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The Caucasian Squirrel, Sciurus anomalus, is the only representative of the Sciuridae family in the Eastern Mediterranean region. In this study, the mitochondrial genome of the Sciurus anomalus species was generated, and we investigate its phylogenetic position within the Sciuridae family. The generated mitogenome sequence is 16,234 bp. It is composed of a control region and a conserved set of 37 genes containing 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes.
Squirrels (family Sciuridae) are globally distributed members of the order Rodentia with wildlife occurrence in indigenous and non-indigenous regions (as invasive species) and frequent presence in zoological gardens and other holdings. Multiple species introductions, strong inter-species competition as well as the recent discovery of a novel zoonotic bornavirus resulted in increased research interest on squirrel pathogens. Therefore we aimed to test a variety of squirrel species for representatives of three virus families.
Sexual size dimorphism (SSD) is a widespread phenomenon in animals including mammals. It has been demonstrated that across species, the direction and magnitude of sexual dimorphism in body size often corresponds to social systems. Moreover, many animal lineages conform to "Rensch's rule", which states that male-biased SSD increases with body size. We tested whether considerable differences in sociality and large variation in body size were connected with the evolution of SSD in the structural body size of ground squirrels, an otherwise ecologically relatively homogenous group of terrestrial rodents.
The Alashan ground squirrel (Spermophilus alashanicus) is primarily distributed in the regions of Inner Mongolia and Ningxia, China. In this study, we present the first complete mitochondrial genome of S. alashanicus. The genome spans 16,464 base pairs and comprises 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a single control region with a marked AT bias. The overall GC content is 35.4%. Phylogenetic analyses indicate that S. alashanicus clusters are closely associated with S. dauricus. This comprehensive characterization of the S. alashanicus mitochondrial genome serves as a foundational resource for future studies on mitochondrial evolution, species identification, population genomics, and phylogenetics.
The flying squirrel genus Biswamoyopterus (Rodentia: Sciuridae: Pteromyini) was once considered to contain three species, Biswamoyopterus biswasi from northeastern India, B. laoensis from central Laos and B. gaoligongensis from southwest China, all identified from morphological characteristics of one or two specimens. However, based on similar morphological characteristics of two samples of the genus Biswamoyopterus collected recently from northern Laos and northern Myanmar, and the small genetic distances on mitochondrial DNA and nuclear DNA between them, the results strongly support these two samples as representatives of the same species. The phylogenetic analyses strongly support Biswamoyopterus as an independent genus of Pteromyini, as a sister group to Aeromys. Biswamoyopterus biswasi is distributed in the northern Indo-China peninsula, where it is exposed to a series of threats, such as intense hunting activity, illegal trade, and rapid habitat loss; this should warrant its classification as critically endangered according to the International Union for Conservation of Nature (IUCN) Red List criteria. Here, the molecular data for genus Biswamoyopterus and two new specimen records from northern Laos and northern Myanmar are presented.
The genus Sciurus, a member of the family Sciuridae, is widely distributed in the Holarctic region. To better understand mitogenomic characteristics and to reveal internal phylogenetic relationships of the genus, 20 complete mitogenomes of Turkish tree squirrels were successfully sequenced for the first time, including 19 for S. anomalus (from 16,505 bp to 16,510 bp) and one for S. vulgaris (16,511 bp). The mitogenomes of two species were AT-biased. All tRNAs for two species displayed a typical clover-leaf structure, except for tRNASer(AGY). The tRNA Serine1 (S1)-GCT structure lacked the dihydrouridine (DHU) loop and stem. Based on mitogenomic dataset for phylogeny of Sciurinae, phylogenetic analyses (Bayesian Inference and Maximum Likelihood) did not support monophyly of Sciurus and proposed that S. anomalus, the most basal taxa in the Sciurini tribe, had at least five mitogenome lineages, which were also supported by network analysis. The dissimilarities among the five lineages of S. anomalus ranged from 0.0042 (0.42%) to 0.0062 (0.62%) using K2P sequence pairwise distances. In addition to this mitogenomic analysis result, phylogenetic analyses using the CYTB + D-loop dataset proposed the existence of at least nine lineages for S. anomalus, which was different than those of the previous studies. The current study proposed that the use of mitogenomic data for reconstructing the phylogeny of Turkey's Sciurus holds an important value for revealing evolutionary relationships.
We present a genome assembly from an individual male Sciurus vulgaris (the Eurasian red squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.88 gigabases in span. The majority of the assembly is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.
