Phylogeography and taxonomy of Afghan pikas Ochotona rufescens in Western Asia were investigated based on a combination of mitochondrial cyt b gene sequences and morphometric analyses. We measured 200 specimens from the whole range of O. rufescens in Western Asia, including the holotypes of O. r. regina, O. r. shukurovi, O. r. vulturna, O. r. vizier and samples from vicinity of the type locality of O. r. rufescens. Principal Component and Factor analyses did not reveal any notable geographical variations. The phylogenetic analysis of mitochondrial cyt b sequence data from 72 specimens of Afghan pikas included six topotypes of three of the recognized subspecies and revealed that divergence between most populations is shallow. The major genetic divergence lay between the samples from Afghanistan and other populations. Previously unrecognized lineages of Afghan pikas were identified in Central Alborz and central east Iran. We demonstrated minor divergence between O. r. regina from Kopet Dagh Mountains, and O. r. shukurovi from the Great Balkhan Mountains, indicating a recent divergence between these two populations. We hypothesize that Pleistocene climate fluctuations in Western Asia are responsible for the diversification in O. rufescens, but that adverse local edaphic conditions in the lowlands may have largely prevented dispersal during glacial periods, thus making dispersal events more infrequent than for comparable populations of pikas in North America.

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