Genome-wide SNP analysis coupled with geographic and reproductive-phenological information reveals panmixia in a classical marine species, the Japanese jack mackerel (Trachurus japonicus)

Identification of genetic population structures in classical marine species—species with large population sizes, wide range distributions, and high dispersal potential—can be a challenging task because of expectedly weak genetic signals of population structure. The Japanese jack mackerel, Trachurus japonicus, is a classical marine species and one of the most important fishery resources in the East Asian seas. In this study, we tested the hypothesis of genetic panmixia in the Japanese jack mackerel using genome-wide SNP analyses coupled with geographic and reproductive phenology information. We generated a highly contiguous genome assembly and performed Genotyping by Random Amplicon Sequencing-Direct (GRAS-Di) to produce at least 19,904 SNPs that were genotyped in 614 samples from seas around the Japanese archipelago. Genetic population structure analyses did not reveal any evidence of genetic differentiation. Neither geographical barriers in the Japanese archipelago nor phenological differences in reproductive timing affected the genetic population structure. Overall, these findings were consistent with the interpretation of genetic panmixia, providing evidence for high genetic connectivity across the population’s distribution. Considering the current knowledge about the distribution and life history of T. japonicus, we suggest that the panmictic status may reflect a metapopulation structure with source-sink dynamics and/or extensive gene flow across the distribution range.