Between an ocean and a high place: coastal drainage isolation generates endemic cryptic species in the Cape kurper Sandelia capensis (Anabantiformes: Anabantidae), Cape Region, South Africa.

This study investigated the range-wide phylogenetics and biogeography of the Cape kurper Sandelia capensis, a primary freshwater fish endemic to and widespread within the Cape Floristic Region (CFR) of South Africa. Maximum likelihood, Bayesian phylogenetic and haplotype network analyses, based on two mitochondrial and two nuclear genes, revealed the existence of three reciprocally monophyletic, deeply divergent and allopatric clades that probably represent cryptic species. The West Coast Clade is largely confined to the Langvlei, Verlorenvlei, Berg and Diep Rivers, the Klein River Clade is endemic to the Klein River and the South Coast Clade is found everywhere else in the range of S. capensis sensu lato. It was hypothesised that divergences within S. capensis sensu lato probably occurred because of isolation of coastal drainages by persistent drainage divides or vicariance of current tributaries by the drowning of their confluences by high sea levels. The current distribution of lineages could be due to historical range expansion and gene flow via river capture or some other mode of transdivide dispersal or dispersal during periods of low sea level via palaeoriver confluences of currently isolated coastal rivers. Comparison of BEAST2 estimated divergence times with the timing of climatic, geological and geomorphological events supported long-term coastal drainage isolation, punctuated by rare transdivide dispersal events and limited palaeoriver dispersal, as the best explanation of current phylogeographic and divergence patterns in S. capensis. Hydrological barriers that block upstream passage in palaeotributaries could hypothetically explain why S. capensis failed to disperse through certain palaeoriver confluences. There were several sites where biogeographic patterns have likely been confounded by human translocation of S. capensis. Alien fish predators and water extraction may threaten the three cryptic species more severely than previously realised, due to their smaller population sizes and inhabitation of only a portion of the range previously ascribed to S. capensis sensu lato. The preponderance of cryptic diversity and endemism in the CFR suggests that additional undescribed cryptic species of obligate freshwater fishes may be found in short coastal river systems around the world, especially in regions with a history of geological stability and a narrow continental shelf.

Molecular and morphological evidence reveals hybridisation between two endemic cyprinid fishes.

The geographic occurrence of moggel Labeo umbratus × mud fish Labeo capensis hybrids and the threat of hybridisation to the genetic integrity of L. umbratus were investigated. Genetic evidence from mtDNA cytb and nDNA s7 intron sequence data indicated probable interspecific hybridisation in two impoundments, Hardap Dam (Orange River Basin, Namibia) and Darlington Dam (Sundays River Basin, Eastern Cape, South Africa). Some putative hybrids were morphologically identifiable on account of their meristic and morphometric intermediacy to the parent species. Human activities appear to drive the observed hybridisation, either through dam construction and direct stocking of L. umbratus or via translocation of Labeo capensis and the previously isolated Orange River lineage of L. umbratus into the southern-flowing systems by inter-basin water transfers. It is recommended that further translocation of fish from these areas should be avoided.

Descriptions of three new species of Marcusenius Gill, 1862 (Teleostei: Mormyridae) from South Africa and Mozambique.

Morphological and genetic studies of mormyrid fishes belonging to the genus Marcusenius from South Africa and Mozambique revealed four species of which three are described as new. Marcusenius pongolensis is widespread throughout the Incomati, Pongola and Kosi river systems, and sparsely represented in the Limpopo River system in South Africa. Marcusenius krameri sp. nov. is endemic to the Limpopo River system, and is the sister taxon of M. caudisquamatus sp. nov. from the Nseleni and Mhlatuze river systems in the KwaZulu-Natal Province of South Africa. The Ruvuma specimens were well differentiated from all southern and eastern African species of Marcusenius, and are therefore recognised as M. lucombesi sp. nov. Phylogenetic analysis of the mitochondrial cytochrome b gene showed that the three new species and M. altisambesi form a monophyletic lineage that is sister to a group containing M. pongolensis and M. macrolepidotus. Marcusenius krameri and M. lucombesi seems to prefer slow flowing reaches of rivers, whereas M. pongolensis and M. caudisquamatus seems to mainly inhabit rapid flowing sections of rivers with a rocky substrate. A key to the southern African species of Marcusenius is provided.

