Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
3,696
datasets available to search
ShareScore release 0.9.0
Dataset results
3,696 results for “Reference”
Power of Bayesian and heuristic tests to detect cross-species introgression with reference to gene flow in the Tamias quadrivittatus group of North American chipmunks
<p>In the past two decades genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used the heuristic method HyDe to detect gene flow, which may suffer from low power. Here we use the Bayesian method implemented in the program bpp to reanalyze these data. We develop a Bayesian test of introgression, calculating the Bayes factor via the Savage-Dickey density ratio using the Markov chain Monte Carlo (MCMC) sample under the model of introgression. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 63%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. We examine the assumptions and performance of HyDe, and demonstrate that it lacks power if gene flow occurs between sister lineages or if the mode of gene flow does not match the assumed hybrid speciation model with symmetrical population sizes. Our analyses highlight the power of likelihood-based inference of cross-species gene flow using genomic sequence data.</p>
DEMIX 1" Reference DEMs version 2.0
<p>This reference data supports the work of the Digital Elevation Model Intercomparison eXercise (DEMIX) working group (Strobl and others, 2021; Guth and others, 2021; Bielski and others, 2023, 2024). </p> <p>The data set consists of:</p> <ul> <li>Excel metadata file with two tabs: <ul> <li>Credits for each of 24 areas for the source of the high resolution data sets, the number of DEMIX tiles (Guth and others, 2023) in that area, the resolution of the source data, and credits for the processing.</li> <li>The national mapping agencies (or equivalent) that provided the free high resolution data, and the files used for the vertical datum transformations.</li> </ul> </li> <li>ZIP file with the 1” grids used to support the DEMIX work and create the DEMIX database (Guth, 2023). The file also includes databases for each area required to use the data in MICRODEM.</li> </ul> <p> </p> <p>Changes to version 2</p> <ol> <li>Version 1 should no longer be used</li> <li>Now contains 236 DEMIX tiles</li> <li>Added 2 new area, Stateline and Canary Islands east which should have minimal differences between the DSM and the DTM and no significant changes over the last 20 years.</li> <li>Added 4 new areas in France from Visioterra</li> <li>Added some additional tiles for a few areas</li> <li>Fixed some anomalies in aggregation to 1” DEMs</li> <li>Now using GDAL to compute the computed datum shift, horizontal and vertical, for USGS 3DEP</li> <li>Recomputed all the reference data and the GIS database (Guth, 2023)</li> </ol> <p>To understand the use of the reference data, see the forthcoming paper (Bielski and others, 2023).</p> <p><strong>References:</strong></p> <p>Bielski, C.; López-Vázquez, C.; Guth. P.L.; Grohmann, C.H. and the TMSG DEMIX Working Group, 2023. DEMIX Wine Contest Method Ranks ALOS AW3D30, COPDEM, and FABDEM as Top 1” Global DEMs: <a href="https://arxiv.org/pdf/2302.08425.pdf">https://arxiv.org/pdf/2302.08425.pdf</a></p> <p><span>Bielski, C.; López-Vázquez, C.; Grohmann, C.H.; Guth. P.L.; Hawker, L.; Gesch, D.; Trevisani, S.; Herrera-Cruz, V.; Riazanoff, S.; Corseaux, A.; Reuter, H.; Strobl, P., 2024. Novel approach for ranking DEMs: Copernicus DEM improves one arc second open global topography. IEEE Transactions on Geoscience & Remote Sensing. </span> <span> vol. 62, pp. 1-22, 2024, Art no. 4503922, </span> <a href="https://doi.org/10.1109/TGRS.2024.3368015"> <span>https://doi.org/10.1109/TGRS.2024.3368015</span></a></p> <p>Guth, P. L., 2023. DEMIX GIS Database Version 2 (2.0) [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.8062008">https://doi.org/10.5281/zenodo.8062008</a></p> <p>Guth, P.L., Strobl, P., Gross, K., & Riazanoff, S. (2023). DEMIX 10k Tile Data Set (1.0) [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.7504791">https://doi.org/10.5281/zenodo.7504791</a></p> <p>Guth, P.L.; Van Niekerk, A.; Grohmann, C.H.; Muller, J.-P.; Hawker, L.; Florinsky, I.V.; Gesch, D.; Reuter, H.I.; Herrera-Cruz, V.; Riazanoff, S.; López-Vázquez, C.; Carabajal, C.C.; Albinet, C.; Strobl, P. Digital Elevation Models: Terminology and Definitions. Remote Sens. 2021, 13, 3581. <a href="https://doi.org/10.3390/rs13183581">https://doi.org/10.3390/rs13183581</a></p> <p>Strobl, P.A.; Bielski, C.; Guth, P.L.; Grohmann, C.H.; Muller, J.P.; López-Vázquez, C.; Gesch, D.B.; Amatulli, G.; Riazanoff, S.; Carabajal, C. The Digital Elevation Model Intercomparison eXperiment DEMIX, a community based approach at global DEM benchmarking. Int. Arch. Photogramm. Remote Sens. Spat. Inf. Sci. 2021, XLIII-B4-2021, 395–400. <a href="https://doi.org/10.5194/isprs-archives-XLIII-B4-2021-395-2021">https://doi.org/10.5194/isprs-archives-XLIII-B4-2021-395-2021</a></p>
Genomic datasets of Laminaria digitata: Paired-end reads from dd-RADseq, reference genome assembly and filtered VCF
