The giant black tiger shrimp (Penaeus monodon) is native to the Indo-Pacific and is the second most farmed penaeid shrimp species globally. Understanding genetic structure, connectivity, and local adaptation among Indo-Pacific black tiger shrimp populations is important for informing sustainable fisheries management and aquaculture breeding programs. Population genetic and outlier detection analyses were undertaken using 10,593 genome-wide single nucleotide polymorphisms (SNPs) from 16 geographically disparate Indo-Pacific P. monodon populations. Levels of genetic diversity were highest for Southeast Asian populations and were lowest for Western Indian Ocean (WIO) populations. Both neutral (n = 9,930) and outlier (n = 663) loci datasets revealed a pattern of strong genetic structure of P. monodon corresponding with broad geographical regions and clear genetic breaks among samples within regions. Neutral loci revealed seven genetic clusters and the separation of Fiji and WIO clusters from all other clusters, whereas outlier loci revealed six genetic clusters and high genetic differentiation among populations. The neutral loci dataset estimated five migration events that indicated migration to Southeast Asia from the WIO, with partial connectivity to populations in both oceans. We also identified 26 putatively adaptive SNPs that exhibited significant Pearson correlation (P < 0.05) between minor allele frequency and maximum or minimum sea surface temperature. Matched transcriptome contig annotations suggest putatively adaptive SNPs involvement in cellular and metabolic processes, pigmentation, immune response, and currently unknown functions. This study provides novel genome-level insights that have direct implications for P. monodon aquaculture and fishery management practices.

中文翻译：

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印度-太平洋地区斑节对虾的种群结构、遗传连通性和局部适应特征

巨型黑虎虾（斑节对虾）原产于印度太平洋地区，是全球第二大养殖对虾品种。了解印度太平洋黑虎虾种群的遗传结构、连通性和当地适应性对于为可持续渔业管理和水产养殖育种计划提供信息非常重要。使用来自 16 个地理上不同的印度-太平洋斑节对虾种群的 10,593 个全基因组单核苷酸多态性 (SNP) 进行种群遗传和异常检测分析。东南亚人群的遗传多样性水平最高，西印度洋（WIO）人群的遗传多样性水平最低。中性（n = 9,930）和离群（n = 663）基因座数据集都揭示了斑节对虾的强遗传结构模式，与广泛的地理区域相对应，并且区域内样本之间存在明显的遗传断裂。中性基因座揭示了七个遗传簇，以及斐济和 WIO 簇与所有其他簇的分离，而离群基因座则揭示了六个遗传簇和种群之间的高度遗传分化。中性位点数据集估计了五次迁徙事件，表明从 WIO 迁徙到东南亚，与两个大洋的种群有部分连接。我们还鉴定了 26 个假定的适应性 SNP，它们在次要等位基因频率与最高或最低海面温度之间表现出显着的 Pearson 相关性 (P < 0.05)。匹配的转录组重叠群注释表明，假定适应性 SNP 参与细胞和代谢过程、色素沉着、免疫反应和目前未知的功能。这项研究提供了新的基因组水平见解，对斑节对虾水产养殖和渔业管理实践具有直接影响。