Cryptic population substructure in Cape Hakes

Genomic information has the potential to aid in the establishment of sustainable management plans for commercially exploited marine fishes, aiding in the long-term conservation of these resources. The southern African hakes (Merluccius capensis and M. paradoxus) are commercially valuable demersal fishes with similar distribution ranges but exhibiting contrasting life histories. Using a comparative framework based on Pool-Seq genome-wide SNP data, we investigated whether the evolutionary processes that shaped extant patterns of diversity and divergence are shared among these two congeneric fishes, or unique to each one. Our findings revealed that M. capensis and M. paradoxus show similar levels of genome-wide diversity, despite different census sizes and life-history features. In addition, M. capensis shows three highly structured geographic populations across the Benguela Current region (one in the northern Benguela and two in the southern Benguela), with no consistent genome-environmen..., Samples used in this study were collected in 2012 for the study of Henriques et al. (2016), from fisheries surveys by the Department of Forestry, Fisheries and Environment (DFFE – South Africa) and the Ministry of Fisheries (Namibia), and ethical clearance for data usage was obtained from the University of Pretoria (NAS217/2021). The sampling design mimicked the main oceanographic features of the Benguela Current system, with samples collected from north and south of the perennial upwelling cell, as well as past Cape Point towards the east in South Africa (Figure 1A). For M. capensis, samples were obtained from northern Namibia to the southern West Coast of South Africa, as previous findings reported a single population break across the Orange River. For M. paradoxus, sampling took place from northern Namibia to southwestern South Africa, as von der Heyden et al. (2007) reported a putative genetic break across Cape Point in South Africa, which was not detected by Henriques et al. (2016)...,

基因组信息可为商业捕捞海水鱼类制定可持续管理方案提供助力，进而助力这类渔业资源的长期保护。南非无须鳕（Merluccius capensis）与歧异无须鳕（Merluccius paradoxus）均为具有商业价值的底栖鱼类，二者分布范围相近，但生活史特征截然不同。本研究基于混池测序（Pool-Seq）全基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据构建比较分析框架，旨在探究塑造这两种同属鱼类现存多样性与分化模式的演化过程，是二者共有还是各自独有。研究结果显示，尽管两种无须鳕的种群普查数量与生活史特征存在差异，但其全基因组多样性水平却较为相似。此外，在本格拉洋流区域内，南非无须鳕（M. capensis）可划分为3个高度分化的地理种群（1个位于北本格拉海域，2个位于南本格拉海域），未发现显著的基因组-环境关联模式（原文此处未完结）。
本研究使用的样本采集于2012年，最初用于Henriques等人（2016）的研究，样本由南非林业、渔业与环境部（DFFE）及纳米比亚渔业部通过渔业调查获取；本研究的数据使用伦理审批由比勒陀利亚大学批准（审批编号：NAS217/2021）。
采样设计覆盖了本格拉洋流系统的主要海洋学特征，样本采集自常年上升流区的南北两侧，以及南非开普角以东海域（图1A）。针对南非无须鳕（M. capensis），样本采集范围覆盖纳米比亚北部至南非西海岸南部，此前研究显示奥兰治河区域存在1个种群分界。针对歧异无须鳕（M. paradoxus），采样范围覆盖纳米比亚北部至南非西南部海域——此前von der Heyden等人（2007）报道称南非开普角区域存在推测的遗传分界，但Henriques等人（2016）未检测到该分界（原文此处未完结）。