Molecular phylogeography of Ruditapes philippinarum in the Northwestern Pacific Ocean based on COI gene

To examine the pattern of phylogeography of Ruditapes philippinarum, a length of 644-bp gene fragment of the mtDNA COI was sequenced. A total of 170 individuals from 19 locations were analyzed yielding 74 haplotypes, most of which were unique. The levels of haplotype diversity and nucleotide diversity for the species ranged from 0.80 +/- 0.16 (Notsuke Bay) to 1.00 +/- 0.13 (Nanao Bay, Miyazu Bay, Dalian 1 and Ariake), and from 0.002 +/- 0.001 (Notsuke Bay) to 0.011 +/- 0.006 (Qingdao), respectively. Both the phylogenetic (NJ tree) and minimum spanning trees (MST) showed three significant genealogical clusters corresponding to sampling localities, a genetic differentiation speculated to be caused by the isolation of the marginal seas of the Northwestern Pacific during Pleistocene low sea-level stands. Both AMOVA and pairwise Fst analyses revealed significant genetic differentiation between the populations from Japan and China. The pattern of isolation by distance was also detected in this species (r = 0.50, P<0.001). Both mismatch distribution analysis and the neutrality tests showed that R. philippinarum had undergone a recent population expansion. The estimate of population expansion time was about 425 kya-1580 kya. (C) 2011 Elsevier B.V. All rights reserved.