Comparative Population Genetics of Chum and Masu Salmon Using Mitochondrial DNA Sequence Variation

population structure Using nucleotide sequence variations found in the 5 ’ half of the control region of the mitochondrial (mt) DNA, genetic diversity of chum (Oncorhynchus keta) and masu salmon (O. masou) was compared to get an insight into the specific difference, if any, in the genetic population structure of these two Pacific salmon species with different lifetime characteristics. Polymerase chain reaction (PCR)-based direct sequence analysis was successfully performed with the primers, tRNAthr-2 and tRNAphe-2, originally designed for chum salmon (Sato et al. 2001) and other sequencing primers for each species. Occasional occurrence of larger PCR products than regular-sized amplified fragments of about 1.0 kb were found in each population of masu salmon, whereas no size polymorphisms of PCR products were observed in chum salmon which constantly showed the regular PCR fragments. The occurrence of such irregular-sized fragments in masu salmon ranged from 3.3 % to 12.5 % in each population examined. Sequence analysis with primers of tRNApro-3, Okdl-L1, Omdl-H1 (designed for masu salmon), and tRNAphe-2 revealed that the irregular-sized PCR fragments were due to the occurrence of one to five repeats of an 80 bp unit in the 3 ’ portion of the control region. Except for the observed sequence repeats, the structure of masu salmon control region and its flanking gene order were in keeping with the previous findings (Shedlock et al. 1992)