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Lakes and rivers in the Baikal ecoregion of central Asia provide particularly interesting models to assess the emergence and maintenance of species diversity, as they display strong contrasts in the composition of their aquatic vertebrate communities. Here, we used RAD-seq to study the recent evolutionary history of five fish species from Lake Hovsgol in Mongolia. This ancient lake was probably recolonized from its outlet following the Last Glacial Maximum, and harbours only ten native fish species. We detected substantial genetic differentiation between the lake and the putative ancestral refuge river in five species but we also found that these species have experienced different population dynamics. Some species appear to have colonized the lake after the Last Glacial Maximum, while others harbour levels of genetic differentiation consistent with the presence of refugia in the lake that could have persisted during glacial maxima or suggestive of colonization from a distinct source. We further demonstrated that fish species have experienced different levels of gene flow following colonization of the lake, suggesting that ecology and habitat use have had a substantial impact on the differentiation of lake populations.

Contrasted patterns of divergence and gene flow among five fish species in a Mongolian rift lake following glaciation