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The Natal multimammate mouse (Mastomys natalensis) is the most widespread rodent species in sub-Saharan Africa, often studied as an agricultural pest and reservoir of viruses. Its mitochondrial (Mt) phylogeny revealed six major lineages parapatrically distributed across open habitats of sub-Saharan Africa. In this study we used 1949 sequences of the mitochondrial cytochrome b gene to elaborate on distribution and evolutionary history of three Mt lineages inhabiting the open habitats of the Zambezian region (corresponding roughly to the African savannas south of the Equator). We describe in more detail contact zones between the lineages—their location and extent of co-occurrence within localities—and infer past population trends. The estimates are interpreted in the light of climatic niche models. The lineages underwent reduction in effective population size during the last glacial, but they spread widely after that: two of them after the last glacial maximum and the last one in mid-Holocene. The centers of expansion, i.e., possible long-term savanna refugia, were estimated to lie close to the Eastern Arc Mountains and lakes of the Great African Rift, geomorphological structures likely to have had long-term influence on geographical distribution of the lineages. Environmental niche modeling shows climate could also affect the broad scale distribution of the lineages but is unlikely to explain the narrow width of the contact zones. The intraspecific Mt differentiation of M. natalensis echoes phylogeographic patterns observed in multiple co-distributed mammal species, which suggests the mammal communities in the region are shaped by the same long-term processes.

The Callewaert’s mouse (Mus callewaerti) is shown as an ancient lineage of the African endemic subgenus Nannomys. Described in 1925 as a large-bodied species with proodont (forward pointing) incisors, it was long known only from a handful of localities in Angola and southern Democratic Republic of the Congo. Here, it is revealed identical with a genetically distinctive Nannomys, provisionally called Mus sp. “Nyika” in previous studies and reported from Nyika Plateau (Malawi) and the Angolan Escarpment. The skull shape analysis clearly associated the holotype of M. callewaerti with other specimens ascribed to the species (including the genotyped ones). It also pinpointed diagnostic features distinguishing M. callewaerti from other large bodied Nannomys, especially its sympatric Mus triton, for which the species was repeatedly mistaken. Mus callewaerti is presumably insectivorous and rare or not easy to capture. The divergence between its Malawian and Angolan populations is relatively shallow, dated to 0.32 million years ago, which suggests that at least in the past the species could be widespread. Mus callewaerti is known from grassy, locally moisty habitats. Together with a handful of other rodent taxa it provides evidence of persistence and historic connection of these habitats across the Zambezian region.

The extremely species-rich genus Trypanosoma has recently been divided into 16 subgenera, most of which show fairly high host specificity, including the subgenus Herpetosoma parasitizing mainly rodents. Although most Herpetosoma spp. are highly host-specific, the best-known representative, Trypanosoma lewisi, has a cosmopolitan distribution and low host specificity. The present study investigates the general diversity of small mammal trypanosomes in East and Central Africa and the penetration of invasive T. lewisi into communities of native rodents. An extensive study of blood and tissue samples from Afrotropical micromammals (1528 rodents, 135 shrews, and five sengis belonging to 37 genera and 133 species) captured in the Central African Republic, Ethiopia, Kenya, Malawi, Mozambique, Tanzania, and Zambia revealed 187 (11.2%) trypanosome-positive individuals. The prevalence of trypanosomes in host genera ranged from 2.1% in Aethomys to 37.1% in Lemniscomys. The only previously known trypanosome detected in our dataset was T. lewisi, newly found in Ethiopia, Kenya, and Tanzania in a wide range of native rodent hosts. Besides T. lewisi, 18S rRNA sequencing revealed 48 additional unique Herpetosoma genotypes representing at least 15 putative new species, which doubles the known sequence-based diversity of this subgenus, and approaches the true species richness in the study area. The other two genotypes represent two new species belonging to the subgenera Ornithotrypanum and Squamatrypanum. The trypanosomes of white-toothed shrews (Crocidura spp.) form a new phylogroup of Herpetosoma, unrelated to flagellates previously detected in insectivores. With 13 documented species, Ethiopia was the richest region for trypanosome diversity, which corresponds to the very diverse environments and generally high biodiversity of this country. We conclude that besides T. lewisi, the subgenus Herpetosoma is highly host-specific (e.g., species parasitizing the rodent genera Acomys and Gerbilliscus). Furthermore, several newly detected trypanosome species are specific to their endemic hosts, such as brush-furred mice (Lophuromys), dormice (Graphiurus), and white-toothed shrews (Crocidura).

