Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent

Due to their limited dispersal ability, fossorial species with predominantly belowground activity usually show increased levels of population subdivision across relatively small spatial scales. This may be exacerbated in harsh mountain ecosystems, where landscape geomorphology limits species' dispersal ability and leads to small effective population sizes, making species relatively vulnerable to environmental change. To better understand the environmental drivers of species' population subdivision in remote mountain ecosystems, particularly in understudied high-elevation systems in Africa, we studied the giant root-rat (Tachyoryctes macrocephalus), a fossorial rodent confined to the afro-alpine ecosystem of the Bale Mountains in Ethiopia. Using mitochondrial and low-coverage nuclear genomes, we investigated 77 giant root-rat individuals sampled from nine localities across its entire ~1000 km2 range. Our data revealed a distinct division into a northern and southern group, with no signs of gene flow, and higher nuclear genetic diversity in the south. Landscape genetic analyses of the mitochondrial and nuclear genomes indicated that population subdivision was driven by slope and elevation differences of up to 500 m across escarpments separating the north and south, potentially reinforced by glaciation of the south during the Late Pleistocene (~42,000-16,000 years ago). Despite this landscape-scale subdivision between the north and south, weak geographic structuring of sampling localities within regions indicated gene flow across distances of at least 16 km at the local scale, suggesting high, aboveground mobility for relatively long distances. Our study highlights that despite the potential for local-scale gene flow in fossorial species, topographic barriers can result in pronounced genetic subdivision. These factors can reduce genetic variability, which should be considered when developing conservation strategies.

Mammalian maxilloturbinal evolution does not reflect thermal biology

The evolution of endothermy in vertebrates is a major research topic in recent decades that has been tackled by a myriad of research disciplines including paleontology, anatomy, physiology, evolutionary and developmental biology. The ability of most mammals to maintain a relatively constant and high body temperature is considered a key adaptation, enabling them to successfully colonize new habitats and harsh environments. It has been proposed that in mammals the anterior nasal cavity, which houses the maxilloturbinal, plays a pivotal role in body temperature maintenance, via a bony system supporting an epithelium involved in heat and moisture conservation. The presence and the relative size of the maxilloturbinal has been proposed to reflect the endothermic conditions and basal metabolic rate in extinct vertebrates. We show that there is no evidence to relate the origin of endothermy and the development of some turbinal bones by using a comprehensive dataset of µCT-derived maxilloturbinals spanning most mammalian orders. Indeed, we demonstrate that neither corrected basal metabolic rate nor body temperature significantly correlate with the relative surface area of the maxilloturbinal. Instead, we identify important variations in the relative surface area, morpho-anatomy, and complexity of the maxilloturbinal across the mammalian phylogeny and species ecology.

Thermal biology in the Upper Galili Mountain blind mole rat (Nannospalax galili) and an overview of spalacine energetics

Several hundred mammalian species thrive in complex burrow systems, which protect them from climatic extremes and predation. At the same time, it is also a stressful environment due to low food supply, high humidity, and, in some cases, a hypoxic and hypercapnic atmosphere. To face such conditions, subterranean rodents have convergently evolved low basal metabolic rate, high minimal thermal conductance and low body temperature. Although these parameters have been intensively studied in the last decades, such information is far from being well-known in one of the most studied groups of subterranean rodents, the blind mole rats of the genus Nannospalax. The lack of information is particularly noticeable for parameters such as the upper critical temperature and the width of the thermoneutral zone. In our study, we analysed the energetics of the Upper Galilee Mountain blind mole rat Nannospalax galili and found its basal metabolic rate of 0.84 ± 0.10 mL O₂×g^-1 × h^-1, thermoneutral zone between 28 and 35 °C, mean T_b within the zone of 36.3 ± 0.6 °C, and minimal thermal conductance equal to 0.082 mL O₂×g^-1 × h^-1 × C^-1. Nannospalax galili is a truly homeothermic rodent well adapted to face lower ambient temperatures, because its T_b was stable down to the lowest temperature measured (10 °C). At the same time, a relatively high basal metabolic rate and relatively low minimal thermal conductance for a subterranean rodent of such body mass, and the difficulty of surviving ambient temperatures slightly above upper critical temperature, indicates problems with sufficient heat dissipation at higher temperatures. This can easily lead to overheating, that is relevant mainly during the hot-dry season. These findings suggest that N. galili can be threatened by ongoing global climate change.

