Molecular systematics of gerbils and deomyines (Rodentia: Gerbillinae, Deomyinae) and a test of desert adaptation in the tympanic bulla

Morphological variations of auditory bullae in otomyine rodents (Rodentia: Otomyini) in southern African biomes

Mammalian middle ear cavities differ from those of other taxa as they comprise three ossicles and in rodents, can be encapsulated by an auditory bulla. In small mammals, the middle ear cavity (bulla) was found to be enlarged in the desert-dwelling species; however, differences in bullar size could have been due to ancestry. In this study, we sampled seven species from three genera (Myotomys, Otomys, and Parotomys) of the African murid tribe Otomyini (laminated-toothed rats), and compared the bullar volumes and shapes between the otomyine species and within the species Myotomys unisulcatus. Photographs of museum skull specimens were taken from ventral and lateral views, and the volumes of the bullae were estimated digitally from the photographs. No sexual dimorphism in bullar volumes was found in any of the species. Corrected bullar volumes were significantly different between species and larger bullae were seen in individuals inhabiting regions with lower annual rainfall. Bullar shape (estimated using geometric morphometrics) was significantly different between the genera and the species. Parotomys have tympanic meatuses that face more anteriorly compared to both, Otomys and Myotomys. When comparing bullae within M. unisulcatus, those inhabiting regions with lower annual rainfall had significantly larger bullar volumes, but no significant difference was found in bullar shape between the regions. This study shows that otomyine rodents in more xeric habitats have different auditory structures to those inhabiting wetter habitats.

Adaptation in brain structure and respiratory and olfactory structures across environmental gradients in African and North American muroid rodents

Morphometric studies of 3D micro CT-scanned images can provide insights into the evolution of the brain and sensory structures but such data are still scarce for the most diverse mammalian order of rodents. From reviewed and new data, we tested for convergence to extreme aridity and high elevation in the sensory and brain morphology of rodents, from morphometric data from micro-CT X-ray scans of 174 crania of 16 species of three distantly related African murid (soft-furred mice, Praomyini, laminate-toothed rats, Otomyini, and gerbils, Gerbillinae) clades and one North American cricetid (deer mice and white-footed mice, Peromyscus) clade. Recent studies demonstrated convergent evolution acting on the oval window area of the cochlea (enlarged in extremely arid-adapted species of Otomyini and Gerbillinae) and on endocranial volume (reduced in high elevation taxa of Otomyini and Peromyscus). However, contrary to our predictions, we did not find evidence of convergence in brain structure to aridity, or in the olfactory/respiratory system (turbinate bones) to high elevation. Brain structure differed, particularly in the petrosal lobules of the cerebellum and the olfactory bulbs, between Otomyini and Gerbillinae, with extreme arid-adapted species in each clade being highly divergent (not convergent) from other species in the same clade. We observed greater "packing" of the maxillary turbinate bones, which have important respiratory functions, in Peromyscus mice from high and low elevations compared to the high-elevation African Praomyini, but more complex patterns within Peromyscus, probably related to trade-offs in respiratory physiology and heat exchange in the nasal epithelium associated with high-elevation adaptation.

Diversity and Evolution of Highly Repetitive DNA Sequences Constituting Chromosome Site-Specific Heterochromatin in Two Gerbillinae Species

Constitutive heterochromatin, consisting of repetitive sequences, diverges very rapidly; therefore, its nucleotide sequences and chromosomal distributions are often largely different, even between closely related species. The chromosome C-banding patterns of two Gerbillinae species, Meriones unguiculatus and Gerbillus perpallidus, vary greatly, even though they belong to the same subfamily. To understand the evolution of C-positive heterochromatin in these species, we isolated highly repetitive sequences, determined their nucleotide sequences, and characterized them using chromosomal and filter hybridization. We obtained a centromeric repeat (MUN-HaeIII) and a chromosome 13-specific repeat (MUN-EcoRI) from M. unguiculatus. We also isolated a centromeric/pericentromeric repeat (GPE-MBD) and an interspersed-type repeat that was predominantly amplified in the X and Y chromosomes (GPE-EcoRI) from G. perpallidus. GPE-MBD was found to contain a 17-bp motif that is essential for binding to the centromere-associated protein CENP-B. This indicates that it may play a role in the formation of a specified structure and/or function of centromeres. The nucleotide sequences of the three sequence families, except GPE-EcoRI, were conserved only in Gerbillinae. GPE-EcoRI was derived from the long interspersed nuclear elements 1 retrotransposon and showed sequence homology throughout Muridae and Cricetidae species, indicating that the repeat sequence occurred at least in the common ancestor of Muridae and Cricetidae. Due to a lack of assembly data of highly repetitive sequences constituting heterochromatin in whole-genome sequences of vertebrate species published to date, the knowledge obtained in this study provides useful information for a deep understanding of the evolution of repetitive sequences in not only rodents but also in mammals.

