Date of Thesis

Fall 2019


Floodplain aquifer systems are diverse and heterogenous ecosystems that serve many ecological functions, including habitat provision to a range of groundwater species. The Flathead River system of northwestern Montana is home to many floodplain aquifers of great ecological importance to the region. The basic biology, population structure, and dispersal patterns of obligate groundwater organisms that reside within the aquifers of the Flathead are still largely unknown. In this study, we investigate the population structure of one such taxon, an undescribed species of the amphipod genus Stygobromus. For our low-coverage RADseq dataset, we tested the suitability of three different analysis pipelines: Stacks, GATK, and ANGSD. We found three distinct genetic groups that corresponded to different floodplains of the Flathead River. These results suggest that geographic separation and possible hydrologic barriers are leading to differentiation of these populations. We discuss the possible role of glacial refugia in promoting genetic diversity and the implications for aquifer research and groundwater conservation.


genomics, population structure, Stygobromus, evolution, climate change, Crown of the Continent

Access Type

Masters Thesis

Degree Type

Master of Science



First Advisor

Steve Jordan