O'Donnell Timothy P, Sullivan Timothy J
Gloucester Marine Genomics Institute Gloucester MA USA.
USDA - National Institute of Food and Agriculture Kansas City MO USA.
Ecol Evol. 2021 Jul 14;11(15):10659-10671. doi: 10.1002/ece3.7878. eCollection 2021 Aug.
Atlantic cod (, Linnaeus 1758) in the western Gulf of Maine are managed as a single stock despite several lines of evidence supporting two spawning groups (spring and winter) that overlap spatially, while exhibiting seasonal spawning isolation. Low-coverage whole-genome sequencing was used to evaluate the genomic population structure of Atlantic cod spawning groups in the western Gulf of Maine and Georges Bank using 222 individuals collected over multiple years. Results indicated low total genomic differentiation, while also showing strong differentiation between spring and winter-spawning groups at specific regions of the genome. Guided regularized random forest and ranked methods were used to select panels of single nucleotide polymorphisms (SNPs) that could reliably distinguish spring and winter-spawning Atlantic cod (88.5% assignment rate), as well as males and females (95.0% assignment rate) collected in the western Gulf of Maine. These SNP panels represent a valuable tool for fisheries research and management of Atlantic cod in the western Gulf of Maine that will aid investigations of stock production and support accuracy of future assessments.
尽管有几条证据支持缅因湾西部存在两个在空间上重叠但具有季节性产卵隔离的产卵群体（春季和冬季），但缅因湾西部的大西洋鳕鱼（Gadus morhua，林奈，1758年）仍作为一个单一种群进行管理。利用多年收集的222个个体，通过低覆盖度全基因组测序来评估缅因湾西部和乔治斯浅滩大西洋鳕鱼产卵群体的基因组种群结构。结果表明，总体基因组分化程度较低，但在基因组的特定区域，春季和冬季产卵群体之间也表现出强烈的分化。使用引导正则化随机森林和排序方法来选择单核苷酸多态性（SNP）面板，这些面板能够可靠地区分缅因湾西部收集的春季和冬季产卵的大西洋鳕鱼（分配率88.5%），以及雄性和雌性（分配率95.0%）。这些SNP面板是缅因湾西部大西洋鳕鱼渔业研究和管理的宝贵工具，将有助于种群产量调查并支持未来评估的准确性。
