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Background  The water rat  Nectomys squamipes  (Cricetidae: Sigmodontinae) is a semiaquatic rodent from eastern South America that shows shallow genetic structure across space, according to some studies. We tested the influence of hydrography and climatic changes on the genetic and phylogeographic structure of this semiaquatic small mammal.    Methods  DNA sequences of two mitochondrial genetic markers (Cyt b and D-loop) and six microsatellite loci from water rats were collected at 50 localities in five river basins in the Atlantic Forest along the eastern coast of South America. We evaluated the genetic structure within and among river basins, and we estimated divergence dates. Species distribution models for the present and past were built to identify possible gene flow paths.    Results  Mitochondrial data and species distribution models showed coherent results. Microsatellite loci showed a more complex pattern of genetic differentiation. The diversification of  N. squamipes  haplotypes occurred during the Pleistocene and the river basin cannot explain most of the genetic structure. We found evidence of population expansion during the last glacial maximum, and gene flow paths indicate historical connections among rivers in the Atlantic Forest.    Discussion  Historical connections among rivers in the Atlantic Forest may have allowed  N. squamipes  to disperse farther across and within basins, leading to shallow genetic structure. Population expansions and gene flow through the emerged continental shelf during glacial period support the Atlantis forest hypothesis, thus challenging the forest refuge hypothesis.

Historical connections among river basins and climatic changes explain the biogeographic history of a water rat