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Abstract Background Previous phylogenetic analyses of African elephants have included limited numbers of forest elephant samples. A large-scale assessment of mitochondrial DNA diversity in forest elephant populations here reveals a more complex evolutionary history in African elephants as a whole than two-taxon models assume. Results We analysed hypervariable region 1 of the mitochondrial control region for 71 new central African forest elephants and the mitochondrial cytochrome b gene from 28 new samples and compare these sequences to other African elephant data. We find that central African forest elephant populations fall into at least two lineages and that west African elephants (both forest and savannah) share their mitochondrial history almost exclusively with central African forest elephants. We also find that central African forest populations show lower genetic diversity than those in savannahs, and infer a recent population expansion. Conclusion Our data do not support the separation of African elephants into two evolutionary lineages. The demographic history of African elephants seems more complex, with a combination of multiple refugial mitochondrial lineages and recurrent hybridization among them rendering a simple forest/savannah elephant split inapplicable to modern African elephant populations.

Over 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 Myr 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. [ABSTRACT FROM AUTHOR]

Nile perch (Lates spp.) was introduced into Lake Victoria only five decades ago but is now well established and distributed throughout the lake. Given the extensive size of the lake, there is a possibility of isolation by distance that can lead to local adaptations. Microsatellite DNA variability was used to assess the genetic diversity and to define the population structure of Nile perch collected from 22 different geographical locations within Lake Victoria. In total, 432 individuals were genotyped at nine microsatellite loci. Analyses of multilocus microsatellite genotypes revealed that genetic diversity of Nile perch of Lake Victoria is relatively high (HE = 0.68). Results also reveal shallow but significant genetic differentiation (FST = 0.029, P < 0.05). STRUCTURE indicated that Nile perch of Lake Victoria was made up of two (K = 2) genetically distinct populations. Separate analysis for each of the two groups also revealed relatively high genetic diversity for each group (HE[N1] = 0.73 and HE[N2] = 0.64). These results are surprising given that Nile perch was only recently introduced and is known to be migratory by nature. We interpret these results in light of multiple introductions from two different source populations of Nile perch and discuss implications of these results for the region's fisheries management. [ABSTRACT FROM AUTHOR]

Jørgensen, A., Madsen, H., Nalugwa, A., Nyakaana, S., Rollinson, D., Stothard, J. R. & Kristensen, T. K. A molecular phylogenetic analysis of Bulinus (Gastropoda: Planorbidae) with conserved nuclear genes. - Zoologica Scripta, 40, 126-136. Mutational saturation of inspected DNA loci and topological incongruence in the phylogenetic inferences have previously confounded attempts to resolve the evolutionary relationships within the freshwater snail genus Bulinus. Traditionally, the 37 species of Bulinus are placed within the four species groups and the evolutionary divergence between groups is substantial. With an intention to shed new light on species group relationships, the present study was designed to investigate the basal divergences in the phylogeny of Bulinus using highly conserved nuclear genes. The resolved phylogeny inferred that the four species groups of Bulinus were monophyletic and Shimodaira-Hasegawa topology tests found them to be significantly supported. The Bulinus truncatus/tropicus species complex and Bulinus wrighti ( Bulinus reticulatus group) formed a well-supported sister-group relationship. The Bulinus africanus species group was the sister-group to the clade ( Bulinus truncatus/tropicus + B. wrighti) with the Bulinus forskalii species group as the sister-group to these taxa. The sister-group relationship between Indoplanorbis and Bulinus was non-significant and the basal clade support of Bulinus improved upon exclusion of Indoplanorbis. The finding of basal long branches of Bulinus species originating from Madagascar strongly suggests the presence of additional cryptic species and an evolutionary scenario influenced by this island's geological vicariance from the African mainland. Speciation by polyploidy was inferred to have evolved within a clade in the Bulinus truncatus/tropicus species complex. Although the monophyletic status of each species group was firmly supported, it was difficult to establish species group concepts equally across the variations and place this precisely in a specific temporal framework. [ABSTRACT FROM AUTHOR]

The article presents a study that used mitochondrial DNA sequence variations to characterize the snail populations of the Bulinus truncatus/tropicus complex sampled in Lake Albert in western Uganda. Included in the study were 39 snail samples collected from five populations, Booma, Bugoigo, Piida, Toonya, and Walukuba. Based on analysis of patterns of sequence variations and evolutionary relationships within localities using a 612 basis point (bp) fragment of the mitochondrial cytochrome oxidase subunit gene, the authors discovered five unique haplotypes defined by 21 polymorphic sites.