<p>The long-term persistence of species in the face of climate change can be evaluated by examining the interplay between selection and genetic drift in the contemporary evolution of populations. In this study, we focused on spatial and temporal genetic variation in four populations of the cold-water kelp Laminaria digitata using thousands of SNPs (ddRAD-seq). These populations were sampled from the center to the south margin in the North Atlantic at two different time points, spanning at least two generations. By conducting genome scans for local adaptation from a single time point, we successfully identified candidate loci that exhibited clinal variation, closely aligned with the latitudinal changes in temperature. This finding suggests that temperature may drive the adaptive response of kelp populations, although other factors, such as the species' demographic history should be considered. Furthermore, we provided compelling evidence of selection through the examination of allele frequency changes over time, by taking into the impact of genetic drift. Specifically, we detected candidate loci exhibiting temporal differentiation that surpassed the levels typically attributed to genetic drift at the south margin, confirmed through simulations. This finding was in sharp contrast with the lack of detection of outlier loci based on temporal differentiation in a population from the North Sea, exhibiting low and decreasing levels of genetic diversity. These contrasting evolutionary scenarios among populations can be primarily attributed to the differential prevalence of selection relative to genetic drift. In conclusion, our study highlights the potential of temporal genomics to gain deeper insights into the contemporary evolution of marine foundation species in response to rapid environmental changes.</p>
Reference datasets for consistency tests of GENAPOPOP 1.0 software: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms.
<p>Datasets companion of the manuscript entitled GenAPoPop 1.0: a user-friendly software to analyse genetic diversity and structure in partially clonal and selfed polyploid organisms, used to achieve consistency test with Spagedi 1.5 software, and used as reference datasets to demonstrate the new possibilities allowed by GenAPoPop software.</p> <p>Raw datasets used for testing GenAPoPop 1.0, A user-friendly software for easily compute genetic analyses of autopolyploid populations packaged for Linux, MacOS and Windows; Results obtained from Spagedi 1.5 (Hardy & Vekemans 2001) and GenAPoPop1.0.</p> <p>Four pseudo-observed genotyping autotetrapolyploid SNP datasets, corresponding respectively to panmictic (A), highly clonal (B), highly selfed (C) and half-clonal-half-selfed (D) reproductive mode scenario. In all these four scenarios, we simulated two populations of 100 individuals each, connected with a migration rate of 0.01 and mutating at a rate of 0.01, genotyped at 10 SNPs. Datasets were recorded 1000 generations after an initial randomly drawing population with equal allele frequencies.</p> <p>One SNP tetraploid genotyping dataset from two French <em>Ludwigia grandiflora subsp. hexapetala</em> populations (aquatic plant from the Angiosperm clade): two populations in which we collected 75 individuals, each genotyped with 36 SNPs using the Hiplex method allowing confident allele dosage (Delord et al. 2018).</p> <p>One microsatellite tetraploid genotyping dataset on two Aulactinia stella populations (sea-anemone from the Cnidaria phylum), sampled on the coast of the arctic ocean. One population of 21 individuals and one population of 15 individuals, both genotyped with 10 microsatellites.</p> <p>We also report here the consistency tests with GenAlex and Spagedi, results of analyses (GPP tab) on 6300 independant simulations and inferences of the quantitative reproductive modes using the bayesian method on CEMP tab made on 6300 another independant simulations.</p>
Measurements on reference materials for SThM measurand versus thermal conductivity calibration curve
<p>This sheet presents the results of measurements carried out on calibration samples using the SThM technique as part of the NanoWires project. The thermal conductivity of the samples was previously characterised using a traceable technique. Measurement results are given with associated standard uncertainty. The thermal conductivity range studied was between 0.187 and 117 W.m<sup>-1</sup>.K<sup>-1</sup>. These measurements were used to construct the thermal conductivity calibration curve for a SThM probe.</p> <p>The 19ENG05 NanoWires project has received funding from the EMPIR programme co-financed by the Participating States and from the European Union’s Horizon 2020 research and innovation programme.</p>
Fig. 59 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Fig. 59 (continued on facing page). One of the 634 most parsimonious trees showing names of transformations for basal nodes. These nodes and characters transformations are identical for all 634 trees. Numbered nodes relate to discussion in the text. Proposed families and subfamilies are named at their respective nodes. Black bars = nonhomoplasious forward change; grey bars = homoplasious forward change; white bars = reversal (whether homoplasious or not). Numbered nodes refer to discussion in text.
