Browsing by Author "Nyakaana, Silvester"
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Item Evolutionary history of Nile perch Lates sp. inferred from mitochondrial DNA variation analyses(Zoological Studies, 2013) Mwanja, Matthew T.; Muwanika, Vincent B.; Masembe, Charles; Nyakaana, Silvester; Waiswa Mwanja, WilsonEvolutionary histories of aquatic species are often characterized by distinct patterns of genetic variation, which in part reflect drainage evolution. In the present study, the consequences of paleo-environmental changes on patterns of genetic variation of the mitochondrial DNA control region in Nile perch Lates sp. sampled from seven water bodies across the African continent were investigated. Results: In a total sample of 124 individual sequences, 37 distinct haplotypes were observed, and 78.4% of these haplotypes were location specific. Haplotypes were found to cluster into two major groups, one composed of individuals sampled from East Africa and another from West Africa, with no haplotypes shared in between. Conclusion: These lineages may have developed in geographical isolation during the Pleistocene and have remained largely allopatric without gene flow (Nm = 0.0) since that time. There was also evidence that both of these genetic lineages have undergone recent population expansions. We interpret these results in light of the recent evolution of Africa's modern drainage network.Item Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene(Molecular Ecology, 2015) Stoffel, Céline; Dufresnes, Christophe; Okello, John Bosco A.; Noirard, Christian; Joly, Pierre; Nyakaana, Silvester; Muwanika, Vincent B.; Alcala, Nicolas; Vuilleumier, Séverine; Siegismund, Hans R.; Fumagalli, LucaOver the past two decades, an increasing amount of phylogeographic work has substantially improved our understanding of African biogeography, in particular the role played by Pleistocene pluvial-drought cycles on terrestrial vertebrates. However, still little is known on the evolutionary history of semi-aquatic animals, which faced tremendous challenges imposed by unpredictable availability of water resources. In this study, we investigate the Late Pleistocene history of the common hippopotamus (Hippopotamus amphibius), using mitochondrial and nuclear DNA sequence variation and range-wide sampling. We documented a global demographic and spatial expansion approximately 0.1-0.3 My ago, most likely associated with an episode of massive drainage overflow. These events presumably enabled a historical continent-wide gene flow among hippopotamus populations, and hence no clear continental-scale genetic structuring remains. Nevertheless, present-day hippopotamus populations are genetically disconnected, probably as a result of the mid- Holocene aridification and contemporary anthropogenic pressures. This unique pattern contrasts with the biogeographic paradigms established for savannah-adapted ungulate mammals and should be further investigated in other water-associated taxa. Our study has important consequences for the conservation of the hippo, an emblematic but threatened species that requires specific protection to curtail its long-term decline.Item Genetic evidence of successful establishment of the Nile perch (Lates spp. L.) in East African lakes and implications for management(Management of Biological Invasions, 2012) Mwanja, Matthew T.; Waiswa Mwanja, Wilson; Muwanika, Vincent B.; Masembe, Charles; Nyakaana, SilvesterNile perch establishment in novel ranges in East Africa is one of the most successful freshwater invasion stories in the recent history. It became ecologically dominant and well established in several lakes in the Lake Victoria Region in a period of less than 5 decades. Genetic diversity of both introduced and native populations were assessed and patterns compared in order to establish the genetic consequences of their introductions. Genetic variation was surveyed at both the mitochondrial control region (CR) and at nine microsatellite loci. A total of 527 Nile perch fish were sampled from 5 East African lakes: native source populations were examined from lakes Albert and Turkana while introduced populations were sampled from lakes Kyoga, Nabugabo and Victoria. Both types of markers revealed higher average genetic diversity for invasive species (HE = 0.70, h = 0.81) than for native source populations (HE = 0.66, h = 0.69). Both populations scored relatively higher than the average for freshwater fishes (HE = 0.62). Both native and introduced populations had 2 underlying genetic groupings in similar proportions as revealed by the STRUCTURE program. The high genetic diversity was most probably a consequence of higher numbers of propagules than outlined by official records of introductions. Use of high number of individuals at stocking is probably the reason for apparently minimized ‘founder effects’ of Nile perch in the introduced ranges. The two underling populations revealed through genetic analysis may be representatives of the two subspecies of Nile perch previously reported in other studies. Implications to the management of this fishery in the East African region is that with the relatively high genetic diversity, the species could be sustainably exploited if it were effectively managed. In addition, further studies of the life histories and other attributes of the two genetic groupings of Nile perch in the region are recommended, as they may require different management plans.Item Population Genetic Structure of Savannah Elephants in Kenya: Conservation and Management Implications(Journal of heredity, 2008) Okello, John B. A.; Masembe, Charles; Rasmussen, Henrik B.; Wittemyer, George; Omondi, Patrick; Kahindi, Onesmas; Muwanika, Vincent B.; Arctander, Peter; Douglas-Hamilton, Iain; Nyakaana, Silvester; Siegismund, Hans R.We investigated population genetic structure and regional differentiation among African savannah elephants in Kenya using mitochondrial and microsatellite markers. We observed mitochondrial DNA (mtDNA) nucleotide diversity of 1.68% and microsatellite variation in terms of average number of alleles, expected and observed heterozygosities in the total study population of 10.20, 0.75, and 0.69, respectively. Hierarchical analysis of molecular variance of mtDNA variation revealed significant differentiation among the 3 geographical regions studied (FCT 5 0.264; P , 0.05) and a relatively lower differentiation among populations within regions (FSC 5 0.218; P , 0.0001). Microsatellite variation significantly differentiated among populations within regions (FSC 5 0.019; P , 0.0001) but not at the regional levels (FCT 5 0.000; P . 