Rodent Diversity Research Articles

Application of a Sensitive Capture Sequencing Approach to Reservoir Surveillance Detects Novel Viruses in Zambian Wild Rodents

We utilized a pan-viral capture sequencing assay, VirCapSeq-VERT, to assess viral diversity in rodents from the Eastern Province of Zambia as a model for pre-pandemic viral reservoir surveillance. We report rodent adeno-, parvo-, paramyxo-, and picornaviruses that represent novel species or isolates, including murine adenovirus 4, two additional species in the genus Chaphamaparvovirus, two paramyxoviruses distantly related to unclassified viruses in the genus Jeilongvirus, and the first Aichivirus A sequence identified from rodents in Africa. Our results emphasize the importance of rodents as a reservoir for potential zoonotic viruses.

Multitrophic Diversity of the Biotic Community Drives Ecosystem Multifunctionality in Alpine Grasslands.

Biodiversity and ecosystem multifunctionality are currently hot topics in ecological research. However, little is known about the role of multitrophic diversity in regulating various ecosystem functions, which limits our ability to predict the impact of biodiversity loss on human well-being and ecosystem multifunctionality. In this study, multitrophic diversity was divided into three categories: plant, animal, and microbial communities (i.e., plant diversity, rodent diversity, and bacterial and fungal diversity). Also, 15 ecosystem functions were divided into four categories-water conservation, soil fertility, nutrient cycling and transformation, and community production-to evaluate the significance of biotic and abiotic variables in maintaining ecosystem multifunctionality. Results indicated that species diversity at multiple trophic levels had a greater positive impact on ecosystem multifunctionality than species diversity at a single trophic level. Notably, the specific nature of this relationship depended on the niche breadths of plants, indicating that plants played a key role in linking above and belowground trophic levels. Abiotic factors such as altitude and pH directly acted on ecosystem multifunctionality and could explain changes in ecosystem functions. Overall, our study offers valuable insights into the critical role of multitrophic species diversity in preserving ecosystem multifunctionality within alpine grassland communities, as well as strong support for the importance of biodiversity protection.

Biodiversity loss in a gradient of urbanization: rodent community structure in a subtropical area of Northern Argentina

Abstract Urbanization promotes habitat degradation because it involves irreversible processes that homogenize habitats and favor the exclusion of native species. This research evaluates rodent community structure at different levels of urbanization in Misiones, Argentina. We expect that rodent communities are less diverse in more highly urbanized areas and that communities differ between each level of urbanization. To assess these hypotheses, rodent capture sessions were carried out from July 2017 to March 2020, totaling 21,985 trap-nights. Alpha and beta diversity were calculated for each level of urbanization. We captured a total of 684 individuals belonging to 8 sylvan-native and 2 commensal-exotic species. Species richness was greatest and evenness was lowest in natural protected areas. The native species Akodon montensis was the most abundant, while the remaining 7 native species represented less than 23% of the total of captures. The rural area showed the second-highest richness, and the community was principally represented by 2 native and 2 exotic species. The periurban area was ranked third in richness and with the highest evenness, dominated by A. montensis followed by Mus musculus and Rattus rattus. The urban area exhibited the lowest richness represented only by the 2 commensal-exotic species. In agreement with our expectations, these results show a negative association between urbanization level and small rodent diversity, evidenced by a reduction in the number of native species in highly urbanized areas.

Impacts of ectoparasite flea infestation on gut microbiota of the Meriones unguiculatus in a rodent-flea system.

