Philosophiae Doctor - PhD / Cichlids are one of the most diverse groups of fishes in the world. The highest concentration of cichlids is found in Lake Malawi, where over 1500 species are recorded to occur, which are dominated by the haplochromine tribe. Several authors proposed that sexual selection has been a major contributor in the high rate of speciation of haplochromine cichlids. However, sexual selection alone may not be sufficient to fully explain high speciation rates among cichlids. Many closely related cichlids in Lake Malawi differ only in coloration, yet occur in sympatry. It is still not fully understood how they remain reproductively isolated. Previous studies suggest that visual cues are primarily used for reproductive isolation and species recognition. In the current study, visual, chemical and acoustic cues were investigated to observe how they may potentially influence species recognition and reproductive isolation between two closely related species, Metriaclima estherae and M. callainos, as well as between alternate colour morphs of M. estherae.

Science and medicine have progressed in unfathomable ways over the past century. Paradoxically, as our result of our advancements in medicine we live in a progressively aging society where the majority of people will have multiple morbidities associated with senescence. The World Health Organization estimates that nearly 100% of the population will suffer dental maladies, which left untreated compound with age. We hope to gain new biomedical insight applicable to the advancing field of dental regenerative therapeutics. This dissertation reveals new dental biology through studying the embryology, genetics and evolution of teeth across patterning, morphogenesis and regeneration. We exploit an innovative model, the Lake Malawi cichlid fishes, to study these processes in a natural system. Malawi cichlids have rapidly evolved diverse species-specific dentitions, ranging from hundreds to thousands of teeth that represent a rainbow of shapes and sizes, yet Malawi cichlid species has nearly identical genomes, offering us a powerful genetic system. Furthermore, unlike classic vertebrate models in embryology such as zebrafish, chicken or mice, cichlids have oral teeth and the ability to replace each tooth constantly throughout their lifetimes. In the first study, we break-down the process of whole de-novo tooth replacement in cichlids. We then explore the re-deployment of initiating gene pathways later in the morphogenesis of each replacement tooth (RT). In the second study we investigate the co-patterning of two placode derived oral organs, teeth and taste buds (TBs), and uncover new genes that may modulate their number and size. We subsequently discover a bipotency of progenitor tissue to form both organs and a later plasticity to trans-fate it through coordination of a Wnt-BMP- Hh genetic hierarchy. In the last study, we explore the stem cells that are responsible for the phenomenon of lifelong cichlid tooth replacement. We describe a common epithelium connected to TBs and rich in stem cells, with a newly discovered stem cell niche at the tip of the RT. We uncover the transcriptomes of both organs, and through differential gene expression informed manipulations, coerce dental cells to display TB characteristics. We hypothesize that TB stem cells may be used in dental therapeutics.

African climate changed considerably throughout the Pleistocene (2.588 million (Ma) to 12 thousand years ago (ka)). The timing, rate, and magnitude of past climate change across the continent impacted the evolutionary and migratory history of many mammalian species, including hominins. Investigating paleoclimatic variability through time at local and regional scales allows for an assessment of the extent to which climate change affected hominin evolution in Africa. This dissertation presents three approaches for increasing the understanding of past climate change in Africa. One method is to critically synthesize the existing literature of African climate (n=85) and hominid demography (n=64) over a restricted time frame (150 ka to 30 ka) and specific spatial scale (regional). Results from this study are two-fold: 1) climate change in Africa during this period was variable by region, responding to different climate-forcing mechanisms, and 2) changes in population and climate were asynchronous and likely created alternating opportunities for migration into adjacent regions, including hominin migrations out of Africa (~140-80 ka). The second approach is to evaluate modern ecological relationships between species and their environment to better quantify interpretations of paleoecological records. A modern distribution study of 33 ostracode species from 104 sites in the southwest arm of Lake Malawi suggest that depth-dependent variables likely define species niches. Relationships between ostracodes, fish and the green algae Botryococcus, were used to inform the paleoecological interpretations in the third study of this dissertation. Additional results suggest that macrocharcoal is likely delivered to the lake basin via river rather than wind-borne methods. The third approach involves primary analysis of climatic indicators from the sedimentary record to chronicle paleoecological and paleoenvironmental change at the basin scale through time. Results from a 380.7 meter-long sediment core recovered from Lake Malawi indicate a change of state likely caused by local tectonism, which affected ostracode assemblages, but had little effect on lake level history through time. Furthermore, the local hydroclimate of Lake Malawi alternately covaried with global glacial/interglacial cycles and local insolation maxima over the past 1.25 Ma. The magnitude and frequency of hydroclimatic variability in the watershed will be further assessed in future research.

