We adopted an integrated systematic approach to delimit evolutionary species and describe phylogeographic, morphometric and ecological relationships in Otomys denti (from the Albertine Rift, Southern Rift in Malawi and the northern Eastern Arc Mountains) and Otomys lacustris (from the Southern Rift in Tanzania and Zambia, and the southern Eastern Arc Mountains). Molecular [cytochrome (cyt) b sequences, 1143 bp, N = 18], craniometric (classical, N = 100 and geometric, N = 60) and ecological (Partial Least Squares regression of shape and ecogeographic variables) approaches show a profound, parallel disjunction between two groups: (1) Eastern Arc and Southern Rift (including the Malawi Rift) (O. lacustris and Otomys denti sungae) and (2) Albertine Rift (Otomys denti denti and Otomys denti kempi) taxa. Within both groups, cyt b sequences or craniometric analysis provided evidence for the differentiation of both southern and northern Eastern Arc from Southern Rift lineages (across the so-called Makambako Gap). Within the Albertine Rift (denti-kempi) lineage, populations from individual mountain ranges differed significantly in skull shape (but not size), but were similar genetically. Over-reliance in the past on very few morphological characters (e.g. number of molar laminae) and a polytypic species concept has obscured phylogenetic relationships and species discrimination in this group. We recognize at least three species in this group, and distinct lineages within two of these species. Each species or lineage was endemic to one of three regions: the Albertine Rift, the Malawi Rift or the Eastern Arc. Our result echo conclusions of recent studies of other mammalian and bird taxa and reflect the geomorphology and palaeoclimatic history of the region.
We combined evidence from biogeography, craniodental traits, linear and geometric morphometrics (233 skulls), cytogenetics (karyotypes of 18 individuals) and mitochondrial DNA sequences (44 cytochrome b and 21 12S rRNA sequences) to test species limits within Otomys typus s.l. (Muridae: Murinae: Otomyini), a complex that is patchily distributed across alpine zones of Ethiopia and East Africa. Our results confirm the specific validity of O. dartmouthi, O. jacksoni, O. orestes, and O. uzungwensis, forms recently removed from synonymy under typus s.l.; support elevation of four other alpine forms to species (O. fortior, O. helleri, O. thomasi, and O. zinki); identify three additional new species (O. cheesmani sp. nov., O. simiensis sp. nov., O. yaldeni sp. nov.); and enable redefinition of O. typus s.s. as a species restricted to certain mountains west of the Great Rift Valley in Ethiopia (Simien and Guna Mountains in the north, extending to the highlands of the western rim of the Rift Valley). Phylogenetic interpretation of the cytochrome b data clearly demonstrates that the alpine morphotype once united under O. typus s.l. has originated independently at high elevations on several mountain ranges in eastern and northeastern Africa; although generally adapted to high-elevation vegetation, such alpine species are ecologically segregated from one another. Patterns of morphometric, genetic, and ecological differentiation among populations once misassigned to nominal O. tropicalis and O. typus more parsimoniously reflect regional cladogenesis along elevational gradients, rather than multiple, successive colonization by different ancestral forms from southern Africa as earlier supposed. Although incomplete and preliminary, information gathered for O. tropicalis indicates that it too is a species composite; several lines of research are discussed to redress its polyphyletic content. Our results, together with other recent taxonomic studies of Otomys, appreciably elevate the level of endemism within eastern Africa and underscore the significance of Africa's eastern highlands to the continental diversification of Otomyini.
BackgroundGolden moles (Chrysochloridae) are small, subterranean, afrotherian mammals from South Africa and neighboring regions. Of the 21 species now recognized, some (e.g., Chrysochloris asiatica, Amblysomus hottentotus) are relatively common, whereas others (e.g., species of Chrysospalax, Cryptochloris, Neamblysomus) are rare and endangered. Here, we use a combined analysis of partial sequences of the nuclear GHR gene and morphological characters to derive a phylogeny of species in the family Chrysochloridae.ResultsAlthough not all nodes of the combined analysis have high support values, the overall pattern of relationships obtained from different methods of phylogeny reconstruction allow us to make several recommendations regarding the current taxonomy of golden moles. We elevate Huetia to generic status to include the species leucorhinus and confirm the use of the Linnean binomial Carpitalpa arendsi, which belongs within Amblysominae along with Amblysomus and Neamblysomus. A second group, Chrysochlorinae, includes Chrysochloris, Cryptochloris, Huetia, Eremitalpa, Chrysospalax, and Calcochloris. Bayesian methods make chrysochlorines paraphyletic by placing the root within them, coinciding with root positions favored by a majority of randomly-generated outgroup taxa. Maximum Parsimony (MP) places the root either between chrysochlorines and amblysomines (with Chlorotalpa as sister taxon to amblysomines), or at Chlorotalpa, with the former two groups reconstructed as monophyletic in all optimal MP trees.ConclusionsThe inclusion of additional genetic loci for this clade is important to confirm our taxonomic results and resolve the chrysochlorid root. Nevertheless, our optimal topologies support a division of chrysochlorids into amblysomines and chrysochlorines, with Chlorotalpa intermediate between the two. Furthermore, evolution of the chrysochlorid malleus exhibits homoplasy. The elongate malleus has evolved just once in the Cryptochloris-Chrysochloris group; other changes in shape have occurred at multiple nodes, regardless of how the root is resolved.
Chromosomal polytypy, morphological conservatism and absence of data have frustrated the taxonomic revision of two species of southern African-endemic laminate-toothed rats (Otomys irroratus and Otomys saundersiae s.l.). New cytogenetic (G-banding and fluorescence in situ hybridization), DNA sequence [cytochrome b (cyt b) gene] and geometric morphometric data demonstrate the synonymy of O. saundersiae from Grahamstown (Eastern Cape, South Africa) under O. irroratus, and the validity of Otomys karoensis from the Fynbos Biome of the Western Cape. Phenotypic dimorphism in pelage colour and cranial morphology in O. irroratus from the climatically unpredictable Albany Thicket (= Savanna) Biome of the Eastern Cape results from the retention of allometric paedomorphic traits in some adults (saundersiae morph) but not others. The same paedomorphic traits are associated with speciation and karyotypic and genetic differentiation in O. karoensis. Within O. irroratus, two phenotypically and genotypically (cyt b divergence = 6.4%) divergent lineages correspond with the Fynbos/Albany Thicket and Grassland biomes. Incipient speciation in O. irroratus seems to be associated with ecology rather than karyotype.
African swine fever virus (ASFV) infection in adult Ornithodoros porcinusWalton (1962) ticks collected from warthog burrows in southern and East Africa was assessed using a duplex genomic amplification approach that is informative with respect to the invertebrate host species and infecting sylvatic cycle virus. DNA extracted from individual ticks was used as template for simultaneous amplification of a C-terminal 478 bp ASFV p72 gene region and a ~313 bp fragment of the tick mitochondrial 16S rRNA gene, under optimised reaction conditions. Within-warthog-burrow infection rates ranged from 0 to 43 % using this approach, whilst phylogenetic analysis of 16S gene sequences revealed the presence of three geographically discrete O. porcinus
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