The Praomyini tribe is one of the most diverse and abundant groups of Old World rodents. Several species are known to be involved in crop damage and in the epidemiology of several human and cattle diseases. Due to the existence of sibling species their identification is often problematic. Thus an easy, fast and accurate species identification tool is needed for non-systematicians to correctly identify Praomyini species. In this study we compare the usefulness of three genes (16S, Cytb, CO1) for identifying species of this tribe. A total of 426 specimens representing 40 species (sampled across their geographical range) were sequenced for the three genes. Nearly all of the species included in our study are monophyletic in the neighbour joining trees. The degree of intra-specific variability tends to be lower than the divergence between species, but no barcoding gap is detected. The success rate of the statistical methods of species identification is excellent (up to 99% or 100% for statistical supervised classification methods as the k-Nearest Neighbour or Random Forest). The 16S gene is 2.5 less variable than the Cytb and CO1 genes. As a result its discriminatory power is smaller. To sum up, our results suggest that using DNA markers for identifying species in the Praomyini tribe is a largely valid approach, and that the CO1 and Cytb genes are better DNA markers than the 16S gene. Our results confirm the usefulness of statistical methods such as the Random Forest and the 1-NN methods to assign a sequence to a species, even when the number of species is relatively large. Based on our NJ trees and the distribution of all intraspecific and interspecific pairwise nucleotide distances, we highlight the presence of several potentially new species within the Praomyini tribe that should be subject to corroboration assessments.
We studied the taxonomy, distribution, and ecology of species within Praomys, a common rodent genus present in rainforests and montane forests in sub-Saharan Africa. The taxonomy of the group is problematic, and for the sampled region of Kisangani (Democratic Republic of Congo) no prior genetic study has been published. We used a combination of molecular (cyt b sequencing) and craniometric techniques (canonical analyses of skull measurements) for the species identification of a total of 654 specimens. We confirm the presence of Praomys minor in the region, up to now only known from the type and paratype specimens. At least seven species are present in the Kisangani region, and two clades occur along both banks of the Congo River. The present-day distribution of the genus seems to be influenced by large-scale rainforest fragmentation related to drier periods in geological history. The Congo River could in this case constitute a modern barrier to gene flow when the climate enabled rainforest expansion. The tributaries of the Congo River play no role in limiting Praomys species distribution, apart from the Aruwimi River for Praomys jacksoni s.l.
A serosurvey involving 2,520 small mammals from Tanzania identified a hot spot of arenavirus circulation in Morogoro. Molecular screening detected a new arenavirus in Natal multimammate mice (Mastomys natalensis), Morogoro virus, related to Mopeia virus. Only a small percentage of mice carry Morogoro virus, although a large proportion shows specific antibodies.
Aim This study aims to reconstruct the evolutionary history of the African rodent genus Malacomys and to identify factors driving diversification within this genus.Location African tropical lowland forest.Methods Analyses were based on sampling representatives from most of the known geographical range of the genus. We assessed genetic structure and historical biogeography using a combination of mitochondrial and nuclear markers. Morphological differences between lineages were analysed using a geometric morphometric approach.Results Three species of Malacomys are recognized within the genus. Two are endemic to West Africa, and one is endemic to Central Africa. Our analyses reveal a strong phylogeographical structure with 13 lineages, most of them allopatric or parapatric. A complex biogeographical history, including dispersalvicariance events, explains the current genetic structure of Malacomys. Discrete divergence events within the genus are dated to the mid-Pliocene (3.7 Ma, 95% range: 2.4-5.2 Ma) and the Pleistocene (less than 1.9 Ma, with most events less than 1 Ma). Morphological variation is partly congruent with genetic structure and may indicate local adaptations.Main conclusions Climatic oscillations, which led to periodic fragmentation of the forest habitat, seem to be the major driver of diversification within this genus. Our results support the existence of multiple small, rather than a few large, forest refugia during glacial maxima. Rivers have played a significant role in shaping boundaries of several regional haplogroups, either by promoting diversification or by preventing secondary contact between previously isolated lineages.
Context The multimammate mouse, Mastomys natalensis (Smith, 1834), is an important agricultural pest in southern and eastern Africa where it can cause significant crop losses. Mastomys natalensis is known to consume a variety of food in response to the availability of food items. However, it is currently unknown whether maize crop growth stages affect the spatio-temporal diet of this species. Aims We examined the foods consumed by M. natalensis in different habitats and seasons in central Tanzania and Swaziland. Methods Diet was investigated in Tanzania in four different habitats (woodland, vegetable gardens, maize fields and fallow land) during different maize crop growth stages between March 2008 and February 2009. In Swaziland, this was conducted in three habitats (fallow land, cultivated fields and pristine land) during three crop growth stages (pre-planting, vegetative stage and post-harvest) between March 2008 and April 2009. Micro-histological examination of undigested fragments from the stomachs of trapped animals was made whereby the preserved stomach content was placed in a Petri dish and sorted using a 25× or 50× magnification binocular stereoscope. Stomach contents were identified as: grain and/or seeds (both grasses and maize), plant material (roots, stems and leaves), invertebrates, pods of seeds, fruits (vegetable fruit such as tomato), animal hairs and unidentified matter. If necessary, a lugol solution was used to determine the presence of starch for maize and grass seeds or grains. Key results In both countries, grain predominated in the diet of M. natalensis. Statistical analyses showed that there were no differences due to seasons or habitats. Therefore, the percentage volume and relative importance were the same across habitats and seasons in both countries. Conclusions Our findings highlight clearly that M. natalensis is a generalist species feeding on available resources depending on the season and the habitat. Its preference for grain may account for its abundance in maize plantations and confirms it as one of the major pests in crop plantations, especially grain. Implications This information offers a useful tool for determining the pest status in different habitats and/or seasons. The findings of this study have implications for agriculture and conservation.
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