Rodent Assemblages Research Articles

Impacts of host phylogeny, diet, and geography on the gut microbiome of rodents.

Mammalian gut microbial communities are thought to play a variety of important roles in health and fitness, including digestion, metabolism, nutrition, immune response, behavior, and pathogen protection. Gut microbiota diversity among hosts is strongly shaped by diet as well as phylogenetic relationships among hosts. Although various host factors may influence microbial community structure, the relative contribution may vary depending on several variables, such as taxonomic scales of the species studied, dietary patterns, geographic location, and gut physiology. The present study focused on 12 species of rodents representing 3 rodent families and 3 dietary guilds (herbivores, granivores, and omnivores) to evaluate the influence of host phylogeny, dietary guild and geography on microbial diversity and community composition. Colon samples were examined from rodents that were collected from 7 different localities in Texas and Oklahoma which were characterized using 16S rRNA gene amplicon sequencing targeting the V1-V3 variable regions. The microbiota of colon samples was largely dominated by the family Porphyromonadaceae (Parabacteriodes, Coprobacter) and herbivorous hosts harbored richer gut microbial communities than granivores and omnivores. Differential abundance analysis showed significant trends in the abundance of several bacterial families when comparing herbivores and granivores to omnivores, however, there were no significant differences observed between herbivores and granivores. The gut microbiotas displayed patterns consistent with phylosymbiosis as host phylogeny explained more variation in gut microbiotas (34%) than host dietary guilds (10%), and geography (3%). Overall, results indicate that among this rodent assemblage, evolutionary relatedness is the major determinant of microbiome compositional variation, but diet and to a lesser extent geographic provenance are also influential.

Subfossil rodents and tenrecs of Children’s Cave, Madagascar

ABSTRACT Madagascar is famous for its exceptional present and past diversity, yet its Holocene small mammal fauna remains poorly documented. In this work we present the first taxonomic study of the Children’s Cave rodent and tenrec subfossil assemblages collected by Forsyth Major as early as 1895 near Antsirabe in the Central Highlands. We found five rodent species, three endemic and two non-native, as well as six species of tenrecids. This assemblage represents one of the earliest records of Rattus rattus and Mus musculus in the Central Highlands of Madagascar. It is also the first record of Macrotarsomys bastardi in that region, a species that does not currently occur there, and which may indicate a slight environmental change with more bush and forest at the time of the site formation. We find that the native and invasive subfossil specimens do not differ in size and morphology from modern representatives, except for Macrotarsomys. Some proportional differences in rodent taxa are evident between the two Central Highland subfossil assemblages of Children’s Cave and the nearby site of Lavajaza, as well as differences in rodent and tenrecid species composition from other sites in southern parts of Madagascar. Therefore, we are unable to draw any conclusions about the contemporaneity of the Lavajaza and Children’s Cave assemblages nor can we attempt to estimate the relative age of the subfossil fauna.

Temporal and behavioural niche partitioning underlies coexistence within a native‐exotic rodent assemblage exploiting a high‐value limited resource

AbstractNiche partitioning is a common strategy species use to avoid competition for limited resources, allowing them to coexist. Rodent species often reduce competition by spatial segregation and trophic differentiation, but behavioural differences, particularly related to foraging, can also be important. Therefore, temporal segregation can also be an important mechanism for species coexistence, as it helps them avoid sub‐optimal habitats. We found three rodent species (the native Octodon degus and O. lunatus, and the exotic Rattus rattus) foraging on endemic palm Jubaea chilensis seeds, a highly valuable but limited resource. We hypothesized that these rodent species could coexist by segregating foraging in time, showing behavioural differences. To test this, we used camera traps to monitor the fate of J. chilensis seeds and rodent activity at 25 feeding stations. From 596 photographic records, we identified 128 as O. degus, 232 as O. lunatus and 236 as R. rattus. Octodon degus had a diurnal activity, while O. lunatus and R. rattus were nocturnal, showing significant temporal segregation. However, we found no spatial association among these rodents. We found significant behavioural differences in decision and handling times and seed removal rates, with O. degus having the greatest seed removal rate. Nevertheless, we found some nocturnal O. degus records in which the three rodent species were co‐foraging, which may suggest that the resource is limited but valuable enough to shift from exploitation to interference competition. Our results suggest that temporal and behavioural differentiation are more important than spatial segregation and trophic differentiation. Thus, niche partition over multiple dimensions might allow for species coexistence.

