Genomic evidence of population genetic differentiation in deep-sea squat lobster Shinkaia crosnieri (crustacea: Decapoda: Anomura) from Northwestern Pacific hydrothermal vent and cold seep

doi:10.1016/j.dsr.2019.103188

CORC > 海洋研究所 > 中国科学院海洋研究所

	Genomic evidence of population genetic differentiation in deep-sea squat lobster Shinkaia crosnieri (crustacea: Decapoda: Anomura) from Northwestern Pacific hydrothermal vent and cold seep
	Cheng, Jiao 1,3; Hui, Min 1,3; Li, Yulong 1,3; Sha, Zhongli 1,2,3
刊名	DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS
	2020-02-01
卷号	156 页码:12
关键词	Chemosynthetic fauna Population connectivity Local adaptation Single nucleotide polymorphism Cytochrome c oxidase subunit I
ISSN号	0967-0637
DOI	10.1016/j.dsr.2019.103188
通讯作者	Sha, Zhongli(shazl@qdio.ac.cn)
英文摘要	The galatheid squat lobster, Shinkaia crosnieri Baba and Williams, 1998, is one of the few dominant species inhabiting both deep-sea hydrothermal vents and cold seeps. Here, we used mitochondrial cytochrome c oxidase subunit I (mtDNA COI) and nuclear genome-wide single nucleotide polymorphism (SNP) as genetic markers to investigate genetic connectivity of S. crosnieri populations from a hydrothermal vent of Okinawa Through and a cold seep of the South China Sea. MtDNA COI sequence analyses indicated that deep-sea vent population of S. crosnieri was genetically divergent from cold seep population. To obtain deep insights into the evolutionary forces driving this genetic break, we performed restriction-site associated DNA analysis to evaluate the extent of genetic differentiation in S. crosnieri inhabiting both environments on a genome-wide scale, and to assess the role of selective processes in shaping this pattern. Using the assembled survey genome of S. crosnieri as a reference, 12,963 SNPs were identified for 30 S. crosnieri specimens. The structural and principle component analyses based on SNPs supported genetic differentiation between the vent and seep populations. Evidence for local adaptation of S. crosnieri populations was confirmed by identifying increased population divergence using F-sT-based outlier tests, which resulted in 54 potentially locally selected SNPs, indicative of an important role for natural selection as a driver of genetic divergence in this species. Further studies revealed that candidate genes containing outlier SNPs were involved in diverse biological processes, including immunity, transposon and metabolic processes. Overall, our results demonstrated significant genetic divergence between the vent and seep S. crosnieri populations in the Northwestern Pacific and provided clues to understand potential genetic basis underlying local adaptation in S. crosnieri during colonization into deep-sea chemosynthetic ecosystems.
资助项目	National Key R&D Program of China[2018YFC0310702] ; National Key R&D Program of China[2018YFC0310802] ; National Natural Science Foundation of China[31872215] ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDA22050302] ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDA22050303] ; Senior User Project of RV KEXUE[KEXUE2018G21]
WOS研究方向	Oceanography
语种	英语
出版者	PERGAMON-ELSEVIER SCIENCE LTD
WOS记录号	WOS:000514247800009
内容类型	期刊论文
源URL	[http://ir.qdio.ac.cn/handle/337002/165544]
专题	中国科学院海洋研究所
通讯作者	Sha, Zhongli
作者单位	1.Chinese Acad Sci, Ctr Ocean Megasci, Qingdao 266071, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao 266237, Peoples R China 3.Chinese Acad Sci, Inst Oceanol, 7 Nanhai Rd, Qingdao 266071, Peoples R China
推荐引用方式 GB/T 7714	Cheng, Jiao,Hui, Min,Li, Yulong,et al. Genomic evidence of population genetic differentiation in deep-sea squat lobster Shinkaia crosnieri (crustacea: Decapoda: Anomura) from Northwestern Pacific hydrothermal vent and cold seep[J]. DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS,2020,156:12.
APA	Cheng, Jiao,Hui, Min,Li, Yulong,&Sha, Zhongli.(2020).Genomic evidence of population genetic differentiation in deep-sea squat lobster Shinkaia crosnieri (crustacea: Decapoda: Anomura) from Northwestern Pacific hydrothermal vent and cold seep.DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS,156,12.
MLA	Cheng, Jiao,et al."Genomic evidence of population genetic differentiation in deep-sea squat lobster Shinkaia crosnieri (crustacea: Decapoda: Anomura) from Northwestern Pacific hydrothermal vent and cold seep".DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS 156(2020):12.