Population structure of obligate groundwater amphipod crustaceans (Stygobromus sp.) in alluvial aquifers

Gravel-bed river floodplains occur in river corridors around the globe. One key habitat of these floodplains are alluvial aquifers that provide habitat for a wide range of obligate groundwater species. Multiple species of the amphipod genus Stygobromus commonly occur in alluvial aquifers, as well as in karstic phreatic systems, but few studies have investigated the population structure and its relevance to the biogeography of the genus. Using reduced representation genome sequencing, RAD-seq, we investigated the population structure and genetic connectivity of an undescribed Stygobromus species in several alluvial aquifers on floodplains of the Flathead River, Montana (USA). Amphipods were genetically similar (pairwise F_ST ranging from 0.0061 to 0.0092) at multiple sites within floodplains but three genetic clusters were segregated among floodplains (pairwise F_ST ranging from 0.0303 to 0.0547), suggesting some geographic isolation of populations. These floodplain aquifers are separated by bedrock canyons that could be migration barriers resulting in the observed spatial segregation of populations.