Despite its biogeographical uniqueness, where two vast savanna regions are separated by the Afromontane mosaic vegetation, there is a significant lack of small mammal sampling in the Tigray region of Ethiopia. Leveraging all our available data on rodents and shrews in the region, we tested the hypothesis that the Afromontane mosaic vegetation in the highlands acts as a barrier to gene flow between taxa found in the Somali-Masai and Sudanian savanna in the southeast and western lowland parts of the region, respectively. Morphological and DNA sequence analysis confirmed the presence of 23 species of small rodents and shrews in the region. We recorded 18 of these species in the Afromontane mosaic vegetation, seven species in the Sudanian savanna, and four species in the Somali-Masai savanna. Notably, the fauna of Sudanian savanna was strikingly different from that of the Somali-Masai savanna at both intraspecific and interspecific level, suggesting northern Ethiopian highlands as very strong biogeographic barrier for taxa adapted to arid lowlands. However, the reported species diversity remains provisional, and additional sampling from unexplored areas is needed. Furthermore, some of the reported taxa, in this study, such as Mus cf. tenellus, Crocidura cf. fuscomurina, Dendromus sp. indet. 2, and Otomys cf. cheesmani, require detailed taxonomic investigation and may represent new species. A robust understanding of the taxonomic diversity and distribution of the small mammals in the region is crucial for effective conservation planning as well as for addressing practical questions related to rodents, such as in public health and pest management.

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.

Mastomys natalensis-borne mammarenaviruses appear specific to subspecific M. natalensis taxa rather than to the whole species. Yet mammarenaviruses carried by M. natalensis are known to spill over and jump hosts in northern sub-Saharan Africa. Phylogeographic studies increasingly show that, like M. natalensis, small mammals in sub-Saharan Africa are often genetically structured into several subspecific taxa. Other mammarenaviruses may thus also form virus-subspecific host taxon associations. To investigate this, and if mammarenaviruses carried by M. natalensis in southern Africa are less prone to spill-over, we screened 1225 non -M. natalensis samples from Tanzania where many small mammal taxa meet. We found mammarenavirus RNA in 6 samples. Genetic/genomic characterisation confirmed they were not spill-over from M. natalensis. We detected host jumps among rodent tribe members and an association between mammarenaviruses and subspecific taxa of Mus minutoides and Grammomys surdaster, indicating host genetic structure may be crucial to understand virus distribution and host specificity.

Crocidura (Eulipotyphla, Soricidae) is the most species-rich genus among mammals, with high cryptic diversity and complicated taxonomy. The hirta-flavescens group of Crocidura represents the most abundant and widespread shrews in savannahs of eastern and southern Africa, making them a suitable phylogeographical model for assessing the role of paleoclimatic changes on current biodiversity in open African habitats. We present the first comprehensive study on the phylogeography, evolutionary history, geographical distribution, systematics, and taxonomy of the group, using the integration of mitochondrial, genome-wide (ddRAD sequencing), morpho-logical and morphometrical data collected from specimens over most of the known geographic distribution. Our genomic data confirmed the monophyly of this group and its sister relationship with the olivieri group of Cro-cidura. There is a substantial genetic variation within the hirta-flavescens group, with three highly supported clades showing parapatric distribution and which can be distinguished morphologically: C. hirta, distributed in both the Zambezian and Somali-Masai bioregions, C. flavescens, known from South Africa and south-western Zambia, and C. cf. flavescens, which is known to occur only in central and western Tanzania. Morphometric data revealed relatively minor differences between C. hirta and C. cf. flavescens, but they differ in the colouration of the pelage. Diversification of the hirta-flavescens group has most likely happened during phases of grassland expansion and contraction during Plio-Pleistocene climatic cycles. Eastern African Rift system, rivers, and the distinctiveness of Zambezian and Somali-Masai bioregions seem to have also shaped the pattern of their di-versity, which is very similar to sympatric rodent species living in open habitats. Finally, we review the group's taxonomy and propose to revalidate C. bloyeti, currently a synonym of C. hirta, including the specimens treated as C. cf. flavescens.

Little is known about the distribution and ecology of small mammals inhabiting Simien Mountains National Park despite the presence of mostly endemic species. Prior to this study, the most comprehensive dataset was collected in 1927. This provides a unique opportunity to assess the possible role of climate change over the last 88 years on the elevational distribution of mammals in the Ethiopian highlands. Between September and November 2015, three of us (EWC, WTS, YM) collected non-volant small mammals at four sites (2900, 3250, 3600, and 4000 m a.s.l.) along the western slope of the Simien Mountains using standardized sampling. Over a four-week period we recorded 13 species, comprising 11 rodents and two shrews, all endemic to the Ethiopian Plateau. We found greatest species richness at mid-elevations (3250 m), consistent with a general pattern found on many other mountains worldwide but less so in Africa. We discovered one potentially new species of shrew. No previously unrecorded rodent species were observed. Finally, we compared our species distribution results to the 1927 dataset and found upward elevational shifts in species ranges, suggesting the role and influence of climate change on the small mammal community. Simien Mountains National Park represents an exceptionally valuable core area of endemism and the best protected natural habitat in northern Ethiopia.

