Ernst R. Swartz

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.

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.

Invasion of a headwater stream by non-native fishes in the Swartkops River system, South Africa.

In South Africa, fishes in headwater streams are increasingly being threatened by non-native fish invasions. These invasions originate primarily from source populations in mainstream rivers and impoundments. In the Blindekloof stream, a Swartkops River headwater tributary, the non-native Micropterus salmoides was eradicated from the stream by conservation authorities in 1989. As a result of this eradication subsequent occurrences of non-native fishes are most likely a result of upstream invasions from the mainstream Swartkops River. The Blindekloof stream therefore provided a unique opportunity to investigate whether M. salmoides would reinvade after its removal in 1989 and if the more recently introduced Clarias gariepinus and Tilapia sparrmanii would invade the Blindekloof stream. During snorkel and electrofishing surveys four non-native species were recorded (M. salmoides, M. dolomieu, T. sparrmanii, C. gariepinus). The large predators, M. salmoides, M. dolomieu and C. gariepinus were neither abundant nor widespread and T. sparrmanii was the only non-native species that had successfully established in the Blindekloof stream. Where M. salmoides and M. dolomieu were observed, all other fish species were absent. By contrast, the native species were present at all sites where C. gariepinus and T. sparrmanii were found. The Pseudobarbus afer population was predominantly limited to a 1.7 km section of the stream that was not invaded and is located above a waterfall. The limited distribution range of this Endangered species makes it particularly vulnerable to predation by non-native fishes. The results of this study indicate that these non-native fishes rapidly invaded the Blindekloof stream following their introduction into the mainstream.

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.

A new species of Slender Stonebasher within the Hippopotamyrus ansorgii complex from the Cunene River in southern Africa (Teleostei: Mormyriformes)

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.

Walking the tightrope: trends in African freshwater systematic ichthyology

Africa is blessed with an abundance and rich diversity of freshwater fishes, reflecting its Gondwanan history and geographical position astride the equator. Africa is, however, relatively poorly serviced scientifically, in this respect presenting a challenge to the tension between conserving biodiversity and sustainable development. Biosystematics has experienced several paradigm shifts in the past half century, including the rise of cladistics and more recently the adoption of molecular DNA applications to taxonomy and phylogeny and the assembly and manipulation of large data sets in an era of major development of bioinformatics. The richness of African biodiversity is a magnet to the global systematic community that, to a degree, offsets the disadvantage of an impoverished indigenous scientific capacity. Conservation biology, however, is rooted more closely to the local situation and therefore requires indigenous taxonomic services that are inevitably scarce. Balancing this network of tensions between scientific knowledge generation and application is like walking a tightrope for existing African scientific resources, and to cope it is essential to embrace modern innovative approaches such as barcoding to identify organisms. This paper considers the historical development of African freshwater ichthyology, presents a suite of recent examples illustrating trends in systematic ichthyology in Africa and draws conclusions to suggest that both traditional and new-age approaches to taxonomy are necessary for a complete understanding and appreciation of African freshwater fish diversity and its conservation. The chosen examples also suggest that the tensions between the approaches can be effectively managed provided exponents work collaboratively. The emerging evidence indicates that the combined skills and insight of complex scientific teams including systematists, ecologists, molecular biologists and earth scientists are needed to resolve the deep complexity of evolution in terms of space, time and form.

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

BackgroundKnowledge 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.ResultsElevation, 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’.ConclusionsThe 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.

Short and long-term strategies to facilitate aerial exposure in a galaxiid

This study investigated two potential strategies to survive short and longer-term aerial exposure in a galaxiid. This scaleless fish possesses cutaneous pores that dilated in the short-term (15 min-3 h) but contracted over longer periods (15 h) out of water, suggesting that these organs are used to cope with shorter durations of air exposure. Pores on the abdominal surface showed the greatest variation while those on the operculum surface hardly changed. Conversely, thickening of the epithelial layer of secondary gill lamellae showed a slower increase but persisted in an approximately linear fashion over the duration of this study, indicating that this is a strategy that facilitates longer-term aerial exposure. Thus, this species has the capacity to accommodate both short and long-term exposure to air.

The genetic legacy of lower sea levels: does the confluence of rivers during the last glacial maximum explain the contemporary distribution of a primary freshwater fish (Pseudobarbus burchelli, Cyprinidae) across isolated river systems?

The primary freshwater fish Pseudobarbus burchelli (Smith 1841) occurs across four presently isolated river systems in the south-western cape floristic region of South Africa. Mitochondrial DNA cytochrome b (701 base pairs) and control region (601 base pairs) genes were sequenced to assess the evolutionary history of P. burchelli and evaluate the role of climatic and landscape changes in shaping patterns of genetic variation in this species. We identified three historically isolated lineages in P. burchelli: a widespread lineage that occurs across three isolated river systems and two geographically restricted lineages. The results were evaluated against predictions of the confluence of river systems during low sea levels of the last glacial maximum. Occurrence of the widespread Breede lineage in the Duiwenhoks River system is consistent with reconstructed palaeoriver systems. However, the occurrence of this lineage in the Goukou river system that formed part of the eastern Gourits–Goukou palaeoriver system can only be explained by translocation or a recent river capture or episodic inundation of low drainage divides. Extreme ecological gradients or the potential presence of instream physical barriers could have prevented an exchange of lineages between the Breede and Heuningnes river systems.