A new redfin species, Pseudobarbus skeltoni (Cyprinidae, Teleostei), from the Cape Floristic Region, South Africa.

A new cyprinid species, Pseudobarbus skeltoni sp. nov, is described from material recently collected in the upper Riviersonderend River (a major tributary of the Breede River system) and the Krom River (a tributary of the Molenaars River in the upper Breede River) in the Cape Floristic Region of South Africa. The new species is readily distinguished from congeners, except P. burgi and P burchelli, by having two pairs of prominent oral barbels. Pseudobarbus skeltoni can be distinguished from P. burgi and P burchelli by the following combination of characters: distinctive terminal (vs. subterminal) mouth in adults; mouth inferior in sub-adults and young adults of P skeltoni but lower lips are unretracted (vs. retracted) and lack a distinct cartilaginous plate; snout prominent; more slender head (head depth 64.2% of HL, vs. 70.1% of HL in P. burchelli and 74.1% of HL in P. burgi); and a longer head relative to standard length (30.5 % vs. 26.8% in P. burchelli and 25.8% in P. burgi). The new species attains the largest size of any Pseudobarbus. The restricted distribution and the small remaining population sizes of P skeltoni indicate that this species is highly threatened and requires immediate conservation attention.

Repeated trans-watershed hybridization among haplochromine cichlids (Cichlidae) was triggered by Neogene landscape evolution.

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.

Contrasting habitat associations of imperilled endemic stream fishes from a global biodiversity hot spot.

BACKGROUND: Knowledge of the factors that drive species distributions provides a fundamental baseline for several areas of research including biogeography, phylogeography and biodiversity conservation. Data from 148 minimally disturbed sites across a large drainage system in the Cape Floristic Region of South Africa were used to test the hypothesis that stream fishes have similar responses to environmental determinants of species distribution. Two complementary statistical approaches, boosted regression trees and hierarchical partitioning, were used to model the responses of four fish species to 11 environmental predictors, and to quantify the independent explanatory power of each predictor. RESULTS: Elevation, slope, stream size, depth and water temperature were identified by both approaches as the most important causal factors for the spatial distribution of the fishes. However, the species showed marked differences in their responses to these environmental variables. Elevation and slope were of primary importance for the laterally compressed Sandelia spp. which had an upstream boundary below 430 m above sea level. The fusiform shaped Pseudobarbus 'Breede' was strongly influenced by stream width and water temperature. The small anguilliform shaped Galaxias 'nebula' was more sensitive to stream size and depth, and also penetrated into reaches at higher elevation than Sandelia spp. and Pseudobarbus 'Breede'. CONCLUSIONS: The hypothesis that stream fishes have a common response to environmental descriptors is rejected. The contrasting habitat associations of stream fishes considered in this study could be a reflection of their morphological divergence which may allow them to exploit specific habitats that differ in their environmental stressors. Findings of this study encourage wider application of complementary methods in ecological studies, as they provide more confidence and deeper insights into the variables that should be managed to achieve desired conservation outcomes.

Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae).

The members of the cyprinid subfamily Danioninae form a diverse and scientifically important group of fishes, which includes the zebrafish, Danio rerio. The diversity of this assemblage has attracted much scientific interest but its monophyly and the relationships among its members are poorly understood. The phylogenetic relationships of the Danioninae are examined herein using sequence data from mitochondrial cytochrome b, mitochondrial cytochrome c oxidase I, nuclear opsin, and nuclear recombination activating gene 1. A combined data matrix of 4117 bp for 270 taxa was compiled and analyzed. The resulting topology supports some conclusions drawn by recent studies on the group and certain portions of the traditional classification, but our results also contradict key aspects of the traditional classification. The subfamily Danioninae is not monophyletic, with putative members scattered throughout Cyprinidae. Therefore, we restrict Danioninae to the monophyletic group that includes the following genera: Amblypharyngodon, Barilius, Cabdio, Chela, Chelaethiops, Danio, Danionella, Devario (including Inlecypris), Esomus, Horadandia, Laubuca, Leptocypris, Luciosoma, Malayochela, Microdevario, Microrasbora, Nematabramis, Neobola, Opsaridium, Opsarius, Paedocypris, Pectenocypris, Raiamas, Rasbora (including Boraras and Trigonostigma), Rasboroides, Salmostoma, Securicula, and Sundadanio. This Danioninae sensu stricto is divided into three major lineages, the tribes Chedrini, Danionini, and Rasborini, where Chedrini is sister to a Danionini-Rasborini clade. Each of these tribes is monophyletic, following the restriction of Danioninae. The tribe Chedrini includes a clade of exclusively African species and contains several genera of uncertain monophyly (Opsarius, Raiamas, Salmostoma). Within the tribe Rasborini, the species-rich genus Rasbora is rendered non-monophyletic by the placement of two monophyletic genera, Boraras and Trigonostigma, hence we synonymize those two genera with Rasbora. In the tribe Danionini, the miniature genus Danionella is recovered as the sister group of Danio, with D. nigrofasciatus sister to D. rerio.

