The genomics of spawning seasonality and seascape in commercially harvested herring (Clupea harengus) in the Northwest Atlantic

我们的目的是确定西北大西洋鲱鱼（Clupea harengus）的地理和时间（季节性）遗传结构。鲱鱼是一种分布广泛、具有重要经济价值的海洋中上层鱼类，具有高度的生物复杂性，即与产卵时间、产卵地点和生活史差异有关的复杂的多样性格局。一些种群在春季繁殖，另一些种群在秋季繁殖，近年来它们的相对丰度发生了变化，这可能是对海洋温度纬度变化的反应。一般而言，渔业管理没有考虑到这种程度的生物复杂性，而忽视多样性在管理单位内的分布，很可能导致对较弱种群组成部分的过度开发，最终导致生物多样性的丧失。我们的目标是了解这种多样性是如何在空间和时间上分布的。大多数先前的研究发现，除了最大的地理范围外，几乎没有证据表明鲱鱼的遗传结构。重新尝试了解这个物种的种群结构是合理的，因为以下三个最近的发展，这使得这个项目独一无二：首先，鲱鱼基因组最近已经完全测序和注释。其次，我们最近不仅发现了秋季和春季产卵鲱鱼之间的基因组差异，而且在加拿大和欧洲的鲱鱼种群中也发现了相同的差异，其中一些差异位于与繁殖光周期调节相关的基因附近。因此，我们确定了可能影响产卵季节的基因组区域，在一些单核苷酸多态性位点（SNPs）的等位基因频率上，秋季产卵者与春季产卵者不同，其中一些与已知功能的基因有关。这是当地适应的证据。这些成就之所以成为可能，是因为最近新一代测序技术的爆炸性发展。我们计划利用这些重大突破来研究西北大西洋鲱鱼的地理和季节结构。加拿大渔业和海洋（DFO）是负责管理加拿大鲱鱼渔业的合作机构，它对拟议的工作很感兴趣。

Our objective is to identify the geographic and temporal (seasonal) genetic structure in herring (Clupea harengus) in the NW Atlantic. Herring, a widely distributed marine pelagic fish of economic importance exhibits a high degree of biocomplexity, i.e., a complex pattern of diversity associated with differences in spawning time and location, and life history. Some populations reproduce in the spring and others in the fall and their relative abundance has changed in recent years likely in response to latitudinal shifts in ocean temperature. Fishery management in general does not consider such a degree of biocomplexity, yet disregard for how diversity is distributed within management units is likely to lead to overexploitation of the weaker population components, ultimately leading to the loss of biodiversity. Our goal is to understand how such diversity is distributed in space and time. Most previous studies found little evidence of genetic structure in herring at all but the largest geographic scales. Renewed attempts to understand population structure in this species are justified because of the following three recent developments, which make this project unique: First the herring genome has recently been completely sequenced and annotated. Second, we recently found not only genomic differences between fall and spring spawning herring but also found the same differences occurring in Canadian and European herring populations, with some differences located near genes linked to photoperiodic regulation of reproduction. We thus identified the genomic regions likely underlying spawning seasonality, with autumn spawners differing from spring spawners in allele frequencies at a number of single nucleotide polymorphic sites (SNPs) some of which are linked to genes of known function. This is evidence of local adaptation. These achievements were possible because of the recent explosive development of Next Generation Sequencing technology. We plan to take advantage of these major breakthroughs to examine the geographic and seasonal structure of herring in the NW Atlantic. The proposed work is of interest to Fisheries and Oceans Canada (DFO), the collaborating institution responsible for the management of the herring fishery in Canada.