Rodent Genus Research Articles

Phylogenetic position of Leimacomys, an enigmatic African rodent genus, reconsidered in the light of morphological and its first genetic data

Abstract The family Muridae represents the most diversified clade of rodents. Their remarkable convergent morphology has challenged taxonomists to establish a robust classification. Thanks to molecular phylogenetic analyses, five subfamilies of murid rodents are hereby defined: Lophiomyinae, Deomyinae, Gerbillinae, Leimacomyinae and Murinae. As the single representative of the subfamily Leimacomyinae, Leimacomys buettneri is known only by the first two specimens collected in 1890. It was classified either as belonging to the Dendromurinae (Nesomyidae), or recently placed in its own subfamily Leimacomyinae (Muridae). Here we present the first molecular genetic analysis of the holotype and the paratype of Leimacomys by genomic skimming and assembly of the mitogenomes. It confirms that Leimacomys belongs to the Muridae as a sister to all extant Deomyinae. As a result, we have re-examined the morphology of type specimens and compared them with deomyine taxa as well as Miocene fossil rodents that are considered as murid-like ancestors. This allows us to propose an updated scenario for the origins of the murid lineages. In the light of our novel genetic and morphological data, we propose to keep the subfamily Leimacomyinae, represented by the monotypic Leimacomys, within the family Muridae.

New data about Calomys tocantinsi (Sigmodontinae) distribution

Calomys is a rodent genus widely distributed in South America comprising 13 species, the most of species associated with savannas and grasslands in Brazil, Bolivia, Peru, Argentina, Paraguay, Uruguay, and Chile. Among Calomys species, two Brazilian endemic species have small distributions, C. cerqueirai and C. tocantinsi, this latter known only for seven localities. Here we extend the distribution of C. tocantinsi in 400km to the north, up to Canaã dos Carajás, in the Brazilian state of Pará. Our data suggest that this species is not endemic to the Cerrado and transition areas, but also occurs in the Amazon domain.

Host sweet host: Rodent communities support similar ectoparasite diversity regardless of anthropogenic disturbance

AbstractRodents are important hosts for ectoparasites, such as fleas, ticks, and mites, which means they are also important intermediate hosts for many zoonotic diseases. As anthropogenic environments bring humans and rodents into closer contact, an understanding of host–ectoparasite ecology is essential to predict and manage disease spillover risks. We aimed to understand how disturbances in vegetation cover affect rodent ectoparasite diversity, prevalence, spatial segregation, host (i.e., sex, genus, size, and habitat domain), and environmental (i.e., vegetation structure, forest cover, and rainfall) variables in the state of Michoacan, Mexico. We investigated these relationships by trapping rodents in five paired disturbed (reduced vegetation cover and regular human activities) and undisturbed (no reduction in vegetation cover) sites in the summer and autumn of 2022. From 110 trapped rodents, we collected 138 ectoparasites on 38 individuals. We found no difference in rodent diversity, ectoparasite diversity, or ectoparasite prevalence between disturbed and undisturbed sites. However, arboreal and male rodents had a higher probability of carrying ectoparasites than ground‐dwelling and female rodents. Rodents with ectoparasites were not spatially clustered; rather, they were randomly distributed across trapping grids. We also identified two rodent genera (Rattus and Sigmodon) that carry ectoparasites of medical importance and that are in close contact with humans. Our results highlight the necessity of constant monitoring of rodents, ectoparasites, and their associated transmittable diseases. Assessing these interactions and how they are affected by anthropogenic disturbance could better inform management decisions and support the need for rodent conservation programmes in the area.

