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Relationships among the historically isolated lineages of Pseudobarbus were reconstructed using molecular and morphological data. Contradictions between the molecular and morphological phylogenies suggest convergent evolution and homoplasy in some morphological characters. The earliest divergence in Pseudobarbus was between P. quathlambae in Lesotho and the rest of the genus associated with the Cape Foristic Region in South Africa. A close relationship between P. phlegethon from the Olifants River system on the west coast of South Africa and a lineage of P. afer from small river systems in Afrotemperate Forests on the south coast, can only be explained through previous occurrence and subsequent extinction of ancestral populations in the Gourits River system. Several river systems had confluences before reaching lower sea levels, most notably during the last glacial maximum about 18,000 years ago, explaining closely related populations across different river systems. Mainly river capture explains shared lineages across river systems that did not share a common confluence during lower sea levels.

Aim  The phylogeography of the two closely related species Pseudobarbus afer and Pseudobarbus phlegethon was investigated to assess the association of evolutionary processes, inferred from mitochondrial DNA (mtDNA) sequence variation, with hypothetical palaeoriver systems and other climatic and landscape changes. Location  One western and several southern river systems in South Africa. Methods  We sampled known populations and confirmed known distribution gaps. This was followed by an assessment of mtDNA control region sequence variation for 31 localities across 17 river systems across the range of the species complex. A map of possible offshore drainage patterns during the last major regression event was constructed based on bathymetry and geological studies. Results  The genetic distinction of four major lineages of P. afer strongly correspond with proposed palaeoriver systems. However, a western ‘Forest’ lineage, is widespread across two such proposed systems and is closely related to P. phlegethon on the west coast of South Africa. Both the ‘Krom’ and ‘St Francis’ lineages were identified in the single palaeoriver system proposed for St Francis Bay. A fourth ‘Mandela’ lineage is restricted to the one or two palaeoriver systems proposed for Nelson Mandela Bay. Four minor lineages were identified within the Forest lineage and two within the Mandela lineage. Main conclusions  The close relationship between P. phlegethon and the Forest lineage of P. afer can only be explained by a series of river captures. We suggest the Gourits River system as a historical link that could account for this relationship. On the south coast, lower sea levels than at present allowed confluence between currently isolated river systems, offering opportunities for dispersal among these populations. At present, isolation between different river systems rather than dispersal appears to have a dominant influence on mtDNA diversity.

This study used phylogenetic analyses of mitochondrial cytochrome b sequences to investigate genetic diversity within three broadly co-distributed freshwater fish genera (Galaxias, Pseudobarbus and Sandelia) to shed some light on the processes that promoted lineage diversification and shaped geographical distribution patterns. A total of 205 sequences of Galaxias, 177 sequences of Pseudobarbus and 98 sequences of Sandelia from 146 localities across nine river systems in the south-western Cape Floristic Region (South Africa) were used. The data were analysed using phylogenetic and haplotype network methods and divergence times for the clades retrieved were estimated using *BEAST. Nine extremely divergent (3.5–25.3%) lineages were found within Galaxias. Similarly, deep phylogeographic divergence was evident within Pseudobarbus, with four markedly distinct (3.8–10.0%) phylogroups identified. Sandelia had two deeply divergent (5.5–5.9%) lineages, but seven minor lineages with strong geographical congruence were also identified. The Miocene-Pliocene major sea-level transgression and the resultant isolation of populations in upland refugia appear to have driven widespread allopatric divergence within the three genera. Subsequent coalescence of rivers during the Pleistocene major sea-level regression as well as intermittent drainage connections during wet periods are proposed to have facilitated range expansion of lineages that currently occur across isolated river systems. The high degree of genetic differentiation recovered from the present and previous studies suggest that freshwater fish diversity within the south-western CFR may be vastly underestimated, and taxonomic revisions are required.

The megadiverse haplochromine cichlid radiations of the East African lakes, famous examples of explosive speciation and adaptive radiation, are according to recent studies, introgressed by different riverine lineages. This study is based on the first comprehensive mitochondrial and nuclear DNA dataset from extensive sampling of riverine haplochromine cichlids. It includes species from the lower River Congo and Angolan (River Kwanza) drainages. Reconstruction of phylogenetic hypotheses revealed the paradox of clearly discordant phylogenetic signals. Closely related mtDNA haplotypes are distributed thousands of kilometres apart and across major African watersheds, whereas some neighbouring species carry drastically divergent mtDNA haplotypes. At shallow and deep phylogenetic layers, strong signals of hybridization are attributed to the complex Late Miocene/Early Pliocene palaeohistory of African rivers. Hybridization of multiple lineages across changing watersheds shaped each of the major haplochromine radiations in lakes Tanganyika, Victoria, Malawi and the Kalahari Palaeolakes, as well as a miniature species flock in the Congo basin (River Fwa). On the basis of our results, introgression occurred not only on a spatially restricted scale, but massively over almost the whole range of the haplochromine distribution. This provides an alternative view on the origin and exceptional high diversity of this enigmatic vertebrate group.

ABSTRACT1. Traditionally headwater streams are surveyed using electrofishing, a potentially harmful sampling method. Increasingly scientists are seeking out the least destructive stream sampling methods, especially when sampling imperilled fishes. It is therefore imperative that the efficacy of alternative, non-destructive sampling methods be investigated.2. This study investigated the potential for using underwater video analysis (UWVA) as an alternative to electrofishing for assessing the diversity and relative abundance of imperilled fishes in clear, relatively shallow (<1.5 m) headwater streams.3. Detection rates using UWVA were higher than with electrofishing, relative abundance estimates between the two methods were significantly correlated, the attractive effect of the camera was negligible and UWVA was logistically feasible for sampling small headwater streams.4. These results have clear conservation implications as it was demonstrated that UWVA is a suitable sampling method for estimating relative abundance of fishes in small, clear headwater streams.

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Previous work has revealed that Hippopotamyrus ansorgii (Boulenger, 1905) is a species complex, with specimens from the Upper Zambezi system (Caprivi Strip in Namibia) that are well differentiated from the Angolan type specimens. Here, we sampled the Cunene River, one of several possible type rivers for H. ansorgii, on the border between Namibia and Angola. The specimens are morphologically differentiated from the six other known morphs within the H. ansorgii species complex, including the types and H. szaboi. The electric organ discharge of the Cunene specimens has a different pulse waveform and associated amplitude spectra to that of the three Upper Zambezi system morphs of the species complex. The Cunene specimens are genetically distinct, but relatively closely related to other taxa of the H. ansorgii complex, such as the Upper Zambezi system morphs. We recognize the Lower Cunene morph as the new species, Hippopotamyrus longilateralis sp. nov.