Data from: A parallel population genomic and hydrodynamic approach to fishery management of highly-dispersive marine invertebrates: the case of the Fijian black-lip pearl oyster Pinctada margaritifera

Fishery management and conservation of marine species increasingly relies on genetic data to delineate biologically relevant stock boundaries. Unfortunately for high gene flow species which may display low, but statistically significant population structure, there is no clear consensus on the level of differentiation required to resolve distinct stocks. The use of fine-scale neutral and adaptive variation, considered together with environmental data can offer additional insights to this problem. Genome-wide genetic data (4,123 SNPs), together with an independent hydrodynamic particle dispersal model were used to inform farm and fishery management in the Fijian black-lip pearl oyster Pinctada margaritifera, where comprehensive fishery management is lacking, and the sustainability of exploitation uncertain. Weak fine-scale patterns of population structure were detected, indicative of broad-scale panmixia among wild oysters, while a hatchery-sourced farmed population exhibited a higher degree of genetic divergence (Fst = 0.0850–0.102). This hatchery-produced population had also experienced a bottleneck (NeLD = 5.1; 95% C.I. = [5.1–5.3]); compared to infinite NeLD estimates for all wild oysters. Simulation of larval transport pathways confirmed the existence of broad-scale mixture by surface ocean currents, correlating well with fine-scale patterns of population structuring. Fst outlier tests failed to detect large numbers of loci supportive of selection, with 2–5 directional outlier SNPs identified (average Fst = 0.116). The lack of biologically significant population genetic structure, absence of evidence for local adaptation and larval dispersal simulation, all indicate the existence of a single genetic stock of P. margaritifera in the Fiji Islands. This approach using independent genomic and oceanographic tools has allowed fundamental insights into stock structure in this species, with transferability to other highly-dispersive marine taxa for their conservation and management.海洋物种的渔业管理与保护愈发依赖遗传数据，以划定具备生物学意义的渔业种群边界。但针对基因流水平较高的物种，即便其种群结构微弱却具备统计学显著性，学界至今仍未就区分独立渔业种群所需的遗传分化程度达成明确共识。结合环境数据开展分析的精细尺度中性与适应性遗传变异，可为该研究难题提供新的解析视角。本研究以斐济黑唇珍珠牡蛎（*Pinctada margaritifera*）为对象，针对其栖息海域缺乏全面渔业管理、捕捞可持续性不明的现状，利用全基因组遗传数据（4123个单核苷酸多态性（Single Nucleotide Polymorphism, SNPs））与独立的水动力颗粒扩散模型，为该物种的养殖与渔业管理提供科学决策依据。研究检测到微弱的精细尺度种群结构特征，表明野生牡蛎群体间存在广泛的泛交现象；而人工繁育场来源的养殖群体则表现出更高水平的遗传分化（固定指数（Fixation Index, Fst）= 0.0850–0.102）。该人工繁育群体还经历了种群瓶颈事件，其基于连锁不平衡估计的有效种群大小（NeLD）为5.1，95%置信区间（95% C.I.）为[5.1–5.3]；相较之下，所有野生牡蛎群体的NeLD估计值均为无穷大。幼虫运输路径模拟结果证实，表层洋流促成了大范围的群体混合，该结果与精细尺度的种群结构模式高度吻合。Fst异常位点检测未发现大量受选择的基因位点，仅鉴定出2-5个定向选择异常SNPs（平均Fst=0.116）。缺乏具备生物学意义的种群遗传结构、未检测到局部适应的相关证据，结合幼虫扩散模拟结果，均表明斐济海域的黑唇珍珠牡蛎仅存在单一遗传渔业种群。本研究结合独立的基因组学与海洋学研究手段，为该物种的种群结构研究提供了基础性见解，该研究方法可推广应用于其他高扩散性海洋类群的保护与管理工作。