The genomic diversity of the Eliurus genus in northern Madagascar with a putative new species

Madagascar exhibits extraordinarily high level of species richness and endemism, while being severely threatened by habitat loss and fragmentation (HL&F). In front of these threats to biodiversity, conservation effort can be directed, for instance, in the documentation of species that are still unknown to science, or in investigating how species respond to HL&F. The tufted-tail rats genus (Eliurus spp.) is the most speciose genus of endemic rodents in Madagascar, with 13 described species, which occupy two major habitat types: dry or humid forests. The large species diversity and association to specific habitat types make the Eliurus genus a suitable model for investigating species adaptation to new environments, as well as response to HL&F (dry vs humid). In the present study, we investigated Eliurus spp. genomic diversity across northern Madagascar, a region covered by both dry and humid fragmented forests. From the mitochondrial DNA (mtDNA) and nuclear genomic (RAD-seq) data of 124 Eliurus individuals sampled in poorly studied forests of northern Madagascar, we identified an undescribed Eliurus taxon (Eliurus sp. nova). We tested the hypothesis of a new Eliurus species using several approaches: i) DNA barcoding; ii) phylogenetic inferences; iii) species delimitation tests based on the Multi-Species Coalescent (MSC) model, iv) genealogical divergence index (gdi); v) an ad-hoc test of isolation-by-distance within versus between sister-taxa, vi) comparisons of %GC content patterns and vii) morphological analyses. All analyses support the recognition of the undescribed lineage as a putative distinct species. In addition, we show that Eliurus myoxinus, a species known from the dry forests of western Madagascar, is, surprisingly, found mostly in humid forests in northern Madagascar. In conclusion, we discuss the implications of such findings in the context of Eliurus species evolution and diversification, and use the distribution of northern Eliurus species as a proxy for reconstructing past changes in forest cover and vegetation type in northern Madagascar.

A new mammalian universal primer for the mitochondrial cytochrome b locus

We designed a set of amplification primers to target the mitochondrial cytochrome b gene of the rodent genus Oligoryzomys. Combinations of two sets of primers successfully amplified complete mitochondrial and partial cytochrome b (MT-CYB), from not only Oligoryzomys, but also other mammalian species from the orders Rodentia, Didelphimorphia, Primates, Chiroptera, Cetacea, Carnivora, and Lagomorpha. Preliminary sequencing analyses revealed that these primers generate informative sequences for several mammalian species important for phylogenetic and species delimitation analyses.

To what extent do physiological tolerances determine elevational range limits of mammals?

A key question in biology concerns the extent to which distributional range limits of species are determined by intrinsic limits of physiological tolerance. Here, we use common-garden data for wild rodents to assess whether species with higher elevational range limits typically have higher thermogenic capacities in comparison to closely related lowland species. Among South American leaf-eared mice (genus Phyllotis), mean thermogenic performance is higher in species with higher elevational range limits, but there is little among-species variation in the magnitude of plasticity in this trait. In the North American rodent genus Peromyscus, highland deer mice (Peromyscus maniculatus) have greater thermogenic maximal oxygen uptake ( ) than lowland white-footed mice (Peromyscus leucopus) at a level of hypoxia that matches the upper elevational range limit of the former species. In highland deer mice, the enhanced thermogenic in hypoxia is attributable to a combination of evolved and plastic changes in physiological pathways that govern the transport and utilization of O2 and metabolic substrates. Experiments with Peromyscus mice also demonstrate that exposure to hypoxia during different stages of development elicits plastic changes in cardiorespiratory traits that improve thermogenic via distinct physiological mechanisms. Evolved differences in thermogenic capacity provide clues about why some species are able to persist in higher-elevation habitats that lie slightly beyond the tolerable limits of other species. Such differences in environmental tolerance also suggest why some species might be more vulnerable to climate change than others.

Novel genomic resources contribute to the systematics of threatened arboreal deer mice of the genus Habromys Hooper & Musser, 1964 (Cricetidae, Neotominae) within a neotomine-peromyscine phylogeny.

