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Figure 6 in Late Oligocene mesotheriids (Mammalia, Notoungulata) from Salla and Lacayani (Bolivia): implications for basal mesotheriid phylogeny and distribution
Figure 6. Isolated left petro-tympanic, MNHN-BOL-V 006906, cerebellar view. Scale bar = 1 cm.
Figure 7. Trachytherus alloxus, SAL 235. A, ventral view. B in Late Oligocene mesotheriids (Mammalia, Notoungulata) from Salla and Lacayani (Bolivia): implications for basal mesotheriid phylogeny and distribution
Figure 7. Trachytherus alloxus, SAL 235. A, ventral view. B, left lateral view. Scale bar = 1 cm.
Figure 2 in Skull anatomy of the Oligocene toothed mysticete Aetioceus weltoni (Mammalia; Cetacea): implications for mysticete evolution and functional anatomy
Figure 2. Aetiocetus weltoni, reconstructed skull in dorsal view showing anatomical features.
Figure 9. Aetiocetus weltoni, UCMP 122900, holotype left dentary. A in Skull anatomy of the Oligocene toothed mysticete Aetioceus weltoni (Mammalia; Cetacea): implications for mysticete evolution and functional anatomy
Figure 9. Aetiocetus weltoni, UCMP 122900, holotype left dentary. A, lateral view; B, medial view.
Genetic variability, management, and conservation implications of the critically endangered Brazilian pitviper Bothrops insularis
<p>Information on demographic, genetic, and environmental parameters of wild and captive animal populations has proven to be crucial to conservation programs and strategies. Genetic approaches in conservation programs of Brazilian snakes remain scarce despite their importance for critically endangered species, such as <i>Bothrops insularis</i>, the golden lancehead, which is endemic to Ilha da Queimada Grande, coast of São Paulo State, Brazil. This study aims to (i) characterize the genetic diversity of <i>ex-situ</i> and <i>in-situ</i> populations of <i>B. insularis</i> using heterologous microsatellites; (ii) investigate genetic structure among and within these populations; and (iii) provide data for the conservation program of the species. Twelve informative microsatellites obtained from three species of the <i>B. neuwiedi</i> group were used to access genetic diversity indexes of <i>ex-situ</i> and <i>in-situ</i> populations. Low-to-medium genetic diversity parameters were found. Both populations showed low — albeit significant — values of system of mating inbreeding coefficient, whereas only the <i>in-situ</i> population showed a significant value of pedigree inbreeding coefficient. Significant values of genetic differentiation indexes suggest a small differentiation between the two populations. Discriminant analysis of principal components (DAPC) recovered five clusters. No geographic relationship was found in the island, suggesting the occurrence of gene flow. Also, our data allowed the establishment of six preferential breeding couples, aiming to minimize inbreeding and elucidate uncertain parental relationships in the captive population. In a conservation perspective, continuous monitoring of both populations is demanded: it involves the incorporation of new individuals from the island into the captive population to avoid inbreeding and to achieve the recommended allelic similarity between the two populations. At last, we recommend that the genetic data support researches as a base to maintain a viable and healthy captive population, highly genetically similar to the <i>in-situ</i> one, which is crucial for considering a reintroduction process into the island.</p>
Imprints of Ocean Chaotic Intrinsic Variability on Bottom Pressure and Implications for Data and Model Analyses
<p>These data are used for the manuscript "Imprints of Ocean Chaotic Intrinsic Variability on Bottom Pressure and Implications for Data and Model Analyses" to be submitted to Geophysical Research Letter. Uploaded data include:</p> <p>[1] ext_int_quater_deg.nc: atmospherically driven and intrinsic variations for subseasonal, intra-annual and mean seasonal bottom pressure signals at model original resolution.</p> <p>[2] ext_int_3deg.nc: atmospherically driven and intrinsic variations for smoothed subseasonal and intra-annual bottom pressure signals at 3*3 degree resolution.</p> <p>[3] ext_int_10deg.nc: atmospherically driven and intrinsic variations for smoothed intra-annual bottom pressure signals at 10*10 degree resolution.</p> <p>[4] meanseason_timeseries.nc: Time series of mean seasonal bottom pressure signals from all 50 ensemble members over Agulhas Current region and Argentine Basin.</p>
The telomere regulatory gene POT1 responds to stress and predicts performance in nature: implications for telomeres and life history evolution