Environmental and climatic drivers of phenotypic evolution and distribution changes in a widely distributed subfamily of subterranean mammals

How environmental factors shape species morphology and distributions is a key issue in ecology, especially in similar environments. Species of Myospalacinae exhibit widespread distribution spanning the eastern Eurasian steppe and the extreme adaptation to the subterranean environment, providing an excellent opportunity for investigating species responses to environmental changes. At the national scale, we here use geometric morphometric and distributional data to assess the environmental and climatic drivers of morphological evolution and distribution of Myospalacinae species in China. Based on phylogenetic relationships of Myospalacinae species constructed using genomic data in China, we integrate geometric morphometrics and ecological niche models to reveal the interspecific variation of skull morphology, trace the ancestral state, and assess factors influencing interspecific variation. Our approach further allows us to project future distributions of Myospalacinae species throughout China. We found that the interspecific morphology variations were mainly concentrated in the temporal ridge, premaxillary-frontal suture, premaxillary-maxillary suture, and molars, and the skull morphology of the two current species in Myospalacinae followed the ancestral state; temperature and precipitation were important environmental variables influencing skull morphology. Elevation, temperature annual range, and precipitation of warmest quarter were identified as dominant factors affecting the distribution of Myospalacinae species in China, and their suitable habitat area will decrease in the future. Collectively, environmental and climate changes have an effect on skull phenotypes of subterranean mammals, highlighting the contribution of phenotypic differentiation in similar environments in the formation of species phenotypes. Climate change will further shrink their habitats under future climate assumptions in the short-term. Our findings provide new insights into effects of environmental and climate change on the morphological evolution and distribution of species as well as a reference for biodiversity conservation and species management.

Counter-gradient variation and the expensive tissue hypothesis explain parallel brain size reductions at high elevation in cricetid and murid rodents

To better understand functional morphological adaptations to high elevation (> 3000 m above sea level) life in both North American and African mountain-associated rodents, we used microCT scanning to acquire 3D images and a 3D morphometric approach to calculate endocranial volumes and skull lengths. This was done on 113 crania of low-elevation and high-elevation populations in species of North American cricetid mice (two Peromyscus species, n = 53), and African murid rodents of two tribes, Otomyini (five species, n = 49) and Praomyini (four species, n = 11). We tested two distinct hypotheses for how endocranial volume might vary in high-elevation populations: the expensive tissue hypothesis, which predicts that brain and endocranial volumes will be reduced to lessen the costs of growing and maintaining a large brain; and the brain-swelling hypothesis, which predicts that endocranial volumes will be increased either as a direct phenotypic effect or as an adaptation to accommodate brain swelling and thus minimize pathological symptoms of altitude sickness. After correcting for general allometric variation in cranial size, we found that in both North American Peromyscus mice and African laminate-toothed (Otomys) rats, highland rodents had smaller endocranial volumes than lower-elevation rodents, consistent with the expensive tissue hypothesis. In the former group, Peromyscus mice, crania were obtained not just from wild-caught mice from high and low elevations but also from those bred in common-garden laboratory conditions from parents caught from either high or low elevations. Our results in these mice showed that brain size responses to elevation might have a strong genetic basis, which counters an opposite but weaker environmental effect on brain volume. These results potentially suggest that selection may act to reduce brain volume across small mammals at high elevations but further experiments are needed to assess the generality of this conclusion and the nature of underlying mechanisms.

RM. The earliest dipodomyine heteromyid in North America and the phylogenetic relationships of geomorph rodents

Dipodomyine heteromyids (kangaroo rats and mice) are a diverse group of arid-adapted ricochetal rodents of North America. Here, a new genus and species of a large dipodomyine is reported from early Miocene-aged deposits of the John Day Formation in Oregon that represents the earliest record of the subfamily. The taxon is known from a single specimen consisting of a nearly complete skull, dentary, partial pes, and caudal vertebra. The specimen is characterized by a mosaic of ancestral and highly derived cranial features of heteromyids. Specifically, the dental morphology and some cranial characteristics are similar to early heteromyids, but other aspects of morphology, including the exceptionally inflated auditory bullae, are more similar to known dipodomyines. This specimen was included in a phylogenetic analysis comprising 96 characters and the broadest sampling of living and extinct geomorph rodents of any morphological phylogenetic analysis to date. Results support the monophyly of crown-group Heteromyidae exclusive of Geomyidae and place the new taxon within Dipodomyinae. The new heteromyid is the largest known member of the family. Analyses suggest that large body size evolved several times within Heteromyidae. Overall, the morphology of the new heteromyid supports a mosaic evolution of the open-habitat adaptations that characterize kangaroo rats and mice, with the inflation of the auditory bulla appearing early in the group, and bipedality/ricochetal locomotion appearing later. We hypothesize that cooling and drying conditions in the late Oligocene and early Miocene favored adaptations for life in more open habitats, resulting in increased locomotor specialization in this lineage over time from a terrestrial ancestor.

