Find research datasets worth reusing

opencc-by-4.0Dec 2023View details →

Fig. 2 in Late Miocene Turtles Of Grytsiv (Western Ukraine) With Rodent Gnaw Marks On The Carapace Surface

Fig. 2. Turtle remains from the late Miocene of Grytsiv: A–B — Emys sp., xiphiplastron NMNHU-P AR402/4 (A), marginal scute NMNHU-P AR 402/1 (B); C–E — Melanochelys cf. M. moldavica Chkhikvadze, 1983, costal plate NMNHU-P AR 403 (C), right xiphiplastron NMNHU-P AR 405 (D–E); F, I — Trionychidae indet., shell fragments NMNHU-P AR 401/1 (F), AR 401/2 (I); G–H — Testudo chernovi Khosatzky, 1948, nuchal NMNHU-P AR 406 (G), type specimen after Khosatzky (1948 a: FIg. 1), modiFIed (not to scale). Scale bars equal 5 mm in A–C, F–G and I, 10 mm in D and E.

opencc-by-4.0Dec 2023View details →

Figs 1–4. 1 in Contribution to the knowledge of beetles (Coleoptera) inhabiting rodent burrows in Turkmenistan

Figs 1–4. 1 – Aleochara jacobsoni, 2 – Orodaliscus transaralicus, 3 – Thinorycter chlamydatus, 4 – Asiocaedius kiseritzkii. Scale bar – 1 mm.

opencc-by-4.0Apr 2024View details →

Impacts of black rat invasion on the primary rodent host of Lassa virus, Mastomys natalensis

Shared here is code and data supporting the manuscript, "Reservoir displacement by an invasive rodent reduces Lassa virus zoonotic spillover risk." 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.

opencc-by-4.0Nov 2012View details →

Figs 3–4 in Dispersal History Of An Invasive Rodent In Hungary - Subfossil Finds Of Rattus Rattus

Figs 3–4. Skull (ventral view) of one of the black rats from site: 3 = Budapest, District XVII, Péceli Road (Roman Period); 4 = Dusnok–Szúnyogosi dűlő (Roman Period). Scale bars 10 mm

opencc-by-4.0Nov 2012View details →

Fig. 1 in Dispersal History Of An Invasive Rodent In Hungary - Subfossil Finds Of Rattus Rattus

Fig. 1. Investigated archaeological sites in Hungary with small mammal fauna. = open air sites with using flotation method, black rat absence; = open air/cave sites with using flotation method,

Fig. 4. A in Cestode fauna of murid and cricetid rodents in Hokkaido, Japan, with assignment of DNA barcodes

Fig. 4. A maximum-likelihood phylogenetic tree of the genus Hymenolepis. The tree was made with sequences of mitochondrial cox1 (456 nucleotide sites) under the substitutional model GTR+G+I. The isolates of this study (18AK285, 19AK270, H22B, JA173, JA175, JA220, and JA244) are shown in bold face. The DNA accession number of each taxon is shown in parenthesis. Rodentolepis nana (accession no. LC063187) was used as an outgroup taxon.

Fig. 8. A in Cestode fauna of murid and cricetid rodents in Hokkaido, Japan, with assignment of DNA barcodes

Fig. 8. A maximum-likelihood phylogenetic tree of the genus Catenotaenia. The tree was made with 28S rDNA sequences (1208 nucleotide sites) under the substitutional model GTR+G. The isolates of this study (AMU, JA212, and JA317) are shown in bold face. The DNA accession number of each taxon is shown in parenthesis. Hymenolepis diminuta (accession no. AY157181) was used as an outgroup taxon.

Fig. 3 in Cestode fauna of murid and cricetid rodents in Hokkaido, Japan, with assignment of DNA barcodes

Fig. 3. Adult tapeworms of Hymenolepis sp. 1, Arostrilepis tenuicirrosa, and Microsomacanthus sp. A, Scolex of Hymenolepis sp. 1; B, mature proglottids of Hymenolepis sp. 1; C, scolex of A. tenuicirrosa; D, mature proglottid of A. tenuicirrosa; E, gravid proglottid of A. tenuicirrosa; F, whole body of Microsomacanthus sp.; G, scolex of Microsomacanthus sp.; H, mature proglottids of Microsomacanthus sp. Scale bars: A, C, G, 200 µm; B, D, 500 µm; E, 1 mm; F, 2 mm; G, 100 µm.

Fig. 6 in Cestode fauna of murid and cricetid rodents in Hokkaido, Japan, with assignment of DNA barcodes

Fig. 6. Adult tapeworms of Paranoplocephala kalelai, Catenotaenia sp., and Raillietina sp. A, Scolex of P. kalelai; B, mature proglottid of P. kalelai; C, gravid proglottid of P. kalelai; D, scolex of Catenotaenia sp.; E, mature proglottid Catenotaenia sp.; F, gravid proglottids of Catenotaenia sp.; G, scolex of Raillietina sp.; H, mature proglottids of Raillietina sp. Scale bars: A–C, E, H, 500 µm; D, G, 200 µm; F, 1 mm.

