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Beyond visual perception, light has non-image-forming effects mediated by melanopsin-expressing, intrinsically photosensitive retinal ganglion cells (ipRGCs). The present study first used multielectrode array recordings to show that in a diurnal rodent, Nile grass rats (Arvicanthis niloticus), ipRGCs generate rod/cone-driven and melanopsin-based photoresponses that stably encode irradiance. Subsequently, two ipRGC-mediated non-image-forming effects, namely entrainment of daily rhythms and light-induced arousal, were examined. Animals were first housed under a 12:12 h light/dark cycle (lights-on at 0600 h) with the light phase generated by a low-irradiance fluorescent light (F12), a daylight spectrum (D65) stimulating all photoreceptors, or a narrowband 480 nm spectrum (480) that maximized melanopsin stimulation and minimized S-cone stimulation (λmax 360 nm) compared to D65. Daily rhythms of locomotor activities showed onset and offset closer to lights-on and lights-off, respectively, in D65 and 480 than in F12, and higher day/night activity ratio under D65 versus 480 and F12, suggesting the importance of S-cone stimulation. To assess light-induced arousal, 3-h light exposures using 4 spectra that stimulated melanopsin equally but S-cones differentially were superimposed on F12 background lighting: D65, 480, 480 + 365 (narrowband 365 nm), and D65 - 365. Compared to the F12-only condition, all four pulses increased in-cage activity and promoted wakefulness, with 480 + 365 having the greatest and longest-lasting wakefulness-promoting effects, again indicating the importance of stimulating S-cones as well as melanopsin. These findings provide insights into the temporal dynamics of photoreceptor contributions to non-image-forming photoresponses in a diurnal rodent that may help guide future studies of lighting environments and phototherapy protocols that promote human health and productivity.

This study examined the fecal samples of striped field mice (Apodemus agrarius coreae) captured in Jeju Special Self-Governing Province. Fecal samples, including the colon and other intestinal organs, were collected and subjected to aerobic culture to investigate the distribution of intestinal microorganisms. Gram staining of the aerobic cultured bacterial colonies from 36 fecal samples revealed the predominant presence of gram-negative bacilli in all samples. Among the 36 samples, gram-negative bacilli were identified in 36 strains (100%), gram-positive cocci in 21 strains (58.3%), and gram-positive bacilli in 15 strains (41.7%), while no gram-negative cocci were observed. The gram-negative bacilli cultured from the 36 samples were identified using the Vitek 2 system, and all were determined to be Escherichia coli (E. coli) strains. In addition, one sample was concurrently identified with E. coli and Enterobacter cloacae strains. The antimicrobial susceptibility testing for the identified E. coli strains did not include all antibiotics, but one strain exhibited intermediate resistance to cefoxitin. No pathogenic bacteria were present in the fecal samples of the scrub typhus-infected rodents, which are vectors for chigger-borne diseases affecting humans and animals.

BACKGROUND: The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic. RESULTS: We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse. CONCLUSIONS: Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.

Four new species of Rattus are described from the Moluccan islands (Maluku) of Indonesia: Rattus taliabuensis and R. feileri, both from the island of Taliabu, and R. halmaheraensis and R. obiensis from the islands of Halmahera and Obi, respectively. These descriptions are presented as part of a taxonomic review of Moluccan Rattus based on all known specimens in museum collections worldwide. Morphological characters, molecular systematics, and geographical distributions are documented for each of these species. Using both morpho-anatomical and morphometric approaches, we found that the Maluku Islands support Rattus taxa with spiny fur and two distinct morphotypes (1) species with a long tail and short rostrum (R. morotaiensis, R. halmaheraensis, R. obiensis, R. feileri) and (2) species with a short tail and long rostrum (R. taliabuensis, R. feliceus, R. ceramicus, R. elaphinus). Most of the new Moluccan species belong to a clade that includes members of the R. xanthurus species group from Sulawesi and the Australo-Papuan Rattus lineages. Their phylogenetic relationships highlight the role of Wallacea as an important area for diversification of Rattus into the Australo-Papuan region. Finally, the morphologically distinctive taxon Nesoromys ceramicus from Seram was found to be sister species to R. feliceus, and we relegate Nesoromys into the synonymy of the genus Rattus. The close affinities between R. ceramicus and R. feliceus may be an example of in situ island speciation, which has not been observed for small mammals on other Maluku Islands. Fabre, Pierre-Henri, Roberto Portela Miguez, Mary Ellen Holden, Yuli S. Fitriana, Gono Semiadi, Guy G. Musser, and Kristofer M. Helgen. 2023. Review of Moluccan Rattus (Rodentia: Muridae) with description of four new species. In Contributions to Mammalogy and Zooarchaeology of Wallacea, ed. K. M. Helgen and R. K. Jones. Records of the Australian Museum 75(5): 673–718.

There is increasing evidence that demographic history and phylogeographic consequences of past climate changes unfolded locally and varied from region to region. Despite the high rodent species diversity and endemism in low latitude Asia, how they have responded to the past climatic fluctuations remains unexplored. In the present study, we trapped 253 murine individuals and sequenced their mitochondrial COI gene sequence. A total of ten species belonging to five genera were recognized through phylogenetic analyses. The results of divergence time estimation showed that the most common ancestors for all recognized species occurred in the Pleistocene. Signals of demographic expansion were detected in six species by at least one test and the events of sharp population size increase occurred asynchronously among species. The demographic expansion during the glaciation periods was corroborated by the expanded suitable distributional areas predicted by ecological niche modelling. The diversified demographic histories of rat communities in low-latitude Asia suggested that species might have responded to past regional environmental changes in an individualistic way. [ABSTRACT FROM AUTHOR]

A comparative analysis of the rates of molecular evolution, transition bias, and its evolutionary compensation was carried out on mitochondrial (D-loop, Cytb, COI, 12S RNA) and nuclear (IRBP, Fv) DNA markers in the Murinae subfamily. According to the levels of variability, the markers can be divided into three classes: (1) hypervariable (D-loop), (2) rapidly evolving (Cytb, COI), and (3) conservative (12S RNA, IRBP, Fv). The nature of nucleotide substitutions appears by the levels of variability. With the D-loop, there is a maximum initial bias, which is already partially compensated for during the early stages of speciation, and completely compensated at the stages of species divergence. The pronounced bias within the Cytb and COI genes is only partially compensated, moreover at the genus levels. The 12S RNA, IRBP, and Fv genes with a low level of transition bias do not show evolutionary compensation as such, and the decrease of the ts/tv index in the evolutionary lineage has a technical character and is a consequence of a relative decrease of the difference in the frequencies of transitions and transversions against the background of an absolute increase in the frequencies of substitutions. The positive relationship between the intensity of nucleotide substitutions, the level of transition bias, and the rates of its evolutionary compensation proves that these phenomena have the same primary basis. [ABSTRACT FROM AUTHOR]

