Today, decisions regarding the management and conservation of populations are often informed to some degree by population genetics. A fundamental measure sought by decisionmakers is the degree of connectivity between populations, which, when approached from a genetic perspective, may be influenced by many factors, making it difficult to generalize across taxa, habitats, or life histories. In the case of freshwaterlimited fauna, the shared constraint of habitat structure (e.g., a dendritic stream network) imposed on all species in the system simplifies the task. A number of models have been proposed that predict how populations of taxa with different life-history traits and dispersal capabilities interact within structured freshwater habitats of this kind. In this article, we summarize these models and illustrate the general patterns of phylogeographic structure expected to occur under different scenarios of freshwater population connectivity. Additionally, we describe how the genetic structure of stream inhabitants can reflect historical changes in the physical structure of streams and thus open a window on past patterns of connectivity. A greater understanding of these concepts will contribute to an improved multidisciplinary approach to managing freshwater ecosystems.

Although most vertebrates reproduce sexually, a small number of fishes, amphibians and reptiles are known in which reproduction is asexual, i.e. without meiotic recombination. In fishes, these so-called unisexual lineages usually comprise only females and utilize co-occurring males of a related sexual species to reproduce via gynogenesis or hybridogenesis. Here, we examine patterns of microsatellite and mitochondrial DNA (mtDNA) variation in a widespread group of freshwater fishes (carp gudgeons; Hypseleotris spp.) to investigate a long-standing proposal that this group includes unisexual forms. We show that the mtDNA genome of most carp gudgeons in tributaries of the Goulburn River belongs to one of two deeply divided clades (∼10% cyt b divergence) and that nuclear variation divides the same individuals into four distinct groups. Group 1 exhibits the genotypic proportions of a random mating population and has a 1:1 sex ratio. Two other groups are extremely sex-biased (98% male, 96% female), exhibit excess heterozygosity at most loci and share at least one allele per locus with group 1. We propose that these two groups represent 'unisexual' hybridogenetic lineages and that both utilize co-occurring group 1 as sexual host. Interestingly, the fourth distinct group appears to represent hybrid offspring of the two putative hybridogenetic lineages. The propagation of clonal haploid genomes by both males and females and the ability of these clones to unite and form sexually mature diploid hybrid offspring may represent a novel mechanism that contributes to the dynamics of coexistence between hybridogenetic lineages and their sexual hosts.

Summary 1. Effective management of aquatic fauna requires knowledge of the ways in which populations in different catchments and sub‐catchments are connected. A powerful way to estimate this is using genetic markers, which provide information on the average amount of genetic connectivity among populations over generations. Although many studies of genetic connectivity have appeared in the literature, there are innumerable species that have not been studied. 2. This study explores whether it is possible to make broad generalisations about population connectivity, based on readily available information in the form of species life history and architecture of the aquatic habitat. 3. A number of models have been proposed to explain the pattern of connectivity shown by aquatic species with different life‐history characteristics, for example, the stream hierarchy model, Isolation by Distance, the Death Valley Model, the headwater model and panmixia. 4. In this study, we propose a dichotomous key to assign species to different models of potential connectivity. The key is based on a few very simple questions about the life history of the species and the geographical arrangement of study sites. We then assessed the performance of the key with 109 data sets of Australian fish and macroinvertebrates, using genetic data to provide an estimate of realised connectivity. 5. The realised connectivity fitted the proposed potential connectivity model in over 70% of cases, and we suggest this might be a useful initial approach for managers where empirical data are lacking.

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Patterns of dispersal in riverine populations of Australian smelt ( Retropinna semoni ) were examined using otolith chemistry (Mg:Ca, Mn:Ca, Sr:Ca, Ba:Ca) and genetic markers (allozymes, mtDNA, microsatellite DNA). During a period of prolonged low flows, young-of-year smelt were collected from 13 streams within three catchments of the southern Murray–Darling Basin, Australia. Spatial differences in otolith core and edge chemical signatures and high levels of genetic assignment to sampling locations were observed, suggesting that most recruits were retained in natal areas after spawning. Following a subsequent period of hydrological connection, the same cohort was sampled as 1-year-olds. Maximum likelihood estimation using otolith core chemistry data from these fish suggested that retention in natal areas was highly variable between years and a similar, though less pronounced, pattern was evident in genetic assignments. Partitioning of genetic variation among catchments was not significant (FCT < 0.004) and probably reflects disequilibrium between migration and genetic drift due to an historical population expansion (~270 000 years ago). Taken together, otolith chemistry and genetic analyses suggest that contemporary dispersal of smelt within these catchments is relatively restricted and may be mediated by changes in hydrological connectivity.