The biology of an isolated Mashona mole-rat population from southern Malawi, with implications for the diversity and biogeography of the genus Fukomys

The Mashona mole-rat, Fukomys darlingi (Thomas, 1895), is a little studied social African mole-rat (Bathyergidae) from south-astern Africa. Here, we present an integrative study characterizing the genetic diversity of populations assigned to F. darlingi with special focus on animals from Nsanje, southern Malawi. These mole-rats show pronounced differences in body mass and general appearance compared to nominate F. darlingi from Zimbabwe and Mozambique, but their taxonomic status has so far remained unclear. A genetic analysis encompassing all major lineages of the genus Fukomys suggests that this population indeed represents a deeply nested lineage within the F. darlingi clade. The karyotype of the Nsanje mole-rats also corresponds to that of the nominate form, being 2n = 54. While both nuclear and mitochondrial data agree about the assignment of the Nsanje mole-rats to F. darlingi, our analyses revealed substantial mitonuclear discordance for other branches within the Fukomys phylogenetic tree. Nsanje mole-rats are significantly larger than nominate F. darlingi and their ontogeny and reproduction closely resemble similar-sized congeneric species rather than the nominate population. The somatic growth of the Nsanje form is the slowest of all African mole-rats. The maximum life span of F. darlingi is at least 19 years. The observed differences between nominate F. darlingi and mole-rats from Nsanje may be attributed mainly to their different body mass. Our study highlights the advantages of an integrative approach for understanding the diversity of African mole-rats and emphasizes the great intraspecific variability that may be encountered in these underground-dwelling rodents.

Longevity of a solitary mole-rat species and its implications for the assumed link between sociality and longevity in African mole-rats (Bathyergidae)

Sociality and cooperative breeding are associated with enhanced longevity in insects and birds, but whether this is also true for mammals is still subject to debate. African mole-rats (Bathyergidae) have recently been claimed to be the only mammalian family in which such an association may exist because cooperatively breeding bathyergids seem to be substantially longer lived than solitary bathyergids. However, although ample longevity data are available for several social bathyergids, almost nothing is known about mortality distribution and lifespan in solitary bathyergids. Here we present robust long-term data on the longevity of a solitary African mole-rat, the silvery mole-rat Heliophobius argenteocinereus. Our findings show that this species is much longer-lived than previously believed. Nonetheless, our comparative analysis suggests that sociality has indeed a positive effect on longevity in this family. We argue that the extreme longevity seen particularly in social bathyergids is probably caused by a combination of subterranean lifestyle and cooperative breeding.

Functional anatomy and disparity of the postcranial skeleton of African mole-rats (Bathyergidae)

The burrowing adaptations of the appendicular system of African mole-rats (Bathyergidae) have been comparatively less investigated than their cranial adaptations. Because bathyergids exhibit different digging modes (scratch-digging and chisel-tooth digging) and social systems (from solitary to highly social), they are a unique group to assess the effects of distinct biomechanical regimes and social organization on morphology. We investigated the morphological diversity and intraspecific variation of the appendicular system of a large dataset of mole-rats (n = 244) including seven species and all six bathyergid genera. Seventeen morpho-functional indices from stylopodial (femur, humerus) and zeugopodial (ulna, tibia-fibula) elements were analyzed with multivariate analysis. We hypothesized that scratch-diggers (i.e., Bathyergus) would exhibit a more specialized skeletal phenotype favoring powerful forelimb digging as compared to the chisel-tooth diggers, and that among chisel-tooth diggers, the social taxa will exhibit decreased limb bone specializations as compared to solitary taxa due to colony members sharing the costs of digging. Our results show that most bathyergids have highly specialized fossorial traits, although such specializations were not more developed in Bathyergus (or solitary species), as predicted. Most chisel tooth-diggers are equally, or more specialized than scratch-diggers. Heterocephalus glaber contrasted significantly from other bathyergids, presenting a surprisingly less specialized fossorial morphology. Our data suggests that despite our expectations, chisel-tooth diggers have a suite of appendicular adaptations that have allowed them to maximize different aspects of burrowing, including shoulder and neck support for forward force production, transport and removal of soils out of the burrow, and bidirectional locomotion. It is probably that both postcranial and cranial adaptations in bathyergids have played an important role in the successful colonization of a wide range of habitats and soil conditions within their present distribution.

