A newly recognized family from the Horn of Africa, the Heterocephalidae (Rodentia: Ctenohystrica)

Genetic diversity of the largest African mole-rat genus, Bathyergus. One, two or four species?

Recent advances in sequencing technology and phylogenetic methods allow us to solve puzzling taxonomic questions using detailed analyses of genetic diversity of populations and gene flow between them. The genus of solitary-living dune mole-rat, Bathyergus, is quite unique among six genera of African mole-rats. The animals are by far the largest and the only scratch digging mole-rat genus possessing a skull less adapted to digging, grooved upper incisors, and more surface locomotor activity. Most authors recognize two species of dune mole-rats, B. suillus and B. janetta, but according to others, the genus is monotypic. In addition, recent molecular studies have revealed cryptic genetic diversity and suggested the existence of up to four species. In our study, we used mitochondrial and genome-wide nuclear data collected throughout the distribution of the genus to investigate the number of species. In agreement with previous studies, we found Bathyergus to be differentiated into several distinct lineages, but we also found evidence for a degree of gene flow between some of them. Furthermore, we confirmed that B. janetta is nested within B. suillus, making the latter paraphyletic and we documented an instance of local mitochondrial introgression between these two nominal species. Phylogeographic structure of the genus was found to be very shallow. Although traditionally dated to the Miocene, we found the first split within the genus to be much younger estimated to 0.82 Ma before present. Genealogical distinctiveness of some lineages was very low, and the coancestry matrix showed extensive sharing of closely related haplotypes throughout the genus. Accordingly, Infomap clustering on the matrix showed all populations to form a single cluster. Overall, our study tends to support the existence of only one species of Bathyergus namely, B. suillus. Environmental niche modelling confirmed its dependence on sandy soils and the preference for soils with relatively high carbon content. Bayesian skyline plots indicate recent population decline in the janetta lineage, probably related to global environmental change.

Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents

Olfactory receptor (OR) genes represent the largest multigenic family in mammalian genomes and encode proteins that bind environmental odorant molecules. The OR repertoire is extremely variable among species and is subject to many gene duplications and losses, which have been linked to ecological adaptations in mammals. Although they have been studied on a broad taxonomic scale (i.e., placental), finer sampling has rarely been explored in order to better capture the mechanisms that drove the evolution of the OR repertoire. Among placental mammals, rodents are well-suited for this task, as they exhibit diverse life history traits, and genomic data are available for most major families and a diverse array of lifestyles. In this study, 53 rodent published genomes were mined for their OR subgenomes. We retrieved more than 85,000 functional and pseudogene OR sequences that were subsequently classified into phylogenetic clusters. Copy number variation among rodents is similar to that of other mammals. Using our OR counts along with comparative phylogenetic approaches, we demonstrated that ecological niches such as diet, period of activity, and a fossorial lifestyle strongly impacted the proportion of OR pseudogenes. Within the OR subgenome, phylogenetic inertia was the main factor explaining the relative variations of the 13 OR gene families. However, a striking exception was a convergent 10-fold expansion of the OR family 14 among the phylogenetically divergent subterranean mole-rat lineages belonging to Bathyergidae and Spalacidae families. This study illustrates how the diversity of the OR repertoire has evolved among rodents, both shaped by selective forces stemming from species life history traits and neutral evolution along the rodent phylogeny.

Muscle architecture and muscle fibre type composition in the forelimb of two African mole-rat species, Bathyergus suillus and Heterocephalus glaber

The scratch-digging Cape dune mole-rat (Bathyergus suillus), and the chisel-toothed digging naked mole-rat (Heterocephalus glaber) are African mole-rats that differ in their digging strategy. The aim of this study was to determine if these behavioural differences are reflected in the muscle architecture and fibre-type composition of the forelimb muscles. Muscle architecture parameters of 39 forelimb muscles in both species were compared. Furthermore, muscle fibre type composition of 21 forelimb muscles were analysed using multiple staining protocols. In B. suillus, muscles involved with the power stroke of digging (limb retractors and scapula elevators), showed higher muscle mass percentage, force output and shortening capacity compared to those in H. glaber. Additionally, significantly higher percentages of glycolytic fibres were observed in the scapular elevators and digital flexors of B. suillus compared to H. glaber, suggesting that the forelimb muscles involved in digging in B. suillus provide fast, powerful motions for effective burrowing. In contrast, the m. sternohyoideus a head and neck flexor, had significantly more oxidative fibres in H. glaber compared to B. suillus. In addition, significantly greater physiological cross-sectional area and fascicle length values were seen in the neck flexor, m. sternocleidomastoideus, in H. glaber compared to B. suillus, which indicates a possible adaptation for chisel-tooth digging. While functional demands may play a significant role in muscle morphology, the phylogenetic differences between the two species may play an additional role which needs further study.

Helminth and protozoan parasites of subterranean rodents (Chordata, Mammalia, Rodentia) of the world

Published studies and ten new unpublished records included herein reveal that approximately 174 species of endoparasites (helminths and protozoans) are known from 65 of 163 species of rodents that occupy the subterranean ecotope globally. Of those, 94 endoparasite species were originally described from these rodents. A total of 282 host-parasite associations are summarized from four major zoogeographic regions including Ethiopian, Palearctic/Oriental, Nearctic, and Neotropical. Thirty-four parasite records from the literature have been identified to only the level of the genus. In this summary, ten new records have been added, and the most current taxonomic status of each parasite species is noted. Interestingly, there are no data on endoparasites from more than 68% of described subterranean rodents, which indicates that discovery and documentation are at an early stage and must continue.

