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

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.

represented with a dash (-). Central clade was not recovered in D-loop and in IB approach with concatenated data. However, MP and ML with concatenated data recovered Central clade with bootstrap of 93% and 58%, respectively. We chose the BI method because it presented higher values of statistical support. Numbers correspond to localities in Appendix S1 and Fig. 1. The circle colors indicate the river basin where samples occur.   Connection 1 is among the Southeast Atlantic and São Francisco basins between the Doce and Das Velhas rivers, a tributary of the São Francisco river. Vieira et al. (2005) counted 12 fish species shared between São Francisco and Southeast Atlantic basins in their study, and the number could be larger if fish fauna of Doce river was better known (Vieira et al., 2005;Vieira, 2010). De Barros et al. 8 (2015) also indicated the connection between Piracicaba river (a tributary of the Doce river) and Das Velhas river as explanation for Cytb haplotypes shared between these different basins in species of the fish genus Oligosarcus Günther.
The sub-basin of the Grande River is a key site in the connection among the Paraná, São Francisco and Southeast Atlantic basins (Connection 2). The fish fauna of the São Francisco River is very similar to that of the Paraná River (Menezes, 1970;Buckup, 2011), indicating a historical contact between these two basins. The high number of fish species shared between the two suggests that the link between the Paraná and São Francisco Rivers is geologically recent (Buckup, 2011). These results are in agreement with those found in the present study because the sub-basin of the Grande River has also served as a recent link between the São Francisco and Paraná populations of N. squamipes.
Moreover, the Grande River sub-basin allowed gene flow between N. squamipes populations through the sub-basin of the Doce and/or Preto rivers (Connections 2 and 3). These connections have been previously reported both for fish (Ribeiro, 2006) and rattlesnakes (Bastos et al., 2005).
The connections among the Paraná, South Atlantic, and Southeast Atlantic basins occurred through the upper Tietê and Paraíba do Sul rivers (Connection 4). The Paraíba do Sul and the upper Paraná river basins were connected in the past though the upper Tietê (Ab 'Saber, 1957;Ribeiro, 2006;Ingenito & Buckup, 2007), and fossil data indicate that this connection is contemporary with the Tremembé Formation in the Late Oligocene or Early Miocene (Gallego & Mesquita, 2000;Vucetich & Ribeiro, 2003;Ribeiro, 2006), long before the origin of N. squamipes. However other connections have been proposed for fishes during the Quaternary Serra et al., 2007;Buckup, 2011), and N. squamipes could have used these recent connections for dispersal across basins.
The connection between the Southeast Atlantic and the East Atlantic (Connection 5) basins may have been mostly influenced by the fluctuations in sea level during the Quaternary. Ocean regressions are frequently called upon to explain the widespread distribution of some fish species throughout the rivers in the coastal region of the Atlantic Forest (Weitzman et al., 1988;Ribeiro, 2006;Menezes et al., 2008;Buckup, 2011) and some phylogeographic patterns of vertebrates (Grazziotin et al., 2006;9 Fitzpatrick et al., 2009). The fish fauna shared among the rivers in these basins are significant, confirming a recent connection (Ribeiro, 2006).

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