Lake Malawi is a great lake not only because of its size (30,800 km2) but also because of its unique fish diversity. The lake contains the highest number of freshwater fish species in the world. The fish species are hypothesized to have radiated within the lake, which is 1-2 million years old. The collapse of the capture fishery in Lake Malawi between the 1970s and 1990s led to the launch of cage culture of indigenous fish species in 2004 in the south east arm of the lake. While cage culture has been practiced for many years in temperate lakes and seas, the fish farm in Lake Malawi is the first in the African Great Lakes and, therefore, not much information currently exists that is relevant to the impact of cage culture on such a large, species-rich tropical lake. Consequently, a study was done between January and December, 2007, at the fish farm in Lake Malawi to determine potential impacts of cage wastes on the environment. The study found that, just like in temperate systems where 70-87% of C, N and P added through feed get dispersed into the environment, discharges from fish cages in Lake Malawi were between 71-88% of the nutrients added through feed. The discharges were proportional to the amount of feed added so that as production and feed supply increase over time, more cage wastes would be generated and released into the environment. The discharges were exacerbated by poor stocking and feeding regimes. Production periods were longer (mean of 376±42 days) than if recommended stocking and feeding rates were followed. Feed quality may also have affected production performance and waste generation in the cages, but was not studied. The cage wastes were incorporated into the food web and support the wild fishes in the vicinity of the fish farm. Impacts of the cage wastes on the water column and sediments in the vicinity of the cages were minimal during the study period, probably because of rapid and efficient dispersion of the wastes by strong water currents, that averaged 9.3 cm s-1, through the cages and high consumption of the cage wastes by large numbers of wild fishes which aggregated around the cages. The wild fishes also helped to disperse the cage wastes over a larger area through consumption, translocation and defecation. However, as production increases, the amount of cage wastes generated may overwhelm mitigation by dispersion by water currents and consumption by wild fishes, particularly if many cages are deployed close together and interfere with current flows. Based on my observations, a fish farm that produces 15,000 tonnes fish/yr in Lake Malawi would generate 1249, 113 and 21 megamoles/yr of C, N and P, respectively, that are comparable or higher than DOC, TDN and TDP loadings observed in the most disturbed large river systems draining into Lake Malawi. The impacts of these river systems in Lake Malawi have been well documented, particularly around river mouths and in the more densely populated and shallower southern portion of the lake, where algal communities and their sedimentation rates have begun to change. Cage culture discharges may accelerate these changes.

Lake Malawi is a great lake not only because of its size (30,800 km2) but also because of its unique fish diversity. The lake contains the highest number of freshwater fish species in the world. The fish species are hypothesized to have radiated within the lake, which is 1-2 million years old. The collapse of the capture fishery in Lake Malawi between the 1970s and 1990s led to the launch of cage culture of indigenous fish species in 2004 in the south east arm of the lake. While cage culture has been practiced for many years in temperate lakes and seas, the fish farm in Lake Malawi is the first in the African Great Lakes and, therefore, not much information currently exists that is relevant to the impact of cage culture on such a large, species-rich tropical lake. Consequently, a study was done between January and December, 2007, at the fish farm in Lake Malawi to determine potential impacts of cage wastes on the environment. The study found that, just like in temperate systems where 70-87% of C, N and P added through feed get dispersed into the environment, discharges from fish cages in Lake Malawi were between 71-88% of the nutrients added through feed. The discharges were proportional to the amount of feed added so that as production and feed supply increase over time, more cage wastes would be generated and released into the environment. The discharges were exacerbated by poor stocking and feeding regimes. Production periods were longer (mean of 376±42 days) than if recommended stocking and feeding rates were followed. Feed quality may also have affected production performance and waste generation in the cages, but was not studied. The cage wastes were incorporated into the food web and support the wild fishes in the vicinity of the fish farm. Impacts of the cage wastes on the water column and sediments in the vicinity of the cages were minimal during the study period, probably because of rapid and efficient dispersion of the wastes by strong water currents, that averaged 9.3 cm s-1, through the cages and high consumption of the cage wastes by large numbers of wild fishes which aggregated around the cages. The wild fishes also helped to disperse the cage wastes over a larger area through consumption, translocation and defecation. However, as production increases, the amount of cage wastes generated may overwhelm mitigation by dispersion by water currents and consumption by wild fishes, particularly if many cages are deployed close together and interfere with current flows. Based on my observations, a fish farm that produces 15,000 tonnes fish/yr in Lake Malawi would generate 1249, 113 and 21 megamoles/yr of C, N and P, respectively, that are comparable or higher than DOC, TDN and TDP loadings observed in the most disturbed large river systems draining into Lake Malawi. The impacts of these river systems in Lake Malawi have been well documented, particularly around river mouths and in the more densely populated and shallower southern portion of the lake, where algal communities and their sedimentation rates have begun to change. Cage culture discharges may accelerate these changes.

