The detailed population genetic structure of the rare endangered latid fish akame Lates japonicus with extremely low genetic diversity revealed from single-nucleotide polymorphisms
The detailed population genetic structure of the rare endangered latid fish akame Lates japonicus with extremely low genetic diversity revealed from single-nucleotide polymorphisms
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DOI：
10.1007/s10592-023-01517-2
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发表时间：
2023-04-17
影响因子：
2.2
通讯作者：
Takahashi，Hiroshi
中科院分区：
文献类型：
--
作者：
Naito，Takuya;Nakayama，Kouji;Takahashi，Hiroshi
对种群空间结构的准确了解对物种保护和管理至关重要，但濒危物种的遗传多样性较低，难以确定这些信息。在已知在脊椎动物中遗传多样性极低的濒危鱼类Lates japonicus中，mtDNA和AFLP标记分析未能明确地将个体划分为两个主要分布区(高知县和宫崎县)，尽管在这些区域之间发现了微弱但显著的遗传差异。在此，我们对高知县和宫崎县四个地点的282只一岁幼崽进行了基于个体的聚类分析和姊妹关系重建，以评估物种的种群遗传结构。我们使用来自双酶切酶切位点相关DNA测序(ddRAD-seq)的单核苷酸多态性(SNP)标记。尽管我们的数据显示阿卡梅的全基因组核苷酸多样性极低(π = 0.00006)，但聚类分析显示这两个地区之间存在明显的遗传差异，有少量的迁徙和具有混合血统的个人。同胞关系分析估计，只有全同胞对个体来自同一县，没有来自不同县的对。这些结果表明，高知县和宫崎县的赤峰种群是不同的管理单元，为了揭示遗传多样性较低的濒危物种详细的种群遗传结构，利用幼体样本和ddRAD-seq中的许多SNP进行基于个体的分析和亲缘关系重建是有效的。
Accurate knowledge of spatial population structure is crucial for species conservation and management, but low genetic diversity of endangered species makes it difficult to ascertain this information. In the Japanese lates or akame,Lates japonicus, an endangered fish known to have extremely low genetic diversity among vertebrates, mtDNA and AFLP marker analyses failed to clearly partition individuals into the two main distribution areas (Kochi and Miyazaki prefectures), although a weak but significant genetic difference between these regions was detected. Here, we conducted individual-based clustering analysis and sibship reconstruction to evaluate the species’ population genetic structure by using 282 yearlings collected from four sites in Kochi and Miyazaki prefectures. We used single nucleotide polymorphism (SNP) markers from double-digest restriction-site-associated DNA sequencing (ddRAD-seq). Although our data revealed extremely low genome-wide nucleotide diversity (π = 0.00006) in akame, the clustering analysis showed a clear genetic difference between the two regions, with a small number of migrants and individuals with admixed ancestry. Sibship analysis estimated that the only full-sib pairs of individuals were from the same prefecture and no pairs were from different prefectures. From these results, we conclude that the akame population of Kochi and Miyazaki prefectures are different management units, and for revealing detailed population genetic structure of endangered species which has low genetic diversity, it is effective to conduct individual-based analysis and sibship reconstruction by using juvenile samples and many SNPs from ddRAD-seq.