Genetic Diversity And Genetic Structure Of The Finless Porpoise Populations Based On D-Loop And Cyt B Gene

Finless porpoise is a kind of small toothed whales, which distribute in coast of Pakistan and India, through southeast Asia and Indonesia, north to China, Korea and Japan. In the study, we sequenced the complete mitochondrial genome of Neophocaena asiaeorientails sunameri by PCR amplification. On the other hand, the part of mt DNA control region and the whole Cyt b gene were obtained by PCR amplification from 11 finless porpoise in the Yangtze Estuary, in combination with other informations of mt DNA control region and Cyt b gene sequences from different geographic populations of the finless porpoise, which have been reported in the Gen Bank. We analyzed the genetic diversity, population structure and population history dynamic of different geographic populations of the finless porpoise.The main results were described as follows:1.The structure and composition analysis of the complete mitochondrial genome of the Neophocaena asiaeorientails sunameri(Phocaenidae: Neophocaena)The circular genome is 16385 bp in length with an A+T content of 59.22%, consisting of 13 protein-coding genes(PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and 2 non-coding areas. Ten protein-coding genes use ATG as the initiation codon, except that ND2 started with ATT, and ND3, ND5 started with ATA. Canonical TAA and TAG termination codons are found in seven protein-coding genes, the remaining four(ND4, ND2, ND3, COIII) have incomplete termination codons(T or TA), in addition, the COI ends with AGG, and the Cty b ends with AGA. All t RNAs could be folded into the typical cloverleaf secondary structure, but the t RNASer(AGY) appears to be missing the “DHU” arm. The necleotide sequence data of 24 mt DNA sequences were used for constructing the phylogenetic tree. It showed that the relationship of Phocoenidae is closer with Delphinidae and Monodontidae.2.The analysis of genetic diversity and population structureBased on the part of mt DNA control region(598bp) from six geographic populations, we found 26 variable sites and 47 unique haplotypes. The average haplotype diversity(Hd=0.625±0.093) and nucleotide diversity(π=0.0021±0.0005) of Taiwan population(TS) were relatively low, and the average nucleotide diversity(π=0.0047±0.0027) of Pearl River Estuarypopulation(PRE) was highest. The index of genetic differentiation(FST) ranged from-0.02032 to 0.70277 between six populations. Analysis of molecular variance of six finless porpoise populations showed that when the geographical population was divided into [NYS]; [YR, YRE]; [NSS, TS]; [PRE], Fct has amaximum value(0.42359), which indicated that this division of geographic group was better at rationalizing to reflect the genetic structure of the finless porpoise populations in Chinese waters.Based on the the whole Cyt b gene(1140bp) from four geographic populations, we found 56 variable sites and 44 unique haplotypes. The average nucleotide diversity(Hd= 0.834±0.027) of Bohai population(NYS) was highest and the average haplotype diversity(Hd=0.286±0.196) and nucleotide diversity(π=0.0015±0.0010) of Yangtze Estuary population(YRE) were relatively low. Analysis of molecular variance indicated that a high proportion of the total genetic variance was attributable within populations(86.69%), whereas 12.64% and 0.67% occurred to variations among regions and among populations within regions, respectively.Based on the the haplotypes of mt DNA control region and Cyt b gene, the phylogenetic trees(NJ) and simple network diagrams were built and showed that the haplotypes didn’t form clades corresponding to the geographical distribution.3. Neutrality test and history dynamic of different geographic populations of the finless porpoiseThe Tajima’s D, Fu & Li’s D* and Fu & Li’s F* were less than zero and non-significant, but the Fu’s Fs was less than zero and significant. Meanwhile, the mismatch distribution had a single-peak curve. These results of neutrality test and mismatch distribution showed that Bohai population(NYS), Yangtze population(YR) and Taiwan population(TS) had experienced the historical population expansion. On the other hand, the Tajima’s D was greater than zero and non-significant, the Fu’s Fs was less than zero and significant, but the Fu & Li’s D*and Fu & Li’s F* were less than zero and non-significant. The result of neutrality test showed that Pearl River Estuary population(PRE) was in dynamic balance and not expanding or remarkable quantity increase.