The genus Gerbillus represents a striking example of successful Pleistocene radiation among rodents, resulting in nearly 50 currently recognised species distributed across Asia (from the Middle East to northwestern India) and Africa (the Saharo-Sahelian region and eastern Africa). Over the past two decades, multiple molecular phylogenetic studies have helped elucidate the complex subgeneric structure of this speciose group. Here, by incorporating into a genetic analysis of mitochondrial and nuclear markers and using samples collected in Somaliland, Ethiopia, Kenya and Tanzania, together with available GenBank sequences of other Gerbillus species we provide, for the first time, genetic data for Microdillus peeli (a taxon whose phylogenetic position has remained unresolved for over a hundred years) and unequivocally demonstrate that it represents an internal lineage within Gerbillus. In addition, we characterise a novel lineage within the genus and attempt to decipher its phylogeographic structure. However, having failed to discriminate between genetically defined lineages using geometric morphometrics and owing to the lack of genetic data for several critically important specimens, we do not undertake a taxonomic revision or describe new taxa within the scope of the present study.

Cryptic diversity - the presence of genetically distinct but morphologically similar taxa - is a key feature of the genus Mastomys, widespread across sub-Saharan Africa. In Ethiopia, three such species are found in sympatry. In this study, geometric morphometrics was applied to 130 genetically identified specimens (skulls). Significant interspecific shape differences were detected, while centroid size largely overlapped. A high level of intraspecific variation was also observed, likely reflecting ecological flexibility and seasonal generation trends. These results suggest that morphological divergence can remain limited in genetically isolated lineages, highlighting the role of cryptic speciation as an important evolutionary process in generalist rodent taxa.

Mitochondria provide most of energy in animal cells through oxidative phosphorylation; therefore, the evaluation of selective pressures on the mitochondrial genome can yield valuable insights into evolution of adaptations to different energy requirements within unique environments. The distribution of East African shrews is directly related to an altitudinal gradient, implying their high level of adaptive divergence and making them a unique model for revealing molecular mechanisms of the adaptation. Here we analysed signs of adaptive evolution in 17 mitogenomes of endemic Ethiopian white-toothed shrews (three ecotypes of Crocidura glassi s.l.) that replace each other in adjacent altitudinal belts of the Bale Massif, possibly indicating large adaptive divergence. To test this hypothesis, we used a combination of different methods besides classic tests of selection; we also analysed physicochemical changes of amino acid properties in protein-coding genes. None of the analyses yielded significant results on positive selection. We can theorize that purifying selection might have been a common selection pattern for mitochondrial genes in C. glassi s.l. ecotypes. Finally, different environmental adaptations – reflecting organisms’ various strategies and possibly important in white-toothed shrews – are discussed.

Naked mole-rats (Heterocephalus glaber) are a species of rodent endemic to the Horn of Africa, notable among mammals for their long lifespans, resistance to a variety of stresses, and eusocial mating behavior. Although their natural range extends across large portions of Kenya, Ethiopia, Somalia, and Djibouti, the large majority of genetic and genomic analyses focus on Kenyan specimens. Here, we constructed a chromosome-scale reference genome assembly for H. glaber, along with new reference assemblies of both the Damaraland mole-rat (Fukomys damarensis) and guinea pig (Cavia porcellus) genomes to aid annotation. We leveraged our H. glaber assembly, along with modern whole-genome sequencing, to characterize the genetic diversity of specimens derived from Kenya, southern Ethiopia, and eastern Ethiopia. We found the Kenyan and southern Ethiopian specimens to be closely related to each other and highly diverged from eastern Ethiopian specimens. We also found specimens collected from nearby locations in southern Ethiopia to be more closely related to Kenyan specimens than to each other. This unexpected distribution of shared genetic diversity highlights the importance of local migration barriers to gene flow in wild H. glaber populations.

The biodiversity of the Ethiopian Highlands features a significant level of endemism. Among its diverse fauna, the genus Crocidura (Soricidae), with many cryptic species, remains poorly documented, particularly for species of minute size. This study describes a newly discovered minute shrew-one of the smallest mammals worldwide-and addresses the taxonomy of the so-called 'Afromontane clade' of Crocidura in Ethiopia. We combined extensive field sampling of recent and historical specimens with advanced genetic analyses (genome skimming, Illumina sequencing, and cytb phylogenetics) and morphological examination (external and craniodental) to delineate the new species and address taxonomic affinities among other minute Crocidura from Ethiopia. One of our newly collected forms represents a distinct genetic lineage, corresponding with unique physical characteristics such as tail length and cranial features. Its discovery highlights the rich, yet still incompletely understood, mammalian diversity in the Ethiopian Highlands and underscores the importance of integrating morphological and molecular data in taxonomic studies.

