Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola

Molecular dating methods of population splits are crucial in evolutionary
biology, but they present important difficulties due to the complexity of
the genealogical relationships of genes and past migrations between
populations. Using the double digest restriction-site associated DNA
(ddRAD) technique and an isolation-with-migration (IM) model, we studied
the evolutionary history of water vole populations of the
genus Arvicola, a group of complex evolution with fossorial and
semi-aquatic ecotypes. To do this, we first estimated mutation rates of
ddRAD loci using a phylogenetic approach. An IM model was then used to
estimate split times and other relevant demographic parameters. A set of
300 ddRAD loci that included 85 calibrated loci resulted in good mixing
and model convergence. The results showed that the two populations
of A. scherman present in the Iberian Peninsula split 34
thousand years ago, during the last glaciation. In addition, the much
greater divergence from its sister species, A. amphibius, may
help to clarify the controversial taxonomy of the genus. We conclude that
this approach, based on ddRAD data and an IM model, is highly useful for
analyzing the origin of populations and species.