First Complete Genome Sequence of a Hare Calicivirus Strain Isolated from Lepus europaeus.
Ontology highlight
ABSTRACT:
SUBMITTER: Droillard C
PROVIDER: S-EPMC6284081 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:In Europe, brown hare (Lepus europaeus) populations have been declining steadily since the 1970s. Gamekeepers can help to support brown hare wild populations by releasing cage-reared hares into the wild. Survival rates of cage-reared hares has been investigated in previous studies, however, survival times in relation to seasonality, which likely plays a crucial role for the efficacy of this management strategy, has not been evaluated. Here we examine the survival duration and daytime home ranges of 22 hares released and radio-tracked during different periods of the year in East Bohemia, Czech Republic. The majority of hares (82%) died within the first six months after release, and 41% individuals died within the first 10 days. Significant differences were found in the duration of survival with respect to the release date. Hares released in the summer months (July and August) survived the longest (on average 103.2 days, SD ± 23.8) and hares released throughout all other months of the year survived for significantly shorter periods of time (on average 20.4 days, SD ± 11.5). The most likely cause of death was red fox predation (38.9%) followed by disease (coccidiosis and other health problems) (27.8%). Three hares (16.6%) were killed by automobile traffic. After six months of radiotracking, we found the average survival time of all hares released was 58 (SD ± 70.9) days. Hares in this study preferred to remain in the vicinity of the release area and the average distance from release point to the center of the home range was 471 m.
| S-EPMC6179284 | biostudies-literature
Project description:We first reported the mitochondrial genome of Lepus yarkandensis. The mitogenome of L. yarkandensis contains 17,011 base pairs. The overall base composition of complete mitogenome is 28.13% A, 27.67% T, 22.02% C, and 22.17% G, with 44.20% of the GC content. All genes exhibit the typical mitochondrial gene arrangement and transcribing directions. Phylogenetic analysis of 9 Lepus species was performed based on the sequence of cytochrome b gene using the Maximum Likelihood method in MEGA 7.0. The results suggested that L. yarkandensis is closely related to Lepus timidus. The results are helpful to future studies on molecular evolution, population genetics, and wildlife protection of L. yarkandensis.
| S-EPMC7707541 | biostudies-literature
Project description:Diseases of the gastrointestinal tract due to changes in the bacterial flora have been described with increasing incidence in the European brown hare. Despite extensive demographic and phylogeographic research, little is known about the composition of its gut microbiota and how it might vary based on potential environmental or host factors. We analysed the intestinal and faecal microbiota of 3 hare populations by Illumina MiSeq 16S rRNA gene amplicon sequencing. The phyla and OTU abundance composition differed significantly between intestinal and faecal samples (PERMANOVA: P = 0.002 and P = 0.031, respectively), but in both sample types Firmicutes and Bacteroidetes dominated the microbial community composition (45.51% and 19.30% relative abundance). Intestinal samples contained an enrichment of Proteobacteria compared with faecal samples (15.71-fold change, P < 0.001). At OTU level, a significant enrichment with best BLAST hits to the Escherichia-Shigella group, Eubacterium limosum, Sphingomonas kyeonggiensis, Flintibacter butyricus and Blautia faecis were detected in intestinal samples (P < 0.05). In our statistical model, geographic location and possibly associated environmental factors had a greater impact on the microbiota composition than host factors. Population had a significant effect on the composition of abundant intestinal and faecal OTUs, and on the abundance of potential pathogenic bacteria of the family Enterobacteriaceae, regularly associated with intestinal dysbiosis in hares, in faecal samples. Our study is the first to describe the microbiota in brown hares and provides a foundation to generate hypothesis aiming to test the role of gut health in population fluctuations of the species.
| S-EPMC6390100 | biostudies-literature
Project description:In female mammals, reproduction, and in particular lactation, is the energetically most exigent life-history phase. Reproduction is strongly controlled by body reserves and food availability, so females with better body condition or food supply are believed to have higher reproductive output. Additionally, the growth and mortality of young mammals depends on their postnatal development. Therefore, the degree of precociality affects energetic demands for both mothers and young. To study the reproductive performance of the precocial European hare (Lepus europaeus), we analysed relationships between six predictor variables describing maternal and environmental effects and nine response variables relating to reproduction from 217 captive females. We compared the data with those of precocial and altricial mammal species from an extensive literature search. For hares, we found: (1) Heavier females had heavier litters at birth. (2) In summer and spring, total litter mass was larger than in winter. (3) At the end of lactation, the litters of multiparous females were heavier than those of primiparous females. (4) Both older females and females giving birth for the first time had relatively high leveret mortality during lactation. Comparing our results with the literature for other mammals revealed that the body condition (i.e., body mass) of females before birth is predictive of reproductive parameters in both precocial and altricial species. In the precocial hare, female body condition is no longer predictive of reproductive parameters at the end of lactation, whereas in altricial species, female body condition remains predictive of reproduction (litter mass at the end of lactation, offspring mortality) until the end of lactation. We conclude that these effects are caused by precocial offspring feeding on solid food soon after birth and, thus, being less dependent on the mother's body condition during lactation than altricial offspring. In line with this, precociality might have evolved as a way of buffering offspring against maternal effects.
