A central goal of the field of artificial life is to build evolving systems that capture interesting dynamics of natural systems, producing evolutionary outcomes such as sophisticated navigation behaviors, novel cooperative strategies, complex ecosystems, or major evolutionary transitions, to name but a few. Such “open-ended” systems are sought after for a number of reasons: 1) For artificial l...

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We describe the evolution of E.coli populations through a Bak-Sneppen type model which incorporates random mutations. We show that, for a value of the mutation level which coincides with the one estimated from experiments, this model reproduces the measures of mean fitness relative to that of a common ancestor, performed for over 10,000 bacterial generations. The last decade has seen a renewed ...

Background: Experimental populations of Escherichia coli have evolved for 20,000 generations in a uniform environment. Their rate of improvement, as measured in competitions with the ancestor in that environment, has declined substantially over this period. This deceleration has been interpreted as the bacteria approaching a peak or plateau in a fitness landscape. Alternatively, this decelerati...

A genetic strategy was designed to examine the occurrence of mutations in stationary-phase populations. In this strategy, a parental population of cells is able to survive under both permissive and restrictive conditions whereas mutants at a particular target locus exhibit a conditional-lethal phenotype. Thus, by growing the population to stationary phase under restrictive conditions and then s...

Experimental evolution of bacteriophage provides a powerful means of studying the genetics of adaptation, as every substitution contributing to adaptation can be identified and characterized. Here, I use experimental evolution of MS2, an RNA bacteriophage, to study its adaptive response to a novel environment. To this end, three lines of MS2 were adapted to rapid growth and lysis at cold temper...

Experimental evolution of bacteriophage provides a powerful means of studying the genetics of adaptation, as every substitution contributing to adaptation can be identified and characterized. Here, I use experimental evolution of MS2, an RNA bacteriophage, to study its adaptive response to a novel environment. To this end, three lines of MS2 were adapted to rapid growth and lysis at cold temper...

Experimental evolution of bacteriophage provides a powerful means of studying the genetics of adaptation, as every substitution contributing to adaptation can be identified and characterized. Here, I use experimental evolution of MS2, an RNA bacteriophage, to study its adaptive response to a novel environment. To this end, three lines of MS2 were adapted to rapid growth and lysis at cold temper...

Pleiotropy and epistasis are central to understanding how genes are expressed. Kauffman’s NK model is used ubiquitously to investigate gene expression in evolution and other contexts; it is widely understood to reflect the results of epistasis, but it is less often used to study pleiotropy. In this paper we introduce the NEP model, a variant of the NK model which allows epistasis and pleiotropy...

Ever since Darwin, understanding evolutionary processes and patterns have been major scientific quests. In the Origin of Species, Darwin explained both adaptation and diversity, and most of his arguments were based on indirect evidence, including comparative approaches. These findings led Darwin to defend that evolution in nature is extremely slow and gradual, hardly being directly observable a...