Population structure, demographic history and local adaptation of the grass carp
Background: Genetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation...
Saved in:
Main Authors: | , , , , , |
---|---|
Other Authors: | |
Format: | Article |
Language: | English |
Published: |
2019
|
Subjects: | |
Online Access: | https://hdl.handle.net/10356/87609 http://hdl.handle.net/10220/49290 |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Institution: | Nanyang Technological University |
Language: | English |
id |
sg-ntu-dr.10356-87609 |
---|---|
record_format |
dspace |
spelling |
sg-ntu-dr.10356-876092023-02-28T17:02:09Z Population structure, demographic history and local adaptation of the grass carp Shen, Yubang Wang, Le Fu, Jianjun Xu, Xiaoyan Yue, Gen Hua Li, Jiale School of Biological Sciences Science::Biological sciences Grass Carp Diversity Background: Genetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the most important freshwater foodfish species for food and water weed control. However, there is as yet no overall picture on genetic variations and population structure of this species, which is important for its aquaculture. Results: We used 43,310 SNPs to infer the population structure, evidence of local adaptation and sources of introduction. The overall genetic differentiation of this species was low. The native populations were differentiated into three genetic clusters, corresponding to the Yangtze, Pearl and Heilongjiang River Systems, respectively. The populations in Malaysia, India and Nepal were introduced from both the Yangtze and Pearl River Systems. Loci and genes involved in putative local selection for native locations were identified. Evidence of both positive and balancing selection was found in the introduced locations. Genes associated with loci under putative selection were involved in many biological functions. Outlier loci were grouped into clusters as genomic islands within some specific genomic regions, which likely agrees with the divergence hitchhiking scenario of divergence-with-gene-flow. Conclusions: This study, for the first time, sheds novel insights on the population differentiation of the grass carp, genetics of its strong ability in adaption to diverse environments and sources of some introduced grass carp populations. Our data also suggests that the natural populations of the grass carp have been affected by the aquaculture besides neutral and adaptive forces. Published version 2019-07-11T06:25:17Z 2019-12-06T16:45:34Z 2019-07-11T06:25:17Z 2019-12-06T16:45:34Z 2019 Journal Article Shen, Y., Wang, L., Fu, J., Xu, X., Yue, G. H., & Li, J. (2019). Population structure, demographic history and local adaptation of the grass carp. BMC Genomics, 20(1), 467-. doi:10.1186/s12864-019-5872-1 https://hdl.handle.net/10356/87609 http://hdl.handle.net/10220/49290 10.1186/s12864-019-5872-1 en BMC Genomics © 2019 The Author(s). This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. 16 p. application/pdf |
institution |
Nanyang Technological University |
building |
NTU Library |
continent |
Asia |
country |
Singapore Singapore |
content_provider |
NTU Library |
collection |
DR-NTU |
language |
English |
topic |
Science::Biological sciences Grass Carp Diversity |
spellingShingle |
Science::Biological sciences Grass Carp Diversity Shen, Yubang Wang, Le Fu, Jianjun Xu, Xiaoyan Yue, Gen Hua Li, Jiale Population structure, demographic history and local adaptation of the grass carp |
description |
Background: Genetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the most important freshwater foodfish species for food and water weed control. However, there is as yet no overall picture on genetic variations and population structure of this species, which is important for its aquaculture. Results: We used 43,310 SNPs to infer the population structure, evidence of local adaptation and sources of introduction. The overall genetic differentiation of this species was low. The native populations were differentiated into three genetic clusters, corresponding to the Yangtze, Pearl and Heilongjiang River Systems, respectively. The populations in Malaysia, India and Nepal were introduced from both the Yangtze and Pearl River Systems. Loci and genes involved in putative local selection for native locations were identified. Evidence of both positive and balancing selection was found in the introduced locations. Genes associated with loci under putative selection were involved in many biological functions. Outlier loci were grouped into clusters as genomic islands within some specific genomic regions, which likely agrees with the divergence hitchhiking scenario of divergence-with-gene-flow. Conclusions: This study, for the first time, sheds novel insights on the population differentiation of the grass carp, genetics of its strong ability in adaption to diverse environments and sources of some introduced grass carp populations. Our data also suggests that the natural populations of the grass carp have been affected by the aquaculture besides neutral and adaptive forces. |
author2 |
School of Biological Sciences |
author_facet |
School of Biological Sciences Shen, Yubang Wang, Le Fu, Jianjun Xu, Xiaoyan Yue, Gen Hua Li, Jiale |
format |
Article |
author |
Shen, Yubang Wang, Le Fu, Jianjun Xu, Xiaoyan Yue, Gen Hua Li, Jiale |
author_sort |
Shen, Yubang |
title |
Population structure, demographic history and local adaptation of the grass carp |
title_short |
Population structure, demographic history and local adaptation of the grass carp |
title_full |
Population structure, demographic history and local adaptation of the grass carp |
title_fullStr |
Population structure, demographic history and local adaptation of the grass carp |
title_full_unstemmed |
Population structure, demographic history and local adaptation of the grass carp |
title_sort |
population structure, demographic history and local adaptation of the grass carp |
publishDate |
2019 |
url |
https://hdl.handle.net/10356/87609 http://hdl.handle.net/10220/49290 |
_version_ |
1759853044836597760 |