International audience; Mammarenaviruses have been a growing concern for public health in Africa since the 1970s when Lassa virus cases in humans were first described in west Africa. In southern Africa, a single outbreak of Lujo virus was reported to date in South Africa in 2008 with a case fatality rate of 80%. The natural reservoir of Lassa virus is Mastomys natalensis while for the Lujo virus the natural host has yet to be identified. Mopeia virus was described for the first time in M. natalensis in the central Mozambique in 1977 but few studies have been conducted in the region. In this study, rodents were trapped between March and November 2019in villages, croplands fields and mopane woodland forest. The aim was to assess the potential circulation and to evaluate the genetic diversity of mammarenaviruses in M. natalensis trapped in the Limpopo National Park and its buffer zone in Massingir district, Mozambique. A total of 534 M. natalensis were screened by RT-PCR and the overall proportion of positive individuals was 16.9%. No significant differences were detected between the sampled habitats (chi 2 = 0.018; DF = 1; p = 0.893). The Mopeia virus (bootstrap value 91%) was the Mammarenavirus circulating in the study area sites, forming a specific sub-clade with eight different sub-clusters. We concluded that Mopeia virus circulates in all habitats investigated and it forms a different sub-clade to the one reported in central Mozambique in 1977.

Background Spiny mice of the genus Acomys are distributed mainly in dry open habitats in Africa and the Middle East, and they are widely used as model taxa for various biological disciplines (e.g. ecology, physiology and evolutionary biology). Despite their importance, large distribution and abundance in local communities, the phylogeny and the species limits in the genus are poorly resolved, and this is especially true for sub-Saharan taxa. The main aims of this study are (1) to reconstruct phylogenetic relationships of Acomys based on the largest available multilocus dataset (700 genotyped individuals from 282 localities), (2) to identify the main biogeographical divides in the distribution of Acomys diversity in dry open habitats in Afro-Arabia, (3) to reconstruct the historical biogeography of the genus, and finally (4) to estimate the species richness of the genus by application of the phylogenetic species concept. Results The multilocus phylogeny based on four genetic markers shows presence of five major groups of Acomys called here subspinosus, spinosissimus, russatus, wilsoni and cahirinus groups. Three of these major groups (spinosissimus, wilsoni and cahirinus) are further sub-structured to phylogenetic lineages with predominantly parapatric distributions. Combination of alternative species delimitation methods suggests the existence of 26 molecular operational taxonomic units (MOTUs), potentially corresponding to separate species. The highest genetic diversity was found in Eastern Africa. The origin of the genus Acomys is dated to late Miocene (ca. 8.7 Ma), when the first split occurred between spiny mice of eastern (Somali-Masai) and south-eastern (Zambezian) savannas. Further diversification, mostly in Plio-Pleistocene, and the current distribution of Acomys were influenced by the interplay of global climatic factors (e.g., Messinian salinity crisis, intensification of Northern Hemisphere glaciation) with local geomorphology (mountain chains, aridity belts, water bodies). Combination of divergence dating, species distribution modelling and historical biogeography analysis suggests repeated “out-of-East-Africa” dispersal events into western Africa, the Mediterranean region and Arabia. Conclusions The genus Acomys is very suitable model for historical phylogeographic and biogeographic reconstructions of dry non-forested environments in Afro-Arabia. We provide the most thorough phylogenetic reconstruction of the genus and identify major factors that influenced its evolutionary history since the late Miocene. We also highlight the urgent need of integrative taxonomic revision of east African taxa. Electronic supplementary material The online version of this article (10.1186/s12862-019-1380-9) contains supplementary material, which is available to authorized users.

Background The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) have been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity and evolution. In this study, we inferred the systematics, phylogeography, and evolutionary history of the L. flavopunctatus group using maximum likelihood and Bayesian phylogenetic inference, divergence times, historical biogeographic reconstruction, and morphometric discriminant tests. We compiled comprehensive datasets of three loci (two mitochondrial [mtDNA] and one nuclear) and two morphometric datasets (linear and geometric) from across the known range of the genus Lophuromys. Results The mtDNA phylogeny supported the division of the genus Lophuromys into three primary groups with nearly equidistant pairwise differentiation: one group corresponding to the subgenus Kivumys (Kivumys group) and two groups corresponding to the subgenus Lophuromys (L. sikapusi group and L. flavopunctatus group). The L. flavopunctatus group comprised the speckled-pelage brush-furred Lophuromys endemic to Ethiopia (Ethiopian L. flavopunctatus members [ETHFLAVO]) and the non-Ethiopian ones (non-Ethiopian L. flavopunctatus members [NONETHFLAVO]) in deeply nested relationships. There were distinctly geographically structured mtDNA clades among the NONETHFLAVO, which were incongruous with the nuclear tree where several clades were unresolved. The morphometric datasets did not systematically assign samples to meaningful taxonomic units or agree with the mtDNA clades. The divergence dating and ancestral range reconstructions showed the NONETHFLAVO colonized the current ranges over two independent dispersal events out of Ethiopia in the early Pleistocene. Conclusion The phylogenetic associations and divergence times of the L. flavopunctatus group support the hypothesis that paleoclimatic impacts and ecosystem refugia during the Pleistocene impacted the evolutionary radiation of these rodents. The overlap in craniodental variation between distinct mtDNA clades among the NONETHFLAVO suggests unraveling underlying ecomorphological drivers is key to reconciling taxonomically informative morphological characters. The genus Lophuromys requires a taxonomic reassessment based on extensive genomic evidence to elucidate the patterns and impacts of genetic isolation at clade contact zones.

