Stock composition of adult chum salmon Oncorhynchus keta caught in a setnet fishery estimated using genetic identification, scale patterns, and otolith thermal marking

Three different techniques for stock identification, namely scale patterns, otolith thermal marks, and single-nucleotide polymorphism (SNP) markers, were applied to the same mixture samples of chum salmon collected in a setnet fishery in the Sea of Okhotsk, off Hokkaido, Japan, to evaluate consistency and accuracy among the techniques. The scale pattern and SNP analyses provided similar estimates for two regional origins (Hokkaido and Honshu) with data for 2011–2013; for each year, the Hokkaido-origin stock was dominant in September and early October, but the Honshu-origin stock was dominant by late October. The SNP analysis specified five geographical origins of chum salmon (the Okhotsk coast, Hokkaido and Honshu coasts of the Sea of Japan, and Hokkaido and Honshu coasts of the Pacific), whereas the other techniques did not identify multi-regional origins. Recaptures of otolith-marked chum salmon were used for estimating the proportions of fish originating from the Hokkaido Sea of Japan region; these estimates differed from those based on the SNP analysis. This study demonstrated that scale pattern and SNP analyses have the potential to provide nearly consistent estimates for the two regional origins, and can possibly help us to understand the interception of migrating chum salmon in Japan.