Population structure and evolutionary history of the greater cane rat (Thryonomys swinderianus) from the Guinean Forests of West Africa

Grasscutter (Thryonomys swinderianus) is a large-body old world rodent found in sub-Saharan Africa. The body size and the unique taste of the meat of this major crop pest have made it a target of intense hunting and a potential consideration as a micro-livestock. However, there is insufficient knowledge on the genetic diversity of its populations across African Guinean forests. Herein, we investigated the genetic diversity, population structures and evolutionary history of seven Nigerian wild grasscutter populations together with individuals from Cameroon, Republic of Benin, and Ghana, using five mitochondrial fragments, including D-loop and cytochrome b (CYTB). D-loop haplotype diversity ranged from 0.571 (± 0.149) in Republic of Benin to 0.921 (± 0.013) in Ghana. Within Nigeria, the haplotype diversity ranged from 0.659 (± 0.059) in Cross River to 0.837 (± 0.075) in Ondo subpopulation. The fixation index (FST), haplotype frequency distribution and analysis of molecular variance revealed varying levels of population structures across populations. No significant signature of population contraction was detected in the grasscutter populations. Evolutionary analyses of CYTB suggests that South African population might have diverged from other populations about 6.1 (2.6-10.18, 95% CI) MYA. Taken together, this study reveals the population status and evolutionary history of grasscutter populations in the region.

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.

Hybridization underlies localized trait evolution in cavefish

Introgressive hybridization may play an integral role in local adaptation and speciation (Taylor and Larson, 2019). In the Mexican tetra Astyanax mexicanus, cave populations have repeatedly evolved traits including eye loss, sleep loss, and albinism. Of the 30 caves inhabited by A. mexicanus, Chica cave is unique because it contains multiple pools inhabited by putative hybrids between surface and cave populations (Mitchell et al., 1977), providing an opportunity to investigate the impact of hybridization on complex trait evolution. We show that hybridization between cave and surface populations may contribute to localized variation in traits associated with cave evolution, including pigmentation, eye development, and sleep. We also uncover an example of convergent evolution in a circadian clock gene in multiple cavefish lineages and burrowing mammals, suggesting a shared genetic mechanism underlying circadian disruption in subterranean vertebrates. Our results provide insight into the role of hybridization in facilitating phenotypic evolution.

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Hybridization leads to a localized difference in sleep duration within a single cave

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Genomic analysis identifies coding differences in Cry1A across cave pools

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Changes in Cry1A appear to be conserved in cavefish and burrowing mammals

The naked truth: a comprehensive clarification and classification of current 'myths' in naked mole-rat biology

The naked mole-rat (Heterocephalus glaber) has fascinated zoologists for at least half a century. It has also generated considerable biomedical interest not only because of its extraordinary longevity, but also because of unusual protective features (e.g. its tolerance of variable oxygen availability), which may be pertinent to several human disease states, including ischemia/reperfusion injury and neurodegeneration. A recent article entitled 'Surprisingly long survival of premature conclusions about naked mole-rat biology' described 28 'myths' which, those authors claimed, are a 'perpetuation of beautiful, but falsified, hypotheses' and impede our understanding of this enigmatic mammal. Here, we re-examine each of these 'myths' based on evidence published in the scientific literature. Following Braude et al., we argue that these 'myths' fall into four main categories: (i) 'myths' that would be better described as oversimplifications, some of which persist solely in the popular press; (ii) 'myths' that are based on incomplete understanding, where more evidence is clearly needed; (iii) 'myths' where the accumulation of evidence over the years has led to a revision in interpretation, but where there is no significant disagreement among scientists currently working in the field; (iv) 'myths' where there is a genuine difference in opinion among active researchers, based on alternative interpretations of the available evidence. The term 'myth' is particularly inappropriate when applied to competing, evidence-based hypotheses, which form part of the normal evolution of scientific knowledge. Here, we provide a comprehensive critical review of naked mole-rat biology and attempt to clarify some of these misconceptions.

New phiocricetomyine rodents (Hystricognathi) from the Jebel Qatrani Formation, Fayum Depression, Egypt

Background

The rich rodent assemblages from the Eocene-Oligocene deposits of the Jebel Qatrani Formation (Fayum Depression, Egypt) have important implications for our understanding of the origin and paleobiogeography of Hystricognathi, a diverse clade that is now represented by the Afro-Asiatic Hystricidae, New World Caviomorpha, and African Phiomorpha.

Methods

Here we present previously undescribed material of the enigmatic hystricognath clade Phiocricetomyinae, from two stratigraphic levels in the lower sequence of the Jebel Qatrani Formation-a new genus and species (Qatranimys safroutus) from the latest Eocene Locality 41 (~34 Ma, the oldest and most productive quarry in the formation) and additional material of Talahphiomys lavocati from that species' type locality, early Oligocene Quarry E (~31-33.2 Ma).

