Philosophical Transactions of the Royal Society B: Biological Sciences

Cooperation is foundational to complex sociality, yet presents profound evolutionary dilemmas - costs and benefits are rarely distributed evenly and the decision to collaborate or defect can involve a complex contextual calculus. These challenges are compounded when cooperation scales from pairs to groups. Group-level cooperation is fundamental to many species success, but how is it sustained and regulated in nature? One promising route to addressing this question is to examine how individuals reorganise their affiliative interactions in anticipation of group-level cooperation. We examine such pre-cooperative reorganisation using long-term data (2013-2018) from three neighbouring groups of wild chimpanzees at the Tai National Park, Cote dIvoire, who routinely cooperate as a collective to defend their territory against other groups. We found that chimpanzees adjusted the distribution of their social contacts in anticipation of risky and proactive territorial defence by forming more broadly connected, yet more diffuse, affiliative networks. Specifically, adult chimpanzees groomed and played with more group members on days of proactive territorial defence, and this pattern was temporally-sensitive, with increased affiliation occurring before, rather than after, the cooperative act. Chimpanzees accessed a broader range of partners through increased interaction efficiency by switching between more partners with shorter interactions per partner. This pattern suggests a shared evolutionary basis of dynamic social readjustment in preparation for group-level social dilemmas in hominids, potentially providing the foundation for the formalized systems of affiliation found in human societies.

BackgroundRecombination rates can be estimated across the genome, underpinning genetic analyses such as identification of regions under selection. Accurate recombination mapping requires observing a large number of recombination events, necessitating large sample sizes to achieve high resolution. This can be prohibitive to some analyses, so population-based estimates can also be used, leveraging the increasing population genomic data available to researchers. ObjectiveThis study aimed to determine the extent to which population-based recombination maps from different human populations are similar and assess to what extent they can be used interchangeably. MethodsWavelet analysis was employed to decompose recombination rate signals along a chromosome and evaluate the proportion of variance explained at different scales. This method also enabled the assessment of correlations across scales and identification of regions with high coherence between datasets. The analysis focused on a region of chromosome 22 in human populations of European and African ancestry. ResultsRecombination rates are not closely conserved across populations, with the greatest divergence observed at fine scales. Coherence between populations varied significantly across all scales. ConclusionAs recombination maps differ substantially between human populations, for genetic analyses involving recombination maps, it is recommended to use maps specific to the population under study.

Frequency-dependent predation helps maintain bacterial diversity, but its stabilizing role may be compromised under climate warming. Whereas theory suggests that warming can weaken predator-prey interactions and destabilize prey coexistence, it remains unclear whether constant and variable warming regimes differentially disrupt predation and alter coexistence outcomes in bacterial communities. Here, we experimentally tested how constant and variable warming (both +4{degrees}C above ambient, but negligible versus high thermal variance) affect the coexistence of two Pseudomonas species in the presence of their lytic phage. Phage predation increased competitive symmetry between the two bacterial species and promoted bacterial coexistence. Under constant warming (negligible variance), this phage-mediated frequency dependence buffered competitive asymmetries and often promoted persistence of the otherwise inferior P. putida, thereby magnifying coexistence. In contrast, variable warming (high variance) weakened phage control, shifted the advantage to P. protegens, and increased competitive exclusion events. The erosion of top-down control under variable warming was consistent with strong thermal sensitivity of phage infection rates, revealed by thermal performance curves. Our findings demonstrate that phage reduction of competitive asymmetry between bacterial hosts is amplified under constant warming but undermined under variable warming, conditions that are becoming increasingly frequent under climate change.

