Submit a preprint


The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variationuse asterix (*) to get italics
Gustavo V Barroso, Julien Y DutheilPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"
<p style="text-align: justify;">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 formalise a causal model of how these micro-evolutionary forces 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 <em>Drosophila melanogaster</em>, 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 robust inferences in population genomics.</p> should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https:// should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https:// should fill this box only if you chose 'Codes have been used in this study'. URL must start with http:// or https://
Sequentially Markovian Coalescent, Mutation rate variation, Linked Selection, Drosophila melanogaster
NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).
Bioinformatics & Computational Biology, Population Genetics / Genomics
No need for them to be recommenders of PCIEvolBiol. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct
e.g. John Doe []
2022-10-30 07:52:07
Fernando Racimo