Non-volant small mammals in Afrotropical regions are a species-rich group of vertebrates, yet their diversity, distribution, and community structure remain insufficiently analysed. Here, we examined them at four locations in Afromontane tropical rainforests in Rwanda across two seasons, with a primary focus on Nyungwe National Park (NNP), comprising Nyungwe and Cyamudongo forests. Using standardised live-trapping and DNA analysis, applied systematically for the first time in this region, we documented 25 species, including 22 rodents, two shrews, and one golden mole. We confirmed most of the species previously recorded in NNP, but sequencing of the mitochondrial cytb gene and comparison with specimens from across Africa revealed one new species record, Lophuromys cinereus, for NNP and the country. The most abundant species were in the genera Praomys, Hybomys, Lophuromys, and Hylomyscus. Our study provides preliminary insights into the effects of season and patch size on non-volant small mammals in NNP: generally, seasonality did not show significant effects on community composition, whereas all species found in the small Cyamudongo fragment were also found in the main forest block of NNP. We highlight gaps worthy of further investigation, including clarification of the influence of biogeographic and ecological factors, e.g. altitudinal ranges, microhabitats, and edge effects, on non-volant small mammals. We also urge the inclusion of non-volant small mammals among target groups to understand the dynamics of Nyungwe ecosystems, demonstrate Afromontane diversity, and inform ecological monitoring and park management plans.

Unraveling how adaptive traits originate and evolve is key to understanding the mechanisms shaping species' diversity and their adaptive potential. Seasonal color molts, from summer-brown to winter-white, evolved in at least 21 mammals and birds to maintain camouflage in environments with seasonal snow, but the occurrence of winter-brown morphs reflects seemingly convergent local adaptation to distinct snow conditions. In the least weasel (Mustela nivalis), alternative winter morphs map to the pigmentation gene MC1R, but the evolutionary history and functional basis of this variation remained unknown. Using in vitro cellular assays, we show that winter-brown coats are caused by a derived protein-coding amino acid substitution that reduces MC1R affinity to its ligands, ASIP and α-MSH. Using targeted enrichment and sequencing, we find that this mutation arose de novo within the species, around one million years ago, and was maintained across the geographically structured populations formed during its evolution in Europe. Using simulations, we show that genetic drift is unlikely to explain the long-term maintenance of this variant at intermediate frequencies, which can be driven by spatially varying selection, anchoring local adaptive responses. Our results underscore how long-standing adaptive variation can fuel recurrent adaptation to heterogeneous environments through time.

Koalas are arboreal herbivorous marsupials, endemic to Australia. During the late 1800s and early 1900s, the number of koalas declined dramatically due to hunting for their furs. In addition, anthropogenic activities have further decimated their available habitat, and decreased population numbers. Here, we utilize 37 historic and 25 modern genomes sampled from across their historic and present geographic range, to gain insights into how their population structure and genetic diversity have changed across time; assess the genetic consequences of the period of intense hunting, and the current genetic status of this iconic Australian species. Our analyses reveal how genome-wide heterozygosity has decreased through time and unveil previously uncharacterized mitochondrial haplotypes and nuclear genotypes in the historic dataset, which are absent from today's koala populations.

Dogs exhibit an exceptional range of morphological diversity as a result of their long-term association with humans. Attempts to identify when dog morphological variation began to expand have been constrained by the limited number of Pleistocene specimens, the fragmentary nature of remains, and difficulties in distinguishing early dogs from wolves on the basis of skeletal morphology. In this study, we used three-dimensional geometric morphometrics to analyze the size and shape of 643 canid crania spanning the past 50,000 years. Our analyses show that a distinctive dog morphology first appeared at about 11,000 calibrated years before present, and substantial phenotypic diversity already existed in early Holocene dogs. Thus, this variation emerged many millennia before the intense human-mediated selection shaping modern dog breeds beginning in the 19th century.

