The effect of landscape processes upon gene flow and genetic diversity in an Australian freshwater fish, Neosilurus hyrtlii J. A. HUEY*, A. M. BAKER † AND J. M. HUGHES* *Australian Rivers Institute, Griffith University, Nathan, Qld, Australia † Queensland University of Technology, Gardens Point Campus, Gardens Point, Qld, Australia SUMMARY 1. Flow regime and riverine architecture are two important landscape characteristics that influence genetic diversity and gene flow in riverine species. 2. Using population genetic markers (mtDNA, microsatellites and allozymes), this study aimed to investigate genetic diversity and gene flow in the freshwater fish, Neosilurus hyrtlii, across two major drainage divisions in northern and central Australia (the Gulf of Carpentaria and Lake Eyre basins). These basins lie adjacent to each other and differ in their hydrological inputs and riverine structure, providing an ideal opportunity to identify the impact of landscape processes upon population dynamics of freshwater fish. 3. Populations were strongly structured among basins, among catchments within basins and were weakly structured within catchments in the Lake Eyre Basin, providing support for the Stream Hierarchy Model. 4. Interestingly, mtDNA and microsatellite diversity was much higher in the Gulf of Carpentaria Basin compared to the Lake Eyre Basin. It was concluded that this difference was due to the extreme hydrological variability in this basin and boom-bust population cycles resulting in smaller effective population sizes in the Lake Eyre Basin. Keywords: dryland rivers, gene flow, genetic diversity, hydrological variability, Neosilurus hyrtlii Introduction Understanding patterns of gene flow and genetic diversity in riverine systems is complex as organismal biology, dendritic stream hierarchies and stochastic physical and biological processes interact to generate diverse evolutionary histories and patterns of genetic structure (Meffe & Vrijenhoek, 1988; Amoros & Bornette, 2002; Robinson, Tockner & Ward, 2002; Ward et al., 2002; Hughes, 2007). Therefore, identify- ing the important mechanisms affecting patterns of gene flow and genetic diversity is vital when consid- ering the long-term management of riverine systems and the species that inhabit them (Moritz, 2002). Flow regime is an important landscape process affecting population dynamics in freshwater fish (Resh et al., 1988; Puckridge et al., 1998; Amoros & Bornette, 2002). The most striking example of this is drought, reducing hydrological connectivity and leav- ing ‘refugia’ to sustain populations until connectivity is restored (Humphries & Baldwin, 2003; Magoulick & Kobza, 2003; Matthews & Marsh-Matthews, 2003). If the drought is severe enough, it may lead to popu- lation bottlenecks, reducing genetic diversity and altering the evolutionary trajectory of a species (Douglas, Brunner & Douglas, 2003). Floods are another important hydrological process (Resh et al., 1988), typically producing connectivity across large geographic areas, particularly in floodplain domi- nated catchments (Puckridge et al., 1998; Balcombe et al., 2007). This hydrological connectivity can facil- itate gene flow among otherwise isolated populations Correspondence: Joel Huey, Australian Rivers Institute, Griffith University, Nathan, Qld 4111, Australia. E-mail: joel.huey@nrw.qld.gov.au Freshwater Biology (2008) 53, 1393–1408 doi:10.1111/j.1365-2427.2008.01971.x Ó 2008 The Authors, Journal compilation Ó 2008 Blackwell Publishing Ltd 1393