Fleas, along with one of their host species, Meriones unguiculatus, possess the capability to act as vectors in the transmission of plague. Parasitism by fleas may markedly influence the physiology and immune system of their hosts. Gut microbiota plays an important role in the growth and development of rodents. However, few studies have explored the impacts of ectoparasitic flea on the gut microbiome of rodents. This study investigated the immunological responses and changes in the gut microbial diversity and composition in both wild and laboratory rodents infested with fleas and laboratory rodents infested with Ctenocephalides felis. We measured immune reactions post-infestation by enzyme-linked immunosorbent assay (ELISA) and explored the effects of ectoparasitic infestation on the diversity and composition of the rodent gut microbiota in microbiome studies by 16S rRNA gene sequencing techniques. After flea infestation, results from 16S rRNA gene sequencing techniques indicated a significant increase in alpha diversity, affecting the composition of the gut microbiota. At the genus level, the abundance of the harmful bacterium Desulfovibrio increased. Beta diversity analyses showed significant differences between the gut microbiota of the experimental and control groups. ELISA results revealed significantly elevated levels of IgG in parasitized mice, while the differences in IgA levels were not significant. Flea infections affect the composition and diversity of the gut microbiota in the M. unguiculatu, and it has been found that the biomarker Desulfovibrio increases following flea infection in these rodents. Our results indicate that the gut microbiota can regulate the stability of the rodent-flea system. These findings may provide a foundation for exploring preventive measures against plague and aid in developing more effective treatments for the infection.

Rodents of Bahir Dar Blue Nile River Millennium Park, Ethiopia.

Rodents are mammals of the order Rodentia, which are found in all continents except Antarctica. They are the most diverse groups of mammals representing 41% of all mammals and they are known with 33 families, 481 genera, and about 2277 species. The present study was conducted from December 2018 to August 2019 both during the dry and wet seasons using Sherman traps and live traps. Four trap sites namely forest, bushland, grassland, and sugarcane plantation were selected for data collection. Shannon-Wiener diversity index (H') was used to compute rodent species diversity, Simpson's index (D) to assess the number and abundance of rodents in the different habitats, and one-way ANOVA and independent samples t-test were used for data analysis. A total of 163 individual rodents were captured in 1776 trap nights of which 125 individuals were captured using live traps in 1176 trap nights and 38 individuals using snap traps in 600 trap nights. Among the total individual rodents captured in the Bahir Dar Blue Nile River Millennium Park, 63.8% (n = 104) were males and 36.2% (n = 59) were females. Males outnumbered females in all the grids and the difference was significant (t = 31.5, df = 10, p < 0.05). The relative abundance of rodent species indicated that 42.4% (n = 53) were Arvicanthis niloticus, 26.4% (n = 33) Rattus rattus, 17.6% (n = 22) Mus musculus, 8% (n = 10) Mastomys natalensis, and 5.6% (n = 7) Arvicanthis abyssinicus. There are more individual specimens of A. niloticus than other species identified in the area (F = 698.22, df = 4, p < 0.05). Distribution of rodents varied among the different habitats. As a result, the bushland habitat showed more diversity of rodents (H = 0.98) and comprised relatively the highest (51.2%, n = 64) number of individuals captured, while the forest habitat supported the lowest number of rodents (4%, n = 5), and the difference showed a significant difference (F = 873.37, df = 3, p < 0.05). Population density with 95% confident interval estimated as 166 individuals/ha (95% CI:164.43-167.57). The present study provides basic information about population dynamics of rodents and contributes to design conservation strategies for rodents in particular and other biota of the area in general.

Rodent diversity in an elevation gradient from grassland to pine forest in the Chihuahuan desert ecoregion in North-Western Mexico

