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Statistica Sinica 17(2007), 1317-1342


Niko Beerenwinkel, Lior Pachter and Bernd Sturmfels

University of California at Berkeley

Abstract: The relationship between the shape of a fitness landscape and the underlying gene interactions, or epistasis, has been extensively studied in the two-locus case. Gene interactions among multiple loci are usually reduced to two-way interactions. We present a geometric theory of shapes of fitness landscapes for multiple loci. A central concept is the genotope, which is the convex hull of all possible allele frequencies in populations. Triangulations of the genotope correspond to different shapes of fitness landscapes and reveal all the gene interactions. The theory is applied to fitness data from HIV and Drosophila melanogaster. In both cases, our findings refine earlier analyses and reveal previously undetected gene interactions.

Key words and phrases: Convex polytope, epistasis, fitness landscape, gene interaction, genotype space, human genotope, population simplex, triangulation.

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