Cargando…
Genomic evidence for local adaptation in the ovoviviparous marine fish Sebastiscus marmoratus with a background of population homogeneity
Advances in next-generation sequencing techniques have allowed for the generation of genome-wide sequence data, to gain insight into the dynamics influencing genetic structure and the local adaptation of marine fish. Here, using genotyping-by-sequencing (GBS) technique, we identified 31,119 single n...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2017
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5431535/ https://www.ncbi.nlm.nih.gov/pubmed/28484228 http://dx.doi.org/10.1038/s41598-017-01742-z |
_version_ | 1783236446563336192 |
---|---|
author | Xu, Shengyong Song, Na Zhao, Linlin Cai, Shanshan Han, Zhiqiang Gao, Tianxiang |
author_facet | Xu, Shengyong Song, Na Zhao, Linlin Cai, Shanshan Han, Zhiqiang Gao, Tianxiang |
author_sort | Xu, Shengyong |
collection | PubMed |
description | Advances in next-generation sequencing techniques have allowed for the generation of genome-wide sequence data, to gain insight into the dynamics influencing genetic structure and the local adaptation of marine fish. Here, using genotyping-by-sequencing (GBS) technique, we identified 31,119 single nucleotide polymorphisms (SNPs) for Sebastiscus marmoratus in 59 individuals from three populations in Chinese coastal waters. Based on all SNPs, there was little evidence of genetic differentiation among populations. However, outlier tests revealed 329 SNPs putatively under divergent selection across populations. Structural and phylogenetic topology analyses based on the outliers showed clear genetic differentiation among populations. Gene Ontology (GO) annotation results revealed that most of these outliers are known or hypothesized to be involved in metabolic process. Together with previous work using mitochondrial cytochrome b sequences, the present results further suggest that the population structure is strongly influenced by locally adaptive pressure. Overall, adaptive evolution in a heterogeneous environment plays an important role in inducing genetic differentiation among local populations. This study increases understanding of the factors (including gene flow and local adaptation) promoting and constraining population genetic differentiation in marine organisms. |
format | Online Article Text |
id | pubmed-5431535 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-54315352017-05-16 Genomic evidence for local adaptation in the ovoviviparous marine fish Sebastiscus marmoratus with a background of population homogeneity Xu, Shengyong Song, Na Zhao, Linlin Cai, Shanshan Han, Zhiqiang Gao, Tianxiang Sci Rep Article Advances in next-generation sequencing techniques have allowed for the generation of genome-wide sequence data, to gain insight into the dynamics influencing genetic structure and the local adaptation of marine fish. Here, using genotyping-by-sequencing (GBS) technique, we identified 31,119 single nucleotide polymorphisms (SNPs) for Sebastiscus marmoratus in 59 individuals from three populations in Chinese coastal waters. Based on all SNPs, there was little evidence of genetic differentiation among populations. However, outlier tests revealed 329 SNPs putatively under divergent selection across populations. Structural and phylogenetic topology analyses based on the outliers showed clear genetic differentiation among populations. Gene Ontology (GO) annotation results revealed that most of these outliers are known or hypothesized to be involved in metabolic process. Together with previous work using mitochondrial cytochrome b sequences, the present results further suggest that the population structure is strongly influenced by locally adaptive pressure. Overall, adaptive evolution in a heterogeneous environment plays an important role in inducing genetic differentiation among local populations. This study increases understanding of the factors (including gene flow and local adaptation) promoting and constraining population genetic differentiation in marine organisms. Nature Publishing Group UK 2017-05-08 /pmc/articles/PMC5431535/ /pubmed/28484228 http://dx.doi.org/10.1038/s41598-017-01742-z Text en © The Author(s) 2017 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 Xu, Shengyong Song, Na Zhao, Linlin Cai, Shanshan Han, Zhiqiang Gao, Tianxiang Genomic evidence for local adaptation in the ovoviviparous marine fish Sebastiscus marmoratus with a background of population homogeneity |
title | Genomic evidence for local adaptation in the ovoviviparous marine fish Sebastiscus marmoratus with a background of population homogeneity |
title_full | Genomic evidence for local adaptation in the ovoviviparous marine fish Sebastiscus marmoratus with a background of population homogeneity |
title_fullStr | Genomic evidence for local adaptation in the ovoviviparous marine fish Sebastiscus marmoratus with a background of population homogeneity |
title_full_unstemmed | Genomic evidence for local adaptation in the ovoviviparous marine fish Sebastiscus marmoratus with a background of population homogeneity |
title_short | Genomic evidence for local adaptation in the ovoviviparous marine fish Sebastiscus marmoratus with a background of population homogeneity |
title_sort | genomic evidence for local adaptation in the ovoviviparous marine fish sebastiscus marmoratus with a background of population homogeneity |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5431535/ https://www.ncbi.nlm.nih.gov/pubmed/28484228 http://dx.doi.org/10.1038/s41598-017-01742-z |
work_keys_str_mv | AT xushengyong genomicevidenceforlocaladaptationintheovoviviparousmarinefishsebastiscusmarmoratuswithabackgroundofpopulationhomogeneity AT songna genomicevidenceforlocaladaptationintheovoviviparousmarinefishsebastiscusmarmoratuswithabackgroundofpopulationhomogeneity AT zhaolinlin genomicevidenceforlocaladaptationintheovoviviparousmarinefishsebastiscusmarmoratuswithabackgroundofpopulationhomogeneity AT caishanshan genomicevidenceforlocaladaptationintheovoviviparousmarinefishsebastiscusmarmoratuswithabackgroundofpopulationhomogeneity AT hanzhiqiang genomicevidenceforlocaladaptationintheovoviviparousmarinefishsebastiscusmarmoratuswithabackgroundofpopulationhomogeneity AT gaotianxiang genomicevidenceforlocaladaptationintheovoviviparousmarinefishsebastiscusmarmoratuswithabackgroundofpopulationhomogeneity |