The Influence of Higher-Order Epistasis on Biological Fitness Landscape Topography

The effect of a mutation on the organism often depends on what other mutations are already present in its genome. Geneticists refer to such mutational interactions as epistasis. Pairwise epistatic effects have been recognized for over a century, and their evolutionary implications have received theoretical attention for nearly as long. However, pairwise epistatic interactions themselves can vary with genomic background. This is called higher-order epistasis, and its consequences for evolution are much less well understood. Here, we assess the influence that higher-order epistasis has on the topography of 16 published, biological fitness landscapes. We find that on average, their effects on fitness landscape declines with order, and suggest that notable exceptions to this trend may deserve experimental scrutiny. We conclude by highlighting opportunities for further theoretical and experimental work dissecting the influence that epistasis of all orders has on fitness landscape topography and on the efficiency of evolution by natural selection.

[1]  J.A.G.M. de Visser,et al.  Deleterious mutations and the evolution of sex , 1996 .

[2]  L. Darrell Whitley,et al.  Predicting Epistasis from Mathematical Models , 1999, Evolutionary Computation.

[3]  Frank J. Poelwijk,et al.  Evolutionary Potential of a Duplicated Repressor-Operator Pair: Simulating Pathways Using Mutation Data , 2006, PLoS Comput. Biol..

[4]  B. Charlesworth,et al.  Why sex and recombination? , 1998, Science.

[5]  R. Punnett,et al.  The Genetical Theory of Natural Selection , 1930, Nature.

[6]  David M. McCandlish,et al.  VISUALIZING FITNESS LANDSCAPES , 2011, Evolution; international journal of organic evolution.

[7]  E. D. Weinberger,et al.  Fourier and Taylor series on fitness landscapes , 1991, Biological Cybernetics.

[8]  R. Lenski,et al.  Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population , 2011, Science.

[9]  Frank J. Poelwijk,et al.  The Context-Dependence of Mutations: A Linkage of Formalisms , 2015, PLoS Comput. Biol..

[10]  P. Stadler Landscapes and their correlation functions , 1996 .

[11]  Nigel F. Delaney,et al.  Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins , 2006, Science.

[12]  S. Wright,et al.  Evolution in Mendelian Populations. , 1931, Genetics.

[13]  S. Holm A Simple Sequentially Rejective Multiple Test Procedure , 1979 .

[14]  Kate B. Cook,et al.  Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity , 2014, Cell.

[15]  J. Krug,et al.  Exploring the Effect of Sex on Empirical Fitness Landscapes , 2009, The American Naturalist.

[16]  Daniel E. Newburger,et al.  Diversity and Complexity in DNA Recognition by Transcription Factors , 2009, Science.

[17]  P. Stadler Spectral Landscape Theory , 1999 .

[18]  A. Dean,et al.  Mechanistic approaches to the study of evolution: the functional synthesis , 2007, Nature Reviews Genetics.

[19]  Michael Baym,et al.  Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes , 2015, Nature Communications.

[20]  L. Avery,et al.  Ordering gene function: the interpretation of epistasis in regulatory hierarchies. , 1992, Trends in genetics : TIG.

[21]  E. D. Weinberger,et al.  The NK model of rugged fitness landscapes and its application to maturation of the immune response. , 1989, Journal of theoretical biology.

[22]  L. Pachter,et al.  EPISTASIS AND SHAPES OF FITNESS LANDSCAPES , 2006, q-bio/0603034.

[23]  A. Kondrashov Deleterious mutations and the evolution of sexual reproduction , 1988, Nature.

[24]  M. Whitlock,et al.  FACTORS AFFECTING THE GENETIC LOAD IN DROSOPHILA: SYNERGISTIC EPISTASIS AND CORRELATIONS AMONG FITNESS COMPONENTS , 2000, Evolution; international journal of organic evolution.

[25]  Richard A. Watson,et al.  PERSPECTIVE:SIGN EPISTASIS AND GENETIC CONSTRAINT ON EVOLUTIONARY TRAJECTORIES , 2005 .

[26]  M. Feldman,et al.  On the evolutionary effect of recombination. , 1970, Theoretical population biology.

[27]  Joshua D. Knowles,et al.  Analysis of a complete DNA–protein affinity landscape , 2010, Journal of The Royal Society Interface.

[28]  Alden H. Wright,et al.  Efficient Linkage Discovery by Limited Probing , 2003, Evolutionary Computation.

[29]  P. Phillips The language of gene interaction. , 1998, Genetics.

[30]  Michael J Harms,et al.  Detecting High-Order Epistasis in Nonlinear Genotype-Phenotype Maps , 2016, Genetics.

[31]  Niko Beerenwinkel,et al.  Inferring Genetic Interactions From Comparative Fitness Data , 2017 .

[32]  D. Weinreich,et al.  Quantitative Description of a Protein Fitness Landscape Based on Molecular Features. , 2015, Molecular biology and evolution.

[33]  Timothy B Sackton,et al.  Genotypic Context and Epistasis in Individuals and Populations , 2016, Cell.

[34]  Organic and GM—Why Not? , 2008, Science.

[35]  J. Gore,et al.  Hidden randomness between fitness landscapes limits reverse evolution. , 2011, Physical review letters.

[36]  M. Kendall A NEW MEASURE OF RANK CORRELATION , 1938 .

