The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation
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 mode...
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2023-04-01
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| Online Access: | https://peercommunityjournal.org/articles/10.24072/pcjournal.267/ |
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| author | Barroso, Gustavo V Dutheil, Julien Y |
| author_facet | Barroso, Gustavo V Dutheil, Julien Y |
| author_sort | Barroso, Gustavo V |
| collection | DOAJ |
| description | 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.
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| format | Article |
| id | doaj-art-cf9922e4971f459ebaa104d82805ef11 |
| institution | Kabale University |
| issn | 2804-3871 |
| language | English |
| publishDate | 2023-04-01 |
| publisher | Peer Community In |
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| series | Peer Community Journal |
| spelling | doaj-art-cf9922e4971f459ebaa104d82805ef112025-02-07T10:16:49ZengPeer Community InPeer Community Journal2804-38712023-04-01310.24072/pcjournal.26710.24072/pcjournal.267The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation Barroso, Gustavo V0https://orcid.org/0000-0002-1943-9297Dutheil, Julien Y1https://orcid.org/0000-0001-7753-4121Max Planck Institute for Evolutionary Biology. Department of Evolutionary Genetics. August-Thienemann-Straße 2 24306 Plön – Germany; University of Wisconsin, Madison. Department of Integrative Biology. 447 Birge Hall – Madison, WI – USAMax Planck Institute for Evolutionary Biology. Department of Evolutionary Genetics. August-Thienemann-Straße 2 24306 Plön – Germany; Unité Mixte de Recherche 5554 Institut des Sciences de l’Evolution, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, FranceWhat 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. https://peercommunityjournal.org/articles/10.24072/pcjournal.267/ |
| spellingShingle | Barroso, Gustavo V Dutheil, Julien Y The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation Peer Community Journal |
| title | The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation
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| title_full | The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation
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| title_fullStr | The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation
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| title_full_unstemmed | The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation
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| title_short | The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation
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| title_sort | landscape of nucleotide diversity in drosophila melanogaster is shaped by mutation rate variation |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.267/ |
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