Dusan Misevic

• Ph.D.
• Managing Director at Center for Research and Interdisciplinarity, French Institute of Health and Medical Research

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 or...

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, e...

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...

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...

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 diffe...

A recent commentary raised concerns about aspects of the model and assumptions used in a previous study which demonstrated that selection can favor chromosomal alleles that confer higher plasmid donation rates. Here, the authors of that previous study respond to the concerns raised.

Evolution provides a creative fount of complex and subtle adaptations that often surprise the scientists who discover them. However, the creativity of evolution is not limited to the natural world: Artificial organisms evolving in computational environments have also elicited surprise and wonder from the researchers studying them. The process of ev...

In many developed countries, human life expectancy has doubled over the last 180 years from ~40 to ~80 years. Underlying this great advance is a change in how we age, yet our understanding of this change remains limited. Here we present a unique database rich with possibilities to study the human ageing process: the AgeGuess.org database on people'...

We are witnessing a dramatic transformation in the way we do science. In recent years, significant flaws with existing scientific methods have come to light, including lack of transparency, insufficient involvement of stakeholders, disconnection from the public, and limited reproducibility of research findings. These concerns have sparked a global...

In bacteria, cooperative genes encoding public good molecules are preferentially located on mobile genetic elements (MGEs), and horizontal transfer of MGEs favours the maintenance of public good cooperation. The rate of horizontal transfer itself can evolve in response to selective pressures acting on both MGEs and bacterial hosts: benefits and cos...

Biological evolution provides a creative fount of complex and subtle adaptations, often surprising the scientists who discover them. However, because evolution is an algorithmic process that transcends the substrate in which it occurs, evolution's creativity is not limited to nature. Indeed, many researchers in the field of digital evolution have o...

Biological evolution provides a creative fount of complex and subtle adaptations, often surprising the scientists who discover them. However, because evolution is an algorithmic process that transcends the substrate in which it occurs, evolution's creativity is not limited to nature. Indeed, many researchers in the field of digital evolution have o...

Switching rate between cooperating and non-cooperating genotypes is a crucial social evolution factor, often neglected by game theory-inspired theoretical and experimental frameworks. We show that the evolution of alleles increasing the mutation or phenotypic switching rates toward cooperation is in itself a social dilemma. Although cooperative off...

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 pa...

Within-population strain dynamics during the transfer phase. A: The change in frequency of the good donor strain D+ from t0 to t1, shown for s1, m, and s2 populations of the experiments presented in Fig 3, suggests that D+ strain fitness is frequency-dependent. Results are shown as means ± SEM (N ≥ 6). B: To confirm the existence of positive freque...

Selection coefficients for the K12 strain in competition with B. Data are from the discrimination experiment, presented in Fig 2C. Data are available from FigShare at http://dx.doi.org/10.6084/m9.figshare.3199252. (TIFF)

Synthetic bacterial strains to study the selection of donor ability. The two competing strains differ in plasmid donor ability: D+ (red) bears FHR plasmid that confers high donor ability (indicated by pili), D− (white) does not bear FHR and can receive plasmids but not transfer them. D+C and D−C cells bear plasmid C that codes for resistance to the...

Parameters governing the selection of donor ability after strong initial dilution. Simulations are the same as the ones described in Fig 4. In A, the change in D+ frequency from t0 to t2 is shown as a function of the proportion of C plasmids present in D+ strain before the selection phase (at t1), each point being the mean of 1,000 replicates. D+ c...

Selection coefficients for D+ strain in a population structured by strong dilution. Data are from the simulations presented in Fig 4. Data are available from FigShare at http://dx.doi.org/10.6084/m9.figshare.3199252. (TIFF)

Effect of the presence of parasitic plasmids on the selection of donor ability. The change in D+ frequency from t0 to t2 is shown from simulation data (see Materials and Methods) as a function of the initial proportion of plasmids that are parasitic plasmids N. Results are shown for different values of C benefits on growth (with high C benefits, th...

Selection coefficient for the D+ strain in competition with D− in a structured population. Data are from the structured population experiment, presented in Fig 3B. Data are available from FigShare at http://dx.doi.org/10.6084/m9.figshare.3199252. (TIFF)

Effect of plasmid presence on the growth rate of E. coli strains used for discrimination experiments. Growth rates were measured in 96-well plates in M9 medium at 37°C, similarly to the conditions of the competition experiment. The maximal growth rate for each strain (A) and plasmid cost derived from the effect on growth rate (B) were computed as m...

Plasmid dynamics during the transfer phase. The change in frequency of D− cells bearing plasmid C-YFP (yellow) and plasmid C-GFP (green) is shown from t0 to t1 for s1, m, and s2 populations of the experiments presented in Fig 3. By design, C-GFP plasmids are initially present in D− only (see Materials and Methods) and decline in frequency as they a...

Dynamics of plasmid linkage to D+ strain with transfer and selection. The metapopulation is the one described in Fig 6. Plasmid linkage to D+ is shown as a function of D+ donor ability and C plasmid benefit on growth (during the selection phase), for both plasmids at t1 (A), and for N plasmid at t2 (B). The linkage values in (A) are the same for C...

Schematic model details and analysis. (DOCX)

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 requ...

Many theories have sought to explain the evolution of sex, but the question remains unanswered owing to the scarcity of compelling empirical tests. Here we summarize the results of two of our published studies investigating the evolution of sex using digital organisms. We used these evolving programs to test the hypothesis that sexual reproduction...

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 o...

The rate of mutation is central to evolution. Mutations are required for adaptation, yet most mutations with phenotypic effects are deleterious. As a consequence, the mutation rate that maximizes adaptation will be some intermediate value. Here, we used digital organisms to investigate the ability of natural selection to adjust and optimize mutatio...

Proceedings from the ninth International Conference on Artificial Life; papers by scientists of many disciplines focusing on the principles of organization and applications of complex, life-like systems. Artificial Life is an interdisciplinary effort to investigate the fundamental properties of living systems through the simulation and synthesis of...

The evolution of sexual reproduction has long been a major problem in biology. According to one theory, sex opposes the fitness-destroying process of Muller's ratchet, which occurs by the stochastic loss of high-fitness genotypes in small populations. Sex opposes the ratchet by allowing genotypes with different deleterious mutations to produce muta...