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. ispartof: VIRUS EVOLUTION vol:7 issue:1 ispartof: location:England status: published

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.

The Ethiopian highlands represent a remarkable biodiversity ‘hot spot’ with a very high number of endemic species, even among vertebrates. Ethiopian representatives of a species complex of speckled brush‐furred rats (Lophuromys flavopunctatus sensu lato) inhabit highland habitats ranging from low‐elevation forests to Afroalpine grasslands. These may serve as a suitable model for understanding evolutionary processes leading to high genetic and ecological diversity in montane biodiversity hot spots. Here, we analyse the most comprehensive genetic data set of this group, comprising 315 specimens (all nine putative Ethiopian Lophuromys taxa sampled across most of their distribution ranges) genotyped at one mitochondrial and four nuclear markers, and thousands of SNPs from ddRAD sequencing. We performed phylogenetic analyses, delimited species and mapped their distribution and estimated divergence time between species (under the species‐tree framework) and mitochondrial lineages. We found significant incongruence between mitochondrial and nuclear phylogenies, most probably caused by multiple interspecific introgression events. We discuss alternative scenarios of Ethiopian Lophuromys evolution, from retention of ancestral polymorphism to hybridization upon secondary contact of partially reproductively isolated lineages leading to reticulate evolution. Finally, we use the diversity of the speckled brush‐furred rats for the description of the main biogeographic patterns in the fauna of the Ethiopian highlands.

Organisms living in high altitude must adapt to environmental conditions with hypoxia and low temperature, e.g. by changes in the structure and function of proteins associated with oxidative phosphorylation in mitochondria. Here we analysed the signs of adaptive evolution in 27 mitogenomes of endemic Ethiopian rats (Stenocephalemys), where individual species adapted to different elevation. Significant signals of positive selection were detected in 10 of the 13 mitochondrial protein-coding genes, with a majority of functional substitutions in the NADH dehydrogenase complex. Higher frequency of positively selected sites was found in phylogenetic lineages corresponding to Afroalpine specialists.

Background: The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) has been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity. In this study, we inferred the systematics, phylogeography, and evolutionary history of the L. flavopunctatus group using maximum likelihood and Bayesian phylogenetic inference, divergence times, historical biogeographic reconstruction, and morphometric discriminant tests. We compiled comprehensive datasets of three loci (two mitochondrial [mtDNA] and one nuclear) and two morphometric datasets (linear and geometric) from across the known range of the genus Lophuromys.Results: The mtDNA phylogeny supported the division of the genus Lophuromys into three primary groups with nearly equidistant pairwise differentiation: one group corresponding to the subgenus Kivumys (Kivumys group) and two groups corresponding to the subgenus Lophuromys (L. sikapusi group and L. flavopunctatus group). The L. flavopunctatus group comprised the speckled-pelage brush-furred Lophuromys endemic to Ethiopia (Ethiopian L. flavopunctatus members [ETHFLAVO]) and the non-Ethiopian ones (non-Ethiopian L. flavopunctatus members [NONETHFLAVO]) in deeply nested relationships. There were distinctly geographically structured mtDNA clades among the NONETHFLAVO, which were incongruous with the nuclear tree where several clades were unresolved. The morphometric datasets did not systematically assign samples to meaningful taxonomic units or agreed with the mtDNA clades. The divergence dating and ancestral range reconstructions showed the NONETHFLAVO colonized the current ranges over two independent dispersal events out of Ethiopia in the early Pleistocene.Conclusion: The phylogenetic associations and divergence times of the L. flavopunctatus group conform to demonstrated hypotheses surrounding the paleoclimatic and ecosystem refugium impacts on the evolutionary radiation of rodents dependent on stably humid conditions in the East Africa region. The overlap in craniodental variation between distinct mtDNA clades among the NONETHFLAVO suggests unraveling underlying ecomorphological drivers is key to reconciling taxonomically informative morphological characters. The genus Lophuromys requires a taxonomic reassessment based on extensive genomic evidence to elucidate the patterns and impacts of genetic isolation at clade contact zones.

International audience; Murine rodents are one of the most evolutionary successful groups of extant mammals. They are also important for human as vectors and reservoirs of zoonoses and agricultural pests. Unfortunately, their fast and relatively recent diversification impedes our understanding of phylogenetic relationships and species limits of many murine taxa, including those with very conspicuous phenotype that has been frequently used for taxonomic purposes. One of such groups are the striped grass mice (genus Lemniscomys), distributed across sub-Saharan Africa in 11 currently recognized species. These are traditionally classified into three morphological groups according to different pelage colouration on the back: (a) L. barbarus group (three species) with several continuous pale longitudinal stripes; (b) L. striatus group (four species) with pale stripes diffused into short lines or dots; and (c) L. griselda group (four species) with a single mid-dorsal black stripe. Here we reconstructed the most comprehensive molecular phylogeny of the genus Lemniscomys to date, using the largest currently available multi-locus genetic dataset of all but two species. The results show four main lineages (=species complexes) with the distribution corresponding to the major biogeographical regions of Africa. Surprisingly, the four phylogenetic lineages are only in partial agreement with the morphological classification, suggesting that the single-stripe and/or multi-striped phenotypes evolved independently in multiple lineages. Divergence dating showed the split of Lemniscomys and Arvicanthis genera at the beginning of Pleistocene; most of subsequent speciation processes within Lemniscomys were affected by Pleistocene climate oscillations, with predominantly allopatric diversification in fragmented savanna biome. We propose taxonomic suggestions and directions for future research of this striking group of African rodents.

