Genetic relationships among collections of the Persian sturgeon, Acipenser persicus, in the south Caspian Sea detected by mitochondrial DNA–Restriction fragment length polymorphisms

In the present study, mitochondrial DNA polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay was used to assess the population structure and genetic relationships among six Persian sturgeon, Acipenser persicus populations from the south Caspian Sea along the Iranian coast. The complete nucleotide dehydrogenase subunit 5 (NADH 5) region of mtDNA amplified by PCR was digested with five restriction enzymes. In total, 154 individuals from six populations including: Guilan (Zone1-2), Mazandaran (Zone 3 and 5), Golestan (Zone 4) and Sefidroud River, from the south Caspian Sea along the Iranian coast were analyzed using five restriction endonucleases (Rsa І, Hinf І, HaeIII, Mbo І and Cfr13І), yielding 17 haplotypes. Samples from Sefidroud River were clearly identified by cluster and molecular variance model (AMOVA) analyses. This collection showed dominant haplotypes that were little in populations from the other geographic areas. The mean haplotype diversity (h) and nucleotide diversity (π) were 0.739±0.038 and 0.0105±0.0043, respectively. Based on heterogeneity test haplotype frequencies of Persian sturgeon populations and Monte-Carlo with 1000 replicates in PCR-RFLP method significant differences were seen (χ2 =37.12, P< 0.0001) and these results showed that haplotype distribution in different location were significant and populations of Sefidroud River were statistically significant (P< 0.0001). This result suggests that the unique genetic structure of Sefidroud River represents a highly valuable genetic resource and should now be treated as demographically independent and managed separately

Genetic diversity in the Persian sturgeon, Acipenser percicus, from the south Caspian Sea based on mitochondrial DNA sequences of the control region

The Persian sturgeon, Acipenser persicus (Borodin, 1897), is an economically important species, which mainly inhabits the Caspian Sea. However, little is known about its population genetic structure. In this study, variation in nucleotide sequences of the mitochondrial DNA (mtDNA) control region of wild stock Persian sturgeon was determined to assess the genetic diversity among different natural populations of this species. The fish (n = 46) were collected from four sites (Astara, Sefidrood, Noshahr and BandareTurkaman) in the south Caspian Sea. As a result 6 haplotypes and 44 variable sites were found. The average haplotype diversity (h) and nucleotide diversity (π) were 0.640±0.028 and 0.0442±0.011, respectively. Analysis of molecular variance (AMOVA) demonstrated that most variations occurred within samples, and the difference between the populations from Astara and Noshahr or Bandare- Turkaman was not significant (p <0.001). Estimates of gene flow indicated reproductive isolation between the Sefidrood River population and the other collections. The divergence might be related to geographical isolation. The results are consistent with the findings from PCR-RFLP analysis (PCR-RFLP) and suggest considerable genetic diversity of the population from Sefidrood River

Population genetic structure of Persian sturgeon (Acipenser persicus) between South Caspian Sea and Sefidrud River using DNA sequencing method

The goal of this study was to analyse the population genetic structure of the Persian sturgeon (Acipenser persicus) between South Caspian Sea and Sefidrud River with mtDNA control region (Dloop gene) and DNA sequencing method during 2010 – 2012 sturgeon stock assessment project. Fish speciemns were collected by bottom trawl net. Extraction of DNA, PCR and DNA sequencing were carried out. Diversity index, the gamma distribution shape parameter for the rate heterogeneity among sites and nucleotide sequence, Fst index, exact test, the historical demographic pattern using neutrality tests and mismatch distribution analysis (D test of Tajima and Fs test of Fu) were analysed. Thirteen haplotypes were obtained, average (±SD) for haplotype diversity was 0.961 ± 0.101, nucleotide diversity was 0.038 ± 0.015, the gamma distribution shape parameter was 0.19, Fst index revealed little genetic structure between populations and the significant Fst value was seen by 10000 permutation only between Sefidrud River and Other Areas (P≤ 0.05) and was confirmed by exact test of population differentiation. Mismatch distribution for Acipenser persicus appeared to be unimodal, which closely matched the expected distributions under the sudden expansion model and supported by the low Harpending’s Raggedness index (0.061). Tajima’s D and Fu’s Fs statistics were -0.84 and - 0.220, respectively, and was not significant. The results of this study showed that the population of Acipenser persicus in Sefidrud River were genetically differentiated from South Caspian Sea and three other areas represented a single panmictic populations. Therefore, fisheries managements of this valuable species should be directed towards conservation of gene pools and increasing different populations

Study on genetic structure of Caspian Sea sturgeons in the stock assessment of sturgeon in Iranian coastline of the south Caspian Sea

The population genetic structure of the Persian sturgeon (Acipenser persicus) in the 2, 3, 4 fisheries regions and Sefidrud River was investigated based on the DNA sequencing method during 2010–2013 sturgeon stock assessment in the south Caspian Sea . DNA samples were extracted using ammonium acetate, the quantity of DNA was measured at 260 and 280 nm using spectrophotometry by Nanodrop (ND 1000 model), and the quality was checked by 1% agarose gel electrophoresis. Two sets of mitochondrial gene (D-loop and cytochrom b) after synthesis were used for polymerase chain reaction (PCR). A Neighbor-Joining (NJ) tree was constructed for all haplotypes according to Kimura 2-parameter model using Mega Version 4.0.1, number of haplotypes, haplotype diversity (Hd) and nucleotide diversity and their corresponding variances, genetic divergence overall and between paired populations (Fst) by 10,000 permutations and exact test, the gamma distribution shape parameter for the rate heterogeneity among sites and nucleotide sequence, the historical demographic pattern of A.persicus using neutrality tests and mismatch distribution analysis (D test of Tajima and Fs test of Fu), also the concordance of the observed with the expected distribution under the sudden population model using the Harpending, s raggedness index (Hri) were analysed. All calculations were conducted using ARLEQUIN version 3.11 and DnaSP 4.0. The aligned mtDNA sequences of D-loop and cytochrom b genes were consisted of 500 and 700 base pairs (bp) respectively. 13 and 4 haplotypes were defined, the average haplotype diversity were 0.961 and 0.419, average nucleotide diversity were 0.038 and 0.002, The gamma distribution shape parameter were 0.19 and 0.20 indicating moderate mutation rate heterogeneity among sites in A.persicus. The lowest value of Fst for D-loop gene was calculated between Sefidrud and four fisheries region (-0.002) and the Fst values observed for cytochrom b gene was 0.04 with Nm=5.37 and not statistically significant. The exact test of population differentiation (non-differentiation exact P values) showed significant differences between Sefidrud and other areas (P ≤0.05) for D-loop gene and for cytochrom b gene was nonsignificant (P ≥0.05). The mismatch analysis produced a unimodal distribution of pairwise differences for both genes which was consistent with the sudden population expansion model. Tajima’s D and Fu’s Fs statistics were significantly negative (D= -0.84 and - 0.99, P>0.01; Fs=-0.220 and -0.079, >0.01). ARLEQUIN calculated the value of t as 13.65 and the time since population expansion was estimated to be approximately 1501 years before present based on the mutation rates for the control region and this value for cytochrom b gene t= 0.98 which population expansion time was 7.84 years before present. The results of this study based on D-loop gene showed that population of A.persicus in the Sefidrud River is differ from other studied areas. Therefore fisheries managements of this unique and valuable stock for restocking and conservation of gene pools is strongly recommended