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Selection-driven tumor evolution with public goods leads to patterns of clonal expansion consistent with neutral growth.

ABSTRACT: Cancers are the result of eco-evolutionary processes fueled by heritable phenotypic diversification and driven by environmentally dependent selection. Space represents a key growth-limiting ecological resource, the ability to explore this resource is likely under strong selection. Using agent-based modeling, we explored the interplay between phenotypic strategies centered on gaining access to new space through cell-extrinsic degradation of extracellular matrix barriers and the exploitation of this resource through maximizing cell proliferation. While cell proliferation is a cell-intrinsic property, newly accessed space represents a public good, which can benefit both producers and non-producers. We found that this interplay results in ecological succession, enabling emergence of large, heterogeneous, and highly proliferative populations. Even though in our simulations both remodeling and proliferation strategies were under strong positive selection, their interplay led to sub-clonal architecture that could be interpreted as evidence for neutral evolution, warranting cautious interpretation of inferences from sequencing of cancer genomes.

SUBMITTER: Edwards J

PROVIDER: S-EPMC7753957 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Evolution of cooperation and consistent personalities in public goods games.

Project description:The evolution of cooperation has remained an important problem in evolutionary theory and social sciences. In this regard, a curious question is why consistent cooperative and defective personalities exist and if they serve a role in the evolution of cooperation? To shed light on these questions, here, I consider a population of individuals who possibly play two consecutive rounds of public goods game, with different enhancement factors. Importantly, individuals have independent strategies in the two rounds. However, their strategy in the first round affects the game they play in the second round. I consider two different scenarios where either only first-round cooperators play a second public goods game, or both first-round cooperators and first-round defectors play a second public goods game, but in different groups. The first scenario can be considered a reward dilemma, and the second can be considered an assortative public goods game but with independent strategies of the individuals in the two rounds. Both models show cooperators can survive either in a fixed point or through different periodic orbits. Interestingly, due to the emergence of a correlation between the strategies of the individuals in the two rounds, individuals develop consistent personalities during the evolution. This, in turn, helps cooperation to flourish. These findings shed new light on the evolution of cooperation and show how consistent cooperative and defective personalities can evolve and play a positive role in solving social dilemmas.

| S-EPMC8660839 | biostudies-literature

Cell-cell contacts confine public goods diffusion inside Pseudomonas aeruginosa clonal microcolonies.

Project description:The maintenance of cooperation in populations where public goods are equally accessible to all but inflict a fitness cost on individual producers is a long-standing puzzle of evolutionary biology. An example of such a scenario is the secretion of siderophores by bacteria into their environment to fetch soluble iron. In a planktonic culture, these molecules diffuse rapidly, such that the same concentration is experienced by all bacteria. However, on solid substrates, bacteria form dense and packed colonies that may alter the diffusion dynamics through cell-cell contact interactions. In Pseudomonas aeruginosa microcolonies growing on solid substrate, we found that the concentration of pyoverdine, a secreted iron chelator, is heterogeneous, with a maximum at the center of the colony. We quantitatively explain the formation of this gradient by local exchange between contacting cells rather than by global diffusion of pyoverdine. In addition, we show that this local trafficking modulates the growth rate of individual cells. Taken together, these data provide a physical basis that explains the stability of public goods production in packed colonies.

| S-EPMC3732961 | biostudies-literature

Group-Level Selection Increases Cooperation in the Public Goods Game.

Project description:When groups compete for resources, some groups will be more successful than others, forcing out less successful groups. Group-level selection is the most extreme form of group competition, where the weaker group ceases to exist, becoming extinct. We implement group-level selection in a controlled laboratory experiment in order to study its impact on human cooperation. The experiment uses variations on the standard linear public goods game. Group-level selection operates through competition for survival: the least successful, lowest-earning groups become extinct, in the sense that they no longer are able to play the game. Additional control treatments include group comparison without extinction, and extinction of the least successful individuals across groups. We find that group-level extinction produces very high contributions to the provision of the public good, while group comparison alone or individual extinction fail to cause higher contributions. Our results provide stark evidence that group-level selection enhances within-group cooperation.

| S-EPMC5004815 | biostudies-literature

Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data.

Project description:Quantification of the effect of spatial tumour sampling on the patterns of mutations detected in next-generation sequencing data is largely lacking. Here we use a spatial stochastic cellular automaton model of tumour growth that accounts for somatic mutations, selection, drift and spatial constraints, to simulate multi-region sequencing data derived from spatial sampling of a neoplasm. We show that the spatial structure of a solid cancer has a major impact on the detection of clonal selection and genetic drift from both bulk and single-cell sequencing data. Our results indicate that spatial constrains can introduce significant sampling biases when performing multi-region bulk sampling and that such bias becomes a major confounding factor for the measurement of the evolutionary dynamics of human tumours. We also propose a statistical inference framework that incorporates spatial effects within a growing tumour and so represents a further step forwards in the inference of evolutionary dynamics from genomic data. Our analysis shows that measuring cancer evolution using next-generation sequencing while accounting for the numerous confounding factors remains challenging. However, mechanistic model-based approaches have the potential to capture the sources of noise and better interpret the data.

| S-EPMC6687187 | biostudies-literature

Bacterial adaptation to public goods cheats

Project description:Adaptation to public goods cheats in Pseudomonas aeruginosa

| PRJEB17843 | ENA

Learning leads to bounded rationality and the evolution of cognitive bias in public goods games.