<p>Telomeres are emerging as correlates of fitness-related traits and may be important mediators of ecologically relevant variation in life history strategies. Growing evidence suggests that telomere dynamics can be more predictive of performance than length itself, but very little work considers how telomere regulatory mechanisms respond to environmental challenges or influence performance in nature. Here, we combine observational and experimental datasets from free-living tree swallows (<i>Tachycineta bicolor</i>) to assess how performance is predicted by the telomere regulatory gene POT1, which encodes a shelterin protein that sterically blocks telomerase from repairing the telomere. First, we show that lower POT1 gene expression was associated with higher female quality, <i>i.e.</i> earlier breeding and heavier body mass. We next challenged mothers with an immune stressor (lipopolysaccharide injection) that led to 'sickness' in mothers and 24h of food restriction in their offspring. While POT1 did not respond to maternal injection, females with lower constitutive POT1 gene expression were better able to maintain feeding rates following treatment. Maternal injection also generated a one-day stressor for chicks, which responded with lower POT1 gene expression and elongated telomeres. Other putatively stress-responsive mechanisms (i.e. glucocorticoids, antioxidants) showed marginal responses in stress-exposed chicks. Model comparisons indicated that POT1 mRNA abundance was a largely better predictor of performance than telomere dynamics, indicating that telomere regulators may be powerful modulators of variation in life history strategies.</p>
Data from: Predicting bushmeat biomass from species composition captured by camera traps: implications for locally-based wildlife monitoring
<p>The 'StatAnalysis.zip' contains the data and model files. We used it for the four analyses below.</p> <p>First, we estimated population densities, the mean body mass and camera-trap capture rates of five main bushmeat targets in a rainforest of southeast Cameroon: Peters's duikers (<em>Cephalophus callipygus</em>), bay duikers (<em>C. dorsalis</em>), blue duikers (<em>Philantomba monticola</em>), brush-tailed porcupines (<em>Atherurus africanus</em>) and Emin's pouched rats (<em>Cricetomys emini</em>). Second, on the basis of the density and body mass estimates, we estimated bushmeat biomass—the total biomass of the five bushmeat species—and its spatial variation. Third, we calculated six bushmeat indicators based on the capture rate estimates. Lastly, we examined the correlation between bushmeat biomass and the indicators.</p> <p>The ZIP file consists of 16 R script files, three CSV files (in the 'data' subfolder) and 135 stan files (in the 'stan' subfolders). It also has two empty folders, 'figure' and 'res', where the figures and R objects of model results will be stored following the analyses. Please see the document 'README.txt' before performing the analysis. This text file gives the ZIP file structure and brief descriptions of the files.</p>
Core-mantle partitioning and the bulk Earth abundances of hydrogen and carbon: implications for their origins
Open the record for dataset details and reuse information.
Supplementary material to "A dynamic flight model for Slocum gliders and implications for turbulence microstructure measurements" by Merckelbach et al.
<p>Supplementary information to the publication "A dynamic flight model for Slocum gliders and implications for turbulence microstructure measurements" by Lucas Merckelbach, Anja Berger, Gerd Krahmann, Marcus Dengler and Jeffrey R. Carpenter, Journal of Atmospheric and Oceanic Technology, 2019, 36(2), DOI: 10.1175/JTECH-D-18-0168.1. The supplementary information consists of the set of glider data and DVL data as used in the manuscript.</p> <p> </p>
Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms
<p><strong>Abstract:</strong> Parkinson's disease (PD) may start in the gut and spread to the brain. To investigate the role of gut microbiome, we conducted a large-scale study, at high taxonomic resolution, using uniform standardized methods from start to end. We enrolled 490 PD and 234 control individuals, conducted deep shotgun sequencing of fecal DNA, followed by metagenome-wide association studies requiring significance by two methods (ANCOM-BC and MaAsLin2) to declare disease association at species and genus level, followed by network analysis to identify polymicrobial clusters, and functional profiling based on microbial genes and pathways. Here we show that over 30% of species, genes and pathways tested have altered abundances in PD, depicting a widespread dysbiosis. PD-associated species form polymicrobial clusters that grow or shrink together, and some compete. PD microbiome is disease permissive, evidenced by overabundance of pathogens and immunogenic components, dysregulated neuroactive signaling, preponderance of molecules that induce alpha-synuclein pathology, and over-production of toxicants; with the reduction in anti-inflammatory and neuroprotective factors limiting the capacity to recover. We validate, in human PD, findings that were observed in experimental models; reconcile and resolve human PD