We investigated genetic variation in mitochondrial cytochrome b within the long-tailed rice field mouse, Mus caroli Bonhote, 1902, across its entire geographic range in Southeast and East Asia with a view to: 1) assessing the pattern and causality of phylogeographic structure in a terrestrial small mammal from continental Southeast Asia; and 2) distinguishing genuine insular relics from cases of human-assisted translocation. We identified five main mtDNA lineages which show a similar level of differentiation as the subspecies of M. musculus and probably diverged during the Middle Pleistocene. Two of the lineages are restricted to large islands (Taiwan and Java) and their existence is explicable in terms of regional palaeogeographic factors including changes in sea level and climate. The remaining lineages are distributed in different regions on mainland Southeast Asia but vicariant explanations are inappropriate given the relatively short time frame. Dispersal across barriers followed by local differentiation probably explains the observed phylogeographic patterning on the mainland. A close genetic link between Okinawan M. caroli and populations in Laos confirms previous suggestions that people carried this species to the Ryukyu Archipelago. However, more intensive regional sampling is needed to identify a precise source area.
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Vol. 32 • No. 2