Genomic data reveal similar genetic differentiation between invertebrates living under and on a riverine floodplain Steve Jordan, Amanda DelVecchia, Brian K. Hand, Laney Hayssen, Clark Nissley, Gordon Luikart, Jack Stanford sdjordan@bucknell.edu amanda.delvecchia@mso.umt.edu brian.hand@flbs.umt.edu ech015@bucknell.edu can@udel.edu gordon.luikart@mso.umt.edu jack.stanford@flbs.umt.edu Abstract Historical and ecological factors influencing population connectivity of stygobiontic and amphibiontic organisms have long been a topic of intense research and speculation. Here we offer RAD-seq data to show that levels of connectivity of a winged stonefly with ground- water larvae and an obligate groundwater amphipod show similar levels of connectivity between floodplains separated by 40 km in the Flathead River basin of NW Montana, USA. This may be due to deep phreatic water connections that enhance movement of organisms between these populations. 1. Introduction In a landmark 1974 paper, Stanford and Gaufin identified several species of large stonefly larvae from a shallow alluvial aquifer supplying domestic water to a Montana community. Over the ensuing decades, researchers have documented diverse communities of macroinvertebrates, meiofauna, and microbes in shallow aquifers in Montana and worldwide [1,2]. These communities include not only insects that spend some time above ground (amphibionts), but crustaceans, oligochaets, mites, and other taxa that never leave interstitial spaces deep below ground (stygobionts). These animals have been documented beneath riverine floodplains at depths of up to 10 meters and up to 1.5 km from the main river channels [3]. The stoneflies spend 1-3 years maturing in the aquifer before emerging as winged, reproductive adults with an aerial lifespan of only a few days [4]. Shallow aquifers are bounded geologically, and both stygobionts and amphibionts have limited above-ground dispersal capabilities, though to different extents. In addition to isolation, groundwater habitats present many other challenges to stygobiontic taxa, including lack of light and reduced autochthonous carbon fixation, variable water flow rates, and reduced nutrient and oxygen availability [5]. Recent stygobiont research has focused on the ecology of the shallow groundwater environment, noting the variable influence of many abiotic and biotic factors on their spatial distribution, including bedrock geology, soil permeability, water chemistry and quality, groundwater levels, adjacent surface flows, riparian vegetation, and climate, among peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/044073 doi: bioRxiv preprint first posted online Mar. 17, 2016;