Clucas Gemma V, Lou R Nicolas, Therkildsen Nina O, Kovach Adrienne I
Natural Resources and the Environment University of New Hampshire Durham NH USA.
Department of Natural Resources Cornell University Ithaca NY USA.
Evol Appl. 2019 Sep 13;12(10):1971-1987. doi: 10.1111/eva.12861. eCollection 2019 Dec.
Selection can create complex patterns of adaptive differentiation among populations in the wild that may be relevant to management. Atlantic cod in the Northwest Atlantic are at a fraction of their historical abundance and a lack of recovery within the Gulf of Maine has created concern regarding the misalignment of fisheries management structures with biological population structure. To address this and investigate genome-wide patterns of variation, we used low-coverage sequencing to perform a region-wide, whole-genome analysis of fine-scale population structure. We sequenced 306 individuals from 20 sampling locations in U.S. and Canadian waters, including the major spawning aggregations in the Gulf of Maine in addition to spawning aggregations from Georges Bank, southern New England, the eastern Scotian Shelf, and St. Pierre Bank. With genotype likelihoods estimated at almost 11 million loci, we found large differences in haplotype frequencies of previously described chromosomal inversions between Canadian and U.S. sampling locations and also among U.S. sampling locations. Our whole-genome resolution also revealed novel outlier peaks, some of which showed significant genetic differentiation among sampling locations. Comparisons between allochronic winter- and spring-spawning populations revealed highly elevated relative ( ) and absolute ( ) genetic differentiation near genes involved in reproduction, particularly genes associated with the brain-pituitary-gonadal axis, which likely control timing of spawning, contributing to prezygotic isolation. We also found genetic differentiation associated with heat shock proteins and other genes of functional relevance, with complex patterns that may point to multifaceted selection pressures and local adaptation among spawning populations. We provide a high-resolution picture of U.S. Atlantic cod population structure, revealing greater complexity than is currently recognized in management. Our genome-scan approach likely underestimates the full suite of adaptive differentiation among sampling locations. Nevertheless, it should inform the revision of stock boundaries to preserve adaptive genetic diversity and evolutionary potential of cod populations.
选择能够在野生种群中创造出复杂的适应性分化模式，这可能与管理相关。西北大西洋的大西洋鳕鱼数量仅为其历史丰度的一小部分，缅因湾内鳕鱼数量缺乏恢复，这引发了人们对渔业管理结构与生物种群结构不一致的担忧。为了解决这一问题并研究全基因组变异模式，我们使用低覆盖度测序对精细尺度的种群结构进行全基因组区域分析。我们对来自美国和加拿大水域20个采样地点的306个个体进行了测序，包括缅因湾的主要产卵群体，以及乔治斯浅滩、新英格兰南部、斯科舍东部陆架和圣皮埃尔浅滩的产卵群体。在估计了近1100万个位点的基因型似然性后，我们发现加拿大和美国采样地点之间以及美国各采样地点之间，先前描述的染色体倒位的单倍型频率存在很大差异。我们的全基因组分辨率还揭示了新的异常值峰值，其中一些在采样地点之间表现出显著的遗传分化。对不同时间冬季和春季产卵种群的比较显示，在参与繁殖的基因附近，尤其是与脑-垂体-性腺轴相关的基因附近，相对（ ）和绝对（ ）遗传分化高度升高，这些基因可能控制产卵时间，导致合子前隔离。我们还发现了与热休克蛋白和其他功能相关基因的遗传分化，其复杂模式可能指向产卵种群之间多方面的选择压力和局部适应性。我们提供了美国大西洋鳕鱼种群结构的高分辨率图谱，揭示了比目前管理中所认识到的更大的复杂性。我们的基因组扫描方法可能低估了采样地点之间适应性分化的全貌。然而，它应该为修订种群边界提供信息，以保护鳕鱼种群的适应性遗传多样性和进化潜力。
