The effects of riverine impoundment on genetic structure and gene flow in two stream fishes in the Mobile River basin BROOK L. FLUKER*, BERNARD R. KUHAJDA* ,1 AND PHILLIP M. HARRIS* *Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, U.S.A. SUMMARY 1. Riverine impoundments (reservoirs) are thought to impede natural migration in small-stream- inhabiting fishes, resulting in spatially and genetically fragmented populations. However, this hypothesis remains poorly tested, and the genetic consequences of riverine impoundment for stream fishes with differing dispersal capabilities are not well understood. 2. This study utilised a combination of microsatellite DNA loci from 479 individuals and the mitochondrial (mt) DNA cytochrome b gene (810–1140 bp) from 83 individuals from eight streams to compare genetic structure and diversity between reservoir-fragmented and non-fragmented groups of two species of stream fishes with differing dispersal capabilities in the Mobile River basin of the south-eastern United States. 3. For both species, analysis of microsatellite loci revealed genetic discontinuities between neighbour- ing tributaries that have been fragmented by reservoir construction. This finding was in stark contrast to the high degree of continuity for both species between reference tributaries in a natural river setting. Results from mtDNA revealed no significant genetic structure within reservoir-frag- mented or non-fragmented groups, indicating a lack of historical genetic structure (i.e. prior to reservoir construction). Microsatellite-based estimates of genetic diversity and migration were differ- entially affected in the two species, indicating that stream fishes with relatively high dispersal abilities may be equally or more susceptible to reservoir fragmentation when compared to species with relatively low dispersal abilities. 4. Collectively, our data revealed that riverine impoundment and reservoir-induced habitat fragmen- tation adversely affect genetic characteristics in small-stream-inhabiting fishes. This is of particular interest in biodiversity hotspots such as the south-eastern United States where hydroelectric and recreational reservoirs restrict connectivity in aquatic systems. Keywords: dams, genetic structure, habitat fragmentation, microsatellites, reservoirs Introduction Habitat fragmentation is one of the leading causes of decline in biodiversity worldwide (Fahrig, 2003; Fischer & Lindenmayer, 2007; Lindenmayer et al., 2008; Heller & Zavaleta, 2009). Anthropogenic habitat alteration often results in the fragmentation of previously continuous migration routes, resources or environmental conditions (Segelbacher et al., 2010). For many organisms, habitat fragmentation and overall loss of favourable habitat leads to subdivision into smaller, isolated populations with reduced or no connectivity (Kindlmann & Burel, 2008). Of particular interest for the conservation of bio- diversity is the degree to which contemporary habitat discontinuity affects functional connectivity via individ- ual exchange and gene flow (Fischer & Lindenmayer, 2007). Reduced gene flow among populations leads to reduced intra-population genetic variation, which can Correspondence: Brook L. Fluker, Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL 35487, U.S.A. E-mail: blfluker@ua.edu 1 Present address: Tennessee Aquarium Conservation Institute, Chattanooga, TN 37402, U.S.A.. 526 © 2013 John Wiley & Sons Ltd Freshwater Biology (2014) 59, 526–543 doi:10.1111/fwb.12283