Pan-African phylogeny of Mus (subgenus Nannomys) reveals one of the most successful mammal radiations in Africa.

BACKGROUND: Rodents of the genus Mus represent one of the most valuable biological models for biomedical and evolutionary research. Out of the four currently recognized subgenera, Nannomys (African pygmy mice, including the smallest rodents in the world) comprises the only original African lineage. Species of this subgenus became important models for the study of sex determination in mammals and they are also hosts of potentially dangerous pathogens. Nannomys ancestors colonized Africa from Asia at the end of Miocene and Eastern Africa should be considered as the place of their first radiation. In sharp contrast with this fact and despite the biological importance of Nannomys, the specimens from Eastern Africa were obviously under-represented in previous studies and the phylogenetic and distributional patterns were thus incomplete. RESULTS: We performed comprehensive genetic analysis of 657 individuals of Nannomys collected at approximately 300 localities across the whole sub-Saharan Africa. Phylogenetic reconstructions based on mitochondrial (CYTB) and nuclear (IRBP) genes identified five species groups and three monotypic ancestral lineages. We provide evidence for important cryptic diversity and we defined and mapped the distribution of 27 molecular operational taxonomic units (MOTUs) that may correspond to presumable species. Biogeographical reconstructions based on data spanning all of Africa modified the previous evolutionary scenarios. First divergences occurred in Eastern African mountains soon after the colonization of the continent and the remnants of these old divergences still occur there, represented by long basal branches of M. (previously Muriculus) imberbis and two undescribed species from Ethiopia and Malawi. The radiation in drier lowland habitats associated with the decrease of body size is much younger, occurred mainly in a single lineage (called the minutoides group, and especially within the species M. minutoides), and was probably linked to aridification and climatic fluctuations in middle Pliocene/Pleistocene. CONCLUSIONS: We discovered very high cryptic diversity in African pygmy mice making the genus Mus one of the richest genera of African mammals. Our taxon sampling allowed reliable phylogenetic and biogeographic reconstructions that (together with detailed distributional data of individual MOTUs) provide a solid basis for further evolutionary, ecological and epidemiological studies of this important group of rodents.

The first large-scale record of gelada's spatial distribution and population size in Mountain chains of Tigray, Northern Ethiopia.

Gelada (Theropithecus gelada) is an Ethiopian endemic mammal whose range was previously believed to be limited to the Bale and Simien Mountain national parks. However, knowledge of the range of the species is still not satisfactory. This study was designed to investigate the distribution and population size of the gelada in selected highlands in Tigray. To achieve this, study areas were divided into census tracts identified for a direct field assessment using habitat-based counting approaches. Moreover, informal interviews were conducted parallel to the direct field assessment in different villages. Our large spatial scale survey, the first of its kind for the region, confirmed the presence of T. gelada in three mountain clusters in Tigray for the first time. A total of 223 individual geladas were recorded in Ganta Afeshum, Hawzen and Welkait escarpments. The highest number of individuals (35.7 ± 3.8) was recorded in Hawzen (with 6.99 individuals/km2), followed by Ganta Afeshum (with 4.3 individuals/km2). Agricultural expansion, settlement and a lack of community awareness are the key threats operating against the conservation of the gelada in its current range in Tigray. Further research on the overall ecology, feeding, and spatial distribution of the species should be projected.

High diversity of RNA viruses in rodents, Ethiopia.

We investigated synanthropic small mammals in the Ethiopian Highlands as potential reservoirs for human pathogens and found that 2 rodent species, the Ethiopian white-footed mouse and Awash multimammate mouse, are carriers of novel Mobala virus strains. The white-footed mouse also carries a novel hantavirus, the second Murinae-associated hantavirus found in Africa.

Prevalence of Orthohantavirus-Reactive Antibodies in Humans and Peri-Domestic Rodents in Northern Ethiopia.

