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Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations
Mutations provide the raw material of evolution, and thus our ability to study evolution depends fundamentally on having precise measurements of mutational rates and patterns. We generate a data set for this purpose using (1) de novo mutations from mutation accumulation experiments and (2) extremely...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5741049/ https://www.ncbi.nlm.nih.gov/pubmed/29079675 http://dx.doi.org/10.1101/gr.219956.116 |
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author | Assaf, Zoe June Tilk, Susanne Park, Jane Siegal, Mark L. Petrov, Dmitri A. |
author_facet | Assaf, Zoe June Tilk, Susanne Park, Jane Siegal, Mark L. Petrov, Dmitri A. |
author_sort | Assaf, Zoe June |
collection | PubMed |
description | Mutations provide the raw material of evolution, and thus our ability to study evolution depends fundamentally on having precise measurements of mutational rates and patterns. We generate a data set for this purpose using (1) de novo mutations from mutation accumulation experiments and (2) extremely rare polymorphisms from natural populations. The first, mutation accumulation (MA) lines are the product of maintaining flies in tiny populations for many generations, therefore rendering natural selection ineffective and allowing new mutations to accrue in the genome. The second, rare genetic variation from natural populations allows the study of mutation because extremely rare polymorphisms are relatively unaffected by the filter of natural selection. We use both methods in Drosophila melanogaster, first generating our own novel data set of sequenced MA lines and performing a meta-analysis of all published MA mutations (∼2000 events) and then identifying a high quality set of ∼70,000 extremely rare (≤0.1%) polymorphisms that are fully validated with resequencing. We use these data sets to precisely measure mutational rates and patterns. Highlights of our results include: a high rate of multinucleotide mutation events at both short (∼5 bp) and long (∼1 kb) genomic distances, showing that mutation drives GC content lower in already GC-poor regions, and using our precise context-dependent mutation rates to predict long-term evolutionary patterns at synonymous sites. We also show that de novo mutations from independent MA experiments display similar patterns of single nucleotide mutation and well match the patterns of mutation found in natural populations. |
format | Online Article Text |
id | pubmed-5741049 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-57410492018-06-01 Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations Assaf, Zoe June Tilk, Susanne Park, Jane Siegal, Mark L. Petrov, Dmitri A. Genome Res Research Mutations provide the raw material of evolution, and thus our ability to study evolution depends fundamentally on having precise measurements of mutational rates and patterns. We generate a data set for this purpose using (1) de novo mutations from mutation accumulation experiments and (2) extremely rare polymorphisms from natural populations. The first, mutation accumulation (MA) lines are the product of maintaining flies in tiny populations for many generations, therefore rendering natural selection ineffective and allowing new mutations to accrue in the genome. The second, rare genetic variation from natural populations allows the study of mutation because extremely rare polymorphisms are relatively unaffected by the filter of natural selection. We use both methods in Drosophila melanogaster, first generating our own novel data set of sequenced MA lines and performing a meta-analysis of all published MA mutations (∼2000 events) and then identifying a high quality set of ∼70,000 extremely rare (≤0.1%) polymorphisms that are fully validated with resequencing. We use these data sets to precisely measure mutational rates and patterns. Highlights of our results include: a high rate of multinucleotide mutation events at both short (∼5 bp) and long (∼1 kb) genomic distances, showing that mutation drives GC content lower in already GC-poor regions, and using our precise context-dependent mutation rates to predict long-term evolutionary patterns at synonymous sites. We also show that de novo mutations from independent MA experiments display similar patterns of single nucleotide mutation and well match the patterns of mutation found in natural populations. Cold Spring Harbor Laboratory Press 2017-12 /pmc/articles/PMC5741049/ /pubmed/29079675 http://dx.doi.org/10.1101/gr.219956.116 Text en © 2017 Assaf et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. |
spellingShingle | Research Assaf, Zoe June Tilk, Susanne Park, Jane Siegal, Mark L. Petrov, Dmitri A. Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations |
title | Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations |
title_full | Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations |
title_fullStr | Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations |
title_full_unstemmed | Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations |
title_short | Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations |
title_sort | deep sequencing of natural and experimental populations of drosophila melanogaster reveals biases in the spectrum of new mutations |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5741049/ https://www.ncbi.nlm.nih.gov/pubmed/29079675 http://dx.doi.org/10.1101/gr.219956.116 |
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