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The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations
Using the data provided by the Drosophila Population Genomics Project, we investigate factors that affect the genetic differentiation between Rwandan and French populations of D. melanogaster. By examining within-population polymorphisms, we show that sites in long introns (especially those >2000...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4270736/ https://www.ncbi.nlm.nih.gov/pubmed/25227256 http://dx.doi.org/10.1038/hdy.2014.80 |
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author | Jackson, B C Campos, J L Zeng, K |
author_facet | Jackson, B C Campos, J L Zeng, K |
author_sort | Jackson, B C |
collection | PubMed |
description | Using the data provided by the Drosophila Population Genomics Project, we investigate factors that affect the genetic differentiation between Rwandan and French populations of D. melanogaster. By examining within-population polymorphisms, we show that sites in long introns (especially those >2000 bp) have significantly lower π (nucleotide diversity) and more low-frequency variants (as measured by Tajima's D, minor allele frequencies, and prevalence of variants that are private to one of the two populations) than short introns, suggesting a positive relationship between intron length and selective constraint. A similar analysis of protein-coding polymorphisms shows that 0-fold (degenerate) sites in more conserved genes are under stronger purifying selection than those in less conserved genes. There is limited evidence that selection on codon bias has an effect on differentiation (as measured by F(ST)) at 4-fold (degenerate) sites, and 4-fold sites and sites in 8–30 bp of short introns ⩽65 bp have comparable F(ST) values. Consistent with the expected effect of purifying selection, sites in long introns and 0-fold sites in conserved genes are less differentiated than those in short introns and less conserved genes, respectively. Genes in non-crossover regions (for example, the fourth chromosome) have very high F(ST) values at both 0-fold and 4-fold degenerate sites, which is probably because of the large reduction in within-population diversity caused by tight linkage between many selected sites. Our analyses also reveal subtle statistical properties of F(ST), which arise when information from multiple single nucleotide polymorphisms is combined and can lead to the masking of important signals of selection. |
format | Online Article Text |
id | pubmed-4270736 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-42707362015-08-01 The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations Jackson, B C Campos, J L Zeng, K Heredity (Edinb) Original Article Using the data provided by the Drosophila Population Genomics Project, we investigate factors that affect the genetic differentiation between Rwandan and French populations of D. melanogaster. By examining within-population polymorphisms, we show that sites in long introns (especially those >2000 bp) have significantly lower π (nucleotide diversity) and more low-frequency variants (as measured by Tajima's D, minor allele frequencies, and prevalence of variants that are private to one of the two populations) than short introns, suggesting a positive relationship between intron length and selective constraint. A similar analysis of protein-coding polymorphisms shows that 0-fold (degenerate) sites in more conserved genes are under stronger purifying selection than those in less conserved genes. There is limited evidence that selection on codon bias has an effect on differentiation (as measured by F(ST)) at 4-fold (degenerate) sites, and 4-fold sites and sites in 8–30 bp of short introns ⩽65 bp have comparable F(ST) values. Consistent with the expected effect of purifying selection, sites in long introns and 0-fold sites in conserved genes are less differentiated than those in short introns and less conserved genes, respectively. Genes in non-crossover regions (for example, the fourth chromosome) have very high F(ST) values at both 0-fold and 4-fold degenerate sites, which is probably because of the large reduction in within-population diversity caused by tight linkage between many selected sites. Our analyses also reveal subtle statistical properties of F(ST), which arise when information from multiple single nucleotide polymorphisms is combined and can lead to the masking of important signals of selection. Nature Publishing Group 2015-02 2014-09-17 /pmc/articles/PMC4270736/ /pubmed/25227256 http://dx.doi.org/10.1038/hdy.2014.80 Text en Copyright © 2015 The Genetics Society http://creativecommons.org/licenses/by/3.0/ This work is licensed under a Creative Commons Attribution 3.0 Unported License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ |
spellingShingle | Original Article Jackson, B C Campos, J L Zeng, K The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations |
title | The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations |
title_full | The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations |
title_fullStr | The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations |
title_full_unstemmed | The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations |
title_short | The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations |
title_sort | effects of purifying selection on patterns of genetic differentiation between drosophila melanogaster populations |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4270736/ https://www.ncbi.nlm.nih.gov/pubmed/25227256 http://dx.doi.org/10.1038/hdy.2014.80 |
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