Year: 2022
Type: article
Abstract: Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences 1 . Here we test this assumption with large surveys of de novo mutations in the plant Arabidopsis thaliana . In contrast to expectations, we find that mutations occur less often in functionally constrained regions of the genome—mutation frequency is reduced by half inside gene bodies and by two-thirds in essential genes. With independent genomic mutation datasets, including from the largest Arabidopsis mutation accumulation experiment conducted to date, we demonstrate that epigenomic and physical features explain over 90% of variance in the genome-wide pattern of mutation bias surrounding genes. Observed mutation frequencies around genes in turn accurately predict patterns of genetic polymorphisms in natural Arabidopsis accessions ( r = 0.96). That mutation bias is the primary force behind patterns of sequence evolution around genes in natural accessions is supported by analyses of allele frequencies. Finally, we find that genes subject to stronger purifying selection have a lower mutation rate. We conclude that epigenome-associated mutation bias 2 reduces the occurrence of deleterious mutations in Arabidopsis , challenging the prevailing paradigm that mutation is a directionless force in evolution.
Source: Nature
Authors: J. Grey Monroe, Thanvi Srikant, Pablo Carbonell-Bejerano, Claude Becker, Mariele Lensink, Moises Exposito-Alonso, Marie Klein, Julia Hildebrandt, Manuela Neumann, Daniel Kliebenstein, Mao-Lun Weng, Eric Imbert, Jon Ågren, Matthew T. Rutter, Charles B. Fenster, Detlef Weigel
Institutions: Max Planck Institute for Biology, University of California, Davis, Ludwig-Maximilians-Universität München, Carnegie Institution for Science, Carnegie Department of Plant Biology, Stanford University, Westfield State University, Université de Montpellier, Institut des Sciences de l'Evolution de Montpellier, Uppsala University, College of Charleston, South Dakota State University
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $11,390
Awards: Predicting and controlling polygenic health traits using probabilistic models and evolution-inspired gene editing, Collaborative: RUI: The natural history of mutations: sequence and fitness data from Arabidopsis thaliana mutation accumulation lines, G4006054706, G6185079379, G6967887928, G8129865752, Collaborative: RUI: The natural history of mutations: sequence and fitness data from Arabidopsis thaliana mutation accumulation lines, Arabidopsis 2010 Collaborative Research: RUI: Quantifying mutation parameters in a fitness landscape: Spontaneous mutation in A. thaliana in its native range., G9000254618, Arabidopsis 2010 Collaborative Research: Quantifying mutation parameters in a fitness landscape: Spontaneous mutation in A. thaliana in its native range.
OpenAlex ID: W4205790736