Lake Malawi is the second largest lake in Africa, supporting diverse populations of endemic cichlids and supplying essential water resources to Malawi, Mozambique and Tanzania. However, population growth, rapid deforestation and intensive agriculture, especially in the southern catchments, have accelerated soil erosion during the last half century. These anthropogenically-disturbed catchments have caused rivers to transport greater sediment loads into Lake Malawi than rivers within forested catchments. Lake Malawi?s immense size and oligotrophic nature may retard detection of inputs of external contaminants. Reversing the effects of increased nutrient loading to Lake Malawi once observed would likely take generations, as the residence time of water is over 140 years. Therefore, sensitive metrics are required to assess the effects of land use change and climate variability in Lake Malawi in advance of deleterious effects. In this study, paleolimnological analyses of four sediment cores collected in 1997 and 1998 along a longitudinal transect of Lake Malawi, dated with ²¹⁰Pb analyses and analyzed for biogenic silica and sedimentary diatom assemblages, were used to create a long-term water quality dataset. These four sites span gradients of land use and latitude in order to reconstruct limnological conditions over the whole lake during the last 300 years. Paleoecological results indicate that patterns of diatom assemblage change are not uniform lake wide. Southern cores contain evidence of nutrient enrichment starting as early as ca. 1940, indicated by increased silica, carbon and nitrogen burial. By ca. 1970, increased rates of sedimentation, diatom influx and changes in diatom community composition, characterized by increased percent abundance of eutrophic diatom taxa, are attributable to accelerated enrichment by terrestrial soil erosion. The succession of diatoms in southern Lake Malawi begins with high percent abundance of <i>Aulacoseira nyassensis</i> and <i>Fragilaria africana</i>, which thrive in nutrient-rich waters, followed by a shift towards diatom taxa with reduced silica requirements by ca. 1980 (e. g. <i>Stephanodiscus nyassae, S. minutulus, S. muelleri, Cyclostephanos</i> and small <i>Nitzschia</i> species. ), a pattern comparable to the eutrophication-induced decline in silica to phosphorus ratios in Lake Victoria. In Lake Malawi, evidence of eutrophication extends to the mid lake as indicated by similar diatom assemblage changes in the sediment core from the central region. Diatom stratigraphies from the north end of the lake indicate no observable impacts of land use change on the northern basin of Lake Malawi during the past 350 years. However, a nine-meter rise in water level ca. 1860 AD appears to have resulted in elevated diatom influxes at that time comparable to the recent eutrophication-induced diatom influxes of the southern cores. The effects of this rise in water level was recorded in all three measured sites, southern, central and northern Lake Malawi, indicating lake-wide increased productivity, yet changes to the diatom community composition were imperceptible. This study shows evidence of recent cultural eutrophication altering limnological conditions with impacts to the biogeochemical cycling of silica, the available silica to phosphorus ratios and the biotic communities of a large portion of Lake Malawi. Thus, providing an early warning that proper stewardship of Lake Malawi requires effective management of land-use practices within the catchment to reduce soil erosion and avoid widespread water quality deterioration of this great lake.

