Abstract: The phylogeography and subspecific situation of the house mouse, Mus musculus in the center and east of the Iranian Plateau has hitherto been neglected due to the hypothesis of commensalism origin of the Iranian house mouse in this region. Meanwhile, geographic bar- riers in central Iran have an important effect on subspe- ciation of the house mouse in this region. In this study, a total of 123 specimens of mice from Iran and Afghanistan were included in the molecular analysis of the mitochon- drial cytochrome b (cytb) gene, 156 specimens of mice were included in geometric morphometrics of the dorsal view of the skull, and 69 specimens of those in outline analysis of the first lower molar (m1). To further explore the relationship among the clades, we selected 19 individ- uals from the four clades and ran a phylogenetic analysis on concatenated sequences of both cytb and the D-loop. Molecular results using maximum likelihood (ML) and Bayesian inference (BI) showed that the Iranian Plateau is occupied with four mitochondrial clades: Mus muscu- lus musculus in northeastern Iran, Mus musculus domes- ticus in western Iran in the Zagros Mountains up to the Persian Gulf basins, clade A (Mus musculus bactrianus) in the east of Iran and Afghanistan, and a new clade B (Mus musculus isatissus) from the center of Iran, which is the sister clade to clade A. This finding demonstrated that the house mouse of central Iran is different from that in the east of Iran and Afghanistan. Geometric morphomet- rics analyses and other morphometric methods of skull and m1 discriminate clade A and clade B. Both molecular and geometric morphometrics analyses separate clade A and clade B. The house mouse of central Iran should be considered as a new subspecies, M. m.  isatissus spp. nov. Our molecular and geometric morphometrics analy- ses concluded that clade A belongs to the subspecies M. m. bactrianus, thereby expanding the distribution of the subspecies from its type locality in the south of Afghani- stan to the east of Iran

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