Transposon insertion sequencing (Tn-seq) has become a powerful tool for assigning gene fitness and essentiality in bacteria, and has recently been extended to bacteriophages. A core but rarely examined assumption of these screens is that fitness is measured in an asocial environment, where each mutant succeeds or fails on its own. Yet many genes act socially: their products can be shared among neighbors, allowing defective mutants to be complemented in trans. In phages multiple genotypes routinely coinfect the same cell. Here we show that social interactions distort gene essentiality. Using paired quorum-sensing microarray and Tn-seq data from Pseudomonas aeruginosa, we find that quorum-sensing-regulated genes are over-represented among genes scored as non-essential, confirming that social genes are under-reported as essential. We then build a stochastic, agent-based model of phage Tn-seq across an MOI gradient, assigning each gene an intrinsic fitness effect and a complementation fraction. Complementable ("social") genes rise in frequency as MOI increases, masking their true fitness cost, whereas non-complementable ("private") genes, do not. Partitioning genes by life-cycle stage and applying a two-round high-then-low-MOI design, further separates gene functions by life cycle stage. We argue that deliberate MOI manipulation turns a confound into a tool, enabling systematic classification of phage sociality.

Classic socio-ecological theory predicts that males and females experience different sources and mechanisms of social competition. Whether these differences translate into sex-specific structural properties of dominance hierarchies remains unclear. Here, we compiled 156 dominance interaction matrices from 80 published studies and extracted three commonly used metrics - hierarchy steepness, linearity and the directional consistency index - to investigate the structural characteristics of male and female dominance hierarchies across primates. All three metrics were strongly affected by methodological and demographic variables. Steepness increased with the number of recorded interactions and group size, linearity decreased as matrices became sparser, and directional consistency declined with increasing numbers of interactions. Steepness covaried positively with both linearity and directional consistency, indicating that groups with steeper hierarchies also exhibited more linear and more directionally consistent relationships. We found no sex differences in steepness, linearity or directional consistency. These results suggest that current metrics primarily reflect variation in the sampling effort and the rate of interaction of the recorded behaviour and appear therefore not to capture potential sex differences in the forms of competition. Our findings highlight the need for alternative measures of power asymmetries that are less confounded by sampling effort and demographic variation to better understand how competition and conflict are structured across primate societies.

During the lifetime of many animals, the microbiota fulfills multiple functions. After death of their hosts, these microbes contribute to cadaver decomposition, with implications for forensics, fossilization and soil nutrient and microbial community dynamics. Here, we draw attention to the possibility that host microbiota can also influence the evolution of pathogen lifestyles. We hypothesized that competition between microbiota and pathogens after host death can reduce benefits to pathogens of killing and decomposing their host. To test this hypothesis, we conducted infection experiments in which we injected the entomopathogenic bacteria Pseudomonas entomophila into Tenebrio molitor larvae. Our results show that bacterial proliferation after pathogen-induced host death occurs in larvae with strongly reduced microbiota, but not in larvae with intact gut microbiota. Strikingly, we found that gut microbiota can suppress the proliferation of an about 100 times larger pathogen population. In addition, we identified a microbiota member that might have mediated competitive suppression of pathogen proliferation after host death. Taken together, our results support our hypothesis that decomposing host microbiota can effectively compete with pathogens, thereby reducing the fitness of pathogens that kill and then exploit dead hosts. Based on a reanalysis of an existing theoretical model, we conclude that the host microbiota can facilitate the evolution of more benign pathogens that are less likely to kill their host for cadaver exploitation. Thus, our findings highlight the potentially important but so far unexplored possibility that pathogen-microbiota interactions in dead hosts can affect living hosts by influencing the evolution of pathogens lifestyles.

Jumping is a challenging locomotive mode, requiring rapid force generation and precise coordination of multiple limbs. Many animals meet this challenge using elastic mechanisms that store and rapidly release energy. Jumping spiders (Salticidae), however, rely on a semi-hydraulic system that constrains how their legs can generate propulsion. Much about how these spiders reliably generate jumps within these mechanical constraints remains unknown. Here, we analyze 46 individuals spanning 14 genera and significant morphological diversity and show that this physically constrained system is coupled to a remarkably stereotyped coordination strategy. Whole-body kinematics and novel graph-based analyses of inter-limb coordination reveal a stereotyped two-stage takeoff sequence: a "swing" driven by extension of the fourth legs, followed by a rapid "fling" by the third legs that generates propulsion for takeoff. We further demonstrate that this pattern is preserved beyond Amazonian species, persisting in salticids from North America and Australia. Our results suggest that physical and biomechanical constraints may canalize locomotor evolution toward a common dynamical solution.

