Long-term fertilization and tillage regimes have limited effects on structuring bacterial and denitrifier communities in a sandy loam UK soil.

Denitrification causes loss of available nitrogen from soil systems, thereby reducing crop productivity and increasing reliance on agrochemicals. The dynamics of denitrification and denitrifying communities are thought to be altered by land management practices, which affect the physicochemical properties of the soil. In this study, we look at the effects of long-term tillage and fertilization regimes on arable soils following 16 years of treatment in a factorial field trial. By studying the bacterial community composition based on 16S rRNA amplicons, absolute bacterial abundance and diversity of denitrification functional genes (nirK, nirS and nosZ), under conditions of minimum/conventional tillage and organic/synthetic mineral fertilizer, we tested how specific land management histories affect the diversity and distribution of both bacteria and denitrification genes. Bacterial and denitrifier communities were largely unaffected by land management history and clustered predominantly by spatial location, indicating that the variability in bacterial community composition in these arable soils is governed by innate environmental differences and Euclidean distance rather than agricultural management intervention.

Social and physical environment independently affect oviposition decisions in Drosophila.

In response to environmental stimuli, including variation in the presence of conspecifics, genotypes show highly plastic responses in behavioral and physiological traits influencing reproduction. Although extensively documented in males, such female responses are rather less studied. We expect females to be highly responsive to environmental variation and to differentially allocate resources to increase offspring fitness, given the major contribution of mothers to offspring number, size, and developmental conditions. Using Drosophila melanogaster, we (a) manipulate exposure to conspecific females, which mothers could use to anticipate the number of potential mates and larval density, and; (b) test how this interacts with the spatial distribution of potential oviposition sites, with females from higher densities expected to prefer clustered resources that can support a larger number of larvae. We found that high density females were slower to start copulating and reduced their copulation duration, the opposite effect to that observed in males. There was a parallel, perhaps related, effect on egg production: females previously housed in groups laid fewer eggs than those housed in solitude. Resource patchiness also influenced oviposition behavior: females preferred aggregated substrate, which attracted more females to lay eggs. However, we found no interaction between prior housing conditions and resource patchiness, indicating that females did not perceive the value of different resource distributions differently when exposed to environments that could signal expected levels of larval competition. We show that, although exposure to consexual competition changes copulatory behaviors of females, the distribution of oviposition resources has a greater effect on oviposition decisions.

Theoretical and Methodological Approaches to Ecological Changes, Social Behaviour and Human Intergroup Tolerance 300,000 to 30,000 BP.

Archaeological evidence suggests that important shifts were taking place in the character of human social behaviours 300,000 to 30,000 years ago. New artefact types appear and are disseminated with greater frequency. Transfers of both raw materials and finished artefacts take place over increasing distances, implying larger scales of regional mobility and more frequent and friendlier interactions between different communities. Whilst these changes occur during a period of increasing environmental variability, the relationship between ecological changes and transformations in social behaviours is elusive. Here, we explore a possible theoretical approach and methodology for understanding how ecological contexts can influence selection pressures acting on intergroup social behaviours. We focus on the relative advantages and disadvantages of intergroup tolerance in different ecological contexts using agent-based modelling (ABM). We assess the relative costs and benefits of different 'tolerance' levels in between-group interactions on survival and resource exploitation in different environments. The results enable us to infer a potential relationship between ecological changes and proposed changes in between-group behavioural dynamics. We conclude that increasingly harsh environments may have driven changes in hormonal and emotional responses in humans leading to increasing intergroup tolerance, i.e. transformations in social behaviour associated with 'self-domestication'. We argue that changes in intergroup tolerance is a more parsimonious explanation for the emergence of what has been seen as 'modern human behaviour' than changes in hard aspects of cognition or other factors such as cognitive adaptability or population size. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10816-020-09503-5.

Spatial Organization of Expanding Bacterial Colonies Is Affected by Contact-Dependent Growth Inhibition.

