Phylogeography, phylogenetics and evolution of the redfins (Teleostei, Cyprinidae, Pseudobarbus) in southern Africa

The present thesis concerns the population history, evolutionary processes and phylogenetic relationships of lineages of the redfin minnow genus Pseudobarbus. First, the population history and evolutionary processes within P. quathlambae were determined, mainly to decide the conservation value of the Mohale population. The Mohale dam threatens its survival. A divergence in mitochondrial control region and cytochrome b sequences and frequency differences in the distribution of major histocompatibility alleles were found between the Mohale population and an “Eastern” lineage. The Mohale population has therefore been historically isolated and was deemed indispensable for the conservation of P. quathlambae. Differentiation among populations of the P. afer and P. phlegethon complex were investigated, in relation to geological and climatic processes. Sea levels were about – 130 m below present levels during the last glacial maximum, about 18 000 years ago. Five historically isolated lineages were identified through analysis of mitochondrial control region sequences. The four P. afer lineages showed a strong association with proposed palaeoriver systems. A “Forest” lineage, however, reaches across two proposed palaeoriver systems. Surprisingly, this lineage is closely related to P. phlegethon. Pseudobarbus asper and P. tenuis were analysed together, because of their close phylogenetic relationship and because they occur in sympatry in the Gourits River system. Pseudobarbus tenuis showed divergence in mitochondrial control region only between the Keurbooms and Bitou River systems compared to the Gourits River system. Within P. asper, divergence was low, suggesting recent inland exchange opportunities between populations of the Gourits and Gamtoos River systems. River capture of south-eastern tributaries of the Gourits River system by the Keurbooms River would have resulted in unidirectional colonization, suggesting that speciation between P. asper and P. tenuis occurred within the Gourits River system with or without the Gamtoos River system being involved. Lower sea levels during the last glacial maximum also played an important role in the population history of P. burchelli. Differentiation in P. burchelli did not occur between two proposed palaeoriver systems, but rather within a western palaeoriver system. Divergence in mitochondrial control region and cytochrome b sequences showed that the “Breede” and “Tradou” lineages diverged within the Breede River system, before the “Heuningnes” lineage became isolated in the Heuningnes River system. Fifteen historically isolated Pseudobarbus lineages were included in a phylogenetic analysis on which biogeographic hypotheses were based. Phylogenetic relationships based on mitochondrial control region, cytochrome b and 16S and a combined dataset of all these were compared to relationships recovered from a previous morphological dataset. Conflicts between the molecular and morphological analyses, suggests that several morphological characters evolved in a complex manner. The molecular phylogenies suggest that the earliest divergence in the Pseudobarbus was between P. quathlambae in the Orange River system and the other species that occur in the Cape Foristic Region. Pseudobarbus lineages with two pairs of barbels and those with a single pair of barbels (excluding P. quathlambae) grouped together. In terms of currently described species, only the two lineages of P. quathlambae and the three lineages of P. burchelli were clearly monophyletic. CopyrightThesis (PhD (Genetics))--University of Pretoria, 2007.Geneticsunrestricte

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.Table Mountain Fund and Prince Bernhard Scholarships, the National Research Foundation (South Africa) and the Claude Leon Foundation.http://link.springer.com/journal/10750hb201

Measurement of the Charged Multiplicities in b, c and Light Quark Events from Z0 Decays

Average charged multiplicities have been measured separately in $b$, $c$ and light quark ($u,d,s$) events from $Z^0$ decays measured in the SLD experiment. Impact parameters of charged tracks were used to select enriched samples of $b$ and light quark events, and reconstructed charmed mesons were used to select $c$ quark events. We measured the charged multiplicities: $\bar{n}_{uds} = 20.21 \pm 0.10 (\rm{stat.})\pm 0.22(\rm{syst.})$, $\bar{n}_{c} = 21.28 \pm 0.46(\rm{stat.}) ^{+0.41}_{-0.36}(\rm{syst.})$ $\bar{n}_{b} = 23.14 \pm 0.10(\rm{stat.}) ^{+0.38}_{-0.37}(\rm{syst.})$, from which we derived the differences between the total average charged multiplicities of $c$ or $b$ quark events and light quark events: $\Delta \bar{n}_c = 1.07 \pm 0.47(\rm{stat.})^{+0.36}_{-0.30}(\rm{syst.})$ and $\Delta \bar{n}_b = 2.93 \pm 0.14(\rm{stat.})^{+0.30}_{-0.29}(\rm{syst.})$. We compared these measurements with those at lower center-of-mass energies and with perturbative QCD predictions. These combined results are in agreement with the QCD expectations and disfavor the hypothesis of flavor-independent fragmentation.Comment: 19 pages LaTex, 4 EPS figures, to appear in Physics Letters

The status and distribution of newly identified endemic galaxiid in the eastern Cape Fold Ecoregion, of South Africa