In 2012, Tigray orthohantavirus was discovered in Ethiopia, but its seasonal infection in small mammals, and whether it poses a risk to humans was unknown. The occurrence of small mammals, rodents and shrews, in human inhabitations in northern Ethiopia is affected by season and presence of stone bunds. We sampled small mammals in two seasons from low- and high-density stone bund fields adjacent to houses and community-protected semi-natural habitats in Atsbi and Hagere Selam, where Tigray orthohantavirus was first discovered. We collected blood samples from both small mammals and residents using filter paper. The presence of orthohantavirus-reactive antibodies in blood was then analyzed using immunofluorescence assay (human samples) and enzyme linked immunosorbent assays (small mammal samples) with Puumala orthohantavirus as antigen. Viral RNA was detected by RT-PCR using small mammal blood samples. Total orthohantavirus prevalence (antibodies or virus RNA) in the small mammals was 3.37%. The positive animals were three Stenocephalemys albipes rats (prevalence in this species = 13.04%). The low prevalence made it impossible to determine whether season and stone bunds were associated with orthohantavirus prevalence in the small mammals. In humans, we report the first detection of orthohantavirus-reactive IgG antibodies in Ethiopia (seroprevalence = 5.26%). S. albipes lives in close proximity to humans, likely increasing the risk of zoonotic transmission.

Bartonella prevalence and genetic diversity in small mammals from Ethiopia.

More than 500 small mammals were trapped at 3 localities in northern Ethiopia to investigate Bartonella infection prevalence and the genetic diversity of the Bartonella spp. We extracted total DNA from liver samples and performed PCR using the primers 1400F and 2300R targeting 852 bp of the Bartonella RNA polymerase beta subunit (rpoB) gene. We used a generalized linear mixed model to relate the probability of Bartonella infection to species, season, locality, habitat, sex, sexual condition, weight, and ectoparasite infestation. Overall, Bartonella infection prevalence among the small mammals was 34.0%. The probability of Bartonella infection varied significantly with species, sex, sexual condition, and some locality, but not with season, elevation, habitat type, animal weight, and ectoparasite infestation. In total, we found 18 unique Bartonella genotypes clustered into 5 clades, 1 clade exclusively Ethiopian, 2 clades clustered with genotypes from central and eastern Africa, and the remaining 2 clades clustered with genotypes and species from Africa and Asia. The close relatedness of several of our Bartonella genotypes obtained from the 3 dominant rodent species in Tigray with the pathogenic Bartonella elizabethae from Rattus spp. in Asia indicates a potential public health threat.

Preliminary investigation on rodent-ectoparasite associations in the highlands of Tigray, Northern Ethiopia: implications for potential zoonoses.

We studied associations between rodents and their arthropod ectoparasites in crop fields and household compounds in the highlands of Tigray, Northern Ethiopia. Ectoparasite infestation indices, such as percent infestation, mean abundance, prevalence and host preferences, were calculated for each taxon. In total, 172 rodents from crop fields and 97 from household compounds were trapped. Rodent species and numbers trapped from the crop fields and household compounds were Mastomys awashensis (Lavrenchenko, Likhnova & Baskevich, 1998) (88 and 44), Arvicanthis dembeensis (Ruppel, 1842) (63 and 37) and Acomys sp. (21 and 16), respectively. A total of 558 insects and acarids (belonging to 11 taxa) were recovered from the rodents trapped in the crop fields, and 296 insects and acarid (belonging to 6 taxa) from the rodents trapped in the household compounds. Approximately 66% of the rodents trapped from the crop fields and 47% of those trapped from the household compounds were infested with ectoparasites. Laelaps sp. (64.9%) and Xenopsylla sp. (20.6%) comprised the highest proportion of the ectoparasites recovered in the crop fields, and the same ectoparasites, but in reverse order, comprised the highest proportions in the household compounds (Xenopsylla [50.3%] and Laelaps sp. [29%]). Our study revealed that crop fields and household compounds in the highlands share similar rodents and several ectoparasites. Furthermore, at least 1 of the rodent species and some of the ectoparasites identified in this study were reported to have posed medical and veterinary threats in other parts of Ethiopia and neighboring countries.