Pseudomonas aeruginosa encodes diverse defence systems against phages and mobile genetic elements, yet their variation across clinical contexts remains unclear. Here, we present a large-scale comparative analysis of the P. aeruginosa defensome across both public and clinically highly relevant datasets, including from patients with chronic lung disease and multidrug-resistant isolates. Our analysis shows that while influences on defensome composition are minor, multidrug-resistant isolates encode more defence systems and cystic fibrosis-associated isolates have fewer. Across phylogenetic clusters, defensome size correlates with cluster abundance, suggesting that defence-rich lineages persist more successfully across environments. Lastly, comparative analysis with other Pseudomonas species reveals enrichment of anti-plasmid systems in P. aeruginosa. Overall, these findings have important implications for phage therapy: multidrug-resistant infections may be more difficult to treat, while cystic-fibrosis-associated isolates may have higher phage susceptibility. This work provides a framework for understanding defensome variation and guiding the decision-making process of phage-based therapies.

Different plasmids exist at different copy numbers per cell, and there is an inverse relationship between a plasmids copy number and its size. Two recent studies quantified this relationship into a scaling law, but both the form and the interpretation of this law are contested. Here, I explore the issues with fitting a single law across plasmid diversity and suggest a consistent synthesis. First, I explore some potential problems with using sequencing-based estimates of copy number. Then, I discuss plasmid copy number through a series of case studies. I argue in favour of interpreting plasmid copy numbers not through a single law, but through the lens of two dominant evolutionary strategies. I suggest that small plasmids which lack active segregation mechanisms have a resulting tradeoff between plasmid inheritance and fitness cost to the host, which is responsible for an inverse relationship between copy number and size. In contrast, larger plasmids with active segregation mechanisms show a much weaker relationship, in line with evidence that their metabolic costs are dominated by the expression of specific genes rather than their size. Where plasmids in the 20-100kb range have higher copy numbers, I argue these probably arise more from selection at the level of the host cell for plasmid-associated phenotypes (e.g. antibiotic resistance) rather than from plasmid-level selection for inheritance.

From animal societies to self-organizing multi-agent systems, collectives adapt their group structure to tasks and environments. However, how they determine appropriate group sizes and the number of subgroups to form remains unclear. We formulate the Group Size and Number Regulation Problem (GSNRP), which asks how individuals regulate group sizes and numbers using only local information. In a first step, we establish a graph-theoretic model demonstrating that simple following behavior suffices to form group structures that match theoretical expectations, but is insufficient for active regulation of group size and number. In a second step, we operationalize individual group-size preferences in a decentralized fission-fusion mechanism based on perceived group size. Through multi-agent simulations, we validate that this mechanism achieves stable convergence across three signaling regimes, from position-only sensing to continuous group-size communication. Using tracking data from wild white-nosed coatis (mammals in the raccoon family), we calibrate individual group-size preferences and show that the controller recovers selected group-size, subgroup-count, and transition statistics. This in-sample case study demonstrates descriptive consistency with natural fission-fusion dynamics without establishing the underlying behavioral mechanism. These results suggest that natural and engineered collectives may share local principles of perception, preference, and response for regulating group structure.

Predicting patterns of behavioural coordination that emerge in small interacting groups is challenging because goal-directed social action is shaped by complex reciprocal and compensatory dynamics. In this study, we examined whether formal symmetry principles derived from group theory could explain coordination patterns among children performing a triadic jumping task. We investigated how geometric symmetries of the task environment and dispositional (a)symmetries associated with leader-follower tendencies jointly constrain collective behaviour. Forty-seven children were classified into symmetric or asymmetric triads based on teacher evaluations of leadership dispositions. Each triad completed multiple trials of a synchronized jumping game requiring movement between adjacent hoops arranged in triangular or square configurations. Results showed that temporal asymmetries in inter-child movement (first, second, or last to jump) were consistent with group-theoretic predictions. In triangular configurations, observed asymmetries corresponded to the highest-order subgroup defined by task and dispositional symmetries. These findings demonstrate that environmental symmetry exerts a hierarchically dominant constraint on collective coordination, within which actor dispositional (a)symmetries further modulate emerging patterns.

