Data from: Restriction site-associated DNA sequencing reveals local adaptation despite high levels of gene flow in Sardinella lemuru (Bleeker, 1853) along the northern coast of Mindanao, Philippines

Stock identification and delineation are important in the management and
conservation of marine resources. These were highlighted as priority
research areas for Bali sardinella (Sardinella lemuru) which is among the
most commercially important fishery resources in the Philippines. Previous
studies have already assessed the stocks of S. lemuru between Northern
Mindanao Region (NMR) and Northern Zamboanga Peninsula (NZP), yielding
conflicting results. Phenotypic variation suggests distinct stocks between
the two regions, while mitochondrial DNA did not detect evidence of
genetic differentiation for this high gene flow species. This paper tested
the hypothesis of regional structuring using genome-wide single nucleotide
polymorphisms (SNPs) acquired through restriction-site associated DNA
sequencing (RADseq). We examined patterns of population genomic structure
using a full panel of 3,573 loci, which was then partitioned into a
neutral panel of 3,348 loci and an outlier panel of 31 loci. Similar
inferences were obtained from the full and neutral panels, which were
contrary to the inferences from the outlier panel. While the full and
neutral panels suggested a panmictic population (global FST ~ 0, p
> 0.05), the outlier panel revealed genetic differentiation between
the two regions (global FST = 0.161, p = 0.001; FCT = 0.263, p <
0.05). This indicated that while gene flow is apparent, selective forces
due to environmental heterogeneity between the two regions play a role in
maintaining adaptive variation. Annotation of the outlier loci returned
five genes that were mostly involved in organismal development. Meanwhile,
three unannotated loci had allele frequencies that correlated with sea
surface temperature. Overall, our results provided support for local
adaptation despite high levels of gene flow in S. lemuru. Management
therefore should not only focus on demographic parameters (e.g., stock
size, catch volume), but also consider the preservation of adaptive
variation.

种群识别与界定（Stock identification and delineation）在海洋资源管理与保护中至关重要。对于菲律宾最具商业价值的渔业资源之一——巴厘沙丁鱼（Sardinella lemuru）而言，这两项研究被列为优先领域。以往研究已评估了北棉兰老岛地区（NMR）与北三宝颜半岛（NZP）之间的巴厘沙丁鱼种群状况，但结果存在矛盾。表型变异表明两区域间存在不同种群，而线粒体DNA（mitochondrial DNA）未检测到这一高基因流物种存在遗传分化的证据。本研究采用限制性位点相关DNA测序（RADseq）获得的全基因组单核苷酸多态性（SNPs），验证了区域种群结构的假设。我们利用包含3573个基因座的全位点组分析种群基因组结构模式，并将其划分为含3348个基因座的中性位点组和含31个基因座的异常位点组。全位点组与中性位点组得出的推论一致，但与异常位点组的推论相反。全位点组与中性位点组显示种群为随机交配种群（全局遗传分化指数FST≈0，p>0.05），而异常位点组则揭示两区域间存在遗传分化（全局FST=0.161，p=0.001；FCT=0.263，p<0.05）。这表明，尽管基因流显著，但两区域环境异质性导致的选择压力在维持适应性变异中发挥作用。异常位点的注释结果得到5个主要参与生物发育的基因。同时，3个未注释的位点其等位基因频率与海表温度相关。综上，研究结果支持巴厘沙丁鱼在高基因流背景下存在局部适应的结论。因此，管理措施不应仅关注种群统计参数（如种群规模、捕捞量），还应考虑保护适应性变异。