Analysis of the Early Pleistocene small mammals from Pirro Nord 13 (Apricena, southern Italy) and their implications for reconstructing the palaeoenvironment of the early human occupation in Europe

Analysis of the Early Pleistocene small mammals from Pirro Nord 13 (Apricena, southern Italy) and their implications for reconstructing the palaeoenvironment of the early human occupation in Europe

Distribution and prevalence of Sin Nombre hantavirus in rodent species in eastern New Mexico.

Orthohantaviruses are diverse zoonotic RNA viruses. Small mammals, such as mice and rats are common chronic, asymptomatic hosts that transmit the virus through their feces and urine. In North America, hantavirus infection primarily causes hantavirus cardiopulmonary syndrome (HCPS), which has a mortality rate of nearly 36%. In the United States of America, New Mexico (NM) is leading the nation in the number of HCPS-reported cases (N = 129). However, no reported cases of HCPS have occurred within eastern NM. In this study, we assessed the prevalence of Sin Nombre virus (SNV) in rodent assemblages across eastern NM, using RT-qPCR. We screened for potential rodent hosts in the region, as well as identified areas that may pose significant infection risk to humans. We captured and collected blood and lung tissues from 738 rodents belonging to 23 species. 167 individuals from 16 different species were positive for SNV RNA by RT-qPCR, including 6 species unreported in the literature: Onychomys leucogaster (Northern grasshopper mouse), Dipodomys merriami (Merriam's kangaroo rat), Dipodomys ordii (Ord's kangaroo rat), Dipodomys spectabilis (Banner-tailed kangaroo rat), Perognathus flavus (Silky pocket mouse), and Chaetodipus hispidus (Hispid pocket mouse). The infection rates did not differ between sexes or rodent families (i.e., Cricetidae vs. Heteromyidae). Generalized linear model showed that disturbed habitat types positively influenced the prevalence of SNV at sites of survey. Overall, the results of this study indicate that many rodent species in east New Mexico have the potential to maintain SNV in the environment, but further research is needed to assess species specific infectivity mechanisms and potential risk to humans.

Beta diversity patterns in Andean rodents: current and historical factors as drivers of turnover and nestedness

Abstract The Andes are known to be one of the most species-rich regions on Earth, with their origination promoting formation of new habitats and acting as climatic barriers. This orogenic event was structured latitudinally with 3 major segments having different formation times and with different environmental and historical conditions. The Andean region has been historically important in the evolutionary history of small mammals and is considered the region of Earth with the highest values of rodent species richness and turnover. Therefore, the region provides an excellent opportunity to evaluate mechanisms involved in structuring rodent assemblages and beta diversity patterns. Here, we assessed spatial patterns of rodent beta diversity along the Andes Mountains, with specific goals of examining patterns of turnover and nestedness as 2 recognized processes that drive species composition. We explored the role of spatial, climate, and historical factors on beta diversity patterns using geographic range maps for 432 rodent species to construct a species presence–absence matrix. We used piecewise regressions to identify latitudinal breakpoints in turnover and nestedness, and conducted multiple regressions and variation-partitioning approaches to assess the contribution of each set of postulated drivers in shaping beta diversity patterns. Beta diversity decreases from north to south. The highest turnover was located at the Northern Andes (5°N and 10°S) and western-central Andes (20°S and 35°S). Nestedness was higher below 40°S and in some areas of the western-central Andes between 15° and 20°S. Turnover and nestedness registered breakpoints coincident with the Central and Southern Andes limit. Turnover explained most of the beta diversity for all segments, although within the Southern Andes there was also some contribution of nestedness. In all segments, beta diversity was mainly explained by spatial factors with minor contributions from spatially structured climate (Northern Andes), interaction of all factors (Central Andes), and the interaction between current climate and history (Southern Andes).

