Genetic polymorphism of mitochondrial control region and cyt b in Trachurus japonicus from Fujian coastal waters

Abstract

Trachurus japonicus is a pelagic fish in Carangidae family mainly distributing in coastal waters of China,Japan and Korea.It has been an important commercially marine fish in China since 1960s.But the natural population genetics and resource quantity of T.japonicas have been declined rapidly due to over-fishing,degrada-tion of its natural habitats and so on in recent years,whereas little knowledge is available about its population ge-netic structure.The distribution of genetic diversity and genetic structure in wild stocks of T.japonicus seems emergent and the conservation strategies should be developed nowadays.The complete mitochondrial DNA con-trol region(861-866 bp) was amplified by means of PCR and sequenced from two T.japonicus populations col-lected from coastal waters in Eastern Fujian(n=30)and Southern Fujian(n=30).The result showed that 66 variable nucleotide sites were detected and 53 haplotypes were identified in two populations for control region sequence,but only three shared haplotypes were observed.The global haplotype diversity(h) and nucleotide diversity() were 0.993 and 1.093,respectively.Thirty-seven variable sites were recoded in the aligned sequences of partial cytochrome b gene(930 bp),and 25 haplotypes were recovered in 41 specimens.The average haplotype diversity(h) and nucleotide diversity() of two populations were 0.937 and 0.336,respectively.Cytochrome b gene en-coded 330 amino acids and the amino acid chain had only one haplotype.Each population had good haplotypic diversity and low nucleotide diversity in both mtDNA control region and cytochrome b,and the genetic diversity in Southern Fujian population was higher than that in Eastern Fujian one.Decapterus maruadsi was chosen as out-group in this study,and neighbor-joining(NJ) phylogenetic tree was constructed based on the haplotypes from the two populations of T.japonicus.The result showed that the two populations might have originated from one clade.Analysis of molecular variance(AMOVA) by ARLEQUIN version 3.1 revealed that the variation occurred mostly within the two populations for no significant population genetic structure existed throughout examined range,which was in consistent with neighbor-joining phylogenetic tree and haplotype network.The pairwise Ki-mura 2-paramter genetic distances calculated by MEGA version 4.0 were also small between the two populations.The demographic history of T.japonicus was examined by using neutrality tests and mismatch distribution analy-sis.The neutral test of Fu' Fs,which is devised specifically to detect population expansion and is sensitive to the presence of singletons in a sample,showed several highly significant negative values and the pairwise nucleotide differences distribution showed a singlet,indicating population expanded 62 000-205 000 years ago.The result showed that T.japonicus had low genetic diversity and genetically homogeneous population structure between the two populations,and this might be caused by population expansion,strong diffusion capacity and oceanographic current in East China.All these results would be very important and useful for making scientific strategy for the natural resource protection and genetic breeding of this fish.