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The analyses of Plio-Pleistocene speciation processes in the Horn of Africa are relevant for understanding the evolution of biodiversity patterns of this understudied part of the world. Here we analyse comprehensive genomic and morphological data of the recently delimited murid genus Ochromyscus , one of the few with Afro-Arabian distribution. Using an integrative taxonomic approach, we delimit three species in the genus: two in eastern Africa (O. brockmani and O. niveiventris) and one in southern Arabia (O. yemeni), and detail their distribution, genetic structure, and evolutionary history. Despite their morphological similarity, the three species split before the Pleistocene, and their interspecific genetic divergence level is comparable to that between sister genera of murine rodents. The split between two taxa living on opposite sides of the Red Sea (O. brockmani vs. O. yemeni) is younger than the separation of their ancestor and O. niveiventris living in eastern Africa. The colonization of Arabia can be explained either by the presence of a relatively recent continental bridge or by the past occurrence of the genus along the eastern coast of the Red Sea and subsequent spreading through the Sinai Peninsula. [ABSTRACT FROM AUTHOR]

Rodents comprise around half of all mammalian species, showcasing their remarkable adaptability to thrive in almost all terrestrial habitats. Their evolutionary success is exemplified by a wide range of morphological features reflecting various feeding and locomotory adaptations. This study examines the functional variation in cranial and mandibular traits as well as locomotion indices in rodent communities within the high-altitude Afroalpine environment of the Ethiopian Highlands. The findings reveal two distinct patterns in cranial and mandibular traits. One pattern is associated with dietary differences, distinguishing the primarily herbivorous species Otomys helleri, Arvicanthis abyssinicus and Lophuromys melanonyx, which are characterised by relatively long molar rows, massive mandibles, and likely enhanced bite force, from the generally omnivorous genus Stenocephalemys and the more faunivorous Lophuromys flavopunctatus. The second pattern indicates that species in the Afroalpine ecosystem have adapted to life in distinct habitats across different elevational zones. Species from the highest elevational zones within the genera Stenocephalemys and Lophuromys exhibit convergent morphological adaptations for life in open habitats, characterised by their larger size, narrower interorbital constriction, and larger orbits. Regarding locomotion, our study emphasises the unique morphology of Otomys, which is characterised by equally long forelimbs and hindlimbs. This corresponds to its predominant fast quadrupedal running. In contrast, Stenocephalemys species are likely to rely more on saltatory locomotion. Among them, the forest-dwelling S. albipes likely demonstrates the most advanced form of this locomotory style. The study highlights significant functional diversification in rodent assemblages from the Ethiopian Highlands, primarily driven by foraging and locomotor ecologies. This morphological variation has likely contributed to shaping the rich rodent communities integral to the Eastern Afromontane Biodiversity Hotspot, globally recognized for its significance in mammal endemism. [ABSTRACT FROM AUTHOR]

We investigated the breeding activity of three sympatric rodent species: Stenocephalemys albipes, Mastomys awashensis, and Acomys cahirinus, in the semi-arid region of Tigray in northern Ethiopia, using mark-recapture data, to determine the influence of rainfall on their breeding patterns within exclosure (i.e., protected area from livestock grazing). Breeding activities of S. albipes and M. awashensis commenced during the wet season, continued into the early dry season, and ceased during the subsequent dry season. The proportion of breeding females reached its peak during the wet season, gradually declining until the dry season. In contrast, A. cahirinus exhibited a different breeding strategy, with year-round breeding, including during the dry season, a period characterized by limited resources. A significant difference in the proportion of breeding females among the three species was observed across seasons. Furthermore, all species shared a common trend of heightened breeding activity, particularly at the conclusion of the wet season and the onset of the early dry season. These findings enhance our understanding of the interplay between rainfall and seasonal breeding within exclosures, while other variables remain constant. Moreover, the region's future plans for managing rodents and the establishment of exclosures must take this information into account. [ABSTRACT FROM AUTHOR]