0.500). We attribute the high differentiation at the mitochondrial genome to the matrilineal social structure of elephant populations, female natal philopatry, and probably ancient vicariance. Lack of significant regional differentiation at the nuclear loci vis-a-vis strong differences at mtDNA loci between regions is likely the effect of subsequent homogenization through male-mediated gene flow. Our results depicting 3 broad regional mtDNA groups and the observed population genetic differentiation as well as connectivity patterns should be incorporated in the planning of future management activities such as translocations.Item Population genetic structure of the common warthog (Phacochoerus africanus) in Uganda: evidence for a strong philopatry among warthogs and social structure breakdown in a disturbed population(African Journal of Ecology, 2007) Muwanika, Vincent B.; Nyakaana, Silvester; Siegismund, Hans R.; Arctander, PeterFine-scale genetic structure of large mammals is rarely analysed. Yet it is potentially important in estimating gene flow between the now fragmented wildlife habitats and in predicting re-colonization following local extinction events. In this study, we examined the extent to which warthog populations from five localities in Uganda are genetically structured using both mitochondrial control region sequence and microsatellite allele length variation. Four of the localities (Queen Elizabeth, Murchison Falls, Lake Mburo and Kidepo Valley) are national parks with relatively good wildlife protection practices and the other (Luwero), not a protected area, is characterized by a great deal of hunting. In the total sample, significant genetic differentiation was observed at both the mtDNA locus (FST ¼ 0.68; P < 0.001) and the microsatellite loci (FST ¼ 0.14; P < 0.001). Despite the relatively short geographical distances between populations, significant genetic differentiation was observed in all pair-wise population comparisons at the two marker sets (mtDNA FST ¼ 0.21–0.79, P < 0.001; microsatellite FST ¼ 0.074–0.191, P < 0.001). Significant heterozygote deficiency was observed at most loci within protected areas while no significant deviation from Hardy–Weinberg expectation was observed in the unprotected Luwero population. WeItem A recent bottleneck in the warthog and elephant populations of Queen Elizabeth National Park, revealed by a comparative study of four mammalian species in Uganda national parks(Animal Conservation, 2003) Muwanika, Vincent B.; Siegismund, Hans R.; Okello, John Bosco A.; Masembe, Charles; Arctander, Peter; Nyakaana, SilvesterUntil 1972, Uganda’s national parks boasted of large numbers of large mammal species. Following the breakdown of law and order between 1972 and 1985, large-scale poaching led to an unprecedented decline in numbers of most large mammals in Uganda’s national parks. However, the extent of decline varied in the different parks across different animal species. We have investigated the genetic effects of these reductions in four mammalian species (the common warthog, African savannah elephant, savannah buffalo and common river hippopotamus) from the three major parks of Uganda using both microsatellite loci (for elephant and warthog populations) and mitochondrial control sequence variation in the warthogs, elephants, buffaloes and hippopotamuses. Queen Elizabeth National Park showed extreme reduction in nucleotide diversity for two species, the common warthog (π = 0.0%) and African elephant (π = 0.4%); no such decrease was found for the two other species, the buffalo (π = 3.7–5.4%) and hippopotamus (π = 1.7–1.9%), in the three parks. Nuclear microsatellite markers on the other hand showed high gene diversity in all populations in the common warthog (mean He 0.66–0.78) and the African savannah elephant (mean He 0.68–0.72). We interpret these results in terms of varying poaching pressure in the different parks, susceptibility of different species to poaching and differences in effective population sizes at the mitochondrial and nuclear lociItem Six new polymorphic microsatellite loci isolated and characterized from the African savannah elephant genome(Molecular Ecology Notes, 2005) Nyakaana, Silvester; Okello, John B. A.; Muwanika, Vincent B.; Siegismund, Hans R.The African savannah elephant (Loxodonta africana) is a ‘keystone’ species that plays a vital role in regulating the dynamics of both plant and animal communities and yet it is endangered and its numbers have been reduced to approximately 500 000 across their entire continental range. Molecular genetic markers are important tools for providing genetic information useful in formulating effective management and conservation strategies for the surviving elephant populations. We describe the isolation and characterization of six new polymorphic microsatellite markers in the African savannah elephant and demonstrate that these loci can be PCR (polymerase chain reaction)-multiplexed, a desirable attribute that saves costs in large-scale microsatellite screening.Item Three genetically divergent lineages of the Oryx in eastern Africa: Evidence for an ancient introgressive hybridization(Conservation Genetics, 2006) Masembe, Charles; Muwanika, Vincent B.; Nyakaana, Silvester; Arctander, Peter; Siegismund, Hans R.Phylogeographic and population genetic studies using sequence information are frequently used to infer species boundaries and history; and to assess hybridization and population level processes. In this study, partial mitochondrial DNA (mtDNA) control region (423 bp) and cytochrome b sequences (666 bp) of Oryx beisa sampled from five isolated localities in its entire current range in Africa were analyzed to investigate the extent of genetic variation and differentiation between populations. We observed high nucleotide diversity at the control region in the total sample (6.3%) but within populations, it varied considerably ranging from 1.6% to 8.1%. Population pairwise genetic differentiation was generally significantly high (ranging from FST = 0.15, P<0.01 to FST = 0.54, P<0.001). In the total sample, 29 and 12 haplotypes were observed in the control region and the cytochrome b data sets respectively. For both data sets, the haplotypes cluster into three distinct clades (sequence divergence ranged from 6.0%–12.9% to 0.8%–1.0% for the control region and cytochrome b sequences, respectively) that do not correspond to sampling locations. Two of these clades are found in the same localities (Samburu and Marsabit), which represent the O.beisa beisa subspecies, whereas the last clade represents the fringe-eared oryx (O. beisa callotis). We interpret these findings in terms of an ancient hybridization and introgression between two formerly isolated taxa of Oryx beisa.