Four new species of Rattus are described from the Moluccan islands (Maluku) of Indonesia: Rattus taliabuensis and R. feileri, both from the island of Taliabu, and R. halmaheraensis and R. obiensis from the islands of Halmahera and Obi, respectively. These descriptions are presented as part of a taxonomic review of Moluccan Rattus based on all known specimens in museum collections worldwide. Morphological characters, molecular systematics, and geographical distributions are documented for each of these species. Using both morpho-anatomical and morphometric approaches, we found that the Maluku Islands support Rattus taxa with spiny fur and two distinct morphotypes (1) species with a long tail and short rostrum (R. morotaiensis, R. halmaheraensis, R. obiensis, R. feileri) and (2) species with a short tail and long rostrum (R. taliabuensis, R. feliceus, R. ceramicus, R. elaphinus). Most of the new Moluccan species belong to a clade that includes members of the R. xanthurus species group from Sulawesi and the Australo-Papuan Rattus lineages. Their phylogenetic relationships highlight the role of Wallacea as an important area for diversification of Rattus into the Australo-Papuan region. Finally, the morphologically distinctive taxon Nesoromys ceramicus from Seram was found to be sister species to R. feliceus, and we relegate Nesoromys into the synonymy of the genus Rattus. The close affinities between R. ceramicus and R. feliceus may be an example of in situ island speciation, which has not been observed for small mammals on other Maluku Islands. [ABSTRACT FROM AUTHOR]

Tissue regeneration is a process that recapitulates and restores organ structure and function. Although previous studies have demonstrated wound-induced hair neogenesis (WIHN) in laboratory mice (Mus), the regeneration is limited to the center of the wound unlike those observed in African spiny (Acomys) mice. Tissue mechanics have been implicated as an integral part of tissue morphogenesis. Here, we use the WIHN model to investigate the mechanical and molecular responses of laboratory and African spiny mice, and report these models demonstrate opposing trends in spatiotemporal morphogenetic field formation with association to wound stiffness landscapes. Transcriptome analysis and K14-Cre-Twist1 transgenic mice show the Twist1 pathway acts as a mediator for both epidermal-dermal interactions and a competence factor for periodic patterning, differing from those used in development. We propose a Turing model based on tissue stiffness that supports a two-scale tissue mechanics process: (1) establishing a morphogenetic field within the wound bed (mm scale) and (2) symmetry breaking of the epidermis and forming periodically arranged hair primordia within the morphogenetic field (μm scale). Thus, we delineate distinct chemo-mechanical events in building a Turing morphogenesis-competent field during WIHN of laboratory and African spiny mice and identify its evo-devo advantages with perspectives for regenerative medicine.

The Bower's Berylmys (Berylmys bowersi) is one of the largest rodent species with a wide distribution range in southern China and the Indochinese Peninsula. The taxonomy and evolutionary history of the B. bowersi is still controversial and confusing. In this study, we used two mitochondrial (Cyt b and COI) and three nuclear (GHR, IRBP, and RAG1) genes to estimate the phylogeny, divergence times, and biogeographic history of B. bowersi. We also explored morphological variations among the specimens collected across China. Our phylogenetic analyses indicated that the traditional B. bowersi contains at least two species: B. bowersi and B. latouchei. Berylmys latouchei was considered a junior synonym of B. bowersi distributed in eastern China, which is confirmed to be distinguishable at specific level because of its larger size, relatively larger and whiter hind feet, and several cranial traits. The estimated split of B. bowersi and B. latouchei was at the early Pleistocene (ca. 2.00 Mya), which might be the outcome of the combined effects of climate change in the early Pleistocene and isolation by the Minjiang River. Our results highlight the Wuyi Mountains in northern Fujian, China, as a glacial refugia during the Pleistocene and call for more intensive surveys and systematic revisions of small mammals in eastern China. The Bowers Berylmys (Berylmys bowersi) is one of the largest rodent species with a wide distribution range in southern China and the Indochinese Peninsula. Our analyses indicated that the traditional B. bowersi is a species complex contains at least two species: B. bowersi and B. latouchei. Also, our results highlight the Wuyi Mountains as the glacial refugia in the Pleistocene and call for more intensive surveys and systematic revisions of small mammals in the eastern China. [ABSTRACT FROM AUTHOR]

Predicting species' capacity to respond to climate change is an essential first step in developing effective conservation strategies. However, conservation prioritization schemes rarely take evolutionary potential into account. Ecotones provide important opportunities for diversifying selection and may thus constitute reservoirs of standing variation, increasing the capacity for future adaptation. Here, we map patterns of environmentally associated genomic and craniometric variation in the central African rodent Praomys misonnei to identify areas with the greatest turnover in genomic composition. We also project patterns of environmentally associated genomic variation under future climate change scenarios to determine where populations may be under the greatest pressure to adapt. While precipitation gradients influence both genomic and craniometric variation, vegetation structure is also an important determinant of craniometric variation. Areas of elevated environmentally associated genomic and craniometric variation overlap with zones of rapid ecological transition underlining their importance as reservoirs of evolutionary potential. We also find that populations in the Sanaga river basin, central Cameroon and coastal Gabon are likely to be under the greatest pressure from climate change. Lastly, we make specific conservation recommendations on how to protect zones of high evolutionary potential and identify areas where populations may be the most susceptible to climate change.

Mastomys are the most widespread African rodent and carriers of various diseases such as the plague or Lassa virus. In addition, mastomys have rapidly gained a large number of mammary glands. Here, we generated a genome, variome, and transcriptomes for Mastomys coucha. As mastomys diverged at similar times from mouse and rat, we demonstrate their utility as a comparative genomic tool for these commonly used animal models. Furthermore, we identified over 500 mastomys accelerated regions, often residing near important mammary developmental genes or within their exons leading to protein sequence changes. Functional characterization of a noncoding mastomys accelerated region, located in the HoxD locus, showed enhancer activity in mouse developing mammary glands. Combined, our results provide genomic resources for mastomys and highlight their potential both as a comparative genomic tool and for the identification of mammary gland number determining factors.

Abstract The Bower's Berylmys (Berylmys bowersi) is one of the largest rodent species with a wide distribution range in southern China and the Indochinese Peninsula. The taxonomy and evolutionary history of the B. bowersi is still controversial and confusing. In this study, we used two mitochondrial (Cyt b and COI) and three nuclear (GHR, IRBP, and RAG1) genes to estimate the phylogeny, divergence times, and biogeographic history of B. bowersi. We also explored morphological variations among the specimens collected across China. Our phylogenetic analyses indicated that the traditional B. bowersi contains at least two species: B. bowersi and B. latouchei. Berylmys latouchei was considered a junior synonym of B. bowersi distributed in eastern China, which is confirmed to be distinguishable at specific level because of its larger size, relatively larger and whiter hind feet, and several cranial traits. The estimated split of B. bowersi and B. latouchei was at the early Pleistocene (ca. 2.00 Mya), which might be the outcome of the combined effects of climate change in the early Pleistocene and isolation by the Minjiang River. Our results highlight the Wuyi Mountains in northern Fujian, China, as a glacial refugia during the Pleistocene and call for more intensive surveys and systematic revisions of small mammals in eastern China.

