Thesis (M. Sc. (Zoology)) -- University of Limpopo, 2012 / The Olifants River System is one of the most polluted river systems in Southern Africa. The Olifants River catchment is characterized by large-scale mining, power generation, heavy industry and inadequate domestic sewage treatment. Fish and crocodile kills have become commonplace over the past decade, especially in the upper catchment and Kruger National Park. The present study was carried out at Loskop and Flag Boshielo dams, two major impoundments in the Olifants River. Water and sediment samples were collected at each dam during winter (July 2011) and summer (November 2011), frozen and sent to an accredited water lab for chemical analysis. Atleast fifteen fish specimens from each dam were collected during each survey using gill nets. To evaluate the health of red-nose labeo, (Labeo rosae) in the two dams, fish organs were assessed macroscopically using the fish Health Assessment Index (HAI) protocol and a section of liver tissue and gills were dissected out, frozen and sent to an accredited water lab for metal analysis. The remainder liver samples were fixed in 10% buffered formalin and sent to University of Pretoria Pathology Laboratory for histopathological analysis. The concentration of nutrients and ions were higher at Loskop Dam whereas most metal concentrations were found to be higher at Flag Boshielo Dam. The present study categorised Flag Boshielo Dam as oligotrophic with Loskop Dam being mesotrophic. The concentration of aluminium, copper, antimony, iron, lead, selenium and strontium was higher at Flag Boshielo Dam with manganese, silica and zinc being higher at Loskop Dam. Although the concentrations of these toxic constituents varied, there were no significant differences between localities (p>0.05). The constituents that showed high concentrations in sediment were iron and aluminium. The general trend of accumulation in sediment was as follows: Fe > Al > Si > Mn > Zn > Cu > Sb > Sr > Pb > Se at Loskop Dam whereas at Flag Boshielo Dam was as follows: Fe > Al > Mn > Si > Zn > Cu > Sr > Pb > Sb > Se. The liver generally accumulated higher concentrations of metals than the other tissue. General trend of liver > gills > muscle was reported for Al, Cu, Fe, Pb, Sb, Se, Si and Zn with gills > liver > muscle trend being reported for Mn and Sr at both localities. Macroscopic abnormalities were observed for some gills and liver at both localities. Parasite (Lernaea cyprinacea) induced lesions on the skin and mild erosion on the tail fin of some fish were recorded at Flag Boshielo Dam. Most of the histopathological alterations were common at both localities but hydropic glycogen and hyaline droplets were observed only at Loskop Dam, with haemosiderin being observed at Flag Boshielo Dam. Both quantitative HAI results and histopathology have shown that the fish population from Flag Boshielo Dam are in better condition/health than the population Abstract Abstract Page iv from Loskop Dam. There might be a correlation between the nutrient levels and fish health. The overall ecological state is better at Flag Boshielo Dam than Loskop Dam.

published_or_final_version / abstract / toc / Zoology / Doctoral / Doctor of Philosophy

Thesis (Ph. D. (Ichthyology & Fisheries Science))--Rhodes University, 2004.

M.Sc. (Zoology) / Please refer to full text to view abstract

D.Phil.

