A Possible More Precise Management Unit Delineation Based on Epigenomic Differentiation of a Long‐Distance‐Migratory Marine Fish Scomberomorus niphonius

ABSTRACT Understanding population structure and adaptive history is critical for designing appropriate management regulations for fisheries and conserving adaptive potential for the future. However, this is not easy for marine fish, especially those with long‐distance migration abilities. In this study, we constructed a high‐quality reference genome for Japanese Spanish mackerel ( Scomberomorus niphonius ) and explored its population structure using whole genomic and epigenomic data. Despite the high depth of the sequence data, we failed to identify geographical genetic differentiation of Japanese Spanish mackerel across Chinese coastal waters. However, whole‐genome bisulphite sequencing can classify this species into the Bohai–Yellow Sea group and the East China Sea–South China Sea group. Genes involved in embryonic skeletal system development, limb morphogenesis functions, and adult locomotory behaviour were differentially methylated in the southern (Zhanjiang, ZJ) and northern (Western Dalian, WDL) populations and may play important roles as drivers of population structure in Japanese Spanish mackerel. Our study not only provides the first reference genome of the Japanese Spanish mackerel and sheds light on population differentiation at the epigenomic level, but also provides a methylome‐based framework for population structure analyses of marine fish with long‐distance migration ability. These findings are expected to facilitate the development of scientific programmes for the successful conservation of marine fishery resources.