Diabetic retinopathy is the most common microvascular complication of diabetes and is a major cause of blindness, but an understanding of the pathogenesis of the disease has been hampered by a lack of accurate animal models. Here, we explore the dynamics of retinal cellular changes in the Nile rat (Arvicanthis niloticus), a carbohydrate-sensitive model for type 2 diabetes. The early retinal changes in diabetic Nile rats included increased acellular capillaries and loss of pericytes that correlated linearly with the duration of diabetes. These vascular changes occurred in the presence of microglial infiltration but in the absence of retinal ganglion cell loss. After a prolonged duration of diabetes, the Nile rat also exhibits a spectrum of retinal lesions commonly seen in the human condition including vascular leakage, capillary non-perfusion, and neovascularization. Our longitudinal study documents a range and progression of retinal lesions in the diabetic Nile rat remarkably similar to those observed in human diabetic retinopathy, and suggests that this model will be valuable in identifying new therapeutic strategies.

Background: In recent years, the African spiny mouse Acomys cahirinus has been shown to regenerate a remarkable array of severe internal and external injuries in the absence of a fibrotic response, including the ability to regenerate full-thickness skin excisions, ear punches, severe kidney injuries, and complete transection of the spinal cord. While skeletal muscle is highly regenerative in adult mammals, Acomys displays superior muscle regeneration properties compared with standard laboratory mice following several injuries, including serial cardiotoxin injections of skeletal muscle and volumetric muscle loss (VML) of the panniculus carnosus muscle following full-thickness excision injuries. VML is an extreme muscle injury defined as the irrecoverable ablation of muscle mass, most commonly resulting from combat injuries or surgical debridement. Barriers to the treatment of VML injury include early and prolonged inflammatory responses that promote fibrotic repair and the loss of structural and mechanical cues that promote muscle regeneration. While the regeneration of the panniculus carnosus in Acomys is impressive, its direct relevance to the study of VML in patients is less clear as this muscle has largely been lost in humans, and, while striated, is not a true skeletal muscle. We therefore sought to test the ability of Acomys to regenerate a skeletal muscle more commonly used in VML injury models., Methods: We performed two different VML injuries of the Acomys tibialis anterior muscle and compared the regenerative response to a standard laboratory mouse strain, Mus C57BL6/J., Results: Neither Acomys nor Mus recovered lost muscle mass or myofiber number within three months following VML injury, and Acomys also failed to recover force production better than Mus. In contrast, Acomys continued to express eMHC within the injured area even three months following injury, whereas Mus ceased expressing eMHC less than one-month post-injury, suggesting that Acomys muscle was primed, but failed, to regenerate., Conclusions: While the panniculus carnosus muscle in Acomys regenerates following VML injury in the context of full-thickness skin excision, this regenerative ability does not translate to regenerative repair of a skeletal muscle., (© 2024. The Author(s).)

It remains unclear how variation in the intensity of sperm competition shapes phenotypic and molecular evolution across clades. Mice and rats in the subfamily Murinae are a rapid radiation exhibiting incredible diversity in sperm morphology and production. We combined phenotypic and genomic data to perform phylogenetic comparisons of male reproductive traits and genes across 78 murine species. We identified several shifts towards smaller relative testes mass, presumably reflecting reduced sperm competition. Several sperm traits were associated with relative testes mass, suggesting that mating system evolution selects for convergent suites of traits related to sperm competitive ability. We predicted that sperm competition would also drive more rapid molecular divergence in species with large testes. Contrary to this, we found that many spermatogenesis genes evolved more rapidly in species with smaller relative testes mass due to relaxed purifying selection. While some reproductive genes evolved rapidly under recurrent positive selection, relaxed selection played a greater role in underlying rapid evolution in small testes species. Our work demonstrates that postcopulatory sexual selection can impose strong purifying selection shaping the evolution of male reproduction, and that broad patterns of molecular evolution may help identify genes that contribute to male fertility., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Society for the Study of Evolution (SSE). All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Relatively little information exists on the effects of mercury on terrestrial wildlife populations. We analyzed 38 free-living small rodent females (Myodes glareolus, Microtus agrestris, and Apodemus flavicolis), of which 11 were pregnant, for total mercury concentrations in combined liver and kidney samples. Using a single-purpose atomic absorption spectrometer for mercury determination, the measured mercury values ranged from 0.006 to 0.079 mg/kg. Pregnant females had significantly (P<0.041) higher mercury levels in liver and kidney than did nonpregnant females. Our results suggest that during mercury biomonitoring studies it is necessary to consider the pregnancy of the analyzed animals., (© Wildlife Disease Association 2024.)

Current research using animal models to investigate retinal cell biology and model retinal degenerative diseases largely utilize small mammals that are nocturnal and lack the ability to restore lost vision. In contrast, the Mongolian gerbil (Meriones) is a diurnal rodent with good photopic vision, and the spiny mouse (Acomys) is a small desert-dwelling rodent with remarkable regenerative capabilities. The goal of this study was to identify antibodies that detect retinal cell classes in Meriones and Acomys, and to describe the retinal anatomy of these two species in comparison to outbred laboratory mice (Mus musculus). Immunohistochemistry was performed on retinal sections with antibodies for various retinal cell types. Sections were imaged by light, fluorescence, and confocal microscopy. Cell density, morphology, and placement were compared between species qualitatively and quantitatively. Our analyses revealed a classic assembly of retinal cells in Meriones and Acomys, with a few deviations compared to Mus. Meriones displayed the highest density of cones and Acomys the lowest. A higher density of bipolar cell bodies in the proximal portion of the inner nuclear layer was observed in both Acomys and Meriones compared to Mus, and both species exhibited an increase in amacrine cell density compared to Mus. Our results provide a foundation for future research into the visual system adaptations of these interesting species., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Using compounded multidose vials (cMDV) is a common practice in the laboratory animal setting, where medications often are diluted to provide appropriate doses to rodents. However, bacterial contamination of MDV has been well established in both the human and veterinary medical literature. For this study, we created 14 cMDV by diluting carprofen into sterile water (dilution, 1:10) and stored 6 cMDV each at 5 and 24 °C. The stoppers of the cMDV were not cleaned with alcohol, and all were punctured twice daily for 28 d. The sterility of the diluted carprofen was evaluated by assessing bacterial growth on days 0, 7, 14, 21, and 28 and by testing for bacterial endotoxin on days 0 and 28. We used liquid chromatography-tandem mass spectrometry to assess the stability of 2 cMDV, with each cMDV being divided into the 2 storage-temperature subsets for days 0, 7, 14, 21, and 28. Neither bacterial contamination nor endotoxin was detected, and drug stability was stable over the 28 d. We suggest that with pragmatic techniques, such as secondary containment and consistent use of new needles, the contents of cMDV can remain sterile and stable for 28 d.

AbstractInbred mice are commonly used to test candidate malaria vaccines, but have been unreliable for predicting efficacy in humans. To establish a more rigorous animal model, we acquired African woodland thicket rats of the genus Grammomys, the natural hosts for Plasmodium berghei. Thicket rats were acquired and identified as Grammomys surdaster by skull and teeth measurements and mitochondrial DNA genotyping. Herein, we demonstrate that thicket rats are highly susceptible to infection by P. berghei, and moderately susceptible to Plasmodium yoelii and Plasmodium chabaudi: 1-2 infected mosquito bites or 25-100 sporozoites administered by intravenous injection consistently resulted in patent parasitemia with P. berghei, and resulted in patent parasitemia with P. yoelii and P. chabaudi strains for at least 50% of animals. We then assessed efficacy of whole-organism vaccines to induce sterile immunity, and compared the thicket rat model to conventional mouse models. Using P. berghei ANKA radiation-attenuated sporozoites, and P. berghei ANKA and P. yoelii chemoprophylaxis vaccination approaches, we found that standard doses of vaccine sufficient to protect laboratory mice for a long duration against malaria challenge, are insufficient to protect thicket rats, which require higher doses of vaccine to achieve even short-term sterile immunity. Thicket rats may offer a more stringent and pertinent model for evaluating whole-organism vaccines.

