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108 results for “rodent host”
Phylogenetic signals in host-parasite associations for Neotropical bats and Nearctic desert rodents
<p>Hosts and their parasites have strong ecological and evolutionary relationships, with hosts representing habitats and resources for parasites. In the present study, we use approaches developed to evaluate the statistical dependence of species trait values on phylogenetic relationships to determine whether host–parasite relationships (i.e. parasite infections) are contingent on host phylogeny. If host–parasite relationships are contingent on the ability of hosts to provide habitat or resources to parasites, and if host phylogeny is an effective surrogate for among-host variation in habitat and resource quality, host–parasite relationships should evince phylogenetic signals (i.e. be contingent on host phylogeny). Because the strength of ecological relationships between parasites and their hosts may affect the likelihood of phylogenetic signals occurring in host–parasite relationships, we hypothesized that (1) host specificity would be positively correlated with the strength of phylogenetic signals and (2) the strength of phylogenetic signals will be greater for parasites that rely more on their host throughout their life cycle. Analyses were conducted for ectoparasites from tropical bats and for ectoparasites, helminths, and coccidians from desert rodents. Phylogenetic signals were evaluated for parasite presence and for parasite prevalence. The frequency of phylogenetic signal occurrence was similar for parasite presence and prevalence, with a signal detected in 24–27% of cases at the species level and in 67% and 15% of cases at the genus level for parasites of bats and rodents, respectively. No differences in signal strength or the likelihood of detecting a signal existed between groups of parasites. Phylogenetic signal strength was correlated with host specificity, suggesting that mechanisms increasing host specificity also increase the likelihood of a phylogenetic signal in host use by parasites. Differences in the transmission mode did not affect signal strength or the likelihood of detecting a signal, indicating that variation in host switching opportunities associated with the transmission mode does not affect signal strength.</p>
Impacts of black rat invasion on the primary rodent host of Lassa virus, Mastomys natalensis
<p>Shared here is code and data supporting the manuscript, "Reservoir displacement by an invasive rodent reduces Lassa virus zoonotic spillover risk."</p> <p>The project directory, which contains numerous large raster data files, was stored as a split zip archive to facilitate upload to Zenodo and consists of the files "rat_invasion.z01", "rat_invasion.z02", "rat_invasion.z03", and "rat_invasion.zip". Following download, these files may need to be decompressed using dedicated archiver software (such as The Unarchiver [https://theunarchiver.com/] on macOS). Note that the entire project repository is ~7 GB when uncompressed. The files shared here mirror the GitHub project repository (https://github.com/eveskew/rat_invasion) with the addition of the large environmental raster data in the "data/environmental" subdirectory.</p>
Fig. 2 in First identification of Echinococcus multilocularis in rodent intermediate hosts in Sweden
Fig. 2. Macroscopic photos of rodent livers containing Echinococcus multilocularis metacestode lesions. The ruler in each picture is in millimeters. (A) Liver from Microtus agrestis with one lesion that contained protoscoleces. (B) Liver from Arvicola amphibius with multiple lesions that did not contain protoscoleces. (C) Liver from Arvicola amphibius with multiple lesions that did contain protoscoleces. (D) Liver from Arvicola amphibius. Arrow points to the only lesion examined for protoscoleces, which were absent.
Fig. 1 in First identification of Echinococcus multilocularis in rodent intermediate hosts in Sweden
Fig. 1. Study areas and positive findings of E. multilocularis in southern Sweden at the beginning of the study, 2013. Boxes show study areas and stars indicate where positive foxes/ fox fecal samples had been found. Circles encompass the study areas where rodents positive for E. multilocularis were captured. The lines are county boundaries. (CRS: WGS 84, QGIS 2.12.3).
Fig. 1 in Host competence of African rodents Arvicanthis neumanni, A. niloticus and Mastomys natalensis for Leishmania major
Fig. 1. Xenodiagnosis and external manifestation of L. major in rodents. Direct xenodiagnosis with P. duboscqi in plastic tubes covered with fine mesh held on the ear of the anaesthetized A. niloticus (A) and external manifestation of L. major LV109 in ear pinnae (site of inoculation) of A. neumanni by week 10 p.i., (B); A. niloticus by week 30 p.i. (C, D) and M. natalensis by week 19 p.i. (E).
