In this study, mtDNA was used to examine the phylogenetic and molecular relationships of the freshwater shrimp family Atyidae. The phylogeographical variations of two landlocked Caridina pseudodenticulata and Neocaridina denticulata were also discussed. Four genera and 32 species of the Atyidae were identified and divided into 6 groups. In addition to 14 previously recorded species, eight of them are new records, while another 10 species remain unconfirmed. The combination of morphological and molecular characteristics can effectively differentiate species within the family Atyidae. Analysis of demographic parameters indicates a recent population expansion of C. pseudodenticulata, but not for N. denticulata. The result of Bayesian skyline plot analysis implies that the expansion of C. pseudodenticulata began about 70,000 years ago, followed by a very recent rapid expansion approximately 4,000-6,000 years ago. Four major geographical regions of N. denticulata can be identified, including: (1) Southern Taiwan group; (2) Hualian group; (3) Northern Taiwan group; and (4) Ilan group. The study on the phylogenetic relationship of Atyidae in Taiwan could provide valuable information for future study of speciation and geological variation in tropical island.

Thesis (M. Sc. (Zoology and Entomology))--Rhodes University, 2005.

Thesis (M.Sc. (Zoology & Entomology)) - Rhodes University, 2007.

South Africa is an arid country and its growing population is putting freshwater resources under increasing pressure. Natural salinization of freshwater systems is being exacerbated by anthropogenic influences. The National Water Act (No. 36 of 1998) stipulates the need for an ecological Reserve, that quantity and quality of freshwater needed to protect freshwater ecosystems while allowing sustainable use of freshwater resources. Water guidelines do exist in the form of the South African Water Quality Guidelines (DWAF, 1996) and more recently, Jooste and Rossouw (2002) compiled benchmark values for water quality variables marking the boundaries between ecological health classes in the 4-category classification system. Predominantly international toxicity data were used to compile the guidelines and the benchmark values. In addition, there is a paucity of chronic toxicity data nationally and internationally. This thesis showed that it is statistically possible to derive protective chronic endpoints for salinity from acute toxicity data through extrapolation. The Acute to Chronic Ratio (ACR), Two-Step Linear Regression (LRA) and Multi-Factor Probit Analysis (MPA) extrapolation methods were investigated to derive chronic toxicity data from acute toxicity data. The authors of LRA and MPA recommend associating a time independent LCx value in the range of LC₀¸₀₁ to LC₁₀ with a Predicted No Effect Concentration (PNOEC). In addition to published methods, this thesis studied the possibility of equating a time independent LC₅₀ value and subjected to a safety factor of 5 (LRA LC₅₀/5), to the PNOEC. Extrapolated chronic toxicity data where the toxicants are NaCl and Na₂SO₄ were derived for indigenous South African macroinvertebrates. NaCl and Na₂SO₄ are salts associated with salinisation in South Africa. In addition, a chronic salinity toxicity test protocol for an indigenous South African aquatic macroinvertebrate was designed and chronic toxicity test were performed using NaCl and Na₂SO₄ as toxicants. The experimental chronic toxicity data produced were used to validate results from the acute to chronic extrapolation methods. Extrapolated chronic toxicity data were inputted into Species Sensitivity Distribution curves, and concentrations that were predicted to protect 95 % of species (PC95) were compared to the sub-lethality benchmarks proposed by Jooste and Rossouw (2002) for NaCl and Na₂SO₄. This study concluded that the LRA LC₅₀/5 extrapolation method is the most protective and accurate and proposed that LRA replace the ACR method in future guideline development for inorganic salts.