Fossorial adaptations in African mole-rats (Bathyergidae) and the unique appendicular phenotype of naked mole-rats

Life underground has constrained the evolution of subterranean mammals to maximize digging performance. However, the mechanisms modulating morphological change and development of fossorial adaptations in such taxa are still poorly known. We assessed the morpho-functional diversity and early postnatal development of fossorial adaptations (bone superstructures) in the appendicular system of the African mole-rats (Bathyergidae), a highly specialized subterranean rodent family. Although bathyergids can use claws or incisors for digging, all genera presented highly specialized bone superstructures associated with scratch-digging behavior. Surprisingly, Heterocephalus glaber differed substantially from other bathyergids, and from fossorial mammals by possessing a less specialized humerus, tibia and fibula. Our data suggest strong functional and developmental constraints driving the selection of limb specializations in most bathyergids, but more relaxed pressures acting on the limbs of H. glaber. A combination of historical, developmental and ecological factors in Heterocephalus are hypothesized to have played important roles in shaping its appendicular phenotype.

Morphological and developmental analyses demonstrated that the naked mole-rats are the least anatomically specialized bathyergid for scratch-digging. Developmental, ecological and historical factors may be involved in such peculiar phenotype

Biogeographical Importance of the Livingstone Mountains in Southern Tanzania: Comparative Genetic Structure of Small Non-volant Mammals

The Livingstone Mountains (LM; also known as the Kipengere Range) found in south-western Tanzania at the northern end of Lake Nyasa are an important region for understanding the biogeography of Eastern Africa. The two branches of the East African Rift Valley meet here and the mountains might represent stepping stones for colonization and migration between different parts of the Eastern Afromontane Biodiversity Hotspot (especially the link between the Eastern Arc Mountains, EAM, and the Southern Rift Mountains, SRM), as well as an efficient barrier to gene flow for taxa living in drier savannahs in lower elevations. Here we combine new mitochondrial sequence data from 610 recently sampled rodents and shrews with available georeferenced genetic data (3538 specimens) from southern Tanzania, northern Malawi/Zambia and northern Mozambique and compare the spatial genetic structure among different taxa. There is no universal phylogeographic pattern in taxa preferring humid montane habitats. For some of them, the Makambako Gap acts as a barrier between the SRM and the EAM, but other taxa can bridge this gap. Barriers within the EAM (frequently) and within the SRM (sometimes) appear more important. The Rukwa rift between the SRM and the ARM is an important barrier that perhaps can only be crossed by taxa that are not that strictly tied to humid montane environments. For mammals living in lower-elevation savannah-like habitats, the LM can act as a strict barrier to gene flow, and together with the Ufipa Plateau, Lake Nyasa and the EAM create a very similar phylogeographic pattern with three recognizable genetic groups in most savannah-dwellers. The Livingstone Mountains thus appear to be one of the most important biogeographic crossroads in Eastern Africa.

Species limits and phylogeographic structure in two genera of solitary African mole-rats Georychus and Heliophobius

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.

Complete mitochondrial genome of the giant root-rat (Tachyoryctes macrocephalus)

The endangered giant root-rat (Tachyoryctes macrocephalus, also known as giant mole rat) is a fossorial rodent endemic to the afro-alpine grasslands of the Bale Mountains in Ethiopia. The species is an important ecosystem engineer with the majority of the global population found within 1000 km². Here, we present the first complete mitochondrial genome of the giant root-rat and the genus Tachyoryctes, recovered using shotgun sequencing and iterative mapping. A phylogenetic analysis including 15 other representatives of the family Spalacidae placed Tachyoryctes as sister genus to Rhizomys with high support. This position is in accordance with a recent study revealing the topology of the Spalacidae family. The full mitochondrial genome of the giant root-rat presents an important resource for further population genetic studies.

Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: First fully resolved phylogeny, evolutionary history and delimitation of extant genera

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.

Ear morphology in two root-rat species (genus Tachyoryctes) differing in the degree of fossoriality

It is supposed that the subterranean lifestyle in mammals is reflected in ear morphology and tuning of hearing to low frequencies. We studied two root-rat species to see if their ear morphology reflects the difference in the amount of their surface activity. Whereas the more subterranean Tachyoryctes splendens possesses shorter pinnae as expected, it has smaller bullae compared to the more epigeic Tachyoryctes macrocephalus. The ratio between the eardrum and the stapedial footplate area and the ratio between the mallear and the incudal lever were lower in T. splendens (19.3 ± 0.3 and 1.9 ± 0.0, respectively) than in T. macrocephalus (21.8 ± 0.6 and 2.1 ± 0.1), probably reflecting the latter's higher surface activity. The cochlea in both species has 3.5 coils, yet the basilar membrane is longer in the smaller T. splendens (13.0 ± 0.5 versus 11.4 ± 0.7 mm), which indicates its wider hearing range and/or higher sensitivity (to some frequencies). In both root-rat species, the highest density of outer hair cells (OHC) was in the apical part of the cochlea, while the highest density of inner hair cells (IHC) was in its middle part. This OHC density pattern corresponds with good low-frequency hearing, whereas the IHC pattern suggests sensitivity to higher frequencies.

