Skolkovo Institute of Science and Technology, Moscow, Russia.
Kharkevich Institute of Information Transmission Problems, Moscow, Russia.
PLoS One. 2020 Dec 2;15(12):e0242225. doi: 10.1371/journal.pone.0242225. eCollection 2020.
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.
生物进化是为了提高适应性，这个过程可以被描述为在适应度景观上攀登。然而，由于环境变化或其他上位相互作用位点的替换，个体位点的适应度景观（即对应于该位点不同变体的适应度值向量）本身可能随时间而改变。虽然有许多模拟器可以用于模拟分子进化的不同方面，但很少有能够适应变化的景观。我们提出了 SELVa，即具有景观变化的进化模拟器，旨在对在一组形成任意形状系统发育的进化谱系中的单一位置适应度景观的变化下的替代过程进行建模。SELVa 用 Java 编写并以可执行的 jar 文件形式分发，它提供了一个灵活的框架，允许用户从许多实现的规则中选择，这些规则用于控制景观的变化。