Results

The multiple specimens of Qatranimys safroutus from L-41 document almost the entire lower and upper dentition, as well as mandibular fragments and the first cranial remains known for a derived phiocricetomyine. Specimens from Quarry E allow us to expand comparisons with specimens from Libya (late Eocene of Dur at-Talah and early Oligocene of Zallah Oasis) that have been placed in T. lavocati, and we show that the Dur at-Talah and Zallah specimens do not pertain to this species. These observations leave the Fayum Quarry E as the only locality where T. lavocati occurs.

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.

Widespread loss of mammalian lineage and dietary diversity in the early Oligocene of Afro-Arabia

Diverse lines of geological and geochemical evidence indicate that the Eocene-Oligocene transition (EOT) marked the onset of a global cooling phase, rapid growth of the Antarctic ice sheet, and a worldwide drop in sea level. Paleontologists have established that shifts in mammalian community structure in Europe and Asia were broadly coincident with these events, but the potential impact of early Oligocene climate change on the mammalian communities of Afro-Arabia has long been unclear. Here we employ dated phylogenies of multiple endemic Afro-Arabian mammal clades (anomaluroid and hystricognath rodents, anthropoid and strepsirrhine primates, and carnivorous hyaenodonts) to investigate lineage diversification and loss since the early Eocene. These analyses provide evidence for widespread mammalian extinction in the early Oligocene of Afro-Arabia, with almost two-thirds of peak late Eocene diversity lost in these clades by ~30 Ma. Using homology-free dental topographic metrics, we further demonstrate that the loss of Afro-Arabian rodent and primate lineages was associated with a major reduction in molar occlusal topographic disparity, suggesting a correlated loss of dietary diversity. These results raise new questions about the relative importance of global versus local influences in shaping the evolutionary trajectories of Afro-Arabia's endemic mammals during the Oligocene.

Two functional epithelial sodium channel isoforms are present in rodents despite pronounced evolutionary pseudogenisation and exon fusion

The epithelial sodium channel (ENaC) plays a key role in salt and water homeostasis in tetrapod vertebrates. There are four ENaC subunits (α, β, γ, δ), forming heterotrimeric αβγ- or δβγ-ENaCs. Although the physiology of αβγ-ENaC is well understood, for decades the field has stalled with respect to δβγ-ENaC due to the lack of mammalian model organisms. The SCNN1D gene coding for δ-ENaC was previously believed to be absent in rodents, hindering studies using standard laboratory animals. We analyzed all currently available rodent genomes and discovered that SCNN1D is present in rodents but was independently lost in five rodent lineages, including the Muridae (mice and rats). The independent loss of SCNN1D in rodent lineages may be constrained by phylogeny and taxon-specific adaptation to dry habitats, however habitat aridity does not provide a selection pressure for maintenance of SCNN1D across Rodentia. A fusion of two exons coding for a structurally flexible region in the extracellular domain of δ-ENaC appeared in the Hystricognathi (a group that includes guinea pigs). This conserved pattern evolved at least 41 Ma and represents a new autapomorphic feature for this clade. Exon fusion does not impair functionality of guinea pig (Cavia porcellus) δβγ-ENaC expressed in Xenopus oocytes. Electrophysiological characterization at the whole-cell and single-channel level revealed conserved biophysical features and mechanisms controlling guinea pig αβγ- and δβγ-ENaC function as compared with human orthologs. Guinea pigs therefore represent commercially available mammalian model animals that will help shed light on the physiological function of δ-ENaC.

Bone remodeling in the longest living rodent, the naked mole-rat: Interelement variation and the effects of reproduction

The pattern of bone remodeling of one of the most peculiar mammals in the world, the naked mole-rat (NMR), was assessed. NMRs are known for their long lifespans among rodents and for having low metabolic rates. We assessed long-term in vivo bone labeling of subordinate individuals, as well as the patterns of bone resorption and bone remodeling in a large sample including reproductive and non-reproductive individuals (n = 70). Over 268 undecalcified thin cross-sections from the midshaft of humerus, ulna, femur and tibia were analyzed with confocal fluorescence and polarized light microscopy. Fluorochrome analysis revealed low osteogenesis, scarce bone resorption and infrequent formation of secondary osteons (Haversian systems) (i.e., slow bone turnover), thus most likely reflecting the low metabolic rates of this species. Secondary osteons occurred regardless of reproductive status. However, considerable differences in the degree of bone remodeling were found between breeders and non-breeders. Pre-reproductive stages (subordinates) exhibited quite stable skeletal homeostasis and bone structure, although the attainment of sexual maturity and beginning of reproductive cycles in female breeders triggered a series of anabolic and catabolic processes that up-regulate bone turnover, most likely associated with the increased metabolic rates of reproduction. Furthermore, bone remodeling was more frequently found in stylopodial elements compared to zeugopodial elements. Despite the limited bone remodeling observed in NMRs, the variation in the pattern of skeletal homeostasis (interelement variation) reported here represents an important aspect to understand the skeletal dynamics of a small mammal with low metabolic rates. Given the relevance of the remodeling process among mammals, this study also permitted the comparison of such process with the well-documented histomorphology of extinct therapsids (i.e., mammalian precursors), thus evidencing that bone remodeling and its endocortical compartmentalization represent ancestral features among the lineage that gave rise to mammals. It is concluded that other factors associated with development (and not uniquely related to biomechanical loading) can also have an important role in the development of bone remodeling.

