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The North American Great Basin is a useful venue for the study of dispersal, vicariance, and rates of molecular evolution among aquatic organisms because its Pleistocene hydrogeographic history is relatively well known. This study examines regional molecular variation in the amphipod Hyalella azteca using mitochondrial (mt) gene sequence (deoxyribonucleic acid [DNA]) data. Populations within several endorheic drainages in the southern Great Basin were analyzed to determine if they represent a monophyletic assemblage with respect to populations from the pluvial Lake Bonneville drainage in the northern Great Basin. We also tested whether the patterns of molecular diversification among populations in the southern Great Basin were consistent with a Pleistocene vicariance hypothesis, and if the magnitude of observed sequence divergence was concordant with standard molecular clock calibrations. Our results show that diversity and endemism among Hyalella populations in the southern Great Basin are high with respect to those in the Lake Bonneville Basin. We further demonstrate that hyalellid populations in the southern Great Basin are a polyphyletic assemblage with respect to their counterparts in the Bonneville Basin, suggesting that dispersal events have been partially responsible for the enigmatic relationships within this assemblage. The relationships among lineages within the southern Great Basin are largely enigmatic and are not concordant with Pleistocene hydrographic history. Our data also indicate that rates of molecular evolution have been heterogeneous; there is a 2.8-fold disparity in relative rates of mtDNA divergence among closely allied lineages. The magnitude of sequence divergence among lineages is inconsistent with standard molecular clock calibrations, and evidence indicates that accelerated rates of divergence may have contributed to the high diversity and endemism among Great Basin hyalellids, complicating reconstruction of the temporal sequence of biogeographic events.

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