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Lacustrine sockeye salmon (Oncorhynchus nerka) are listed as an endangered species in Japan despite little genetic information on their population structure. In order to clarify the genetic diversity and structure of Japanese populations for evaluating on the bottleneck effect and an endangered species, we analyzed the ND5 region of mitochondrial DNA (mtDNA) and 45 single nucleotide polymorphisms (SNPs) in 640 lacustrine sockeye salmon in Japan and 80 anadromous sockeye salmon in Iliamna Lake of Alaska. The genetic diversity of the Japanese population in both mtDNA and SNPs was significantly less than that of the Iliamna Lake population. Moreover, all Japanese populations had SNP loci deviating from the HWE. In spite of low genetic diversity, the SNP analyses resulted that the Japanese population was significantly divided into three groups. These suggest that Japanese sockeye salmon populations should be protected as an endangered species and genetically disturbed by the hatchery program and transplantations.

This 20th Wakefield Symposium, ‘The genetics of subpolar fish and invertebrates’, is the successor of the 11th Wakefield Symposium, ‘Genetics of sub- arctic fish and shellfish’, which was held in Juneau, Alaska in 1993. In the introduction to that sympo- sium (Gharrett & Smoker 1994), it was noted that: ‘beginning in the 1960s, modern tools of genetic analysis began to be broadly applied in fisheries science’, and that ‘within the past decade (referring to the 1980s), fisheries genetics had entered the main- stream of fisheries resource utilization’. That obser- vation may be an understatement in today’s world of fisheries science. Once-vigorous fisheries in many parts of the world have failed, growing demand for fisheries products has led to full utilization of many remaining capture resources and is driving an increase in aquaculture productivity, and the role of aquacul- ture has increased dramatically ([FAO 2002]). Looming over concerns of lost stocks and persistent erosion of genetic variability are predictions of global warming, which may further tax genetic resources. One of the consequences of these developments is an increased interest in and reliance on genetic applications to many aspects of fisheries management, aquaculture, and conservation.