Freshwater systems offer important opportunities to investigate the consequences of intrinsic biological and extrinsic environmental factors on the distribution of genetic variation, and hence population genetic structure.

I examined three species from three families of Australian freshwater fish, Pseudomugil signifer (Pseudomugilidae), Craterocephalus stercusmuscarum (Atherinidae) and Hypseleotris compressa (Gobiidae). These species are abundant, have wide overlapping distributions and qualitatively different dispersal capabilities. I was interested in attempting to unravel how the biological, environmental and historical factors had served to influence the patterns and extent of genetic diversity within each species, thereby inferring some of the important evolutionary processes which have affected Australia's freshwater fauna. I used allozyme and 500-650bp sequences from the ATPase6 mitochondrial DNA (mtDNA) gene to quantify the patterns of genetic variation at several hierarchical levels: within populations, among populations within drainages and among drainages. I collected fish at several spatial scales, from species wide to multiple samples within drainages; samples were collected from the Northern Territory, Queensland and New South Wales.

The species with the highest potential for dispersal, H. compressa, exhibited the lowest levels of genetic differentiation as measured at several allozyme loci (H. compressa: FST=0.014; P. signifer FST=0.58; C. stercusmuscarum FST=0.74). Populations of H. compressa also had low levels of mtDNA differentiation, with many recently derived haplotypes which were widespread along the coast of Queensland. This suggested either considerable gene flow occurs or recent demographic change in the populations sampled. As there was no relationship between geographic distance and genetic differentiation, the populations appeared to be out of genetic drift - gene flow equilibrium, assuming a two-dimensional stepping stone model of gene flow. It was concluded that there has been greater connectivity among populations of H. compressa in the recent past than either of the other study species.

Populations of P. signifer showed considerable genetic subdivision at different hierarchical levels throughout the sampled range, indicating gene flow was restricted, especially between separate drainages. Two widely divergent regional groups were identified and mirrored previous taxonomic designations. There was also significant subdivision among drainages within regional groups. I examined population structure within drainages of two essentially independent, but geographically close systems. Results suggested that a confluence between subcatchments was not a barrier to gene flow, but that distance was an important component in the determination of the distribution of genetic diversity within drainages in P. signifer.

For C. stercusmuscarum the genetic data suggested that populations in upland areas of easterly flowing rivers resulted from invasions via the diversion of western flowing rivers. Indeed, it appeared that there may have been two independent invasions into the upland areas of rivers in North Queensland. Second, population structure of lowland east coast populations was consistent with there being many small, isolated subpopulations over the range. Third, populations in south east Queensland, appeared to be derived from western flowing streams, and not via dispersal from other lowland east coast populations.