Fig. 5. A in Cestode fauna of murid and cricetid rodents in Hokkaido, Japan, with assignment of DNA barcodes

Fig. 5. A maximum-likelihood phylogenetic tree of the genus Arostrilepis. The tree was made with sequences of mitochondrial cytb (558 nucleotide sites) under the substitutional model GTR+G+I. The isolates of this study (19AK170, 19AK439, 19AK454, and 19AK459) are shown in bold face. The DNA accession number of each taxon is shown in parenthesis. Hymenolepis diminuta (accession no. AF314223) was used as an outgroup taxon.

Fig. 2. A in Cestode fauna of murid and cricetid rodents in Hokkaido, Japan, with assignment of DNA barcodes

Fig. 2. A maximum likelihood phylogenetic tree of the families Hymenolepididae, Anoplocephalidae, Catenotaeniidae, and Davaineidae. The tree was made with sequences of 28S rDNA (1137 nucleotide sites) under the substitutional model GTR+G. The isolates of this study (19AK270, JA175, 19AK170, JA313, 19AK378, AMU, and Para33SI) are shown in bold face. The DNA accession number of each taxon is shown in parenthesis. Bootstrap percentages are shown on each node. Scale bar indicates the number of substitutions per nucleotide site. Dibothriocephalus nihonkaiensis (accession no. LC474508) was used as an outgroup taxon.

Fig. 1 in Cestode fauna of murid and cricetid rodents in Hokkaido, Japan, with assignment of DNA barcodes

Fig. 1. Maps of the Japanese Archipelago and Hokkaido. Arrows indicate the southward and northward movements of terrestrial mammals in the Pleistocene glacial epoch. Rodent sampling sites are shown as open circles.

opencc-by-4.0Dec 2020View details →

Fig. 1 in Dynamics Of Mouse-Like Rodent Communities In Anthropogenically Disturbed Territories Of The Southeast Of Western Siberia (Kemerovo Region, Russia)

Fig. 1. The dynamics of similarity of small mammal populations in deforested zones compared to the initial population in taiga (using the Czekanowsky-SØrensen coefficient calculated for species' percentage in the community).

opencc-by-4.0May 2022View details →

The genetic structure and connectivity in two sympatric rodent species with different life histories are similarly affected by land use disturbances

Microsatellite dataset of the wood mouse (Apodemus sylvaticus) and the bank vole (Myodes glareolus). The dataset of the wood mouse is constituted of 194 samples and 7 microsatellite markers: WM_194ind_7STRs.txt The dataset of the bank vole is constituted of 199 samples and 8 microsatellite markers: BV_199ind_8STRs.txt Each locus is encoded in the three-digit format (e.g., 126126) and each column corresponds to a locus specified in the order at the beginning of the file, following the GENEPOP format. Pop indicates the beginning of a new location.   Locus name in WM_194ind_7STRs.txt Locus_1    AS-7-FAM Locus_2    AS-12-PET Locus_3    AS-20-NED Locus_4    AS-34-FAM Locus_5    GTTD9A-PET Locus_6    AS-11-VIC Locus_7    MS-AF-8-NED   Locus name in BV_199ind_8STRs.txt Locus_1    Cg13B8-F_FAM Locus_2    Cg6A1-F_VIC Locus_3    Cg3F12-F_PET Locus_4    Cg13H9-F_PET Locus_5    Cg2E2-F_VIC Locus_6    Cg3E10-F_FAM Locus_7    Cg2A4-F_FAM Locus_8    Cg3A8-F_NED

opencc-zeroMay 2022View details →

Bridging macroecology and macroevolution in the radiation of sigmodontine rodents

Investigations of phenotypic disparity across geography often ignore macroevolutionary processes. As a corollary, the random null expectations to which disparity is compared and interpreted may be unrealistic. We tackle this issue by representing, in geographical space, distinct processes of phenotypic evolution underlying ecological disparity. Under divergent natural selection, assemblages in a given region should have empirical disparity higher than expected under an evolutionarily-oriented null model, while the opposite may indicate constraints on phenotypic evolution. We gathered phylogenies, biogeographic distributions, and data on the skull morphology of sigmodontine rodents to discover which regions of the Neotropics were more influenced by divergent, neutral, or constrained phenotypic evolution. We found that regions with higher disparity than expected by the evolutionary-oriented null model, in terms of both size and shape, were concentrated in the Atlantic Forest, suggesting a larger role for divergent natural selection there. Phenotypic disparity in the rest of South America, mainly the Amazon basin, northeastern Brazil and Southern Andes, was constrained — lower than predicted by the evolutionary model. We also demonstrated equivalence between the disparity produced by randomization-based null models and constrained-evolution null models. Therefore, including evolutionary simulations into the null modeling framework used in ecophylogenetics can strengthen inferences on the processes underlying phenotypic evolution.

