Philosophical Transactions of the Royal Society B

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.

Gender inequality has been documented across a variety of high-prestige professions. Both structural bias (e.g., lack of proportionate representation) and interpersonal bias (e.g., sexism, discrimination) generate costs to underrepresented minorities. How can we estimate these costs and what interventions are most effective for reducing them? We used agent-based simulations, removing gender differences in interpersonal bias to isolate and quantify the impact and costs of structural bias (unequal gender ratios) on individuals and institutions. We compared the long-term impact of bias-confrontation strategies. Unequal gender ratios led to higher costs for female agents and institutions and increased sexism among male agents. Confronting interpersonal bias by targets and allies attenuated the impact of structural bias. However, bias persisted even after a structural intervention to suddenly make previously unequal institutions equal (50% women) unless the probability of interpersonal bias-confrontation was further increased among targets and allies. This computational approach allows for comparison of various policies to attenuate structural equality, and informs the design of new experiments to estimate parameters for more accurate predictions.

Bacterial growth rates are constrained by genome replication, yet the role of replication kinetics in bacterial growth rates remains incompletely understood. Here, we examine if genome size, replichore organization, and nucleotide compositional asymmetry are reasonable predictors of bacterial doubling times. In free-living bacteria, both genome size and the length of the longest replichore are found to correlate positively with doubling time, pointing to an influence of replication dynamics on bacterial growth rates. Moreover, fast-growing bacteria are shown to exhibit stronger nucleotide compositional skew. Incorporating skew into the model substantially improves predictive accuracy, suggesting that compositional asymmetry in genomes may facilitate replication fork progression and thereby enhance growth rates. Based on these observations, we speculate that nucleotide skew may play a potential adaptive role in bacterial genome replication. To assess whether the observed association between genome architecture and growth rate reflects an evolutionary signature or a mechanistic link, we reconstructed ancestral states and found that the model fits ancestral traits more strongly, with predictive strength (R2) decreasing progressively along the evolutionary tree as successive speciations occur. We speculate that this association has been stronger early in bacterial evolution and became subsequently screened as organisms diversified and increased in ecological and physiological complexity.

The link between fitness and reproduction rate is a central tenet in microbiology, and indeed evolutionary biology: Mutants reproducing faster than the dominant wild-type are favoured by selection, but otherwise the mutation is lost. This link was given by Ronald Fisher in 1930 under the assumption that fitness can only change through mutations that boost or hinder growth rate, whence the use of logarithms on growth data by experimentalists. Here I show that logarithms are highly sensitive to sampling times, resulting in fitness estimates that are not constant over the growth of bacterial cultures. This variability invalidates typical selection measurements, and unfit mutants can be co-maintained if they reach their equilibrium. And this is what I observed in competition assays between two Escherichia coli constructs, one of which harbours a non-transmissible plasmid that protects against tetracycline (pGW155B), without using the antibiotic. Despite growing 40% slower than its drug-sensitive counterpart, the construct harbouring the plasmid persisted throughout the competition. And, perhaps more importantly, maintained the plasmid. My study suggests that reliance on growth rate masks that selection on plasmid carriage may be stronger than previously thought--explaining the seemingly-paradoxical abundance of plasmids in nature.

Acoustic signal complexity varies widely in the animal kingdom for reasons that remain unclear. In birds, it is widely proposed that vocal complexity evolves as an honest signal of individual quality driven by sexual selection. Other hypotheses related to social interactions include competition for ecological resources (social selection) and intra-group communication in group- living animals, both of which may favour signal complexity. However, these hypotheses are rarely explored at macroevolutionary scales, particularly in the context of constraints on sound production, transmission and detection, leading to ongoing uncertainty about the evolutionary origins of complex vocal signals. Using Bayesian phylogenetic models, we test whether different forms of social communication and ecological constraints predict the temporal and spectral complexity of songs in 1,288 species of suboscine passerine birds. We found that song complexity was reduced by sexual selection, along with other limiting factors including large body size and dense vegetation. Conversely, territoriality boosted the temporal complexity of songs. These findings challenge the common assumption that sexual selection is the main driver of increased signal complexity, and instead highlight the role of social selection as a key component of multiple inter-related drivers and constraints.