The influence of habitat heterogeneity and rainfall on small mammal diversity and reproduction was studied in Chimit Kola. Data were collected using a grid and line trapping design in six representative habitats. Species identification and data analysis were performed using molecular techniques and R programming software. A total of 11 species were captured with an overall trap success of 25.6%. Mastomys awashensis was the most abundant, followed by Acomys louisae, and the least was Crocidura parvipes. Species richness and diversity were the highest in the riverine forest and the least in the fallowland habitats. The riverine forest had the highest abundance, followed by grassland and the least was in the forest. The abundance and reproductive activities of most small mammals were significantly higher during the wet season than during the dry season. Pregnancy was biased towards the right uterine horn compared to the left. The diversity and reproduction of small mammals are influenced by habitat productivity, which in turn is associated with seasonal rainfall, reflecting the significance of habitat heterogeneity and seasonal resource availability for the conservation of species.

Complete mitochondrial genomes of the Ethiopian endemic shrew Crocidura yaldeni s.l. were assembled for the first time. We provide data concerning the sequencing, assembly, and annotation of the obtained mitochondrial genomes. The phylogenetic analysis revealed the existence of several lineages within C. yaldeni s.l. that was consistent with the previous studies based on mitochondrial gene cytochrome b. These data provide a basis for further studies on phylogeny and mechanisms of the presumable mitochondrial DNA introgression of this group.

The naked mole-rat Heterocephalus, a hairless, subterranean rodent from the Horn of Africa, has attracted scientific interest due to its cooperative breeding, poikilothermy, longevity, resistance to cancer, and tolerance to pain and hypoxia, among others. Genomic analyses of H. glaber, traditionally considered a single species, reveal three highly divergent lineages. One of these, identified as H. phillipsi Thomas 1885, shows deep genetic divergence ( 4.1 Ma) and distinct morphology, notably reduced third molars, warranting recognition as a distinct species. The remaining two lineages, previously designated as the subspecies H. g. glaber Rüppell 1842 and H. g. ansorgei Thomas 1903, diverged around 2.3 Ma and their morphological differentiation is less pronounced. Each of the lineages occupies distinct environmental conditions, with H. phillipsi inhabiting extremely harsh habitats. The finding of an unexpected diversity within this key biomedical model opens new avenues across various fields of research. Genomic and morphological data reveal that the naked mole-rat comprises three deeply diverged lineages, including the revalidated species Heterocephalus phillipsi, reshaping our understanding of its evolution and biomedical potential.

Environmental conditions modulate the energy regimes of organisms, which affects their energetic mitochondrial functions. New regimes may reinforce adaptive increased ATP production, such as in high-elevation mammals, to offset their elevated thermoregulatory costs, increased erythropoiesis, or enlarged lung capacity. ATP production can be increased by higher densities of mitochondria in cells. This study investigated factors affecting inter-and intraspecific variation in the copy number of mtDNA in seven rodent species (genera Stenocephalemys and Lophuromys) from two regions of the Ethiopian Highlands. Quantitative PCR was used to assess the relative quantity of mtDNA (RQ) in liver and muscle tissues (n = 81 specimens). Overall, liver and thigh muscle tissue differed in the amount of mtDNA in a species-, genus-and area-specific manner. All species from the Choqa region had higher RQ in the liver than in the muscle. In contrast, two high-elevation specialists in the Guassa region had a higher number of mitochondria in muscle than in the liver, corresponding to other studies on rodents. In addition, the genus Lophuromys had an overall higher copy number of mtDNA than Stenocephalemys, and the tissue-specific relationship was altitude-dependent, with an absence of difference at high altitudes. This study provides the first data on the mtDNA copy number of Ethiopian rodents and demonstrates the complex relationship of mitochondrial quantity with species, life history, and area of origin.

