Chromosomal inversions in the Atlantic cod genome: implications for management of Canada’s Northern cod stock

Following stock collapse and over twenty years of moratoria, the state of Canada’s Northern Atlantic cod (Gadus morhua) remains precarious. To test if recent stock growth was of endogenous or exogenous origin, we performed a whole genome scan (ddRAD) on 135 adults captured in 2015 at three offshore spawning locations spanning the range of the offshore stock along the northeastern Newfoundland and Labrador shelf (Hawke Channel, Notre Dame Channel and Bonavista Corridor), with an additional 105 adults from three more southern locations (St. Anns Bank, Browns Bank and Bay of Fundy). Population structure analysis using 5,077 single nucleotide polymorphisms (SNPs) detected a distinct genetic break off the coast of Nova Scotia near 45 °N. Gene flow between groups north and south of this divide appears to be limited despite the presence of several northern-type and admixed individuals present in the southern area. North of the genetic divide, allele frequencies of neutral loci were indicative ...在种群崩溃与长达二十余年的禁渔期之后，加拿大大西洋北部鳕鱼（Gadus morhua）的种群现状仍岌岌可危。为验证近期种群增长是内源性还是外源性所致，我们对2015年捕获的135尾成年个体开展了全基因组扫描（ddRAD），样本采集自纽芬兰与拉布拉多东北陆架海域离岸种群分布范围内的3个离岸产卵位点（霍克海峡、圣母海峡与博纳维斯塔走廊），另采集了来自南部3个位点的105尾成年个体（圣安斯银行、布朗斯银行与芬迪湾）。基于5077个单核苷酸多态性（single nucleotide polymorphisms, SNPs）的种群结构分析显示，在北纬45°附近的新斯科舍省近海海域存在显著的遗传分界。尽管南部海域存在若干北方型个体与混合血统个体，但该分界南北两侧种群间的基因交流似乎十分有限。在遗传分界以北区域，中性位点的等位基因频率呈现出……