Lake Malawi is the second largest lake in Africa, supporting diverse populations of endemic cichlids and supplying essential water resources to Malawi, Mozambique and Tanzania. However, population growth, rapid deforestation and intensive agriculture, especially in the southern catchments, have accelerated soil erosion during the last half century. These anthropogenically-disturbed catchments have caused rivers to transport greater sediment loads into Lake Malawi than rivers within forested catchments. Lake Malawi?s immense size and oligotrophic nature may retard detection of inputs of external contaminants. Reversing the effects of increased nutrient loading to Lake Malawi once observed would likely take generations, as the residence time of water is over 140 years. Therefore, sensitive metrics are required to assess the effects of land use change and climate variability in Lake Malawi in advance of deleterious effects. In this study, paleolimnological analyses of four sediment cores collected in 1997 and 1998 along a longitudinal transect of Lake Malawi, dated with ²¹⁰Pb analyses and analyzed for biogenic silica and sedimentary diatom assemblages, were used to create a long-term water quality dataset. These four sites span gradients of land use and latitude in order to reconstruct limnological conditions over the whole lake during the last 300 years. Paleoecological results indicate that patterns of diatom assemblage change are not uniform lake wide. Southern cores contain evidence of nutrient enrichment starting as early as ca. 1940, indicated by increased silica, carbon and nitrogen burial. By ca. 1970, increased rates of sedimentation, diatom influx and changes in diatom community composition, characterized by increased percent abundance of eutrophic diatom taxa, are attributable to accelerated enrichment by terrestrial soil erosion. The succession of diatoms in southern Lake Malawi begins with high percent abundance of <i>Aulacoseira nyassensis</i> and <i>Fragilaria africana</i>, which thrive in nutrient-rich waters, followed by a shift towards diatom taxa with reduced silica requirements by ca. 1980 (e. g. <i>Stephanodiscus nyassae, S. minutulus, S. muelleri, Cyclostephanos</i> and small <i>Nitzschia</i> species. ), a pattern comparable to the eutrophication-induced decline in silica to phosphorus ratios in Lake Victoria. In Lake Malawi, evidence of eutrophication extends to the mid lake as indicated by similar diatom assemblage changes in the sediment core from the central region. Diatom stratigraphies from the north end of the lake indicate no observable impacts of land use change on the northern basin of Lake Malawi during the past 350 years. However, a nine-meter rise in water level ca. 1860 AD appears to have resulted in elevated diatom influxes at that time comparable to the recent eutrophication-induced diatom influxes of the southern cores. The effects of this rise in water level was recorded in all three measured sites, southern, central and northern Lake Malawi, indicating lake-wide increased productivity, yet changes to the diatom community composition were imperceptible. This study shows evidence of recent cultural eutrophication altering limnological conditions with impacts to the biogeochemical cycling of silica, the available silica to phosphorus ratios and the biotic communities of a large portion of Lake Malawi. Thus, providing an early warning that proper stewardship of Lake Malawi requires effective management of land-use practices within the catchment to reduce soil erosion and avoid widespread water quality deterioration of this great lake.

Mechanisms controlling the productivity, abundançe and taxonomic composition of phytoplankton in tropical Lake Malawi were examined by monitoring phytoplankton dynamics in 8 regions covering the length of the lake (560 km) over a 10-12 month period, and relating these dynamics to spatio-temporal changes in thermal structure, nutrient availability, and meteorological conditions. In addition, nearshore benthic photosynthetic rates were measured in 7 different months.Spatial and temporal changes in areal photosynthetic rates were due almost entirely to changes in the efficiency of light utilization by the phyroplankton community. An evaluation of potential factors which might influence tight utilization indicates that nutrient availabitity is the most important. Most of the photosynthetic N and P demand is met by internal recycling within the upper 200 m, and therefore spatio-temporal variation of phytoplankton photosynthetic rate is closely related to changes in mixing regime. It is shown that the dominant meteorological factors responsible for changes in the mixing regime were solar radiation and windspeed. A comparison with previous photosynthesis data for Lake Malawi indicates that windspeed is a dominant factor controlling interannual variability. Shallow areas of the lake were more productive than deep areas, due to more intense upwelling and more efficient internal nutrient recycling in shallow waters. Within the littoral zone, benthic photosynthetic rates were very high, accounting for 14% to 28% of total net photosynthesis within the shallow southeast arm. Phytoplankton biomass was not correlated with photosynthetic rate, indicating that biomass loss processes were important in controlling biomass variability. Changes in phytoplankton taxonomic composition were related to changes in mixing regime. Cyanobacteria and chlorophytes were dominant throughout much of the study period, but diatoms made up a significant proportion of total biomass during periods of increased turbulence and nutrient availability. An analysis of phytoplankton surface area : volume ratios revealed that organism shape and size are important determinants in species succession. Previous studies have emphasized the low variability of phytoplankton biomass and photosynthetic rates in tropical lakes, relative to temperate lakes. An inter-lake comparison reveals that this tenet does not apply to large lakes. Fluctuations in the mixing regime of large tropical lakes have an effect on phytoplankton variability similar in magnitude to the effect of fluctuating solar irradiance in large temperate lakes.