How microevolutionary processes translate to macroevolutionary patterns is a central question in evolutionary biology. Macroevolutionary and biogeographic studies often rely on species trees to make inferences about diversification, but gene flow can lead to incorrect phylogenetic inference. Under a range of biogeographic conditions, gene flow may not occur uniformly across space during diversification, which could lead to macroevolutionary misinferences. For example, whenever a "peripheral" population is relatively isolated and inferred as sister to a "core" clade of populations that exchange migrants, it might solely reflect gene flow, as opposed to macroevolutionary processes such as the order of biogeographic dispersal events. We use simulations of the hypothetical case of spatially heterogeneous gene flow described above and found that relatively low levels of gene flow led to monophyly of the adjacent populations, with longer branches for peripheral taxa, regardless of the true divergence history. We highlight an empirical example wherein lowland antbirds (Family: Thamnophilidae)-a clade known for dynamic gene flow in Amazonia-tend to be young in Amazonia, but older at Amazonias periphery. Although it is challenging to know if the simulated bias applies here, our work suggests a distinguishability problem for any nodes stemming from radiations in geographically heterogeneous environments.

Debates about public trust in science often contrast deficit-based models, which emphasize the role of scientific knowledge, with constructivist perspectives that highlight the coexistence of multiple epistemologies. However, both approaches tend to overlook the mechanisms that link scientific knowledge, alternative epistemic orientations, and mistrust in science. To address this gap, the study applies a multilevel structural equation model within a multidimensional framework to examine conspiratorial reasoning as a key mechanism through which scientific knowledge influences science mistrust. Using cross-national survey data from Europe during the COVID-19 pandemic, the analysis also considers how this pathway is moderated by individual cognitive, motivational, and ideological traits, as well as macro-level political, cultural and economic factors. The findings reveal that conspiratorial reasoning significantly mediates the relationship between scientific knowledge and mistrust at both individual and regional levels. Moreover, the strength of these associations is conditioned by factors like informational engagement, regional value climates, and religiosity. Overall, the results suggest that scientific knowledge serves as a conditional epistemic resource, rather than a consistent buffer against mistrust in science.

Plasmids play an important role in bacterial genome evolution by transferring genes between lineages. Fitness costs associated with plasmid acquisition are expected to be a barrier to gene exchange, but the causes of plasmid fitness costs are poorly understood. Single compensatory mutations are often sufficient to completely ameliorate plasmid fitness costs, suggesting that such costs are caused by specific genetic conflicts rather than generic properties of plasmids, such as their size, metabolic burden, or expression level. Here we show -- using a combination of experimental evolution, reverse genetics, and transcriptomics -- that fitness costs of two divergent large plasmids in Pseudomonas fluorescens are caused by inducing maladaptive expression of a chromosomal tailocin toxin operon. Mutations in single genes unrelated to the toxin operon, and located on either the chromosome or the plasmid, ameliorated the disruption associated with plasmid acquisition. We identify one of these compensatory loci, the chromosomal gene PFLU4242, as the key mediator of the fitness costs of both plasmids, with the other compensatory loci either reducing expression of this gene or mitigating its deleterious effects by upregulating a putative plasmid-borne ParAB operon. The chromosomal mobile genetic element Tn6291, which uses plasmids for transmission, remained upregulated even in compensated strains, suggesting that mobile genetic elements communicate through pathways independent of general physiological disruption. Plasmid fitness costs caused by specific genetic conflicts are unlikely to act as a long-term barrier to horizontal gene transfer due to their propensity for amelioration by single compensatory mutations, explaining why plasmids are so common in bacterial genomes.

Human populations rely on cultural artifacts and complex cumulative culture for their survival. Populations vary dramatically in the size of their tool repertoires, and the determinants of these cultural repertoire sizes have been the focus of extensive study in recent years. A prominent hypothesis, supported by computational models of cultural evolution, asserts that tool repertoire size increases with population size. However, not all empirical studies seeking to test this hypothesis have found such a correlation; this has led to a contentious and ongoing debate. As a possible resolution to this longstanding controversy, we suggest that accounting for even rare cultural migration events that allow sharing of knowledge between different-sized populations may help explain why a populations size might not always predict its cultural repertoire size. Using an agent-based model to explore different assumptions about the effects of population size and migration on tool repertoires, we find that connectivity of one population to others, particularly to large populations, may significantly boost its tool repertoire size when population interactions lead to cultural exchange. Thus, two populations of identical size may have drastically different tool repertoire sizes, hinging upon their access to other groups knowledge. Intermittent contact between populations boosts cultural repertoire size and still allows for the development of unique tool repertoires that have limited overlap between populations.