Montemys delectorum is the only member of the genus Montemys within the family Muridae, which is an endemic rodent of the Eastern Africa Highlands. It is a threatened species due to habitat loss, and its current conservation status is uncertain. We studied the breeding pattern and population size of M. delectorum, two of the most important factors in understanding the conservation status of a species. Capture-mark-release studies were conducted from February 2021 to June 2022 in open patchy forests and dense forest habitats. Montemys delectorum showed bimodal breeding seasonality: a low rate for the short interval between December and February and a pronounced rate for May-July, following the high rainfall in April. This shows that rainfall promotes vegetation availability, which stimulates breeding activity and adds offspring to the population, resulting in increased population abundance. The population of M. delectorum is not stable in this landscape, as indicated by the significant differences in population size between the two forest types, with a significantly greater population in the patchy open forest. This indicates that the patchy open forest should be considered an essential refuge for the species. [ABSTRACT FROM AUTHOR]

The Ethiopian Highlands represent one of the most important centres of endemism on Earth. Six endemic species of laminate-toothed rats have been reported from Ethiopia in a previous study based mostly on morphological analyses. Largely missing genetic data for some of the species, insufficient sampling across Ethiopia, and presence of a pseudogene on cytochrome b created knowledge gaps in basic taxonomy, distribution, and phylogenetic position of the Ethiopian taxa. Here we perform an integrative taxonomic revision of the group by using the largest available sets of genomic and morphological data. We first reconstructed the mitochondrial phylogeny of the whole genus, delimited major clades, and evidenced two independent colonization events of Otomys to Ethiopia. By using genome-scale SNPs, we delimited putative Ethiopian species and analysed their phylogenetic relationships. In genetically characterized specimens we assessed morphological variation of skulls. We confirmed the presence of six previously reported species and significantly extended the known distributional range for some of them. Furthermore, we discovered a genetically and morphologically distinct lineage in northern Ethiopia, probably representing a new species. The speciation processes are similar to other Afromontane Ethiopian endemic rodent clades, with prevailing allopatric diversification combined with reticulate processes. [ABSTRACT FROM AUTHOR]

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The Ethiopian highlands represent the largest part of the Eastern Afromontane Biodiversity Hotspot (EAMBH). Their fauna and flora are largely unique. Particularly, Afroalpine habitats on isolated mountains are known to harbour a large number of highly specialized endemic species. In contrast to intensively studied Afroalpine ecosystems, the forests in southern and southwestern parts of the Ethiopian highlands remain neglected in terms of biodiversity research, even though they represent the only remaining natural large-scale forests in this part of EAMBH. Here, we performed an integrative taxonomic revision (combining multi-locus phylogenetic analysis with classical and geometric morphometrics) and analysis of the evolutionary history of ancient lineages of the genus Mus, with a special focus on the taxon discovered in moist Ethiopian forests. We unequivocally showed that this taxon forms a very distinct gene pool separated from other taxa by the mid-Pliocene, substantially differentiated from both sympatric and sister species by external and cranial morphology. None of the available type specimens (including synonym types) can be unambiguously classified to this taxon according to both skull and body form. Therefore, we describe it as a new mammal species, narrowly endemic to two most humid forests in southern (Harenna) and southwestern (Chingawa) part of the Ethiopian highlands. The description of such paleo-endemic taxa will add incentives to embark on urgent conservation action for formal protection of these unique forests within the EAMBH. [ABSTRACT FROM AUTHOR]