Fine-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 = 0.68; P < 0.001) and the microsatellite loci ( FST = 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 = 0.21–0.79, P < 0.001; microsatellite FST = 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. We explain these results in terms of: (i) a strong philopatry among warthogs, (ii) a Wahlund effect resulting from the sampling regime and (iii) break down of social structure in the disturbed Luwero population. [ABSTRACT FROM AUTHOR]

Labeo victorianus, a fish species endemic to the Lake Victoria basin, once supported a commercial fishery. Since the 1950s landings have, however, declined due to overfishing. Recent surveys have found only two extant populations in Uganda; one in the Sio River and a second in the Kagera River. Fish from the Kagera River populations are significantly larger and exhibit differences in their reproductive biology. Using both genetic (control region sequences of mitochondrial DNA) and morphometric (truss and non-truss) characters, we investigated the level of genetic and morphological distinctiveness of the two remaining populations. Analyses of the mitochondrial control region sequence data (446 base pairs) did not show clear genetic differentiation between the populations (FST, =-0.002, P > 0.05). Nonetheless, several private haplotypes were observed (16 haplotypes out of a total of 19) suggesting that a substantial amount of genetic distinctiveness exists between the two populations. Principal component analysis of twenty truss and nine non-truss variables, and heteroscedastic f-tests on all but one measurement, indicated that 'size' rather than 'shape' separate out fish from the two rivers. There was, therefore, a substantial degree of congruence between genetic and morphological data. These results have been interpreted in light of the recent population history of L. victorianus in Lake Victoria. [ABSTRACT FROM AUTHOR]

The spectacular diversity of sub-Saharan Africa's large mammals was hit by constant social strife and civil war over three decades (1970s-1990s) leading to localized extinctions and drastic reductions in population sizes for many species. These localized extinctions and reduction in population sizes undermine the ability of species to evolve and adapt to changing environments as a result of genetic erosion. The genetic consequences of the widespread reduction of population sizes as a result of social strife in sub-Saharan Africa are not well documented. Here we review past molecular genetic data that are relevant to understanding of the genetic effects of war and social strife on Africa's wildlife. Uganda was probably one of the worst affected countries. Before 1972, Uganda had large herds and a variety of mammals. However, following the breakdown of law and order, some large mammals were exterminated while other populations were decimated. Recent results of genetic surveys in five large mammals in Uganda (the common warthog, savanna elephant, savanna buffalo, common hippopotamus and Uganda kob) suggest a substantial erosion of genetic diversity in the elephants and warthogs of Queen Elizabeth National Park. Although the rest of the studied mammals show no direct loss of genetic diversity, strong genetic differentiation was observed among most populations separated by even short geographical distances, indicating an increase in the 'between' component of genetic diversity that could have been accelerated by genetic erosion due to decrease in population sizes. [ABSTRACT FROM AUTHOR]

Geological data show that Lake Victoria dried out some 15 000 years ago. These data suggest that the entire faunal diversity within the lake has evolved since this time. However, mitochondrial DNA sequence diversity in the endemic cyprinid fish, Labeo victorianus, was high (24 haplotypes in 38 individuals; percentage sequence divergence of 0.74%), suggesting that the evolution of this species predates this Late Pleistocene climatological event. This finding is consistent with what has been reported earlier for cichlid fishes in the lake. [ABSTRACT FROM AUTHOR]

Investigates the isolation and characteristics of microsatellite loci from the African elephant using a hybrid-capture enrichment as isolation method. Exctraction of genomic DNA; Sequencing of recombinant clones; Analysis of alleles at each polymorphic locus.