Environmental implications of Ptolemaic Period rodents and shrews from the Sacred Falcon Necropolis at Quesna, Egypt (Mammalia: Muridae and Soricidae)

BACKGROUND

Assemblages of mummified and preserved animals in necropoleis of Ptolemaic Period Egypt (ca. 332-30 BC) document some aspects of the ceremonial and religious practices of the ancient Egyptians, but study of these animal remains can also provide insight into the local environments in which the animals and humans lived.

RESULTS

Excavations of the Sacred Falcon Necropolis at Quesna in the Nile Delta have yielded many thousands of animal remains, mostly of raptors, but also of a lesser number of small, wild mammals. Among the latter, we identified four species of murid rodents (Rodentia: Muridae) and five species of shrews (Eulipotyphla: Soricidae). The soricids are of particular interest because they represent a more diverse assemblage of species than occurs in the delta today. They include one species, Crocidura gueldenstaedtii (Pallas, 1811), that no longer occurs in the delta and another, C. fulvastra (Sundevall, 1843), that is now extirpated from Egypt.

CONCLUSIONS

The coexistence of this diverse small mammal community suggests that a greater availability and variety of mesic habitats were present during the Ptolemaic Period than occur there now. The local mammal faunas recovered at Quesna and other well-studied ancient Egyptian sites together provide evidence of a richer, more complex regional environment along the Nile Valley. They also provide important insight regarding the biogeography of the individual species comprising the faunas and about the extent of faunal turnover since the Ptolemaic Period.

Characterization of Two New Apodemus Mitogenomes (Rodentia: Muridae) and Mitochondrial Phylogeny of Muridae

Apodemus is the most common small rodent species in the Palearctic realm and an ideal species for biogeographical research and understanding environmental changes. Elucidating phylogenetic relationships will help us better understand species adaptation and genetic evolution. Due to its stable structure, maternal inheritance, and rapid evolution, the mitogenome has become a hot spot for taxonomic and evolutionary studies. In this research, we determined the mitochondrial genome of Apodemus agrarius ningpoensis and Apodemus draco draco and studied the phylogeny of Muridae using ML and BI trees based on all known complete mitogenomes. The mitochondrial genome of Apodemus agrarius ningpoensis was 16,262 bp, whereas that of Apodemus draco draco was 16,222 bp, and both encoded 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Analysis of base composition showed a clear A-T preference. All tRNAs except tRNASer and tRNALys formed a typical trilobal structure. All protein-coding genes contained T- and TAA as stop codons. Phylogeny analysis revealed two main branches in the Muridae family. Apodemus agrarius ningpoensis formed sister species with Apodemus chevrieri, whereas Apodemus draco draco with Apodemus latronum. Our findings provide theoretical basis for future studies focusing on the mitogenome evolution of Apodemus.

Skull variation in populations of the Indian gerbil Tatera indica (Gerbillinae, Rodentia) sampled across its broad geographic range

Populations of broadly distributed species often exhibit geographic structuring, which is sometimes reflected in phenotype. The monotypic Indian gerbil (Tatera indica) is an example of a widely distributed species, with its range encompassing much of Asia. This study aims to determine if T. indica populations exhibit marked variation in skull morphology—this structure is particularly adaptable and thus could be amenable to show such variation. Furthermore, the potential drivers of skull variation are examined, including the role of climate and geography. To achieve these goals, 21 linear measurements were measured on the skulls of 509 specimens, coming from 111 different localities, across this species wide range. The specimens were then assigned into one of four broad geographic groups (≈ populations) based on their geographic proximity, and the overall and the pairwise differences in the 21 skull measurements among these groups were assessed. Specimens from Pakistan significantly differed from those belonging to the West Iran, East Iran, and India populations, which in turn did not significantly differ from each other. Pairwise bioclimatic and geographic distances between the localities explained a significant, yet small amount of variation in the measurements. Thus, while the Pakistani T. indica population was distinct in skull measurements, both climatic and non-climatic spatial factors seem not to account largely for its distinctiveness (from the other populations).