Identifying how microbes are able to manipulate, survive, and thrive in complex multispecies communities has expanded our understanding of how microbial ecosystems impact human health and the environment. The ability of bacteria to negatively affect neighbors, through explicit toxin delivery systems, provides them with an opportunity to manipulate the composition of growing microbial communities. Contact-dependent inhibition (CDI) systems (a Type Vb secretion system) are a distinct subset of competition systems whose contribution to shaping the development of spatially structured bacterial communities are yet to be fully understood. Here, we compare the impact of different CDI systems, at both the single-cell and population level, to determine the key drivers of CDI-mediated competition within spatially structured bacterial populations. Through an iterative approach using both an Escherichia coli experimental system and computational modeling, we show that CDI systems have subtle and system-specific effects at the single-cell level, generating single-cell-wide boundaries between CDI-expressing inhibitor cells and their neighboring targets. Despite the subtle effects of CDI at a single-cell level, CDI systems greatly diminished the ability of susceptible targets to expand their range during colony growth. The inoculum density of the population, together with the CDI system-specific variables of the speed of inhibition after contact and biological cost of CDI, strongly affects CDI-mediated competition. In contrast, the magnitude of the toxin-induced growth retardation of target cells only weakly impacts the composition of the population. Our work reveals how distinct CDI systems can differentially affect the composition and spatial arrangement of bacterial populations.

Climate-induced phenology shifts linked to range expansions in species with multiple reproductive cycles per year.

Advances in phenology (the annual timing of species' life-cycles) in response to climate change are generally viewed as bioindicators of climate change, but have not been considered as predictors of range expansions. Here, we show that phenology advances combine with the number of reproductive cycles per year (voltinism) to shape abundance and distribution trends in 130 species of British Lepidoptera, in response to ~0.5 °C spring-temperature warming between 1995 and 2014. Early adult emergence in warm years resulted in increased within- and between-year population growth for species with multiple reproductive cycles per year (n = 39 multivoltine species). By contrast, early emergence had neutral or negative consequences for species with a single annual reproductive cycle (n = 91 univoltine species), depending on habitat specialisation. We conclude that phenology advances facilitate polewards range expansions in species exhibiting plasticity for both phenology and voltinism, but may inhibit expansion by less flexible species.

Differing effects of age and starvation on reproductive performance in Drosophila melanogaster.

Successful reproduction requires the completion of many, often condition-dependent, stages, from mate searching and courtship through to sperm transfer, fertilisation and offspring production. Animals can plastically adjust their investment in each stage according to the physical and social environment, their own condition, their future reproductive potential, and the condition of their partner. Here we manipulate age and condition, through a nutritional challenge early or late in life, of both male and female Drosophila melanogaster and measure the effects on courtship, mating, and fitness when paired with a standardized (unmanipulated) partner. Older males were slower to start courting and mating, and courted at a slower rate, but males were indifferent to female age or condition despite older females laying and hatching fewer eggs. Female condition had a substantial effect on mating acceptance rate, which dropped dramatically after starvation, and particularly recent starvation experience. In contrast, male condition had little effect on any of the components of reproductive performance we measured. Intriguingly, we found no evidence for additive or multiplicative effects of ageing and starvation: the only significant interaction between these variables was on male latency to initiate courtship - older males were slower to start courting unless they had experienced starvation early in life. These results indicate that the immediate costs of mating differ between males and females, and that the sexes differ in their perception of the opportunity cost sustained by refusing a mating opportunity. Our results support the idea that ageing has more wide-ranging impact on reproductive behaviours than does nutritional challenge.

Population and evolutionary dynamics in spatially structured seasonally varying environments.