opencc-zeroMay 2022View details →

Niche overlap in rodents increases with competition but not ecological opportunity: A role of inter-individual difference

<div> Niche variation at population level mediates niche packing (i.e., patterns of species' spread within the niche space) and species coexistence at community level. Competition and ecological opportunity (resource diversity) are two of the main mechanisms underlying niche variation. Dense niche packing could occur through increased niche partitioning or increased niche overlap. In this study we used stable carbon and nitrogen isotope data of 635 individual rodents from 4 species across 9 sites in the montane region of a subtropical island to test the effects of competition and ecological opportunity on population isotope niche size, inter-individual niche difference within population, and inter-specific niche overlap within community. We used the Bayesian Standard Ellipse Area (SEAB, the ellipse area enclosed by carbon and nitrogen isotope values of organisms on a bi-plot) to estimate population niche size and inter-specific niche overlap. Inter-individual niche difference within population was quantified as isotopic divergence and isotopic uniqueness. We used rodent abundance (the number of unique individuals captured) to measure competition and plant isotope niche size (plant SEAB) to measure ecological opportunity. The rodents experienced competition as evidenced by a negative relationship between population change rate and conspecific abundance. Rodent population niche size increased with ecological opportunity but not competition. The inter-individual niche difference (isotopic uniqueness) increased with competition (inter-specific competition only) but not ecological opportunity. At community level, inter-specific niche overlap (herbivore—omnivore pair only) increased with competition (the combined abundance of the pair) but not ecological opportunity. This study demonstrated that isotope niche variation of the rodents could be hierarchically influenced by ecological opportunity and competition, with the former setting the limit of population niche size across communities and the latter shaping inter-individual niche difference and inter-specific niche overlap within communities. Under strong intra-specific competition and limited ecological opportunity for niche expansion, individuals may choose to increase their isotopic uniqueness from conspecifics at the cost of overlapping with heterospecifics of different trophic roles within the community niche space as overall competition increases. Denser niche packing of these rodent communities might be achieved through increased niche overlap. </div>

opencc-zeroSep 2022View details →

Thermal adaptation of pelage in desert rodents balances cooling and insulation

Phenotypic convergence across distantly related taxa can be driven by similar selective pressures from the environment or intrinsic constraints. The roles of these processes on physiological strategies, such as homeothermy, are poorly understood. We studied the evolution of thermal properties of mammalian pelage in a diverse community of rodents inhabiting the Mojave Desert, U.S.A. We used a heat flux device to measure the thermal insulation of museum specimens and determined whether thermal properties were associated with habitat preferences while assessing phylogenetic dependence. Species that prefer arid habitats exhibited significantly lower conductivity and thinner pelage relative to species with other habitat preferences. Despite having thinner pelage, the low conductivity imparted comparable insulation to species with other habitat preferences. Thus, arid species retain insulative pelage while simultaneously benefitting from thin pelage that promotes heat loss via convective cooling. We found no evidence of intrinsic constraints or phylogenetic dependence. Heat flux models designed to simulate body temperature regulation demonstrated that arid specialists saved 14.5% of their annual energy required for homeothermy by evolving lower conductivity, providing support for adaptive evolution of pelage. Our study indicates that selection for lower energetic requirements of homeothermy has shaped evolution of pelage thermal properties.