Complex reticulate evolution of speckled brush-furred rats (Lophuromys) in the Ethiopian centre of endemism

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.

Molecular systematics and biogeographic history of the African climbing-mouse complex (Dendromus)

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.

Heat dissipation in subterranean rodents: the role of body region and social organisation

The relatively warm and very humid environment of burrows presents a challenge for thermoregulation of its mammalian inhabitants. It was found that African mole-rats dissipate body heat mainly through their venter, and social mole-rats dissipate more body heat compared to solitary species at lower temperatures. In addition, the pattern of the ventral surface temperature was suggested to be homogeneous in social mole-rats compared to a heterogeneous pattern in solitary mole-rats. To investigate this for subterranean rodents generally, we measured the surface temperatures of seven species with different degrees of sociality, phylogeny, and climate using infrared thermography. In all species, heat dissipation occurred mainly through the venter and the feet. Whereas the feet dissipated body heat at higher ambient temperatures and conserved it at lower ambient temperatures, the ventral surface temperature was relatively high in all temperatures indicating that heat dissipation to the environment through this body region is regulated mainly by behavioural means. Solitary species dissipated less heat through their dorsum than social species, and a tendency for this pattern was observed for the venter. The pattern of heterogeneity of surface temperature through the venter was not related to sociality of the various species. Our results demonstrate a general pattern of body heat exchange through the three studied body regions in subterranean rodents. Besides, isolated individuals of social species are less able to defend themselves against low ambient temperatures, which may handicap them if staying alone for a longer period, such as during and after dispersal events.

Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini)

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.

Are southern African solitary mole-rats homeothermic or heterothermic under natural field conditions?

Abandoning of a stable body temperature (T_b), a phenomenon known as heterothermy, is an adaptation to cope mainly with a lack of food and water, especially in species inhabiting daily or seasonally variable environments. There is increasing evidence that African mammals avoid adverse conditions by heterothermy and eventually by entering torpor. Members of subterranean rodent family, the African mole-rats (Bathyergidae), are suitable candidates to study both phenomena, because of the diversity of their strategies in respect of maintaining stable T_b ranging from homeothermic species to a mammal with the most labile T_b, the naked mole-rat. Currently, there are field data on daily and seasonal T_b in one social species only and such information are lacking for any solitary mole-rat. In our study, we recorded yearly T_b in two solitary bathyergids, the Cape mole-rat Georychus capensis and the Cape dune mole-rat Bathyergus suillus from South Africa using intraperitoneally implanted dataloggers. Since this region is characterised by changing ecological characteristics, we expected either decreases of T_b within 24 h indicating daily torpor and/or longer-term decreases of T_b, which would indicate multiday torpor. Although we found seasonally phase shifted low amplitude daily T_b cycles, we did not find any remarkable and regular daily and/or seasonal T_b deviations, likely showing an absence of torpor in both species. Due to absence of this energy saving mechanism, we may speculate that both species could be vulnerable to ongoing global climatic change.

Multilocus phylogeny of African striped grass mice (Lemniscomys): Stripe pattern only partly reflects evolutionary relationships

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.

Gas composition and its daily changes within burrows and nests of an Afroalpine fossorial rodent, the giant root-rat Tachyoryctes macrocephalus

Fossorial mammals are supposed to face hypoxic and hypercapnic conditions, but such conditions have been rarely encountered in their natural burrow systems. Gas composition in burrows after heavy rains, deeper burrows and especially nest chambers, where animals usually spend most of the day, could be even more challenging than in shallow burrows. Such situations, however, have been rarely surveyed in the wild. In our study, we determined concentrations of O₂, CO₂ and CH₄ in active burrows and nests of the giant root-rat Tachyoryctes macrocephalus, a large fossorial rodent endemic to the Afroalpine zone of the Bale Mountains in Ethiopia. We were able to determine the precise location of nests by tracking individuals equipped with radio-collars. To the best of our knowledge, this is the first study that analyses air samples taken directly from the nests of actually occupied burrow systems in any free-living fossorial mammal. We found no evidence for environmental hypoxia in the examined burrows and nests (range 19.7-21.6% O₂). Concentrations of CO₂ in the burrows increased after the burrows were plugged in the evening, but did not reach physiologically problematic levels. The highest CO₂ concentrations in burrows were detected in the evening during a wet period (up to 0.44%). In root-rat nest chambers, the highest (but still harmless) CO₂ concentrations (up to 1.31%) were detected in the morning (measured in the late dry season only) together with an elevated concentration (up to 13.5ppm) of CH₄. Regular surface activity of giant root-rats, combined with the relatively large dimensions of their nest chambers and tunnels, and the absence of heavy soils, may contribute to harmless atmospheres within their burrow systems.