Project description:In social interactions, including cooperation and conflict, individuals can adjust their behaviour over the shorter term through learning within a generation, and natural selection can change behaviour over the longer term of many generations. Here we investigate the evolution of cognitive bias by individuals investing into a project that delivers joint benefits. For members of a group that learn how much to invest using the costs and benefits they experience in repeated interactions, we show that overestimation of the cost of investing can evolve. The bias causes individuals to invest less into the project. Our explanation is that learning responds to immediate rather than longer-term rewards. There are thus cognitive limitations in learning, which can be seen as bounded rationality. Over a time horizon of several rounds of interaction, individuals respond to each other's investments, for instance by partially compensating for another's shortfall. However, learning individuals fail to strategically take into account that social partners respond in this way. Learning instead converges to a one-shot Nash equilibrium of a game with perceived rewards as payoffs. Evolution of bias can then compensate for the cognitive limitations of learning.

| S-EPMC6841956 | biostudies-literature

How public can public goods be? Environmental context shapes the evolutionary ecology of partially private goods.

Project description:The production of costly public goods (as distinct from metabolic byproducts) has largely been understood through the realization that spatial structure can minimize losses to non-producing "cheaters" by allowing for the positive assortment of producers. In well-mixed systems, where positive assortment is not possible, the stable production of public goods has been proposed to depend on lineages that become indispensable as the sole producers of those goods while their neighbors lose production capacity through genome streamlining (the Black Queen Hypothesis). Here, we develop consumer-resource models motivated by nitrogen-fixing, siderophore-producing bacteria that consider the role of colimitation in shaping eco-evolutionary dynamics. Our models demonstrate that in well-mixed environments, single "public goods" can only be ecologically and evolutionarily stable if they are partially privatized (i.e., if producers reserve a portion of the product pool for private use). Colimitation introduces the possibility of subsidy: strains producing a fully public good can exclude non-producing strains so long as the producing strain derives sufficient benefit from the production of a second partially private good. We derive a lower bound for the degree of privatization necessary for production to be advantageous, which depends on external resource concentrations. Highly privatized, low-investment goods, in environments where the good is limiting, are especially likely to be stably produced. Coexistence emerges more rarely in our mechanistic model of the external environment than in past phenomenological approaches. Broadly, we show that the viability of production depends critically on the environmental context (i.e., external resource concentrations), with production of shared resources favored in environments where a partially-privatized resource is scarce.

| S-EPMC9651594 | biostudies-literature

Clonal selection confers distinct evolutionary trajectories in BRAF-driven cancers.

Project description:Molecular determinants governing the evolution of tumor subclones toward phylogenetic branches or fixation remain unknown. Using sequencing data, we model the propagation and selection of clones expressing distinct categories of BRAF mutations to estimate their evolutionary trajectories. We show that strongly activating BRAF mutations demonstrate hard sweep dynamics, whereas mutations with less pronounced activation of the BRAF signaling pathway confer soft sweeps or are subclonal. We use clonal reconstructions to estimate the strength of "driver" selection in individual tumors. Using tumors cells and human-derived murine xenografts, we show that tumor sweep dynamics can significantly affect responses to targeted inhibitors of BRAF/MEK or DNA damaging agents. Our study uncovers patterns of distinct BRAF clonal evolutionary dynamics and nominates therapeutic strategies based on the identity of the BRAF mutation and its clonal composition.

| S-EPMC6853924 | biostudies-literature

Spatial dilemmas of diffusible public goods.

Project description:The emergence of cooperation is a central question in evolutionary biology. Microorganisms often cooperate by producing a chemical resource (a public good) that benefits other cells. The sharing of public goods depends on their diffusion through space. Previous theory suggests that spatial structure can promote evolution of cooperation, but the diffusion of public goods introduces new phenomena that must be modeled explicitly. We develop an approach where colony geometry and public good diffusion are described by graphs. We find that the success of cooperation depends on a simple relation between the benefits and costs of the public good, the amount retained by a producer, and the average amount retained by each of the producer's neighbors. These quantities are derived as analytic functions of the graph topology and diffusion rate. In general, cooperation is favored for small diffusion rates, low colony dimensionality, and small rates of decay of the public good. DOI: http://dx.doi.org/10.7554/eLife.01169.001.

| S-EPMC3865686 | biostudies-literature

Spatial dynamics of ecological public goods.

Project description:The production, consumption, and exploitation of common resources ranging from extracellular products in microorganisms to global issues of climate change refer to public goods interactions. Individuals can cooperate and sustain common resources at some cost or defect and exploit the resources without contributing. This generates a conflict of interest, which characterizes social dilemmas: Individual selection favors defectors, but for the community, it is best if everybody cooperates. Traditional models of public goods do not take into account that benefits of the common resource enable cooperators to maintain higher population densities. This leads to a natural feedback between population dynamics and interaction group sizes as captured by "ecological public goods." Here, we show that the spatial evolutionary dynamics of ecological public goods in "selection-diffusion" systems promotes cooperation based on different types of pattern formation processes. In spatial settings, individuals can migrate (diffuse) to populate new territories. Slow diffusion of cooperators fosters aggregation in highly productive patches (activation), whereas fast diffusion enables defectors to readily locate and exploit these patches (inhibition). These antagonistic forces promote coexistence of cooperators and defectors in static or dynamic patterns, including spatial chaos of ever-changing configurations. The local environment of cooperators and defectors is shaped by the production or consumption of common resources. Hence, diffusion-induced self-organization into spatial patterns not only enhances cooperation but also provides simple mechanisms for the spontaneous generation of habitat diversity, which denotes a crucial determinant of the viability of ecological systems.

| S-EPMC2683138 | biostudies-literature

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