The Crested-tailed deer mouse, Habromyslophurus, is one of seven arboreal species within the genus Habromys. Species of this genus are monotypic, relatively rare, and occur in low densities. Their geographical distribution is highly fragmented due to being restricted to montane cloud forest in Mesoamerica and they are of conservation concern. All Habromys species are endemic to Mexico, except H.lophurus, which is also distributed in Guatemala and El Salvador. In this study, we obtained and characterized the first mitogenome and several thousand nuclear ultraconserved elements (UCEs) of H.lophurus to determine its phylogenetic position within neotomine-peromyscine mice. Its mitogenome sequence (16,509 bp) is only the second complete mitogenome obtained for this poorly known genus. We also obtained the first nuclear genomic data for H.lophurus, including 3,654 UCE loci, as well as a partial mitogenome of H.simulatus (6,349 bp), and 2,186 UCE for the outgroup Holochilussciureus. Phylogenetic analyses that included our newly generated genomic data coupled with previously published data from other neotomine-peromyscine mice confirm the placement of H.lophurus, H.simulatus, and H.ixtlani within a highly supported clade. The Habromys clade was nested within a clade that also contains members of the genus Peromyscus and provides further support for the hypothesis of the paraphyly of Peromyscus. These genomic resources will contribute to future phylogenomic studies that aim to further elucidate the evolutionary history of this rare and critically endangered genus of rodents.

Establishing the availability of the mammalian genus name Antillomys and species name Antillomys rayi (Rodentia, Cricetidae)

The rodent genus name Antillomys and the species name Antillomys rayi (Cricetidae: Sigmodontinae) are unavailable, given that the publication where it originally appears did not satisfy the requirements of the International Code of Zoological Nomenclature. The names were formally described in the supplementary information (electronic online text) in Word format, and the work itself did not contain evidence that it was registered in Zoobank, as per Article 8.5.3 (amended) of the International Code of Zoological Nomenclature. In this note we establish the availability of the names Antillomys and Antillomys rayi, by fulfilling ICZN´s requirements.

An integrative approach to explore species limits in Laelaps mazzai Fonseca, 1939 (Mesostigmata, Laelapidae), a South American widespread mite parasitizing the cricetid Calomys Waterhouse, 1837

Laelaps mazzai Fonseca, 1939 (Mesostigmata, Laelapidae) parasitizes several species of the widespread South American rodent genus Calomys Waterhouse, 1837. Morphological variation has been noticed within this laelapid but has yet to be analyzed. Since several other species of laelapids that initially were considered generalists have resulted in host-specific species, after further analyses, herein we explored, through morphology and genetics, the variation of this parasite across six species of Calomys, trying to establish if it constitutes a polymorphic species or a complex of cryptic host specific-species. An integrative approach was applied, including principal component and discriminant analyses of females and males and DNA sequences (nuclear region ITS and the COI gene). The obtained results indicate that female mites tend to differentiate only the sizes of their dorsal shield among host species but with extensive overlapping. At the same time the males lack metrical differentiation, and the genetic evidence failed to resolve specific-species clades. We conclude that L. mazzai is a single widespread mite with little genetic and phenotypic differentiation.

A new genus and species of arvicolid rodent (Mammalia) from the early Pleistocene of Spain

In this paper, a new genus and species of arvicolid rodent is described from the late early Pleistocene levels of the sections of Fuente Nueva 3 (Guadix-Baza Basin, Granada, southern Iberian Peninsula), and Quibas (Murcia, southeastern Iberian Peninsula). The majority of Manchenomys n. gen. molars lacks roots, and the morphology of the first lower molar (m1) is simple, with a short and rounded anteroconid complex and widely confluent triangles four and five (T4 and T5) fields.

Evolution in reproductive tempo and investment across the Peromyscus radiation.

Mammals display diverse reproductive strategies, however, the ultimate and proximate mechanisms that underlie this diversity and its composite traits remain poorly understood from both evolutionary and physiological perspectives. The Peromyscus genus of rodents, which is found throughout the north and central Americas, has diversified along life history gradients, varying both within and among species in reproductive strategies. This variation provides a useful model for studying reproductive diversity. Here, we combine a literature review with new analyses of captive colony breeding records from sixPeromyscus species to assess our current understanding of how plasticity and local adaptation contribute to diversity in two classes of reproductive traits: phenology and litter investment. There is substantial evidence that many traits underlying phenology and litter investment have diverged among populations in ways that are likely to be locally adaptive, though plasticity in these traits remains common. However, these conclusions are largely based on data collected from the two most widespread Peromyscus species: P. maniculatus and P. leucopus. The majority of Peromyscus species diversity remains understudied regarding reproductive phenology and litter traits. We conclude by discussing key challenges and considerations relevant to using Peromyscus as a mammalian model for reproductive trait diversity and evolution moving forward.