The aim of this thesis is to use phylogenetic analyses of mitochondrial DNA to investigate the biogeography and evolutionary relationships within the freshwater shrimp family Atyidae in Australia at a nested series of scales, both geographic and systematic. At the largest scale, the relationships between Australian and Indo-West Pacific species were inferred using the two most common atyid genera in Australia, Caridina and Paratya. Most atyids are hypothesised to have colonised Australia from Southeast Asia, but Paratya may be a Gondwanan relict given its distribution. Australian Paratya all form a strong clade, with a sister relationship to species from Tasman Sea islands. Molecular clock estimates place all of the splits within Paratya after the break-up of Gondwana, with Australia being colonised once 3½-8½ million years ago. This transoceanic dispersal is conjectured to have taken place through oceanic currents because of the amphidromous life cycle of some taxa of Paratya. Caridina has a very different biogeographic history in Australia, as numerous Australian species have close evolutionary relationships with non-Australian taxa from locations throughout the region. This implies many colonisations to or from Australia over a long period, and thus highlights the surprising adeptness of freshwater shrimp in dispersal across ocean barriers and the unity of much of the region's freshwater biota. A number of potential species radiations within Australia were also identified. This agrees with patterns detected for a large number of Australian freshwater taxa, and implies a vicariant explanation due to the development of colder, dryer climates. The systematic relationships of the remaining two Australian surface genera (Caridinides, Australatya) and two subterranean genera (Parisia, Pycnisia) were also investigated. Australatya forms a strong clade with Pacific 'Atya-like' genera, and Caridinides falls within a clade containing Australian Caridina. The hypogean genera, Parisia and Pycnisia, form a strong clade in all analyses, implying an Australian subterranean speciation. The possibility of a relationship between Parisia/Pycnisia and some Australian Caridina species may have implications for the monophyly of the highly disjunct genus Parisia, as it may descend from local Caridina species and represent convergent morphologies. The common and speciose genus Caridina was used as a model taxon for analyses within Australia. At the medium scale, molecular taxonomic techniques were used to uncover cryptic species within a problematic east Australian species complex. At least five species were detected. Phylogeographic and population genetic analyses were carried out on each of these five cryptic species, which diverged from each other in the late Miocene/Pliocene. There were very large differences between the species in the scales of overall geographic distribution, intraspecific divergence and population structure. These were characterised as either: 1) species with large ranges, low intraspecific divergence, limited phylogeographic structuring (Caridina sp. D); 2) species with large ranges, high intraspecific divergence, a high level of phylogeographic structuring (sp. B); 3) species with a limited range, low intraspecific divergence, no phylogeographic structuring (sp. E); or 4) species with limited ranges, high intraspecific divergences, a high level of phylogeographic structuring (sp. A & C). These patterns reflect a combination of large-scale factors, such as landscape structure and climate change, and small-scale factors, such as species-specific tolerances to local conditions and differing dispersal capabilities. Life history variation (egg size) between species may be correlated with different dispersal abilities. Species with the smallest eggs have the least intraspecific divergence and largest distribution, while those with the biggest eggs have the most divergence and smallest distribution, with medium-sized egg species in between. At the smallest phylogeographic scale, C. sp. C from the sand dune islands of Moreton Bay in southeastern Queensland was further analysed. Two different lineages (C1, C2) were found which diverged from each other during the late Miocene/Pliocene and so are older than the current landscape in which they are found. Small-scale phylogeographic analyses within C1, C2 and a sympatric fish identified divergences dating to the Pleistocene (about 100-300 thousand years ago). This implies that ice age sea-level changes may have structured these populations, although there is little observable influence of the last glacial maximum (about 18 thousand years ago). This study has highlighted a number of taxonomic anomalies within the Atyidae. The detection of many cryptic species implies that biodiversity within freshwater invertebrates is higher than currently appreciated. The evolutionary and biogeographic relationships of Australian atyids have proved complex, with many taxa having their own individual histories. At the large Indo-Pacific scale, dispersal is most evident, but within Australia, both vicariance and dispersal have been responsible for structuring all taxa at every scale.

