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.

渔业管理与海洋物种保护愈发依赖遗传数据，以划定具有生物学意义的渔业种群边界。遗憾的是，对于那些基因流水平较高、仅表现出微弱但具统计学显著性群体结构的物种而言，学界尚未就分辨其不同渔业种群所需的遗传分化程度达成明确共识。若将精细尺度的中性与适应性遗传变异与环境数据结合分析，可为解决这一难题提供新的研究视角。本研究以斐济黑唇珍珠贝（*Pinctada margaritifera*）为研究对象，该物种尚未建立完善的渔业管理制度，其捕捞可持续性尚不明确。研究采用全基因组遗传数据（4123个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点），结合独立的水动力粒子扩散模型，为其养殖与渔业管理提供科学支撑。研究检测到微弱的精细尺度群体结构特征，表明野生珠贝群体整体处于随机泛交状态；而一个孵化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）。与所有野生群体的无限有效种群大小（基于连锁不平衡估计的有效种群大小NeLD）估计值相比，该孵化繁育群体还经历了瓶颈效应（NeLD = 5.1；95%置信区间（C.I.）= [5.1~5.3]）。幼虫扩散路径的模拟结果证实，表层洋流会形成大范围的幼虫混合现象，这与群体结构的精细尺度分布模式高度吻合。Fst异常位点检测未发现大量受选择的基因座，仅鉴定出2~5个定向选择的异常SNPs（平均Fst = 0.116）。缺乏具有生物学意义的群体遗传结构、未检测到局部适应的证据，结合幼虫扩散模拟结果，均表明斐济海域的*P. margaritifera*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，为该物种种群结构的解析提供了基础性认知，该方法也可为其他高扩散性海洋类群的保护与管理提供借鉴。