Increasingly imperative objectives in ecology are to understand and forecast population dynamic and evolutionary responses to seasonal environmental variation and change. Such population and evolutionary dynamics result from immediate and lagged responses of all key life-history traits, and resulting demographic rates that affect population growth rate, to seasonal environmental conditions and population density. However, existing population dynamic and eco-evolutionary theory and models have not yet fully encompassed within-individual and among-individual variation, covariation, structure and heterogeneity, and ongoing evolution, in a critical life-history trait that allows individuals to respond to seasonal environmental conditions: seasonal migration. Meanwhile, empirical studies aided by new animal-tracking technologies are increasingly demonstrating substantial within-population variation in the occurrence and form of migration versus year-round residence, generating diverse forms of 'partial migration' spanning diverse species, habitats and spatial scales. Such partially migratory systems form a continuum between the extreme scenarios of full migration and full year-round residence, and are commonplace in nature. Here, we first review basic scenarios of partial migration and associated models designed to identify conditions that facilitate the maintenance of migratory polymorphism. We highlight that such models have been fundamental to the development of partial migration theory, but are spatially and demographically simplistic compared to the rich bodies of population dynamic theory and models that consider spatially structured populations with dispersal but no migration, or consider populations experiencing strong seasonality and full obligate migration. Second, to provide an overarching conceptual framework for spatio-temporal population dynamics, we define a 'partially migratory meta-population' system as a spatially structured set of locations that can be occupied by different sets of resident and migrant individuals in different seasons, and where locations that can support reproduction can also be linked by dispersal. We outline key forms of within-individual and among-individual variation and structure in migration that could arise within such systems and interact with variation in individual survival, reproduction and dispersal to create complex population dynamics and evolutionary responses across locations, seasons, years and generations. Third, we review approaches by which population dynamic and eco-evolutionary models could be developed to test hypotheses regarding the dynamics and persistence of partially migratory meta-populations given diverse forms of seasonal environmental variation and change, and to forecast system-specific dynamics. To demonstrate one such approach, we use an evolutionary individual-based model to illustrate that multiple forms of partial migration can readily co-exist in a simple spatially structured landscape. Finally, we summarise recent empirical studies that demonstrate key components of demographic structure in partial migration, and demonstrate diverse associations with reproduction and survival. We thereby identify key theoretical and empirical knowledge gaps that remain, and consider multiple complementary approaches by which these gaps can be filled in order to elucidate population dynamic and eco-evolutionary responses to spatio-temporal seasonal environmental variation and change.

The evolution of plasmid stability: Are infectious transmission and compensatory evolution competing evolutionary trajectories?

Conjugative plasmids are widespread and play an important role in bacterial evolution by accelerating adaptation through horizontal gene transfer. However, explaining the long-term stability of plasmids remains challenging because segregational loss and the costs of plasmid carriage should drive the loss of plasmids though purifying selection. Theoretical and experimental studies suggest two key evolutionary routes to plasmid stability: First, the evolution of high conjugation rates would allow plasmids to survive through horizontal transmission as infectious agents, and second, compensatory evolution to ameliorate the cost of plasmid carriage can weaken purifying selection against plasmids. How these two evolutionary strategies for plasmid stability interact is unclear. Here, we summarise the literature on the evolution of plasmid stability and then use individual based modelling to investigate the evolutionary interplay between the evolution of plasmid conjugation rate and cost amelioration. We find that, individually, both strategies promote plasmid stability, and that they act together to increase the likelihood of plasmid survival. However, due to the inherent costs of increasing conjugation rate, particularly where conjugation is unlikely to be successful, our model predicts that amelioration is the more likely long-term solution to evolving stable bacteria-plasmid associations. Our model therefore suggests that bacteria-plasmid relationships should evolve towards lower plasmid costs that may forestall the evolution of highly conjugative, 'infectious' plasmids.

Climate change, climatic variation and extreme biological responses.

Extreme climatic events could be major drivers of biodiversity change, but it is unclear whether extreme biological changes are (i) individualistic (species- or group-specific), (ii) commonly associated with unusual climatic events and/or (iii) important determinants of long-term population trends. Using population time series for 238 widespread species (207 Lepidoptera and 31 birds) in England since 1968, we found that population 'crashes' (outliers in terms of species' year-to-year population changes) were 46% more frequent than population 'explosions'. (i) Every year, at least three species experienced extreme changes in population size, and in 41 of the 44 years considered, some species experienced population crashes while others simultaneously experienced population explosions. This suggests that, even within the same broad taxonomic groups, species are exhibiting individualistic dynamics, most probably driven by their responses to different, short-term events associated with climatic variability. (ii) Six out of 44 years showed a significant excess of species experiencing extreme population changes (5 years for Lepidoptera, 1 for birds). These 'consensus years' were associated with climatically extreme years, consistent with a link between extreme population responses and climatic variability, although not all climatically extreme years generated excess numbers of extreme population responses. (iii) Links between extreme population changes and long-term population trends were absent in Lepidoptera and modest (but significant) in birds. We conclude that extreme biological responses are individualistic, in the sense that the extreme population changes of most species are taking place in different years, and that long-term trends of widespread species have not, to date, been dominated by these extreme changes.This article is part of the themed issue 'Behavioural, ecological and evolutionary responses to extreme climatic events'.