In the last years, a murine identified as Paraethomys aff. abaigari has been repeatedly recognized in several early Pliocene localities of the Iberian Peninsula. We have revised these occurrences, as well as other samples of similar morphology, and propose that all these records correspond to a new species. We diagnose Paraethomys baeticus sp. nov. based on a large sample from the early Ruscinian site of Baza-1 (Guadix-Baza Basin, Spain). It is a medium-sized representative of the genus, with relatively well-developed longitudinal connections both in upper and lower molars, but incomplete stephanodonty. M1 displays high tubercles t6–t9 and low t4–t8 connections. M1 and, to a lesser extent, M2 have posterior spurs on t1 and t3. The t9 and t12 are absent in M2. In m1, a round islet of enamel between the anteroconid and the protoconid-metaconid is regularly observed, as well as a general lack of medial anteroconid, moderate labial cingulum with large posterior accessory cuspid, and longitudinal spur. The new species differs from other European representatives of the genus Paraethomys mainly in its size, which is intermediate between that of the small-sized Paraethomys meini and the large-sized Paraethomys abaigari. In addition, both the size and relative width are smaller than those of Paraethomys jaegeri. The frequency of posterior spurs on t1 and t3 of M1 and M2 is higher than that of P. meini and lower than that of P. jaegeri. The new species here described represents a key biochronological and biostratigraphic marker, since it is restricted to levels of late early Ruscinian age. Thus, this species is useful for establishing divisions within the early Ruscinian, and becomes a characteristic taxon for the early Pliocene in the terrestrial record of the Iberian Peninsula. Magnetobiostratigraphic correlations suggest a chronological range for P. baeticus sp. nov. between ca. 4.6 and 4.3 Ma.

The spread of Lassa virus (LASV) in Guinea, Liberia and Sierra Leone, which together are named the Mano River Union (MRU) area, was examined phylogeographically. To provide a reliable evolutionary scenario, new rodent-derived, whole LASV sequences were included. These were generated by metatranscriptomic next-generation sequencing from rodents sampled between 2003 and 2020 in 21 localities of Guinea and Sierra Leone. An analysis was performed using BEAST to perform continuous phylogeographic inference and EvoLaps v36 to visualize spatio-temporal spread. LASV was identified as expected in its primary host reservoir, the Natal multimammate mouse ( Mastomys natalensis ), and also in two Guinean multimammate mice ( Mastomys erythroleucus ) in northern Sierra Leone and two rusty-bellied brush-furred mice ( Lophuromys sikapusi ) in southern Sierra Leone. This finding is consistent with the latter two species being secondary host reservoirs. The strains in these three species were very closely related in LASV lineage IV. Phylogenetic analysis indicated that the most recent common ancestor of lineage IV existed 316-374 years ago and revealed distinct, well-supported clades from Sierra Leone (Bo, Kabala and Kenema), Guinea (Faranah, Kissidougou-Guekedou and Macenta) and Liberia (Phebe-Ganta). The phylogeographic scenario suggests southern Guinea as the point of origin of LASV in the MRU area, with subsequent spread to towards Mali, Liberia and Sierra Leone at a mean speed of 1.6 to 1.1 km/year.

The Natal multimammate mouse ( Mastomys natalensis ) is the host of Lassa mammarenavirus, causing Lassa haemorrhagic fever in West Africa. As there is currently no operational vaccine and therapeutic drugs are limited, we explored rodent control as an alternative to prevent Lassa virus spillover in Upper Guinea, where the disease is highly endemic in rural areas. In a seven-year experiment, we distributed rodenticides for 10-30 days once a year and, in the last year, added intensive snap trapping for three months in all the houses of one village. We also captured rodents both before and after the intervention period to assess their effectiveness by examining alterations in trapping success and infection rates (Lassa virus RNA and IgG antibodies). We found that both interventions reduced the rodent population by 74-92% but swiftly rebounded to pre-treatment levels, even already six months after the last snap-trapping control. Furthermore, while we observed that chemical control modestly decreased Lassa virus infection rates annually (a reduction of 5% in seroprevalence per year), the intensive trapping unexpectedly led to a significantly higher infection rate (from a seroprevalence of 28% before to 67% after snap trapping control). After seven years, we conclude that annual chemical control, alone or with intensive trapping, is ineffective and sometimes counterproductive in preventing Lassa virus spillover in rural villages. These unexpected findings may result from density-dependent breeding compensation following culling and the survival of a small percentage of chronically infected rodents that may spread the virus to a new susceptible generation of mice.

Formosan wood mice (Apodemus semotus) are endemic rodents in Taiwan. Recently Formosan wood mice exhibit similar locomotor behaviors in the laboratory environment as in the field environment has shown. Contemporaneously, Formosan wood mice have higher moving distances of and central dopaminergic (DAergic) activities than C57BL/6 mice in behavioral test. This study tried to compare the behavioral responses between male Formosan wood mice and male C57BL/6 mice in the light-dark exploration tests. We also measured the levels of DA and 3,4-dihydroxyphenylacetic acid (DOPAC), the primary metabolite of DA, to assess the dopaminergic activity of the medial prefrontal cortex, striatum, and nucleus accumbens. Our data show that Formosan wood mice revealed higher exploration and central DAergic activities than did C57BL/6 mice in the light-dark exploration tests, and diazepam (an anxiolytics) treatment reduced the exploratory activity and central dopaminergic activities in Formosan wood mice, but not in C57BL/6 mice. After repeated exposure to light-dark exploration tests, the latency to dark zone was increased, and the duration in light zone as well as the central DAergic activity were decreased in C57BL/6 mice. This study provides comparative findings; Formosan wood mice showed the higher exploratory activities than C57BL/6 mice did, and their central DAergic activities were related to the behavioral responses in these two mice. This could potentially shed light on the reasons behind the prevalence of higher exploration and central dopaminergic activities. Using Formosan wood mice as a model to study human diseases related to hyperactivity adds significant value to the potential research., Competing Interests: Declaration of competing interest The authors have declared that no competing interests exist., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Understanding the cellular and molecular determinants of mammalian tissue regeneration and repair is crucial for developing effective therapies that restore tissue architecture and function. In this review, we focus on the cell types involved in scarless wound response and regeneration of spiny mice (Acomys). Comparative -omics approaches with scar-prone mammals have revealed species-specific peculiarities in cellular behavior during the divergent healing trajectories. We discuss the developing views on which cell types engage in restoring the architecture of spiny mouse tissues through a co-ordinated spatiotemporal response to injury. While yet at the beginning of understanding how cells interact in these fascinating animals to regenerate tissues, spiny mice hold great promise for scar prevention and anti-fibrotic treatments., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