We present a genome assembly from an individual male Sciurus carolinensis (the eastern grey squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.82 gigabases in span. The majority of the assembly (92.3%) is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.
Beilong virus (BeiV), a member of the newly recognized genus Jeilongvirus of family Paramyxoviridae, has been reported with limited geographic and host scopes, only in Hongkong, China and from two rat species. Here, by next-generation sequencing (NGS) on dominant wild small animal species in 4 provinces in China, we obtained a complete sequence of BeiV strain from Rattus norvegicus in Guangdong, neighboring HongKong, China. We then made an expanded epidemiological investigation in 11 provinces to obtain the geographic distribution and genetic features of this virus. Altogether 7168 samples from 2005 animals (1903 rodents, 100 shrews, 2 mustelidaes) that belonged to 33 species of Cricetidae, Muridae, Sciuridae and Dipodidae family of Rodentia, 3 species of Soricidae family of Soricomorpha, 2 species of Mustelidae family of Carnivora were examined by RT-PCR and sequencing. A positive rate of 3.7% (266/7168) was obtained that was detected from 22 animal species, including 5 species of Cricetidae family, 12 species of Muridae family, 2 species of Sciuridae family and 3 species of Soricidae family. Phylogenetic analyses based on 154 partial Large gene sequences grouped the current BeiV into two lineages, that were related to their geographic regions and animal hosts. Our study showed the wide distribution of BeiV in common species of wild rodents and shrews in China, highlighting the necessity of epidemiological study in wider regions.
Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by systematists is likely a product of the difficulties in assessing morphological informative traits and of the scarcity or unavailability of fresh tissue samples for DNA sequencing. The highly discrepant taxonomic arrangements are a consequence of the lack of phylogenies and the exclusive phenotypic-based classifications, which can be misleading in a group with conservative morphology. Here we used high-throughput sequencing and an unprecedented sampling of museum specimens to provide the first comprehensive phylogeny of tree squirrels, with a special emphasis on Neotropical taxa.
B1 SINEs were studied in 22 families covering all major rodent lineages. The number of B1 copies considerably varies, from 1 x 10(4) in Geomyidae to 1 x 10(6) in Myodonta. B1 sequences can be divided into three main structural variants: B1 with a 20-bp tandem duplication (found in Gliridae, Sciuridae, and Aplodontidae), B1 with a 29-bp duplication (found in other families), and proto-B1 without duplication (pB1). These variants can be further subdivided according to their characters, including specific 7-, 9-, or 10-bp deletions. Different B1 subfamilies predominate in different rodent families. The analysis of B1 variants allowed us to propose possible pathways for the evolution of this SINE in the context of rodent evolution.
These data provide additional information relevant to the frequency of fisher detections by camera traps, and single-season occupancy and local persistence of fishers in small patches of forest habitats detailed elsewhere, "Landscape Fuel Reduction, Forest Fire, and Biophysical Linkages to Local Habitat Use and Local Persistence of Fishers (Pekania pennanti) in Sierra Nevada Mixed-conifer Forests" [10]. The data provides insight on camera trap detections of 3 fisher predators (bobcat [Lynx rufus]). Coyote [Canis latrans], mountain lion [Puma concolor], 5 mesocarnivores in the same foraging guild as fishers (gray fox [Urocyon cinereoargenteus]) ringtail [Bassariscus astutus], marten [Martes americana], striped skunk [Mephitis mephitis] spotted skunk [Spilogale gracilis], and 5 Sciuridae rodents that fishers consume as prey (Douglas squirrel [Tamiasciurus douglasii]), gray squirrel [Sciurus griseus], northern flying squirrel [Glaucomys sabrinus], long-eared chipmunk [Neotamias quadrimaculatus], California ground squirrel [Spermophilus beecheyi]. We used these data to identify basic patterns of co-occurrence with fishers, and to evaluate the relative importance of presence of competing mesocarnivores, rodent prey, and predators for fisher occupancy of small, 1 km(2) grid cells of forest habitat.
We present Champagne, a whole-genome method for generating character matrices for phylogenomic analysis using large genomic indel events. By rigorously picking orthologous genes and locating large insertion and deletion events, Champagne delivers a character matrix that considerably reduces homoplasy compared with morphological and nucleotide-based matrices, on both established phylogenies and difficult-to-resolve nodes in the mammalian tree. Champagne provides ample evidence in the form of genomic structural variation to support incomplete lineage sorting and possible introgression in Paenungulata and human-chimp-gorilla which were previously inferred primarily through matrices composed of aligned single-nucleotide characters. Champagne also offers further evidence for Myomorpha as sister to Sciuridae and Hystricomorpha in the rodent tree. Champagne harbors distinct theoretical advantages as an automated method that produces nearly homoplasy-free character matrices on the whole-genome scale.
