The detailed population genetic structure of the rare endangered latid fish akame Lates japonicus with extremely low genetic diversity revealed from single-nucleotide polymorphisms

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.