Non-equilibrium molecular dynamics of steady-state fluid transport through a 2D membrane driven by a concentration gradient.

We use a novel non-equilibrium algorithm to simulate steady-state fluid transport through a two-dimensional (2D) membrane due to a concentration gradient by molecular dynamics (MD) for the first time. We confirm that, as required by the Onsager reciprocal relations in the linear-response regime, the solution flux obtained using this algorithm agrees with the excess solute flux obtained from an established non-equilibrium MD algorithm for pressure-driven flow. In addition, we show that the concentration-gradient-driven solution flux in this regime is quantified far more efficiently by explicitly applying a transmembrane concentration difference using our algorithm than by applying Onsager reciprocity to pressure-driven flow. The simulated fluid fluxes are captured with reasonable quantitative accuracy by our previously derived continuum theory of concentration-gradient-driven fluid transport through a 2D membrane [D. J. Rankin, L. Bocquet, and D. M. Huang, J. Chem. Phys. 151, 044705 (2019)] for a wide range of solution and membrane parameters, even though the simulated pore sizes are only several times the size of the fluid particles. The simulations deviate from the theory for strong solute-membrane interactions relative to thermal energy, for which the theoretical approximations breakdown. Our findings will be beneficial for a molecular-level understanding of fluid transport driven by concentration gradients through membranes made from 2D materials, which have diverse applications in energy harvesting, molecular separations, and biosensing.

Entrance effects in concentration-gradient-driven flow through an ultrathin porous membrane.

Transport of liquid mixtures through porous membranes is central to processes such as desalination, chemical separations, and energy harvesting, with ultrathin membranes made from novel 2D nanomaterials showing exceptional promise. Here, we derive, for the first time, general equations for the solution and solute fluxes through a circular pore in an ultrathin planar membrane induced by a solute concentration gradient. We show that the equations accurately capture the fluid fluxes measured in finite-element numerical simulations for weak solute-membrane interactions. We also derive scaling laws for these fluxes as a function of the pore size and the strength and range of solute-membrane interactions. These scaling relationships differ markedly from those for concentration-gradient-driven flow through a long cylindrical pore or for flow induced by a pressure gradient or an electric field through a pore in an ultrathin membrane. These results have broad implications for transport of liquid mixtures through membranes with thickness on the order of the characteristic pore size.

Human cooperation based on punishment reputation.

The threat of punishment usually promotes cooperation. However, punishing itself is costly, rare in nonhuman animals, and humans who punish often finish with low payoffs in economic experiments. The evolution of punishment has therefore been unclear. Recent theoretical developments suggest that punishment has evolved in the context of reputation games. We tested this idea in a simple helping game with observers and with punishment and punishment reputation (experimentally controlling for other possible reputational effects). We show that punishers fully compensate their costs as they receive help more often. The more likely defection is punished within a group, the higher the level of within-group cooperation. These beneficial effects perish if the punishment reputation is removed. We conclude that reputation is key to the evolution of punishment.

The interplay between relatedness and horizontal gene transfer drives the evolution of plasmid-carried public goods.

Plasmids carry a wide range of genes that are often involved in bacterial social behaviour. The question of why such genes are frequently mobile has received increasing attention. Here, we use an explicit population genetic approach to model the evolution of plasmid-borne bacterial public goods production. Our findings highlight the importance of both transmission and relatedness as factors driving the evolution of plasmid-borne public goods production. We partition the effects of plasmid transfer of social traits into those of infectivity and the effect of increased relatedness. Our results demonstrate that, owing to its effect on relatedness, plasmid mobility increases the invasion and stability of public goods, in a way not seen in individually beneficial traits. In addition, we show that plasmid transfer increases relatedness when public goods production is rare but this effect declines when production is common, with both scenarios leading to an increase in the frequency of plasmid-borne public goods. Plasmids remain important vectors for the spread of social genes involved in bacterial virulence thus an understanding of their dynamics is highly relevant from a public health perspective.

Renaissance model of an epidemic with quarantine.

Quarantine is one possible solution to limit the propagation of an emerging infectious disease. Typically, infected individuals are removed from the population by avoiding physical contact with healthy individuals. A key factor for the success of a quarantine strategy is the carrying capacity of the facility. This is often a known parameter, while other parameters such as those defining the population structure are more difficult to assess. Here we develop a model where we explicitly introduce the carrying capacity of the quarantine facility into a susceptible-infected-recovered (SIR) framework. We show how the model can address the propagation and control of contact and sexually transmitted infections. We illustrate this by a case study of the city of Zurich during the 16th century, when it had to face an epidemic of syphilis. After Swiss mercenaries came back from a war in Naples in 1495, the authorities of the city addressed subsequent epidemics by, among others, placing infected members of the population in quarantine. Our results suggest that a modestly sized quarantine facility can successfully prevent or reduce an epidemic. However, false detection can present a real impediment for this solution. Indiscriminate quarantine of individuals can lead to the overfilling of the facility, and prevent the intake of infected individuals. This results in the failure of the quarantine policy. Hence, improving the rate of true over false detection becomes the key factor for quarantine strategies. Moreover, in the case of sexually transmitted infections, asymmetries in the male to female ratio, and the force of infection pertaining to each sex and class of sexual encounter can alter the effectiveness of quarantine measures. For example, a heterosexually transmitted disease that mainly affects one sex is harder to control in a population with more individuals of the opposite sex. Hence an imbalance in the sex ratios as seen in situations such as mining colonies, or populations at war, can present impediments for the success of quarantine policies.