Flying squirrels are the only group of gliding mammals with a remarkable diversity and wide geographical range. However, their evolutionary story is not well known. Thus far, identification of extinct flying squirrels has been exclusively based on dental features, which, contrary to certain postcranial characters, are not unique to them. Therefore, fossils attributed to this clade may indeed belong to other squirrel groups. Here we report the oldest fossil skeleton of a flying squirrel (11.6 Ma) that displays the gliding-related diagnostic features shared by extant forms and allows for a recalibration of the divergence time between tree and flying squirrels. Our phylogenetic analyses combining morphological and molecular data generally support older dates than previous molecular estimates (~23 Ma), being congruent with the inclusion of some of the earliest fossils (~36 Ma) into this clade. They also show that flying squirrels experienced little morphological change for almost 12 million years.
The utility of DNA Barcoding for species identification and discovery has catalyzed a concerted effort to build the global reference library; however, many animal groups of economical or conservational importance remain poorly represented. This study aims to contribute DNA barcode records for all ground squirrel species (Xerinae, Sciuridae, Rodentia) inhabiting Eurasia and to test efficiency of this approach for species discrimination. Cytochrome c oxidase subunit 1 (COI) gene sequences were obtained for 97 individuals representing 16 ground squirrel species of which 12 were correctly identified. Taxonomic allocation of some specimens within four species was complicated by geographically restricted mtDNA introgression. Exclusion of individuals with introgressed mtDNA allowed reaching a 91.6% identification success rate. Significant COI divergence (3.5-4.4%) was observed within the most widespread ground squirrel species (Spermophilus erythrogenys, S. pygmaeus, S. suslicus, Urocitellus undulatus), suggesting the presence of cryptic species. A single putative NUMT (nuclear mitochondrial pseudogene) sequence was recovered during molecular analysis; mitochondrial COI from this sample was amplified following re-extraction of DNA. Our data show high discrimination ability of 100 bp COI fragments for Eurasian ground squirrels (84.3%) with no incorrect assessments, underscoring the potential utility of the existing reference librariy for the development of diagnostic 'mini-barcodes'.
The role of facial vibrissae (whiskers) in the behavior of terrestrial mammals is principally as a supplement or substitute for short-distance vision. Each whisker in the array functions as a mechanical transducer, conveying forces applied along the shaft to mechanoreceptors in the follicle at the whisker base. Subsequent processing of mechanoreceptor output in the trigeminal nucleus and somatosensory cortex allows high accuracy discriminations of object distance, direction, and surface texture. The whiskers of terrestrial mammals are tapered and approximately circular in cross section. We characterize the taper of whiskers in nine mammal species, measure the mechanical deflection of isolated felid whiskers, and discuss the mechanics of a single whisker under static and oscillatory deflections. We argue that a tapered whisker provides some advantages for tactile perception (as compared to a hypothetical untapered whisker), and that this may explain why the taper has been preserved during the evolution of terrestrial mammals.
Rodent-borne disease surveillance was conducted at Nightmare Range (NM-R), near the demilitarized zone in northeast Gyeonggi Province, Republic of Korea, to identify hemorrhagic fever with renal syndrome (HFRS) risks for a mountainous high-elevation (500 m) military training site. Monthly surveys were conducted from January 2008-December 2009. A total of 1,720 small mammals were captured belonging to the Orders Rodentia [Families, Sciuridae (1 species) and Muridae (7 species)] and Soricomorpha [Family, Soricidae (1species)]. Apodemus agrarius, the primary reservoir for Hantaan virus (HTNV), accounted for 89.9% (1,546) of all small mammals captured, followed by Myodes regulus (4.0%), Crocidura lasiura (3.9%), Micromys minutus (1.4%), Mus musculus (0.3%), Microtus fortis (0.2%), Apodemus peninsulae (0.2%), Tamias sibiricus (0.1%), and Rattus norvegicus (<0.1%). Three species were antibody-positive (Ab+) for hantaviruses: A. agrarius (8.2%), M. minutus (4.2%), and C. lasiura (1.5%). HTNV specific RNA was detected in 93/127 Ab+ A. agrarius, while Imjin virus specific RNA was detected in 1/1 Ab+ C. lasiura. Overall, hantavirus Ab+ rates for A. agrarius increased with weight (age) and were significantly higher among males (10.9%) than females (5.1%) (P<0.0001). High A. agrarius gravid rates during the fall (August-September) were associated with peak numbers of HFRS cases in Korea that followed high gravid rates. From 79 RT-PCR positive A. agrarius, 12 HTNV RNA samples were sequenced and compared phylogenetically based on a 320 nt sequence from the GC glycoprotein-encoding M segment. These results demonstrate that the HTNV isolates from NM-R are distinctly separated from HTNV isolated from the People's Republic of China. These studies provide for improved disease risk assessments that identify military activities, rodent HTNV rates, and other factors associated with the transmission of hantaviruses during field training exercises.