| S-EPMC7888652 | biostudies-literature
Project description:BackgroundIn Europe the mountain hare (Lepus timidus) exists in Great Britain, Norway, Sweden, Finland, parts of the Alps and in Eastern Europe, but not in Denmark. Interspecific hybridization has been demonstrated between native Swedish mountain hares and introduced brown hares (Lepus europaeus). During the data collection in a study concerning Danish brown hares we identified 16 hares with a single very divergent haplotype.ResultsPhylogenetic analysis shows that the divergent Danish haplotype is most closely related to the Swedish mountain hare. The frequency of Lepus timidus mtDNA haplotype in the Eastern Danish hare populations is estimated to 6%.ConclusionIn contrast to what is known, the Danish hare populations are not pure L. europaeus populations but include introgressed brown hares with Swedish L. timidus mtDNA. The most probable explanation of this is natural migration or translocation of introgressed brown hares from Sweden. The impurity of hare populations has implications for conservation and population genetics.
| S-EPMC1654140 | biostudies-literature
Project description:In this study, we report on the complete mitochondrial genome of the Arctic hare, Lepus arcticus (Leporidae; Lagomorpha) a large lagomorph endemic to the northernmost regions of Greenland. The complete mitogenome of L. arcticus was 16,972 bp long and was typical of genus Lepus mitogenomes in genomic content and structure, as the entire mitogenome contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and one control region. The phylogenetic analysis of the Arctic hare within Leporidae confirmed the sister relationship among Lepus species. This mitogenome sequence will provide a useful resource for investigations of biogeography, phylogenetic distance, and evolutionary history in lagomorphs.
| S-EPMC7707595 | biostudies-literature
Project description:Here, we report the complete genome of a feline calicivirus (FCV) originating from household cats in Guangxi, southern China, in September 2013. To understand its genetic characteristics, we isolated FCV strain GX01-2013 from MDCK cells and determined its complete genome sequence.
| S-EPMC5034133 | biostudies-literature
Project description:The genes of the major histocompatibility complex (MHC) are attractive candidates for investigating the link between adaptive variation and individual fitness. High levels of diversity at the MHC are thought to be the result of parasite-mediated selection and there is growing evidence to support this theory. Most studies, however, target just a single gene within the MHC and infer any evidence of selection to be representative of the entire gene region. Here we present data from three MHC class II beta genes (DPB, DQB, and DRB) for brown hares in two geographic regions and compare them against previous results from a class II alpha-chain gene (DQA). We report moderate levels of diversity and high levels of population differentiation in the DQB and DRB genes (Na ?=? 11, D (est)?=? 0.071 and Na ?= 15, D (est)?=? 0.409, respectively), but not for the DPB gene (Na ?=? 4, D (est)?=? 0.00). We also detected evidence of positive selection within the peptide binding region of the DQB and DRB genes (95% CI, ? ?>? 1.0) but found no signature of selection for DPB. Mutation and recombination were both found to be important processes shaping the evolution of the class II genes. Our findings suggest that while diversifying selection is a significant contributor to the generally high levels of MHC diversity, it does not act in a uniform manner across the entire MHC class II region. The beta-chain genes that we have characterized provide a valuable set of MHC class II markers for future studies of the evolution of adaptive variation in Leporids.
| S-EPMC3190090 | biostudies-literature
Project description:European hares of both sexes rely on fat reserves, particularly during the reproduc-tive season. Therefore, hares should select dietary plants rich in fat and energy. However, hares also require essential polyunsaturated fatty acids (PUFA) such as linoleic acid (LA) and alpha-linolenic acid (ALA) to reproduce and survive. Although hares are able to absorb PUFA selectively in their gastrointestinal tract, it is unknown whether this mechanism is sufficient to guarantee PUFA supply. Thus, diet selection may involve a trade-off between a preference for energy versus a preference for crucial nutrients, namely PUFA. We compared plant and nutrient availability and use by hares in an arable landscape in Austria over three years. We found that European hares selected their diet for high energy content (crude fat and crude protein), and avoided crude fibre. There was no evidence of a preference for plants rich in LA and ALA. We conclude that fat is the limiting resource for this herbivorous mammal, whereas levels of LA and ALA in forage are sufficiently high to meet daily requirements, especially since their uptake is enhanced by physiological mechanisms. Animals selected several plant taxa all year round, and preferences did not simply correlate with crude fat content. Hence, European hares might not only select for plant taxa rich in fat, but also for high-fat parts of preferred plant taxa. As hares preferred weeds/grasses and various crop types while avoiding cereals, we suggest that promoting heterogeneous habitats with high crop diversity and set-asides may help stop the decline of European hares throughout Europe.
| S-EPMC4521881 | biostudies-literature
Project description:Numerous studies have shown that the phylogeography of many species, including European brown hare, has been affected by the climatic oscillations of the Pleistocene. During this period the Balkans acted as a major refugium offering habitable conditions for many species. However, few studies have focused on the specific role of the Greek peninsula in the phylogeographic history of species in this southernmost margin of Balkans. We, therefore analyzed a 528 bp fragment of the D-loop region of mitochondrial DNA in 154 wild brown hare individuals from unsampled areas from both mainland and island Greece and compared it to 310 available brown hare sequences (including 110 Greek samples). Newly identified haplotypes show characteristic distribution in specific Greek areas reinforcing the theory that Greece can be considered as a subrefuge within Balkans for a number of species, with several "refugia within refugia" spots, holding significant genetic diversity. No haplotypes from wild Greek individuals clustered with the Central and Western Europe group revealing a minimal contribution of this area to the colonization of central Europe. One hundred and ten reared brown hares were also analyzed to elucidate the impact of introductions on local populations. Most of these samples presented close genetic affinity with haplotypes from Central and Western Europe indicating that farms in Greece use breeders from those areas. Therefore, despite human translocation of individuals, the genetic structure of brown hare has mostly been influenced by paleoclimatic conditions and minimally by human actions.
| S-EPMC6209229 | biostudies-literature