microbiome literature, and provide a broad foundation with a wealth of concrete testable hypotheses to discern the role of the gut microbiome in PD. </p> <p><strong>Zenodo contents:</strong> In this Zenodo archive we provide (1) post sequence QC and post taxonomic and functional profiling "Source Data" used to generate tables and figures in the manuscript and (2) "Supplementary Code" that contains the workflow and code used to perform bioinformatic processing of shotgun sequences and statistical analyses of microbial profiles and subject metadata. The code provided here is the same "Supplementary Code" that is provided in the supplement of the manuscript. Individual level raw shotgun sequences and metadata are available on NCBI Sequence Read Archive (SRA) under BioProject ID <a href="https://www.ncbi.nlm.nih.gov/bioproject/834801">PRJNA834801</a>.</p>
Broad diversity in monoterpene-sesquiterpene balance across wild sunflowers: implications of leaf and floral volatiles for biotic interactions
<p>• <strong>Premise of the study:</strong> As plant lineages diversify across environmental gradients, species are predicted to encounter divergent biotic pressures. This study investigates the evolution of volatile secondary metabolism across <em>Helianthus</em> genus. <br>• <strong>Methods:</strong> Leaves and petals of 40 species of wild <em>Helianthus</em> were analyzed via gas chromatography-mass-spectrometry to describe volatile secondary metabolite profiles. <br>• <strong>Key results:</strong> Across all species, 500 compounds were identified including 40% sesquiterpenes, 18% monoterpenes, 3% diterpenes, 4% fatty acid derivatives, and 35% other compounds such as phenolics and small organic compounds. Qualitatively, annuals and species from more arid western climates had leaf compositions with a higher proportion of total monoterpenes, while erect perennials and species from more mesic eastern habitats contained a higher proportion of total sesquiterpenes. Among species, mass-based leaf monoterpene and sesquiterpene abundance were identified as largely orthogonal axes of variation by principal components analysis. Leaf and petal profiles were not strongly correlated. <br>• <strong>Conclusions:</strong> Wide diversity in volatile metabolism was observed among wild <em>Helianthus</em>, indicating value of this genus as a model system, and a rich genetic resource. The independence of leaf and petal volatile profiles indicates a low level of phenotypic integration between vegetative and reproductive structures, implying vegetative defense and reproductive defense or pollinator attraction functions mediated by terpenoid profiles in these two organs can evolve without major tradeoffs. The major biosynthetic pathways manufacturing major terpenoids identified in wild <em>Helianthus </em>have been well described to date, providing a road map to deeper inquiry into the drivers of this diversity.</p>
Fig. 35 in Morphology of larvae and pupae of the genus Autocrates (Coleoptera: Trictenotomidae) and its phylogenetic implications
Fig. 35. Bayesian inference tree of trictenotomid species based on combined COI and 16S sequences.
Supporting data for: Limited genetic differentiation of Mycetomoellerius mikromelanos in Parc National Soberanía, Panama: Implications for queen dispersal
<p>The coevolutionary relationship between fungus-growing ants (Formicidae: Attini: Attina) and their symbionts has been well-studied in the Panamanian rainforests. To further understand the ecological context of these evolutionary relationships, we have examined the population genetic structure of the fungus-growing ant species<em> Mycetomoellerius</em> <em>mikromelanos</em> Cardenas, Schultz, & Adams 2021, in the Panama Canal Zone. We specifically investigated the presence of population structure, the significance of geographic features (i.e., creeks) limiting gene flow, and relatedness between ant colonies. To accomplish this, we genotyped 85 ant colonies from nine creeks across an approximately 30 km transect in Parque National Soberanía, Panama using double digest restriction-site associated DNA sequencing. We did not find distinct population structures using two genetic clustering methods; however, we did detect an effect of isolation by distance. Furthermore, related colonies were frequently detected on the same creek or neighboring creeks, and some at further geographic distances. Collectively, these findings demonstrate that new colonies tend to establish on natal creeks and occasionally on distant creeks following long-distance dispersal events. We discuss how population genetic patterns reveal the natural history of <em>M</em>. <em>mikromelanos</em> in Parque National Soberanía and how these results fit into the context of fungus-growing ant mutualisms.</p>
A meta-analysis of pre-pregnancy maternal body mass index and placental DNA methylation identifies 27 CpG sites with implications for mother-child health