The coevolution of toxin and antitoxin genes drives the dynamics of bacterial addiction complexes and intragenomic conflict.

Bacterial genomes commonly contain 'addiction' gene complexes that code for both a toxin and a corresponding antitoxin. As long as both genes are expressed, cells carrying the complex can remain healthy. However, loss of the complex (including segregational loss in daughter cells) can entail death of the cell. We develop a theoretical model to explore a number of evolutionary puzzles posed by toxin-antitoxin (TA) population biology. We first extend earlier results demonstrating that TA complexes can spread on plasmids, as an adaptation to plasmid competition in spatially structured environments, and highlight the role of kin selection. We then considered the emergence of TA complexes on plasmids from previously unlinked toxin and antitoxin genes. We find that one of these traits must offer at least initially a direct advantage in some but not all environments encountered by the evolving plasmid population. Finally, our study predicts non-transitive 'rock-paper-scissors' dynamics to be a feature of intragenomic conflict mediated by TA complexes. Intragenomic conflict could be sufficient to select deleterious genes on chromosomes and helps to explain the previously perplexing observation that many TA genes are found on bacterial chromosomes.

The evolution of conflict resolution between plasmids and their bacterial hosts.

It has recently been proposed that mobile elements may be a significant driver of cooperation in microorganisms. This may drive a potential conflict, where cooperative genes are transmitted independently of the rest of the genome, resulting in scenarios where horizontally spread cooperative genes are favored, whereas a chromosomal equivalent would not be. This can lead to the whole genome being exploited by surrounding noncooperative individuals. Given that there are costs associated with mobile elements themselves, infection with a plasmid carrying a cooperative trait may lead to a significant conflict within the host genome. Here, we model the mechanisms that allow the host to resolve this conflict, either by exhibiting complete resistance to the mobile element or by controlling its gene expression via a chromosomally based suppressor. We find that the gene suppression mechanism will be more stable than full resistance, implying that suppressing the expression of costly genes within a cell is preferable to preventing the acquisition of the mobile element, for the resolution of conflict within a genome.

Differences in cell division rates drive the evolution of terminal differentiation in microbes.

Multicellular differentiated organisms are composed of cells that begin by developing from a single pluripotent germ cell. In many organisms, a proportion of cells differentiate into specialized somatic cells. Whether these cells lose their pluripotency or are able to reverse their differentiated state has important consequences. Reversibly differentiated cells can potentially regenerate parts of an organism and allow reproduction through fragmentation. In many organisms, however, somatic differentiation is terminal, thereby restricting the developmental paths to reproduction. The reason why terminal differentiation is a common developmental strategy remains unexplored. To understand the conditions that affect the evolution of terminal versus reversible differentiation, we developed a computational model inspired by differentiating cyanobacteria. We simulated the evolution of a population of two cell types -nitrogen fixing or photosynthetic- that exchange resources. The traits that control differentiation rates between cell types are allowed to evolve in the model. Although the topology of cell interactions and differentiation costs play a role in the evolution of terminal and reversible differentiation, the most important factor is the difference in division rates between cell types. Faster dividing cells always evolve to become the germ line. Our results explain why most multicellular differentiated cyanobacteria have terminally differentiated cells, while some have reversibly differentiated cells. We further observed that symbioses involving two cooperating lineages can evolve under conditions where aggregate size, connectivity, and differentiation costs are high. This may explain why plants engage in symbiotic interactions with diazotrophic bacteria.

Kin selection and the evolution of social information use in animal conflict.

Animals often use social information about conspecifics in making decisions about cooperation and conflict. While the importance of kin selection in the evolution of intraspecific cooperation and conflict is widely acknowledged, few studies have examined how relatedness influences the evolution of social information use. Here we specifically examine how relatedness affects the evolution of a stylised form of social information use known as eavesdropping. Eavesdropping involves individuals escalating conflicts with rivals observed to have lost their last encounter and avoiding fights with those seen to have won. We use a game theoretical model to examine how relatedness affects the evolution of eavesdropping, both when strategies are discrete and when they are continuous or mixed. We show that relatedness influences the evolution of eavesdropping, such that information use peaks at intermediate relatedness. Our study highlights the importance of considering kin selection when exploring the evolution of complex forms of information use.

