivation: replaying events past, present and future'.

Neural activity patterns of recent experiences are reactivated during sleep in structures critical for memory storage, including hippocampus and neocortex. This reactivation process is thought to aid memory consolidation. Although synaptic rearrangement dynamics following learning involve an interplay between slow-wave sleep (SWS) and rapid eye movement (REM) sleep, most physiological evidence implicates SWS directly following experience as a preferred window for reactivation. Here, we show that reactivation occurs in both REM and SWS and that coordination of REM and SWS activation on the same day is associated with rapid learning of a motor skill. We performed 6 h recordings from cells in rats' motor cortex as they were trained daily on a skilled reaching task. In addition to SWS following training, reactivation occurred in REM, primarily during the pre-task rest period, and REM and SWS reactivation occurred on the same day in rats that acquired the skill rapidly. Both pre-task REM and post-task SWS activation were coordinated with muscle activity during sleep, suggesting a functional role for reactivation in skill learning. Our results provide the first demonstration that reactivation in REM sleep occurs during motor skill learning and that coordinated reactivation in both sleep states on the same day, although at different times, is beneficial for skill learning. This article is part of the Theo Murphy meeting issue 'Memory reactivation: replaying events past, present and future'.

Interaction between hippocampal sharp-wave ripples (SWRs) and UP states, possibly by coordinated reactivation of memory traces, is conjectured to play an important role in memory consolidation. Recently, it was reported that SWRs were differentiated into multiple subtypes. However, whether cortical UP states can also be classified into subtypes is not known. Here, we analysed neural ensemble activity from the medial prefrontal cortex from rats trained to run a spatial sequence-memory task. Application of the hidden Markov model (HMM) with three states to epochs of UP-DOWN oscillations identified DOWN states and two subtypes of UP state (UP-1 and UP-2). The two UP subtypes were distinguished by differences in duration, with UP-1 having a longer duration than UP-2, as well as differences in the speed of population vector (PV) decorrelation, with UP-1 decorrelating more slowly than UP-2. Reactivation of recent memory sequences predominantly occurred in UP-2. Short-duration reactivating UP states were dominated by UP-2 whereas long-duration ones exhibit transitions from UP-1 to UP-2. Thus, recent memory reactivation, if it occurred within long-duration UP states, typically was preceded by a period of slow PV evolution not related to recent experience, and which we speculate may be related to previously encoded information. If that is the case, then the transition from UP-1 to UP-2 subtypes may help gradual integration of recent experience with pre-existing cortical memories by interleaving the two in the same UP state. This article is part of the Theo Murphy meeting issue 'Memory reactivation: replaying events past, present and future'.

The brain likely uses offline periods to consolidate recent memories. One hypothesis holds that the hippocampal output provides a unique, global linking or 'index' code for each memory, and that this code is stored in the cortex in association with locally encoded attributes of each memory. Activation of the index code is hypothesized to evoke coordinated memory trace reactivation thus facilitating consolidation. Retrosplenial cortex (RSC) is a major recipient of hippocampal outflow and we have described populations of neurons there with sparse and orthogonal coding characteristics that resemble hippocampal 'place' cells, and whose expression depends on an intact hippocampus. Using two-photon Ca2+ imaging, we recorded ensembles of neurons in the RSC during periods of immobility before and after active running on a familiar linear treadmill track. Synchronous bursting of distinct groups of neurons occurred during rest both prior to and after running. In the second rest epoch, these patterns were associated with the locations of tactile landmarks and reward. Complementing established views on the functions of the RSC, our findings indicate that the structure is involved with processing landmark information during rest. This article is part of the Theo Murphy meeting issue 'Memory reactivation: replaying events past, present and future'.

Soil bacterial communities are altered by anthropogenic drivers such as climate change-related warming and fertilization. However, we lack a predictive understanding of how bacterial communities respond to such global changes. Here, we tested whether phylogenetic information might be more predictive of the response of bacterial taxa to some forms of global change than others. We analysed the composition of soil bacterial communities from perturbation experiments that simulated warming, drought, elevated CO2 concentration and phosphorus (P) addition. Bacterial responses were phylogenetically conserved to all perturbations. The phylogenetic depth of these responses varied minimally among the types of perturbations and was similar when merging data across locations, implying that the context of particular locations did not affect the phylogenetic pattern of response. We further identified taxonomic groups that responded consistently to each type of perturbation. These patterns revealed that, at the level of family and above, most groups responded consistently to only one or two types of perturbations, suggesting that traits with different patterns of phylogenetic conservation underlie the responses to different perturbations. We conclude that a phylogenetic approach may be useful in predicting how soil bacterial communities respond to a variety of global changes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Linking 'omics measurements with biogeochemical cycles is a widespread challenge in microbial community ecology. Here, we propose applying genomic adaptation as 'biosensors' for microbial investments to overcome nutrient stress. We then integrate this genomic information with a trait-based model to predict regional shifts in the elemental composition of marine plankton communities. We evaluated this approach using metagenomic and particulate organic matter samples from the Atlantic, Indian and Pacific Oceans. We find that our genome-based trait model significantly improves our prediction of particulate C : P (carbon : phosphorus) across ocean regions. Furthermore, we detect previously unrecognized ocean areas of iron, nitrogen and phosphorus stress. In many ecosystems, it can be very challenging to quantify microbial stress. Thus, a carefully calibrated genomic approach could become a widespread tool for understanding microbial responses to environmental changes and the biogeochemical outcomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

The Price equation describes the change in populations. Change concerns some value, such as biological fitness, information or physical work. The Price equation reveals universal aspects for the nature of change, independently of the meaning ascribed to values. By understanding those universal aspects, we can see more clearly why fundamental mathematical results in different disciplines often share a common form. We can also interpret more clearly the meaning of key results within each discipline. For example, the mathematics of natural selection in biology has a form closely related to information theory and physical entropy. Does that mean that natural selection is about information or entropy? Or do natural selection, information and entropy arise as interpretations of a common underlying abstraction? The Price equation suggests the latter. The Price equation achieves its abstract generality by partitioning change into two terms. The first term naturally associates with the direct forces that cause change. The second term naturally associates with the changing frame of reference. In the Price equation's canonical form, total change remains zero because the conservation of total probability requires that all probabilities invariantly sum to one. Much of the shared common form for the mathematics of different disciplines may arise from that seemingly trivial invariance of total probability, which leads to the partitioning of total change into equal and opposite components of the direct forces and the changing frame of reference. This article is part of the theme issue 'Fifty years of the Price equation'.