Lake Victoria, the largest tropical lake, has faced an unprecedented assault on its ecosystem through a variety of anthropomorphic causes that include the introduction of Nile perch Lates niloticus and over-fishing. As a result there have been species extinctions and declining fish population trends. This thesis explores options for reversing these declining population trends and the restoration of collapsed fisheries based on indigenous non-cichlid species. A candidate species was chosen - the cyprinid fish Labeo victorianus. This thesis studied various aspects of L. victorianus' reproductive biology in two geographically distant populations. These included general reproductive patterns in relation to proximate environmental conditions, gonadal development and recrudescence, sex development, characterisation of genetic and morphological diversity, and induced spawning. Fish from both populations were found to be potamodrometic, and highly fecund, iteroparous spawners. L. victorianus was also shown to be an undifferentiated gonochorist, where all individuals pass through an intersexual juvenile stage prior to differentiation, and maturation to either sex. Sexual maturity was attained at a significantly larger size within the Kagera River than that of Sio River fish – possibly as a response to genotypic and/or phenotypic differences. Spawning seemed to be synchronised with rainfall in Kagera River - a pattern that was not strictly adhered to with the Sio River. Thorough microscopic investigation of recrudescence patterns indicated there was uninterrupted spawning in fish from the Kagera River followed by Type I oocyte atresia. In contrast, there was a 90% spawning failure, as characterised by Type II oocyte atresia, within the Sio River population. Aspects of spermatogenesis and sperm ultrastructure using light- and ultramicrotomic methods are described. Although the populations had varying reproductive biology parameters and were morphologically distinct, they remained undifferentiated at the mitochondrial level. Both populations were characterised by low nucleotide diversity – a feature attributed to a bottleneck event. The option of captive breeding was explored by conducting induced spawning experiments. Success was only achieved with a decapeptide Gonadotropic Releasing Hormone ([D-Arg⁶, Pro⁹-NEt])-sGnRH) in combination with a water-soluble dopamine receptor antagonist metoclopramide. This thesis stresses the importance of a research-oriented approach in the conservation of Lake Victoria's indigenous fish resources. It was concluded that information needed for the development of management policies can be generated within a reasonably short time period, of approximately three years, with modest levels of funding support.

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. Copyright / Thesis (PhD (Genetics))--University of Pretoria, 2007. / Genetics / unrestricted

This dissertation outlines the contribution of evolutionary and environmental factors on North American freshwater fish morphological variation. A more thorough understanding of the factors which result in morphological variation is essential to describing patterns of evolutionary diversification, distribution, ecological niche, ontogeny, sexual dimorphism, ecosystem role, community assembly, invasion dynamics, and conservation. This dissertation makes a unique contribution to understanding morphological diversity in freshwater fishes by linking intraspecific and interspecific variation to phylogeny, allometry, sex, habitat niche, geographic niche, hydrology, and long term environmental change. This dissertation is comprised of three chapters which detail large scale macroevolutionary patterns in morphological variation for North American freshwater fishes, long term morphological changes with hydrological alterations in Cyprinidae, and phenotypic plasticity of freshwater drum in the Wabash River. Overall, North American fishes tend to be deeper bodied and more robust with larger body size, in females, in low flow and lentic hydrological conditions, and in taxa with smaller geographic range that occupy more specialized habitat niches. Further, macroevolutionary analysis suggests that the majority of morphological diversification occurred relatively early on in the evolutionary history of North American fishes. / Evolution of North American freshwater fish morphology with variation in habitat use and geographic range -- 100 years of hydrologic alterations and morphological variation in Cyprinidae -- Effects of allometry, sex and river location on morphological variation of freshwater drum Aplodinotus grunniens in the Wabash River, USA. / Department of Biology

This thesis explores the biology, ecology, and life-history styles of two closely-related redfin minnows, Pseudobarbus afer and P. asper (pisces; Cyprinidae), which both occur in the Gamtoos River system of South Africa. Five of the seven species of flexible-rayed redfin minnows are in the South African Red Data Book - Fishes. This investigation was designed to provide the data which would enable conservation authorities to manage the remaining populations of the Pseudobarbus species. A thorough understanding of the Gamtoos River system was necessary to properly interpret the findings of this study. The palaeo river systems and the changing climates since the break-up of Gondwanaland are discussed so that the present day environments could be considered as well as the past environmental changes. P. afer and P. asper occur in the Gamtoos River system with no physical barrier separating the two species. P. afer only occurs in the clear mountain streams of the Cape Fold Mountain Belt whereas P. asper occurs in the highly saline and turbid Karoo section of the system. P. afer were found to be the more precocial form of the sister species. They had bigger eggs, lower relative fecundity, shorter breeding season, lower gonadosomatic indices, larger first feeding larval fish, matured later and had a longer life-span than did P. asper, which had more altricial life-history attributes. They differ in their tradeoffs with P. asper devoting more resources earlier to reproduction and having a shorter lifespan. The improvement in the one aspect of fitness (early maturity) leads to the deterioration in another, namely lifespan. Both species undertake breeding migrations to riffle areas where they spawn in mid-channel immediately above a pool after an increase in water flow. P. afer and P. asper are non-guarders of their non-adhesive eggs and young, open substrate spawners on coarse substrates (rocks) and have photophobic free embryos. The breeding season is shorter for P. afer whereas P. asper can spawn as late as April and impoundment releases can induce them to spawn. A study of comparative neuroecology revealed that of the four groups of fish analyzed (males and females of both species) male P. afer had the largest brains, especially the optic lobes and cerebellum. P. asper females had the smallest brains. No neural compensation in the external gustatory centre, the facial lobe, was found for P. asper inhabiting the turbid waters. P. afer also had significantly larger eyes and longer barbels. P. afer males were also found to have the highest density and largest nuptial tubercles as well as the most pronounced breeding colouration. It was concluded that P. asper is the more derived of the sister species pair with regard to life-history attributes. It is further suggested that investment per offspring is important in determining the life-history trajectories. Paedomorphosis has occurred and by this mechanism variability has been restored to the redfin minnows in the Groot River which enables them to survive in the highly variable, intermittent Karoo stream. The more precocial P. afer do not require this variability in the more constant and predictable environment of the Wit River.