The African spiny mouse (Acomys cahirinus) is a unique mammalian model of tissue regeneration, regenerating 4 mm ear-hole punches with cartilage, adipocytes, hair follicles, and muscle. However, the time to regenerate ear tissue varies from 20 to 90 days and muscle regeneration is inconsistent. Some report that older spiny mice have delayed regeneration without investigation on the regenerative capacity of muscle. We thought that delayed regeneration and inconsistent muscle regeneration could be linked via age-related nerve degeneration. While the current study found that spiny mice aged 6-9 months had delayed regeneration compared to 3-4 month-old spiny mice, the capacity of muscle regeneration was unrelated to age, and there was little evidence for age-related nerve degeneration. Instead, the regeneration of muscle, cartilage and adipocytes was spatially heterogeneous, declining in amount from the proximal to distal region of the regenerated tissue. Also, cartilage regeneration in the distal region was decreased in ≥22-month-old Acomys and adipocyte regeneration was decreased in those older than 6 months, compared to 3-4 month olds. While the underlying mechanisms for delayed and spatially heterogenous regeneration remain unclear, age and the spatial region of the regenerated tissue should be considered in experimental designs with spiny mice., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2024. Published by The Company of Biologists Ltd.)

[Display omitted] • Eimeria of 2 ecologically similar rodent groups form a complex system of genetic lineages with different host specificities. • The lineages retained their host specificities while spreading across large geographic areas. • The genetic structure is only partially reflected by morphological traits. Interplay between conserved host specificity and occasional host switches is an important process determining the evolution of host-parasite systems. Here, we address the dynamics of host switches at the population level in rodent-associated Eimeria. Focusing mainly on two ecologically similar host groups, Murinae and Arvicolinae, we show that the Eimeria infecting those hosts form a complex system of many genetic lineages with different host specificities. The broad geographic distribution of lineages indicates that they are well-established genetic forms which retained their host specificities while spreading across large geographic areas. We also demonstrate that genetic structure is only partially reflected by morphological traits. [ABSTRACT FROM AUTHOR]

Adaptive radiations are characterized by the diversification and ecological differentiation of species, and replicated cases of this process provide natural experiments for understanding the repeatability and pace of molecular evolution. During adaptive radiation, genes related to ecological specialization may be subject to recurrent positive directional selection. However, it is not clear to what extent patterns of lineage-specific ecological specialization (including phenotypic convergence) are correlated with shared signatures of molecular evolution. To test this, we sequenced whole exomes from a phylogenetically dispersed sample of 38 murine rodent species, a group characterized by multiple, nested adaptive radiations comprising extensive ecological and phenotypic diversity. We found that genes associated with immunity, reproduction, diet, digestion, and taste have been subject to pervasive positive selection during the diversification of murine rodents. We also found a significant correlation between genome-wide positive selection and dietary specialization, with a higher proportion of positively selected codon sites in derived dietary forms (i.e. carnivores and herbivores) than in ancestral forms (i.e. omnivores). Despite striking convergent evolution of skull morphology and dentition in two distantly related worm-eating specialists, we did not detect more genes with shared signatures of positive or relaxed selection than in a nonconvergent species comparison. Although a small number of the genes we detected can be incidentally linked to craniofacial morphology or diet, protein-coding regions are unlikely to be the primary genetic basis of this complex convergent phenotype. Our results suggest a link between positive selection and derived ecological phenotypes, and highlight specific genes and general functional categories that may have played an integral role in the extensive and rapid diversification of murine rodents. [ABSTRACT FROM AUTHOR]

Endometriosis is characterized by the presence of endometrial glands and stroma in extrauterine sites. Our objective was to determine whether endometriotic lesions (ELs) from women with endometriosis have altered retinoid levels compared with their eutopic endometrium, and to test the hypothesis that defects in all-trans retinoic acid (ATRA) biosynthesis in EL is related to reduced expression of cellular retinol-binding protein type 1 (RBP1). Retinoids were evaluated by liquid chromatography-tandem mass spectrometry and high-performance liquid chromatography in eutopic endometrial biopsies (EBs) and ELs from 42 patients with pathologically confirmed endometriosis. The ATRA levels were reduced, whereas the retinol and retinyl ester concentrations were elevated in EL compared with EB tissue. Similar results were found in a mouse model of endometriosis that used green fluorescent protein-positive endometrial tissue injected into the peritoneum of syngeneic hosts to mimic retrograde menses. The ATRA biosynthesis in vitro in retinol-treated primary human endometrial stromal cell (ESC) cultures derived from ELs was reduced compared with that of ESCs derived from patient-matched EBs. Correspondingly, RBP1 expression was reduced in tissue and ESCs derived from EL versus EB. Rbp1(-/-) mice showed reduced endometrial ATRA concentrations compared with wild type, associated with loss of tissue organization and hypercellularity. These findings provide the first quantitative measurements of ATRA in human endometrium and endometriosis, demonstrating reduced ATRA in ectopic tissue and corresponding ESC cultures. Quantitation of retinoids in murine endometriosis and in Rbp1(-/-) mice supports the contention that impaired ATRA synthesis caused by reduced RBP1 promotes an "endometriosis phenotype" that enables cells to implant and grow at ectopic sites.

In many species males display alternative reproductive tactics (ARTs). While males of different tactics differ behaviorally in the field, it is often not known whether these behavioral differences would also occur under standardized laboratory conditions, nor how ARTs are regulated by the brain. In the present study we kept male African striped mice (Rhabdomys pumilio) in captivity either in family groups or solitary, to mimic ARTs observed in the field. This allowed us to study these males behaviorally under standardized conditions, to replicate physiological findings from the field, and to study the expression of the arginine vasopressin 1a receptor (AVPR1a) in their brains. Changes in either peptide release or receptor expression (or both) might regulate ARTs with differential timelines, with peptide secretion being faster than receptor expression. As observed in the field, family living males had higher corticosterone but lower testosterone levels than singly housed males. Surprisingly, singly housed males were less aggressive while at the same time having higher testosterone levels. We found no differences in AVPR1a expression. In a previous study it was shown that singly housed males have higher levels of AVP stored in their brain, which potentially could be secreted when the social situation changes, for example to establish social bonds. Our study on AVPR1a suggests the hypothesis that, given that the receptor distribution and expression of singly housed males do not differ from that of family-living males, the brains of singly-housed males have a similar capacity to be responsive to AVP when given the chance to interact socially.