Behavioural synchronization of large-scale animal movements - disperse alone, but migrate together?

Dispersal and migration are superficially similar large-scale movements, but which appear to differ in terms of inter-individual behavioural synchronization. Seasonal migration is a striking example of coordinated behaviour, enabling animal populations to track spatio-temporal variation in ecological conditions. By contrast, for dispersal, while social context may influence an individual's emigration and settlement decisions, transience is believed to be mostly a solitary behaviour. Here, we review differences in drivers that may explain why migration appears to be more synchronized than dispersal. We derive the prediction that the contrast in the importance of behavioural synchronization between dispersal and migration is linked to differences in the selection pressures that drive their respective evolution. Although documented examples of collective dispersal are rare, this behaviour may be more common than currently believed, with important consequences for eco-evolutionary dynamics. Crucially, to date, there is little available theory for predicting when we should expect collective dispersal to evolve, and we also lack empirical data to test predictions across species. By reviewing the state of the art in research on migration and collective movements, we identify how we can harness these advances, both in terms of theory and data collection, to broaden our understanding of synchronized dispersal and its importance in the context of global change.

Rapid compensatory evolution promotes the survival of conjugative plasmids.

Conjugative plasmids play a vital role in bacterial adaptation through horizontal gene transfer. Explaining how plasmids persist in host populations however is difficult, given the high costs often associated with plasmid carriage. Compensatory evolution to ameliorate this cost can rescue plasmids from extinction. In a recently published study we showed that compensatory evolution repeatedly targeted the same bacterial regulatory system, GacA/GacS, in populations of plasmid-carrying bacteria evolving across a range of selective environments. Mutations in these genes arose rapidly and completely eliminated the cost of plasmid carriage. Here we extend our analysis using an individual based model to explore the dynamics of compensatory evolution in this system. We show that mutations which ameliorate the cost of plasmid carriage can prevent both the loss of plasmids from the population and the fixation of accessory traits on the bacterial chromosome. We discuss how dependent the outcome of compensatory evolution is on the strength and availability of such mutations and the rate at which beneficial accessory traits integrate on the host chromosome.

Understanding how biodiversity unfolds through time under neutral theory.

Theoretical predictions for biodiversity patterns are typically derived under the assumption that ecological systems have reached a dynamic equilibrium. Yet, there is increasing evidence that various aspects of ecological systems, including (but not limited to) species richness, are not at equilibrium. Here, we use simulations to analyse how biodiversity patterns unfold through time. In particular, we focus on the relative time required for various biodiversity patterns (macroecological or phylogenetic) to reach equilibrium. We simulate spatially explicit metacommunities according to the Neutral Theory of Biodiversity (NTB) under three modes of speciation, which differ in how evenly a parent species is split between its two daughter species. We find that species richness stabilizes first, followed by species area relationships (SAR) and finally species abundance distributions (SAD). The difference in timing of equilibrium between these different macroecological patterns is the largest when the split of individuals between sibling species at speciation is the most uneven. Phylogenetic patterns of biodiversity take even longer to stabilize (tens to hundreds of times longer than species richness) so that equilibrium predictions from neutral theory for these patterns are unlikely to be relevant. Our results suggest that it may be unwise to assume that biodiversity patterns are at equilibrium and provide a first step in studying how these patterns unfold through time.

Bacteriophages limit the existence conditions for conjugative plasmids.

