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Weak Correlation between Nucleotide Variation and Recombination Rate across the House Mouse Genome

Positive selection and purifying selection reduce levels of variation at linked neutral loci. One consequence of these processes is that the amount of neutral diversity and the meiotic recombination rate are predicted to be positively correlated across the genome—a prediction met in some species but...

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Autores principales: Kartje, Michael E, Jing, Peicheng, Payseur, Bret A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186785/
https://www.ncbi.nlm.nih.gov/pubmed/32108880
http://dx.doi.org/10.1093/gbe/evaa045
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author Kartje, Michael E
Jing, Peicheng
Payseur, Bret A
author_facet Kartje, Michael E
Jing, Peicheng
Payseur, Bret A
author_sort Kartje, Michael E
collection PubMed
description Positive selection and purifying selection reduce levels of variation at linked neutral loci. One consequence of these processes is that the amount of neutral diversity and the meiotic recombination rate are predicted to be positively correlated across the genome—a prediction met in some species but not others. To better document the prevalence of selection at linked sites, we used new and published whole-genome sequences to survey nucleotide variation in population samples of the western European house mouse (Mus musculus domesticus) from Germany, France, and Gough Island, a remote volcanic island in the south Atlantic. Correlations between sequence variation and recombination rates estimated independently from dense linkage maps were consistently very weak (ρ ≤ 0.06), though they exceeded conventional significance thresholds. This pattern persisted in comparisons between genomic regions with the highest and lowest recombination rates, as well as in models incorporating the density of transcribed sites, the density of CpG dinucleotides, and divergence between mouse and rat as covariates. We conclude that natural selection affects linked neutral variation in a restricted manner in the western European house mouse.
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spelling pubmed-71867852020-05-01 Weak Correlation between Nucleotide Variation and Recombination Rate across the House Mouse Genome Kartje, Michael E Jing, Peicheng Payseur, Bret A Genome Biol Evol Letter Positive selection and purifying selection reduce levels of variation at linked neutral loci. One consequence of these processes is that the amount of neutral diversity and the meiotic recombination rate are predicted to be positively correlated across the genome—a prediction met in some species but not others. To better document the prevalence of selection at linked sites, we used new and published whole-genome sequences to survey nucleotide variation in population samples of the western European house mouse (Mus musculus domesticus) from Germany, France, and Gough Island, a remote volcanic island in the south Atlantic. Correlations between sequence variation and recombination rates estimated independently from dense linkage maps were consistently very weak (ρ ≤ 0.06), though they exceeded conventional significance thresholds. This pattern persisted in comparisons between genomic regions with the highest and lowest recombination rates, as well as in models incorporating the density of transcribed sites, the density of CpG dinucleotides, and divergence between mouse and rat as covariates. We conclude that natural selection affects linked neutral variation in a restricted manner in the western European house mouse. Oxford University Press 2020-02-28 /pmc/articles/PMC7186785/ /pubmed/32108880 http://dx.doi.org/10.1093/gbe/evaa045 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Letter
Kartje, Michael E
Jing, Peicheng
Payseur, Bret A
Weak Correlation between Nucleotide Variation and Recombination Rate across the House Mouse Genome
title Weak Correlation between Nucleotide Variation and Recombination Rate across the House Mouse Genome
title_full Weak Correlation between Nucleotide Variation and Recombination Rate across the House Mouse Genome
title_fullStr Weak Correlation between Nucleotide Variation and Recombination Rate across the House Mouse Genome
title_full_unstemmed Weak Correlation between Nucleotide Variation and Recombination Rate across the House Mouse Genome
title_short Weak Correlation between Nucleotide Variation and Recombination Rate across the House Mouse Genome
title_sort weak correlation between nucleotide variation and recombination rate across the house mouse genome
topic Letter
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186785/
https://www.ncbi.nlm.nih.gov/pubmed/32108880
http://dx.doi.org/10.1093/gbe/evaa045
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