Population genetic structure of Sardinella lemuru in Philippine waters was examined using mitochondrial DNA markers, control region (CR) and cytochrome oxidase I (COI). The sampling effort was focused along the northern coast of Mindanao where the species was previously reported to have regionally structured stocks. Sequences from online databases were included to expand geographic coverage of the analyses. Phylogeographic and population genetic inferences revealed the presence of genetically structured sympatric haplogroups across the archipelago (CR: n $=$ 493, K $=$ 3, between-group genetic distance = 0.038 – 0.054, global ${\Phi }_{\mathrm{ST}}=0.41$ p < 0.001; COI: n $=$ 159, K $=$ 2, between-group genetic distance = 0.012, global ${\Phi }_{\mathrm{ST}}=0.77$, p $<$ 0.001). In contrast, little to no genetic differentiation was inferred when samples were assigned based on geographic location (CR global ${\Phi }_{\mathrm{ST}}=0.01$, p < 0.05; COI global ${\Phi }_{\mathrm{ST}}=0.001$, p > 0.05). These results suggest that (1) gene flow occurs across space, but is limited among sympatric haplogroups, (2) these sympatric haplogroups do not correspond to cryptic species, and (3) differences in mutation rates between the two markers may have led to a different number of haplogroups being recovered. High haplotype diversity (H${}_{\mathrm{CR}}=0.99$; H${}_{\mathrm{COI}}=0$.798), low nucleotide diversity (${\pi }_{\mathrm{CR}}=0.041$; ${\pi }_{\mathrm{COI}}=0.005$), and significantly negative Fu’s F${}_{\mathrm{S}}$ values implied demographic expansion for all haplogroups. The mismatch distribution and Bayesian Skyline plot indicated that expansion occurred during the late Pleistocene. Based on our results, we hypothesize that the Philippines is a secondary contact zone for S. lemuru, and testing this requires that samples be obtained from the entire habitat range of the species along the Indo-West Pacific Region.

使用线粒体DNA标记，控制区（CR）和细胞色素氧化酶I（COI）检测了菲律宾水域沙丁鱼的种群遗传结构。采样工作集中在棉兰老岛的北海岸，以前据报道该物种具有区域结构的种群。包括来自在线数据库的序列，以扩大分析的地理覆盖范围。文献记载和种群遗传推论揭示了整个群岛存在遗传结构同胞单倍群（CR：n $=$ 493，K $=$ 3，群体间遗传距离= 0.038 – 0.054，全球 ${\Phi }_{\mathrm{ST}}=0。41$p <0.001；硬币$=$ 159，K $=$ 2，组间遗传距离= 0.012，整体 ${\Phi }_{\mathrm{ST}}=0。77$p $<$ 0.001）。相反，根据地理位置分配样品时，几乎没有或没有遗传分化的推断（CR全球${\Phi }_{\mathrm{ST}}=0。01$，p <0.05；全球COI${\Phi }_{\mathrm{ST}}=0。001$，p> 0.05）。这些结果表明（1）基因流动跨空间发生，但在同胞单倍群中受到限制；（2）这些同胞单倍群不对应于隐性物种；（3）两个标记之间的突变率差异可能导致恢复的单倍组数不同。高单倍型多样性（H${}_{\mathrm{CR}}=0。99$; H${}_{\mathrm{COI}}=0$.798），核苷酸多样性低（${\pi }_{\mathrm{CR}}=0。041$; ${\pi }_{\mathrm{COI}}=0。005$），并显着负付氏F${}_{\mathrm{小号}}$值暗示所有单倍群的人口扩展。不匹配分布和贝叶斯天际线图表明扩张发生在更新世晚期。根据我们的结果，我们假设菲律宾是柠檬猴的次生接触区，而要对此进行测试，则需要从印度洋-西太平洋地区物种的整个栖息地范围中获取样本。