UNLABELLED: Bacteriophages are a major cause of bacterial mortality and impose strong selection on natural bacterial populations, yet their effects on the dynamics of conjugative plasmids have rarely been tested. We combined experimental evolution, mathematical modeling, and individual-based simulations to explain how the ecological and population genetics effects of bacteriophages upon bacteria interact to determine the dynamics of conjugative plasmids and their persistence. The ecological effects of bacteriophages on bacteria are predicted to limit the existence conditions for conjugative plasmids, preventing persistence under weak selection for plasmid accessory traits. Experiments showed that phages drove faster extinction of plasmids in environments where the plasmid conferred no benefit, but they also revealed more complex effects of phages on plasmid dynamics under these conditions, specifically, the temporary maintenance of plasmids at fixation followed by rapid loss. We hypothesized that the population genetic effects of bacteriophages, specifically, selection for phage resistance mutations, may have caused this. Further mathematical modeling and individual-based simulations supported our hypothesis, showing that conjugative plasmids may hitchhike with phage resistance mutations in the bacterial chromosome. IMPORTANCE: Conjugative plasmids are infectious loops of DNA capable of transmitting DNA between bacterial cells and between species. Because plasmids often carry extra genes that allow bacteria to live in otherwise-inhospitable environments, their dynamics are central to understanding bacterial adaptive evolution. The plasmid-bacterium interaction has typically been studied in isolation, but in natural bacterial communities, bacteriophages, viruses that infect bacteria, are ubiquitous. Using experiments, mathematical models, and computer simulations we show that bacteriophages drive plasmid dynamics through their ecological and evolutionary effects on bacteria and ultimately limit the conditions allowing plasmid existence. These results advance our understanding of bacterial adaptation and show that bacteriophages could be used to select against plasmids carrying undesirable traits, such as antibiotic resistance.

Sperm production responds to perceived sperm competition risk in male Drosophila melanogaster.

Postcopulatory sexual selection arising from female multiple mating leads to the evolution of ejaculates that maximize a male's reproductive success under sperm competition. Where the risk of sperm competition is variable, optimal fitness may be achieved by plastically altering ejaculate characteristics in response to the prevailing sperm competition environment. In the model species Drosophila melanogaster, males expecting to encounter sperm competition mate for longer and transfer more accessory proteins and sperm. Here we show that after being housed with a single rival for one week, the seminal vesicles of male D. melanogaster contain a significantly greater proportion of live sperm than those of males maintained alone, indicating adaptive adjustment of sperm quality in response to the perceived risk of sperm competition. This effect is due to an increase in the number of live sperm produced, indicating that males upregulate sperm production in response to the presence of rivals. Our data suggest that males show plasticity in the rate of spermatogenesis that is adaptive in the context of a fluctuating sperm competition environment.

Inter-annual variability influences the eco-evolutionary dynamics of range-shifting.

Understanding the eco-evolutionary dynamics of species under rapid climate change is vital for both accurate forecasting of biodiversity responses and for developing effective management strategies. Using an individual-based model we demonstrate that the presence and form (colour) of inter-annual variability in environmental conditions can impact the evolution of dispersal during range shifts. Under stable climate, temporal variability typically results in higher dispersal. However, at expanding margins, inter-annual variability actually inhibits the evolution of higher emigration propensities by disrupting the spatial sorting and natural selection processes. These results emphasize the need for future theoretical studies, as well as predictive modelling, to account for the potential impacts of inter-annual variability.

Exposure to sperm competition risk improves survival of virgin males.

Sperm competition between the ejaculates of multiple males for the fertilization of a given set of ova is taxonomically widespread. Males have evolved remarkable adaptations to increase their reproductive success under postcopulatory sexual selection, which in many species includes the ability to modify behaviour and ejaculate characteristics plastically to match the perceived level of sperm competition. Males of the model species Drosophila melanogaster increase mating duration and modify seminal fluid composition in response to short-term changes in sperm competition risk. If these responses increase a male's total investment in reproduction, he must either trade-off this cost against other life-history traits or suffer reduced survival. We tested whether mounting a plastic sperm competition response bears an instantaneous survival cost, and instead found that male D. melanogaster exposed to a high risk of sperm competition survive 12 per cent longer than those at low risk, equating to a 49 per cent reduction in the hourly hazard of death. This striking effect was found only among virgins: the high cost of mating in this species eliminates any such benefit among non-virgin males. Our results suggest that the improvement in survival found among virgins may be a product of males' tactical responses to sperm competition.

Female choosiness leads to the evolution of individually distinctive males.