1. DNA‐based studies have uncovered cryptic species and lineages within almost all freshwater fishes studied thus far from the Cape Fold Ecoregion (CFE) of South Africa. These studies have changed the way the CFE is viewed, as almost all stream fishes that were previously considered to be of low conservation priority, because they were perceived to have broad geographical ranges, contain multiple historically isolated lineages, many of which are narrow‐range endemics. 2. As stream fishes of the CFE are of conservation concern owing to threats mainly posed by habitat degradation, invasion by alien species and hydrological modification, re‐evaluation of the distribution and conservation status of newly identified unique lineages is required to inform the development and implementation of effective conservation and management strategies. 3. The present study conducted an IUCN Red List conservation assessment of a newly identified lineage of the Galaxias zebratus species complex (hereafter referred to as Galaxias sp. ‘Joubertina’) to identify key threats and provide recommendations to conservation authorities on appropriate measures to reduce extinction risk. 4. The lineage met the qualifying threshold for the Endangered category because of its very restricted geographic range, few remaining secure populations, small known population sizes and the intensity of threats to most of the populations. Only six populations remain, one of which could be an ‘extralimital’ population potentially established through an inter‐basin water transfer scheme. 5. Galaxias sp. ‘Joubertina’ is threatened by invasive piscivores, habitat degradation and excessive water abstraction. These impacts have fragmented remnant populations, raising concerns about potential long‐term adverse impacts on genetic diversity and evolutionary potential of this lineage. 6. Immediate conservation measures should protect remnant populations from further impacts, while long‐term measures should aim to restore historical connectivity to reduce the potential deleterious effects of inbreeding in the small isolated populations

Invasion status of Florida bass Micropterus floridanus (Lesueur, 1822) in South Africa

Largemouth bass Micropterus salmoides are a popular North American angling species that was introduced into South Africa in 1928. To enhance the largemouth bass fisheries, Florida bass Micropterus floridanus were introduced into KwaZulu Natal, South Africa, in 1980. Knowledge on the status of M. floridanus in South Africa is required, because it lives longer and reaches larger sizes than M. salmoides, which may result in heightened impacts on native biota. Because M. floridanus are morphologically similar, but genetically distinct from M. salmoides, the distribution of this species was assessed by genetically screening 185 Micropterus sp. individuals sampled from 20 localities across South Africa using the mitochondrial ND2 gene. Individuals with mitochondrial DNA matching M. salmoides were recovered from 16 localities, whereas M. floridanus mitochondrial DNA was recovered from 13 localities. At nine localities (45%), the mitochondrial DNA of both species was detected. These results demonstrate M. floridanus dispersal to multiple sites across South Africa

Using a unified invasion framework to characterize Africa’s first loricariid catfish invasion

Record of a new invasion and assessment of stateThis paper presents evidence of establishment of a loricariid population in the Nseleni River in South Africa and uses a unified framework to determine its invasion stage. Specimens were identified morphologically as Pterygioplichthys disjunctivus (Weber 1991), but genetic barcoding results indicated close association with specimens that may have a hybrid history. The species was introduced into South Africa via the pet trade and the first record of introduction into the wild was in 2004. Samples collected in 2011 and 2012 demonstrated that there were multiple length cohorts in the population including juveniles (12–130 mm total length TL) and large ([300 mm TL) adult fish. Gonadal assessment of adults demonstrated the presence of reproduction capable specimens. The concurrent occurrence of mature adults and juvenile fish demonstrated establishment. Locality records indicate that P. disjunctivus has already spread between two rivers through an inter basin water transfer. Using a unified framework for invasions this invasion was categorized as a self sustaining population in the wild with individuals surviving and reproducing a significant distance from their original point of introduction. Containment is suggested as potential management strategy.Ezemvelo KZN Wildlife; South African Institute for Aquatic Biodiversity; DST/NRF Centre of Excellence in Invasion Biology (CIB); Department of Environmental Affairs Working for Water (WfW) programme; Canadian Centre for DNA Barcoding at the University of Guelph, the sponsors of the FISH-BOL project (listed at www.bolnet.ca)

Reconstruction of the historical distribution ranges of imperilled stream fishes from a global endemic hotspot based on molecular data: Implications for conservation of threatened taxa

Understanding historical distribution patterns of freshwater fishes prior to human impacts is crucial for informing effective strategies for biodiversity conservation. However, incomplete information on species occurrence records, the existence of cryptic species and sensitivity to small sample sizes limit the application of historical records in natural history collections as well as conventional species distribution modelling algorithms to infer past distributions of species. This study used molecular data as an alternative and objective approach to reconstruct the historical distribution ranges of four stream fishes from the Breede River system in the Cape Fold Ecoregion, a global hotspot of imperilled endemic freshwater biodiversity in southern Africa. The study used 249 occurrence records and 208 mitochondrial cytochrome b sequences to reconstruct the potential historical ranges of four taxa: Galaxias sp. 'zebratus nebula', Galaxias sp. 'zebratus Riviersonderend', Pseudobarbus sp. 'burchelli Breede' and Pseudobarbus skeltoni. All four taxa historically had broader distribution ranges across the Breede River system before human impacts, but they have suffered severe attrition as the main-stem populations have been extirpated. The severe decline in the historical ranges of these four taxa is a result of multiple impacts, particularly hydrological modification, habitat degradation and the introduction of non-native species, which are also global challenges for freshwater ecosystems. The approach presented in this study has great potential for reconstructing historical ranges of stream-dwelling taxa from disparate regions where fragmentation has resulted from human-mediated impacts. This information is crucial for identifying appropriate conservation strategies such as river rehabilitation and eradication of non-native species, as well as guiding reintroductions and informing assisted gene flow where these are deemed necessary interventions

Sea-level changes, river capture and the evolution of populations of the Eastern Cape and fiery redfins (Pseudobarbus afer and Pseudobarbus phlegethon, Cyprinidae) across multiple river systems in South Africa

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