Surprisingly long survival of premature conclusions about naked mole-rat biology

Naked mole-rats express many unusual traits for such a small rodent. Their morphology, social behaviour, physiology, and ageing have been well studied over the past half-century. Many early findings and speculations about this subterranean species persist in the literature, although some have been repeatedly questioned or refuted. While the popularity of this species as a natural-history curiosity, and oversimplified story-telling in science journalism, might have fuelled the perpetuation of such misconceptions, an accurate understanding of their biology is especially important for this new biomedical model organism. We review 28 of these persistent myths about naked mole-rat sensory abilities, ecophysiology, social behaviour, development and ageing, and where possible we explain how these misunderstandings came about.

Social Evolution in African Mole-Rats - A Comparative Overview

The African mole-rat superfamily are a unique group of subterranean rodents that are remarkable for their adaptations to a subterranean lifestyle and their range in sociality, spanning strictly solitary species to the naked mole-rat, the most social of all rodents. Widely distributed through sub-Saharan Africa their occurrence is associated with the presence of food resources in the form of underground roots, bulbs and tubers, which form their staple diet. African mole-rats have an ancient Oligocene/Eocene origin, with the naked mole-rat, the extant species with the earliest divergence from the common ancestor of the clade. As a consequence of its early evolution the naked mole-rat appears to have acquired many extraordinary biological features, even when compared with other mole-rats. Molecular phylogenies indicate that complex sociality and cooperative breeding has been convergently gained and/or lost more than once among African mole-rats, making them a fascinating group for comparative studies of social evolution. Ultimately, ecological constraints on digging and finding food have played a role in increasing cooperative behavior and social complexity, from what was most likely a monogamous ancestor living in family groups. Phylogenetically controlled comparisons suggest that proximate control of their lifestyle shows both conservation and divergence in the underlying mechanisms.

Comparative forelimb morphology of scratch-digging and chisel-tooth digging African mole-rat species

Bathyergus suillus (Cape dune mole-rat) and Heterocephalus glaber (naked mole-rat) are two species of subterranean burrowing rodents. Bathyergus suillus occurs in soft sandy soils and is regarded as a scratch-digger, while H. glaber is found in hard, compact soils and is a chisel-tooth digging species. The present study aimed to determine musculoskeletal differences in the forelimb of these two species. The muscles of the forelimb, back and neck were dissected to the points of origin and insertion in the left and right forelimbs, B. suillus (n = 7) and H. glaber (n = 5). Dissected muscles were photographed before maceration to demonstrate muscle attachments. The scapular spine, acromion process and clavicle were relatively straight in B. suillus. In comparison a curved scapular spine, acromion process and clavicle were observed in H. glaber. In both species, the clavicle rested on the greater tuberosity of the humerus. In B. suillus, the deltoid tuberosity was prominent and situated more distally on the humeral shaft compared to the indistinct, more proximally situated deltoid tuberosity in H. glaber. A prominent bony structure underlying the thenar pad as well as a cartilaginous protrusion beneath the hypothenar pad were observed on the palmar surface of the manus in B. suillus. Prominent claws were observed in B. suillus. A robust m. sternohyoideus was observed in H. glaber while mm. tensor fasciae antebrachii and coracobrachialis were absent. The flexors of the antebrachium of B. suillus had additional and enlarged attachment sites. The forelimb of B. suillus may be morphologically adapted for scratch-digging with relatively large and additional forelimb muscles and robust bones. In comparison, H. glaber had a reduction in the relative size, amount of muscles as well as number of attachment sites in the forelimb muscles, while the well-developed ventral neck muscles may facilitate neck and head stabilisation during chisel-tooth digging.

A phylogenomic rodent tree reveals the repeated evolution of masseter architectures

Understanding the number of times a trait has evolved is a necessary foundation for comprehending its potential relationships with selective regimes, developmental constraints and evolutionary diversification. Rodents make up over 40% of extant mammalian species, and their ecological and evolutionary success has been partially attributed to the increase in biting efficiency that resulted from a forward shift of one or two portions of the masseter muscle from the zygomatic arch onto the rostrum. This forward shift has occurred in three discrete ways, but the number of times it has occurred has never been explicitly quantified. We estimated an ultrametric phylogeny, the first to include all rodent families, using thousands of ultraconserved elements. We examined support for evolutionary relationships among the five rodent suborders and then incorporated relevant fossils, fitted models of character evolution, and used stochastic character mapping to determine that a portion of the masseter muscle has moved forward onto the rostrum at least seven times (with one reversal) during the approximately 70 Myr history of rodents. Combined, the repeated evolution of this key innovation, its increasing prevalence through time, and the species diversity of clades with this character underscores the adaptive value of improved biting efficiency and the relative ease with which some advantageous traits arise.