Museomics and the holotype of a critically endangered cricetid rodent provide key evidence of an undescribed genus

Historical DNA obtained from voucher specimens housed in natural history museums worldwide have allowed the study of elusive, rare or even extinct species that in many cases are solely represented by museum holdings. This has resulted in the increase of taxonomic representation of many taxa, has led to the discovery of new species, and has yielded stunning novel insights into the evolutionary history of cryptic or even undescribed species. Peromyscus mekisturus, is a critically endangered cricetid rodent endemic to Mexico and is only known from two museum specimens collected in 1898 and 1947. Intensive field work efforts to attempt to determine if viable populations still exist have failed, suggesting that this species is extinct or is nearing extinction. In addition, a recent study using mitogenomes demonstrated that P. mekisturus forms a well-supported clade outside the genus Peromyscus and hypothesized that this taxon is the sister group of the genus Reithrodontomys. Here, we used target enrichment and high-throughput sequencing of several thousand nuclear ultraconserved elements and mitogenomes to reconstruct dated phylogenies to test the previous phylogenetic hypothesis. We analyzed the holotype and the only other known specimen of P. mekisturus and museum samples from other peromyscine rodents to test the phylogenetic position of the species. Our results confirm that the only two specimens known to science of P. mekisturus belong to the same species and support the hypothesis that this species belongs to an undescribed genus of cricetid rodents that is sister to the genus Reithrodontomys. We dated the origin of P. mekisturus together with other speciation events in peromyscines during the late Pliocene – early Pleistocene and related these events with the Pleistocene climatic cycles. In light of our results, we recommend a taxonomic re-evaluation of this enigmatic species to properly recognize its taxonomic status as a new genus. We also acknowledge the relevance of generating genomic data from type specimens and highlight the need and importance of continuing to build the scientific heritage of the collections to study and better understand past, present, and future biodiversity.

A new genus and species of shrew-like mouse (Rodentia: Muridae) from a new center of endemism in eastern Mindanao, Philippines.

The Philippine archipelago hosts an exceptional diversity of murid rodents that have diversified following several independent colonization events. Here, we report the discovery of a new species of rodent from Mt. Kampalili on eastern Mindanao Island. Molecular and craniodental analyses reveal this species as a member of a Philippine "New Endemic" clade consisting of Tarsomys, Limnomys, and Rattus everetti (tribe Rattini). This new species of "shrew-mouse" is easily distinguished from its relatives in both craniodental and external characteristics including a long, narrow snout; small eyes and ears; short, dark, dense fur dorsally and ventrally; stout body with a tapering, visibly haired tail shorter than head and body length; stout forepaws; bulbous and nearly smooth braincase; narrow, tapering rostrum; short incisive foramina; slender mandible; and narrow, slightly opisthodont incisors. This new genus and species of murid rodent illustrates that murids of the tribe Rattini have exhibited greater species and morphological diversification within the Philippines than previously known and provides evidence that Mt. Kampalili represents a previously unrecognized center of mammalian endemism on Mindanao Island that is deserving of conservation action.

Fluorescence and UV–visible reflectance in the fur of several Rodentia genera

Mammals are generally brown in colour, but recent publications are showing that they may not be as uniform as once assumed. Monotremes, marsupials, and a handful of eutherians reflect various colours when lit with UV light, mostly purple. Because of these still scarce records, we aimed to explore UV reflectance among rodent genera, the most diverse mammalian group, and the group of eutherians with the most common records of biofluorescence. Here we report structures like nails and quills reflected green, but for most genera, it was faded. However, Hystrix, Erethizon, and Ctenomys showed intense and contrasting green glow, while Chaetomys presented a vivid orange anogenital. The main available explanation of fluorescence in mammals relies on porphyrin. This explanation applies to the cases like Chaetomys, where specimens showed anogenital orange biofluorescence, but does not apply to the green biofluorescence we observed. In our sample, because the structures that reflected green were all keratinized, we have reasons to believe that biofluorescence results from keratinization and is a structurally-based colouration. However, not all spines/quills equally biofluoresced, so we cannot rule out other explanations. Since Rodentia is the most common mammalian group with reports on biofluorescence, this trait likely serves various functions that match the species diversity of this group.