Environmental and climatic inferences for Marine Isotope Stage 2 of southern Belgium (Meuse valley, Namur Province) based on rodent assemblages

Environmental and climatic inferences for Marine Isotope Stage 2 of southern Belgium (Meuse valley, Namur Province) based on rodent assemblages

Additions to the late Eocene Süngülü mammal fauna in Easternmost Anatolia and the Eocene-Oligocene transition at the periphery of Balkanatolia

The Eocene-Oligocene transition marks a period of dramatic global climatic change correlated with pronounced mammalian faunal change. Fossil evidence is indispensable for studying the distribution of taxa through time, and determining how abiotic parameters shaped ancient biodiversity. Here we report ruminant artiodactyls and a new anthropoid primate from Süngülü, a locality in Eastern Anatolia that has yielded a diversified and largely endemic assemblage of rodents. Three taxa of ­ruminants are recognized, the tragulid Iberomeryx parvus Gabunia, 1964, a larger species of Iberomeryx Gabunia, 1964, and a bachitheriid referred to cf. Bachitherium sp. A lower molar is identified as the new eosimiid primate Sungulusimias unayae n. gen., n. sp., which is the first occurrence of Paleogene anthropoids in western Asia. The lower molar of Sungulusimias unayae n. gen., n. sp. is characterized by protoconid and metaconid closely spaced and of similar height and volume, paraconid cuspidate and nearly connate with metaconid, strong mesiobuccal cingulid, and entoconid without strong connection to hypoconulid via the postcristid. The composition of this assemblage together with rodents indicates a probable Latest Eocene age for Süngülü, although an early Oligocene age cannot be completely ruled out. The rodent fauna from Süngülü suggests that endemism persisted at the periphery of Balkanatolia until the latest Eocene while Eastern Anatolia was situated in a strategic corridor for faunal exchanges between eastern Asia, Indo-Pakistan and Europe. During the Eocene-Oligocene transition, Balkanatolia probably functioned as a “holding pen” where various taxa were confined for significant intervals of time before proceeding to colonize Western Europe at the Grande Coupure.

Squirrels (Rodentia, Sciuridae) from the Late Miocene Pavlodar fossil site in northern Kazakhstan: implications for cranial anatomy and evolutionary history of the early marmotine ground squirrel genus Sinotamias

ABSTRACT Although sciurids are among the most distinctive rodents of the Neogene age in Eurasia and North America, there remain significant gaps in knowledge of their fossil record, particularly that of Central Asia. Here we report on Sciuridae specimens from the Pavlodar (Gusinyi Perelet) fossil site in northern Kazakhstan (western Siberia), which pertain to Sinotamias orientalis, a basal marmotine ground squirrel genus from the Middle Miocene – Early Pliocene of Eastern Europe and Eastern Asia. The new specimens document the previously unknown cranial (maxillary and palatine) features of Sinotamias, which confirms the distinctiveness of the genus from chipmunks (subtribe Tamiina), suggesting a close phylogenetic relationship between Sinotamias and basal extant Marmotina genera Ammospermophilus and Callospermophilus. We review the rodent assemblage of Pavlodar 1A and propose the latest Miocene, Baodean age for the locality, correlative to the late Turolian, 7.5–6.5 Mya.