Masticatory musculature of the African mole-rats (Rodentia: Bathyergidae)

The Bathyergidae, commonly known as blesmols or African mole-rats, is a family of rodents well-known for their subterranean lifestyle and tunnelling behaviour. Four of the five extant bathyergid genera (Cryptomys, Fukomys, Georychus and Heliophobius) are chisel-tooth diggers, that is they dig through soil with their enlarged incisors, whereas the remaining genus (Bathyergus) is a scratch-digger, only using its forelimbs for burrowing. Heterocephalus glaber, the naked mole-rat, is also a chisel-tooth digger and was until recently included within the Bathyergidae (as the most basally branching genus), but has now been placed by some researchers into its own family, the Heterocephalidae. Given the importance of the masticatory apparatus in habitat construction in this group, knowledge and understanding of the morphology and arrangement of the jaw-closing muscles in Bathyergidae is vital for future functional analyses. Here, we use diffusible iodine-based contrast-enhanced microCT to reveal and describe the muscles of mastication in representative specimens of each genus of bathyergid mole-rat and to compare them to the previously described musculature of the naked mole-rat. In all bathyergids, as in all rodents, the masseter muscle is the most dominant component of the masticatory musculature. However, the temporalis is also a relatively large muscle, a condition normally associated with sciuromorphous rodents. Unlike their hystricomorphous relatives, the bathyergids do not show an extension of the masseter through the infraorbital foramen on to the rostrum (other than a very slight protrusion in Cryptomys and Fukomys). Thus, morphologically, bathyergids are protrogomorphous, although this is thought to be secondarily derived rather than retained from ancestral rodents. Overall, the relative proportions of the jaw-closing muscles were found to be fairly consistent between genera except in Bathyergus, which was found to have an enlarged superficial masseter and relatively smaller pterygoid muscles. It is concluded that these differences may be a reflection of the behaviour of Bathyergus which, uniquely in the family, does not use its incisors for digging.

Revision of Oligocene ‘Paraphiomys’ and an origin for crown Thryonomyoidea (Rodentia: Hystricognathi: Phiomorpha) near the Oligocene–Miocene boundary in Africa

‘Paraphiomys’ simonsi is a phiomorph rodent from the early Oligocene of Egypt (~29–30 Mya) that has historically been aligned with much younger (< ~20 Mya) Miocene species of the genera Paraphiomys and Neosciuromys. Here, we use Bayesian tip-dating analysis of a 109-character morphological matrix containing 57 living and extinct ctenohystricans to test these proposed placements for ‘Paraphiomys’ simonsi. Our analyses provide support for the exclusion of ‘Paraphiomys’ simonsi from both Paraphiomys and Neosciuromys and justify the establishment of a new genus (Monamys gen. nov.) for this stem thryonomyoid. These analyses also indicate that the divergence of the extant dassie rat Petromus from the extant cane rat Thryonomys (i.e. origin of crown Thryonomyoidea) occurred ~23.7 Mya, close to the Oligocene–Miocene boundary and in close agreement with recent molecular estimates for this split. Miocene Neosciuromys, Paraulacodus, Protohummus and the type species of Paraphiomys are identified as stem thryonomyids, whereas the Namibian species Apodecter stromeri, Tufamys woodi, ‘Paraphiomys’ australis and ‘Paraphiomys’ roessneri are identified for the first time as stem petromurids, raising the possibility of a long period of endemic petromurid evolution in south-west Africa. Comparison of molecular divergence estimates with our optimal tip-dated topology suggests that stem bathyergoids are most likely to have arisen from late Eocene and early Oligocene ‘phiomyids’.

Rapid molecular evolution of pain insensitivity in multiple African rodents

Noxious substances, called algogens, cause pain and are used as defensive weapons by plants and stinging insects. We identified four previously unknown instances of algogen-insensitivity by screening eight African rodent species related to the naked mole-rat with the painful substances capsaicin, acid (hydrogen chloride, pH 3.5), and allyl isothiocyanate (AITC). Using RNA sequencing, we traced the emergence of sequence variants in transduction channels, like transient receptor potential channel TRPA1 and voltage-gated sodium channel Na_v1.7, that accompany algogen insensitivity. In addition, the AITC-insensitive highveld mole-rat exhibited overexpression of the leak channel NALCN (sodium leak channel, nonselective), ablating AITC detection by nociceptors. These molecular changes likely rendered highveld mole-rats immune to the stings of the Natal droptail ant. Our study reveals how evolution can be used as a discovery tool to find molecular mechanisms that shut down pain.

Emergence of hystricognathous rodents: Palaeogene fossil record, phylogeny, dental evolution and historical biogeography

Although phylogenetic trees imply Asia as the ancestral homeland of the Hystricognathi clade (Rodentia: Ctenohystrica), curiously the oldest known fossil occurrences of hystricognathous rodents are not from Asia, but from Africa and South America, where they appear suddenly in the fossil record of both landmasses by the Late Middle Eocene. Here we performed cladistic and Bayesian (standard and tip-dating analyses) assessments of the dental evidence documenting early ctenohystricans, including several Asian ‘ctenodactyloids’, virtually all Palaeogene Asian and African hystricognaths known thus far and two representatives of the earliest known South American hystricognaths. Our results provide a phylogenetic context of early hystricognaths (with implications on systematics) and suggest that some Eocene Asian ‘ctenodactyloids’ could be considered as stem hystricognaths and pre-hystricognaths, although they were not recognized as such originally. However, this view does not fill the gap of the Eocene Asian hystricognath record, as the proposed results imply many ghost lineages extending back to the Middle Eocene for several Asian and African taxa. They also imply a complex early historical biogeography of the group, involving multiple dispersal events from Asia to Africa (and possibly from Africa back to Asia) and then to South America sometime during the Middle Eocene. Based on these phylogenetic considerations, we discuss the emergence of hystricognathous rodents from a morpho-anatomical perspective by analysing the differentiation of their masticatory apparatus and chewing movements, notably through the evolution of their dental patterns.

