Population structure and demographic history of Pacific herring Clupea pallasii around Japan inferred from mitochondrial DNA sequences

Using the mitochondrial DNA control region sequences of 549 bp for 618 Pacific herring from 16 spatiotemporal samples collected at nine spawning sites in the Hokkaido and Tohoku areas of Japan during the spawning period between 2003 and 2014, we estimated the contemporary population structure and demographic history of the Japanese herring. Neighbor-joining unrooted phylogenetic trees based on the empirical Bayes pairwise F-ST values showed three large clusters consisting of six local samples in Hokkaido, Lake Obuchi-numa, and Miyako Bay/Matsushima Bay in Tohoku. Hokkaido samples had higher genetic diversity than Honshu samples. The haplotype frequency of Miyako Bay after the Great Tohoku earthquake was substantially different to that before the earthquake, but similar to that of Lake Obuchi-numa. Our demographic analyses inferred that the effective population size (N-e) has expanded since at least similar to 600 kyr ago in Hokkaido but is stable in Honshu, but a rapid and simultaneous decrease in N-e has occurred since similar to 20 kyr ago in Japanese herring, corresponding to the warming after the Last Glacial Maximum.