We describe two new species of white-toothed shrews from south-western and central Ethiopia, based on recent collections and an application of morphological and genetic methods, Crocidura similiturba sp. nov. and Crocidura makeda sp. nov. Comparisons are provided with other Crocidura species known to occur in the country. Both new species are currently known only from the Ethiopian Highlands. Furthermore, we provide new geographical records and discuss biogeographical patterns in the country. New molecular data, even if based primarily on mitochondrial cytochrome b, suggests substantial divergence within afrotropical Suncus megalura, suggesting that the East African lineage might be considered separated at the species level – Suncus sorella (Thomas, 1897), stat. nov. Molecular data support a monophyly of the clade, grouping most Crocidura species endemic to Ethiopia (the East African subclade of the Old World clade), but also indicates additional colonisations of Ethiopian Plateau from East and Central Africa in the past. The remarkable number of endemics shows that Ethiopia is an important centre for the Crocidura radiation, as is the case for other groups of non-flying terrestrial vertebrates.

Hepatitis C virus (HCV; genus Hepacivirus) represents a major public health problem, infecting about 3 % of the human population (± 185,000,000 people). Because no plausible animal reservoir carrying closely related hepaciviruses has been identified, the zoonotic origins of HCV still remain elusive. Motivated by recent findings of divergent hepaciviruses in rodents and a plausible African origin of HCV genotypes, we have screened a comprehensive collection of small mammals samples from seven sub-Saharan African countries. Out of 4,303 samples screened, 80 were found positive for the presence of hepaciviruses in 29 different host species. We here report 56 novel genomes that considerably increase the diversity of three divergent rodent hepacivirus lineages, which previously were almost exclusively represented by New World and European hepaciviruses. Further-more, we provide undisputable evidence for hepacivirus co-infections in rodents, which remarkably, we exclusively but repeatedly found in four sampled species of brush-furred mice. We also point at hepacivirus co-infections indirectly in different animal hosts by demonstrating evidence for recombination within specific host lineages. Our study considerably expands the available hepacivirus genomic data and elucidates the relatively deep evolutionary history that these pathogens have in rodents compared to other mammalian hosts. Overall, our results emphasize the importance of rodents as a potential hepacivirus reservoir and as models for investigating HCV infection dynamics.

Mastomys natalensis is widespread in sub-Saharan Africa and hosts several arenavirus species, including the pathogenic zoonotic Lassa virus in West Africa. Mitochondrial lineages sub-divide the range of M. natalensis and have been associated with cryptic structure within the species. To test specificity of arenaviruses to hosts carrying these lineages, we screened 1772 M. natalensis in a large area of Tanzania where three mitochondrial lineages meet. We detected fifty-two individuals that were positive for one of three arenaviruses: Gairo, Morogoro, and Luna virus. This is the first record of Luna virus in Tanzania. We confirmed the specificity of each arenavirus to a distinct host mitochondrial lineage except for three cases in one locality at the centre of a host hybrid zone. No arenaviruses were detected in a large part of the study area. Morogoro and Gairo virus showed differences in prevalence (Morogoro virus lower than Gairo virus) and in genetic structure (Morogoro virus more structured than Gairo virus). However, both viruses have genetic neighbourhood size estimates of the same order of magnitude as Lassa virus. While differences in arenavirus and/or host evolutionary and ecological dynamics may exist, Tanzanian arenaviruses could be suited to model Lassa virus dynamics in M. natalensis.

The tribe Arvicanthini (Muridae: Murinae) is a highly diversified group of rodents (ca. 100 species) and with 18 African genera (plus one Asiatic) represents probably the most successful adaptive radiation of extant mammals in Africa. They colonized a broad spectrum of habitats (from rainforests to semi-deserts) in whole sub-Saharan Africa and their members often belong to most abundant parts of mammal communities. Despite intensive efforts, the phylogenetic relationships among major lineages (i.e. genera) remained obscured, which was likely caused by the intensive radiation of the group, dated to the Late Miocene. Here we used genomic scale data (377 nuclear loci; 581,030 bp) and produced the first fully resolved species tree containing all currently delimited genera of the tribe. Mitogenomes were also extracted, and while the results were largely congruent, there was less resolution at basal nodes of the mitochondrial phylogeny. Results of a fossil-based divergence dating analysis suggest that the African radiation started early after the colonization of Africa by a single arvicanthine ancestor from Asia during the Messinian stage (ca. 7 Ma), and was likely linked with a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forest, while many others successfully colonized broad spectrum of new open habitats (e.g. savannas, wetlands or montane moorlands) that appeared at the beginning of Pliocene. One lineage even evolved partially arboricolous life style in savanna woodlands, which allowed them to re-colonize equatorial forests. We also discuss delimitation of genera in Arvicanthini and propose corresponding taxonomic changes.