The evolution of plasmid-carried antibiotic resistance.

BACKGROUND: Antibiotic resistance represents a significant public health problem. When resistance genes are mobile, being carried on plasmids or phages, their spread can be greatly accelerated. Plasmids in particular have been implicated in the spread of antibiotic resistance genes. However, the selective pressures which favour plasmid-carried resistance genes have not been fully established. Here we address this issue with mathematical models of plasmid dynamics in response to different antibiotic treatment regimes. RESULTS: We show that transmission of plasmids is a key factor influencing plasmid-borne antibiotic resistance, but the dosage and interval between treatments is also important. Our results also hold when plasmids carrying the resistance gene are in competition with other plasmids that do not carry the resistance gene. By altering the interval between antibiotic treatments, and the dosage of antibiotic, we show that different treatment regimes can select for either plasmid-carried, or chromosome-carried, resistance. CONCLUSIONS: Our research addresses the effect of environmental variation on the evolution of plasmid-carried antibiotic resistance.

Sexual conflict and the tragedy of the commons.

It is widely understood that the costs and benefits of mating can affect the fecundity and survival of individuals. Sexual conflict may have profound consequences for populations as a result of the negative effects it causes males and females to have on one another's fitness. Here we present a model describing the evolution of sexual conflict, in which males inflict a direct cost on female fitness. We show that these costs can drive the entire population to extinction. To males, females are an essential but finite resource over which they have to compete. Population extinction owing to sexual conflict can therefore be seen as an evolutionary tragedy of the commons. Our model shows that a positive feedback between harassment and the operational sex ratio is responsible for the demise of females and, thus, for population extinction. We further show that the evolution of female resistance to counter harassment can prevent a tragedy of the commons. Our findings not only demonstrate that sexual conflict can drive a population to extinction but also highlight how simple mechanisms, such as harassment costs to males and females and the coevolution between harassment and resistance, can help avert a tragedy of the commons caused by sexual conflict.

The evolution of punishment through reputation.

Punishment of non-cooperators has been observed to promote cooperation. Such punishment is an evolutionary puzzle because it is costly to the punisher while beneficial to others, for example, through increased social cohesion. Recent studies have concluded that punishing strategies usually pay less than some non-punishing strategies. These findings suggest that punishment could not have directly evolved to promote cooperation. However, while it is well established that reputation plays a key role in human cooperation, the simple threat from a reputation of being a punisher may not have been sufficiently explored yet in order to explain the evolution of costly punishment. Here, we first show analytically that punishment can lead to long-term benefits if it influences one's reputation and thereby makes the punisher more likely to receive help in future interactions. Then, in computer simulations, we incorporate up to 40 more complex strategies that use different kinds of reputations (e.g. from generous actions), or strategies that not only include punitive behaviours directed towards defectors but also towards cooperators for example. Our findings demonstrate that punishment can directly evolve through a simple reputation system. We conclude that reputation is crucial for the evolution of punishment by making a punisher more likely to receive help in future interactions, and that experiments investigating the beneficial effects of punishment in humans should include reputation as an explicit feature.

Horizontal gene transfer and the evolution of bacterial cooperation.

Bacteria frequently exhibit cooperative behaviors but cooperative strains are vulnerable to invasion by cheater strains that reap the benefits of cooperation but do not perform the cooperative behavior themselves. Bacterial genomes often contain mobile genetic elements such as plasmids. When a gene for cooperative behavior exists on a plasmid, cheaters can be forced to cooperate by infection with this plasmid, rescuing cooperation in a population in which mutation or migration has allowed cheaters to arise. Here we introduce a second plasmid that does not code for cooperation and show that the social dilemma repeats itself at the plasmid level in both within-patch and metapopulation scenarios, and under various scenarios of plasmid incompatibility. Our results suggest that although plasmid carriage of cooperative genes can provide a transient defense against defection in structured environments, plasmid and chromosomal defection remain the only stable strategies in an unstructured environment. We discuss our results in the light of recent bioinformatic evidence that cooperative genes are overrepresented on mobile elements.

The social side of Homo economicus.

Many recent experiments in the field of behavioural economics appear to demonstrate a willingness of humans to behave altruistically, even when it is not in their interest to do so. This has led to the assertion that humans have evolved a special predisposition towards altruism. Recent studies have questioned this, and demonstrated that selfless cooperation does not hold up in controlled experiments. As I discuss here, this calls for more economic 'field experiments' and highlights the need for greater integration of the evolutionary and economic sciences.

Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence.