Composition of non‐volant small mammals inhabiting a degradation gradient in a lowland tropical forest in Uganda

A study aimed at assessing the structure of rodent and shrew assemblages inhabiting a degradation gradient while considering rainfall patterns, was conducted in one of few remaining lowland tropical forests in eastern Africa. We collected a unique dataset of rodents and shrews, representing 24 species (19 rodents, 5 shrews). The most abundant species alternated in dominance as species abundance significantly fluctuated across the study period following a degradation gradient. While only generalist species were observed near the degraded forest edge, habitat specialists such as Deomys ferrugineus, Malacomys longipes and Scutisorex congicus, were observed in the primary forest interior suggesting a significant association between species and their associated habitats and habitat attributes. There was also an observed correlation between rainfall patterns and species abundance. Capturing more species in adjacent fallows and along the degraded forest edge suggests that many species are able to live in degraded habitats that offer a variety of food resources. The study has highlighted the importance of habitat heterogeneity through species associations and also recommend an assessment of the effect of habitat homogeneity due to the proliferation of paper mulberry on small mammal community.

Demographic processes, refugia and dispersal routes during the Pleistocene in a sigmodontine rodent assemblage from the South American Pampas

Abstract The Pampas of South America represents one of the most extended subtropical–temperate grasslands in the world. This ecoregion was influenced by Pleistocene climate oscillations. The sigmodontine rodent assemblage inhabiting this region is a good model system to analyse the impact of these climate changes on evolutionary histories. We performed a comparative phylogeographical study on seven species to evaluate the concordance of phylogeographical patterns among them, to assess if they experienced congruent and synchronous demographic changes, and posit putative centres of origin and dispersal routes. Four species (Calomys musculinus, Oligoryzomys flavescens, Oxymycterus nasutus and Oligoryzomys nigripes) showed evidence of demographic expansion. In the first three, population increases started during Marine Isotope Stage 5 (MIS 5) while in Ol. nigripes, the rise started during MIS 7; this rise would have continued to the present in all cases. Necromys lasiurus, Scapteromys tumidus and Scapteromys aquaticus did not show a pattern of expansion. Four centres of origin were identified; in general, populations sharing the same putative refugium followed common dispersal routes. Our results indicate that the Pampas offered relatively stable habitats over time, mainly in areas associated with watercourses or coastlines, suggesting that recent Pleistocene climate oscillations have had a moderate impact on this ecoregion compared to other regions of South America.

DIVERSITY PATTERNS OF RODENT ASSEMBLAGES IN THE NORTH OF FAZAO-MALFAKASSA NATIONAL PARK (TOGO)

The rodent assemblages were studied in different habitat types in the northern part of the Fazao-Malfakassa National Park located in central-western Togo, West Africa. A suite of different methods was applied, including face-by-face interviews with local hunters, live trapping along standardized transects and opportunistic observations. A total of 20 rodent species were recorded based on the surveys carried out in villages, including 6 families and 17 genera. There was a clear gradient pattern in the univariate diversity indices by habitat type: Dominance index was remarkably higher in Urban/plantation than in the other habitat types whereas Evenness index was remarkably higher in gallery forest than in the other habitat types. According to a Canonical Correspondence Analysis, three “ecological groups” (= guilds) of species were formed: a group from wooded habitats (savannahs and semiforests), a group from grassy savannah and a group from urban/plantation habitats. Null model analyses revealed that species tend to non-randomly congregate in some habitat types and/or localities. The ecological implications of these data were presented.

A Comparison of Small Rodent Assemblages after a 20 Year Interval in the Alps.

Human-induced environmental alterations in the Alps may importantly affect small mammal species, but evidence in this sense is limited. We live-trapped small rodents in the Central-Eastern Italian Alps in three close-by habitat types (rocky scree, alpine grassland, and heath) at 2100 m a.s.l. during summer-fall, in 1997 and 2016. We compared small rodent assemblages through a Redundancy Detrended Analysis (RDA). In both surveys, we detected two specialist species, i.e., the common vole (Microtus arvalis) and the snow vole (Chionomys nivalis), and, unexpectedly, the forest generalist bank vole (Myodes glareolus). In 1997, grassland was mainly occupied by the common vole, while the bank vole and the snow vole were sympatric in the other habitats. In 2016, the snow vole was detected only in the scree, while other species did not show distribution changes. We discuss a series of hypotheses that might have driven the differences observed across decades, among which is a species-specific response to abiotic and biotic environmental alterations, with the alpine habitat specialist moving out of sub-optimal habitats. We encourage further research on this topic, e.g., via long-term longitudinal studies.

