Dusan Misevic

Sexual reproduction reshapes the genetic architecture of digital organisms

Modularity and epistasis, as well as other aspects of genetic architecture, have emerged as central themes in evolutionary biology. Theory suggests that modularity promotes evolvability, and that aggravating (synergistic) epistasis among deleterious mutations facilitates the evolution of sex. Here, by contrast, we investigate the evolution of different genetic architectures using digital organisms, which are computer programs that self-replicate, mutate, compete and evolve. Specifically, we investigate how genetic architecture is shaped by reproductive mode. We allowed 200 populations of digital organisms to evolve for over 10 000 generations while reproducing either asexually or sexually. For 10 randomly chosen organisms from each population, we constructed and analysed all possible single mutants as well as one million mutants at each mutational distance from 2 to 10. The genomes of sexual organisms were more modular than asexual ones; sites encoding different functional traits had less overlap and sites encoding a particular trait were more tightly clustered. Net directional epistasis was alleviating (antagonistic) in both groups, although the overall strength of this epistasis was weaker in sexual than in asexual organisms. Our results show that sexual reproduction profoundly influences the evolution of the genetic architecture.

Genetic information transfer promotes cooperation in bacteria

Significance Bacteria often cooperate through the production of public goods that change their environment. These processes can affect human health by increasing virulence or antibiotic resistance. Public good production is costly, making cooperation susceptible to invasion by nonproducing “cheater” individuals. Bacteria also readily share genes, even among distinct species. Our experiments and models converge to show that when both cheating and cooperative genes are transferred, cooperators win against cheaters because transfer increases assortment among alleles, favoring cooperation. This can explain why genes for cooperation are often mobile, and suggests that, in addition to reducing antibiotic resistance spread, preventing gene mobility could reduce cooperative virulence. Many bacterial species are social, producing costly secreted “public good” molecules that enhance the growth of neighboring cells. The genes coding for these cooperative traits are often propagated via mobile genetic elements and can be virulence factors from a biomedical perspective. Here, we present an experimental framework that links genetic information exchange and the selection of cooperative traits. Using simulations and experiments based on a synthetic bacterial system to control public good secretion and plasmid conjugation, we demonstrate that horizontal gene transfer can favor cooperation. In a well-mixed environment, horizontal transfer brings a direct infectious advantage to any gene, regardless of its cooperation properties. However, in a structured population transfer selects specifically for cooperation by increasing the assortment among cooperative alleles. Conjugation allows cooperative alleles to overcome rarity thresholds and invade bacterial populations structured purely by stochastic dilution effects. Our results provide an explanation for the prevalence of cooperative genes on mobile elements, and suggest a previously unidentified benefit of horizontal gene transfer for bacteria.

Experiments with Digital Organisms on the Origin and Maintenance of Sex in Changing Environments

Many theories have been proposed to explain the evolution of sex, but the question remains unsettled owing to a paucity of compelling empirical tests. The crux of the problem is to understand the prevalence of sexual reproduction in the natural world, despite obvious costs relative to asexual reproduction. Here we perform experiments with digital organisms (evolving computer programs) to test the hypothesis that sexual reproduction is advantageous in changing environments. We varied the frequency and magnitude of environmental change, while the digital organisms could evolve their mode of reproduction as well as the traits affecting their fitness (reproductive rate) under the various conditions. Sex became the dominant mode of reproduction only when the environment changed rapidly and substantially (with particular functions changing from maladaptive to adaptive and vice versa). Even under these conditions, it was easier to maintain sexual reproduction than for sex to invade a formerly asexual population, although sometimes sex did invade and spread despite the obstacles to becoming established. Several diverse properties of the ancestral genomes, including epistasis and modularity, had no effect on the subsequent evolution of reproductive mode. Our study provides some limited support for the importance of changing environments to the evolution of sex, while also reinforcing the difficulty of evolving and maintaining sexual reproduction.