Tnni3k alleles influence ventricular mononuclear diploid cardiomyocyte frequency

Recent evidence implicates mononuclear diploid cardiomyocytes as a proliferative and regenerative subpopulation of the postnatal heart. The number of these cardiomyocytes is a complex trait showing substantial natural variation among inbred mouse strains based on the combined influences of multiple polymorphic genes. One gene confirmed to influence this parameter is the cardiomyocyte-specific kinase Tnni3k. Here, we have studied Tnni3k alleles across a number of species. Using a newly-generated kinase-dead allele in mice, we show that Tnni3k function is dependent on its kinase activity. In an in vitro kinase assay, we show that several common human TNNI3K kinase domain variants substantially compromise kinase activity, suggesting that TNNI3K may influence human heart regenerative capacity and potentially also other aspects of human heart disease. We show that two kinase domain frameshift mutations in mice cause loss-of-function consequences by nonsense-mediated decay. We further show that the Tnni3k gene in two species of mole-rat has independently devolved into a pseudogene, presumably associated with the transition of these species to a low metabolism and hypoxic subterranean life. This may be explained by the observation that Tnni3k function in mice converges with oxidative stress to regulate mononuclear diploid cardiomyocyte frequency. Unlike other studied rodents, naked mole-rats have a surprisingly high (30%) mononuclear cardiomyocyte level but most of their mononuclear cardiomyocytes are polyploid; their mononuclear diploid cardiomyocyte level (7%) is within the known range (2–10%) of inbred mouse strains. Naked mole-rats provide further insight on a recent proposal that cardiomyocyte polyploidy is associated with evolutionary acquisition of endothermy.

Embryonic cardiomyocytes have one diploid nucleus (like most cells of the body), but most adult cardiomyocytes are polyploid. Most adult cardiomyocytes are also post-mitotic and nonregenerative, and as a result, heart injury (such as from a heart attack) is followed by scarring and impaired function rather than by regeneration. A subset of cardiomyocytes in the adult heart remains mononuclear diploid, and recent evidence indicates that this subpopulation has proliferative and regenerative capacity. Our previous work in mice showed that the percentage of this cell population in the adult heart is a complex trait subject to the combined influence of a number of polymorphic genes. One gene that influences variation in this trait is a kinase gene known as Tnni3k. This study addresses the consequences of a number of Tnni3k alleles, both newly engineered in mice and naturally occurring in a number of species, including human and mole-rat, and studied at the phenotypic and biochemical level. These results provide insight into inter- and intra-species variation in the cardiomyocyte composition of the adult heart, and may be relevant to understanding heart regenerative ability in humans and across other species.

Brain atlas of the African mole-rat Fukomys anselli

African mole-rats are subterranean rodents that spend their whole life in underground burrow systems. They show a range of morphological and physiological adaptations to their ecotope, for instance severely reduced eyes and specialized somatosensory, olfactory, and auditory systems. These adaptations are also reflected in the accessory sensory pathways in the brain that process the input coming from the sensory organs. So far, a brain atlas was available only for the naked mole-rat (Heterocephalus glaber). The Ansell's mole-rat (Fukomys anselli) has been the subject of many investigations in various disciplines (ethology, sensory physiology, and anatomy) including magnetic orientation. It is therefore surprising that an atlas of the brain of this species was not available so far. Here, we present a comprehensive atlas of the Ansell's mole-rat brain based on Nissl and Klüver-Barrera stained sections. We identify and label 375 brain regions and discuss selected differences from the brain of the closely related naked mole-rat as well as from epigeic mammals (rat), with a particular focus on the auditory brainstem. This atlas can serve as a reference for future neuroanatomical investigations of subterranean mammals.

Human cancer, the naked mole rat and faunal turnovers

We argue that the human evolutionary heritage with frequent adaptations through geological time to environmental change has affected a trade‐off between offspring variability and cancer resistance, and thus favored cancer‐prone individuals. We turn the attention to a factor setting the highly cancer‐resistant naked mole rat apart from most other mammals: it has remained phenotypically largely unchanged since 30‐50 million years ago. Research focusing on DNA stability mechanisms in ‘living fossil’ animals may help us find tools for cancer prevention and treatment.

The usage of subgenera in mammalian taxonomy

In this note, I discuss the advantages of the usage of subgenera as a practical taxonomic rank in mammalian taxonomy. Use of this category preserves traditional usage, reduces nomenclatural instability and avoids unnecessary change of names. Subgenera are useful to label diagnosable clades of closely related species, especially in morphologically and ecologically diverse monophyletic genera, without alteration of traditional binomial usage. Contrary to informal names such as “divisions” or “groups”, subgenera are governed by the rules of the International Commission on Zoological Nomenclature (ICZN), having usage constrained (and stability promoted) by typification and priority.

Sociality does not drive the evolution of large brains in eusocial African mole-rats

The social brain hypothesis (SBH) posits that the demands imposed on individuals by living in cohesive social groups exert a selection pressure favouring the evolution of large brains and complex cognitive abilities. Using volumetry and the isotropic fractionator to determine the size of and numbers of neurons in specific brain regions, here we test this hypothesis in African mole-rats (Bathyergidae). These subterranean rodents exhibit a broad spectrum of social complexity, ranging from strictly solitary through to eusocial cooperative breeders, but feature similar ecologies and life history traits. We found no positive association between sociality and neuroanatomical correlates of information-processing capacity. Solitary species are larger, tend to have greater absolute brain size and have more neurons in the forebrain than social species. The neocortex ratio and neuronal counts correlate negatively with social group size. These results are clearly inconsistent with the SBH and show that the challenges coupled with sociality in this group of rodents do not require brain enlargement or fundamental reorganization. These findings suggest that group living or pair bonding per se does not select strongly for brain enlargement unless coupled with Machiavellian interactions affecting individual fitness.

