McCandlish, D. M. (June 2011) Visualizing fitness landscapes. Evolution, 65 (6). pp. 1544-58. ISSN 1558-5646 (Electronic)0014-3820 (Linking)
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: | https://repository.cshl.edu/id/eprint/34044 |
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