Fossil records generally inform paleobiologists about extinct taxa and rates of evolution measured at the scale of millions of years. Good records that are densely sampled through time can reveal species level details such as longevity in local sections. Yet fossil data normally do not address details of lineage microevolution because the density through time of lineage sampling is insufficient to perceive patterns at a precision finer than 106 years in most cases. This study concerns details of a splitting event in the evolution of murine rodents, an event for which multiple fossil samples dated to a precision of 105 years fortuitously document the tempo and mode of origin of sister species, the stems of two extant tribes of mice. Evolution of early Murinae in the northern part of the biogeographically restricted Indian subcontinent between 11.6 and 10.5 Ma involved cladogenesis of two crown taxa, the extant tribes Murini and Arvicanthini. Large samples of fossil rodent teeth document their divergence from a common morphological pool. Definitive basal Murini and Arvicanthini at 10.5 Ma are similar in size and differ by subtle features of the dentition. Those features occur sporadically in the common pool of older fossil teeth at 11.2, 11.4, and 11.6 Ma as inconsistent polymorphisms. Interpreted as a single lineage in the 11.6–11.2 Ma interval, variability of this abundant murine incorporated the roots of the two crown tribes. The pattern through time suggests morphological stasis for several hundred thousand years prior to splitting. This special case informs us on one example of evolution and shows that the tempo of splitting evolution in some cases may be measured in hundreds of thousands of years, followed by stasis once daughter species have differentiated morphologically.

For organisms to survive and prosper in a harsh environment, particularly under rapid climate change, poses tremendous challenges. Recent studies have highlighted the continued loss of megafauna in terrestrial ecosystems and the subsequent surge of small mammals, such as rodents, bats, lagomorphs, and insectivores. However, the ecological partitioning of these animals will likely lead to large variation in their responses to environmental change. In the present study, we investigated the evolutionary history and genetic adaptations of white-bellied rats (Niviventer Marshall, 1976), which are widespread in the natural terrestrial ecosystems in Asia but also known as important zoonotic pathogen vectors and transmitters. The southeastern Qinghai-Tibet Plateau was inferred as the origin center of this genus, with parallel diversification in temperate and tropical niches. Demographic history analyses from mitochondrial and nuclear sequences of Niviventer demonstrated population size increases and range expansion for species in Southeast Asia, and habitat generalists elsewhere. Unexpectedly, population increases were seen in N. eha , which inhabits the highest elevation among Niviventer species. Genome scans of nuclear exons revealed that among the congeneric species, N. eha has the largest number of positively selected genes. Protein functions of these genes are mainly related to olfaction, taste, and tumor suppression. Extensive genetic modification presents a major strategy in response to global changes in these alpine species. [ABSTRACT FROM AUTHOR]

The relationship between organismal function and form is a cornerstone of biology because functional diversity is key to generating and maintaining ecological diversity. Morphological changes often occur in unison with behavioral or ecological transitions, and this process may foster diversification, but alternately could trap a species on an adaptive peak. We estimated the most comprehensive phylogenetic hypothesis of Murinae, a young (∼15 million years) and diverse (∼700 species) clade of mammals. We then tested for correlated evolution among four morphological traits with potential links to locomotor modes (Arboreal, General, Terrestrial, and Amphibious), then investigated the effects of locomotion on morphological and lineage diversification. We found unique combinations of trait values for each locomotor mode, including strong covariance between the tail and hindfoot lengths of specialized Arboreal and ecologically flexible General species. Low diversification rates and long branch lengths suggest that specialized lineages represent stable evolutionary "cul‐de‐sacs." General species, characterized by the classic "rat‐like" body plan and broad locomotor abilities, have narrow optimal trait values and slow phenotypic evolution, but high lineage diversification rates. Our findings suggest that versatile, generalist forms act as seeds of species diversity and morphological specialization, which together build ecologically diverse radiations. [ABSTRACT FROM AUTHOR]

The Niviventer fulvescens species complex (NFSC), a group of abundant and taxonomically ambiguous rodent taxa, is distributed from Southeast Asia to south-eastern China. We combined molecular and morphological datasets to clarify the species composition and variation of the NFSC. Our phylogenetic analyses, using molecular data, recovered eight genetic lineages in the NFSC, including a novel, distinct lineage from Jilong, Tibet, China, which is described as a new species , N. fengi sp. nov. The species status of N. fengi is supported by a species delimitation analysis, and it is morphologically distinguished from other members of the NFSC by its greyish dorsal fur, soft hairs covering the whole body and a hairy tail. NFSC species bearing well-developed spines are found at lower elevations. A comprehensive taxonomic revision of the NFSC within China is provided, represented by five species: N. cremoriventer , N. fulvescens , N. huang , N. mekongis comb. nov. and N. fengi. A further study of this species complex, including samples from Southeast Asia, is needed. [ABSTRACT FROM AUTHOR]

We first sequenced and characterised the complete mitochondrial genome of Toxocara apodeme, then studied the evolutionary relationship of the species within Toxocaridae. The complete mitochondrial genome was amplified using PCR with 14 specific primers. The mitogenome length was 14303 bp in size, including 12 PCGs (encoding 3,423 amino acids), 22 tRNAs, 2 rRNAs, and 2 NCRs, with 68.38% A+T contents. The mt genomes of T. apodemi had relatively compact structures with 11 intergenic spacers and 5 overlaps. Comparative analyses of the nucleotide sequences of complete mt genomes showed that T. apodemi had higher identities with T. canis than other congeners. A sliding window analysis of 12 PCGs among 5 Toxocara species indicated that nad 4 had the highest sequence divergence, and cox 1 was the least variable gene. Relative synonymous codon usage showed that UUG, ACU, CCU, CGU, and UCU most frequently occurred in the complete genomes of T. apodemi. The Ka/Ks ratio showed that all Toxocara mt genes were subject to purification selection. The largest genetic distance between T. apodemi and the other 4 congeneric species was found in nad 2, and the smallest was found in cox 2. Phylogenetic analyses based on the concatenated amino acid sequences of 12 PCGs demonstrated that T. apodemi formed a distinct branch and was always a sister taxon to other congeneric species. The present study determined the complete mt genome sequences of T. apodemi , which provide novel genetic markers for further studies of the taxonomy, population genetics, and systematics of the Toxocaridae nematodes.

Adiaspiromycosis is a nontransmissible infectious pulmonary disease caused by the inhalation of propagules from fungal species belonging to the family Ajellomicetaceae, especially Emergomyces crescens. Adiaspiromycosis caused by E. crescens has been recorded in a broad number of species worldwide, with small burrowing mammals being considered the main hosts for this environmental pathogen. Only a handful of studies on adiaspiromycosis in European wildlife has been published to date. We assessed the occurrence of adiaspiromycosis in wild rodents (Murinae and Arvicolinae) from the central Spanish Pyrenees (NE Spain). The lungs of 302 mice and 46 voles were screened for the presence of adiaspores through histopathologic examination. Pulmonary adiaspiromycosis was recorded in 21.6% of all individuals (75/348), corresponding to 63/299 wood mice (Apodemus sylvaticus) and 12/40 bank voles (Myodes glareolus). Adiaspore burden varied highly between animals, with a mean of 0.19 spores/mm2 and a percentage of affected lung tissue ranging from <0.01% to >8%. These results show that the infection is present in wild rodents from the central Spanish Pyrenees. Although the impact of this infection on nonendangered species is potentially mild, it might contribute to genetic diversity loss in endangered species., (© Wildlife Disease Association 2024.)

