Old world ground squirrels (genus Spermophilus) are distributed throughout the Holarctic and Palearctic regions, of which two Iranian species, the Yellow ground squirrel S. fulvus and the Asia Minor ground squirrel S. xanthoprymnus, comprise the southernmost distribution of the genus in the Palearctic. The two species are found in fragmented populations from northeastern to northwestern Iran, with S. fulvus being more common and widespread in the country. The enormous geographical distance (more than 1000 km) between Yellow ground squirrel’s patchy populations in eastern and western Iran has led to ambiguous evolutionary relationships and consequently uncertain conservation planning for the species. We studied the phylogenetic relationships and spatial genetic structure of the isolated populations using the mitochondrial Cytochrome b (cyt b) among 79 individuals. Our phylogenetic analysis found that S. fulvus was divided into three main mtDNA clades in Iran. Molecular dating suggested an ancestral expansion from high latitudes towards Iran during the cold periods (before the Holsteinian temperate period), followed by contraction of populations into interglacial refugia around the Holsteinian temperate period (430-350 Kya), leading to their isolation from their ancestral pool about 427 Kya. Furthermore, we found a non-deep phylogenetic divergence between patchy isolated populations of the species in Iran. A major genetic break was detected between populations of eastern Iran (steppes in Hezar Masjed and Binalud mountains, near Iran-Turkmenistan-Afghanistan borderline) and the others, probably associated with their confinement to interglacial refugia during the Domnitz temperate period (340-300 Kya). However, the recent divergence between northeastern and western populations of Iran probably resulted from their contraction into interglacial refugia in the Saale/Drenthe temperate period (250-190 Kya). These results may suggest that populations of the Yellow ground squi