Understanding species distribution across elevational gradients is crucial for developing conservation strategies for montane biotic systems. A survey of small mammals was conducted on Mount Meru at six elevations, ranging between 1500 m and 3650 m. A total of 803 small mammal individuals, including 2 shrew species and 13 rodent species, were documented. Of these, Crocidura newmarki and Lophuromys verhageni were endemic on Mount Meru. Species richness was highest at mid–elevations, which is in line with the global pattern for small mammals. Prior to our study, the most complete data on small mammals on Mount Meru was collected in 2009. Our study provides an opportunity to show how small mammal elevational distribution has changed, over the last decade. We found six species (Arvicanthis niloticus, Mastomys natalensis, Lemniscomys striatus, Dasymys incomtus, Cricetomys ansorgei, and Montemys delectorum), which were not documented in 2009, but did not find Otomys tropicalis. Interestingly, the community composition at higher elevations in 2021 resembles that at lower elevations in 2009, suggesting that small mammal species have moved their range upward over time. Climate change could be a factor associated with the distributional shift found. [ABSTRACT FROM AUTHOR]

Considering climate change and high population increase, the conversion of natural habitats into arable land is rising at an alarming rate in the Ethiopian highlands. The impact on the diversity of rodents and shrews is difficult to measure since historical data are often unavailable. However, the relative effects of such land-use changes could be contemplated by comparing with data from similar natural habitats in adjacent areas. Between October to November 2018, we randomly setup 20 infrared camera traps in wheat fields located near Mount Guna at about 3350 m elevation, as part of a large research project investigating the efficacy of rodent repellent botanicals. We recorded six rodent species (Arvicanthis abyssinicus, Dendromus lovati, Dendromus mystacalis, Hystrix cristata, Mus mahomet and Stenocephalemys albipes) and two shrew species (Crocidura cf. baileyi and Crocidura olivieri). A. abyssinicus, H. cristata and S. albipes are known to occur in agricultural fields. D. lovati was recorded from anthropogenic habitat for the first time in this study. The species has been described as rare or difficult to capture with conventional traps. We call for rigorous biodiversity studies and conservation measures in agroecosystems in the Ethiopian highlands to avert further losses in biodiversity and ecosystem services. [ABSTRACT FROM AUTHOR]

The Afar Triangle in easternmost Africa is one of biogeographically important regions, whose recent biota is virtually unknown. Here we evaluated the level of evolutionary uniqueness of biodiversity of this region in a wide regional and continental biogeographical context, using rodents as a model group. By combining our recent collections with historical records, and based on genetic data and phylogenetic approaches, we specifically tested whether and to what extent the geographical isolation of the Afar Depression is reflected in allopatric diversification of arid-adapted mammals. We documented the presence of 16 rodent species (four are reported for the first time in Ethiopia and one rediscovered there after more than 100 years) and eight additional species are likely present based on literature data. Comparative phylogeographic analysis suggests that the Afar Triangle can be considered as a part of a larger Somalian biogeographical region, but its fauna is genetically distinct, including the presence of narrow Afar endemics. To a lesser extent, there are taxa with evolutionary affinities to the eastern Sahara–Sahelian region and to the southern Arabian Peninsula. Compared to the Ethiopian Highlands, the rodent fauna of Afar is relatively poor. However, similarly to highlands, the evolutionary distinctiveness of mammals in the Afar Triangle is very high and it can be considered a unique centre of endemism. Our first comprehensive summary of Afar rodents significantly fills the gap in the knowledge of the mammalian fauna of arid regions in Ethiopia and the Horn of Africa in general and highlights the significance of the region for nature conservation. [ABSTRACT FROM AUTHOR]