Microbes often generate by-products that inhibit own or consortial growth. Such imposing constraints can be alleviated by symbiotic partnerships where the partner consumes the limiting factor resulting in mutually beneficial cooperation. Theories of mitochondrial origin envisage such metabolic syntrophy of partners as the initial interaction, often coupled with mechanistic membrane gymnastics to trap the alphaproteobacterial symbiont to ensure vertical inheritance and as a prerequisite or vestibule of endosymbiosis. Yet we do not know how this happened. Here, using a mathematical model, we investigate how such metabolic self-inhibition enables and facilitates the evolution of compact physical integration between syntrophic partners. We show that when one species produces a metabolite that is self-inhibitory, selection favors increasingly tight spatial association of a detoxifying partner to mitigate local accumulation of the self-limiting product. Under a broad parameter range, this process drives the emergence of surface-associated configurations promoting morphological adaptations such as membrane protrusions or invaginations that increase inter-partner contact area. Our results prove that such costly host membrane contortions can evolve as a means to improve benefits of inhibition reduction by protective syntrophic ectosymbionts. Additionally, a unilateral syntrophic interaction between parties is sufficient for the transition; a mutualistic (or bilateral) one is not necessary. Our model establishes a direct evolutionary link between metabolic coupling and physical integration, suggesting that the need to alleviate (self-generated) inhibition can be a primary driver of ectosymbiotic attachment and its transition toward more intimate associations. Our findings provide a general theoretical framework for understanding how microbial consortia evolve structural complexity from initially loose metabolic interactions, with implications for the origins of stable symbioses and the early steps toward cellular integration.

1. Passive acoustic monitoring (PAM) is increasingly used for ecological research, biodiversity monitoring, assessment, and reporting. Automated species classifiers make it feasible to process large audio datasets but generate numerous detections that often need validation before use in downstream analyses or formal outputs. 2. Method development in PAM has focused on classifier building and downstream models that account for imperfect detection, yet the practical step between these - post-classification validation - remains weakly supported and is often implemented through ad hoc workflows. This increases manual handling, creates scope for transcription or consolidation errors, limits transparency and makes it difficult to document what was reviewed. 3. We introduce PAMalytics, an open-source, no-code, local browser-based application to support post-classification validation as a standardised workflow stage. PAMalytics ingests detections from any classifier, allows users to define how detections are sampled for review, and presents selected detections alongside their spectrograms with audio playback in one unified interface. Sampling strategy and review decisions are tracked alongside reviewer identity improving traceability and reproducibility across the validation workflow. 4. Case studies with Conservation International Cambodia and Imperial College London demonstrate PAMalytics in two validation settings. In Cambodia, gibbon predictions from a large, uneven dataset were sampled within sites, with likely classifier errors prioritised for validation. At Imperial, Amazon bird detections were sampled across each species classifier-confidence range before biodiversity metrics were derived. In both cases, PAMalytics reduced manual handling and validation time. By turning an ad hoc step into an accessible, structured workflow for conservation practitioners, PAMalytics fills a practical gap in the PAM bioacoustics pipeline and strengthens the link between automated detections and evidence used in biodiversity monitoring and reporting.