Le but de notre étude était de mettre en place une méthode qui puisse nous permettre d’identifier, en aveugle, des perturbateurs de voies biologiques, et qui soit d’une part généralisable pour toute espèce de poissons et d’autre part applicable quel que soit le cours d’eau considéré. Nous nous sommes intéressés aux gènes différentiellement exprimés dans le foie, en utilisant la technologie du séquençage Illumina de banques ADNc. Nous avons étudié trois espèces de cyprinidae (C. nasus, P. toxostoma, S. cephalus) dans le bassin de la Durance, servant à l’alimentation en eau de plusieurs millions de personnes. Nous avons mis en place une suite logicielle pour inférer un transcriptome pour chacune des trois espèces étudiées, et effectué un travail en bioinformatique pour l’identification des spécimens hybrides. Cette méthode nous permet d’assigner les 596 millions de séquences générées (293 spécimens) à l’une des trois espèces et à 16606 gènes identifiés. Les résultats biologiques montrent des variations de l’expression de gènes touchant des voies biologiques associées à des réponses aux xénobiotiques le long de l’axe amont-aval de la rivière. Ils montrent aussi que les spécimens échantillonnés dans le canal EDF présentent des réponses atténuées aux xénobiotiques par rapport aux individus en rivière. Ce résultat peut s’expliquer par l’effet de dilution des polluants dans une masse d’eau plus importante. Cette étude met en évidence les capacités adaptatives des populations de poissons à court terme, via des modifications de l’expression des gènes à un ensemble de perturbateurs environnementaux. Ce travail permet d’envisager la mise en place d’un outil de gestion incontournable. / The aim of our study was to establish a method that allows the identification (in blind) of biologicalpathway disrupters, for all species of fish and applicable regardless of the watercourse considered. Wefocused on differentially expressed genes (and the biological pathways in which they act) in the liver,using the Illumina sequencing technology of cDNA libraries. We studied three species of cyprinidae (C.nasus, P. toxostoma, S. cephalus) in the Durance basin that constitutes water resource for several millionpeople. We have implemented a pipeline to infer the transcriptome for each of the three species studied,and developed a bioinformatics framework for the identification of hybrid specimens. This methodallows us to assign the 596 million sequences generated (representing 293 specimens) to one of the threespecies and to 16,606 identified genes. The biological results display variations in the expression of genesaffecting biological pathways associated with xenobiotic responses (estrogens, Hap, heavy metals) alongthe upstream-downstream axis of the river. They also yield that the specimens sampled in the EDFchannel displayed an attenuated responses to xenobiotics, in comparison to individuals that inhabitethe river, possibly a benefit of the dilution effect of pollutants in a larger body of water. This studyhighlights short-term adaptive capacities (acclimation) of fish populations to a set of environmentaldisrupters via changes in gene expression levels. It will open a way to an essential tool for managementpolicies.