opencc-by-4.0Jul 2023View details →

Enhanced atlases and flatmaps of rodent neocortex

Flatmaps of mouse isocortex and barrel column annotations in CCFv3 space (10 µm resolution) <ul> <li>annotation_barrels.nrrd: Pre-generated annotations of barrel columns divided into layers, can be transplanted directly into the CCFv3 atlas.</li> <li>barrel_positions.feather: 3D coordinates of segmented barrel voxels used to create annotations.</li> <li>central-streamlines.feather: Central streamlines used to calculate barrel cortex metrics.</li> <li>depth.nrrd: Streamline-derived absolute cortical depth in µm.</li> <li>flatmap_authalic_shaped_256.nrrd: Discretized flatmap for use in flatmap comparison notebook (256x256 pixel resolution, shape-match border). </li> <li>flatmap_authalic_square_256.nrrd: Discretized flatmap for use in flatmap comparison notebook (256x256 pixel resolution, square border).</li> <li>flatmap_both_shaped.nrrd: Flatmap of mouse isocortex in both hemispheres (shape-match border).</li> <li>flatmap_both_square.nrrd: Flatmap of mouse isocortex in both hemispheres (square border).</li> <li>flatmap_shaped.nrrd: Flatmap of mouse isocortex in a single hemisphere (shape-match border).</li> <li>flatmap_square.nrrd: Flatmap of mouse isocortex in a single hemisphere (square border).</li> <li>hexgrid.nrrd: Decomposition of mouse isocortex into 1307 hexagonal columns of roughly equal size.</li> <li>hierarchy.json: Region hierarchy in AIBS format extended with barrel annotations.</li> <li>isocortex.nrrd: Annotations of mouse isocortex regions in a single hemisphere (1-based, consecutive) for plotting in ITK-SNAP.</li> <li>isocortex.label: Accompanying label file for plotting isocortex.nrrd in ITK-SNAP.</li> <li>thickness.nrrd: Streamline-derived cortical thickness in µm.</li> <li>flatmap_input/Makefile: Pipeline to derive inputs for the flatmapping algorithm from CCFv3 datasets.</li> <li>flatmap_input/border_points.txt: Border points for the shape-match flatmap, a convex approximation to the shape of the CCFv3 flatmap.</li> <li>flatmap_input/config_shaped.mk: Configuration file for the flatmapping algorithm (shape-match border).</li> <li>flatmap_input/config_square.mk: Configuration file for the flatmapping algorithm (square border).</li> </ul>   Enhanced atlas and flatmap of P14 rat somatosensory cortex <ul> <li>brain_regions.nrrd: Annotated regions in rat somatosensory cortex, divided into layers.</li> <li>flatmap.nrrd: Flatmap of rat somatosensory cortex in a single hemisphere (square border).</li> <li>hexgrid.nrrd: Decomposition of rat somatosensory cortex into 263 hexagonal columns of roughly equal size.</li> <li>hierarchy.json: Region hierarchy in AIBS format.</li> <li>orientation.nrrd: Local orientation towards pia, stored as a quaternion.</li> <li>relative_depth.nrrd: Relative cortical depth in the range [0,1].</li> <li>sscx.nrrd: Annotations of rat somatosensory cortex regions in a single hemisphere (1-based, consecutive) for plotting in ITK-SNAP.</li> <li>sscx.label: Accompanying label file for plotting sscx.nrrd in ITK-SNAP.</li> <li>thickness.nrrd: Cortical thickness in µm.</li> <li>flatmap_input/config.mk: Configuration file for the flatmapping algorithm.</li> <li>flatmap_input/annotations.nrrd: Annotations of rat somatosensory cortex regions (0-based, consecutive).</li> <li>flatmap_input/mask.nrrd: Labeling of source volume into interior, exterior, top/bottom/sides boundaries.</li> <li>flatmap_input/orientation_{x,y,z}.nrrd: Components of the orientation vector, as input to the flatmapping algorithm.</li> <li>flatmap_input/relative_depth.nrrd: Relative depth field, as input to the flatmapping algorithm.</li> </ul>   Code to generate flatmaps and barrel cortex annotations can be found in a <a href="https://github.com/BlueBrain/atlas-enhancement" target="_blank" rel="noopener">software repository</a> under a free software license.

opencc-zeroJun 2024View details →

Physical seed damage, not rodent's saliva, accelerates seed germination of trees in a subtropical forest

Many tree species adopt fast seed germination to escape the predation risk by rodents. Physical seed damage and the saliva of rodents on partially consumed seeds may also act as cues for the seed to accelerate the germination process. However, the impacts of these factors on seed germination rate and speed remain unclear. In this study, we investigated such impacts on the germination rate and speed (reversal of germination time) of four tree species (Quercus variabilis, Q. serrata, Q. acutissima, and Q. glauca) after partial consumption by four rodent species, through a series of experiments. We also examined how seed traits may affect the damage degree by rodents by analyzing the relationship between the germination rate and time of rodent-damaged seeds and the traits. We found that artificially and rodent-damaged seeds exhibited a significantly higher seed germination rate and speed, compared to intact seeds. Also, the rodent saliva on seeds showed no significant effect on seed germination rate and speed. Furthermore, We observed significant positive correlations between several seed traits (including seed mass, coat thickness, and protein content) and seed germination rate, but these seed traits had a positive correlation with the germination rate and speed. These correlations are likely due to the beneficial traits countering seed damage by rodents. Overall, our results highlight the significant role of physical seed damage by rodents (rather than their saliva) in facilitating seed germination of tree species and potential mutualism between rodents and trees. Additionally, our results may have some implications in forest restoration, such that intentionally sowing or dispersing slightly damaged seeds by humans or drones may increase the likelihood of successful seed regeneration.