This study examines the postcanine enamel microstructures in three Eocene Sparnotheriodontidae taxa (Notiolofos arquinotiensis, Phoradiadius divortiensis, Sparnotheriodontidae indet.), comparing their schmelzmuster with other early-diverging South American Native Ungulates (SANUs) exhibiting vertical Hunter-Schreger bands (HSB). All three sparnotheriodontid taxa exhibit a highly derived schmelzmuster with three zones, inner and outer radial enamel and thick vertical HSB with broad transition zones. This latter trait differs from the narrow transition zones in most comparative taxa, except the lower molar of Astrapotherium. The Andean Phoradiadius divortiensis shares enamel features with the Antarctic Notiolofos arquinotiensis (acute-angled IPM in inner radial enamel and in HSB) and Sparnotheriodontidae indet. (enamel thickness, prism-parallel IPM in outer radial enamel). However, P. divortiensis uniquely shows low and steep prism inclination in the outer enamel. This acute-angled IPM, absent in comparative SANU taxa, further suggests Sparnotheriodontidae as an apomorphic branch within Litopterna, akin to specialised families in Perissodactyla. Comparisons with Astrapotheria, Carodnia vieirai (Xenungulata), Pyrotherium romeroi (Pyrotheria), and Didolodontidae (possible Litopterna) highlight the unique features of Sparnotheriodontidae, including exclusively vertical HSB combined with acute-angled IPM. Didolodontidae show plesiomorphic features such as no HSB or transverse HSB, and therefore occupy a basal evolutionary position. Pyrotherium and Carodnia exhibit divergent schmelzmuster traits, reinforcing the distinctiveness of Sparnotheriodontidae. Our findings suggest Sparnotheriodontidae represents one of the stratigraphically oldest SANU clades to develop schmelzmuster with exclusively vertical HSB, underscoring their unique evolutionary trajectory within the broader context of Litopterna.

This paper provides an upgrade of Hystrix parvae, which so far is the smallest and oldest extinct species of Hystrix s. str. The new data derive from the exceptionally rich new fossil collection of the locality Kohfidisch in Austria, that comprises more than 100 fossils. The detailed descriptions are supported by enamel microstructure analysis of incisors, and x-ray microcomputed images (microCT) of the partial skull, upper and lower jaws and teeth. The tooth pattern and sizes show wide ranges, depending on the ontogenetic stage, tooth position and stage of wear. The deciduous D4/d4 and the permanent lower p4-m3 are identified as low crowned or brachydont. The mean hypsodonty index of m1/2 is 69%. The permanent upper P4-M3 are brachydont to mesodont. The mean hypsodonty index of M1/2 is 114%. The karstic cave and fissure system of Kohfidisch provided an ideal nursery environment as evidenced by numerous deciduous teeth in different ontogenetic stages. The age of the fauna is Late Miocene (lower Turolian, MN11), around 8.6 million years.

Low genomic diversity is generally indicative of small population size and is considered detrimental by decreasing long-term adaptability.1,2,3,4,5,6 Moreover, small population size may promote gene flow with congeners and outbreeding depression.7,8,9,10,11,12,13 Here, we examine the connection between habitat availability, effective population size (Ne), and extinction by generating a 40× nuclear genome from the extinct blue antelope (Hippotragus leucophaeus). Historically endemic to the relatively small Cape Floristic Region in southernmost Africa,14,15 populations were thought to have expanded and contracted across glacial-interglacial cycles, tracking suitable habitat.16,17,18 However, we found long-term low Ne, unaffected by glacial cycles, suggesting persistence with low genomic diversity for many millennia prior to extinction in ∼AD 1800. A lack of inbreeding, alongside high levels of genetic purging, suggests adaptation to this long-term low Ne and that human impacts during the colonial era (e.g., hunting and landscape transformation), rather than longer-term ecological processes, were central to its extinction. Phylogenomic analyses uncovered gene flow between roan (H. equinus) and blue antelope, as well as between roan and sable antelope (H. niger), approximately at the time of divergence of blue and sable antelope (∼1.9 Ma). Finally, we identified the LYST and ASIP genes as candidates for the eponymous bluish pelt color of the blue antelope. Our results revise numerous aspects of our understanding of the interplay between genomic diversity and evolutionary history and provide the resources for uncovering the genetic basis of this extinct species’ unique traits.