A geometric morphometric analysis of geographic variation in the Cape Short-eared gerbil, Desmodillus auricularis (Rodentia: Gerbillinae)

The genus Desmodillus is monospecific, consisting of only the Cape short-eared gerbil (Desmodillus auricularis). Despite being widely distributed across southern Africa, previous studies did not find evidence of intraspecific phenotypic geographic differentiation. The objectives of this study is to use geometric morphometrics to investigate if and how the skull of D. auricularis varies spatially. It examines the covariation of skull morphology with broad spatial (latitude and longitude) and climatic variables, based on a sample of 580 specimens from southern Africa (Botswana, Namibia, and South Africa). The results did not support the differentiation of D. auricularis populations into distinct geographically isolated phenotypic groups. However, there is strong evidence for clinal variation in skull morphology; the most prominent pattern being a decrease in size from the west (closest to the South Atlantic coast) to the east (towards the continent’s interior). Shape variation was not localized in any skull region and seem to be driven mostly by size (allometry), although it also covaried significantly with latitude and longitude. Statistically significant skull shape sexual dimorphism was also detected, with males having larger crania than females. Spatial clinal variation in skull morphology was mostly associated with differences in the aridity of the habitats relative to their distance from the coast as evidenced by precipitation-related bioclimatic variables—annual precipitation (BIO12), precipitation of driest month (BIO14), and precipitation of driest quarter (BIO17)—covarying the most with skull morphology. This could be driven by either the climate influencing local resources available to populations or by the climate directly instigating phenotypic climatic adaptations.

Uncovering the diversity of endemic Ethiopian fauna: complete mitochondrial genomes of four Lophuromys species (Rodentia, Muridae)

Complete mitochondrial genomes of four species of Ethiopian speckled brush-furred rats Lophuromys (L. chrysopus, L. menageshae, L. melanonyx, and L. simensis) were assembled for the first time. We provide data concerning the sequencing, assembly, and annotation of the obtained mitogenomes; compare two widely used circular-genome annotation tools (MITOS and MitoZ), and discuss relevant points concerning relationships within both Ethiopian Lophuromys and the Muridae family.

Species-typical group size differentially influences social reward neural circuitry during nonreproductive social interactions

We investigated whether nonreproductive social interactions may be rewarding for colonial but not non-colonial species. We found that the colonial spiny mouse (Acomys cahirinus) is significantly more gregarious, more prosocial, and less aggressive than its non-colonial relative, the Mongolian gerbil (Meriones unguiculatus). In an immediate-early gene study, we examined oxytocin (OT) and tyrosine hydroxylase (TH) neural responses to interactions with a novel, same-sex conspecific or a novel object. The paraventricular nucleus of the hypothalamus (PVN) OT cell group was more responsive to interactions with a conspecific compared to a novel object in both species. However, the ventral tegmental area (VTA) TH cell group showed differential responses only in spiny mice. Further, PVN OT and VTA TH neural responses positively correlated in spiny mice, suggesting functional connectivity. These results suggest that colonial species may have evolved neural mechanisms associated with reward in novel, nonreproductive social contexts to promote large group-living.

Evolution of Guanylate Binding Protein (GBP) Genes in Muroid Rodents (Muridae and Cricetidae) Reveals an Outstanding Pattern of Gain and Loss

Guanylate binding proteins (GBPs) are paramount in the host immunity by providing defense against invading pathogens. Multigene families related to the immune system usually show that the duplicated genes can either undergo deletion, gain new functions, or become non-functional. Here, we show that in muroids, the Gbp genes followed an unusual pattern of gain and loss of genes. Muroids present a high diversity and plasticity regarding Gbp synteny, with most species presenting two Gbp gene clusters. The phylogenetic analyses revealed seven different Gbps groups. Three of them clustered with GBP2, GBP5 and GBP6 of primates. Four new Gbp genes that appear to be exclusive to muroids were identified as Gbpa, b, c and d. A duplication event occurred in the Gbpa group in the common ancestor of Muridae and Cricetidae (~20 Mya), but both copies were deleted from the genome of Mus musculus, M. caroli and Cricetulus griseus. The Gbpb gene emerged in the ancestor of Muridae and Cricetidae and evolved independently originating Gbpb1 in Muridae, Gbpb2 and Gbpb3 in Cricetidae. Since Gbpc appears only in three species, we hypothesize that it was present in the common ancestor and deleted from most muroid genomes. The second Gbp gene cluster, Gbp6, is widespread across all muroids, indicating that this cluster emerged before the Muridae and Cricetidae radiation. An expansion of Gbp6 occurred in M. musculus and M. caroli probably to compensate the loss of Gbpa and b. Gbpd is divided in three groups and is present in most muroids suggesting that a duplication event occurred in the common ancestor of Muridae and Cricetidae. However, in Grammomys surdaster and Mus caroli, Gbpd2 is absent, and in Arvicanthis niloticus, Gbpd1 appears to have been deleted. Our results further demonstrated that primate GBP1, GBP3 and GBP7 are absent from the genome of muroids and showed that the Gbp gene annotations in muroids were incorrect. We propose a new classification based on the phylogenetic analyses and the divergence between the groups. Extrapolations to humans based on functional studies of muroid Gbps should be re-evaluated. The evolutionary analyses of muroid Gbp genes provided new insights about the evolution and function of these genes.