The genus Gerbillus represents an example of the successful Pleistocene radiation among rodents, leading to the emergence of almost 50 currently recognized species inhabiting Asia (from the Middle East to northwest India) and Africa (the Saharo-Sahelian region and eastern Africa). During the last two decades, multiple molecular phylogenetic studies helped to decipher the complex subgeneric structure of this speciose group. However, questions concerning the number of phylogenetic lineages (species) within the genus and their evolutionary relationships remained open, especially because of the lack of genetic material from the Horn of Africa. Here we provide for the first time genetic information on Microdillus peeli (being for more than a hundred years a taxon with an unresolved phylogenetic position) and unequivocally show that it is an internal lineage of Gerbillus. Together with one additional newly characterized lineage of apparently subgenus rank (proposed here as subgenus 'Pusillus'), endemic to Somali-Masai region in eastern Africa, these findings document that the Horn of Africa is the center of evolutionary diversity of gerbils in general, and of the genus Gerbillus in particular. ### Competing Interest Statement The authors have declared no competing interest. Czech Science Foundation, 23-06116S

The Ethiopian highlands represent a wide spectrum of ecological gradients that provide suitable conditions for gradient speciation. Previous studies support the gradient model of speciation for two Ethiopian shrew species: Crocidura thalia and C. glassi. Here, we aimed to elucidate for the first time the phylogenetic position of C. afeworkbekelei and to test the gradient model of speciation for these three species. On the basis of a dataset collected from the whole south slope of the Bale Mountains, we reconstructed phylogenetic relationships among these species using mitochondrial and nuclear markers. Additionally, we examined shape and size differentiation of the skull and mandible. The molecular data revealed a similarity of the three species with lack of reciprocal monophyly among them. We demonstrated differences both in size and shape of the skull and mandible between low- and high-elevation forms albeit without a significant morphological hiatus. We identified the most changeable parts of the skull and mandible, which imply adaptive shifts in diet. We revealed the distribution, phylogenetic and morphological patterns that match predictions of the gradient model of speciation for three mammalian forms. Our data suggest intense processes of adaptation to the markedly different habitats along the considerable altitudinal gradient that fit the first stage of the gradient model of speciation. We believe that C. afeworkbekelei and C. thalia should be regarded as different ecotypes, and these species names must be reduced to junior synonyms of C. glassi.

Thicket rats of the genus Grammomys are partly arboreal rodents distributed across a large part of sub-Saharan Africa. Previous work showed that their highest diversity is in forests and woodlands of Eastern Africa, that the evolutionary history of the genus roughly mirrors the evolution of African forests, and that the currently delimited species (names) do not correspond to major genetic clades. We used thousands of single nucleotide polymorphisms to perform phylogenomic analysis and to delimit genomic pools (i.e. candidate biological species). The resulting molecular operational taxonomic units were then compared with the most comprehensive sets of other available data (mitochondrial DNA variability, ecological requirements, morphology, karyotypes, sequences from the type material, etc.) and used for an integrative solution to the taxonomy of the genus. Our revision delimited seven species, which is less than the 12 recognized in the most recent literature on African rodents. We conclude that the African thicket rats represent a classic example of challenging problems in current integrative taxonomy. It is now relatively easy to obtain genomic data and to delimit candidate species, but it is much more complicated to give them species names using the valid rules of zoological nomenclature.

There is increasing evidence that the Ethiopian highlands have functioned as a long-term refugium for many montane taxa. They also served as a source of colonization for other mountain blocks in eastern Africa during warm and humid Plio-Pleistocene episodes. The climbing mice (Dendromus) are widely distributed in grassy habitats across most African mountain regions, making them a suitable model to investigate how climate and topography have impacted the evolution of diversity in the Eastern Afromontane Biodiversity Hotspot. A recent phylogenetic study based mostly on mitochondrial DNA sequences identified a monophyletic Dendromus clade that grouped all known Ethiopian taxa plus two lineages outside Ethiopia. However, the species limits in this group, phylogenetic relationships, and biogeography remained unresolved. Here, we analyse the genomic variability at thousands of double-digest restriction-site-associated DNA (ddRAD) loci, sequences of the mitochondrial gene for cytochrome b, and morphological data from all major phylogenetic lineages in this clade, sampled from across their known distribution ranges, with an aim to delimit species and assess their distribution and evolutionary history. Both nuclear and mitochondrial phylogenies provide congruent results, i.e. the presence of seven well-supported major lineages (putative species), which are morphologically and ecologically distinguishable. We also provide a taxonomic revision (including sequencing of the mitogenome of the holotype of D. mystacalis) that resulted in the re-description of D. mystacalis, the description of two new species, and the resurrection of one species from synonymy. The most likely evolutionary scenario included a radiation in the Ethiopian highlands, followed by an “out-of-Ethiopia” dispersal event of a montane lineage, leading to the colonization of Imatong Mts. and Mt. Kilimanjaro.