The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.

Mazama simplicicornis argentina is the name that was given to describe a gray brocket collected by Lönberg in 1919 in the central Chaco region of Argentina. Subsequent authors, based on morphological similarities, considered this name to be a synonym for the species Subulo gouazoubira Fischer, 1814 from Paraguay. In the absence of genetic analyses to compare the Argentinian and Paraguayan gray brockets, we aimed to clarify the taxonomy of M. simplicicornis argentina through an integrative assessment using morphological, cytogenetical, and molecular data from its holotype and a current topotype. Qualitative skull features and cranio-morphometric results of M. simplicicornis argentina showed a great similarity with the S. gouazoubira neotype characters. The diploid chromosome number of M. simplicicornis argentina topotype corresponded with the karyotypical pattern of S. gouazoubira with 2n = 70 and FN = 70, showing a great similarity in all classic and molecular cytogenetic results and revealing the homologies between karyotypes. The phylogenetic analysis of mitochondrial genes used in this study (concatenated partial ND5 and Cytb gene) allocated the M. simplicicornis argentina specimens in the monophyletic clade of S. gouazoubira with a branch value of 100%. These results show that there is no discontinuity between the Argentinian and Paraguayan gray brockets. Therefore, the individuals originally described as M. simplicicornis argentina should be recognized as S. gouazoubira.

Examples of photoluminescence (PL) are being reported with increasing frequency in a wide range of organisms from diverse ecosystems. However, the chemical basis of this PL remains poorly defined, and our understanding of its potential ecological function is still superficial. Among mammals, recent analyses have identified free-base porphyrins as the compounds responsible for the reddish ultraviolet-induced photoluminescence (UV-PL) observed in the pelage of springhares and hedgehogs. However, the localization of the pigments within the hair largely remains to be determined. Here, we use photoluminescence multispectral imaging emission and excitation spectroscopy to detect, map, and characterize porphyrinic compounds in skin appendages in situ. We also document new cases of mammalian UV-PL caused by free-base porphyrins in distantly related species. Spatial distribution of the UV-PL is strongly suggestive of an endogenous origin of the porphyrinic compounds. We argue that reddish UV-PL is predominantly observed in crepuscular and nocturnal mammals because porphyrins are photodegradable. Consequently, this phenomenon may not have a specific function in intra- or interspecific communication but rather represents a byproduct of potentially widespread physiological processes.

Analyzing the δ2H values in individual amino acids of proteins extracted from vertebrates, we unexpectedly found in some samples, notably bone collagen from seals, more than twice as much deuterium in proline and hydroxyproline residues than in seawater. This corresponds to at least 4 times higher δ2H than in any previously reported biogenic sample. We ruled out diet as a plausible mechanism for such anomalous enrichment. This finding puts into question the old adage that "you are what you eat".

Microsatellite data for "Genetic variation between and within two populations of bat-eared foxes (Otocyon megalotis Desmarest, 1822) in South Africa" African Zoology doi:10.1080/15627020.2021.1942204

The lower incisor enamel microstructure of the fossil rodent family Eomyidae was believed to be three‐layered and highly derived but rather uniform throughout the clade. Here, we describe a new four‐layered schmelzmuster in Eomyidae consisting of a three‐fold portio interna with longitudinal oriented, uniserial Hunter‐Schreger bands and a one‐fold portio externa, accounting for a unique enamel microstructure character combination in Rodentia. This new schmelzmuster type has developed early in eomyid evolution and is detectable already in the late Eocene (Chadronian) of North America. In European eomyids, it first occurs in the early Miocene (MN 3), implying that this four‐layered schmelzmuster was not present in all members of the family but restricted to species included in Eomyini and some genera currently considered Eomyidae incertae sedis within Eomyidae. Additionally, our analysis recognizes three taxa with schmelzmuster divergent from all other eomyids. Incisor enamel microstructure does not advocate a close phylogenetic relationship of Eomyidae to either fossil or extant Heteromyidae and Geomyidae, nor to fossil Heliscomyidae and Florentiamyidae. Our results rather support the view that Eomyidae are placed outside Geomorpha.

