Visualizing fitness landscapes

McCandlish, D. M. (June 2011) Visualizing fitness landscapes. Evolution, 65 (6). pp. 1544-58. ISSN 1558-5646 (Electronic)0014-3820 (Linking)

URL: https://www.ncbi.nlm.nih.gov/pubmed/21644947
DOI: 10.1111/j.1558-5646.2011.01236.x

Abstract

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.

Item Type: Paper
Uncontrolled Keywords: Codon/genetics Evolution, Molecular *Genetic Fitness Genetics, Population/*methods Genotype Models, Genetic Phenotype Protein Structure, Secondary RNA/chemistry/genetics *Selection, Genetic Serine/genetics
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification
evolution
CSHL Authors:
Communities: CSHL labs > McCandlish lab
Depositing User: Matt Covey
Date: June 2011
Date Deposited: 18 Jan 2017 20:38
Last Modified: 18 Jan 2017 20:38
PMCID: PMC3668694
Related URLs:
URI: http://repository.cshl.edu/id/eprint/34044

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