Genetic structure of Afghan Pika (Ochotona rufescens) populations based on D-loop region of the mitochondrial genome in Northern Khorasan Province

This study was carried out for genetic diversity of Afghan Pika (Ochotona rufescens) among four different populations in Northern Khorasan Province using D-Loop region of mitochondrial gene. The sixteen specimens were trapped from four different sanctuaries (Ghorkhod، Golol-Sarani، Salouk and Sarigol) and transferred to Laboratory. The intra and inter population genetic factors (haplotype and nucleotide diversity، haplotype differentiation among populations، Fst، Nm، gamma distribution parameter، mismatch distribution، Tajima''D neutrality test and Isolation by distance) were estimated and the results were compared among the populations. Finally، data set with 483 bp was used for each individual. The results showed 25 polymorphic، 457 conserved sites and 10 different haplotypes. The low value of Fst (Fst=0. 21، P<0. 05) among populations based on D-Loop region of mitochondrial gene showed that genetic differentiation among populations were low and gene flow between populations were high. Mantel test (10000 irritations) showed that the relationship between distance and genetic matrix among all individuals (r=0. 172، P=0. 057) and among populations (r=-0. 64، P=0. 159) were not significance and IBD did not occur. Discrete gamma distribution for estimating heterogeneity rate among populations was 200 which indicated low mutation or heterogeneity rate among the four populations. The Rogers-Harpending index for mismatch distribution (0. 08، P>0. 5) and Tajima ''D test (0. 37، P>0. 1) showed no population expansion and relatively stable population sizes.