Abstract:

The complex geology and hydrological evolution of Africa has resulted in a landscape characterised by some of the world's largest freshwater lakes and rivers. These freshwater
habitats contain diverse fish fauna from which commercial inland fisheries support
millions of people in Africa and other parts of the world through fish exports. Despite the
extreme importance of African fisheries, versus increased threats that have led to their
stagnation and decline, fisheries conservation and management based
knowledge of stock structure has remained poorly studied and understood in Africa. It is
clear though, that biogeography of fish fauna will often follow patterns of stock structure
along gradients of interconnected,
structure and diversity of commercial fish species along these gradients in Africa is vital
in identifying management units (MUs) for sustainable management and potential
aquaculture development of aquatic species.
The widely distributed bagrid catfishes (Bagrus docmak. and B. bayad) and the Nile perch,
Lates niloticus, have been identified as model species that could be used to not only
understand the biogeography of the African aquatic fauna, but are also important
commercial fisheries and candidate species for aquaculture development. These fish
species are indigenous to Africa and valued for food, as well as important components of
recreational-based fisheries. These three species have been overexploited in their natural
environments, with the Nile perch also in decline within environments where it has been
translocated.
The overarching objective of this thesis was to develop and utilise new genetic resources
freshwater fishes and further understanding on how genetic population structure has been
_ .
shaped by both the geology and anthropological (i.e., translocations), especially in the
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or fragmented habitats. Understanding the genetic
on geneticThe overarching objective of this thesis was to develop and utilise new genetic resources
freshwater fishes and further understanding on how genetic population structure has been
_ .
shaped by both the geology and anthropological (i.e., translocations), especially in the
xii
or fragmented habitats. Understanding the genetic
on genetic
The complex geology and hydrological evolution of Africa has resulted in a landscape
to understand the genetic structure and biogeography of these three important African
Great Lakes Region of Africa. The knowledge acquired will be useful for the
management and conservation of existing fisheries and aquaculture development
programmes.
Firstly, to address the lack of genetic resources for important commercial fish species in
Africa, high throughput Next Generation Sequencing (NGS) was used to generate novel
genomic resources for two commercially important fish species, L. niloticus and B.
docmak. Roche 454 GS-FLX shotgun sequencing was used to generate over 160,000
sequence fragments for B. docmak. from which hundreds of microsatellites markers with
primers were in silico mined. Of these a subset of 20 novel microsatellite loci were tested
in the laboratory from which 15 markers successfully amplified and were characterized
in B docmak individuals from Lake Albert in East Africa (mean allelic richness (Mi) of
4.5, mean Ho. and He. of 0.535 ± 0.37 and 0.605 ± 0.028, respectively). These 15 loci also
Whilst there is some understanding of how macroevolutionary drivers have shaped teleost
speciation in East Africa, there is a paucity of research into how the same biogeographical
factors have affected microevolution (ie evolution of populations within a species). To
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were
East
Africa, within two major drainage basins; the Albertine Rift and Lake Victoria Basin.
Individuals (N = 175) were genotyped at 12 microsatellite loci and 93 individuals
sequenced at the mitochondrial DNA control region. Results suggested populations from
Lakes Edward and Victoria had undergone a severe historic bottleneck resulting in very
low nucleotide diversity (it = 0.004 and 0.006 respectively) and negatively significant Fit
detected at both historical (mtDNA (psr = 0.62, P = 0.000) and contemporary
(microsatellite Fsr= 0.46, P = 0.000) levels. Patterns of low genetic diversity and strong
population structure revealed are consistent with speciation patterns that have been linked
to the complex biogeography of East Africa, suggesting that these biogeographical
features have operated as both macro- and micro-evolutionary forces in the formation of
the East African teleost fauna.
Thirdly, in order to understand the population genetic structure of Nile perch, an iconic
species of high commercial importance, both in the species’ native range and where it
has been translocated, Nile perch tissue samples were acquired from two West (Senegal
River and Lake Kainji on the Niger River) and four East African (Lakes Albert, K.yoga,
Victoria and Turkana) locations. Nineteen polymorphic microsatellite loci were used to
study the genetic variation among populations across regions (West and East Africa), as
well as between native and introduced populations within East Africa. Results revealed
strong and significant genetic structuring among populations across the sampled
distribution (divergence across regions, Fct = 0.26, P =.0.000). STRUCTURE analysis
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values (-3.769 and-5.049, at P < 0.05). High genetic structuring between drainages was
Overall this thesis provides the first comprehensive set of species-specific genomic
resources developed for the freshwater African bagrids (5. docmak and B. bayad) and the
Nile Perch, L. niloticus. Using the genomic resources developed, the three freshwater
species examined, showed strong phylogeographic and genetic structure patterns that
enabled the successful identification of management units (MUs). The identification of
these management units will be useful in the formulation of future conservation strategies
and identification of stocks suitable for aquaculture development for these species. The
molecular data generated herein is central to the management of freshwater fisheries in
Africa, especially West and East Africa (that have been identified each as a unique
genetic group) and contributes to the understanding of microevolutionary forces in
shaping the evolution of the African freshwater fish fauna.