Cargando…
Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences
Disentangling the effect on genomic diversity of natural selection from that of demography is notoriously difficult, but necessary to properly reconstruct the history of species. Here, we use high-quality human genomic data to show that purifying selection at linked sites (i.e. background selection,...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
eLife Sciences Publications, Ltd
2018
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177262/ https://www.ncbi.nlm.nih.gov/pubmed/30125248 http://dx.doi.org/10.7554/eLife.36317 |
_version_ | 1783361839390785536 |
---|---|
author | Pouyet, Fanny Aeschbacher, Simon Thiéry, Alexandre Excoffier, Laurent |
author_facet | Pouyet, Fanny Aeschbacher, Simon Thiéry, Alexandre Excoffier, Laurent |
author_sort | Pouyet, Fanny |
collection | PubMed |
description | Disentangling the effect on genomic diversity of natural selection from that of demography is notoriously difficult, but necessary to properly reconstruct the history of species. Here, we use high-quality human genomic data to show that purifying selection at linked sites (i.e. background selection, BGS) and GC-biased gene conversion (gBGC) together affect as much as 95% of the variants of our genome. We find that the magnitude and relative importance of BGS and gBGC are largely determined by variation in recombination rate and base composition. Importantly, synonymous sites and non-transcribed regions are also affected, albeit to different degrees. Their use for demographic inference can lead to strong biases. However, by conditioning on genomic regions with recombination rates above 1.5 cM/Mb and mutation types (C↔G, A↔T), we identify a set of SNPs that is mostly unaffected by BGS or gBGC, and that avoids these biases in the reconstruction of human history. |
format | Online Article Text |
id | pubmed-6177262 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-61772622018-10-17 Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences Pouyet, Fanny Aeschbacher, Simon Thiéry, Alexandre Excoffier, Laurent eLife Genetics and Genomics Disentangling the effect on genomic diversity of natural selection from that of demography is notoriously difficult, but necessary to properly reconstruct the history of species. Here, we use high-quality human genomic data to show that purifying selection at linked sites (i.e. background selection, BGS) and GC-biased gene conversion (gBGC) together affect as much as 95% of the variants of our genome. We find that the magnitude and relative importance of BGS and gBGC are largely determined by variation in recombination rate and base composition. Importantly, synonymous sites and non-transcribed regions are also affected, albeit to different degrees. Their use for demographic inference can lead to strong biases. However, by conditioning on genomic regions with recombination rates above 1.5 cM/Mb and mutation types (C↔G, A↔T), we identify a set of SNPs that is mostly unaffected by BGS or gBGC, and that avoids these biases in the reconstruction of human history. eLife Sciences Publications, Ltd 2018-08-23 /pmc/articles/PMC6177262/ /pubmed/30125248 http://dx.doi.org/10.7554/eLife.36317 Text en © 2018, Pouyet et al http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited. |
spellingShingle | Genetics and Genomics Pouyet, Fanny Aeschbacher, Simon Thiéry, Alexandre Excoffier, Laurent Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences |
title | Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences |
title_full | Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences |
title_fullStr | Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences |
title_full_unstemmed | Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences |
title_short | Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences |
title_sort | background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences |
topic | Genetics and Genomics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177262/ https://www.ncbi.nlm.nih.gov/pubmed/30125248 http://dx.doi.org/10.7554/eLife.36317 |
work_keys_str_mv | AT pouyetfanny backgroundselectionandbiasedgeneconversionaffectmorethan95ofthehumangenomeandbiasdemographicinferences AT aeschbachersimon backgroundselectionandbiasedgeneconversionaffectmorethan95ofthehumangenomeandbiasdemographicinferences AT thieryalexandre backgroundselectionandbiasedgeneconversionaffectmorethan95ofthehumangenomeandbiasdemographicinferences AT excoffierlaurent backgroundselectionandbiasedgeneconversionaffectmorethan95ofthehumangenomeandbiasdemographicinferences |