Abstract:

The Sub-Saharan Great Lakes Region has a rich ichthyofauna most notably, the cichlids. Among the cichlids, the most important and commercially exploited are the tilapine species of which O. niloticus Linn, 1758 (Nile tilapia) is the most common. This vital resource has been subjected to immense anthropogenic threats primarily through fish translocations, overfishing, habitat destruction, climate change, alien invasive aquatic weeds etc. Hereby, the broader aim of this thesis was to investigate the impact of anthropogenic activities on the evolutionary trajectory of the East African O. niloticus particularly in nonnative habitats following the aforementioned activities in the region. This was investigated using the hypothesis that anthropogenic activities might have altered the natural morphology and genetic structure of O. niloticus through admixture and introgression with the indigenous congeneric species. Geometric morphometries and molecular genetic markers were used to delineate the cichlid in the region from different East African localities, covering low and high-altitude environments. Samples were collected from three locality types; farms, lakes with natural but non-native (introduced) fish and lakes with native (indigenous) fish. The farms and non-native localities were only limited to Uganda. Additionally, samples at the continental level were collected, including populations from the West African country of Burkina Faso and Ethiopia to test and compare the genetic structure with the East African ones. For morphometric analysis only the East African populations were included. During geometric morphometries analysis, two thin plate spline (Tps) programs; Tps Utility (TpsUtil) and Tps digitizer (TpsDig) were utilized. These programs were used to acquire landmarks on fish digital photographs and henceforth generation of x, y coordinates which were then imported into MorphoJ program for subsequent multivariate analyses (chapter 2). At molecular level, 64 microsatellites (SSR) loci were developed and 26 were employed to test the four East African/Uganda populations. Here, the latest genotyping by sequencing approach using SSR loci (SSR-GBS) was compared with the traditional fragmented length analysis by assessing the information content recovered with the two approaches (Chapter 3). SSR-GBS was then applied in Chapter four to investigate all the sub-Saharan Nile tilapia populations. A total of 40 SSR loci were used for amplifying all the present studied populations. Geometric morphometric analysis generally revealed that all the East African populations were somewhat homogeneous in shape, implying close relation. However, when principle component scores (PC1 and PC2) were plotted against the axes, it was clear that the non-natives; Victoria and Kyoga, were morphologically divergent from for instance some native populations (Kazinga Channel and Edward). But the non-native Victoria and Kyoga appeared undifferentiated from some natives like Albert, George, River Nile and Turkana. The shape variation among the East African Nile tilapia populations was suspected to admixture and hybridization, partly induced by anthropogenic activities. However, other environmental cues like water turbulences (for example in River Nile), predation threat effects (e.g. Nile perch in native lakes; Albert and Turkana), severe and adverse environmental conditions (like declined water levels aggravated by high temperatures in L. Turkana), were taken into consideration. Apparently, use of SSR-GBS genotyping approach yielded more information content than the traditional based amplicon length procedures. For instance, SSR-GBS method did better to reveal the genetic diversity of the East African O. niloticus than the conventional amplicon length (AL). These results were consistent with a detailed genetic structure generated by SSR-GBS which was undetectable with AL. Additionally, based on polymorphic information content (PIC), it was evident that the SSR-GBS showed more polymorphic loci compared to AL. More importantly the markers developed in this thesis and the genotyping techniques were demonstrated how they may contribute useful information for further investigations regarding the East African Nile tilapia for sustainable exploitation and conservation. By evaluating the genetic diversity and variability patterns among Nile tilapia populations at sub-Saharan level, the Ethiopian populations were indicated more divergent than the East African ones. This was particularly prominent for lake Tana which indicated a high level of distinctiveness. In East Africa, genetic structure analyses revealed four O. niloticus groups which were consistently supported by Fst results. Moreover, the East African populations genetically differed from their Ethiopian and West African counterparts. Also, O. niloticus from Lake Turkana (Kenya) was isolated, while the Ugandan populations were grouped according to geographical locations/water catchments and anthropogenic activities i. Signals of genetic erosion were detected in Ethiopian and some East African populations being likely a consequence of either bottlenecks associated with fragmentation or founder effects. O. niloticus in Lakes Tana, Victoria and the cluster of Lakes Edward, George as well as Kazinga Channel, may require further exploration for taxonomic recognition. Apart from Lake Tana, the level of isolation of the cichlid in Lake Victoria and the genetic group in the western Rift Valley Lakes have not been reported before. This thesis indicates that anthropogenic activities have contributed to a significant change in the genotypic composition of O. niloticus which may compromise the species’ sustainability. Overall, the molecular analyses were congruent to the geometric morphometries, which shows the robustness and importance of the current approach in understanding the state the of the East African O. niloticus. In the ongoing work, out of scope of this thesis, these populations are followed at mitochondrial genome level to precisely investigate the extent of introgression and phyletic patterns.