BACKGROUND: Microbes engage in a remarkable array of cooperative behaviors, secreting shared proteins that are essential for foraging, shelter, microbial warfare, and virulence. These proteins are costly, rendering populations of cooperators vulnerable to exploitation by nonproducing cheaters arising by gene loss or migration. In such conditions, how can cooperation persist? RESULTS: Our model predicts that differential gene mobility drives intragenomic variation in investment in cooperative traits. More mobile loci generate stronger among-individual genetic correlations at these loci (higher relatedness) and thereby allow the maintenance of more cooperative traits via kin selection. By analyzing 21 Escherichia genomes, we confirm that genes coding for secreted proteins-the secretome-are very frequently lost and gained and are associated with mobile elements. We show that homologs of the secretome are overrepresented among human gut metagenomics samples, consistent with increased relatedness at secretome loci across multiple species. The biosynthetic cost of secreted proteins is shown to be under intense selective pressure, even more than for highly expressed proteins, consistent with a cost of cooperation driving social dilemmas. Finally, we demonstrate that mobile elements are in conflict with their chromosomal hosts over the chimeric ensemble's social strategy, with mobile elements enforcing cooperation on their otherwise selfish hosts via the cotransfer of secretome genes with "mafia strategy" addictive systems (toxin-antitoxin and restriction-modification). CONCLUSION: Our analysis matches the predictions of our model suggesting that horizontal transfer promotes cooperation, as transmission increases local genetic relatedness at mobile loci and enforces cooperation on the resident genes. As a consequence, horizontal transfer promoted by agents such as plasmids, phages, or integrons drives microbial cooperation.

Assortment and the evolution of generalized reciprocity.

Reciprocity is often invoked to explain cooperation. Reciprocity is cognitively demanding, and both direct and indirect reciprocity require that individuals store information about the propensity of their partners to cooperate. By contrast, generalized reciprocity, wherein individuals help on the condition that they received help previously, only relies on whether an individual received help in a previous encounter. Such anonymous information makes generalized reciprocity hard to evolve in a well-mixed population, as the strategy will lose out to pure defectors. Here we analyze a model for the evolution of generalized reciprocity, incorporating assortment of encounters, to investigate the conditions under which it will evolve. We show that, in a well-mixed population, generalized reciprocity cannot evolve. However, incorporating assortment of encounters can favor the evolution of generalized reciprocity in which indiscriminate cooperation and defection are both unstable. We show that generalized reciprocity can evolve under both the prisoner's dilemma and the snowdrift game.

The evolution of judgement bias in indirect reciprocity.

Indirect reciprocity is a form of reciprocity where help is given to individuals based on their reputation. In indirect reciprocity, bad acts (such as not helping) reduce an individual's reputation while good acts (such as helping) increase an individual's reputation. Studies of indirect reciprocity assume that good acts and bad acts are weighted equally when assessing the reputation of an individual. As different information can be processed in different ways, this is not likely to be the case, and it is possible that an individual could bias an actor's reputation by putting more weight to acts of defection (not helping) than acts of co-operation (helping) or vice versa. We term this difference 'judgement bias', and build an individual-based model of image scoring to investigate the conditions under which it may evolve. We find that, if the benefits of co-operation are small, judgement bias is weighted towards acts perceived to be bad; if the benefits are high, the reverse is true. Our result is consistent under both scoring and standing strategies, and we find that allowing judgement bias to evolve increases the level of co-operation in the population.

The coevolution of cooperation and dispersal in social groups and its implications for the emergence of multicellularity.

BACKGROUND: Recent work on the complexity of life highlights the roles played by evolutionary forces at different levels of individuality. One of the central puzzles in explaining transitions in individuality for entities ranging from complex cells, to multicellular organisms and societies, is how different autonomous units relinquish control over their functions to others in the group. In addition to the necessity of reducing conflict over effecting specialized tasks, differentiating groups must control the exploitation of the commons, or else be out-competed by more fit groups. RESULTS: We propose that two forms of conflict - access to resources within groups and representation in germ line - may be resolved in tandem through individual and group-level selective effects. Specifically, we employ an optimization model to show the conditions under which different within-group social behaviors (cooperators producing a public good or cheaters exploiting the public good) may be selected to disperse, thereby not affecting the commons and functioning as germ line. We find that partial or complete dispersal specialization of cheaters is a general outcome. The propensity for cheaters to disperse is highest with intermediate benefit:cost ratios of cooperative acts and with high relatedness. An examination of a range of real biological systems tends to support our theory, although additional study is required to provide robust tests. CONCLUSION: We suggest that trait linkage between dispersal and cheating should be operative regardless of whether groups ever achieve higher levels of individuality, because individual selection will always tend to increase exploitation, and stronger group structure will tend to increase overall cooperation through kin selected benefits. Cheater specialization as dispersers offers simultaneous solutions to the evolution of cooperation in social groups and the origin of specialization of germ and soma in multicellular organisms.