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Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations
Signatures of spatially varying selection have been investigated both at the genomic and transcriptomic level in several organisms. In Drosophila melanogaster, the majority of these studies have analyzed North American and Australian populations, leading to the identification of several loci and tra...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6212444/ https://www.ncbi.nlm.nih.gov/pubmed/30385770 http://dx.doi.org/10.1038/s41598-018-34267-0 |
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author | Mateo, Lidia Rech, Gabriel E. González, Josefa |
author_facet | Mateo, Lidia Rech, Gabriel E. González, Josefa |
author_sort | Mateo, Lidia |
collection | PubMed |
description | Signatures of spatially varying selection have been investigated both at the genomic and transcriptomic level in several organisms. In Drosophila melanogaster, the majority of these studies have analyzed North American and Australian populations, leading to the identification of several loci and traits under selection. However, several studies based mainly in North American populations showed evidence of admixture that likely contributed to the observed population differentiation patterns. Thus, disentangling demography from selection might be challenging when analyzing these populations. European populations could help identify loci under spatially varying selection provided that no recent admixture from African populations would have occurred. In this work, we individually sequence the genome of 42 European strains collected in populations from contrasting environments: Stockholm (Sweden) and Castellana Grotte (Southern Italy). We found low levels of population structure and no evidence of recent African admixture in these two populations. We thus look for patterns of spatially varying selection affecting individual genes and gene sets. Besides single nucleotide polymorphisms, we also investigated the role of transposable elements in local adaptation. We concluded that European populations are a good dataset to identify candidate loci under spatially varying selection. The analysis of the two populations sequenced in this work in the context of all the available D. melanogaster data allowed us to pinpoint genes and biological processes likely to be relevant for local adaptation. Identifying and analyzing populations with low levels of population structure and admixture should help to disentangle selective from non-selective forces underlying patterns of population differentiation in other species as well. |
format | Online Article Text |
id | pubmed-6212444 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-62124442018-11-06 Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations Mateo, Lidia Rech, Gabriel E. González, Josefa Sci Rep Article Signatures of spatially varying selection have been investigated both at the genomic and transcriptomic level in several organisms. In Drosophila melanogaster, the majority of these studies have analyzed North American and Australian populations, leading to the identification of several loci and traits under selection. However, several studies based mainly in North American populations showed evidence of admixture that likely contributed to the observed population differentiation patterns. Thus, disentangling demography from selection might be challenging when analyzing these populations. European populations could help identify loci under spatially varying selection provided that no recent admixture from African populations would have occurred. In this work, we individually sequence the genome of 42 European strains collected in populations from contrasting environments: Stockholm (Sweden) and Castellana Grotte (Southern Italy). We found low levels of population structure and no evidence of recent African admixture in these two populations. We thus look for patterns of spatially varying selection affecting individual genes and gene sets. Besides single nucleotide polymorphisms, we also investigated the role of transposable elements in local adaptation. We concluded that European populations are a good dataset to identify candidate loci under spatially varying selection. The analysis of the two populations sequenced in this work in the context of all the available D. melanogaster data allowed us to pinpoint genes and biological processes likely to be relevant for local adaptation. Identifying and analyzing populations with low levels of population structure and admixture should help to disentangle selective from non-selective forces underlying patterns of population differentiation in other species as well. Nature Publishing Group UK 2018-11-01 /pmc/articles/PMC6212444/ /pubmed/30385770 http://dx.doi.org/10.1038/s41598-018-34267-0 Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Mateo, Lidia Rech, Gabriel E. González, Josefa Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations |
title | Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations |
title_full | Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations |
title_fullStr | Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations |
title_full_unstemmed | Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations |
title_short | Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations |
title_sort | genome-wide patterns of local adaptation in western european drosophila melanogaster natural populations |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6212444/ https://www.ncbi.nlm.nih.gov/pubmed/30385770 http://dx.doi.org/10.1038/s41598-018-34267-0 |
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