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Mutation accumulation (MA) experiments, in which de novo mutations are sampled and subsequently characterized, are an essential tool in understanding the processes underlying evolution. In microbial populations, MA protocols typically involve a period of population growth between severe bottlenecks, such that a single individual can form a visible colony. While it has long been appreciated that the action of positive selection during this growth phase cannot be eliminated, it is typically assumed to be negligible. Here, we quantify the effect of both positive and negative selection in MA studies, demonstrating that selective effects can substantially bias the distribution of fitness effects (DFE) and mutation rates estimated from typical MA protocols in microbes. We then present a simple correction for this bias that applies to both beneficial and deleterious mutations, and can be used to correct the observed DFE in multiple environments. We use simulated MA experiments to illustrate the extent to which the MA‐inferred DFE differs from the underlying true DFE, and demonstrate that the proposed correction accurately reconstructs the true DFE over a wide range of scenarios; we also provide an example of these corrections applied to experimental data. These results highlight that positive selection during microbial MA experiments is in fact not negligible, but can be corrected to gain a more accurate understanding of fundamental evolutionary parameters. [ABSTRACT FROM AUTHOR]

Lytic viruses infect and kill host cells, producing a large number of viral copies. Temperate viruses, in contrast, are able to integrate viral genetic material into the host cell DNA, leaving a viable host cell. The evolutionary advantage of this strategy, lysogeny, has been demonstrated in complex environments that include spatial structure, oscillating population dynamics, or periodic environmental collapse. Here, we examine the evolutionary stability of the lysis–lysogeny decision, that is, we predict the long‐term outcome of the evolution of lysogeny rates. We demonstrate that viruses with high rates of lysogeny are stable against invasion by more virulent viral strains even in simple environments, as long as the pool of susceptible hosts is not unlimited. This mirrors well‐known results in both r‐K selection theory and virulence evolution: although virulent viruses have a faster potential growth rate, temperate strains are able to maintain positive growth on a lower density of the limiting resource, susceptible hosts. We then outline scenarios in which the rate of lysogeny is predicted to evolve either toward full lysogeny or full lysis. Finally, we demonstrate conditions under which intermediate rates of lysogeny, as observed in temperate viruses in nature, can be sustained long‐term. In general, intermediate lysogeny rates persist when the coupling between susceptible host density and virus density is relaxed. [ABSTRACT FROM AUTHOR]

Sequencing of bacterial genomes has revealed an abundance of prophage sequences in many bacterial species. Since these sequences are accessible, through recombination, to infecting phages, bacteria carry an arsenal of genetic material that can be used by these viruses. We develop a mathematical model to isolate the effects of this phenomenon on the coevolution of temperate phage and bacteria. The model predicts that prophage sequences may play a key role in maintaining the phage population in situations that would otherwise favor host cell resistance. In addition, prophage recombination facilitates the existence of multiple phage types, thus promoting diverse co-existence in the phage-host ecosystem. Finally, because the host carries an archive of previous phage strategies, prophage recombination can drive waves of innovation in the host cell population. [ABSTRACT FROM AUTHOR]

The rate at which a population adapts to its environment is a cornerstone of evolutionary theory, and recent experimental advances in microbial populations have renewed interest in predicting and testing this rate. Efforts to understand the adaptation rate theoretically are complicated by high mutation rates, to both beneficial and deleterious mutations, and by the fact that beneficial mutations compete with each other in asexual populations (clonal interference). Testable predictions must also include the effects of population bottlenecks, repeated reductions in population size imposed by the experimental protocol. In this contribution, we integrate previous work that addresses each of these issues, developing an overall prediction for the adaptation rate that includes: beneficial mutations with probabilistically distributed effects, deleterious mutations of arbitrary effect, population bottlenecks, and clonal interference. [ABSTRACT FROM AUTHOR]

We use a branching process approach to estimate the substitution rate, the rate at which beneficial mutations occur and fix, in populations of lytic viruses whose growth is controlled by periodic population bottlenecks. Our model predicts that substitution rates, and by extension adaptation rates, are profoundly affected by the survival of infected host cells at the bottleneck. In particular, we find that direct transfer (or environmental) bottlenecks, in which some fraction of both free virus and host cells are preserved, are associated with relatively slow adaptation rates for the virus. In contrast, viruses can adapt much more quickly when only free virus is transferred to a new host population, as is typical in an epidemiological setting. Finally, when premature lysis of the host-cell population is induced at the bottleneck, we predict that adaptation rates for the virus will, in general, be faster still. These results hold irrespective of the life-history trait affected by the beneficial mutation. The substitution rates in the presence of environmental bottlenecks are predicted to be as much as an order of magnitude lower than in the other two cases. [ABSTRACT FROM AUTHOR]

Sperm competition is a major force of sexual selection, but its implications for mating system and life-history evolution are just beginning to be understood. Of particular importance is understanding the mechanisms of sperm competition. Models have been developed to determine if sperm competition operates in a fair raffle process, whereby each sperm from competing males has an equal chance of fertilizing a female's ova, or if it operates in a loaded raffle process, whereby one male's sperm has a fertilization advantage. These models require data on relative sperm and offspring (paternity) numbers of competing males. Here we develop a model based on maximum-likelihood methods for differentiating between the fair and loaded raffle processes. The model calculates the relative competitiveness of two males' sperm (loadings) as well as the economy of scale (nonlinear returns to sperm number). Previous models implicitly assumed that there is no economy of scale, which may not be the case when there is cooperation or interference among sperm from a given male. We demonstrate that our model has superior power--in some instances more than double--than previous models. We apply our model to an example of sperm competition in the guppy (Poecilia reticulata) and show that the system may be characterized by a loaded raffle attributable to effects of second male precedence. [ABSTRACT FROM AUTHOR]

Presents a study that derived the ultimate probability of extinction for a beneficial mutation in a periodically bottlenecked population, using both discrete and continuous approaches. Effects of population bottlenecks on the dynamics of evolution; Information on the approximate expression for an effective population size; Implications for the quantitative analysis of experimental evolution.