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Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker

The large yellow croaker (Larimichthys crocea) is one of the most economically valuable marine fish in China and is a notable species in ecological studies owing to a serious collapse of wild germplasm in the past few decades. The stock division and species distribution, which have important implica...

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Autores principales: Chen, Baohua, Bai, Yulin, Wang, Jiaying, Ke, Qiaozhen, Zhou, Zhixiong, Zhou, Tao, Pan, Ying, Wu, Renxie, Wu, Xiongfei, Zheng, Weiqiang, Xu, Peng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Nature Singapore 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10232709/
https://www.ncbi.nlm.nih.gov/pubmed/37275538
http://dx.doi.org/10.1007/s42995-023-00165-2
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author Chen, Baohua
Bai, Yulin
Wang, Jiaying
Ke, Qiaozhen
Zhou, Zhixiong
Zhou, Tao
Pan, Ying
Wu, Renxie
Wu, Xiongfei
Zheng, Weiqiang
Xu, Peng
author_facet Chen, Baohua
Bai, Yulin
Wang, Jiaying
Ke, Qiaozhen
Zhou, Zhixiong
Zhou, Tao
Pan, Ying
Wu, Renxie
Wu, Xiongfei
Zheng, Weiqiang
Xu, Peng
author_sort Chen, Baohua
collection PubMed
description The large yellow croaker (Larimichthys crocea) is one of the most economically valuable marine fish in China and is a notable species in ecological studies owing to a serious collapse of wild germplasm in the past few decades. The stock division and species distribution, which have important implications for ecological protection, germplasm recovery, and fishery resource management, have been debated since the 1960s. However, it is still uncertain even how many stocks exist in this species. To address this, we evaluated the fine-scale genetic structure of large yellow croaker populations distributed along the eastern and southern Chinese coastline based on 7.64 million SNP markers. Compared with the widely accepted stock boundaries proposed in the 1960s, our results revealed that a climate-driven habitat change probably occurred between the Naozhou (Nanhai) Stock and the Ming-Yuedong (Mindong) Stock. The boundary between these two stocks might have shifted northwards from the Pearl River Estuary to the northern area of the Taiwan Strait, accompanied by highly asymmetric introgression. In addition, we found divergent landscapes of natural selection between the stocks inhabiting northern and southern areas. The northern population exhibited highly agminated signatures of strong natural selection in genes related to developmental processes, whereas moderate and interspersed selective signatures were detected in many immune-related genes in the southern populations. These findings establish the stock status and genome-wide evolutionary landscapes of large yellow croaker, providing a basis for conservation, fisheries management and further evolutionary biology studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-023-00165-2.
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spelling pubmed-102327092023-06-02 Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker Chen, Baohua Bai, Yulin Wang, Jiaying Ke, Qiaozhen Zhou, Zhixiong Zhou, Tao Pan, Ying Wu, Renxie Wu, Xiongfei Zheng, Weiqiang Xu, Peng Mar Life Sci Technol Research Paper The large yellow croaker (Larimichthys crocea) is one of the most economically valuable marine fish in China and is a notable species in ecological studies owing to a serious collapse of wild germplasm in the past few decades. The stock division and species distribution, which have important implications for ecological protection, germplasm recovery, and fishery resource management, have been debated since the 1960s. However, it is still uncertain even how many stocks exist in this species. To address this, we evaluated the fine-scale genetic structure of large yellow croaker populations distributed along the eastern and southern Chinese coastline based on 7.64 million SNP markers. Compared with the widely accepted stock boundaries proposed in the 1960s, our results revealed that a climate-driven habitat change probably occurred between the Naozhou (Nanhai) Stock and the Ming-Yuedong (Mindong) Stock. The boundary between these two stocks might have shifted northwards from the Pearl River Estuary to the northern area of the Taiwan Strait, accompanied by highly asymmetric introgression. In addition, we found divergent landscapes of natural selection between the stocks inhabiting northern and southern areas. The northern population exhibited highly agminated signatures of strong natural selection in genes related to developmental processes, whereas moderate and interspersed selective signatures were detected in many immune-related genes in the southern populations. These findings establish the stock status and genome-wide evolutionary landscapes of large yellow croaker, providing a basis for conservation, fisheries management and further evolutionary biology studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-023-00165-2. Springer Nature Singapore 2023-04-07 /pmc/articles/PMC10232709/ /pubmed/37275538 http://dx.doi.org/10.1007/s42995-023-00165-2 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Research Paper
Chen, Baohua
Bai, Yulin
Wang, Jiaying
Ke, Qiaozhen
Zhou, Zhixiong
Zhou, Tao
Pan, Ying
Wu, Renxie
Wu, Xiongfei
Zheng, Weiqiang
Xu, Peng
Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker
title Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker
title_full Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker
title_fullStr Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker
title_full_unstemmed Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker
title_short Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker
title_sort population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10232709/
https://www.ncbi.nlm.nih.gov/pubmed/37275538
http://dx.doi.org/10.1007/s42995-023-00165-2
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