Climbing mice in the genus Dendromus (sensu lato) are widely distributed in Africa, south of the Saharan Desert. The 17 currently recognized species in the genus range from widespread taxa to single-mountain endemics, and there is considerable variation across species with respect to habitats occupied. These habitats range from arid grasslands and savannahs to sub-alpine and alpine vegetation. Using the most comprehensive geographic and genetic survey to date and after reviewing many type specimens, we assess the systematics and biogeography of Dendromus. Given the structure of our molecular phylogenetic hypotheses, in which we recover six major clades, we propose the recognition of three genera within the Dendromus group (sensu lato): in addition to Dendromus (26 lineages), we suggest the retention of Megadendromus (monotypic) and the resurrection of the genus Poemys (six lineages). From our model-based molecular phylogenetic results and morphological comparisons, we suggest that six formerly synonymized taxa should be resurrected, and we highlight 14 previously undescribed lineages. We also constructed time-calibrations on our phylogeny, and performed ancestral area reconstructions using BioGeoBEARS. Based on fossil evidence, Dendromus appears to have had a widespread African distribution dating back to the Late Miocene (8–10 Ma), and our basal ancestral area reconstruction (Ethiopians Highlands + Eastern African Mountains + Zambezian region) supports this. Divergence of the six major clades we recover (Poemys, Megadendromus and four within Dendromus) occurred prior to or at the Miocene-Pliocene boundary 5.3 Ma. Biogeographically, Megadendromus is restricted to the Ethiopian Highlands. The ancestral area for Poemys is reconstructed as the Zambezian region, with species distributions ranging from South Africa to Western Africa. The ancestral area for Dendromus is reconstructed as the Ethiopian Highlands, with the ancestral areas of the four major clades being reconstructed as Ethiopian Highlands, Albertine Rift, South Africa or Western Africa. None of the four Dendromus clades are reciprocally monophyletic with respect to distributional area.

The murid rodent Praomys daltoni is widespread in Sudanian savanna and woodlands of West Africa, and previous study of mitochondrial DNA variability suggested that it encompasses the phenotypically (small, grey-bellied) and ecologically (commensal) distinct form, Praomys derooi. Here, we comprehensively examined the genetic and morphological diversity within the complex. Six mitochondrial lineages showed a fine-scale phylogeographical pattern, whereas delimitation based on nuclear loci pooled four of them into a single widespread unit. A newly discovered lineage from southern Mauritania stands apart from the rest of the complex and might represent an unrecognized species. At the same time, the internal position of P. derooi (C2 mitochondrial lineage) was confirmed by the multilocus analysis. The magnitude of genetic distances between major phylogeographical lineages was typical for interspecific divergence in other clades of Praomys, despite the little differences among them in morphology (skull and upper molar row shapes). The most pronounced morphological shift was associated with a transition to commensalism, especially in P. derooi, but also in other lineages. This makes the whole complex a suitable model for the study of phenotypic novelty, the evolution of commensalism and conditions for ecological speciation.

International audience; Wood mice of the genus Hylomyscus, are small-sized rodents widely distributed in lowland and montane rainforests in tropical Africa, where they can be locally abundant. Recent morphological and molecular studies have increased the number of recognized species from 8 to 18 during the last 15 years. We used complete mitochondrial genomes and five nuclear genes to infer the number of candidate species within this genus and depict its evolutionary history. In terms of gene sampling and geographical and taxonomic coverage, this is the most comprehensive review of the genus Hylomyscus to date. The six species groups (aeta, alleni, anselli, baeri, denniae and parvus) defined on morphological grounds are monophyletic. Species delimitation analyses highlight undescribed diversity within this genus: perhaps up to 10 taxa need description or elevation from synonymy, pending review of type specimens. Our divergence dating and biogeographical analyses show that diversification of the genus occurred after the end of the Miocene and is closely linked to the history of the African forest. The formation of the Rift Valley combined with the declining global temperatures during the Late Miocene caused the fragmentation of the forests and explains the first split between the denniae group and remaining lineages. Subsequently, periods of increased climatic instability during Plio-Pleistocene probably resulted in elevated diversification in both lowland and montane forest taxa.

The 13th African Small Mammal Symposium (ASMS) was organized on September 16-21, 2019, at Mekelle University in Mekelle, Tigray, Ethiopia. Starting in 1977, these symposia are organized every four years and since 2003 have been held in tropical Africa. The aim of the meetings is to promote communication among researchers and students interested in various aspects of the biology of African small mammals (mainly rodents, insectivores, bats, afrotherians, small carnivores and primates), which are significantly understudied in comparison with their larger relatives.In this editorial contribution, which introduces a special issue of Journal of Vertebrate Biology on African small mammals, we would like to briefly summarize the history of these meetings and to pinpoint the major trends in research on African small mammals, based on an analysis of the presentations at these meetings.

