RAD genotyping reveals fine-scale population structure and provides evidence for adaptive divergence in a commercially important fish from the northwestern Pacific Ocean

doi:10.7717/peerj.7242

	RAD genotyping reveals fine-scale population structure and provides evidence for adaptive divergence in a commercially important fish from the northwestern Pacific Ocean
	Zhang, Bai-Dong; Xue, Dong-Xiu; Li, Yu-Long; Liu, Jin-Xian 1
	2019-07-03
Source Publication	PEERJ
ISSN	2167-8359
Volume	7 Pages:23
Corresponding Author	Liu, Jin-Xian(jinxianliu@gmail.com)
Abstract	Exploring factors shaping genetic structure of marine fish is challenging due to fewer barriers to gene flow in the ocean. However, genome-wide sequence data can greatly enhance our ability to delineate previously unidentified population structure as well as potential adaptive divergence. The small yellow croaker (Larimichthys polyactis) is a commercially important fish species with high gene flow and its overwintering populations experience heterogeneous environment, suggesting possible population differentiation and adaptive divergence. To delineate patterns of population structure as well as test for signatures of local adaptation, a total of 68,666 quality filtered SNP markers were identified for 80 individuals from four overwintering populations by using restriction site-associated DNA sequencing (RAD-seq). Significant genetic differentiation among overwintering populations from the Central Yellow Sea, the South Yellow Sea and the North East China Sea were detected (Pair-wise F-ST: 0.00036-0.00390), which were consistent with population division of overwintering groups inferred from traditional ecological approaches. In addition, a total of 126 unique SNPs were detected to be significantly associated with environmental parameters (temperature, salinity and turbidity). These candidate SNPs were involved in multiple pathways such as energy metabolism and phagocytosis, suggesting they may play key roles in growth and innate immunity. Our results suggested the existence of hitherto unrecognized cryptic population structure and local adaptation in this high gene flow marine fish and thus gain new insights into the design of management strategies.
Keyword	Population genomics Single-nucleotide polymorphisms RAD-seq Local adaptation Larimichthys polyactis
DOI	10.7717/peerj.7242
Indexed By	SCI
Language	英语
Funding Project	National Natural Science Foundation of China-Shandong Joint Fund for Marine Ecology and Environmental Sciences[U1606404] ; National Natural Science Foundation of China[41706162] ; AoShan Talents Program ; Qingdao National Laboratory of Marine Science and Technology[2015ASTP-ES05] ; China Postdoctoral Science Foundation[2018M632734]
WOS Research Area	Science & Technology - Other Topics
WOS Subject	Multidisciplinary Sciences
WOS ID	WOS:000473602400004
Publisher	PEERJ INC
Citation statistics
Document Type	期刊论文
Identifier	http://ir.qdio.ac.cn/handle/337002/161957
Collection	海洋生态与环境科学重点实验室
Corresponding Author	Liu, Jin-Xian
Affiliation	1.Chinese Acad Sci, Inst Oceanol, CAS Key Lab Marine Ecol & Environm Sci, Qingdao, Shandong, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Ecol & Environm Sci, Qingdao, Shandong, Peoples R China 3.Chinese Acad Sci, Ctr Ocean Mega Sci, Qingdao, Shandong, Peoples R China
Corresponding Author Affilication	Institute of Oceanology, Chinese Academy of Sciences
Recommended Citation GB/T 7714	Zhang, Bai-Dong,Xue, Dong-Xiu,Li, Yu-Long,et al. RAD genotyping reveals fine-scale population structure and provides evidence for adaptive divergence in a commercially important fish from the northwestern Pacific Ocean[J]. PEERJ,2019,7:23.
APA	Zhang, Bai-Dong,Xue, Dong-Xiu,Li, Yu-Long,&Liu, Jin-Xian.(2019).RAD genotyping reveals fine-scale population structure and provides evidence for adaptive divergence in a commercially important fish from the northwestern Pacific Ocean.PEERJ,7,23.
MLA	Zhang, Bai-Dong,et al."RAD genotyping reveals fine-scale population structure and provides evidence for adaptive divergence in a commercially important fish from the northwestern Pacific Ocean".PEERJ 7(2019):23.

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