Urbanization is a fast and dramatic transformation of habitat that generally forces native fauna into novel ecological challenges. The biological prerequisites necessary to establish in urban areas have been widely studied, but the macroevolutionary characteristics of traits that allow urban colonization remain poorly understood. Urban colonization might be facilitated by traits that are evolutionarily conserved and which lead to a diversity of closely related species. Alternatively, urban colonization might be associated with labile traits that frequently arise and are lost. In a large data set from passerine birds, we find that urban colonization has a signal of highly labile traits, despite many traits associated with colonization being highly conserved. Urban colonization is associated with traits that allow faster speciation than non-urban-colonizing counterparts, and more frequently transition to non-urban trait states than in the opposite direction. Overall, the traits that facilitate urban colonization are a mix of highly conserved and labile traits and appear to provide an evolutionarily successful strategy.

1Engineered gene drive techniques for population replacement and/or suppression have potential for tackling complex challenges, including reducing the spread of diseases and invasive species. Unfortunately, the self-propelled behavior of drives can lead to the spread of transgenic elements beyond the target population, which is concerning. Gene drive systems with a low threshold frequency for invasion, such as homing-based gene drive systems, require initially few transgenic individuals to spread and are therefore easy to implement. However their ease of spread presents a double-edged sword; their low threshold makes these drives much more susceptible to spread outside of the target population (spillover). We model a proposed drive system that transitions in time from a low threshold drive system (homing-based gene drive) to a high threshold drive system (underdominance) using daisy chain technology. This combination leads to a spatially restricted drive strategy, while maintaining an attainable release threshold. We develop and analyze a discrete-time model as proof of concept and find that this technique effectively generates stable local population suppression, while preventing the spread of transgenic elements beyond the target population under biologically realistic parameters.

Fluctuating sea levels during the Pleistocene led to habitat loss and fragmentation, impacting the evolutionary trajectories of reef fishes. Species with specialized ecological requirements or habitat preferences, like clownfishes (Amphiprioninae), may have been particularly vulnerable due to their intricate dependence on sea anemones. The diverse host specializations within this group likely contributed distinct responses to sea-level fluctuations, differentially shaping their recent evolutionary histories. Leveraging a comprehensive genomic dataset, we reveal demographic patterns and connectivity dynamics across multiple populations of ten clownfish species under different host specializations. Host-generalist species demonstrated strong resilience to habitat perturbations, while those specialized on single hosts suffered dramatic bottlenecks linked to sea-level fluctuations. Spatial analyses revealed the significant role of oceanic currents in shaping clownfish genetic diversity landscapes. Dispersal barriers were driven by environmental variables, with the Coral Triangle emerging as a hub of genetic diversity. Our results reveal how clownfish associative behavior influences their population dynamics, holding major implications for their conservation such as the need to consider their mutualism with sea anemones, particularly on host-specialists, to ensure their survival in the face of climate threats. These findings extend broader principles of conservation, improving our understanding of species responses to ecological constraints and environmental changes over evolutionary timescales.

Birdsong has historically been characterized as a sexually selected, primarily male behavior. More recent findings suggest female song is widespread, raising questions about how social functions of birdsong shape song evolution. Certain breeding systems, like cooperative breeding, change social dynamics and selection pressures on both sexes, providing important contexts for studying song evolution. Here, we use phylogenetic comparative analyses across 1041 songbird species to examine relationships between cooperative breeding, female song, and male song characteristics. Here, we show robust bidirectional co-evolutionary dynamics between cooperative breeding and female song that persist when controlling for territoriality, allometry, and geographic sampling biases. Importantly, when examining intensity of territorial defense, we find this relationship is context-dependent: while cooperative breeding and female song commonly co-occur in strongly territorial systems, their association is especially pronounced in weakly territorial systems, where they co-occur much more often than expected by chance. Additionally, we observe that male song repertoire size evolves more slowly in cooperative-breeding lineages. These findings demonstrate that cooperative breeding shapes the evolution of vocal communication differently based on territorial context and sex, with female song potentially serving crucial but understudied functions related to social cohesion in cooperative systems, particularly in species where territorial conflict is reduced.