Modern biomedical research is characterised by a need for new animal models1 and particularly those from unique or challenging environments and with peculiar characteristics seems to be the most promising2,3. Among mammals, the naked mole-rat Heterocephalus glaber from the Horn of Africa is one of such candidates. Although this small hairless exclusively subterranean rodent has attracted the attention of the scientific community for decades, mainly due to its poikilothermy and eusociality, the exponential trajectory of research started in 21st century with discoveries of its longevity, resistance to cancer and tolerance to pain and hypoxia, in addition to many other intriguing phenomena4–6. The genus Heterocephalus has traditionally been considered to include only a single species, but surprisingly, little is known about genetic differences among its natural populations. Here, we report from mitochondrial and nuclear genomic data across its distributional range, the existence of three species of naked mole-rat, namely: H. glaber, H. ansorgei, and H. philipsi. Among them, H. philipsi stands out as being the most distinct. Its divergence from the rest is 4.1 Ma before the present making it considerably older than most recent mammalian species, cf.7. The existence of three species that inhabit different environmental conditions, and especially the occurrence of H. philipsi in extremely harsh areas, opens up new horizons for the use of this model in biomedical and other fields of research.

This paper records new locality data for six species of ectoparasitic mites and ticks from bats in Ethiopia – Spinturnix scotophili, Spinturnix faini, Spinturnix semilunaris, Chelanyssus aethiopicus, Ixodes simplex, Carios vespertilionis. Five new host-parasite associations are recorded – Spinturnix scotophili on Myotis bocagei; Spinturnix faini on Miniopterus cf. arenarius; Spinturnix semilunaris on Miniopterus arenarius; Ixodes simplex on Rhinolophus landeri; Carios vespertilionis on Mops midas.

Hepatitis E virus (HEY; family Hepeviridae) infections cause >40,000 human deaths annually. Zoonotic infections predominantly originate from ungulates and occasionally from rats, highlighting the zoonotic potential of rodent- associated hepeviruses. We conducted host genomic data mining and uncovered two genetically divergent rodent- associated hepeviruses, and two bat- associated hepeviruses genetically related to known bat- associated strains. We thus analyzed 2,565 liver specimens from 108 rodent and shrew species sampled from globally understudied regions and hosts in Africa, Asia, and Latin America during 2011- 2018 for hepeviruses by RT-PCR. We detected 63 positive field samples (2.5%, 95% CI 1.9- 3.1) from 14 animal species, including two coinfections with genetically divergent strains and significant variation (X-2, P < 0.001) in detection rates between study sites. Strain- specific qRT-PCR assays showed virus concentrations between 9.2 x 10(2) and 3.2 x 10(9) copies/g. We recovered 24 near- complete hepeviral genomes from rodents, shrews, and bats, all showing three partially overlapping open reading frames (ORFs), some including putative late domains that may be associated with quasi- envelopment. Rodent- derived hepeviruses grouped into five clades clustering in basal sister relationship to human- (31 to 84% distance in translated ORF1-3) and rat- associated HEY. Parsimony- based analyses and cophylogenetic reconciliations revealed that rodents were predominant sources of hepeviral cross- order host shifts. Bayesian ancestral state reconstructions substantiated a direct origin of human- associated HEY in ungulates such as swine and camelids (posterior probability 0.8), whereas the nonrecent evolutionary origins of human- and ungulate- associated HEYwere projected to rodent hosts (posterior probability > 0.9). Our results elucidate the genealogy of human HEY and warrant increased surveillance and experimental risk assessments for rodent- associated hepeviruses.

Patterns of introgression of several genetic markers across the hybrid zone between allied species of the common vole Microtus arvalis s. str. и M. obscurus were studied in four its sections: in northwest Nizhny Novgorod region, east Vladimir and southwest of Nizhny Novgorod regions, south Lipetsk region, and northwest Voronezh region. Analysis of the clinal variability for three molecular-genetic markers (cytb, tp53, SMCY11) and for karyotypes showed a structural similarity between the “Vladimir – Nizhny Novgorod”, “Nizhny Novgorod”, and “Voronezh” sections. The maximal width was shown for the cytb cline, the minimal width – for the SMCY11 cline; the tp53 cline and chromosomal cline occupy intermediate position for this parameter. Furthermore, in these transects the centre of the cline for the cytb is shifted southeastward (into the distribution range of M. obscurus) from the centres of three other clines. The revealed asymmetric introgression of mitochondrial genome from M. arvalis to M. obscurus may be explained by the fact that the hybrid zone was formed as a result of invasion of M. obscurus into the range of M. arvalis. The “Lipetsk” transect differs from three above-mentioned transects by very narrow clines with nearly coinciding centres. Such characteristics of the “Lipetsk” transect are obviously caused by localization of the hybrid zone in this section along river Voronezh. The obtained results led us to suppose that the structure of the studied hybrid zone is determined mainly by coinciding (or non-coinciding) of its centre with local physical barriers.