<p>Higher maternal pre-pregnancy body mass index (ppBMI) is associated with increased neonatal morbidity, as well as with pregnancy complications and metabolic outcomes in offspring later in life. Placenta is a key organ in fetal development and has been proposed to act as a mediator between the mother and different health outcomes in children. The overall aim of the present work is to investigate the association of ppBMI with epigenome-wide placental DNA methylation (DNAm) in 10 studies from the PACE consortium, amounting to 2,631 mother-child pairs. We identify 27 CpG sites at which we observe placental DNAm variations of up to 2.0% per 10 ppBMI-unit. The CpGs that are differentially methylated in placenta do not overlap with CpGs identified in previous studies in cord blood DNAm related to ppBMI. Many of the identified CpGs are located in open sea regions, are often close to obesity-related genes such as GPX1 and LGR4 and altogether, are enriched in cancer and oxidative stress pathways. Our findings suggest that placental DNAm could be one of the mechanisms by which maternal obesity is associated with metabolic health outcomes in newborns and children, although further studies will be needed in order to corroborate these findings.</p> <p>File descriptions:</p> <ul> <li>ppBMI_placenta_unadjustedmodel_NFJ.csv = EWAS summary statistics for the EWAS of ppBMI using the unadjusted model</li> <li>ppBMI_placenta_adjustedmodel_NFJ.csv = EWAS summary statistics for the EWAS of ppBMI using the adjusted model</li> </ul> <p>Upload of this dataset was completed by The EWAS Catalog team. The data can be queried along with hundreds of other EWAS at ewascatalog.org. To upload your EWAS summary statistics and have a Zenodo DOI generated for you go to ewascatalog.org/upload.</p>
Temperature as a likely driver shaping global patterns in mineralogical composition in bryozoans: Implications for marine calcifiers under Global Change
<p><span>The Southern Ocean is showing one of the most rapid responses to human-induced global change, thus acting as a sentinel of the effects on marine species and ecosystems. Ocean warming and acidification are already impacting benthic species with carbonate skeletons, but the magnitude of these changes to species and ecosystems remains largely unknown. Here we provide the largest carbonate mineralogical dataset to date for Southern Ocean bryozoans, which are diverse, abundant and important as carbonate producers, thus making them excellent for monitoring the effects of ocean warming and acidification. </span><span>To</span><span> improve our </span><span>understanding of how bryozoans might respond to ocean warming and acidification,</span><span> we assess latitudinal and seafloor temperature patterns of skeletal mineralogy using bryozoan species occurrences together with temperature data for the first time. Our findings, combining new mineralogical data with published data from warmer regions, show that the proportions of high-Mg calcite and bimineralic species increase significantly towards lower latitudes and with increasing seawater temperature. These patterns are consistent with the hypothesis that seawater temperature is likely a significant driver of variations in bryozoan mineralogy at a global scale.</span></p>
Discovery of Ultra-depleted Melt Inclusion in Late Cretaceous Intracontinental Basaltic Andesites in South China: Implications for Recycling of Lower Oceanic Crust
<p><strong>Contents of this file </strong></p> <p><strong>S1. Supplementary Text:</strong></p> <p><strong>1. </strong>Data compilation and statistical analysis</p> <p><strong>2.</strong> Reconstructing the chemical compositions of melt inclusion</p> <p><strong>3.</strong> Batch melting calculation</p> <p><strong>4.</strong> Melt-plagioclase diffusive interaction model</p> <p><strong>S2. Supplementary Table:</strong></p> <p><strong>Table S1. </strong>The parameters used in batch melting calculation.</p> <p><strong>Table S2. </strong>Parameters used in the melt-plagioclase diffusive interaction model</p> <p><strong>Table S3. </strong>Input and output data for the melt-plagioclase diffusive interaction model.</p> <p><strong>S3. Supplementary Figure:</strong></p> <p><strong>Figure S1. </strong>Primitive mantle-normalized trace element patterns.</p> <p><strong>S4. Supplementary Dataset (uploaded separately):</strong></p> <p><strong>Dataset S1. </strong>Compiled data including basaltic rocks from South China, MORBs, and Hawaiian OIBs.</p> <p><strong>Dataset S2. </strong>Olivine chemical compositions.</p> <p><strong>Dataset S3. </strong>Bulk-rock major oxide, trace element, and Sr-Nd-Pb-Hf isotopic compositions.</p> <p><strong>Dataset S4. </strong>Measured and corrected major element compositions of melt inclusion.</p> <p><strong>Dataset S5. </strong>Measured and corrected trace element compositions of melt inclusion.</p> <p><strong>Dataset S6. </strong>Pb isotopic compositions of melt inclusion.</p>