Fig. 3 in Host biology and environmental variables differentially predict flea abundances for two rodent hosts in a plague-relevant system
Fig. 3. Cumulative distribution plots divided by year for (A) T. alpinus and (B) T. speciosus. For each species 2013 is shown in red, 2014 in teal, 2015 in pink. The x-axis represents each host individual, ordered from least to most flea infested, and the y-axis shows the cumulative proportion of total flea counts. The dotted line indicates individuals in the 90th percentile of flea abundances, illustrating that the top 10% most infected chipmunks usually account for close to 50% of all counted fleas. The proportion of individuals without fleas in each year is represented graphically as the proportion at which each colored line departs from the x-axis. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 4 in Host biology and environmental variables differentially predict flea abundances for two rodent hosts in a plague-relevant system
Fig. 4. Relationships between fecal glucocorticoid metabolite levels, sex, and flea abundance for (A) T. alpinus and (B) T. speciosus. Points show the mean ± S.E. number of fleas counted for female (white) and male (black) individuals within FGM categories (FGM values were rounded to the nearest 10). Lines of best fit (based on all raw data points) ± 95% confidence intervals are overlaid for each sex.
Fig. 2 in Host biology and environmental variables differentially predict flea abundances for two rodent hosts in a plague-relevant system
Fig. 2. Patterns of flea abundance across years, hosts, and flea species. Overall average flea abundances (A–B) and abundances of each flea species (C–D) in each year for T. alpinus (A, C) and T. speciosus (B, D). Abundances of each flea species on hosts of each sex (Males: closed circles, Females: open circles) on T. alpinus (E) and T. speciosus (F).
Fig. 5 in Host biology and environmental variables differentially predict flea abundances for two rodent hosts in a plague-relevant system
Fig. 5. Relationships between flea abundances and (A) the second principal component of temperature data; or (B) elevation for T. alpinus (white) and T. speciosus (black). Points show the mean ± S.E. number of fleas counted for a given study site in a given year. For each study site in each year, a mean ± S.E. temperature or elevation value is shown. Lines of best fit (based on all raw data points) ± 95% confidence intervals are overlaid for each species.
Fig. 1 in Host biology and environmental variables differentially predict flea abundances for two rodent hosts in a plague-relevant system
Fig. 1. Map showing study sites. Sites (see Supplementary Data S1 for more information) located in and around Yosemite National Park (green) were visited either in all three years (2013, 2014, and 2015; black), in two of the years (yellow), or in only one year (red). Yellow and black lines show significant roadways in the area. Lakes are shown in blue, including Mono Lake at top right. Inset shows Yosemite National Park (green) on a map of California. Site codes: AL: Arrowhead Lake; CL: Cathedral Lake (upper); GA: Glen Aulin; GL: Gaylor Lakes; HC: Hoffmann Creek; MA: Mammoth Lakes; ML: May Lake; PC: Porcupine Creek; SL: Saddlebag Lake; SLN: Saddlebag Lake, north-side (Greenstone and Steelhead Lakes); TM: Tuolumne Meadows. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in Eco-epidemiological screening of multi-host wild rodent communities in the UK reveals pathogen strains of zoonotic interest
Fig. 3. Bayesian phylogenetic tree of 18S ribosomal RNA sequences of Babesia microti isolates, indicating the position of the Munich strain-like isolate obtained from the tick Ixodes trianguliceps from a bank vole in Ceredigion, Wales. Sequences of the cogeneric species B. vulpes and B. rodhaini are used as outgroups.
Fig. 2 in Eco-epidemiological screening of multi-host wild rodent communities in the UK reveals pathogen strains of zoonotic interest
Fig. 2. Flea diversity. Percentage of flea genera collected during the two sampling seasons. *p <0.05.
Fig. 1 in Eco-epidemiological screening of multi-host wild rodent communities in the UK reveals pathogen strains of zoonotic interest
Fig. 1. Percentage of tick life stages across seasons collected from all rodent species. a) Total percentage of ticks found in the two study seasons. Light grey: larvae; dark grey: nymphs; black: adults. b) Percentage of tick life stages in each sampling season.
Phylogenetic signals in host-parasite associations for Neotropical bats and Nearctic desert rodents
Open the record for dataset details and reuse information.
