Although essential for fisheries resources management, little is known about the population structure of the Japanese conger Conger myriaster. To search for useful molecular markers for the study of population structures, mitochondrial (mt) and nuclear DNA diversities in the Japanese conger were examined using DNA sequencing and amplified fragment length polymorphism (AFLP) analysis, respectively. A region spanning from part of the 3' end of the cytochrome b gene to the central part of the control region (apprx585 base pairs/individual) was sequenced for 73 individuals from five different localities around Japan. A total of 99 variable positions were found, and a total of 67 haplotypes were identified in the 73 individuals. The average sequence differences within samples (1.8-2.4%) was comparable to those between samples (1.9-2.3%). The results of a hierarchical analysis of the sequence data did not suggest clear genetic subdivision among the local samples. Although a total of 499 bands were detected in the AFLP analysis from 58 individuals with three primer sets, no genetic structuring could be suggested. Nonetheless, to elucidate the subtle structure of populations, if any, many more individuals from more localities should be examined in detail. The genetic variations detected in the present study would serve as useful molecular markers for such studies.
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