Diversity patterns of rodent communities across elevational ranges have been analyzed in the Chihuahuan Desert. However, detailed local variations in community composition and species turnover across these ranges are unknown. Anthropogenic pressures in a landscape differ depending on ecosystem type, and therefore, effective conservation initiatives must incorporate an understanding of where these biotic transitions occur. We estimated the rodent diversity in a prairie-to-mountain continuum of four ecosystem types in the Chihuahuan Desert: oak forest (Quercus spp.), pine forest (Pinus spp.), grasslands, and scrublands. We hypothesized that solid habitat associations of the rodent community in each ecosystem are strong drivers that differentiate community groups across ecosystem types. We speculated that the inherent differences between prairie and mountain ecosystems will likely yield a more significant species turnover than between communities within ecosystem types. We studied the rodent communities in each of the four ecosystem types during the dry, wet, and winter seasons in the Janos Biosphere Reserve in Chihuahua, Mexico, across an elevational range from 1,300 to 2,600 m asl. The grassland rodent communities were subdivided into two groups: those with and those without black-tailed prairie dogs (Cynomys ludovicianus). We estimated species richness, number of dominant species, and species turnover for each ecosystem type across the elevational range. Our study revealed that while the prairie and mountain ecosystems support two distinctly different rodent communities, there were significant differences in community composition in each ecosystem type, except the grassland communities, where the presence/absence of the prairie dogs did not appear to influence community composition. The rodent community in the scrublands was the most species-rich and included all the grassland species and a species shared with oak and pine forests. In contrast, the mountain oak and pine forests were less diverse ecosystems dominated by habitat specialists.

Diversity and Conservation of Rodents in Saudi Arabia

Diversity and Conservation of Rodents in Saudi Arabia

Rodent communities in a neglected grassland landscape: Investigating species-specific responses of grassland rodents to habitat type and shrub presence

Arid grasslands worldwide are transitioning to scrublands due to shrub encroachment, resulting in habitats with varying shrub cover. Shrubs play a crucial role in grassland ecosystems, offering trade-offs to rodents in terms of visibility, shelter, and food availability, thereby affecting their occurrence and distribution. This study explores the link between habitat characteristics and rodent activity and density, focusing on shrub presence. In the Tirunelveli district of southern India, we measured rodent density and activity across three grassland types with increasing shrub presence. Our findings reveal species-specific responses to shrub density. The Soft-furred rat (Millardia meltada) dominated, showing adaptability to different shrub levels, while the black rat (Rattus Rattus) was least represented. Fine-scale analysis indicates a positive association between shrub presence and rodent captures. Grassland obligate species like the Indian gerbil (Tatera indica) exhibited reduced activity in densely shrubbed sites, whereas semi-arboreal species like the Indian palm squirrel (Funumbulus palmarum) showed increased activity. This study underscores the importance of considering habitat structure in grassland ecosystem management for the conservation of rodent diversity and ecosystem health.

Population genetics and demography of the endemic mouse species of Cyprus, Mus cypriacus

AbstractMus cypriacus is one of three small palaeoendemic mammals that have survived the Mediterranean islands’ anthropization. This species, endemic to Cyprus, was described in 2006 and stands out as one of the last mammal species to have been discovered in Europe. Despite scarce data on its genetics, ecology, and life-history traits, Mus cypriacus is assessed as Least Concern LC in the IUCN Red List, partly due to its morphological similarity with the sympatric house mouse that prevented earlier identification. Our study uses mitochondrial and microsatellite markers to investigate this small rodent's population genetic structure and diversity. Our analysis did not identify any population genetic structure and suggested a high genetic diversity across Cyprus. When inferring habitat preference using sample locations, it appeared that M. cypriacus utilizes a diverse variety of habitats, covering more than 80% of the island. Although these results are encouraging for the conservation status of the species, they still need to be cautiously applied as potential threats may arise due to increasing habitat destruction and changes in land use. Consequently, our encouraging results should be applied judiciously. Additional ecological data are urgently needed to gain a more comprehensive understanding of this inconspicuous endemic species.

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.

Effects of overgrazing on the functional diversity of rodents in desert areas.