In sub-Saharan Africa, agricultural intensification and urbanization have increased the risk of proliferation of rodents in rural and urban habitats. Management of rodent populations is a challenge in terms of food security and public health. However, conventional efforts to manage rodents are currently reactive and based on the inadequate use of synthetic chemical rodenticides, including first- and second-generation anticoagulants and acute rodenticides. This approach carries substantial environmental and health risks and has yielded limited success in terms of reduction of rodent populations sustainably. In this paper, which is the second part of a diptych, we advocate for a shift towards more sustainable and environmentally friendly approaches, such as Ecologically-Based Rodent Management (EBRM), as a realistic alternative to synthetic rodenticides. This method is based on a good knowledge of habitat use, species diversity and population dynamics of major rodent pests, and involves community-based interventions aimed at reducing rodent abundance to economically and hygienically acceptable levels in the long term. We present for the first time a comprehensive compilation of published and unpublished information derived from observational field studies conducted in Ethiopia, Niger, Nigeria, Benin, Mali, Mauritania and Senegal with the aim to provide an overview of EBRM case studies in these countries of sub-Saharan Africa. This paper intends to serve as a catalyst for change, encouraging the transformation of rodent management practices towards sustainable methods. We aim at stimulating further research and interventions that promote EBRM in Africa, ultimately fostering more environmentally conscious and effective solutions. [Display omitted] • In Africa, agricultural intensification and urbanization are major changes. • These changes increase the risk of rodent proliferation in rural and urban habitats. • Conventional rodent control relies on reactive, inappropriate use of rodenticides. • Ecologically-Based Rodent Management has been poorly tested in sub-Saharan Africa. • This method can be a realistic, sustainable and environment-friendly alternative. [ABSTRACT FROM AUTHOR]

Hepatitis C virus (HCV; genus Hepacivirus) represents a major public health problem, infecting about three per cent of the human population. Because no animal reservoir carrying closely related hepaciviruses has been identified, the zoonotic origins of HCV still remain unresolved. Motivated by recent findings of divergent hepaciviruses in rodents and a plausible African origin of HCV genotypes, we have screened a large collection of small mammals samples from seven sub-Saharan African countries. Out of 4,303 samples screened, eighty were found positive for the presence of hepaciviruses in twenty-nine different host species. We, here, report fifty-six novel genomes that considerably increase the diversity of three divergent rodent hepacivirus lineages. Furthermore, we provide strong evidence for hepacivirus co-infections in rodents, which were exclusively found in four sampled species of brush-furred mice. We also detect evidence of recombination within specific host lineages. Our study expands the available hepacivirus genomic data and contributes insights into the relatively deep evolutionary history of these pathogens in rodents. Overall, our results emphasize the importance of rodents as a potential hepacivirus reservoir and as models for investigating HCV infection dynamics. [ABSTRACT FROM AUTHOR]

The abundance and microhabitat use of rodents were investigated in four different habitats: two rain-fed crop fields with differing stone bund density, an irrigated field and bushland. A total of 444 individual small mammals belonging to six rodent and one shrew species were recorded in trapping grids and line transects. Of these, 230 individuals (52%) belonged to three pest rodent species of crop fields in northern Ethiopia: Stenocephalemys albipes (65%), Mastomys awashensis (25%) and Arvicanthis niloticus (10%). Population abundance of the three species was higher in the early dry season compared to the rainy season. While the bushland was significantly (p < 0.05) favoured by S. albipes and M. awashensis in both seasons, the irrigated field was preferred by Arvicanthis niloticus in the early dry season. In the early dry season, the microhabitat use of A. niloticus was strongly associated with the type of ground cover (herb) (R²adj = 0.152, P < 0.01). While M. awashensis was associated with vegetation density (R²adj = 0.13, P < 0.01), S. albipes was associated with vegetation cover (R²adj = 0.102, P < 0.001). The findings indicate that co-occurring pest rodent species prefer different microhabitats. Understanding their co-occurrence particularly in crop fields is vital for crop protection as they are known serious agricultural pests in northern Ethiopia. [ABSTRACT FROM AUTHOR]

Orthohantaviruses are RNA viruses that some members are known to cause severe zoonotic diseases in humans. Orthohantaviruses are hosted by rodents, soricomorphs (shrews and moles), and bats. Only two orthohantaviruses associated with murid rodents are known in Africa, Sangassou orthohantavirus (SANGV) in two species of African wood mice (Hylomyscus), and Tigray orthohantavirus (TIGV) in the Ethiopian white-footed rat (Stenocephalemys albipes). In this article, we report evidence that, like SANGV, two strains of TIGV occur in two genetically related rodent species, S. albipes and S. sp. A, occupying different elevational zones in the same mountain. Investigating the other members of the genus Stenocephalemys for TIGV could reveal the real diversity of TIGV in the genus. [ABSTRACT FROM AUTHOR]