A small assemblage of early Oligocene rodents and insectivores from the Sivas basin, Turkey

The assemblage of small mammals from a site near Yeniköy (Anatolia) is described. The assemblage was collected by screen-washing a sample from a locality in the Selimye Formation (Sivas basin). The site has a magneto-stratigraphic calibrated age of 29 Ma (younger part of the early Oligocene). The murids dominate in this relatively small collection with Eucricetodon and Pseudocricetodon. In addition, a dipodid, an unidentified erinaceide and the new baluchimyin hystricognath genus and species Zorania milosi nov. gen. et nov. sp. are present. The study of Eucricetodon, Pseudocricetodon and Zorania nov. sp. includes an analysis of incisor enamel microstructure. The incisor microstructure of Eucricetodon shows that there are several parallel long-living lineages within the genus. The Anatolia-Balkans biogeography of the late Eocene-Oligocene is reviewed. Its rodent assemblages are characterised by dominance of murids and presence of taxa that are known from low-latitude Asia. The Paleogene Anatolia-Balkans biogeographic province, is therefore rather different from those of western European and the Indian subcontinent.

Tropical savanna small mammals respond to loss of cover following disturbance: A global review of field studies

Small-mammal faunas of tropical savannas consist of endemic assemblages of murid rodents, small marsupials, and insectivores on four continents. Small mammals in tropical savannas are understudied compared to other tropical habitats and other taxonomic groups (e.g., Afrotropical megafauna or Neotropical rainforest mammals). Their importance as prey, ecosystem engineers, disease reservoirs, and declining members of endemic biodiversity in tropical savannas compels us to understand the factors that regulate their abundance and diversity. We reviewed field studies published in the last 35 years that examined, mostly experimentally, the effects of varying three primary endogenous disturbances in tropical savanna ecosystems—fire, large mammalian herbivory (LMH), and drought—on abundance and diversity of non-volant small mammals. These disturbances are most likely to affect habitat structure (cover or concealment), food availability, or both, for ground-dwelling small mammalian herbivores, omnivores, and insectivores. Of 63 studies (included in 55 published papers) meeting these criteria from the Afrotropics, Neotropics, and northern Australia (none was found from southern Asia), 29 studies concluded that small mammals responded (mostly negatively) to a loss of cover (mostly from LMH and fire); four found evidence of increased predation on small mammals in lower-cover treatments (e.g., grazed or burned). Eighteen studies concluded a combination of food- and cover-limitation explained small-mammal responses to endogenous disturbances. Only two studies concluded small-mammal declines in response to habitat-altering disturbance were caused by food limitation and not related to cover reduction. Evidence to date indicates that abundance and richness of small savanna mammals, in general (with important exceptions), is enhanced by vegetative cover (especially tall grass, but sometimes shrub cover) as refugia for these prey species amid a “landscape of fear,” particularly for diurnal, non-cursorial, and non-fossorial species. These species have been called “decreasers” in response to cover reduction, whereas a minority of small-mammal species have been shown to be “increasers” or disturbance-tolerant. Complex relationships between endogenous disturbances and small-mammal food resources are important secondary factors, but only six studies manipulated or measured food resources simultaneous to habitat manipulations. While more such studies are needed, designing effective ones for cryptic consumer communities of omnivorous dietary opportunists is a significant challenge.