Experimental parasite community perturbation reveals associations between Sin Nombre virus and gastrointestinal nematodes in a rodent reservoir host
<p>Individuals are often co-infected with several parasite species, yet measuring within-host interactions remains difficult in the wild. Consequently, the impact of such interactions on host fitness and epidemiology are often unknown. We used anthelmintic drugs to experimentally reduce nematode infection and measured the effects on both nematodes and the important zoonosis Sin Nombre virus (SNV) in its primary reservoir (<i>Peromyscus spp.</i>). Treatment significantly reduced nematode infection, but increased SNV seroprevalence. Furthermore, mice that were co-infected with both nematodes and SNV were in better condition and survived up to four times longer than uninfected or singly-infected mice. These results highlight the importance of investigating multiple parasites for understanding interindividual variation and epidemiological dynamics in reservoir populations with zoonotic transmission potential.</p>
Combining GWAS and FST-based approaches to identify targets of Borrelia-mediated selection in natural rodent hosts
Recent advances in high-throughput sequencing technologies provide opportunities to gain novel insights into the genetic basis of phenotypic trait variation. Yet to date, progress in our understanding of genotype-phenotype associations in non-model organisms in general and natural vertebrate populations in particular has been hampered by small sample sizes typically available for wildlife populations and a resulting lack of statistical power, as well as a limited ability to control for false positive signals. Here we propose to combine a genome-wide association (GWAS) and FST-based approach with population-level replication to partly overcome these limitations. We present a case study in which we used this approach in combination with Genotyping-by-Sequencing (GBS) SNP data to identify genomic regions associated with Borrelia afzelii resistance or susceptibility in the natural rodent host of this Lyme disease-causing spirochete, the bank vole (Myodes glareolus). Using this combined approach we identified four consensus SNPs located in exonic regions of the genes Slc26a4, Tns3, Wscd1 and Espnl, which were significantly associated with the voles' Borrelia infectious status within and across populations. Functional links between host responses to bacterial infections and most of these genes have previously been demonstrated in other rodent systems, making them promising new candidates for the study of evolutionary host responses to Borrelia emergence. Our approach is applicable to other systems and may facilitate the identification of genetic variants underlying disease resistance or susceptibility, as well as other ecologically relevant traits, in wildlife populations.
Data from: Genome-wide support for incipient Tula orthohantavirus species within a single rodent host lineage
<p>Evolutionary divergence of viruses is most commonly driven by co-divergence with their hosts or through isolation of transmission after host-shifts. It remains mostly unknown, however, whether divergent phylogenetic clades within named virus species represent functionally equivalent byproducts of high evolutionary rates or rather incipient virus species. Here, we test these alternatives with genomic data from two widespread phylogenetic clades in Tula orthohantavirus (TULV) within a single evolutionary lineage of their natural rodent host, the common vole Microtus arvalis. We examined voles from 42 locations in the contact region between clades for TULV infection by RT-PCR. Sequencing yielded 23 TULV Central North and 21 TULV Central South genomes which differed by 14.9-18.5% at the nucleotide and 2.2-3.7% at the amino acid level without evidence of recombination or reassortment. Geographic cline analyses demonstrated an abrupt (<1 km wide) transition between the parapatric TULV clades in continuous landscape. This transition was located within the Central mitochondrial lineage of M. arvalis and genomic SNPs showed gradual mixing of host populations across it. Genomic differentiation of hosts was much weaker across the TULV Central North to South transition than across the nearby hybrid zone between two evolutionary lineages in the host. We suggest that these parapatric TULV clades represent functionally distinct, incipient species which are likely differently affected by genetic polymorphisms in the host. This highlights the potential of natural viral contact zones as systems for investigating of the genetic and evolutionary factors enabling or restricting the transmission of RNA viruses.</p>
Data sets for Polyplax serrata article "Highly-resolved genomes of two closely related lineages of the rodent louse Polyplax serrata with different host specificities"
<p><strong>Supplementary data for Polyplax serrata article 2023</strong></p> <p>Data included in this repository were generated and used in various genomic and phylogenetic analysis presented by the publication "<strong>Highly-resolved genomes of two closely related lineages of the louse </strong><em><strong>Polyplax serrata</strong></em><strong> with different host specificities</strong>"</p> <p><strong>Description of the data and file structure</strong></p> <p>Data provided for each analyzed taxa include:</p> <p>- Annotation table.</p> <p>- fasta format files for transcripts (CDS and mRNA).</p> <p>- fasta format file for genome.</p> <p>- protein fasta file.</p> <p>- gbk format file that includes the genome with its corresponding annotations.</p> <p>Additionally,</p> <p>- repeat families in fasta format were included for <em>Polyplax serrata</em> S and N lineages.