Phylogeny and biogeography of the genus Pseudobarbus (Cyprinidae): shedding light on the drainage history of rivers associated with the Cape Floristic Region.

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.

A new species catfish, Amphilius pagei (Siluriformes: Amphiliidae) from Angola.

Amphilius pagei, a new species of amphiliid catfish is described from the Cuanza River basin in Angola. It is distinguished from all other species of Amphilius by the combination of presence (vs. absence) of an epidermal fold at the base of the caudal fin, 6+7 (i,5,6,i) principal caudal-fin rays (vs. 7+8 or 8+9), a variably mottled body coloration that includes dark saddles (vs. body coloration not mottled with dark saddles), head and body heavily spotted (vs. head and body not heavily spotted), epidermal fold smooth (vs. crenelations present on epidermal fold), branchiostegal rays usually eight or nine, and total gill rakers usually 12-16. It is most similar to A. lentiginosus which has a crenelated epidermal fold and fewer branchiostegal rays.

Historical abiotic events or human-aided dispersal: inferring the evolutionary history of a newly discovered galaxiid fish.

Range expansion of obligate freshwater fishes in the Cape Floristic Region (CFR) of South Africa has mostly been attributed to river capture events and confluence of rivers following sea-level regression. The role of low drainage divides and interbasin water transfers has received less attention. This study analyzed mitochondrial and nuclear DNA sequences to assess the processes that could have influenced the phylogeographic patterns of a newly discovered lineage of Galaxias zebratus (hereafter Galaxias zebratus "Joubertina") that occurs across two currently isolated river systems close to the Joubertina area in the eastern CFR. Results from both analyses revealed that observed genetic differentiation cannot be explained by isolation between the two river systems. No genetic differentiation was found between the Krom River system and a population from one of the Gamtoos tributaries. Shallow genetic differentiation was found between the Krom and the other Gamtoos populations. Historical river capture events and sea-level changes do not explain the present distribution of Galaxias zebratus "Joubertina" across the Krom and Gamtoos River systems. Interbasin dispersal during pluvial periods, recent river capture, or recent human-mediated translocation seems to be the most plausible explanations.

A new species of redfin (Teleostei, Cyprinidae, Pseudobarbus) from the Verlorenvlei River system, South Africa.

Pseudobarbusverloreni, a new species, is described from material collected in the Verlorenvlei River system on the west coast of South Africa. It differs from its congeners (except Pseudobarbusskeltoni, Pseudobarbusburchelli, and Pseudobarbusburgi) by the presence of two pairs of oral barbels. Pseudobarbusverloreni sp. n. can be distinguished from the three currently described double barbeled Pseudobarbus species by the following combination of characters: pigment pattern, generally deeper body relative to standard length, a longer intestine associated with the deeper body form, shorter snout relative to head length, and much shorter anterior barbels relative to head length. The new species is distinguished from Pseudobarbusburgi in the neighbouring Berg River system by its longer head and longer pre-dorsal length. It seems as if Pseudobarbusverloreni sp. n. has been extirpated from the Langvlei River system and face several threats to its survival in the Verlorenvlei River system.

Evolutionary drivers of diversification and distribution of a southern temperate stream fish assemblage: testing the role of historical isolation and spatial range expansion.

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.