Aquatic toxicity tests are increasingly being used in water resource management worldwide, and currently in South Africa, policy and legislation are being drafted to reflect this international trend. While standard toxicity test methods and test organisms are being considered to develop and set water quality guidelines and effluent discharge limits, it is not clear whether guidelines and discharge limits set using these standard test organisms will be sufficient to protect South Africa’s scarce water resources. As part of ongoing research to investigate the use of indigenous riverine organisms as toxicity test organisms a number of potential species have been identified, including the freshwater shrimp Caridina nilotica. For much of the history of aquatic toxicological data the bulk of the data has been generated by acute toxicity testing, based on short exposures and using mortality as the response end point. There are relatively few chronic, longterm tests with sub-lethal endpoints. However, it was recognized that information about longer exposure durations and non lethal response endpoints was needed, instead of mortality. Chronic tests can provide a more environmentally realistic measure of chemical toxicity than acute toxicity tests. Caridina nilotica has been identified as a potential standard toxicity test organism, as it is widely distributed, easy to find and it occurs in flowing waters. It is an indigenous species which can be easily cultured and maintained in the laboratory and is also ecologically important. Both adults and juveniles have been used successfully in acute toxicity tests at the Institute for Water Research (Rhodes University) and the ability to rear the organisms under laboratory conditions has allowed the development of chronic toxicity tests using C. nilotica. Chronic early life stage tests include continuous exposure of the early life stages, which are presumed to be the most sensitive for aquatic organisms. This study reports on the embryonic development of C. nilotica at the culture temperature of 24⁰C. Morphological developmental stages were monitored and measured and 7 developmental stages were identified. Based on the measurements of the features that were identified, toxicity tests using the reference chemicals sodium chloride (NaCl), sodium sulphate (Na₂SO₄) and cadmium chloride (CdCl₂) were undertaken to test the suitability of C. nilotica embryonic development for chronic toxicity tests for use in water resource management. The length, width, length:width ratios and area of the features decreased in size when exposed to the chemicals. The Lowest Observed Effect Concentration (LOEC) values were 2000mg/L for Na₂SO₄, 3000mg/L for NaCl and 0.31mg/L for CdCl₂. The No Observed Effect Concentration (NOEC) values were 1000mg/L for Na₂SO₄, 2000mg/L for NaCl and <0.31mg/L for CdCl₂. Further research on the teratogenic effects of single chemicals and industrial effluent on developing C. nilotica embryos needs to be undertaken in order to evaluate the described test protocol for use in water resource management.