A new rodent chronology for the late Neogene of Spain

A new rodent chronology for the late Neogene of Spain

Dispersal ability is associated with contrasting patterns of beta diversity in African small mammal communities

AbstractAimSpatial processes and environmental filtering are important factors shaping community composition, but their effects are rarely tested across all aspects and components of beta diversity. We investigate both of these factors to explain patterns of taxonomic, functional and phylogenetic beta diversity of small mammals across Sub‐Saharan Africa. We predict that groups with poorest dispersal ability will experience the highest taxonomic and phylogenetic turnover but a nesting of functional diversity independent of dispersal.LocationAfrica.TaxaRodents, bats, shrews.MethodsWe amassed a continent‐spanning dataset of 97 bat assemblages, 166 rodent assemblages and 153 shrew assemblages comprising a total of 183, 225 and 109 species, respectively, from six bioregions of Sub‐Saharan Africa. We calculated three aspects of beta diversity: taxonomic, functional and phylogenetic. For each of these, we first calculated total beta diversity based on the Sørensen index (βsor) and then decomposed this into turnover (βsim) and nestedness (βnes) components. We then used Moran's Eigenvector Maps to examine the relationships between each aspect of beta diversity and environmental gradients (environmental filtering) and geographical distance between sites (spatial processes).ResultsWe found consistent patterns across the three taxa in all aspects of beta diversity, with taxonomic beta diversity being greatest and phylogenetic beta diversity being lowest. The turnover component was typically greater than the nestedness component for taxonomic and functional beta diversity, but not for phylogenetic beta diversity, for all three groups. Beta diversity was also linked with the dispersal ability of the three groups, with the highest levels of beta diversity found in shrews, intermediate levels in rodents and the lowest levels in bats.Main ConclusionsSpatial processes, which are linked to the dispersal abilities of the three taxa of small mammal, dominate environmental drivers in structuring African small‐mammal communities with phylogenetic comparisons suggesting a relatively permeable continent.

Biostratigraphy and biochronology of late Cenozoic North American rodent assemblages

Biostratigraphy and biochronology of late Cenozoic North American rodent assemblages

Cricetodontinae (Rodentia, Mammalia) of the Miocene Tagay fauna (Olkhon Island, Lake Baikal, Eastern Siberia)

The collection of fossil Rodentia from the Miocene Tagay fauna comprises Aplodontidae, Mylagaulidae, Sciuridae, Gliridae, Castoridae, Eomyidae and Cricetodontinae. Represented by three taxa the Cricetodontinae dominate the rodent assemblage of the Tagay fauna. The fossils were collected by wet-screening of test samples along the section Tagay-1 at Tagay Bay of Olkhon Island. Here, we report on the medium-sized Democricetodon cf. lindsayi, the very small Democricetodon sp. and the large Gobicricetodon filippovi. The primitive dental pattern of D. cf. lindsayi and G. filippovi suggest archaic members of the genera, and an age around the Early/Middle Miocene transition.

A new Late Miocene hystricognath rodent assemblage (Caviidae, Dinomyidae, and Neoepiblemidae) from northern Brazil and its biostratigraphic relevance

ABSTRACT The Neogene strata of the Solimões Formation (northern Brazil) have revealed an astonishing diversity of extinct caviomorph rodents. The main exposures of this formation are found along the Juruá, Acre, and Purus rivers, and some road cuts in the State of Acre. In this paper, we reported a new locality containing a rodent assemblage. The outcrop (Coqueiro locality) is located in the Envira River, central region of State of Acre, Brazil. During fieldwork in 2010 and 2019, several isolated cheek teeth and bones of mammals were recovered in conglomeratic levels from this locality. Here, we described specimens assigned to Cardiatherium sp. (Caviidae: Hydrochoerinae), Potamarchus sp. and cf. Pseudopotamarchus (Dinomyidae: Potamarchinae), and Neoepiblema sp. (Neoepiblemidae). The locality is not yet dated by radiometric methods but based on the biostratigraphic information of the taxa here reported, we suggest that the fossil-bearing levels of this locality were deposited during the Late Miocene.