Human activities are increasingly altering ecosystems, and are especially severe in streams where flow modification can affect environments far downstream and can interact with other pressures, such as species invasions. This has led to a disproportionately high number of threatened species in streams (e.g., native galaxiid fishes in New Zealand). I investigated how threatened bignose galaxias (Galaxias macronasus) and upland longjaw galaxias (Galaxias prognathus) were affected by flow-related influences in their habitats. A survey of sub-catchments in the Mackenzie Basin showed that flow regulation played a strong role in influencing fish occurrence; native fishes dominated unregulated rivers and introduced species dominated regulated rivers. Upland longjaw galaxias (ULG) were sparsely distributed and only found in unmodified braided rivers. Targeted surveys in these rivers indicated their habitat selection was weak, and although habitat availability was high, individual habitats were only occupied for short periods because floods frequently reconfigured the river bed. Thus, disturbances played a major role in ULG populations, forcing a strategy of weak habitat selection and frequent movement. This also makes them vulnerable to large-scale flow changes making the habitat more benign and potentially increasing competition (e.g., from invasive trout). Bignose galaxias were only locally abundant in very low discharge habitats lacking other fishes, so were restricted to very small parts of the river network. An experiment manipulating flows showed bignose galaxias moved into slower habitats over the short-term, suggesting a slow-flow preference, but not excluding the competitive influences of other fish like trout. Overall, this work shows these threatened fishes are susceptible to many of the current and future global changes affecting freshwaters like habitat alteration and invaders, but the above knowledge should allow targeted management of these influences for these highly threatened endemic fish.

The dispersal of freshwater fishes in the Cape Floristic Region of South Africa has been attributed to river capture events and confluence of rivers during sea level regression. The role of low drainage divides and inter-basin water transfers have received less attention. A unique lineage of Galaxias zebratus (hereafter the Joubertina galaxias) occurs in two currently isolated river systems, the Gamtoos and Krom. The present study mapped the distribution of the Joubertina galaxias and used mitochondrial and nuclear DNA sequences to assess the processes that could have influenced its current distribution pattern. Analyses of both mitochondrial cytochrome ♭ and nuclear (S7) sequences revealed that observed genetic differentiation cannot be explained by isolation between the Gamtoos and Krom River systems. No genetic differentiation was found between the Krom River System and the Twee River (a tributary of the Gamtoos River System). Shallow genetic differentiation (0.4% for cytochrome ♭ and 0.3% for S7) was found between the Krom and the remaining populations in the Gamtoos River System. High levels of genetic structuring were observed within the Gamtoos River System with most tributaries having one or more unique alleles. Inter-basin dispersal during pluvial periods or recent human mediated translocation seems to be the most plausible explanations for presence of the Joubertina galaxias in the Krom River System. The present study also assessed the threats and habitat preferences of the Joubertina galaxias, and an evaluation of the conservation status of this lineage was done. The Joubertina galaxias is threatened mainly by alien fish invasion, habitat loss and loss of genetic diversity due to fragmentation of its populations. Due to its very restricted geographic range, small known population sizes and the intensity of threats to this lineage’s survival, this lineage has been assessed as Endangered. The lineage has a restricted Area of Occupancy (AOO) and Extent of Occurrence (EOO). The extent of occurrence has declined in all tributaries and is continuing to decline in all except two tributaries that are secure. The lineage may have had natural fragmentation among its populations, but recent threats have completely isolated the populations. The threats affect the lineage’s survival potential in the four tributaries which have small populations that are not presently viable. The densities observed for the Joubertina galaxias ranged from 0.16 - 1.3 fish /m² and the number of mature individuals for the whole population seems to be less than 2500 mature individuals. There is therefore a need for specific conservation actions to ensure the long-term survival of this unique lineage.

To test competing hypotheses about the relative roles of vicariance and dispersal in the freshwater fishes in Galaxiidae, a phylogenetic framework and a time scale for species divergence were estimated using mitochondrial and nuclear DNA sequences. Relaxed clock dating revealed that the Galaxiidae originated in Gondwana in the late Cretaceous and thus vicariance cannot be ruled out for the two basal lineages, Galaxiella and Brachygalaxias. These two lineages are ancient relicts that rafted to their present distributions or were fragmented by the separation of Australia from South America via Antarctica. The opening of the Drake passage between South America and Antarctica initiated the proto-Antarctic Circumpolar Current (pACC) and counter-clockwise circulation in the South Atlantic, on which marine stage ancestors could have dispersed to South Africa and New Zealand via Australia during the late Eocene. Thus dispersal explains the disjunct distribution of the clade comprised of G. platei, G. zebratus and Neochanna spp. in South America, South Africa, and Australasia. The narrowing of the Drake passage and collapse of the pACC from about 24-14 Mya likely prevented further contact between South America and South Africa. Tectonic events around the globe produced an anomalous warming event, which along with the uplift of New Zealand provided empty niches and promoted the radiation of Galaxias. Most of the speciation in the other clades occurred during this time. When the Antarctic Circumpolar Current was reactivated at the end of the Mid-Miocene Climatic Optimum (MMCO) about 15–14 Mya, it provided a marine conveyor belt for the dispersal of the ancestor of Galaxias maculatus from Australia to South America, and later to Australia and New Zealand. The integration of divergence times estimated on the phylogeny with ancestral area reconstruction supports an origin in Gondwana and subsequent oceanic dispersal as the explanation for the distribution of the Galaxiidae across the southern continents.

To test competing hypotheses about the relative roles of vicariance and dispersal in the freshwater fishes in Galaxiidae, a phylogenetic framework and a time scale for species divergence were estimated using mitochondrial and nuclear DNA sequences. Relaxed clock dating revealed that the Galaxiidae originated in Gondwana in the late Cretaceous and thus vicariance cannot be ruled out for the two basal lineages, Galaxiella and Brachygalaxias. These two lineages are ancient relicts that rafted to their present distributions or were fragmented by the separation of Australia from South America via Antarctica. The opening of the Drake passage between South America and Antarctica initiated the proto-Antarctic Circumpolar Current (pACC) and counter-clockwise circulation in the South Atlantic, on which marine stage ancestors could have dispersed to South Africa and New Zealand via Australia during the late Eocene. Thus dispersal explains the disjunct distribution of the clade comprised of G. platei, G. zebratus and Neochanna spp. in South America, South Africa, and Australasia. The narrowing of the Drake passage and collapse of the pACC from about 24-14 Mya likely prevented further contact between South America and South Africa. Tectonic events around the globe produced an anomalous warming event, which along with the uplift of New Zealand provided empty niches and promoted the radiation of Galaxias. Most of the speciation in the other clades occurred during this time. When the Antarctic Circumpolar Current was reactivated at the end of the Mid-Miocene Climatic Optimum (MMCO) about 15–14 Mya, it provided a marine conveyor belt for the dispersal of the ancestor of Galaxias maculatus from Australia to South America, and later to Australia and New Zealand. The integration of divergence times estimated on the phylogeny with ancestral area reconstruction supports an origin in Gondwana and subsequent oceanic dispersal as the explanation for the distribution of the Galaxiidae across the southern continents.