Exploring the preparation of multifunctional hydrogels from a bionic perspective is an appealing strategy. Here, a multifunctional hydrogel dressing inspired by the characteristics of porous extracellular matrix produced during Acomys wound healing is prepared. These dressings are printed by digital light processing printing of hydrogels composed of gelatin methacrylate, hyaluronic acid methacrylate, and pretreated platelet-rich plasma (PRP) to shape out triply periodic minimal surface structures, which are freeze-dried for long-term storage. These dressings mimic the porous extracellular matrix of Acomys, while the freeze-drying technique effectively extends the storage duration of PRP viability. Through in vivo and in vitro experiments, the biomimetic dressings developed in this study modulate cell behavior and facilitate wound healing. Consequently, this research offers a novel approach for the advancement of regenerative wound dressings., (© 2023 Wiley‐VCH GmbH.)

Background: The geographic distribution and host-parasite interaction networks of Sarcocystis spp. in small mammals in eastern Asia remain incompletely known., Methods: Experimental infections, morphological and molecular characterizations were used for discrimination of a new Sarcocystis species isolated from colubrid snakes and small mammals collected in Thailand, Borneo and China., Results: We identified a new species, Sarcocystis muricoelognathis sp. nov., that features a relatively wide geographic distribution and infects both commensal and forest-inhabiting intermediate hosts. Sarcocystis sporocysts collected from rat snakes (Coelognathus radiatus, C. flavolineatus) in Thailand induced development of sarcocysts in experimental SD rats showing a type 10a cyst wall ultrastructure that was identical with those found in Rattus norvegicus from China and the forest rat Maxomys whiteheadi in Borneo. Its cystozoites had equal sizes in all intermediate hosts and locations, while sporocysts and cystozoites were distinct from other Sarcocystis species. Partial 28S rRNA sequences of S. muricoelognathis from M. whiteheadi were largely identical to those from R. norvegicus in China but distinct from newly sequenced Sarcocystis zuoi. The phylogeny of the nuclear 18S rRNA gene placed S. muricoelognathis within the so-called S. zuoi complex, including Sarcocystis attenuati, S. kani, S. scandentiborneensis and S. zuoi, while the latter clustered with the new species. However, the phylogeny of the ITS1-region confirmed the distinction between S. muricoelognathis and S. zuoi. Moreover, all three gene trees suggested that an isolate previously addressed as S. zuoi from Thailand (KU341120) is conspecific with S. muricoelognathis. Partial mitochondrial cox1 sequences of S. muricoelognathis were almost identical with those from other members of the group suggesting a shared, recent ancestry. Additionally, we isolated two partial 28S rRNA Sarcocystis sequences from Low's squirrel Sundasciurus lowii that clustered with those of S. scandentiborneensis from treeshews., Conclusions: Our results provide strong evidence of broad geographic distributions of rodent-associated Sarcocystis and host shifts between commensal and forest small mammal species, even if the known host associations remain likely only snapshots of the true associations., (© 2024. The Author(s).)

The genus Acomys is of growing importance to many research fields. Previous research has shown that individuals differ when exploring new environments and that these behavioural strategies are consistent in time. In this study, we subjected 60 commensal Acomys cahirinus (37 males, 23 females) to a series of seven tests (free exploration, forced exploration under bright illumination, forced exploration under low illumination, hole board test, vertical activity test, elevated plus maze, and voluntary wheel running) to acquire independent behavioural traits and investigate whether and how personality develops in spiny mice. The full series of experiments was performed twice during ontogeny: once in the sub-adult stage (tested at 62-72 days of age) and once in the adult stage (102-112 days of age). We found that behaviour of the animals was repeatable both within (range of R values from 0.155 to 0.726) and across the two life-stages (0.238 to 0.563). While the structure of behaviour in adults was rather clear, it had not been fully crystalized in sub-adults, suggesting personality changes during maturation, even though some individual traits might be repeatable across ontogeny. Notably, the most consistent behavioural traits across the different tests were jumping and rearing, which are not commonly reported., (Copyright © 2024 Elsevier B.V. All rights reserved.)

In mammalian research, it has been debated what can initiate an evolutionary tradeoff between different senses, and the phenomenon of sensory tradeoff in rodents, the most abundant mammalian clade, is not evident. The Nile rat (Arvicanthis niloticus), a murid rodent, recently adapted to a diurnal niche through an evolutionary acquisition of daylight vision with enhanced visual acuity. As such, this model provides an opportunity for a cross-species investigation where comparative morphological and multi-omic analyses of the Nile rat are made with its closely related nocturnal species, e.g. the mouse (Mus musculus) and the rat (Rattus norvegicus). Thus, morphological examinations were performed, and evolutionary reductions in relative sizes of turbinal bone surfaces, the cribriform plate, and the olfactory bulb were discovered in Nile rats. Subsequently, we compared multiple murid genomes, and profiled olfactory epithelium transcriptomes of mice and Nile rats at various ages with RNA sequencing. The results further demonstrate that, in comparison with mouse olfactory receptor (OR) genes, Nile rat OR genes have experienced less frequent gain, more frequent loss, and more frequent expression reduction during their evolution. Furthermore, functional degeneration of coding sequences in the Nile rat lineage was found in OR genes, yet not in other genes. Taken together, these results suggest that acquisition of improved vision in the Nile rat has been accompanied by degeneration of both olfaction-related anatomical structures and OR gene repertoires, consistent with the hypothesis of an olfaction-vision tradeoff initiated by the switch from a nocturnal to a diurnal lifestyle in mammals., Competing Interests: Conflict of Interest The authors declare no competing interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

The Rocahepevirus ratti hepatitis E virus genotype C1 (HEV-C1) has been documented to infect humans. However, the understanding of HEV-C1 remains constrained. This study aims to determine the prevalence and genomic characteristics of HEV-C1 in small animals in Yunnan province of southwestern China. A total of 444 liver tissues were collected from animals covering the orders Rodentia, Soricomorpha, Scandentia and Erinaceomorpha in three regions in Yunnan. Then Paslahepevirus balayani and Rocahepevirus were examined using RT-qPCR. The detection rate of Rocahepevirus was 12.95 % (36/278) in animals of order Rodentia, with 14.77 % (35/237) in Rattus tanezumi and 33.33 % (1/3) in Niviventer fulvescens. No Paslahepevirus balayani was detected. Additionally, two full-length Rocahepevirus sequences (MSE-17 and LHK-54) and thirty-three partial ORF1 sequences were amplified and determined to be HEV-C1. MSE-17 and LHK-54 shared moderate nucleotide identity (78.9 %-80.3 %) with HEV-C1 isolated in rats and humans. The HEV-C1 isolated from Niviventer fulvescens demonstrated a 100 % nucleotide identity with that from Rattus tanezumi. The rat HEV-C1 sequences isolated in our study and other Asian HEV-C1 sequences were phylogenetically distant from those isolated in North America and Europe. Furthermore, the two full-length sequences isolated in our study had less amino acid substitutions in the motifs of RNA-dependent RNA polymerase domain (F 204 L and L 238 F), compared with other Asian sequences. In summary, HEV-C1 commonly spreads in rats in Yunnan province of China. Our findings suggest a spatially associated phylogeny, and potential cross-species transmission of HEV-C1., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

