Genetic Variation in One Bottlenecked and Two Wild Populations of the Japanese Scallop (Patinopecten yessoensis): Empirical Parameter Estimates from Coding Regions of Mitochondrial DNA

Abstract

Restriction analysis of the mitochondrial genome of 16 Japanese scallop (Patinopecten yessoensis) provided unique genotypes for each individual, mostly due to length variation. Fragment length variation was common, probably because tandemly repeated elements of noncoding mtDNA mutate to a different number of copies at high rates. To accurately estimate genetic diversity, we used the polymerase chain reaction (PCR) to selectively amplify coding mtDNA fragments and performed restriction analysis on these. Four pairs of PCR primers were used to amplify fragments encoding: (1) most of ATP synthetase subunit 6 and most of cytochrome c oxidase subunit 3, (2) part of cytochrome b apoenzyme, (3) tRNA for threonine, and (4) most of the large (16S) ribosomal gene. We used this technique to compare the genetic diversity of a population bred in a small experimental hatchery in British Columbia for three generations with its wild source population at Mutsu Bay, Aomori, Japan, and with a second wild population at Uchiura Bay, Hokkaido, Japan. The three populations were similar in the frequency distributions of the 11 mitochondrial clonal lines. This suggests that the experimental hatchery stock was not severely inbred and that gene flow between the two wild Japanese populations has been sufficient to prevent divergence.