Functional histology of the skin in the subterranean African giant mole-rat: thermal windows are determined solely by pelage characteristics

Excavation of burrows is an extremely physically demanding activity producing a large amount of metabolic heat. Dissipation of its surplus is crucial to avoid the risk of overheating, but in subterranean mammals it is complicated due to the absence of notable body extremities and high humidity in their burrows. IR-thermography in a previous study on two species of African mole-rats revealed that body heat was dissipated mainly through the ventral body part, which is notably less furred. Here, we analyzed the dorsal and ventral skin morphology, to test if dermal characteristics could contribute to higher heat dissipation through the ventral body part. The thickness of the epidermis and dermis and the presence, extent and connectivity of fat tissue in the dermis were examined using routine histological methods, while vascular density was evaluated using fluorescent dye and confocal microscopy in the giant mole-rat Fukomys mechowii. As in other hitherto studied subterranean mammals, no subcutaneous adipose tissue was found. All examined skin characteristics were very similar for both dorsal and ventral regions: relative content of adipose tissue in the dermis (14.4 ± 3.7% dorsally and 11.0 ± 4.0% ventrally), connectivity of dermal fat (98.5 ± 2.8% and 95.5 ± 6.8%), vascular density (26.5 ± 3.3% and 22.7 ± 2.3%). Absence of large differences in measured characteristics between particular body regions indicates that the thermal windows are determined mainly by the pelage characteristics.

Burrowing below ground: interaction between soil mechanics and evolution of subterranean mammals

The evolution of species is governed by complex phenomena in which biological and environmental features may interact dynamically. Subterranean mammals dig tunnels whose diameter minimizes energetic costs during excavations and display anatomical adaptations in order to burrow structurally stable tunnels according to specific features of the soil. These animals weight from less than 50 g up to 1-2 kg, and dig tunnels with diameters from 3 to 15 cm. The use of allometric laws has enabled these data to be correlated. However, since tunnels need to be stable with respect to the geomechanical characteristics of the resident soils, a mathematical treatment linking the admissible dimensions of tunnels to the environment here suggests a mechanically grounded correlation between the body mass of subterranean mammals and the maximum dimensions of tunnels. Remarkably, such theoretical findings reflect very well the empirical allometric relationship and contribute to explain the wide differences observed in body sizes of subterranean mammals. In this respect, a far from ancillary role of environmental mechanics on the morphological evolution of subterranean mammals can be hypothesized.

Multiple radiations of spiny mice (Rodentia: Acomys) in dry open habitats of Afro-Arabia: evidence from a multi-locus phylogeny

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.

Biogeographic implications of small mammals from Northern Highlands in Tanzania with first data from the volcanic Mount Kitumbeine

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 asLophuromys makundiand probablyOtomys 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. montisandLophuromys 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.

Phylogeography of a widespread sub-Saharan murid rodent Aethomys chrysophilus: the role of geographic barriers and paleoclimate in the Zambezian bioregion

Murid rodents of the genus Aethomys are one of the most common rodents in drier habitats in sub-Saharan Africa. Among them, the red veld rat Aethomys chrysophilus is the most widespread species with the core distribution located in the Zambezian bioregion. In this study, we describe phylogeographic structure of the species and estimate its age from a time-calibrated phylogeny of the genus. Seven parapatric clades were identified in the mitochondrial cytochrome b phylogeny, where some of the distributions of these clades have been separated by previously described biogeographical divides (Zambezi-Kafue river system, Rukwa Rift and the Eastern Arc Mountains). One internal clade corresponded to populations previously described as a distinct species, Aethomys ineptus. The whole A. chrysophilus complex was estimated to be 1.3 (0.5–2.4) Mya old, with A. ineptus originating 0.7 (0.1–1.4) Mya before present. The internal position of A. ineptus was also recovered in phylogenetic reconstruction based on two nuclear genes and thus it is not a consequence of mitochondrial introgression. In addition, we analyzed skull form variation across the species’ distributional range and found no significant difference between A. ineptus and the rest of A. chrysophilus complex.