The article provides a brief overview of the main results of studies on mammals in Ethiopia performed by the Joint Ethio-Russian Biological Expedition. The mammals of the country represent a suitable model for studying the processes of evolution and speciation in the mountainous tropics, as well as ways to adapt to the conditions of the highlands. The results obtained are of particular importance for the development of a number of areas of evolutionary biology, as well as nature conservation and medical biology: exploring mechanisms for the emergence of high biodiversity and endemism; empirical verification of alternative speciation hypotheses; assessment of the role of introgressive hybridization in evolution; study of coevolution of functionally related mitochondrial and nuclear genes. Using the example of the Ethiopian Highlands, the prospects for further studies of the processes of conjugate evolution of small mammals and their specific arena- and hantaviruses in conditions of long-term isolation are demonstrated.

Aim:The Eastern Afromontane Biodiversity Hotspot (EABH) offers an ideal location to investigate the evolutionary mechanisms producing a high level of endemic biodiversity. We tested the hypothesis that the cradle of Eastern Afromontane diversity is in the largest sub-region of the EABH montane archipelago, that is the Ethiopian Highlands. Further, we expected that climate oscillations followed by elevational shifts in montane habitats facilitated the dispersal of small mammal populations across unsuitable arid lowlands. Location:Mountains and highlands of East Africa. Taxon:Shrews of the genus Crocidura (Eastern Afromontane phylogenetic clade). Methods:We collected comprehensive genetic data from 511 (mitochondrial gene for cytochrome b) and 147 (double digest Restriction-Associated DNA sequencing) samples of Crocidura shrews across the EABH. We estimated phylogenetic relationships with Bayesian and Maximum Likelihood approaches. Population genetic analyses were performed in STRUCTURE to evaluate the internal structure of species outside Ethiopia. Ancestral area and dispersal routes were analysed by the BioGeoBears package. Results:Six major phylogenomic clades were delimited based on concatenated nuclear loci. The mitochondrial phylogeny roughly matches nuclear phylogenies, but with poorer resolution. Five of the six revealed clades are restricted to the Ethiopian Highlands, which is unambiguously the cradle of the diversity of this group of mammals (also confirmed by the biogeographic analysis). All non-Ethiopian and a single Ethiopian species fall into the sixth clade with poorly resolved internal relationships. Detailed population genetic analysis of SNP data revealed a pronounced structure with multiple gene pools in this clade; however, this structure only partly corresponds with the current taxonomy. Main Conclusions:Eastern Afromontane Crocidura shrews originated in the Ethiopian Highlands. They radiated there, and through a single southward dispersal event across the Turkana depression, they colonised the rest of the EABH in response to diverse geomorphology and climatic changes during the Plio-Pleistocene.

The chigger mites of Ethiopia were investigated based on materials collected in the field and museum depositories of alcohol-fixed mammals. Previously, only two chigger species were known from the country. In total, we collected 21 chigger species, mainly from rodents, occasionally insectivores, and one bat, from nine localities, and raised the number of trombiculids known from Ethiopia to 22. Three new species were described: Gahrliepia bochkovi sp. n. from a high-mountain locality of the Arsi Mountains National Park, Schoutedenichia borenensis sp. n. from Borena National Park, and Microtrombicula abaturovi sp. n. from Lake Koka located in the Great Rift Valley. Seventeen species were recorded in Ethiopia for the first time; four of them were for the first time recorded on the African continent - Leptotrombidium paradux Vercammen-Grandjean and Langston, 1976, Schoutedenichia asirensis Stekolnikov, Al-Ghamdi, Alagaili and Makepeace, 2019, S. originalis Kudryashova, 1976, and Microtrombicula saperoi (Radford, 1954).http://www.zoobank.org/urn:lsid:zoobank.org:pub:D79DC5A0-8340-4CC2-B9FD-F16A7CC38FE2