Section: Evolutionary Biology
Topic: Evolution, Genetics/Genomics, Population biology

The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation

10.24072/pcjournal.267 - Peer Community Journal, Volume 3 (2023), article no. e40.

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What shapes the distribution of nucleotide diversity along the genome? Attempts to answer this question have sparked debate about the roles of neutral stochastic processes and natural selection in molecular evolution. However, the mechanisms of evolution do not act in isolation, and integrative models that simultaneously consider the influence of multiple factors on diversity are lacking; without them, confounding factors lurk in the estimates. Here we present a new statistical method that jointly infers the genomic landscapes of genealogies, recombination rates and mutation rates. In doing so, our model captures the effects of genetic drift, linked selection and local mutation rates on patterns of genomic variation. We then formalize a causal model of how these micro-evolutionary mechanisms interact, and cast it as a linear regression to estimate their individual contributions to levels of diversity along the genome. Our analyses reclaim the well-established signature of linked selection in Drosophila melanogaster, but we estimate that the mutation landscape is the major driver of the genome-wide distribution of diversity in this species. Furthermore, our simulation results suggest that in many evolutionary scenarios the mutation landscape will be a crucial factor shaping diversity, depending notably on the genomic window size. We argue that incorporating mutation rate variation into the null model of molecular evolution will lead to more realistic inferences in population genomics.

Published online:
DOI: 10.24072/pcjournal.267
Type: Research article
Keywords: Mutation rate variation, Linked selection, Sequentially Markovian coalescent, Drosophila melanogaster
Barroso, Gustavo V 1, 2; Dutheil, Julien Y 1, 3

1 Max Planck Institute for Evolutionary Biology. Department of Evolutionary Genetics. August-Thienemann-Straße 2 24306 Plön – Germany
2 University of Wisconsin, Madison. Department of Integrative Biology. 447 Birge Hall – Madison, WI – USA
3 Unité Mixte de Recherche 5554 Institut des Sciences de l’Evolution, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
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     title = {The landscape of nucleotide diversity in {\protect\emph{Drosophila} melanogaster} is shaped by mutation rate variation},
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Barroso, Gustavo V; Dutheil, Julien Y. The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation. Peer Community Journal, Volume 3 (2023), article  no. e40. doi : 10.24072/pcjournal.267.

Peer reviewed and recommended by PCI : 10.24072/pci.evolbiol.100636

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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