Sexual behavior of Ctenomys pearsoni (Rodentia: Ctenomyidae) in “Carrasco” population (Montevideo - Uruguay)

Ctenomys is a genus of South American subterranean rodents that is distributed from Peru to southern Argentina and Uruguay. The present work studies the reproductive behavior (courtship and copula) of Ctenomys pearsoni (Carrasco population, Uruguay). To carry out the characterization, we used an ethogram with 19 behavioral units grouped into different categories. By studying 10 couples we quantified the frequency of occurrence and the time invested in each behavioral unit during the development of the interaction. Through the analysis of the results, the roles of each partner and the importance of each one's role in the development of reproductive behavior are inferred. The results obtained are compared with the data available for other populations of the species and other species of the genus. We discussed the relevance of classifying the reproductive pattern on the basis of the Dewsbury classification. Finally, the importance of each sex in the development and molding of reproductive behavior is discussed.

A century of stasis: Taxonomy of Ctenomys (Rodentia: Hystricomorpha) populations in northeastern Patagonia limits, Argentina

The South American rodent genus Ctenomys is well represented throughout much of southern Patagonia by the polytypic “magellanicus” lineage. In western Argentina, members of this lineage occur from 35 °S to 54 °S latitude. In comparison, the taxonomy of Ctenomys in northeastern Patagonia remains poorly known. This ∼160,000 km2 region consists primarily of mostly flat, homogenous tracts of austral Monte desert covering a gravel substrate and is cut by two major fluvial systems associated with the Colorado and the Negro rivers. Here, we use mitochondrial sequences and morphological comparisons to describe phylogenetic relationships among recently sampled populations of Ctenomys from this region. These analyses indicate that the “magellanicus” lineage extends into northeastern Patagonia to at least the Negro river (40°S). Contained within this lineage are three latitudinally distinct clades that are separated by geographic features such as rivers and basaltic plateaus. Identification of these clades generates new insights into the phylogeographic history of the “magellanicus” lineage and marks the end to nearly a century of stasis regarding taxonomic studies of Ctenomys from northeastern Patagonia.

Variable social organization among tuco-tucos (genusCtenomys) in theopimusclade

AbstractComparative studies of closely related species provide a powerful means of identifying the ecological and demographic factors associated with variation in mammalian social systems. Although most members of the subterranean rodent genus Ctenomys are thought to be solitary, the highland tuco-tuco (C. opimus) is group living, meaning that multiple adults share a burrow system and underground nest site. These animals are part of the opimus clade, a monophyletic collection of four named species that occur in northwestern Argentina and adjacent portions of Chile and Bolivia. As a first step toward generating a comparative assessment of social organization within this clade, we characterized spatial relationships among members of a population of Ctenomys at Antofagasta de la Sierra, Catamarca Province, Argentina. Based on geographic location and natural history, these animals were expected to be part of the opimus clade; analyses of mitochondrial cytochrome-b sequences from our study population confirmed this general phylogenetic placement. Radiotelemetry data indicated that the animals at Antofagasta were group living, with up to three adult females and one adult male sharing a burrow system. In contrast to other group-living ctenomyids, however, individuals did not consistently share nest sites. Comparisons of these data with re-analyses of spatial relationships among members of the population of C. opimus studied by O’Brien et al. (2020) revealed several intriguing differences in social organization, potential explanations for which include short-term responses to variable demographic and ecological conditions as well as more enduring responses to differences in local selective pressures. Further comparative analyses of these populations and, more generally, members of this subclade of Ctenomys will help to elucidate the factors contributing to variation in social behavior within this speciose and geographically widespread genus.

Variation in brain volume in nine populations and three taxa of the African striped mouse Rhabdomys.

