Conditional cooperation with longer memory.

Direct reciprocity is a wide-spread mechanism for the evolution of cooperation. In repeated interactions, players can condition their behavior on previous outcomes. A well-known approach is given by reactive strategies, which respond to the coplayer's previous move.

Fixation times on directed graphs.

Computing the rate of evolution in spatially structured populations is difficult. A key quantity is the fixation time of a single mutant with relative reproduction rate r which invades a population of residents. We say that the fixation time is "fast" if it is at most a polynomial function in terms of the population size N.

The mutagenic forces shaping the genomic landscape of lung cancer in never smokers.

Lung cancer in never smokers (LCINS) accounts for up to 25% of all lung cancers and has been associated with exposure to secondhand tobacco smoke and air pollution in observational studies. Here, we evaluate the mutagenic exposures in LCINS by examining deep whole-genome sequencing data from a large international cohort of 871 treatment-naïve LCINS recruited from 28 geographical locations within the Sherlock- study. mutations were 3.

The evolutionary safety of mutagenic drugs should be assessed before drug approval.

Some drugs increase the mutation rate of their target pathogen, a potentially concerning mechanism as the pathogen might evolve faster toward an undesired phenotype. We suggest a four-step assessment of evolutionary safety for the approval of such treatments.

A geometric process of evolutionary game dynamics.

Many evolutionary processes occur in phenotype spaces which are continuous. It is therefore of interest to explore how selection operates in continuous spaces. One approach is adaptive dynamics, which assumes that mutants are local.

Evolutionary dynamics of mutants that modify population structure.

Natural selection is usually studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we explore how natural selection acts on mutants that have the same reproductive rate, but different population structures. In our framework, population structure is given by a graph that specifies where offspring can disperse.

Gene drives for the extinction of wild metapopulations.

Population-suppressing gene drives may be capable of extinguishing wild populations, with proposed applications in conservation, agriculture, and public health. However, unintended and potentially disastrous consequences of release of drive-engineered individuals are extremely difficult to predict. We propose a model for the dynamics of a sex ratio-biasing drive, and using simulations, we show that failure of the suppression drive is often a natural outcome due to stochastic and spatial effects.

Correction: A spatial vaccination strategy to reduce the risk of vaccine-resistant variants.

[This corrects the article DOI: 10.1371/journal.pcbi.

Vacancies in growing habitats promote the evolution of cooperation.

We study evolutionary game dynamics in a growing habitat with vacancies. Fitness is determined by the global effect of the environment and a local prisoner's dilemma among neighbors. We study population growth on a one-dimensional lattice and analyze how the environment affects evolutionary competition.

Trust based attachment.

In social systems subject to indirect reciprocity, a positive reputation is key for increasing one's likelihood of future positive interactions [1-13]. The flow of gossip can amplify the impact of a person's actions on their reputation depending on how widely it spreads across the social network, which leads to a percolation problem [14]. To quantify this notion, we calculate the expected number of individuals, the "audience", who find out about a particular interaction.

Evolutionary safety of lethal mutagenesis driven by antiviral treatment.

Nucleoside analogs are a major class of antiviral drugs. Some act by increasing the viral mutation rate causing lethal mutagenesis of the virus. Their mutagenic capacity, however, may lead to an evolutionary safety concern.

The effect of environmental information on evolution of cooperation in stochastic games.

Many human interactions feature the characteristics of social dilemmas where individual actions have consequences for the group and the environment. The feedback between behavior and environment can be studied with the framework of stochastic games. In stochastic games, the state of the environment can change, depending on the choices made by group members.

Adaptive dynamics of memory-one strategies in the repeated donation game.

Human interactions can take the form of social dilemmas: collectively, people fare best if all cooperate but each individual is tempted to free ride. Social dilemmas can be resolved when individuals interact repeatedly. Repetition allows them to adopt reciprocal strategies which incentivize cooperation.

Mutation enhances cooperation in direct reciprocity.

Direct reciprocity is a powerful mechanism for the evolution of cooperation based on repeated interactions between the same individuals. But high levels of cooperation evolve only if the benefit-to-cost ratio exceeds a certain threshold that depends on memory length. For the best-explored case of one-round memory, that threshold is two.

Recombination and selection against introgressed DNA.

Introgressed DNA is often deleterious at many loci in the recipient species' genome, and is therefore purged by selection. Here, we use mathematical modeling and whole-genome simulations to study the influence of recombination on this process. We find that aggregate recombination controls the genome-wide rate of purging in the early generations after admixture, when purging is most rapid.

A spatial vaccination strategy to reduce the risk of vaccine-resistant variants.

The COVID-19 pandemic demonstrated that the process of global vaccination against a novel virus can be a prolonged one. Social distancing measures, that are initially adopted to control the pandemic, are gradually relaxed as vaccination progresses and population immunity increases. The result is a prolonged period of high disease prevalence combined with a fitness advantage for vaccine-resistant variants, which together lead to a considerably increased probability for vaccine escape.

Direct reciprocity between individuals that use different strategy spaces.

In repeated interactions, players can use strategies that respond to the outcome of previous rounds. Much of the existing literature on direct reciprocity assumes that all competing individuals use the same strategy space. Here, we study both learning and evolutionary dynamics of players that differ in the strategy space they explore.

Evolution of resistance to COVID-19 vaccination with dynamic social distancing.

The greatest hope for a return to normalcy following the COVID-19 pandemic is worldwide vaccination. Yet, a relaxation of social distancing that allows increased transmissibility, coupled with selection pressure due to vaccination, will probably lead to the emergence of vaccine resistance. We analyse the evolutionary dynamics of COVID-19 in the presence of dynamic contact reduction and in response to vaccination.

Cooperation in alternating interactions with memory constraints.

In repeated social interactions, individuals often employ reciprocal strategies to maintain cooperation. To explore the emergence of reciprocity, many theoretical models assume synchronized decision making. In each round, individuals decide simultaneously whether to cooperate or not.

Infection dynamics of COVID-19 virus under lockdown and reopening.

Motivated by COVID-19, we develop and analyze a simple stochastic model for the spread of disease in human population. We track how the number of infected and critically ill people develops over time in order to estimate the demand that is imposed on the hospital system. To keep this demand under control, we consider a class of simple policies for slowing down and reopening society and we compare their efficiency in mitigating the spread of the virus from several different points of view.

Fast and strong amplifiers of natural selection.

Selection and random drift determine the probability that novel mutations fixate in a population. Population structure is known to affect the dynamics of the evolutionary process. Amplifiers of selection are population structures that increase the fixation probability of beneficial mutants compared to well-mixed populations.

The Great Oxygenation Event as a consequence of ecological dynamics modulated by planetary change.

The Great Oxygenation Event (GOE), ca. 2.4 billion years ago, transformed life and environments on Earth.

A unified framework of direct and indirect reciprocity.

Direct and indirect reciprocity are key mechanisms for the evolution of cooperation. Direct reciprocity means that individuals use their own experience to decide whether to cooperate with another person. Indirect reciprocity means that they also consider the experiences of others.

Increased stem cell proliferation in atherosclerosis accelerates clonal hematopoiesis.

Clonal hematopoiesis, a condition in which individual hematopoietic stem cell clones generate a disproportionate fraction of blood leukocytes, correlates with higher risk for cardiovascular disease. The mechanisms behind this association are incompletely understood. Here, we show that hematopoietic stem cell division rates are increased in mice and humans with atherosclerosis.