Predicting the Evolution of Sex on Complex Fitness Landscapes

Most population genetic theories on the evolution of sex or recombination are based on fairly restrictive assumptions about the nature of the underlying fitness landscapes. Here we use computer simulations to study the evolution of sex on fitness landscapes with different degrees of complexity and epistasis. We evaluate predictors of the evolution of sex, which are derived from the conditions established in the population genetic literature for the evolution of sex on simpler fitness landscapes. These predictors are based on quantities such as the variance of Hamming distance, mean fitness, additive genetic variance, and epistasis. We show that for complex fitness landscapes all the predictors generally perform poorly. Interestingly, while the simplest predictor, ΔVarHD, also suffers from a lack of accuracy, it turns out to be the most robust across different types of fitness landscapes. ΔVarHD is based on the change in Hamming distance variance induced by recombination and thus does not require individual fitness measurements. The presence of loci that are not under selection can, however, severely diminish predictor accuracy. Our study thus highlights the difficulty of establishing reliable criteria for the evolution of sex on complex fitness landscapes and illustrates the challenge for both theoretical and experimental research on the origin and maintenance of sexual reproduction.

Genetic Architecture Promotes the Evolution and Maintenance of Cooperation

When cooperation has a direct cost and an indirect benefit, a selfish behavior is more likely to be selected for than an altruistic one. Kin and group selection do provide evolutionary explanations for the stability of cooperation in nature, but we still lack the full understanding of the genomic mechanisms that can prevent cheater invasion. In our study we used Aevol, an agent-based, in silico genomic platform to evolve populations of digital organisms that compete, reproduce, and cooperate by secreting a public good for tens of thousands of generations. We found that cooperating individuals may share a phenotype, defined as the amount of public good produced, but have very different abilities to resist cheater invasion. To understand the underlying genetic differences between cooperator types, we performed bio-inspired genomics analyses of our digital organisms by recording and comparing the locations of metabolic and secretion genes, as well as the relevant promoters and terminators. Association between metabolic and secretion genes (promoter sharing, overlap via frame shift or sense-antisense encoding) was characteristic for populations with robust cooperation and was more likely to evolve when secretion was costly. In mutational analysis experiments, we demonstrated the potential evolutionary consequences of the genetic association by performing a large number of mutations and measuring their phenotypic and fitness effects. The non-cooperating mutants arising from the individuals with genetic association were more likely to have metabolic deleterious mutations that eventually lead to selection eliminating such mutants from the population due to the accompanying fitness decrease. Effectively, cooperation evolved to be protected and robust to mutations through entangled genetic architecture. Our results confirm the importance of second-order selection on evolutionary outcomes, uncover an important genetic mechanism for the evolution and maintenance of cooperation, and suggest promising methods for preventing gene loss in synthetically engineered organisms.

Effects of public good properties on the evolution of cooperation

Cooperation is a still unsolved and ever-controversial topic in evolutionary biology. Why do organisms engage in activities with long-term communal benefits but short-term individual cost? A general answer remains elusive, suggesting many important factors must still be examined and better understood. Here we study cooperation based on the secretion of a public good molecule using Aevol, a digital platform inspired by microbial cooperation systems. Specifically, we focus on the environmental and physical properties of the public good itself, its mobility, durability, and cost. The intensity of cooperation that evolves in our digital populations, as measured by the amount of the public good molecule organisms secrete, strongly depends on the properties of such a molecule. Specifically, and somewhat counter intuitively, digital organisms evolve to secrete more when public good degrades or diffuses quickly. The evolution of secretion also depends on the interactions between the population structure and public good properties, not just their individual values. Environmental factors affecting population diversity have been extensively studied in the past, but here we show that physical aspects of the cooperation mechanism itself may be equally if not more important. Given the wide range of substrates and environments that support microbial cooperation in nature, our results highlight the need for careful consideration of public good properties when studying the evolution of cooperation in bacterial or computational models.

Robustness and evolvability of cooperation

Robustness and evolvability are indirectly selected properties of biological systems that still play a significant role in determining evolutionary trajectories. Understanding such second order evolution is even more challenging when considering traits related to cooperation, as the evolution of cooperation itself is governed by indirect selection. To examine the robustness and evolvability of cooperation, we used an agent-based model of digital evolution, Aevol. In Aevol individuals capable of cooperating via costly public good secretion evolve for thousands of generations in a classical tragedy of the commons scenario. We varied the cost of secreting the public good molecule between and within individual experiments and constructed and evaluated millions of mutants to quantify the organisms’ position in the fitness landscape. Populations initially evolved at different regimes selecting against secretion, and then continued the evolution at a reasonably low cost of secretion. The populations that experienced a very strong selection against cooperation evolved less secretion than the ones that initially experienced a less drastic selection against cooperation via a high secretion cost. The mutational analysis revealed a correlation between the number of mutants with increased secretion and the secretion level across all costs of secretion. We also evolved several clones of each population to highlight a strong effect of history in general on cooperation. Our work shows that the history of cooperative interactions has an effect on evolutionary dynamics, a result likely to be relevant in any cooperative systems that are frequently experiencing changes in cost and benefit of cooperation.