Individual recognition is a taxonomically widespread ability that underlies a diverse suite of behaviors including the identification of individual nest-mates, agonistic opponents, and mating partners. However, as yet relatively little is known about the circumstances under which the requisite signal diversity can evolve. Here, we develop a model describing a novel mechanism of individual identity evolution via sexual selection. Females choose among a subset of males, but can select the most attractive male only when he bears a unique identity signal. This mimics a species in which mate assessment and choice are temporally separate, such as when females observe males in direct conflict and must subsequently locate the winner. When females in our model are choosy at least 10% of the time, diversity at individuality signaling loci evolves as a by-product of selection on male attractiveness more rapidly than does diversity at equivalent loci evolving only under neutral processes. Even at lower discrimination rates, drifting signal diversity gives the female choice mechanism sufficient traction to drive up average male attractiveness. The mechanism we describe here can significantly increase signal diversity at even low rates of discrimination by females.

The speed of range shifts in fragmented landscapes.

Species may be driven extinct by climate change, unless their populations are able to shift fast enough to track regions of suitable climate. Shifting will be faster as the proportion of suitable habitat in the landscape increases. However, it is not known how the spatial arrangement of habitat will affect the speed of range advance, especially when habitat is scarce, as is the case for many specialist species. We develop methods for calculating the speed of advance that are appropriate for highly fragmented, stochastic systems. We reveal that spatial aggregation of habitat tends to reduce the speed of advance throughout a wide range of species parameters: different dispersal distances and dispersal kernel shapes, and high and low extinction probabilities. In contrast, aggregation increases the steady-state proportion of habitat that is occupied (without climate change). Nonetheless, we find that it is possible to achieve both rapid advance and relatively high patch occupancy when the habitat has a "channeled" pattern, resembling corridors or chains of stepping stones. We adapt techniques from electrical circuit theory to predict the rate of advance efficiently for complex, realistic landscape patterns, whereas the rate cannot be predicted by any simple statistic of aggregation or fragmentation. Conservationists are already advocating corridors and stepping stones as important conservation tools under climate change, but they are vaguely defined and have so far lacked a convincing basis in fundamental population biology. Our work shows how to discriminate properties of a landscape's spatial pattern that affect the speed of colonization (including, but not limited to, patterns like corridors and chains of stepping stones), and properties that affect a species' probability of persistence once established. We can therefore point the way to better land use planning approaches, which will provide functional habitat linkages and also maintain local population viability.

Costs of dispersal.

Dispersal costs can be classified into energetic, time, risk and opportunity costs and may be levied directly or deferred during departure, transfer and settlement. They may equally be incurred during life stages before the actual dispersal event through investments in special morphologies. Because costs will eventually determine the performance of dispersing individuals and the evolution of dispersal, we here provide an extensive review on the different cost types that occur during dispersal in a wide array of organisms, ranging from micro-organisms to plants, invertebrates and vertebrates. In general, costs of transfer have been more widely documented in actively dispersing organisms, in contrast to a greater focus on costs during departure and settlement in plants and animals with a passive transfer phase. Costs related to the development of specific dispersal attributes appear to be much more prominent than previously accepted. Because costs induce trade-offs, they give rise to covariation between dispersal and other life-history traits at different scales of organismal organisation. The consequences of (i) the presence and magnitude of different costs during different phases of the dispersal process, and (ii) their internal organisation through covariation with other life-history traits, are synthesised with respect to potential consequences for species conservation and the need for development of a new generation of spatial simulation models.

A metapopulation paradox: partial improvement of habitat may reduce metapopulation persistence.

The adverse influence of habitat degradation on the survival of populations may sometimes be amplified by rapid evolution over ecological timescales. This phenomenon of "evolutionary suicide" has been described in theoretical as well as empirical studies. However, no studies have suggested that habitat improvement could possibly also trigger an evolutionary response that would result in a decline in population size. We use individual-based simulations to demonstrate the potential for such a paradoxical response. An increase in the quality, size, or stability of only a fraction of the habitat patches in a metapopulation may result in an evolutionary decline in the dispersal propensity of individuals, followed by a decrease in recolonization, a reduction in the number of patches occupied, a decline in overall population size, and even extinction. Thus, well-intended conservation efforts that ignore potential evolutionary consequences of habitat management may increase the extinction risk of populations.