The libyan jird is one of the most widely distributed species among wild rodents, with its range extending from Morocco to China. Fifteen subspecies were described but their validity and the phylogenetic relationships among them are uncertain. Based on a comprehensive sampling, this study aims to define subspecies limits within M. libycus and to discuss the factors driving subspecific diversification. We used an integrative approach combining molecular (Cytochrome b and Cytochrome Oxidase Subunit 1 genes) and geometric morphometric data. Genetic and morphometric data allowed us to identify three allopatric lineages within M. libycus : Western lineage in North Africa, Central lineage in Saudi Arabia, Jordan and Syria, and Eastern lineage in Iran, Afghanistan and China. Our results support the existence of at least three subspecies within the Lybian Jird: M. l. libycus, M. l. syrius and M. l. erythrourus. All divergence events within M. libycus occurred during the Pleistocene, after 1.533 Ma. Quaternary climate fluctuations in the Sinai Peninsula explain the differentiation between the African M. l. libycus and the Levant-Arabian M. l. syrius. The differentiation of M. l. syrius with respect to the eastern M. l. erythrourus is putatively linked to the climatic fluctuations and tectonic activity of the Zagros Mountains and/or the Mesopotamia Plain of Iraq during the Pleistocene.

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