Environmental stressors and disturbances can cause changes in an ecosystem's community structure, which can be reflected in its functional diversity. As grazing intensity increases, this causes changes in the environment that inevitably lead to changes in the community structure, which can especially affect rodents due to their sensitivity to the environment. The effects of grazing prohibition and overgrazing on the functional diversity of desert rodent communities in Alxa were studied in April, July, and October of 2018-2020. The trap-day method was used to study rodent communities in disturbed habitats. Five functional traits were selected and quantified: nutrition, life history, physiology, morphology, and activity rhythm. The results showed that: (1) The species composition of rodent communities in the Alxa Desert in spring and autumn was significantly correlated with the functional traits of the hibernation, reproductive cycle, and feeding habits. The species composition in the summer was only significantly correlated with the functional traits of reproductive cycle and diet. (2) The effects of overgrazing on the functional diversity of rodents in desert areas have significant temporal and spatial characteristics. (3) In spring and summer, overgrazing made the Functional Richness index of the rodent community lower than that of areas where grazing is prohibited, but the Functional Evenness index was higher than that of grazing-prohibition areas. In autumn, overgrazing increased the Functional Richness index of the rodent community and decreased the Functional Evenness index. The Functional Divergence index was higher in overgrazing areas than in grazing-prohibited ones. These results suggest that, in spring and summer, overgrazing reduced the ecological space utilization ability of rodent communities; however, the impact on the degree of utilization of community resources is more comprehensive. In autumn, overgrazing increases the ability of rodent communities to use ecological space but reduces resource efficiency. Overgrazing makes the niche differentiation of rodent communities higher, the degree of overlap lower, and the competition between species weaker. Therefore, overgrazing will affect the functional diversity of the community through the utilization of ecological space, resource utilization, interspecific competition, and niche.

Forest holds high rodent diversity than other habitats under a rapidly changing and fragmenting landscape in Quirimbas National Park, Mozambique

Habitat loss and fragmentation have widely recognised as the major challenge for biodiversity conservation across the world. This is particularly true in Quirimbas National Park (QNP) where holds unique fauna, and anthropogenic factors have been intensifying leading to a significant loss of biodiversity, especially rodents which play a vital role for the functioning of ecosystems. However, studies assessing rodent diversity, and deeply analysing spatiotemporal dynamics of this vulnerable landscape are still lacking although they are decisive for successful wildlife management and monitoring. This study aimed to assess the rodent diversity, change intensity and its driving forces, and fragmentation of different habitat types in QNP. Multi-temporal satellite images and field data were used to analyse the habitat fragmentation and change intensities at three levels (time interval, category, and transition) from 1990 to 2020. The stratified sampling and capture-recapture approaches were used to survey rodents in three habitats: forest, grassland and cropland. Ecological metrics were employed to measure rodent diversity, distribution and composition. Statistical tests were applied to check differences in rodent abundance and diversity among habitats. The findings revealed an increase in fragmentation of all habitats, and forest experienced the highest losses (107.3 km2) during 1990–2020. The annual rate change intensity was fast from 2010 to 2020. Cropland and built-up land experienced greater intensively gains and losses, while the annual change intensity of forest was dormant over time. Cropland and built-up land expanded at the expense of forest from 2010 to 2020, whereas from 2000 to 2010, cropland's gain targeted intensively grassland, built-up land and water body, and avoided forest. We recorded four rodent species: Acomys spinosissimus, Mastomys verreauxii, Dasymys incomtus and Aethomys chrysophilus; the last three species are new records for the park. Forest revealed the highest rodent diversity (Shannon entropy = 3.0), and the total species richness was comparable to previous studies in eastern Africa. We found significant differences in rodent abundance among habitats. Turnover and nestedness were the main cause of the overall beta diversity. This study can provide vital information for wildlife managers to better understand the process of habitat loss and fragmentation and its implication to biodiversity, which is crucial for applying appropriate conservation management.