Brain size can vary between populations in different environments because of different selection pressures on behaviours, such as learning and memory, related to spatial, social and environmental differences. We investigated the variation in total and broad-scale regional brain size in the murid rodent genus Rhabdomys from different environments. We assessed taxon-, population- and sex-level differences in total and regional brain volume in three populations each of three taxa (arid-occurring Rhabdomys pumilio and mesic-occurring Rhabdomys dilectus chakae and R. d. dilectus) originating across southern Africa. We μCT-scanned crania obtained from museums in South Africa and used digital software to create endocasts and extract total endocranium and regional volumes: olfactory bulb, anterior cerebrum, posterior cerebrum, cerebellum volume and petrosal volume. Total endocranial volume scaled with basal skull length and all-region volumes scaled with total endocranial volume. We found taxon-, and population-level differences in total endocranial volume. Relative anterior and posterior cerebrum volume did not differ significantly between taxa or populations, but relative cerebellum volume was larger in arid populations than mesic populations. Relative olfactory bulb volume was larger in mesic R. dilectus than in the R. pumilio, but petrosal lobule volume was larger in R. pumilio populations than in R. dilectus. Males had larger total endocranial volumes than females. Drivers of larger total endocranial volumes in R. pumilio are not immediately clear from our results. Environmental seasonality of food availability, cognitive buffering and locomotion may all correlate with total endocranial volume size, whereas the influence of sociality cannot be excluded. The environment and degree of semi-arboreality are likely driving variation in cerebellum, olfactory bulb and petrosal lobule volumes.

Erratum to: Systematics of the rodent genus Neacomys Thomas (Cricetidae: Sigmodontinae): two new species and a discussion on carotid patterns

Erratum to: Systematics of the rodent genus Neacomys Thomas (Cricetidae: Sigmodontinae): two new species and a discussion on carotid patterns

Zoonotic vector-borne bacteria in wild rodents and associated ectoparasites from Tunisia.

Wild rodents are considered as potential carriers of several zoonotic vector-borne bacteria but their epidemiology is poorly understood in Tunisia. A total of 305 biological samples (100 spleens, 100 livers, 100 kidneys, and 5 pooled ectoparasites (Xenopsylla cheopis, Laelaps echidninus, Ornithonyssus sp., Hoplopleura sp. and eggs of the rat fleas)) were collected from 100 wild rodents from three Tunisian governorates. Molecular screening was performed to reveal infections with main vector-borne bacteria. Captured rodents belonged to three rodent genera and species including Rattus rattus (n=51, 51%), Meriones shawi (n=24, 24%) and Mus musculus (n=25, 25%). Examined rodents were found to be heavily infested by the rat flea X. cheopis (n=32, 47%) and the rat mite L. echidninus (n=22, 32.3%). However, the rat mite Ornithonyssus sp. (n=13, 19.1%) and the rat lice Hoplopleura sp. (n=1, 1.5%) were rarely identified. Based on 16S rRNA and msp4 genes, infection with Anaplasmataceae bacteria was detected in six specimens of R. rattus and one M. shawi. Pathogenic A. phagocytophilum (n=1), A. phagocytophilum-like 1 (Anaplasma sp. Japan) (n=1), and A. ovis (n=5) were identified. On the basis of ompB, ompA and gltA genes, infection with Rickettsia spp. was identified in three specimens of R. rattus and one of M. shawi. Five Rickettsia species of the spotted fever group, corresponding to R. monacensis, R. helvetica, R. massiliae, R. africae, and R. aeschlimannii, were detected in mixed infections. Bartonella henselae DNA was also found in two R. rattus, based on rpoB partial sequences. All revealed Anaplasma, Rickettsia and Bartonella bacteria were detected in spleen samples. Ehrlichia, Coxiella and Borrelia spp. were not identified in any of the tested samples. In Tunisia, this is the first report indicating infections with Anaplasma, Rickettsia and Bartonella spp. in wild rodents, particularly present alongside domestic livestock and human. This represents a serious risk of potential bacterial transmission. Thus, controlling rodent population in animal herds, residential areas and sensitizing local people to this risk seem absolutely necessary.