Unraveling the gut microbiome of the long-lived naked mole-rat

The naked mole-rat (Heterocephalus glaber) is a subterranean mouse-sized African mammal that shows astonishingly few age-related degenerative changes and seems to not be affected by cancer. These features make this wild rodent an excellent model to study the biology of healthy aging and longevity. Here we characterize for the first time the intestinal microbial ecosystem of the naked mole-rat in comparison to humans and other mammals, highlighting peculiarities related to the specific living environment, such as the enrichment in bacteria able to utilize soil sulfate as a terminal electron acceptor to sustain an anaerobic oxidative metabolism. Interestingly, some compositional gut microbiota peculiarities were also shared with human gut microbial ecosystems of centenarians and Hadza hunter-gatherers, considered as models of a healthy gut microbiome and of a homeostatic and highly adaptive gut microbiota-host relationship, respectively. In addition, we found an enrichment of short-chain fatty acids and carbohydrate degradation products in naked mole-rat compared to human samples. These data confirm the importance of the gut microbial ecosystem as an adaptive partner for the mammalian biology and health, independently of the host phylogeny.

Slow aging in mammals-Lessons from African mole-rats and bats

Traditionally, the main mammalian models used in aging research have been mice and rats, i.e. short-lived species that obviously lack effective maintenance mechanisms to keep their soma in a functional state for prolonged periods of time. It is doubtful that life-extending mechanisms identified only in such short-lived species adequately reflect the diversity of longevity pathways that have naturally evolved in mammals, or that they have much relevance for long-lived species such as humans. Therefore, some complementary, long-lived mammalian models have been introduced to aging research in the past 15-20 years, particularly naked mole-rats (and to a lesser extent also other mole-rats) and bats. Here, I summarize and compare the most important results regarding various aspects of aging - oxidative stress, molecular homeostasis and repair, and endocrinology - that have been obtained from studies using these new mammalian models of high longevity. I argue that the inclusion of these models was an important step forward, because it drew researchers' attention to certain oversimplifications of existing aging theories and to several features that appear to be universal components of enhanced longevity in mammals. However, even among mammals with high longevity, considerable variation exists with respect to other candidate mechanisms that also must be taken into account if inadequate generalizations are to be avoided.

Neoteny, Prolongation of Youth: From Naked Mole Rats to “Naked Apes” (Humans)

It has been suggested that highly social mammals, such as naked mole rats and humans, are long-lived due to neoteny (the prolongation of youth). In both species, aging cannot operate as a mechanism facilitating natural selection because the pressure of this selection is strongly reduced due to 1) a specific social structure where only the “queen” and her “husband(s)” are involved in reproduction (naked mole rats) or 2) substituting fast technological progress for slow biological evolution (humans). Lists of numerous traits of youth that do not disappear with age in naked mole rats and humans are presented and discussed. A high resistance of naked mole rats to cancer, diabetes, cardiovascular and brain diseases, and many infections explains why their mortality rate is very low and almost age-independent and why their lifespan is more than 30 years, versus 3 years in mice. In young humans, curves of mortality versus age start at extremely low values. However, in the elderly, human mortality strongly increases. High mortality rates in other primates are observed at much younger ages than in humans. The inhibition of the aging process in humans by specific drugs seems to be a promising approach to prolong our healthspan. This might be a way to retard aging, which is already partially accomplished via the natural physiological phenomenon neoteny.

Unraveling the message: insights into comparative genomics of the naked mole-rat

Animals have evolved to survive, and even thrive, in different environments. Genetic adaptations may have indirectly created phenotypes that also resulted in a longer lifespan. One example of this phenomenon is the preternaturally long-lived naked mole-rat. This strictly subterranean rodent tolerates hypoxia, hypercapnia, and soil-based toxins. Naked mole-rats also exhibit pronounced resistance to cancer and an attenuated decline of many physiological characteristics that often decline as mammals age. Elucidating mechanisms that give rise to their unique phenotypes will lead to better understanding of subterranean ecophysiology and biology of aging. Comparative genomics could be a useful tool in this regard. Since the publication of a naked mole-rat genome assembly in 2011, analyses of genomic and transcriptomic data have enabled a clearer understanding of mole-rat evolutionary history and suggested molecular pathways (e.g., NRF2-signaling activation and DNA damage repair mechanisms) that may explain the extraordinarily longevity and unique health traits of this species. However, careful scrutiny and re-analysis suggest that some identified features result from incorrect or imprecise annotation and assembly of the naked mole-rat genome: in addition, some of these conclusions (e.g., genes involved in cancer resistance and hairlessness) are rejected when the analysis includes additional, more closely related species. We describe how the combination of better study design, improved genomic sequencing techniques, and new bioinformatic and data analytical tools will improve comparative genomics and ultimately bridge the gap between traditional model and nonmodel organisms.