Ecological correlates of the morphology of the auditory bulla in rodents: Application to the fossil record

For rodents, hearing is essential to survival. It enables predator evasion, prey detection, and conspecific recognition; it is also likely to be constrained by the physical environment. The resulting hypothetical link between tympanic bulla morphology and ecology has never been investigated across a broad array of rodent species before. Such link may enable the determination of the ecological affinities of many fossil species only known from partial skulls. In this study, we used geometric morphometrics to quantify the shape of the auditory bulla of 197 specimens representing 91 species from 17 families of extant rodents across four different locomotory modes. We used landmarks and semi-landmarks on the ventral and lateral views of the skull to capture morphological characteristics of the bulla and external auditory meatus (EAM). Our results demonstrate an association between bullar morphology and locomotion in rodents. Bullar shape enables the correct classification of 76% of the species in our training set. Fossorial taxa, in particular, show a characteristic morphology including an asymmetric bulla with a dorsally located and laterally expanded EAM that has a small opening diameter. A phylogenetically informed flexible discriminant analysis shows a weak phylogenetic effect on tympanic morphology. There is no evidence for differences in bullar hypertrophy across locomotory categories. The application of this approach to select fossil rodents from the Oligo-Miocene shows broad agreements with prior studies and yields new locomotory inferences for 14 fossil species, including the first proposed locomotion for members of the family Florentiamyidae. Such results call for the timing of burrowing diversification in rodents to be reevaluated.

A remarkable rodent: Regeneration and reproduction in spiny mice (Acomys)

Although certain organisms are chosen and employed to better understand a specific problem in biology (so-called model organisms), sometimes an animal model reveals its' biomedical importance by happenstance. In many ways, the advent of spiny mice (Acomys) as an emerging model to study regeneration and menstruation stands as a case study in scientific pseudoserendipity (Diaz de Chumaceiro, 1995). As we recount in this chapter, the discovery of these phenotypes, while not entirely accidental, was nonetheless unexpected. In addition to recounting how we uncovered these unusual mammalian traits, we outline recent work by our groups and others that has begun to outline the cellular and genetic mechanisms underlying bonafide mammalian tissue regeneration and a human-like mode of reproduction in spiny mice.

Comparative Mitogenome Analysis of Gerbils and the Mitogenome Phylogeny of Gerbillinae (Rodentia: Muridae)

To enrich the mitogenomic database of Gerbillinae (Rodentia: Muridae), mitogenomes of three gerbils from different genera, Meriones tamariscinus (16,393 bp), Brachiones przewalskii (16,357 bp), and Rhombomys opimus (16,352 bp), were elaborated and compared with those of other gerbils in the present study. The three gerbil mitogenomes consisted of 2 ribosomal RNA genes, 13 protein-coding genes (PCGs), 22 transfer RNA genes, and one control region. Here, gerbil mitogenomes have shown unique characteristics in terms of base composition, codon usage, non-coding region, and the replication origin of the light strand. There was no significant correlation between the nucleotide percentage of G + C and the phylogenetic status in gerbils, and between the GC content of PCGs and the leucine count. Phylogenetic relationships of the subfamily Gerbillinae were reconstructed by 7 gerbils that represented four genera based on concatenated mitochondrial DNA data using both Bayesian Inference and Maximum Likelihood. The phylogenetic analysis indicated that M. tamariscinus was phylogenetically distant from the genus Meriones, but has a close relationship with R. opimus. B. przewalskii was closely related to the genus Meriones rather than that of R. opimus.

Skull morphological evolution in Malagasy endemic Nesomyinae rodents

Madagascar is a large island to the south-east of Africa and in many ways continental in size and ecological complexity. Here we aim to define how skull morphology of an endemic and monophyletic clade of rodents (sub-family Nesomyinae), that show considerable morphological variation, have evolved and how their disparity is characterized in context of the geographical and ecological complexity of the island. We performed a two-dimensional geometric morphometric analysis on 370 dorsal and 399 ventral skull images of 19 species (comprising all nine extant endemic genera) and tested the influence of three ecological parameters (climate, locomotor habitat and nychthemeral cycle) in a phylogenetic context on size and shape. The results indicate that skull shape appears to importantly reflect phylogeny, whereas skull size does not carry a significant phylogenetic signal. Skull shape is significantly influenced by climate while, skull size is not impacted by any of the ecological factors tested, which is controversial to expectations in an insular context. In conclusion, Nesomyinae must have evolved under unusual types of local constraints, preventing this radiation from demonstrating strong ecological release.

