Population structure of elongate ilisha Ilisha elongata along the Northwestern Pacific Coast revealed by mitochondrial control region sequences

The elongate ilisha Ilisha elongata is an economically important species broadly distributed from the Western Pacific to the Java Sea off Sarawak. The fishery of elongate ilisha has been declining in recent years in terms of total catch, size of harvested fish, as well as absence of the fish from previously distributed areas. The knowledge about population structure and genetic diversity of elongate ilisha is important for managing sustainable fisheries. Only two studies have investigated the population genetics of elongate ilisha but both with limited sampling. In the present study, we sampled 16 sites from the coast of China, Korea and Japan. We sequenced the whole mitochondrial control region (D-loop), which showed a remarkably high polymorphism. The average haplotype diversity was 0.98 and the nucleotide diversity (pi) was 0.006. Neutrality tests suggested past population expansions. Populations were weakly differentiated (I broken vertical bar (ST) = 0.0612). This result, together with a lack of association between clades and locations (R (2) = 0.0591), indicated a weak population structure of the elongate ilisha. The only exception was from the population of Dandong in the West Korean Bay, which was different from all other populations in its D-loop sequence. We did not find genetic differences between the fish with a bottom-sword caudal fin and the fish with a double-sword caudal fin.