Oceanic islands have been used as model systems for studies of evolution and speciation as the range of island sizes coupled with their known geological chronosequence make them ideal systems for the study of spatial and temporal variations in species diversity and distributions. These processes also occur on continental islands and mainland habitats but features of oceanic islands, notably their clearly delimited boundaries, natural isolation and simple geological composition make them more amenable to study. The perched dune lakes of Fraser Island, Australia share many of the properties of oceanic islands. The naturally isolated formation of the perched lakes, clearly delimited boundaries of the freshwater habitat and phase difference compared to the surrounding, terrestrial environment have significant implications for the biota these lakes support. Inhabitants of the perched dune lakes consist of the aquatic and semi-aquatic descendents of colonisers that were able to traverse a land barrier and survive in the oligotrophic, acidic waters over subsequent generations. Barriers to ongoing gene flow among lake populations, are however likely to be different for species with different life history characteristics. I therefore sought to assess the effects of three different life history characteristics on post-colonisation interpopulation gene flow. A representative species was selected to represent one of each of the following life history characteristics: * Aquatic species confined to lake for entire life cycle - freshwater shrimp Caridina indistincta. * Semi-aquatic species capable of terrestrial dispersal - freshwater turtle Emydura krefftii. * Semi-aquatic species capable of aerial dispersal - odonate Orthetrum Boumiera. 137-250 individuals were sampled per species across six lakes separated by 1-6km. Regions of the mitochondrial genome were targeted and molecular screening methods developed and employed to assess the relative levels of post-colonisation gene flow among lake populations. Parsimony analysis of the 25 unique haplotypes identified in the species with no apparent inter-lake dispersal mechanism, the freshwater shrimp Caridina indistincta, demonstrated that there was no sharing of derived haplotypes among lake populations. Star shaped genealogies were identified in four lake populations indicative of a population expansion and mismatch distribution analysis confirmed a recent population expansion estimated to have occurred no more than 200,000 years ago. This demonstrates that each of the perched dune lakes was colonised by C.indistincta soon after their inception but that no ongoing gene flow among lake populations has occurred. The population genetic structure of the species assessed which is capable of terrestrial dispersal suggests that although this species of freshwater turtle, Emydura krefftii, is capable of overland dispersal, gene flow among lake populations is limited. Even at the small spatial scale examined in this study, E.krefftii populations displayed a pattern of isolation by distance (r=0.854, p&lt0.03). Nested clade analysis also suggested a pattern of restricted gene flow with some long distance dispersal in recent times with long distance dispersal and a possible range expansion occurring historically. The species examined in this study that displayed the most extensive gene flow among lake populations was the dragonfly Orthetrum boumiera. No relationship was found between genetic and geographic distance (r= -0.0852, p&gt0.05) and nested clade analysis could not identify a geographical association among haplotypes, indicative of panmixia. While larval life stages of this species are fully aquatic, the winged adult stages of this species appear to be connecting seemingly isolated lake populations, at least at the spatial scale examined here. The results of this study have demonstrated that these perched dune lakes provide 'island like' models for recent biogeographic processes. The pattern of colonisation and subsequent diversification identified in these populations takes the form of insitu 'genetic radiations' with those populations that are isolated forming monophyletic clades endemic to a single lake. The genetic diversity and endemism identified in this study has occurred over much smaller temporal (&lt500,000 years) and spatial (&lt6.5km) scales than in studies of oceanic island fauna. However, the mode of formation of the perched dune lakes and the implications that their natural isolation and abiotic genesis have for the evolution of colonisers of these unique habitats has resulted in them being analogous to true oceanic islands.

Although the use of pesticides is necessary to meet the socio-economic needs of many developing countries, especially in Africa, side effects of these bio-active chemicals have contributed to contaminating aquatic and terrestrial ecosystems. Environmental water quality degradation by pesticides interferes with ecosystem health and poses numerous risks to aquatic life. In South Africa, glyphosate-based herbicides are frequently used to control weeds and invading alien plants, but ultimately end up in freshwater ecosystems. However, there are no South African-based environmental water quality management strategies to regulate these bio-active chemicals. Therefore, this study sought to provide a sound scientific background for the environmental water quality management of glyphosate-based herbicides in South Africa, by conducting both laboratory and field investigations. In the laboratory investigations, aquatic ecotoxicological methods were used to evaluate responses of the freshwater aquatic shrimp Caridina nilotica exposed to Roundup® at different biological system scales, and the responses of multiple South African aquatic species exposed to Roundup® through species sensitivity distribution (SSD). In the field investigations, the effect of Kilo Max WSG on the physicochemical and biological conditions of three selected sites in the Swartkops River before and after a spray episode by Working for Water were evaluated through biomonitoring, using the South African Scoring System version 5 (SASS5) as a sampling protocol. Both Roundup® and Kilo Max WSG are glyphosate-based herbicides. All the data were subjected to relevant statistical analyses. Findings of this study revealed that Roundup® elicited responses at different biological system scales in C. nilotica, while SSD estimates were used to derive proposed water quality guidelines for glyphosate-based herbicides in South Africa. The biomonitoring revealed that using glyphosate-based herbicides to control water hyacinth within the Swartkops River had a negligible impact on the physicochemical and biological conditions. Based on these findings, a conceptual framework that can be used for the integrated environmental water quality management of glyphosate-based herbicides in South Africa was developed as part of integrated water resource management (IWRM). The combined data sets contribute to a sound scientific basis for the environmental water quality management of glyphosate-based herbicides in South Africa.