Mechanisms controlling the productivity, abundançe and taxonomic composition of phytoplankton in tropical Lake Malawi were examined by monitoring phytoplankton dynamics in 8 regions covering the length of the lake (560 km) over a 10-12 month period, and relating these dynamics to spatio-temporal changes in thermal structure, nutrient availability, and meteorological conditions. In addition, nearshore benthic photosynthetic rates were measured in 7 different months.Spatial and temporal changes in areal photosynthetic rates were due almost entirely to changes in the efficiency of light utilization by the phyroplankton community. An evaluation of potential factors which might influence tight utilization indicates that nutrient availabitity is the most important. Most of the photosynthetic N and P demand is met by internal recycling within the upper 200 m, and therefore spatio-temporal variation of phytoplankton photosynthetic rate is closely related to changes in mixing regime. It is shown that the dominant meteorological factors responsible for changes in the mixing regime were solar radiation and windspeed. A comparison with previous photosynthesis data for Lake Malawi indicates that windspeed is a dominant factor controlling interannual variability. Shallow areas of the lake were more productive than deep areas, due to more intense upwelling and more efficient internal nutrient recycling in shallow waters. Within the littoral zone, benthic photosynthetic rates were very high, accounting for 14% to 28% of total net photosynthesis within the shallow southeast arm. Phytoplankton biomass was not correlated with photosynthetic rate, indicating that biomass loss processes were important in controlling biomass variability. Changes in phytoplankton taxonomic composition were related to changes in mixing regime. Cyanobacteria and chlorophytes were dominant throughout much of the study period, but diatoms made up a significant proportion of total biomass during periods of increased turbulence and nutrient availability. An analysis of phytoplankton surface area : volume ratios revealed that organism shape and size are important determinants in species succession. Previous studies have emphasized the low variability of phytoplankton biomass and photosynthetic rates in tropical lakes, relative to temperate lakes. An inter-lake comparison reveals that this tenet does not apply to large lakes. Fluctuations in the mixing regime of large tropical lakes have an effect on phytoplankton variability similar in magnitude to the effect of fluctuating solar irradiance in large temperate lakes.

The potential role of sanctuary areas for biological control of Schistosomiasis and development of sustainable fisheries was investigated at Cape Maclear, Lake Malawi National Park (LMNP). There has been a recent increase in the incidence of schistosomiasis infection which is a threat to the local community as well as the tourism industry which is the major source of income to LMNP as well as Chembe Village. At the same place there is increasing fishing pressure due to growing human population and declining fish resource. The increase in the incidence of schistosomiasis transmission was attributed in part to over-fishing of the molluscivorous fish which are believed to control the vector snails for schistosomiasis. Four molluscivorous fish species, Trematocranus placodon; Trematocranus microstoma; Mylochromis sphaerodon and Mylochromis anaphyrmus were reported to account for more than 90% of the fishes (by numerical abundance) which feed on the gastropods above 15 metre depth. The gastropod numbers was reported to be highest at 1.5 to 4.5 metre depth. Of the four molluscivores, T. placodon was proposed as a biological control agent for schistosomiasis based upon the previous observations of its feeding habits in artificial conditions. Captive propagation of T. placodon for reintroduction at Cape Maclear in Lake Malawi has been proposed. The present study aimed at providing baseline data required to test the hypotheses that: 1) Over-fishing of the molluscivorous fish has resulted to the increased incidence of schistosomiasis at Cape Maclear. A sub hypothesis to this was that an extension of the LMNP can act as a sanctuary area for the biological control of schistosomiasis by protecting molluscivorous fish which could control schistosomiasis vector snails. 