African mole-rats (Bathyergidae) are an intensively studied family of subterranean rodents including three highly social and three solitary genera. Although their phylogenetic interrelations are clear, genetic diversity and the number of species within each genus is much less certain. Among the solitary genera, Heliophobius and Georychus were for a long time considered as monotypic, but molecular studies demonstrated strong phylogeographic structure within each genus and proposed that they represent complexes of cryptic species. The present study re-evaluates their internal genetic/phylogenetic structure using a combination of methodological approaches. We generated datasets of one mitochondrial and six specifically selected nuclear markers as well as of a large number of double digest restriction site associated (ddRAD) loci and then applied species delimitation analyses based on the multispecies coalescent model or clustering on co-ancestry matrices. The population structure was largely congruent across all analyses, but the methods differed in their resolution scale when determining distinct gene pools. While the multispecies coalescent model distinguished five Georychus and between eleven to thirteen Heliophobius gene pools in both Sanger sequenced and ddRAD loci, two clustering algorithms revealed significantly finer or coarser structure in ddRAD based co-ancestry matrices. Tens of clusters were distinguished by fineRADstructure and one (in Georychus) or two clusters (in Heliophobius) by Infomap. The divergence dating of the bathyergid phylogeny estimated that diversification within both genera coincided with the onset of the Pleistocene and was likely driven by repeated large-scale climatic changes. Based on this updated genetic evidence, we suggest recognizing one species of Georychus and two species of Heliophobius, corresponding to a northern and southern major lineage, separated by the Eastern Arc Mountains. Yet, the final taxonomic revision should await integrated evidence stemming from e.g.. morphological, ecological, or behavioral datasets.

Even though populations of many large carnivores are expanding throughout Europe, the Eurasian lynx population in the Western Carpathians seems unable to spread beyond the western boundaries of its current distributional range. Many factors, both extrinsic and intrinsic, can influence the potential for range expansion: landscape fragmentation, natal philopatry, low natural fecundity and high mortality, and low and sex-biased dispersal rates. In this study we used non-invasive genetic sampling to determine population size fluctuation, sub-structuring and social organisation of the peripheral lynx population at the Czech–Slovak border. Even though the population size has been relatively stable over the period studied (2010–2016), the individual inbreeding coefficients of residents at the end of the study were much higher than those of founders at the beginning of the study. While non-resident individuals (predominantly males) occurred regularly in the study population, only resident individuals with well-established home ranges participated in breeding and produced offspring. Almost half the offspring detected in the study (predominantly females) settled in or near the natal area. Subsequent incestuous mating resulted in production of inbred individuals, reduction of effective population size of the population, and sub-structuring of the population through formation of two distinct family lineages. Our study illustrates how social constraints, such as territoriality, breeding of residents and natal philopatry of females, lead to incestuous mating in small-sized populations, especially at the periphery of their distribution. This threat should be taken into account in planning of conservation and population recovery of species with similar social structure.

The silvery mole-rat (Heliophobius argenteocinereus) is a solitary subterranean rodent with its distribution centred mainly in miombo woodlands of eastern Africa. This part of the continent was significantly influenced by the formation of the East African Rift System (EARS) during the last 25 Mya and by pronounced climatic changes in the Plio-Pleistocene that have caused genetic differentiation leading even to speciation events in many organisms. Recently, based on analysis of mitochondrial (mt) DNA sequences, it was suggested that H. argenteocinereus is a complex of six to eight species that diverged from the early to middle Miocene. In the present study, we significantly extended the sampling, re-analysed mtDNA datasets and analysed nuclear markers with the aim to assess the evolutionary history of Heliophobius. If we do not consider the old museum samples from south-eastern Democratic Republic of Congo (very divergent short mtDNA sequences obtained from ancient DNA, requiring further study from fresh material), the genus Heliophobius is composed of three major mtDNA lineages with parapatric distribution. The Rukwa Rift (+Mbeya triple junction) at the Zambia-Tanzania border, Lake Malawi, and the Eastern Arc Mountains form the biogeographical divides among these clades. The relatively shallow differences among the mitochondrial clades, divergence dating based on the use of the fossilised birth-death ratio model and a multi-locus dataset, and a very similar pattern of genetic structure to other rodents inhabiting the same area and habitat, suggest that the evolutionary history of the extant silvery mole-rat was predominantly influenced by the climatic fluctuations in the Plio-Pleistocene. Awaiting further studies employing genomiC., ecological, morphological or behavioural data, we advocate for using the single name H. argenteocinereus for all evolutionary lineages within this taxon, because ( 1 ) comparison of the genetic structure observed in mtDNA and nuclear markers suggest hybridization between at least some mtDNA lineages in the contact zones; and (2) new samples close to the type localities suggest incorrect use of previous names.