Among vertebrates, placental mammals are particularly variable in the covariance between cranial shape and body size (allometry), with rodents being a major exception. Australian murid rodents allow an assessment of the cause of this anomaly because they radiated on an ecologically diverse continent notably lacking other terrestrial placentals. Here, we use 3D geometric morphometrics to quantify species-level and evolutionary allometries in 38 species (317 crania) from all Australian murid genera. We ask whether ecological opportunity resulted in greater allometric diversity compared with other rodents or whether conserved allometry suggests intrinsic constraints and/or stabilizing selection. We also assess whether cranial shape variation follows the proposed rule of craniofacial evolutionary allometry (CREA), whereby larger species have relatively longer snouts and smaller braincases. To ensure we could differentiate parallel versus nonparallel species-level allometric slopes, we compared the slopes of rarefied samples across all clades. We found exceedingly conserved allometry and CREA-like patterns across the 10-million-year split between Mus and Australian murids. This could support both intrinsic-constraint and stabilizing-selection hypotheses for conserved allometry. Large-bodied frugivores evolved faster than other species along the allometric trajectory, which could suggest stabilizing selection on the shape of the masticatory apparatus as body size changes. [ABSTRACT FROM AUTHOR]

In the last years, a murine identified as Paraethomys aff. abaigari has been repeatedly recognized in several early Pliocene localities of the Iberian Peninsula. We have revised these occurrences, as well as other samples of similar morphology, and propose that all these records correspond to a new species. We diagnose Paraethomys baeticus sp. nov. based on a large sample from the early Ruscinian site of Baza-1 (Guadix-Baza Basin, Spain). It is a medium-sized representative of the genus, with relatively well-developed longitudinal connections both in upper and lower molars, but incomplete stephanodonty. M1 displays high tubercles t6-t9 and low t4-t8 connections. M1 and, to a lesser extent, M2 have posterior spurs on t1 and t3. The t9 and t12 are absent in M2. In m1, a round islet of enamel between the anteroconid and the protoconid-metaconid is regularly observed, as well as a general lack of medial anteroconid, moderate labial cingulum with large posterior accessory cuspid, and longitudinal spur. The new species differs from other European representatives of the genus Paraethomys mainly in its size, which is intermediate between that of the small-sized Paraethomys meini and the large-sized Paraethomys abaigari. In addition, both the size and relative width are smaller than those of Paraethomys jaegeri. The frequency of posterior spurs on t1 and t3 of M1 and M2 is higher than that of P. meini and lower than that of P. jaegeri. The new species here described represents a key biochronological and biostratigraphic marker, since it is restricted to levels of late early Ruscinian age. Thus, this species is useful for establishing divisions within the early Ruscinian, and becomes a characteristic taxon for the early Pliocene in the terrestrial record of the Iberian Peninsula. Magnetobiostratigraphic correlations suggest a chronological range for P. baeticus sp. nov. between ca. 4.6 and 4.3 Ma. [ABSTRACT FROM AUTHOR]

The estimation of robust and accurate measures of branch support has proven challenging in the era of phylogenomics. In data sets of potentially millions of sites, bootstrap support for bifurcating relationships around very short internal branches can be inappropriately inflated. Such overestimation of branch support may be particularly problematic in rapid radiations, where phylogenetic signal is low and incomplete lineage sorting severe. Here, we explore this issue by comparing various branch support estimates under both concatenated and coalescent frameworks, in the recent radiation Australo-Papuan murine rodents (Muridae: Hydromyini). Using nucleotide sequence data from 1245 independent loci and several phylogenomic inference methods, we unequivocally resolve the majority of genus-level relationships within Hydromyini. However, at four nodes we recover inconsistency in branch support estimates both within and among concatenated and coalescent approaches. In most cases, concatenated likelihood approaches using standard fast bootstrap algorithms did not detect any uncertainty at these four nodes, regardless of partitioning strategy. However, we found this could be overcome with two-stage resampling, that is, across genes and sites within genes (using -bsam GENESITE in IQ-TREE). In addition, low confidence at recalcitrant nodes was recovered using UFBoot2, a recent revision to the bootstrap protocol in IQ-TREE, but this depended on partitioning strategy. Summary coalescent approaches also failed to detect uncertainty under some circumstances. For each of four recalcitrant nodes, an equivalent (or close to equivalent) number of genes were in strong support (⁠|$>$| 75% bootstrap) of both the primary and at least one alternative topological hypothesis, suggesting notable phylogenetic conflict among loci not detected using some standard branch support metrics. Recent debate has focused on the appropriateness of concatenated versus multigenealogical approaches to resolving species relationships, but less so on accurately estimating uncertainty in large data sets. Our results demonstrate the importance of employing multiple approaches when assessing confidence and highlight the need for greater attention to the development of robust measures of uncertainty in the era of phylogenomics. [ABSTRACT FROM AUTHOR]

Skeletal growth rates reconstructed from bone histology in extinct insular hippopotamids, elephants, bovids and sauropods have been used to infer dwarfism as a response to island conditions. Limited published records of osteocyte lacunae densities (Ot.Dn), a proxy for living osteocyte proliferation, have suggested a slower rate of bone metabolism in giant mammals. Here, we test whether insularity might have affected bone metabolism in a series of small to giant murine rodents from Timor. Ten adult femora were selected from a fossil assemblage dated to the Late Quaternary (~5000–18 000 years old). Femur morphometric data were used in computing phylogenetically informed body mass regressions, although the phylogenetic signal was very low (Pagel's λ = 0.03). Estimates of body weight calculated from these femora ranged from 75 to 1188 g. Osteocyte lacunae densities from histological sections of the midshaft femur were evaluated against bone size and estimated body weight. Statistically significant (P  < 0.05) and strongly negative relationships between Ot.Dn, femur size and estimated weight were found. Larger specimens were characterized by lower Ot.Dn, indicating that giant murines from Timor might have had a relatively slow pace of bone metabolic activity, consistent with predictions made by the island rule. [ABSTRACT FROM AUTHOR]

Closely related species that occur across steep environmental gradients often display clear body size differences, and examining this pattern is crucial to understanding how environmental variation shapes diversity. Australian endemic rodents in the Pseudomys Division (Muridae: Murinae) have repeatedly colonized the arid, monsoon, and mesic biomes over the last 5 million years. Using occurrence records, body mass data, and Bayesian phylogenetic models, we test whether body mass of 31 species in the Pseudomys Division can be predicted by their biome association. We also model the effect of eight environmental variables on body mass. Despite high phylogenetic signal in body mass evolution across the phylogeny, we find that mass predictably increases in the mesic biome and decreases in arid and monsoon biomes. As per Bergmann's rule, temperature is strongly correlated with body mass, as well as several other variables. Our results highlight two important findings. First, body size in Australian rodents has tracked with climate through the Pleistocene, likely due to several environmental variables rather than a single factor. Second, support for both Brownian motion and predictable change at different taxonomic levels in the Pseudomys Division phylogeny demonstrates how the level at which we test hypotheses can alter interpretation of evolutionary processes. [ABSTRACT FROM AUTHOR]

We conducted a national human serologic study of a hantavirus detected in Madagascar rodents using a commercial kit and a new ELISA targeting the virus. Our results suggest a conservative estimate of 2.7% (46/1,680) IgG seroprevalence. A second single-district study using the new ELISA revealed a higher prevalence (7.2%; 10/139). [ABSTRACT FROM AUTHOR]