Identity and density of parasite exposures alter the outcome of co-infections: Implications for management
<p>1) Although research has focused on density-dependent responses of hosts to single-parasite infections, hosts are exposed to numerous parasites simultaneously under natural conditions and if these exposures lead to infections, they can threaten host populations and ecosystem stability. Moreover, spatiotemporal variation in abundance of co-occurring parasites might influence host infection intensity. If interactions are consistent between different co-infecting parasites, then these patterns could give managers another tool to control disease spread and even predict problematic disease emergences.</p> <p>2) We investigated how parasite density and identity alter within-host co-infection dynamics. To test this, we simultaneously exposed Cuban treefrogs (Osteopilus septentrionalis) as a model amphibian species to all pairwise combinations of three problematic parasites that commonly co-infect amphibians: the fungus Batrachochytrium dendrobatidis (Bd), the nematode Aplectana hamatospicula, and Ranavirus. Hosts were exposed to one parasite at a fixed dose and another parasite at a range of five doses.</p> <p>3) Higher doses of Bd decreased Ranaviral and A. hamatospicula loads, but Bd load was not influenced by the dose of either parasite. Ranaviral load was negatively associated with A. hamatospicula dose, but A. hamatospicula load was not affected by Ranaviral dose. We found that all the pairwise co-infections were dependent on parasite density and that pairwise interactions were highly asymmetric – strong in one direction and weak in the other – consistent with interactions dominating food webs.</p> <p>4) Synthesis and applications: We also revealed that the exposure dose of A. hamatospicula was positively associated with host tolerance to Bd infection and negatively associated with Ranaviral load in hosts. Ranavirus and Bd cause mass die-offs in amphibians, but A. hamatospicula does not. Therefore, in systems where these parasites coexist, maintaining or increasing densities of A. hamatospicula could reduce the negative effects of Bd and Ranavirus infections. Additionally, if these asymmetric and density dependent patterns from community ecology are applicable to other amphibian co-infections or co-infections in other systems, this should allow conservation organizations and resource managers to predict outbreaks and manage host declines associated with deadly parasites by modifying the abundance of co-infecting parasites that might be easier to manage.</p>
Qatar Peninsula' High Vulnerability to Oil Spills and its Implication for the Potential Disruption in Global Gas Supply (Datasets)
<p>Outputs of oil spill dispersal simulations performed backward in time using OpenDrift for the following study:</p> <p>Anselain, T., Heggy, E., Dobbelaere, T., & Hanert, E. (2022). Qatar Peninsula’ High Vulnerability to Oil Spills and its Implication for the Potential Disruption in Global Gas Supply. <em>Nature Sustainability</em>. In press.</p>
Warburg effect characterizes the skeletal muscle in Fabry Disease: experimental evidence and clinical implications
<p>Skeletal muscle (SM) pain and fatigue are common in Fabry disease (FD), and strongly impact the patient’s quality of life. Still, the SM in FD is poorly investigated. Although energetic alterations are reported in cells from FD patients, they have never been related to fatigue and pain. Given the pivotal relevance of energetics for SM health, we undertook the investigation of the SM. We consistently observed a reduced tolerance to aerobic activity and lactate accumulation in FD-humanized mouse model and patients. Accordingly, in sedentary mouse FD SM we detected an increase in fast/glycolytic-fibers, mirrored by an upregulation of glycolytic enzymes and glucose-transporters. In fibroblasts derived from FD patients, we confirmed a high glycolytic-rate and accordingly, metabolomic/lipidomic-analysis revealed that lipids are underutilized as energetic fuel in FD-patients. In the quest for a tentative mechanism, we explored analogies with genetic myopathies, that show altered expression of energetic metabolism. Specifically, we explored HIF-1 upregulation and found it increased in FD mice and patients. From a screening of miRNAs associated with metabolic stress, we found the significant upregulation of miR-17, which has been previously associated with HIF-1 up-regulation. A specific antagomir targeting miR-17 was able to inhibit HIF-1 accumulation and revert metabolic-remodeling in FD-cells. Our findings unveil an anaerobic glycolytic-switch under normoxia, known as Warburg Effect, which is induced by miR-17-mediated-upregulation of HIF-1. The miR-17/HIF-1 pathway can be a new therapeutic target in FD, and Exercise-testing and blood lactate may become a new diagnostic and monitoring-tool in FD.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.