The blue antelope ( Hippotragus leucophaeus ) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan ( H. equinus ) or sable ( H. niger ) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are unfavourable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4x mean coverage from a historical specimen (~200 years old) and one at 2.1x mean coverage from a fossil specimen dating to 9,800–9,300 cal BP, making it currently the oldest palaeogenome from Africa. Phylogenomics show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelopes, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely a decisive factor in the blue antelope’s extinction.

Native to southern Africa, the blue antelope ( Hippotragus leucophaeus ) is the only large African mammal species known to have become extinct in historical times. However, it was poorly documented prior to its extinction ~ 1800 AD, and many of the small number of museum specimens attributed to it are taxonomically contentious. This places limitations on our understanding of its morphology, ecology, and the mechanisms responsible for its demise. We retrieved genetic information from ten of the sixteen putative blue antelope museum specimens using both shotgun sequencing and mitochondrial genome target capture in an attempt to resolve the uncertainty surrounding the identification of these specimens. We found that only four of the ten investigated specimens, and not a single skull, represent the blue antelope. This indicates that the true number of historical museum specimens of the blue antelope is even smaller than previously thought, and therefore hardly any reference material is available for morphometric, comparative and genetic studies. Our study highlights how genetics can be used to identify rare species in natural history collections where other methods may fail or when records are scarce. Additionally, we present an improved mitochondrial reference genome for the blue antelope as well as one complete and two partial mitochondrial genomes. A first analysis of these mitochondrial genomes indicates low levels of maternal genetic diversity in the ‘museum population’, possibly confirming previous results that blue antelope population size was already low at the time of the European colonization of South Africa.

Information on genetic variation within and among populations is relevant for a broad range of topics in biology. We use a combination of mitochondrial and nuclear microsatellite markers to evaluate genetic variation within and between two populations of bat-eared foxes (Otocyon megalotis Desmarest, 1822) in South Africa. The bat-eared fox is a small canid occurring in southern and eastern Africa. The species is currently not threatened with extinction, but a lack of information on genetic diversity has been identified as a deficit for its future conservation. We observed low to moderate genetic differentiation between the two geographically separated populations, but neither mitochondrial nor nuclear microsatellite markers suggested that there have been dispersal barriers between them. Similar genetic diversity within both populations was contrasted by interpopulational differences in relatedness variation among males and females. A high genetic relatedness within both populations, indicated by mitochondrial data, is likely caused by a common historical origin or a combination of species-specific social organization and environmental dispersal constraints. We call for further research on the genetic divergence of bat-eared fox populations as well as on the genetic consequences of interactions between environmental characteristics and social organization in this species.

Abstract The enamel microstructure of fossil and extant Geomyoidea (Geomyidae, Heteromyidae) lower incisors incorporates three‐ or two‐layered schmelzmusters with uniserial, transverse Hunter‐Schreger bands having parallel and perpendicular or exclusively perpendicular oriented interprismatic matrix. Phylogenetically, these schmelzmusters are regarded as moderately (enamel type 2) to highly derived (enamel type 3). Our analysis detected a zone of modified radial enamel close to the enamel–dentine junction. Modified radial enamel shows a strong phylogenetic signal within the clade Geomorpha as it is restricted to fossil and extant Geomyoidea and absent in Heliscomyidae, Florentiamyidae, and Eomyidae. This character dates back to at least the early Oligocene (early Arikareean, 29 Ma), where it occurs in entoptychine gophers. We contend that this specialized incisor enamel architecture developed as a biomechanical adaptation to regular burrowing activities including chisel‐tooth digging and a fiber‐rich diet and was probably present in the common ancestor of the clade. We regard the occurrence of modified radial enamel in lower incisors of scratch‐digging Geomyidae and Heteromyidae as the retention of a plesiomorphic character that is selectively neutral. The shared occurrence of modified radial enamel is a strong, genetically anchored argument for the close phylogenetic relationship of Geomyidae and Heteromyidae on the dental microstructure level.