Desmodilliscus braueri crania compared to Pachyuromys duprasi (Desmodilliscini, Gerbillinae, Rodentia)

Molecular phylogenies support the monophyly of Desmodilliscus braueri and Pachyuromys duprasi as a clade basally split from all other gerbillines. While this monophyly supports their placement in a single tribe (Desmodilliscini), no morphological synapomorphies exist among desmodilliscines. This study compares the scale-independent cranial shapes of these two species using geometric morphometrics to determine how they differ and/or converge. Tribal synapomorphies, should they exist, may appear as interspecifically invariable cranial regions. No such invariable cranial regions were detected. The two species significantly differed in cranial size and shape. A small part of shape variation was allometric, with a weak unique allometric effect. No sexual size nor shape dimorphism was found. The sister taxa greatly differed in almost all cranial features, with Pachyuromys (when compared to Desmodilliscus) having a larger-sized cranium, with a larger bulla and suprameatal triangle, a more posteriorly placed palatine foramina, and more anteriorly shifted (and reduced) rostral cranial structures, due to being crowded by the hypertrophied bulla. Cranial variation patterns are consistent with the literature. The extreme morphological divergence among these species is explained by the distant divergence time and ecological differences. Absence of cranial shape synapomorphies does not preclude synapomorphies in other craniodental morphological features (e.g., detailed morphology of the dentition and cranial foramina) or in other morphological structures, such as the postcranial skeleton.

Keeping an ear out: size relationship of the tympanic bullae and pinnae in bandicoots and bilbies (Marsupialia: Peramelemorphia)

Bandicoots and bilbies (Order Peramelemorphia) occupy a broad range of habitats across Australia and New Guinea, from open, arid deserts to dense forests. This once diverse group has been particularly vulnerable to habitat loss and introduced eutherian predators, and numerous species extinctions and range retractions have occurred. Understanding reasons for this loss requires greater understanding of their biology. Morphology of the pinnae and tympanic bullae varies markedly among species. As hearing is important for both predator avoidance and prey location, the variability in ear morphology could reflect specialization and adaptation to specific environments, and therefore be of conservation relevance. We measured 798 museum specimens representing 29 species of Peramelemorphia. Controlling for phylogenetic relatedness and head length, pinna surface area was weakly negatively correlated with average precipitation (rainfall being our surrogate measure of vegetation productivity/complexity), and there were no environmental correlates with effective diameter (pinna width). Controlling for phylogenetic relatedness and skull length, tympanic bulla volume was negatively correlated with precipitation. Species that inhabited drier habitats, which would be open and allow sound to carry further with less obstruction, had relatively larger pinnae and tympanic bullae. In contrast, species from higher rainfall habitats, where sounds would be attenuated and diffused by dense vegetation, had the smallest pinnae and bullae, suggesting that low-frequency hearing is not as important in these habitats. Associations with temperature did not reach statistical significance. These findings highlight linkages between hearing traits and habitat that can inform conservation and management strategies for threatened species.

Diversification of the cranium and mandible of spiny rats of the genus Trinomys (Rodentia: Echimyidae) in an environmental and phylogenetic context

Evolutionary constraints and ecological pressures influence species’ morphological diversity. The aim of this study was to explore patterns of morphological variation, to investigate the influence of environmental variables on morphological differentiation, and assess the strength of phylogenetic signal for the cranium and mandible in spiny rats of the genus Trinomys. We examined 377 crania and mandibles of all species of the genus Trinomys. We used geometric morphometric methods based on two-dimensional anatomical landmarks to describe cranium and mandible shape and size. Phylogenetic signal was tested using the K statistics and associations between morphology and environmental variables were made using a phylogenetic partial least squares analysis. We found marked differences in size and shape in the synchranium among species, especially in the segregation of T. albispinus and T. yonenagae from the other species, which in turn greatly overlapped both in size and shape spaces. We found a weak phylogenetic signal for size of the synchranium and intermediate phylogenetic signals for shape, a pattern similar to other studies. Differentiation of the synchranium shape in Trinomys was associated largely with precipitation-related variables, while the association between size and environmental variables was weak. Notably, Trinomys species inhabiting xeric environments had relatively larger tympanic bullae.

Distribution of Vasopressin and Oxytocin Neurons in the Basal Forebrain and Midbrain of Spiny Mice (Acomys cahirinus)

The nonapeptides vasopressin (VP) and oxytocin (OT) are present in some form in most vertebrates. VP and OT play critical roles in modulating physiology and are well-studied for their influences on a variety of social behaviors, ranging from affiliation to aggression. Their anatomical distributions have been mapped for numerous species across taxa, demonstrating relatively strong evolutionary conservation in distributions throughout the basal forebrain and midbrain. Here we examined the distribution of VP-immunoreactive (-ir) and OT-ir neurons in a gregarious, cooperatively breeding rodent species, the spiny mouse (Acomys cahirinus), for which nonapeptide mapping does not yet exist. Immunohistochemical techniques revealed VP-ir and OT-ir neuronal populations throughout the hypothalamus and amygdala of males and females that are consistent with those of other rodents. However, a novel population of OT-ir neurons was observed in the median preoptic nucleus of both sexes, located dorsally to the anterior commissure. Furthermore, we found widespread sex differences in OT neuronal populations, with males having significantly more OT-ir neurons than females. However, we observed a sex difference in only one VP cell group - that of the bed nucleus of the stria terminalis (BST), a VP neuronal population that exhibits a phylogenetically widespread sexual dimorphism. These findings provide mapping distributions of VP and OT neurons in Acomys cahirinus. Spiny mice lend themselves to the study of mammalian cooperation and sociality, and the nonapeptide neuronal mapping presented here can serve as a basic foundation for the study of nonapeptide-mediated behavior in a group of highly social rodents.