[37]  Robert B. Heckendorn,et al.  Should evolutionary geneticists worry about higher-order , 2013 .

[38]  D. Weinreich,et al.  RAPID EVOLUTIONARY ESCAPE BY LARGE POPULATIONS FROM LOCAL FITNESS PEAKS IS LIKELY IN NATURE , 2005, Evolution; international journal of organic evolution.

[39]  M. Nowak,et al.  Stochastic Tunnels in Evolutionary Dynamics , 2004, Genetics.

[40]  Tim F. Cooper,et al.  The Environment Affects Epistatic Interactions to Alter the Topology of an Empirical Fitness Landscape , 2013, PLoS genetics.

[41]  J. W. Thornton,et al.  Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites , 2015, eLife.

[42]  Tyler N. Starr,et al.  Epistasis in protein evolution , 2016, Protein science : a publication of the Protein Society.

[43]  J. Meza,et al.  Adaptive Landscapes of Resistance Genes Change as Antibiotic Concentrations Change. , 2015, Molecular biology and evolution.

[44]  J. Krug,et al.  Quantitative analyses of empirical fitness landscapes , 2012, 1202.4378.

[45]  Sayan Mukherjee,et al.  Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits , 2016, bioRxiv.

[46]  Michael J. Harms,et al.  High-order epistasis shapes evolutionary trajectories , 2017, PLoS Comput. Biol..

[47]  M. Wade,et al.  Epistasis and the Evolutionary Process , 2000 .

[48]  J. Noel,et al.  Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases , 2008, Nature chemical biology.

[49]  N. Barton,et al.  Why sex and recombination? , 2009, Cold Spring Harbor symposia on quantitative biology.

[50]  David W Hall,et al.  Fitness epistasis among 6 biosynthetic loci in the budding yeast Saccharomyces cerevisiae. , 2010, The Journal of heredity.

[51]  Thanat Chookajorn,et al.  Stepwise acquisition of pyrimethamine resistance in the malaria parasite , 2009, Proceedings of the National Academy of Sciences.

[52]  P. Phillips Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems , 2008, Nature Reviews Genetics.

[53]  D. J. Kiviet,et al.  Empirical fitness landscapes reveal accessible evolutionary paths , 2007, Nature.

[54]  D. Hartl,et al.  Fitness Trade-Offs in the Evolution of Dihydrofolate Reductase and Drug Resistance in Plasmodium falciparum , 2011, PloS one.

[55]  P. Stadler,et al.  Random field models for fitness landscapes , 1999 .

[56]  Elena R. Lozovsky,et al.  Compensatory mutations restore fitness during the evolution of dihydrofolate reductase. , 2010, Molecular biology and evolution.

[57]  D. Mosier,et al.  Fitness Epistasis and Constraints on Adaptation in a Human Immunodeficiency Virus Type 1 Protein Region , 2010, Genetics.

[58]  W. Provine Sewall Wright and evolutionary biology , 1987 .

[59]  J. Krug,et al.  Empirical fitness landscapes and the predictability of evolution , 2014, Nature Reviews Genetics.

[60]  J. Krug,et al.  Exact results for amplitude spectra of fitness landscapes. , 2013, Journal of theoretical biology.

[61]  Ronald M. Nelson,et al.  Higher order interactions: detection of epistasis using machine learning and evolutionary computation. , 2013, Methods in molecular biology.

[62]  E. Ortlund,et al.  An epistatic ratchet constrains the direction of glucocorticoid receptor evolution , 2009, Nature.

[63]  Elena R. Lozovsky,et al.  Accessible Mutational Trajectories for the Evolution of Pyrimethamine Resistance in the Malaria Parasite Plasmodium vivax , 2013, Journal of Molecular Evolution.

[64]  Robert B. Heckendorn,et al.  Should evolutionary geneticists worry about higher-order epistasis? , 2013, Current opinion in genetics & development.

[65]  J. Jensen,et al.  On the (un-)predictability of a large intragenic fitness landscape , 2016, bioRxiv.

[66]  R. Greenberg Biometry , 1969, The Yale Journal of Biology and Medicine.

[67]  Nigel F. Delaney,et al.  Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation , 2011, Science.

[68]  Kyung-Ah Sohn,et al.  Fast detection of high-order epistatic interactions in genome-wide association studies using information theoretic measure , 2014, Comput. Biol. Chem..

[69]  Brian W. Matthews,et al.  Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing , 1990, Nature.

[70]  B. Shraiman,et al.  Competition between recombination and epistasis can cause a transition from allele to genotype selection , 2009, Proceedings of the National Academy of Sciences.

[71]  H. A. Orr,et al.  Fitness and its role in evolutionary genetics , 2009, Nature Reviews Genetics.

[72]  Yuanying Chen,et al.  Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary , 2023, bioRxiv.

[73]  Stephen P. Miller,et al.  The Biochemical Architecture of an Ancient Adaptive Landscape , 2005, Science.

[74]  Jennifer L. Knies,et al.  Enzyme Efficiency but Not Thermostability Drives Cefotaxime Resistance Evolution in TEM-1 β-Lactamase , 2017, Molecular biology and evolution.

[75]  John Maynard Smith,et al.  Natural Selection and the Concept of a Protein Space , 1970, Nature.