Department of Biology, Duke University, Box 90338 Durham, North Carolina 27708, USA.
Evolution. 2011 Jun;65(6):1544-58. doi: 10.1111/j.1558-5646.2011.01236.x. Epub 2011 Mar 1.
Fitness landscapes are a classical concept for thinking about the relationship between genotype and fitness. However, because the space of genotypes is typically high-dimensional, the structure of fitness landscapes can be difficult to understand and the heuristic approach of thinking about fitness landscapes as low-dimensional, continuous surfaces may be misleading. Here, I present a rigorous method for creating low-dimensional representations of fitness landscapes. The basic idea is to plot the genotypes in a manner that reflects the ease or difficulty of evolving from one genotype to another. Such a layout can be constructed using the eigenvectors of the transition matrix describing the evolution of a population on the fitness landscape when mutation is weak. In addition, the eigendecomposition of this transition matrix provides a new, high-level view of evolution on a fitness landscape. I demonstrate these techniques by visualizing the fitness landscape for selection for the amino acid serine and by visualizing a neutral network derived from the RNA secondary structure genotype-phenotype map.
适应景观是思考基因型与适应度之间关系的一个经典概念。然而,由于基因型的空间通常是高维的,适应景观的结构可能难以理解,并且将适应景观视为低维、连续表面的启发式方法可能具有误导性。在这里,我提出了一种创建适应景观低维表示的严格方法。基本思想是以反映从一种基因型进化到另一种基因型的容易程度的方式来绘制基因型。这种布局可以使用描述当突变较弱时种群在适应景观上进化的转移矩阵的特征向量来构建。此外,该转移矩阵的特征分解提供了适应景观上进化的新的高级视图。我通过可视化选择丝氨酸的适应景观以及通过可视化源自 RNA 二级结构基因型-表型图的中性网络来演示这些技术。