Pup ultrasonic isolation calls of six gerbil species and the relationship between acoustic traits and body size

Among Gerbillinae rodents, ultrasonic calls of adults of small-sized species are typically higher frequency than those of adults of large-sized species. This study investigates whether a similar relationship can be found in pups of six gerbil species (Dipodillus campestris, Gerbillus perpallidus, Meriones unguiculatus, Meriones vinogradovi, Sekeetamys calurus and Pachyuromys duprasi). We compared the average values of acoustic variables (duration, fundamental and peak frequency) of ultrasonic calls (20 calls per pup, 1200 in total) recorded from 6- to 10-day-old pups (10 pups per species, 60 in total) isolated for 2 min at 22°C and then weighed and measured for body variables. The longest calls (56 ± 33 ms) were found in the largest species, and the highest frequency calls (74.8 ± 5.59 kHz) were found in the smallest species. However, across species, call duration (ranging from 56 to 159 ms among species) did not display a significant relationship with pup body size; and, among frequency variables, only the minimum fundamental frequency depended on pup body size. Discriminant analysis assigned 100% of calls to the correct species. The effect of species identity on the acoustics was stronger than the effect of body size. We discuss these results with the hypotheses of acoustic adaptation, social complexity, hearing ranges and phylogeny.

Habitat productivity is a poor predictor of body size in rodents

The “resource availability hypothesis” predicts occurrence of larger rodents in more productive habitats. This prediction was tested in a dataset of 1,301 rodent species. We used adult body mass as a measure of body size and normalized difference vegetation index (NDVI) as a measure of habitat productivity. We utilized a cross-species approach to investigate the association between these variables. This was done at both the order level (Rodentia) and at narrower taxonomic scales. We applied phylogenetic generalized least squares (PGLS) to correct for phylogenetic relationships. The relationship between body mas and NDVI was also investigated across rodent assemblages. We controlled for spatial autocorrelation using generalized least squares (GLS) analysis. The cross-species approach found extremely low support for the resource availability hypothesis. This was reflected by a weak positive association between body mass and NDVI at the order level. We find a positive association in only a minority of rodent subtaxa. The best fit GLS model detected no significant association between body mass and NDVI across assemblages. Thus, our results do not support the view that resource availability plays a major role in explaining geographic variation in rodent body size.

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.

Associated tympanic bullar and cochlear hypertrophy define adaptations to true deserts in African gerbils and laminate-toothed rats (Muridae: Gerbillinae and Murinae)

Hearing capabilities in desert rodents such as gerbils and heteromyids have been inferred from both anatomical and ecological aspects and tested with experiments and theoretical models. However, very few studies have focused on other desert-adapted species. In this study, a refined three-dimensional morphometric approach was used on three African rodent tribes (Otomyini, Taterillini and Gerbillini) to describe the cochlear and tympanic bullar morphology, and to explore the role of phylogeny, allometry and ecology to better understand the underlying mechanism of any observed trends of hypertrophy in the bulla and associated changes in the cochlea. As a result, desert-adapted species could be distinguished from mesic and semi-arid taxa by the gross cochlear dimensions, particularly the oval window, which is larger in desert species. Bullar and cochlear modifications between species could be explained by environment (bulla and oval window), phylogeny (cochlear curvature gradient) and/or allometry (cochlear relative length, oval window and bulla) with some exceptions. Based on their ear anatomy, we predict that Desmodillus auricularis and Parotomys brantsii should be sensitive to low-frequency sounds, with D. auricularis sensitive to high-frequency sounds, too. This study concludes that in both arid and semi-arid adapted laminate-toothed rats and gerbils there is bulla and associated cochlea hypertrophy, particularly in true desert species. Gerbils also show tightly coiled cochlea but the significance of this is debatable and may have nothing to do with adaptations to any specific acoustics in the desert environment.

