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Sequence analyses on the complete mitochondrial DNA (mtDNA) control region (992 bp) were conducted to elucidate the population structure of kuruma prawns (Penaeus japonicus) in East Asia. Five populations including 95 individuals were collected. They are separated into the Japan Sea (JS), the north and south of the East China Sea (NECS and SECS), the Taiwan Strait (TS), and the north of the South China Sea (NSCS) populations. There are 292 variable sites without any insertions and deletions. Nucleotide diversity in the total populations is 2.51 ± 0.07%, and the variations within populations ranged from 2.61 ± 0.93% (SECS) to 2.29 ± 0.16% (JS). FST values between the JS and the rest of the populations, between the NECS and NSCS populations, and between the SECS and NSCS populations show significant differences. The UPGMA tree of these five populations shows three distinct clusters; one includes the JS population; another includes the NECS population; the third includes populations from the rest of the areas. The analysis of molecular variance (AMOVA) shows clear genetic difference between the JS and the rest of the populations. Additional AMOVA analysis excluding the JS population indicates significant variation between the NECS population and the other three populations. We, therefore, conclude that three distinct populations exist in East Asia; one is in the JS; another is in the NECS; and the third is distributed in SECS, TS and NSCS.

Population genetic structure of the kuruma prawn (Penaeus japonicus) in East Asia inferred from mitochondrial DNA sequences