Severely depleted genetic diversity and population structure of a large predatory marine fish (Lates japonicus) endemic to Japan

Marine fish generally show higher genetic diversity and shallower population structure than freshwater fish, but data for rare species are lacking. A latid fish, akame (Lates japonicus), is a rare, large predatory fish endemic to Japan, occurring mainly in the estuaries and coastal waters of Kochi and Miyazaki prefectures. Among species of Lates, akame is the only one adapted to temperate waters, while the others are distributed in tropical waters. Despite conservation concerns for this species, almost nothing is known about its population genetic characteristics. We used amplified fragment length polymorphism (AFLP) and mitochondrial DNA (mtDNA) markers to describe the genetic variation and its partitioning among juvenile samples collected from multiple localities and over different years. Twenty-four primer combinations detected a total of 522 AFLP loci, only 40 (7.7 %) of which were polymorphic. Sequence analysis of the entire mtDNA control region identified only five haplotypes defined by four variable sites. The level of genetic diversity revealed by both genetic markers was unusually low compared to other marine fish and comparable to levels observed for some endangered freshwater fish exhibiting some of the lowest levels of genetic diversity among vertebrate populations. Analysis of molecular variance for the AFLP data indicated a weak but significant population structure (F (CT) = 0.07, P < 0.001) between the Kochi and Miyazaki regions. Our results highlight the need for in situ conservation efforts for akame across its entire distribution range and throughout its entire life cycle to minimize extinction risks associated with environmental and demographic stochasticity.