Mobile genetic elements are involved in bacterial sociality

Mobile genetic elements in bacteria are enriched in genes participating in social behaviors, suggesting an evolutionary link between gene mobility and social evolution. Cooperative behaviors, like the production of secreted public good molecules, are susceptible to the invasion of non-cooperative individuals, and their evolutionary maintenance requires mechanisms ensuring that benefits are directed preferentially to cooperators. In order to investigate the reasons for the mobility of public good genes, we designed a synthetic bacterial system where we control and quantify the transfer of public good production genes. In our recent study, we have experimentally shown that horizontal transfer helps maintain public good production in the face of both non-producer organisms and non-producer plasmids. Transfer spreads genes to neighboring cells, thus increasing relatedness and directing a higher proportion of public good benefits to producers. The effect is the strongest when public good genes undergo epidemics dynamics, making horizontal transfer especially relevant for pathogenic bacteria that repeatedly infect new hosts and base their virulence on costly public goods. The promotion of cooperation may be a general consequence of horizontal gene transfer in prokaryotes. Our work has an intriguing parallel, cultural transmission, where horizontal transfer, such as teaching, may preferentially promote cooperative behaviors.

Shape matters: Lifecycle of cooperative patches promotes cooperation in bulky populations

Natural cooperative systems take many forms, ranging from one‐dimensional cyanobacteria arrays to fractal‐like biofilms. We use in silico experimental systems to study a previously overlooked factor in the evolution of cooperation, physical shape of the population. We compare the emergence and maintenance of cooperation in populations of digital organisms that inhabit bulky (100 × 100 cells) or slender (4 × 2500) toroidal grids. Although more isolated subpopulations of secretors in a slender population could be expected to favor cooperation, we find the opposite: secretion evolves to higher levels in bulky populations. We identify the mechanistic explanation for the shape effect by analyzing the lifecycle and dynamics of cooperator patches, from their emergence and growth, to invasion by noncooperators and extinction. Because they are constrained by the population shape, the cooperator patches expand less in slender than in bulky populations, leading to fewer cooperators, less public good secretion, and generally lower cooperation. The patch dynamics and mechanisms of shape effect are robust across several digital cooperation systems and independent of the underlying basis for cooperation (public good secretion or a cooperation game). Our results urge for a greater consideration of population shape in the study of the evolution of cooperation across experimental and modeling systems.

Indirect Fitness Benefits Enable the Spread of Host Genes Promoting Costly Transfer of Beneficial Plasmids

Bacterial genes that confer crucial phenotypes, such as antibiotic resistance, can spread horizontally by residing on mobile genetic elements (MGEs). Although many mobile genes provide strong benefits to their hosts, the fitness consequences of the process of transfer itself are less clear. In previous studies, transfer has been interpreted as a parasitic trait of the MGEs because of its costs to the host but also as a trait benefiting host populations through the sharing of a common gene pool. Here, we show that costly donation is an altruistic act when it spreads beneficial MGEs favoured when it increases the inclusive fitness of donor ability alleles. We show mathematically that donor ability can be selected when relatedness at the locus modulating transfer is sufficiently high between donor and recipients, ensuring high frequency of transfer between cells sharing donor alleles. We further experimentally demonstrate that either population structure or discrimination in transfer can increase relatedness to a level selecting for chromosomal transfer alleles. Both mechanisms are likely to occur in natural environments. The simple process of strong dilution can create sufficient population structure to select for donor ability. Another mechanism observed in natural isolates, discrimination in transfer, can emerge through coselection of transfer and discrimination alleles. Our work shows that horizontal gene transfer in bacteria can be promoted by bacterial hosts themselves and not only by MGEs. In the longer term, the success of cells bearing beneficial MGEs combined with biased transfer leads to an association between high donor ability, discrimination, and mobile beneficial genes. However, in conditions that do not select for altruism, host bacteria promoting transfer are outcompeted by hosts with lower transfer rate, an aspect that could be relevant in the fight against the spread of antibiotic resistance.