Social behaviours can allow individuals to flexibly respond to environmental change, potentially buffering adverse effects. However, individuals may respond differently to the same environmental stimulus, complicating predictions for population-level response to environmental change. Here we show that bottlenose dolphins (Tursiops truncatus) alter their social behaviour at yearly and monthly scales in response to a proxy for food availability (salmon abundance) but do not respond to variation in a proxy for climate (the North Atlantic Oscillation index). There was also individual variation in plasticity for gregariousness and connectedness to distant parts of the social network, although these traits showed limited repeatability. In contrast, individuals showed consistent differences in clustering with their immediate social environment at the yearly scale but no individual variation in plasticity for this trait at either time scale. These results indicate that social behaviour in free-ranging cetaceans can be highly resource dependent with individuals increasing their connectedness over short timescales but possibly reducing their wider range of connection at longer timescales. Some social traits showed more individual variation in plasticity or mean behaviour than others, highlighting how predictions for the responses of populations to environmental variation must consider the type of individual variation present in the population.

Rates of diversification differ between angiosperm lineages. To date, attempts to explain this heterogeneity have focused on the potential correlation between speciation and extinction rates and particular key traits. However, an often-overlooked explanation is that evolutionary lability, here defined as the rates of trait change, may be a better predictor of speciation and extinction rate heterogeneity than the observed traits themselves. Here, we show how this can be tested by using hidden Markov models (HMMs), which allow for several rate classes associated with speciation, extinction, and transition between trait states across a phylogeny. Using a phylogenetic dataset of 13 angiosperm clades including 10,474 species, we show that higher rates of change between open and closed-canopy biomes is consistently associated with higher lineage turnover rates (speciation + extinction rates) across clades. We demonstrate how HMMs can be leveraged in ways that go beyond their conventional use as null models in diversification analyses, and that comparing different rate classes can unveil novel patterns of biological interest. These patterns result in a shift in focus from static traits to dynamic evolutionary processes and may provide a more comprehensive understanding into how biodiversity is generated and maintained, in angiosperms and other organisms.

Sex differences in cooperation are widespread, but their evolution remains poorly understood. Here we use phylogenetic comparative methods to test the Dispersal hypothesis for the evolution of sex differences in contributions to cooperative care across the cooperatively breeding birds and mammals. The Dispersal hypothesis predicts that, where non-breeding individuals of both sexes help to rear offspring within their natal group, the more dispersive sex will contribute less (either because leaving the natal group earlier reduces the downstream direct benefit from cooperation or because dispersal activities trade-off against cooperation). Our analyses reveal (i) support for the Dispersal hypothesis (sex biases in dispersal predict sex biases in natal cooperation across taxa), and (ii) that this pattern cannot be readily attributed to alternative hypothesized drivers of sex differences in cooperation (kin selection, heterogamety, paternity uncertainty, patterns of parental care or differences between birds and mammals). Our findings help to clarify the evolutionary drivers of sex differences in cooperation and highlight the need for single-species studies to now tease apart whether sex differences in dispersal predict sex differences in natal cooperation because dispersal impacts the direct benefits of natal cooperation (as is often proposed) or because activities that promote dispersal trade-off against natal cooperation.

INTRODUCTIONThe original brain lag hypothesis proposed that primate brain evolution depended on spare energy derivative of savings of scale enabled by increasing body size. Deaner & Nunn [1] concluded that, in fact, there was no evidence for a brain lag. However, their result may have been due to a number of possible confounds in their analysis. METHODSI revisit their analysis to test for potential confounds using updated datasets. I also ask how primates paid for the energy costs incurred by changes in brain and body mass, and whether the impetus for these changes was predation risk. Finally, I ask whether the observed patterns explain the brain/body size ratio trajectory observed in fossil hominins. RESULTSI show that using statistically more appropriate statistics and updated data yields a significant brain lag effect. However, contrary to the original brain lag hypothesis, the brain/body ratio does not converge back on the allometric regression line, but continues to evolve beyond it. Increases in brain size are correlated with exploiting large group size rather than body size as the principal defence against predation risk, with significant growth in brain size (but not body size) only being possible if species adopted a more frugivorous diet. Finally, I show that hominins followed a similar trajectory from an australopithecine baseline that fell on the relevant allometric regression. CONCLUSIONThe brain lag effect is much more complicated than the original hypothesis proposed, with a distinctive switch from body to brain over evolutionary time.