Late Pleistocene echimyid rodents (Rodentia, Hystricognathi) from northern Brazil

ABSTRACT Echimyidae (spiny rats, tree rats and the coypu) is the most diverse family of extant South American hystricognath rodents (caviomorphs). Today, they live in tropical forests (Amazonian, coastal and Andean forests), occasionally in more open xeric habitats in the Cerrado and Caatinga of northern South America, and open areas across the southern portion of the continent (Myocastor). The Quaternary fossil record of this family remains poorly studied. Here, we describe the fossil echimyids found in karst deposits from southern Tocantins, northern Brazil. The analyzed specimens are assigned to Thrichomys sp., Makalata cf. didelphoides and Proechimys sp. This is the first time that a fossil of Makalata is reported. The Pleistocene record of echimyids from this area is represented by fragmentary remains, which hinders their determination at specific levels. The data reported here contributes to the understanding of the ancient diversity of rodents of this region, evidenced until now in other groups, such as the artiodactyls, cingulates, carnivores, marsupials, and squamate reptiles.

New phiomorph rodents from the latest Eocene of Egypt, and the impact of Bayesian "clock"-based phylogenetic methods on estimates of basal hystricognath relationships and biochronology

The Fayum Depression of Egypt has yielded fossils of hystricognathous rodents from multiple Eocene and Oligocene horizons that range in age from ∼37 to ∼30 Ma and document several phases in the early evolution of crown Hystricognathi and one of its major subclades, Phiomorpha. Here we describe two new genera and species of basal phiomorphs, Birkamys korai and Mubhammys vadumensis, based on rostra and maxillary and mandibular remains from the terminal Eocene (∼34 Ma) Fayum Locality 41 (L-41). Birkamys is the smallest known Paleogene hystricognath, has very simple molars, and, like derived Oligocene-to-Recent phiomorphs (but unlike contemporaneous and older taxa) apparently retained dP(4)∕4 late into life, with no evidence for P(4)∕4 eruption or formation. Mubhammys is very similar in dental morphology to Birkamys, and also shows no evidence for P(4)∕4 formation or eruption, but is considerably larger. Though parsimony analysis with all characters equally weighted places Birkamys and Mubhammys as sister taxa of extant Thryonomys to the exclusion of much younger relatives of that genus, all other methods (standard Bayesian inference, Bayesian "tip-dating," and parsimony analysis with scaled transitions between "fixed" and polymorphic states) place these species in more basal positions within Hystricognathi, as sister taxa of Oligocene-to-Recent phiomorphs. We also employ tip-dating as a means for estimating the ages of early hystricognath-bearing localities, many of which are not well-constrained by geological, geochronological, or biostratigraphic evidence. By simultaneously taking into account phylogeny, evolutionary rates, and uniform priors that appropriately encompass the range of possible ages for fossil localities, dating of tips in this Bayesian framework allows paleontologists to move beyond vague and assumption-laden "stage of evolution" arguments in biochronology to provide relatively rigorous age assessments of poorly-constrained faunas. This approach should become increasingly robust as estimates are combined from multiple independent analyses of distantly related clades, and is broadly applicable across the tree of life; as such it is deserving of paleontologists' close attention. Notably, in the example provided here, hystricognathous rodents from Libya and Namibia that are controversially considered to be of middle Eocene age are instead estimated to be of late Eocene and late Oligocene age, respectively. Finally, we reconstruct the evolution of first lower molar size among Paleogene African hystricognaths using a Bayesian approach; the results of this analysis reconstruct a rapid latest Eocene dwarfing event along the lineage leading to Birkamys.

Towards a uniform nomenclature for ground squirrels: the status of the Holarctic chipmunks

The chipmunks are a Holarctic group of ground squirrels currently allocated to the genus

Dental peculiarities in the silvery mole-rat: an original model for studying the evolutionary and biological origins of continuous dental generation in mammals

Unravelling the evolutionary and developmental mechanisms that have impacted the mammalian dentition, since more than 200 Ma, is an intricate issue. Interestingly, a few mammal species, including the silvery mole-rat Heliophobius argenteocinereus, are able to replace their dentition by the addition of supernumerary molars at the back of jaw migrating then toward the front. The aim here was to demonstrate the potential interest of further studying this rodent in order to better understand the origins of continuous dental replacement in mammals, which could also provide interesting data concerning the evolution of limited dental generation occurring in first mammals. In the present study, we described the main stages of the dental eruptive sequence in the silvery mole-rat and the associated characteristics of horizontal replacement using X-ray microtomography. This was coupled to the investigation of other African mole-rats which have no dental replacement. This method permitted to establish evidence that the initial development of the dentition in Heliophobius is comparable to what it is observed in most of African mole-rats. This rodent first has premolars, but then identical additional molars, a mechanism convergent to manatees and the pygmy rock-wallaby. Evidence of continuous replacement and strong dental dynamics were also illustrated in Heliophobius, and stressed the need to deeply investigate these aspects for evolutionary, functional and developmental purposes. We also noticed that two groups of extinct non-mammalian synapsids convergently acquired this dental mechanism, but in a way differing from extant mammals. The discussion on the diverse evolutionary origins of horizontal dental replacement put emphasis on the necessity of focusing on biological parameters potentially involved in both continuous and limited developments of teeth in mammals. In that context, the silvery mole-rat could appear as the most appropriate candidate to do so.