Research on prosocial behaviour in nonhuman primates faces two related but distinct problems. First, empirical findings are heterogeneous: studies report instrumental helping, targeted tool transfer, food provisioning, consolation, and collaborative action, whereas others report little or no concern for partner welfare in low-cost prosocial-choice paradigms. These differences may reflect paradigm-specific variation in recipient need, action cost, actor benefit, joint payoff, solicitation, relationship context, competition, affordance clarity, and response bias rather than disagreement about one mechanism. Second, the interpretive vocabulary is underconstrained. Terms such as altruism, empathy, prosocial motivation, helping, and collaboration are often defined from behavioural outcomes and then treated as if they identified distinct latent mechanisms. This manuscript proposes a computational reframing of the problem. Prosocial behaviour is formalised as socially gated action selection. In the model, instrumental helping, low-cost prosocial choice, costly recipient benefit, strict altruism-like outcomes, need-sensitive empathy-like responding, and coordinated joint action are task and outcome profiles generated by different configurations of independently specified variables. These include need detection, goal inference, affordance recognition, action cost, actor benefit, relationship and tolerance effects, competition, request context, social feedback, joint payoff, action selection, and motor or apparatus bias. An illustrative simulation shows how low-cost instrumental helping, cost- or risk-suppressed recipient benefit, false-positive prosocial choice, and reliable-partner collaboration can arise from the same architecture. The framework identifies which task variables must be measured or manipulated before stronger claims about other-regarding motivation, empathy-like responding, or collaboration are justified.

Gene drives are potentially powerful tools, able to spread throughout target populations. They could be used to modify or suppress disease vectors, invasive species, and agricultural pests. Yet, in many scenarios, confinement of the drive to only a target population is required. Several types of drives are capable of this, among the most promising of which are CRISPR toxin-antidote drives. Though showing good performance in simple models, such drives have not been thoroughly assessed in spatially structured populations. Here we evaluate three modification drive variants with varying levels of confinement. We find that Toxin-Antidote Recessive Embryo (TARE) drive and 2-locus TARE drives can usually spread in connected populations or from a single sufficiently large release. However, they can still be stopped by a migration corridor or by a sufficiently high population density gradient. 1-locus 2-drive TARE, on the other hand, will not be able to spread outside of release areas and indeed will often retreat in the face of wild-type alleles. When these drives arrive at a point source such as a port, only the standard TARE drive has a significant chance of establishing if releases occur at sufficiently high frequency and quantity. However, in models with parental care among a limited number of offspring, TARE drives become more invasive, with lower introduction thresholds. Overall, we find that spatial and other ecological factors can substantially affect the outcome of a confined CRISPR toxin-antidote drive release.

Environmental disturbances are ubiquitous in microbial ecosystems, yet their effects on community composition and interactions remain poorly understood. Here, we combine analytical derivations and large-scale generalized Lotka-Volterra simulations to examine how recurrent disturbances, varying in intensity (C), frequency (1/T), regularity, and evenness, affect microbial communities. We find that context-dependent interactions (ICD)--representing the net effect of the entire community on each species--are robust to changes in disturbance intensity and frequency. Community composition is influenced by disturbance, but this effect is primarily captured by a single composite parameter T/log(C), reducing the two-dimensional disturbance space onto a one-dimensional axis. Species abundances and ICD remain largely independent of specific values of T and C except near critical transition regions (survival thresholds and no-interaction zones). Sensitivity analyses show that disturbance-sensitive cases occur in the vicinity of these boundaries. This robustness extends to when the disturbance is irregular (even up to 50% stochastic variation in T or C), with uneven disturbances, when the disturbance is species-specific, and holds at any time point throughout the inter-disturbance growth phase. The patterns are independent of species richness, growth rates, carrying capacities, and interaction strengths. Our findings highlight that microbial community organization is largely conserved under recurrent environmental stress, with extinction acting as the dominant route by which disturbances reshape communities. These findings indicate that disturbance is not a strong driver of community structure and that minor variations in experimental or environmental conditions or sampling time are not expected to substantially impact microbiome composition.

Reputation plays a major role in supporting cooperation among unrelated individuals through indirect reciprocity. By helping others, individuals build a good personal reputation and receive greater benefits from future partners. Most models of indirect reciprocity assume that a person's reputation reflects only their own behaviour. Yet in many societies, people are also judged by their family's reputation. How family reputation affects the evolution of cooperation, and whether reliance on it can itself evolve, remain unclear. Here we show that reputation inheritance expands the conditions under which indirect reciprocity favours cooperation, increasing helping and favouring greater reciprocity. Greater reciprocity in turn favours stronger reliance on inherited reputation, creating a positive feedback that stabilises cooperation, especially when interactions are infrequent or personal behaviour is difficult to observe. This feedback arises because cooperation generates future benefits both for the individual, through their personal reputation, and for their descendants, through inherited reputation. Reputation inheritance thereby provides a route via which kin selection and reciprocity, often treated as alternative explanations for cooperation, can reinforce one another. Our model helps explain why family-based reputation occurs across diverse human societies and provides an evolutionary framework for studying phenomena organised around family standing, including kin-based institutions, feuds between families and honour-based violence within them.