Group living and social interactions among animals provide key benefits, such as the exchange of beneficial social information and novel behaviours, but also pose the risk of spreading costly infectious diseases, presenting a social trade-off. While both information and infections spread across social networks, they typically have distinct mechanisms of transmission. Here, we model social information and behaviour spread as a complex contagion governed by a conformist learning rule, while pathogen transmission follows a simple contagion mechanism. Building on theoretical foundations, our study applies computational models to examine how subgroup structure (modularity) influences the spread of these contagions across diverse animal social structures sourced from the Animal Social Network Repository (ASNR). Our findings reveal that high modularity and subgroup structure slow simple contagion spread, whereas complex contagions are less impeded by this fragmentation. Consequently, our results suggest that social networks divided into small groups or subgroups can help balance the competing pressures of acquiring social information and avoiding infectious disease in real-world networks.

The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses remain unclear. Moreover, statistical analyses on this topic have typically been limited to a narrow diversity of bacteria and archaea without considering the potential bias introduced by the shared recent ancestry of many lineages. In this study, we used a phylogenetic generalized least-squares (PGLS) analysis to evaluate the effect of different factors on the genome size of a broad diversity of bacteria and archaea. We used dN/dS to estimate the strength of purifying selection, and 16S copy number as a proxy for ecological strategy, which have both been postulated to play a role in shaping genome size. After model fit, Pagels lambda indicated a strong phylogenetic signal in genome size, suggesting that the diversification of this trait is strongly influenced by shared evolutionary histories. As a predictor variable, dN/dS showed a poor predictability and non-significance when phylogeny was considered, consistent with the view that genome reduction can occur under either weak or strong purifying selection depending on the ecological context. Copies of 16S rRNA showed poor predictability but maintained significance when accounting for non-independence in residuals, suggesting that ecological strategy as approximated from 16S rRNA copies might play a minor role in genome size variation. Altogether, our results indicate that genome size is a complex trait that is not driven by any singular underlying evolutionary force, but rather depends on lineage- and niche-specific factors that will vary widely across bacteria and archaea. Author SummaryThe evolutionary forces driving genome size in bacteria and archaea have been subject to debate during the last decades. Independent comparative analyses have suggested that unique variables, such as the strength of selection, environmental complexity, and mutation rate, are the main drivers of this trait, which complicates generalizations across the Tree of Life. Here, we applied a phylogeny-based statistical approach to assess how tightly genome size is linked to evolutionary history in bacteria and archaea. Moreover, we also evaluated the predictability of genome size from the strength of purifying selection and ecological strategy on a broad diversity of bacteria and archaea genomes. Our approach indicates that genome size in prokaryotes is strongly dependent on phylogenetic history, and that genome size is the result of the interaction of variables like past events, current selection regimes, and environmental complexity that are clade dependent.

DNA supercoiling acts as a global transcriptional regulator, which contributes to the rapid transcriptional response of bacteria to many environmental changes. Although a large fraction of promoters from distant species respond to superhelical variations, the sequence or structural determinants of this behaviour remain elusive. Here, we propose the sequence of the "discriminator" element located downstream of the -10 hexamer to play an important role in this response, by modulating the facility of open-complex formation during transcription initiation. We develop a quantitative model of this regulatory mechanism relying on known parameters of DNA thermodynamics, and show that its predictions quantitatively match the in vitro and in vivo supercoiling response of stable RNA promoters previously measured, as well as the in vivo response of selected mRNA promoters with mutated discriminator sequences. We then test the universality of this mechanism by statistical analysis of promoter sequences in transcriptomes of phylogenetically distant bacteria under conditions of supercoiling variations, (1) by gyrase inhibitors, (2) by environmental stresses, (3) inherited in the longest-running evolution experiment. In all cases, we identify a robust and significant sequence signature in the discriminator region, suggesting that promoter opening underpins an ubiquitous regulatory mechanism in the prokaryotic kingdom, based on the fundamental mechanical properties of DNA.