A Baseline Study on the Diversity of Rodents in Rural Mountain Areas of the Gilgit District, Pakistan

A Baseline Study on the Diversity of Rodents in Rural Mountain Areas of the Gilgit District, Pakistan

Maritime international trade and bioinvasions: A three‐year long survey of small mammals in Autonomous Port of Cotonou, Benin

Abstract International trade has been favouring the dissemination of a wide suite of invasive alien species. Upstream prevention through the monitoring of entry points is identified as an appropriate strategy to achieve control of bioinvasions and their consequences. Maritime transportation has been responsible for the introduction worldwide of exotic rodents that are major pests for crops and food stocks as well as reservoirs of many zoonotic pathogens. In order to limit further dissemination, the International Health Regulation constrains decisions makers and socio‐economic stakeholders to manage ship‐mediated import/export of rodents within seaports. Unfortunately, eco‐evolutionary insights into rodent introduction events that could guide preventive actions in seaports are very scarce. In order to bridge this gap, we here describe the results of a 3 year‐long survey of small mammals conducted in the Port of Cotonou, Benin. Our aim was to assess the spatiotemporal distribution, diversity and relative abundance of invasive and native rodents. 960 small mammal individuals were captured in nine within‐seaport sites. We found (i) a marked predominance of invasive species (84% of the individuals belonging to Mus musculus, Rattus rattus, R. norvegicus), (ii) with native species (i.e. Mastomys natalensis and the shrew Crocidura olivieri) essentially restricted to peripheral non‐industrial areas, as well as (iii) a fine‐scale spatial segregation stable over time between the invasive Norway rats and house mice on the one hand, and the black rats and shrews on the other hand. Furthermore, trapping before and after two successive rodent control campaigns indicates that they were ineffective and that subsequent rodent recolonisation occurred 6–12 months following intervention. Synthesis and applications. Our results are discussed in terms of ecological processes at play (e.g. interspecific interactions) and operational recommendations (e.g. assessment of proper eradication units, environmental modifications).

Small mammal abundance and diversity along an altitudinal gradient in the Simien Mountains National Park, Ethiopia

Abstract Species richness, abundance, diversity, and distribution of rodents and shrews along altitudinal gradients in the Simien mountains national park, Ethiopia, were studied using Sherman traps. Rodents and shrews were trapped at four altitudinal ranges (2,800 m a.s.l., 3,200 m a.s.l., 3,600 m a.s.l. and 4,000 m a.sl.). A total of 202 individuals were captured, comprising 184 rodents and 18 shrews. In total, there were eight species of rodents and one shrew species. The relative abundances of Lophuromys simensis and Stenocephalemys albipes were the highest in the early dry season, dry season, and wet season. The relative abundances of Desmomys harringitoni (7.43%), Dendromys lovati (4.46%), and Mus imberbis (1.98%) were the lowest across the study area. The highest species diversity was recorded at an altitude of 2,800 m a.s.l. (H’ = 1.82). Species composition of rodents and shrews found at altitudes of 2,800 m a.s.l. and 3,200 m a.s.l. were highly similar (Sij = 0.97363). In contrast, the least similar species composition was between altitudes of 2,800 m a.s.l. and 4,000 m a.s.l. (Sij = 0.15632). The abundance, distribution, and diversity of rodents and shrews were significantly correlated with altitude (p = 0.000). Species abundance, distribution, and diversity in the Simien Mountains National Park were significantly correlated with altitude (0.377) and habitat types (0.306). Species composition of small mammals varied among altitudes, seasons, and habitat types, with six rodents and one shrew species being endemic. Notably, the park is subjected to various environmental disturbances, such as fires, grazing, and agriculture, which can negatively impact these small mammals, particularly the endemic species.