</p> <p>- rRNA in fasta format were included for <em>Polyplax serrata</em> S and N lineages, <em>Pediculus humanus, Columbicola columbae </em>and <em>Brueelia nebulsa</em>. </p> <p><strong>Sharing/Access information</strong></p> <p>GenBank accession number of analyzed taxa:</p> <p>· <em>Aedes Aegypti</em> (GenBank accession no. GCF_002204515.2).</p> <p>· <em>Brueelia nebulsa</em> ( GenBank accession no. GCA_028293925.1).</p> <p>· <em>Columbicola columbae</em> (GenBank accession no. GCA_016920875.1).</p> <p>· <em>Cimex lectularis</em> (GenBank accession no. GCF_000648675.2).</p> <p>· <em>Glossina morsitans</em> (GenBank accession no. GCA_001077435.1).</p> <p>· <em>Pediculus humanus</em> (GenBank accession no. GCA_000006295.1).</p> <p>· <em>Rhodnius prolixus</em> (GenBank accession no. GCA_000181055.3).</p> <p>· <em>Polyplax serrata S lineage</em> (GenBank accession no. JAWJWF000000000).</p> <p>· <em>Polyplax serrata N lineage</em> (GenBank accession no. JAWJWE000000000).</p> <p> </p> <p>Note: All the latter genomes except for the two genomes of <em>Polyplax serrata</em> S and N lineages, were acquired from GenBank database and were subjected to the same gene prediction and annotation workflow as <em>P. serrata</em> genomes to maintain methodological consistence in downstream analysis of the annotation results.</p> <p><strong>Software</strong></p> <p>- Gene prediction and annotation was performed using Funannotate v1.18.14 (<a href="https://github.com/nextgenusfs/funannotate">https://github.com/nextgenusfs/funannotate)</a>).</p> <p>- Repeat were identified in the genomes of P. serrata S and N lineages using RepeatModeler v2.0.3.</p>
Borrelia burgdorferi strain and host sex influence pathogen prevalence and abundance in the tissues of a laboratory rodent host
<p class="MsoNormal">Experimental infections with different pathogen strains give insight into pathogen life history traits. The purpose of our study was to compare variation in tissue infection prevalence and spirochete abundance among strains of <em>B. burgdorferi</em> in a rodent host (<em>Mus musculus</em>, C3H/HeJ). Male and female mice were experimentally infected via tick bite with one of 12 strains. Ear tissue biopsies were taken at days 29, 59, and 89 post-infection (PI), and 7 tissues were collected at necropsy. The presence and abundance of spirochetes in the mouse tissues were measured by qPCR. To determine the frequencies of our strains in nature, their MLSTs were matched to published datasets.</p> <p class="MsoNormal">For the infected mice, 56.6% of the tissues were infected with <em>B. burgdorferi</em>. The mean spirochete load in the mouse necropsy tissues varied 4.8-fold between the strains with the lowest and highest values. The mean spirochete load in the ear tissue biopsies decreased rapidly over time for some strains. <span>The percentage of infected tissues in male mice (65.4%) was significantly higher compared to female mice (50.5%). The </span>mean spirochete load in the 7 tissues <span>was 1.5x higher in male mice compared to female mice; this male bias was 15.3x higher in the ventral skin. </span>Across the 11 strains, the mean spirochete loads in the infected mouse tissues were positively correlated with the strain-specific frequencies in their tick vector populations. Our study suggests that laboratory-based estimates of pathogen abundance in host tissues can predict the strain composition of this important tick-borne pathogen in nature.</p>
Data from: Forecasting potential emergence of zoonotic diseases in Southeast Asia: network analysis identifies key rodent hosts
1. Within complex ecological systems, identifying animal species likely to play a key role in the emergence of infectious zoonotic diseases remains a major challenge. One approach consists of using information on current ecological and parasitological similarities among host species in order to predict the most likely pathways for future pathogen spillover. 2. Using field data acquired from 15 sympatric rodent species in various habitats in Thailand, Cambodia and Laos, we built networks based on shared parasites (17 helminth and 15 microparasite species) and shared habitats among rodent species and humans. We investigated the architectures of bipartite and unipartite networks using modularity, subgroups partitioning or node centrality, to assess the relative epidemiological importance of particular rodent species. 3. Our results showed that Rattus tanezumi, Bandicota savilei and R. exulans were consistently found to be members of subgroups that included humans in unipartite and bipartite networks on zoonotic agents and shared habitats. High values of centrality in shared zoonotic agents were found for the same three rodent species, whereas high values of shared habitats were observed for two of them. Although phylogenetically related rodent species likely shared both habitats and parasites, a lack of habitat specialisation was associated with increased zoonotic parasite sharing. 4. Our results emphasize the disproportionate importance of these three rodent species, through their high degree of connectivity with humans, which may represent a high risk for direct zoonotic spillover. Moreover, due to its high centrality in habitats, R. tanezumi may also play a key role as a bridge host. 5. The recent discovery of new arenaviruses in rodents in Southeast Asia, with associated disease in humans in Cambodia, provides an opportunity to test this empirically. The three rodent species identified using our network approach are some of the potential maintenance hosts for these new emerging arenaviruses. 6. Synthesis and applications. Our results on rodents and their pathogens in Southeast Asia show that network analysis has a high potential to improve the surveillance of emerging zoonotic pathogens by targeting key host species and potential "emerging' pathogen–rodent interactions in complex and heterogeneous landscapes.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.