2) A park initially designed to protect the colourful rock dwelling fish and for promotion of tourism may not effectively protect the food fish. To test the first hypothesis, the biology and ecology of T. placodon were investigated with a view to evaluating the effect this species could have on the schistosomiasis vector snail population and hence the control of bilharzia in the lake. The proportions of various gastropod species at Cape Maclear was compared with those found in T. placodon guts. Comparisons of T. placodon abundance and demographic structure inside and outside LMNP were made. To test the second hypothesis, this study investigated the food fish species that use LMNP 100 m protected zone and some basic ecological factors to appreciate the extent to which the adjacent fishery might benefit from their use of the park waters. T. placodon numerical abundance (number of individuals per unit area) ranged from 5.7 to 40.5 /200 m² and it significantly (P< 0.05) varied between sampling sites. Otter Point and Mitande which are inside the park had the lowest abundance as compared to the other three sites; Nguli inside the park; Fisheries and Nchenga outside the park. Two sites in the park, Otter Point and Mitande, had a greater proportion of mature T. placodon individuals than all other sites. The abundance of T. placodon fluctuated significantly from month to month at Nchenga, Nguli and Fisheries (X² test, P<0.0001 for all the three sites) and insignificantly (P>0.05) at Otter Point and Mitande (X² test). T. placodon densities found in the present study corresponded to the peak density of 30 individuals / 200 m² reported in 1986 but did not correspond to that of 1.0 / 200 m² for 1994. There was no evidence to support the previous reports that T. placodon abundance had decreased tremendously from 1986. The reason suggested to account for the discrepancies of T. placodon abundance reported in the present study and other studies was inadequate sampling in the previous studies which did not take into account spatial and temporal variability in T. placodon abundance. The findings reported in this thesis show that there is no need for captive propagation of T. placodon to be reintroduced into the lake at Cape Maclear and that it may prove to be unsuccessful. However, since juvenile T. placodon dominated in abundance at the three sites along the major beach which is outside the park boundaries, it is suggested that the park boundaries be extended to this area so that T. placodon should be protected to allow individuals to grow to bigger size which would be more effective for gastropod control. T. placodon between 60 mm and 80 mm TL fed on benthic insects, phytoplankton and from detritus material. Individuals between 80 mm and 100 mm fed on a mixture of benthic insects, fish scales and small gastropods and at sizes greater than 100 mm individuals specialized feeding on gastropods. Gastropods of five genera were taken and they were: Melanoides , Bulinus, Gabiella, Lanistes and Bellamya. Of these genera Melanoides fonned the greatest part of T. placodon diet. Bulinus was the second most abundant genus but compared to Melanoides its proportion was very small. Of the three Bulinus species taken by T. placodon, B. globosus, is a confirmed vector for Schistosoma haematobium which is prevalent at Cape Maclear. This species was eaten in the least quantities. A comparison ofthe five gastropod proportions in T. placodon diet and in the habitats they occupy showed that Melanoides were taken in proportionately more quantities than Bulinus at most sites. These findings contrasted the previous reports that T. placodon preferred Bulinus to Melanoides. By applying the optimal foraging theory which predicts that an animal species searching for food will go for the type of prey with the highest profitability, it is concluded that the Bulinus cannot be eliminated completely by molluscivores because if their population size falls below a certain level, the fish will switch to other gastropod types. It is concluded that the increase in schistosomiasis may not be necessarily due to overfishing the molluscivorous fish but could be due to the fact that there has been an increase in the proportion of the B. globosus albeit in small numbers which are infected with schistosomiasis parasites. An integrated approach to schistosomiasis control at Cape Maclear comprising vector control, improved water supply, sanitation and health education is suggested since no method can be effective in isolation. Few food fish species were observed to use the park at various times, varying from one species to another with regards to duration, life history stages and abundance. Only a few fish species taken by the adjacent artisanal and commercial fisheries were represented among those observed in the park. This was attributed to the limited diversity of habitat types covered. Only small population size of some species visited the protected area and only part of the life cycle of some species were observed in the park. The use of the park area was seasonal for some species and the protected zone boundaries can be crossed more than once within a day because 100 m distance is just a few minutes swim by fish. Under such circumstances the park cannot function as an effective sanctuary for food fish. An increase of the park size may be a better option to effectively protect the food fish.