Study On Species Validities Of Chinese Coilia And Population Genetic Structure Of Coilia Nasus

This paper analyzed the COⅠgene sequences of 214 individuals of Coilia nasus, C. nasus taihuensis, C. brachygnathus, C. grayii and C. mystus, which from 9 populations, including Changjiang and Zhujiang population. The bias of base composition of codon is obvious, and the GC content follow the order 1st>2nd>3rd, while the difference of base composition among populations is not apparent. There are 71 haplotypes detected in the analyzed sample of Coilia nasus, C. nasus taihuensis, C. brachygnathus, and the haplotype-shared phenomenon is common. The single mutation site was mainly localized around 100bp and 600bp. The genetic distances among Coilia nasus, C. nasus taihuensis and C. brachygnathus, ranging from 0. 253% to 0.557%, close to the intra-population distance, but it is lower than 2% significantly, which is the threshold of the DNA barcoding species identification, and this is not conform to the“10×”law of species indentification. It indicates that these three populations are all C. nasus. However, the genetic distance between two C. mystus populations is 5.08% and far beyond 2%, it suggests that these two C. mystus populations could be considered at the species or subspecies level. Engraulis japonicas as out-group, Neighbor-joining,Maximum Parsimony and Maximum Likelihood methods were employed for phylogenetics analysis,respectively. Phylogenic analyses showed that C. nasus, C .nasus taihuensis, and C. brachygnathus could not form monophyletic clades respectively, whereas the two C.mystus populations were divided into two branch according to geographical sites, and the C. grayii population forms monophyletic clades. These results suggest that the barcode of COⅠgene could be used to identify the Coilia species of China. In addition, we researched the genetic structure and evolutionary history of six C.nasus populations (ZS, JJ, TH, JD, PYH, AR) on the premise that C .nasus taihuensis, and C. brachygnathus are the synonym of C. nasus. The populations differentiation index (Fst) and the gene intercourse index (Nm) are 0.17%- 48.1% and 0.54-288 respectively. The Fst value of PYH is significantly larger than that of other five populations, while the Nm value is significantly lower. The analyse results of K-2-P genetic distance, AMOVA and neighbor-joining tree based on the sequence of COⅠbarcode indicate that there is significant differentiation between the midstream population (PYH) and the downstream populations (ZS,JJ,TH,JD,), but not between the downstream populations and Ariake population(AR). The neutrality test and network analyses indicate a late Pleistocene population expansion for C. nasus (0.038-0.028 million years ago), it is possible that climatic oscillations during the Pleistocene ice ages produced great changes in this species’geographical distribution and abundance.The PIMA(PCR isolation of microsatellite arrays)was employed to isolate the polymorphic microsatellite loci in Coilia nasus. 102 microsatellite loci which contained more than 5 repeats were isolated, then 21 pairs of microsatellite loci amplify primers were designed, and only 11 pairs of polymorphic and stable primers are qualified for genetic structure and populations history analysis in six C.nasus populations (ZS,JJ,TH,JD, PYH,AR). The average PIC (Polymorphism Information Content) of 11 microsatellite loci is 0.7485 . The NA(number of allele) amplified by loci is from 4 to 15,with an average of 8.45. No null allele was found by the Micro-checker. PYH and AR populations showed lower genetic diversity, the average NA and PIC index of PYH (5.273、0.598) and AR (5.455、0.6082) are significant lower than the that of other 4 populations. Deviation from HWE (Hardy-Weinberg equilibrium) occurred in all loci except Micro 639. The number of deviation from HWE for ZS, JJ, TH, JD, PYH populations is 4, 4, 4, 3, 4, respectively, while there is only one loci deviation from HWE in AR population. The populations differentiation index (Fst) and the gene intercourse index (Nm) are 0.39%-13.4% and 1.5223-63.5255 respectively. The average Fst between PYH, AR and other 4 populations are significant larger while the Nm are pronounced lower than that among the other 4 populations. Besides, AMOVA and the clustering outcome based on the Bayesian model both suggest that the differentiation occurred between the PYH, AR population and the populations lived in the downstream of Yangzi river (ZS, JJ, TH, JD). Furthermore, the differentiation between PYH and other populations is much more remarkable while little differentiation founded among ZS, JJ, TH and JD population. The Bottleneck analysis found a violent bottleneck effect striking on all the C. nasus populations except AR. So we suggest that some of the C.nasus distributed in the range from Yangzi estuary to western Japan originally experienced the sharply decline of sea level and were trapped in south-western of Kyushu coast during the Pleistocene ice ages. And then they differentiated with the Yangzi population because of the ascending sea level and the strong Tsushima Strait followed during interglacial period, forming the Ariake bay population.