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African wild pigs have a contentious evolutionary and biogeographic history. Until recently, desert warthog (Phacochoerus aethiopicus) and common warthog (P. africanus) were considered a single species. Molecular evidence surprisingly suggested they diverged at least 4.4 million years ago, and possibly outside of Africa. We sequenced the first whole-genomes of four desert warthogs and 35 common warthogs from throughout their range. We show that these two species diverged much later than previously estimated, 400,000–1,700,000 years ago depending on assumptions of gene flow. This brings it into agreement with the paleontological record. We found that the common warthog originated in western Africa and subsequently colonized eastern and southern Africa. During this range expansion, the common warthog interbred with the desert warthog, presumably in eastern Africa, underlining this region's importance in African biogeography. We found that immune system–related genes may have adaptively introgressed into common warthogs, indicating that resistance to novel diseases was one of the most potent drivers of evolution as common warthogs expanded their range. Hence, we solve some of the key controversies surrounding warthog evolution and reveal a complex evolutionary history involving range expansion, introgression, and adaptation to new diseases. [ABSTRACT FROM AUTHOR]

Abstract: In tropical Africa, woody species provide products and services that millions of people depend on. However, many of these species are also threatened and declining and this can have serious livelihood consequences for communities who depend on them. Identifying which species are most at risk and which ones are being conserved is therefore critical. In this study, we undertook a survey in Nawaikoke Sub-county, Uganda to assess which of 26 most preferred species are managed on farmland, to identify what environmental factors influence their availability, and to describe their conservation statuses. Individuals of these species were enumerated and measured in 320 plots across the eight parishes of Nawaikoke. Seven of the 26 species were not encountered in any plots. The rest were found close to homesteads in homegardens, in crop gardens and in young fallows on well drained soils. Only Combretum collinum and Acacia seyal were associated with old fallows and poorly drained clay loamy soils. Mangifera indica, Milicia excelsa, Ficus natalensis, Ficus sycomorus, Artocarpus heterophyllus and Albizia coriaria were found in numerous plots in at least six of the eight parishes, and at relatively high densities and we consider them to be at the lowest risk of disappearance from the landscape. Size-class distributions of all preferred species, regardless of their abundance, exhibited little recruitment from juvenile life stages. We conclude that most of the species face some level of threat through destruction of seedlings and saplings and that for these species to persist into the future there is need to work with farmers to encourage them to plant or spare those found growing naturally. There is a high potential for these species to increase in abundance because they grow in a wide diversity of farm niches. For the farmers to become more involved, focus should primarily be on native species that provide shade, fruits and timber. Some of these target species also play ecological roles, increasing their functionality. Lastly, there is need to protect non-crop habitats like fallows and wetlands. [Copyright &y& Elsevier]

Background: In East Africa, foot-and-mouth disease virus serotype SAT 1 is responsible for occasional severe outbreaks in livestock and is known to be maintained within the buffalo populations. Little is known about the evolutionary forces underlying its epidemiology in the region. To enhance our appreciation of the epidemiological status of serotype SAT 1 virus in the region, we inferred its evolutionary and phylogeographic history by means of genealogy-based coalescent methods using 53 VP1 coding sequences covering a sampling period from 1948-2007. Results: The VP1 coding sequence of 11 serotype SAT 1 FMD viruses from East Africa has been determined and compared with known sequences derived from other SAT 1 viruses from sub-Saharan Africa. Purifying (negative) selection and low substitution rates characterized the SAT 1 virus isolates in East Africa. Two virus groups with probable independent introductions from southern Africa were identified from a maximum clade credibility tree. One group was exclusive to Uganda while the other was present within Kenya and Tanzania. Conclusions: Our results provide a baseline characterization of the inter-regional spread of SAT 1 in sub-Saharan Africa and highlight the importance of a regional approach to trans-boundary animal disease control in order to monitor circulating strains and apply appropriate vaccines. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

With the emergence of analytical software for the inference of viral evolution, a number of studies have focused on estimating important parameters such as the substitution rate and the time to the most recent common ancestor (tMRCA) for rapidly evolving viruses. Coupled with an increasing abundance of sequence data sampled under widely different schemes, an effort to keep results consistent and comparable is needed. This study emphasizes commonly disregarded problems in the inference of evolutionary rates in viral sequence data when sampling is unevenly distributed on a temporal scale through a study of the foot-and-mouth (FMD) disease virus serotypes SAT 1 and SAT 2. Our study shows that clustered temporal sampling in phylogenetic analyses of FMD viruses will strongly bias the inferences of substitution rates and tMRCA because the inferred rates in such data sets reflect a rate closer to the mutation rate rather than the substitution rate. Estimating evolutionary parameters from viral sequences should be performed with due consideration of the differences in short-term and longer-term evolutionary processes occurring within sets of temporally sampled viruses, and studies should carefully consider how samples are combined.

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., (© 2015 John Wiley & Sons Ltd.)