Violent conflicts increasingly involve multiple armed actors competing for influence over shared civilian populations, creating complex dynamics that challenge conventional security analysis and policy design. We present a framework that adapts epidemiological methods informed by the conflict landscape in Nigeria to model multi-actor violent conflict as an epidemic process. We derive a basic insecurity reproduction number ($R_0$), identify violence-free and persistent-violence equilibria, and introduce a novel Civilian Harm Index (CHI) to quantify humanitarian impact. Sensitivity analyses identify recruitment, ideological support from civilian populations, and abduction as the key drivers of conflict persistence and civilian harm. The framework reveals several counterintuitive findings. Interventions that most effectively suppress violence transmission are not necessarily those that minimise civilian harm, demonstrating that epidemic control and humanitarian protection may require distinct optimisation criteria. Likewise, interventions effective against one armed actor may be ineffective, or even counterproductive, when applied uniformly across groups. In addition, prisoner exchange and ransom payments increase violence persistence and civilian harm. Although developed as an illustrative rather than predictive framework, our results show that epidemiological methods provide quantitative metrics for evaluating intervention priorities and trade-offs in complex multi-actor conflicts.

Across different modalities, signals play a core role in attracting mates and influencing mating success. In several non-human primate species, females produce calls during mating that are thought to promote male competition over receptive females. The extent to which social system characteristics modulate the function of copulation calls remains less clear. We studied copulation calls in wild Guinea baboons (Papio papio), who live in a multilevel society structured around units in which females associate and mate almost exclusively with a single male. We hypothesised that females use copulation calls as an indirect form of mate competition, with competition increasing in larger units. In addition, we hypothesised that females are more likely to mate again after calling. We analysed 6116 copulations between 2014 and 2025, involving 99 reproductively active females and 78 subadult and adult males. Females produced copulation calls in 72.7% of copulations, with large inter-individual variation. Neither unit size nor its interaction with the female's swelling size or the presence of simultaneously receptive females affected the probability of calling. A survival analysis with a subset of the data (2353 copulations) revealed no effect of calling on the latency to the next mating. Our results render the hypothesis that female Guinea baboons use calls in indirect mate competition unlikely. Yet, the probability of calling varied with sexual swelling size, suggesting that calls signal female fertility. Possibly, Guinea baboon copulation calls represent an evolutionary remnant, no longer under selective pressure, and can be considered index signals of female fertility.

Collective escape responses are widespread in animal groups, yet how threat-related information spreads from a few informed individuals to the collective remains poorly understood because the identities of the individuals who initially detect danger are rarely experimentally controlled. Here, we combined aversive conditioning, behavioural tracking, and computational modelling to investigate how escape information propagates through schools of Puntigrus tetrazona. We conditioned selected fish to associate a green light with an aversive stimulus. Subsequently, we tested the escape response of schools containing one informed and four naive fish to the green light. One informed fish was sufficient to trigger a collective escape response. Upon stimulus onset, conditioned fish accelerated and crossed the hurdle, after which naive fish sequentially increased their speed and followed. Temporal correlations in speed revealed a hierarchical leader-follower structure mostly aligned with hurdle-crossing order. Neither initial distance, viewing angle, nor relative orientation to informed fish predicted the order of the escape sequence. An agent-based model incorporating local alignment and distance regulation reproduced experimental observations and suggested that the informed individual likely remains partly attentive to its neighbours during escape. Overall, our work provides a general framework for experimentally dissecting information transfer in animal groups and identifying the behavioural mechanisms underlying collective escape dynamics.