Pallas's squirrel (Callosciurus erythraeus) was introduced in Japan in the 1930s and has since established itself in several areas across the country. Although wild Sciuridae populations have been demonstrated to be potential reservoirs for zoonotic enteric protozoa, epidemiological studies of such pathogens in Japan are scarce. Here, we examined 423 fecal samples from Pallas's squirrels captured in Kanagawa Prefecture, Japan, using PCR and DNA sequencing to determine the occurrence of Cryptosporidium spp., Enterocytozoon bieneusi, and Blastocystis. The overall prevalence of Cryptosporidium spp., E. bieneusi, and Blastocystis was 4.3% (18/423 samples), 13.0% (55/423 samples), and 44.0% (186/423 samples), respectively. The prevalence of Blastocystis and E. bieneusi was significantly higher in spring (60.1% and 17.4%, respectively) than in winter (27.6% and 8.6%, respectively [P < 0.01]). Sequence analysis of Cryptosporidium spp., targeting the partial small subunit ribosomal RNA gene (SSU rDNA), showed 100% identity (541/541 bp) to Cryptosporidium ubiquitum, and analysis of the gp60 gene showed 99.76% (833/835 bp) identity to C. ubiquitum subtype XIIh. The sequences of the ribosomal internal transcribed spacer region of E. bieneusi and the partial SSU rDNA of Blastocystis were identified as E. bieneusi genotype SCC-2 and Blastocystis subtype 4, respectively. This study confirmed the presence of C. ubiquitum, E. bieneusi, and Blastocystis in Pallas's squirrels in Kanagawa Prefecture. Because Pallas's squirrels inhabit urban areas, living close to humans, the species may serve as a potential source of infection in human populations. IMPORTANCE Pallas's squirrel is designated a "regulated organism" under the Invasive Alien Species Act in Japan, and municipal authorities are introducing control measures to reduce its populations. It has been suggested that wild mammals may play a role in contaminating the environment with zoonotic pathogens. The present study detected the enteric pathogens Cryptosporidium ubiquitum, Enterocytozoon bieneusi, and Blastocystis in the feces of Pallas's squirrels inhabiting Kanagawa Prefecture, Japan. These pathogens persist in the environment and contaminate soils and water, which may potentially infect humans. Because Pallas's squirrels in Kanagawa Prefecture are found in urban areas, where they are in close contact with human populations, continued monitoring of zoonotic diseases among squirrel populations will be important for evaluating the significance of wildlife in pathogen transmission.
Some species responded successfully to prehistoric changes in climate [1, 2], while others failed to adapt and became extinct [3]. The factors that determine successful climate adaptation remain poorly understood. We constructed a reference genome and studied physiological adaptations in the Alpine marmot (Marmota marmota), a large ground-dwelling squirrel exquisitely adapted to the "ice-age" climate of the Pleistocene steppe [4, 5]. Since the disappearance of this habitat, the rodent persists in large numbers in the high-altitude Alpine meadow [6, 7]. Genome and metabolome showed evidence of adaptation consistent with cold climate, affecting white adipose tissue. Conversely, however, we found that the Alpine marmot has levels of genetic variation that are among the lowest for mammals, such that deleterious mutations are less effectively purged. Our data rule out typical explanations for low diversity, such as high levels of consanguineous mating, or a very recent bottleneck. Instead, ancient demographic reconstruction revealed that genetic diversity was lost during the climate shifts of the Pleistocene and has not recovered, despite the current high population size. We attribute this slow recovery to the marmot's adaptive life history. The case of the Alpine marmot reveals a complicated relationship between climatic changes, genetic diversity, and conservation status. It shows that species of extremely low genetic diversity can be very successful and persist over thousands of years, but also that climate-adapted life history can trap a species in a persistent state of low genetic diversity.
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