Ancient Evolutionary Origin and Positive Selection of the Retroviral Restriction Factor Fv1 in Muroid Rodents

The laboratory mouse Fv1 gene encodes a retroviral restriction factor that mediates resistance to murine leukemia viruses (MLVs). Sequence similarity between Fv1 and the gag protein of the murine endogenous retrovirus L (MuERV-L) family of ERVs suggests that Fv1 was coopted from an ancient provirus. Previous evolutionary studies found Fv1 orthologs only in the genus Mus Here, we describe identification of orthologous Fv1 sequences in several species belonging to multiple families of rodents outside the genus Mus We show that these Fv1 orthologs are in the same region of conserved synteny, between the genes Miip and Mfn2, suggesting a minimum insertion time of 45 million years for the ancient progenitor of Fv1 Our analysis also revealed that Fv1 was not detectable or heavily mutated in some lineages in the superfamily Muroidea, while, in concert with previous findings in the genus Mus, we found strong evidence of positive selection of Fv1 in the African clade in the subfamily Muridae Residues identified as evolving under positive selection include those that have been previously found to be important for restriction of multiple retroviral lineages. Taken together, these findings suggest that the evolutionary origin of Fv1 substantially predates Mus evolution, that the rodent Fv1 has been shaped by lineage-specific differential selection pressures, and that Fv1 has long been evolving under positive selection in the rodent family Muridae, supporting a defensive role that significantly antedates exposure to MLVs.IMPORTANCE Retroviruses have adapted to living in concert with their hosts throughout vertebrate evolution. Over the years, the study of these relationships revealed the presence of host proteins called restriction factors that inhibit retroviral replication in host cells. The first of these restriction factors to be identified, encoded by the Fv1 gene found in mice, was thought to have originated in the genus Mus In this study, we utilized genome database searches and DNA sequencing to identify Fv1 copies in multiple rodent lineages. Our findings suggest a minimum time of insertion into the genome of rodents of 45 million years for the ancestral progenitor of Fv1 While Fv1 is not detectable in some lineages, we also identified full-length orthologs showing signatures of a molecular "arms race" in a family of rodent species indigenous to Africa. This finding suggests that Fv1 in these species has been coevolving with unidentified retroviruses for millions of years.

Phylogenetic heritability of geographic range size in haematophagous ectoparasites: time of divergence and variation among continents

To understand existence, patterns and mechanisms behind phylogenetic heritability in the geographic range size (GRS) of parasites, we measured phylogenetic signal (PS) in the sizes of both regional (within a region) and continental (within a continent) geographic ranges of fleas in five regions. We asked whether (a) GRS is phylogenetically heritable and (b) the manifestation of PS varies between regions. We also asked whether geographic variation in PS reflects the effects of the environment's spatiotemporal stability (e.g. glaciation disrupting geographic ranges) or is associated with time since divergence (accumulation differences among species over time). Support for the former hypothesis would be indicated by stronger PS in southern than in northern regions, whereas support for the latter hypothesis would be shown by stronger PS in regions with a large proportion of species belonging to the derived lineages than in regions with a large proportion of species belonging to the basal lineages. We detected significant PS in both regional and continental GRSs of fleas from Canada and in continental GRS of fleas from Mongolia. No PS was found in the GRS of fleas from Australia and Southern Africa. Venezuelan fleas demonstrated significant PS in regional GRS only. Local Indicators of Phylogenetic Association detected significant local positive autocorrelations of GRS in some clades even in regions in which PS has not been detected across the entire phylogeny. This was mainly characteristic of younger taxa.

Taxonomic hypotheses regarding the genus Gerbillus (Rodentia, Muridae, Gerbillinae) based on molecular analyses of museum specimens

Methodological improvements now allow routine analyses of highly degraded DNA samples as found in museum specimens. Using these methods could be useful in studying such groups as rodents of the genus Gerbillus for which i) the taxonomy is still highly debated, ii) collection of fresh specimens may prove difficult. Here we address precise taxonomic questions using a small portion of the cytochrome b gene obtained from 45 dry skin/skull museum samples (from 1913 to 1974) originating from two African and three Asian countries. The specimens were labelled Gerbillusgerbillus, Gerbillusandersoni, Gerbillusnanus, Gerbillusamoenus, Gerbillusperpallidus and Gerbilluspyramidum, and molecular results mostly confirmed these assignations. The close relationship between Gerbillusnanus (Asian origin) and Gerbillusamoenus (African origin) confirmed that they represent vicariant sibling species which differentiated in allopatry on either side of the Red Sea. In the closely related Gerbillusperpallidus and Gerbilluspyramidum, specimens considered as belonging to one Gerbilluspyramidum subspecies (Gerbilluspyramidumfloweri) appeared closer to Gerbillusperpallidus suggesting that they (Gerbilluspyramidumfloweri and Gerbillusperpallidus) may represent a unique species, distributed on both sides of the Nile River, for which the correct name should be Gerbillusfloweri. Furthermore, the three other Gerbilluspyramidum subspecies grouped together with no apparent genetic structure suggesting that they may not yet represent genetically differentiated lineages. This study confirms the importance of using these methods on museum samples, which can open new perspectives in this particular group as well as in other groups of interest.