We provide an annotated checklist of rodents of Ethiopia. For each species we show a distributional map based on critically revised data from: (1) published literature; (2) museum collections, including records in the Global Biodiversity Information Facility (GBIF); and (3) recent field surveys performed in the last three decades as part of the Joint Ethio-Russian Biological Expedition (JERBE) and Ethio-Czech Research Projects. In most cases recent material was analysed in detail using genetic and/or morphometric approaches. In total, the Ethiopian rodent fauna consists of 104 species (40 genera, 10 families). Compared to previous studies we were not able to confirm the presence of 12 species, probably due to a lack of data from arid lowland areas, though some of these species may be extinct. We report the occurrence of > 40 species not previously included in a checklist published in 1996 (with many species still requiring formal description). Of the total number of species recorded, a high proportion are endemics of Ethiopian Highlands (43 species = 41.3 %), followed by those living in Somali-Masai (27) and Sudanian (13) savanna. The checklist confirms an unusually high level of Ethiopian rodent biodiversity, which should serve as a basis for conservation. [ABSTRACT FROM AUTHOR]

Aim The rodent genus Gerbilliscus is widespread in savannas throughout sub-Saharan Africa. The eastern clade comprises four species with distributions centred in the Somali-Masai biogeographical region of East Africa. We investigated the genetic diversity of the group with a view to illuminating the historical (Plio-Pleistocene) processes that formed contemporary biota of the understudied Somali-Masai region. Location Somali-Masai savanna, East Africa. Methods We performed multilocus genetic analyses of 240 samples from 112 localities, combining genotyping of recently collected samples ( N = 145), 454-pyrosequencing of museum material ( N = 34) and published sequences ( N = 61). We used Bayesian and maximum likelihood approaches for phylogenetic reconstructions, and coalescent-based methods to delimit species. We also estimated divergence times and modelled recent and past distributions to reconstruct the major evolutionary influences in the Somali-Masai region during the Plio-Pleistocene. Results Genetic analyses provided evidence for six lineages, possibly corresponding to distinct species. The two main species groups (with two and four putative species, respectively) have overlapping distributions, but species within each group are distributed parapatrically. The origin of the eastern clade dates back to the Pliocene, while individual species diverged in the Pleistocene. The distribution of genetic diversity and ecological niche modelling point to the importance of the Rift Valley and the presence of unsuitable xeric habitats in the allopatric diversification of Gerbilliscus in the Somali-Masai savanna within the last 5 Myr. Conclusions This is the first detailed phylo(bio-)geographical study of animals with predominant distribution in the Somali-Masai region. It revealed currently underestimated diversity of eastern clade of Gerbilliscus and proposed a scenario of its evolution during Plio-Pleistocene. Conspicuous genetic structure of these taxa can be now used to test detailed phylogeographical hypotheses related to Plio-Pleistocene history of gerbils and, to some extent, also biota of Somali-Masai bioregion in general. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Ethiopian rats (genus Stenocephalemys) represent a monophyletic group of Ethiopian endemic rodents that diverged in the Ethiopian Highlands during the Pleistocene. Because of the frequent occurrence of socalled reticulate evolution (i.e. repeated hybridization of partially diverged populations), their taxonomy has not been adequately resolved, despite the fact that they belong to the most abundant rodent genus in Ethiopia and are important as pests and carriers of pathogens (e.g. hantaviruses). Here we analysed material for 623 Stenocephalemys specimens using integrative taxonomy composed of genomic analyses (388 nuclear markers and complete mitogenomes), 2D-geometric morphometry of skulls and classical morphometry of external traits. The genus consists of six clearly defined gene pools (= species), characterized by specific morphology, ecology and distribution. Two of them, described here as new species, live in fragmented populations in Afroalpine habitats in the north-western part of the Ethiopian Highlands. We also showed that mitochondrial DNA is not applicable as a universal diagnostic tool for species discrimination in Stenocephalemys, because of multiple cases of mitochondrial introgression. This finding illustrates the utility of the genus as a suitable model for future studies of mito-nuclear coevolution along an elevational gradient. [ABSTRACT FROM AUTHOR]

