Measuring epistasis in fitness landscapes: The correlation of fitness effects of mutations

被引：49

作者：

Ferretti, Luca ^{[1
,2
,3
,4
]}

Schmiegelt, Benjamin ^{[5
]}

Weinreich, Daniel ^{[6
]}

Yamauchi, Atsushi ^{[7
]}

Kobayashi, Yutaka ^{[8
]}

Tajima, Fumio ^{[9
]}

Achaz, Guillaume ^{[1
,2
,3
]}

机构：

[1] UPMC, Evolut Paris Seine UMR 7138, Paris, France

[2] UPMC, Atelier Bioinformat, Paris, France

[3] Coll France, SMILE, CIRB UMR 7241, F-75231 Paris, France

[4] Pirbright Inst, Woking, Surrey, England

[5] Univ Cologne, Inst Theoret Phys, Cologne, Germany

[6] Brown Univ, Ecol & Evolutionary Biol, Providence, RI 02912 USA

[7] Kyoto Univ, Ctr Ecol Res, Kyoto 6068501, Japan

[8] Kochi Univ Technol, Kami, Kochi, Japan

[9] Univ Tokyo, Dept Biol Sci, Tokyo 1138654, Japan

来源：

JOURNAL OF THEORETICAL BIOLOGY | 2016年 / 396卷

基金：

英国生物技术与生命科学研究理事会;

关键词：

Epistasis; Fitness; Mutations; Ruggedness; ACCESSIBLE PATHS; MODEL; EVOLUTION;

D O I：

10.1016/j.jtbi.2016.01.037

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Genotypic fitness landscapes are constructed by assessing the fitness of all possible combinations of a given number of mutations. In the last years, several experimental fitness landscapes have been completely resolved. As fitness landscapes are high-dimensional, simple measures of their structure are used as statistics in empirical applications. Epistasis is one of the most relevant features of fitness landscapes. Here we propose a new natural measure of the amount of epistasis based on the correlation of fitness effects of mutations. This measure has a natural interpretation, captures well the interaction between mutations and can be obtained analytically for most landscape models. We discuss how this measure is related to previous measures of epistasis (number of peaks, roughness/slope, fraction of sign epistasis, Fourier Walsh spectrum) and how it can be easily extended to landscapes with missing data or with fitness ranks only. Furthermore, the dependence of the correlation of fitness effects on mutational distance contains interesting information about the patterns of epistasis. This dependence can be used to uncover the amount and nature of epistatic interactions in a landscape or to discriminate between different landscape models. (C) 2016 Elsevier Ltd. All rights reserved.

引用

页码：132 / 143

页数：12

共 42 条

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