Viral diversity in wild and urban rodents of Yunnan Province, China

ABSTRACT Rodents represent over 40% of known mammal species and are found in various terrestrial habitats. They are significant reservoirs for zoonotic viruses, including harmful pathogens such as arenaviruses and hantaviruses, yet knowledge of their hosts and distributions is limited. Therefore, characterizing the virome profile in these animals is invaluable for outbreak preparedness, especially in potential hotspots of mammal diversity. This study included 681 organs from 124 rodents and one Chinese tree shrew collected from Yunnan Province, China, during 2020-2021. Metagenomic analysis revealed unique features of mammalian viruses in rodent organs across habitats with varying human disturbances. R. tanezumi in locations with high anthropogenic disturbance exhibited the highest mammal viral diversity, with spleen and lung samples showing the highest diversities for these viruses at the organ level. Mammal viral diversity for both commensal and non-commensal rats was identified to positively correlate with landscape disturbance. Some virus families were associated with particular organs or host species, suggesting tropism for these pathogens. Notably, known and novel viral species that are likely to infect humans were identified. R. tanezumi was identified as a reservoir and carrier for various zoonotic viruses, including porcine bocavirus, hantavirus, cardiovirus, and lyssavirus. These findings highlight the influence of rodent community composition and anthropogenic activities on diverse virome profiles, with R. tanezumi as an important reservoir for zoonotic viruses.

RNA virus diversity in rodents.

Many zoonotic disease emergencies are associated with RNA viruses in rodents that substantially impact public health. With the widespread application of meta-genomics and meta-transcriptomics for virus discovery over the last decade, viral sequences deposited in public databases have expanded rapidly, and the number of novel viruses discovered in rodents has increased. As important reservoirs of zoonotic viruses, rodents have attracted increasing attention for the risk of potential spillover of rodent-borne viruses. However, knowledge of rodent viral diversity and the major factors contributing to the risk of zoonotic epidemic outbreaks remains limited. Therefore, this study analyzes the diversity and composition of rodent RNA viruses using virus records from the Database of Rodent-associated Viruses (DRodVir/ZOVER), which covers the published literatures and records in GenBank database, reviews the main rodent RNA virus-induced human infectious diseases, and discusses potential challenges in this field.

Quaternary rodents of South Africa: A companion guide for cranio-dental identification.

Rodentia is the most species-rich order among mammals. The Republic of South Africa harbours a high rodent diversity whose taxonomy and phylogeny have been extensively studied using genetic tools. Such advances have led to the establishment of new faunal lists for the country. Because rodents are frequently recovered from archaeological cave site material and owl pellets, and constitute prime material for studying both past and present environmental conditions, it is necessary to characterize their osteological remains. The skull and teeth are the most useful diagnostic skeletal elements preserved in modern and fossil accumulations. This key provides updated craniodental criteria for identifying rodent genera found in Quaternary deposits, and modern material from the Republic of South Africa, thus facilitating research on past and present rodent diversity.

The Genetic Diversity and Interspecific Transmission of Circovirus in Rhizomys sinensis in Guangdong, Southern China

Circoviruses are a group of small circular, single-stranded DNA viruses that belong to the family Circoviridae. They are known to infect a wide variety of animals. Rhizomys sinensis is a species of rodent that is the reservoir of many zoonotic pathogens. Our previous study identified many sequencing reads mapped to the genome of viruses in Circoviridae in R. sinensis. However, little is known about the circulation and genetic characterization of circoviruses in R. sinensis. This study identified three different circoviruses in samples from 195 R. sinensis. First, the bamboo rat circovirus is widely prevalent in R. sinensis in Guangdong Province, and all strains could be divided into three clades based on nucleotide substitutions at specific sites. Second, and more important, porcine circovirus 2 (PCV2) was isolated for the first time from R. sinensis, which expanded the host range of PCV2 and indicated extra procedures would be required to protect livestock from this virus. Finally, a novel circovirus phylogenetically close to the dromedary stool-associated circular ssDNA virus was detected in 86 (44.1%) samples, which may represent a new circovirus species. These results not only expand our understanding of the circovirus diversity in rodents, particularly in R. sinensis, but also underscore the importance of continued surveillance of viruses in wildlife populations, particularly in rodents, to prevent and control the spread of zoonotic pathogens.

The abundance and diversity of rodents in forest sites invaded and uninvaded by Maesopsis eminii trees in Amani Nature Reserve, Tanzania

The abundance and diversity of rodents in forest sites invaded and uninvaded by Maesopsis eminii trees in Amani Nature Reserve, Tanzania