Multimammate mice of the genus Mastomys are widespread in sub-Saharan Africa and occur in a wide range of open habitats. Representatives of this genus are the most common African rodents, the main vertebrate agricultural pests and vectors of human pathogens. In Ethiopia, the biogeographically most complex eastern African country, several species have been reported, but their distribution has never been described because of their cryptic morphology. Here we present genetically identified species from 377 Ethiopian Mastomys specimens and analyse their distributional patterns. The genus, represented by four species, inhabits most of the country, with the exception of the highest mountains and dry areas, such as the Afar triangle and the Somali region. For the first time we document M. kollmannspergeri from a single locality in the northernmost part of Ethiopia. Three previously recorded species are more widespread – M. erythroleucus was found at 32 localities, M. natalensis at 13 localities and the Ethiopian endemic species M. awashensis at 18 localities. Phylogenetic analysis of mitochondrial cytochrome b gene sequences indicates that only one of the six phylogroups of M. natalensis and one of the four phylogroups of M. erythroleucus are represented in Ethiopia. Haplotype network analysis indicates two subclades of Ethiopian M. erythroleucus separated by the Ethiopian Rift Valley. Using presence records, we constructed distribution models for the species and analysed the level of overlap. The predicted distribution shows most overlap between M. awashensis and M. natalensis, which is in agreement with empirical data as both species were found in sympatry at four localities. A medium level of overlap was predicted between M. natalensis and M. erythroleucus and both species were found co-existing at two localities. This study not only presents the first detailed distribution of cryptic Mastomys species, but also clearly identifies multimammate mice as model taxa for future evolutionary studies (e.g. the evolution of coexistence or host-parasite interactions) and indicates the regions suitable for such studies. [ABSTRACT FROM AUTHOR]

[Display omitted] • Fully resolved phylogeny of a highly diversified group of African mammals using genome-scale data. • Mechanisms of adaptive radiation in Late Miocene/Early Pliocene. • Delimitation of monophyletic genera in Praomyini rodents. • Discovery of a new mammal genus in Ethiopian forests. The tribe Praomyini is a diversified group including 64 species and eight extant rodent genera. They live in a broad spectrum of habitats across whole sub-Saharan Africa. Members of this tribe are often very abundant, they have a key ecological role in ecosystems, they are hosts of many potentially pathogenic microorganisms and comprise numerous agricultural pests. Although this tribe is well supported by both molecular and morphological data, its intergeneric relationships and the species contents of several genera are not yet fully resolved. Recent molecular data suggest that at least three genera in current sense are paraphyletic. However, in these studies the species sampling was sparse and the resolution of relationships among genera was poor, probably due to a fast radiation of the tribe dated to the Miocene and insufficient amount of genetic data. Here we used genomic scale data (395 nuclear loci = 610,965 bp long alignment and mitogenomes = 14,745 bp) and produced the first fully resolved species tree containing most major lineages of the Praomyini tribe (i.e. all but one currently delimited genera and major intrageneric clades). Results of a fossil-based divergence dating analysis suggest that the radiation started during the Messinian stage (ca. 7 Ma) and was likely linked to a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forests, while many others adapted to a broad spectrum of new open lowland and montane habitats that appeared at the beginning of Pliocene. Our analyses clearly confirmed the presence of three polyphyletic genera (Praomys , Myomyscus and Mastomys). We review current knowledge of these three genera and suggest corresponding taxonomic changes. To keep genera monophyletic, we propose taxonomic re-arrangements and delimit four new genera. Furthermore, we discovered a new highly divergent genetic lineage of Praomyini in southwestern Ethiopia, which is described as a new species and genus. [ABSTRACT FROM AUTHOR]