SELVa: Simulator of evolution with landscape variation

Abstract

Organisms evolve to increase their fitness, a process that may be described as climbing the fitness landscape. However, the fitness landscape of an individual site, i.e., the vector of fitness values corresponding to different variants at this site, can itself change with time due to changes in the environment or substitutions at other epistatically interacting sites. While there exist a number of simulators for modeling different aspects of molecular evolution, very few can accommodate changing landscapes. We present SELVa, the Simulator of Evolution with Landscape Variation, aimed at modeling the substitution process under a changing single-position fitness landscape in a set of evolving lineages that form a phylogeny of arbitrary shape. Written in Java and distributed as an executable jar file, SELVa provides a flexible framework that allows the user to choose from a number of implemented rules governing landscape change.