The Arsi Mountains (Southeastern Ethiopian mountain block) are a unique region comprising a range of habitats, including natural montane forest, extensive ericaceous scrub and small, restricted patches of Afroalpine ecosystem. During 3 years of sampling small mammals, 13 rodent species were recorded, including the extremely rare Mus imberbis and Dendromus nikolausi. Genetic analysis was used to shed light on the taxonomic diversity of rodents in the Arsi Mountains and their evolutionary associations with populations from other Ethiopian montane massifs (including the neighbouring Bale Mountains). All species recorded are endemic to the Ethiopian highlands. The results of this study provide the first genetically confirmed data on the occurrence of such endemic species as Lophuromys melanonyx, L. chrysopus and a yet undescribed Dendromus species in the Arsi Mountains. The genetic affinities of some Arsi rodents with their conspecifics in the neighbouring Bale Mountains were also explored. The results suggest the Arsi Mountains as one of the most important hotspots of unique Ethiopian mammal diversity.

Despite the high degree of biological diversity in the Zambezian region, little information is available regarding the evolutionary history of its biota, and this is especially true for the fauna and flora of non-forested habitats. Here we use the most comprehensive multi-locus genetic dataset available to (1) reconstruct the phylogeny of spiny mice of the Acomys spinosissimus complex and to describe the spa-tial distribution of its genetic diversity; (2) to assess the level of reproductive isolation between genetic clades; (3) to analyse differences in climatic niche between potential species; and (4) to model their current and past distribution. The complex comprises four main genetic clades that correspond to four nominal species living in the east of the Zambezian region. Their distribution is delimited by important geographical divides including the Eastern Arc Mountains, Lake Malawi and the Zambezi River. Two species considered Tanzanian endemics, A. ngurui and A. muzei, are now known to be more widespread than previously thought and they have their centres of genetic diversity just north of the Zambezi. The first split between the extant members of the A. spinosissimus complex is estimated at 3 Mya. Most intraspecific diversification events are thought to have occurred in the Pleistocene, suggesting that climatic oscillations played an important role in their diversification. The climatic niches of parapatric taxa differ significantly; hence, local adaptations have likely played an important role in reproductive isolation. Species distribution modelling predicts a dramatic reduction of occurrence probability across the area during the last interglacial period, facilitating allopatric diversification of fragmented populations. Our results strongly suggest the combined role of Pleistocene climatic change, biogeographical barriers and local adaptation in forming current taxa diversity in east African savannah-like habitats. While such processes have frequently been observed in forest-living organisms (theory of allopatric diversification in forest refugia), similar mechanisms were likely also working in open ecosystems (savannah refugia).

Positive selection acting on Toll‐like receptors (TLRs) has been recently investigated to reveal evolutionary mechanisms of host–pathogen molecular co‐adaptation. Much of this research, however, has focused mainly on the identification of sites predicted to be under positive selection, bringing little insight into the functional differences and similarities among species and a limited understanding of convergent evolution in the innate immune molecules. In this study, we provide evidence of phenotypic variability in the avian TLR4 ligand‐binding region (LBR), the direct interface between host and pathogen molecular structures. We show that 55 passerine species vary substantially in the distribution of electrostatic potential on the surface of the receptor, and based on these distinct patterns, we identified four species clusters. Seven of the 34 evolutionarily nonconservative and positively selected residues correspond topologically to sites previously identified as being important for lipopolysaccharide, lipid IVa or MD‐2 binding. Five of these positions codetermine the identity of the charge clusters. Groups of species that host‐related communities of pathogens were predicted to cluster based on their TLR4 LBR charge. Despite some evidence for convergence among taxa, there were no clear associations between the TLR4 LBR charge distribution and any of the general ecological characteristics compared (migration, latitudinal distribution and diet). Closely related species, however, mostly belonged to the same surface charge cluster indicating that phylogenetic constraints are key determinants shaping TLR4 adaptive evolution. Our results suggest that host innate immune evolution is consistent with Fahrenholz's rule on the cospeciation of hosts and their parasites.

Small terrestrial mammals and their biogeographical affinities were studied on Mount Kitumbeine, one of the little known volcanoes in the Gregory Rift Valley (northern Tanzania). In June, 2015, a total of 10 species, two insectivores and eight rodents, were recorded during a short-time sampling in two high altitude habitats. Taxonomic identification was based on genetic data allowing zoogeographic interpretations. For most of the taxa, there was a clear link with fauna of the northern part of the Eastern Arc Mountains, but there were also species with their core distributions in the Albertine Rift Mountains (Crocidura montis) as well as taxa endemic to the volcanic Northern Highlands (e.g. Hanang or Ngorongoro), such as Lophuromys makundi and probably Otomys angoniensis. Comparison of genotyped small mammals from Kitumbeine and neighboring hills with previously collected data revealed the first genetically confirmed Tanzanian records of two species (C. montis and Lophuromys stanleyi) and one species (Lophuromys sabunii) is reported for the first time from Zambia. The present study thus showed that, even in such well-studied areas like northern Tanzania, a basic faunistic survey of mammals can still bring interesting results stressing the need to study biota in small and poorly known areas.