Teeth of vertebrates are under constant use and therefore show wear-induced traces on the surface. According to Williams (2005), the mechanism by which wear occurs is a mechanical and/or chemical process resulting in material loss. Wear facets, the smooth and polished contact areas between opposing teeth, form during force-fit chewing activity between antagonists due to attritional (tooth-tooth) and abrasional (tooth-substrate-tooth) contacts involving either some kind of resistant alimentary bolus or some other dental behavior with an empty mouth cavity (Maier & Schneck 1981). In mammals, the occlusion of dental surfaces produces characteristic facet patterns on the crown’s surface. Orientation and inclination of a facet are determined by tooth morphology, while the texture of the surface (e. g., complexity and roughness) is the result of the food ingested (e. g., Schulz et al. 2010, Winkler et al. 2019, Schulz-Kornas et al. 2020, this volume). Complementary patterns of wear facets on the occlusal surface of opposing teeth change in shape and size during ontogeny and therefore can be used for age determination (e. g., Baumann 1949, Grau et al. 1970, Habermehl 1985, Anders et al. 2011a,b, Ruf et al. 2020, this volume). Wear facet patterns begin to form as soon as the tooth crown erupts and antagonists occlude. Fortelius (1985) differentiated between primary and secondary occlusal surfaces. Facets on primary surfaces develop gradually on the enamel cover (i. e., enamel facets) and only later expose the dentin with increasing wear due to age. In those cases, the exposed dentin has no explicit function. Facets on a secondary surface are composed of enamel and dentin. Dentin exposure happens relatively fast and it forms depressions in close proximity to protruding enamel, and the combination of both has a specific function. Those facets remain constant for a relatively long period of time in the life of an animal (i. e., dentin facets interrupted and/ or surrounded by enamel bands). Facets on secondary surfaces are specialized occlusal surfaces that are mostly developed in herbivorous taxa with a horizontal power stroke movement, regardless of the direction (Koenigswald 2020, this volume). In these specialized cases enamel and exposed dentin function as a unit, and neighboring facets merge and may cover large areas composed of both tissues (e. g., occlusal surface of elephant molars). In correspondence, some mammal groups developed specialized dentitions (e. g., hypsodonty, euhypsodonty, A new wear facet terminology for mammalian dentitions

Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore suffered a remarkable population reduction in the last 150 years due to human activities. The two white rhinoceros subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly after the onset of the decline, while the SWR recovered after a severe bottleneck. Such demographic events are predicted to have an erosive effect at the genomic level, in connection with the extirpation of diversity, and increased genetic drift and inbreeding. However there is currently little empirical data available that allows us to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore to assess these effects, we generated a whole-genome, temporal dataset consisting of 52 re-sequenced white rhinoceros genomes, that represents both subspecies at two time windows: before and during/after the bottleneck. Our data not only reveals previously unknown population substructure within both subspecies, but allowed us to quantify the genomic erosion undergone by both, with post-bottleneck white rhinoceroses harbouring significantly fewer heterozygous sites, and showing higher inbreeding coefficients than pre-bottleneck individuals. Moreover, the effective population size suffered a decrease of two and three orders of magnitude in the NWR and SWR respectively, due to the recent bottleneck. Our data therefore provides much needed empirical support for theoretical predictions about the genomic consequences of shrinking populations, information that is relevant for understanding the process of population extinction. Furthermore, our findings have the potential to inform management approaches for the conservation of the remaining white rhinoceroses.