Fig. 60. Character transformations within clade 4 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Fig. 60. Character transformations within clade 4 of the same tree shown in Fig. 59. Numbered nodes relate to discussion in the text. Note that resolution within this clade differs little from the strict consensus tree shown in Fig. 56. Tribal groupings are those proposed under this study. Black bars = non-homoplasious forward change; grey bars = homoplasious forward change; white bars = reversal (whether homoplasious or not).
Fig. 58 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Fig. 58. Strict consensus tree showing current tribal placements for genera, together with their proposed tribal placements under the revised classifications derived from this study. Numbered nodes are those referred to in the text.
Fig. 62. Character transformations within clade 13 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Fig. 62. Character transformations within clade 13 of the same tree shown in Fig. 59. Note that resolution within this clade differs little from the strict consensus tree shown in Fig. 56. Numbered nodes relate to discussion in the text. The tribal grouping is that proposed under this study. Black bars = nonhomoplasious forward change; grey bars = homoplasious forward change; white bars = reversal (whether homoplasious or not).
Figs. 54–55 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Figs. 54–55. Cyclochila australasiae: (54) stridulatory file on underside of lateral angles of pronotal collar; (55) stridulatory scraper on fore wing base.
Fig. 56 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Fig. 56. Strict consensus of the 634 most parsimonious trees with all characters unordered and equally weighted. Numbered nodes (bold print) relate to discussion in the text. Other numbers at nodes are jackknife values from 1000 jackknife replications (above) and T-PTP scores from 100 replications (below). Nodes lacking jackknife or bootstrap percentages fall below 50%.
Fig. 57 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Fig. 57. Strict consensus tree showing current subfamily placements for genera, together with their proposed subfamily placements under the revised classification derived from this study. Numbered nodes are those referred to in the text.
Fig. 52. Character 85 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Fig. 52. Character 85. Male reproductive system, accessory glands, states 0–2: (0) absent; (1) short; (2) long.
Fig. 51. Character 79 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Fig. 51. Character 79. Apical part of theca, states 0 and 1: (0) without leaf-like lobes; (1) with a pair of leaf-like lateral lobes.
Fig. 53. Character 86 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Fig. 53. Character 86. Female reproductive system, accessory glands of common oviduct, states 0–2: (0) absent; (1) short; (2) long.
Fig. 49. Character 71. Basal plate attachment, states 0–2 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Fig. 49. Character 71. Basal plate attachment, states 0–2: (0) entirely membranous, loosely attached; (1) completely fused with no mobility; (2) with a functional membranous "hinge".
Fig. 48. Character 70 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Fig. 48. Character 70. Aedeagal basal plate in lateral view showing ventral rib, states 0 and 1: (0) completely fused with basal plate; (1) rod-like, suspended with attachment only at ends.
Fig. 61. Character transformations within clade 7 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Fig. 61. Character transformations within clade 7 of the same tree shown in Fig. 59. Numbered nodes relate to discussion in the text. Note that resolution within this clade differs little from the strict consensus tree shown in Fig. 56. Tribal groupings are those proposed under this study. Black bars = non-homoplasious forward change; grey bars = homoplasious forward change; white bars = reversal (whether homoplasious or not).
Fig. 50. Character 75. Thecal pseudoparameres, states 0–3 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Fig. 50. Character 75. Thecal pseudoparameres, states 0–3: (0) dorsal of theca, originating closer to theca than its base, always much longer than theca; (1) dorsal of theca, originating near thecal base; (2) entirely lateral of theca, filiform or flat and usually very long; (3) lateral of theca, dorsally fused to near their apices.
Fig. 47. Character 68 in An Appraisal of the Higher Classification of Cicadas (Hemiptera: Cicadoidea) with Special Reference to the Australian Fauna
Fig. 47. Character 68. Aedeagal basal plate in dorsal view (apex at top), states 0–9: (0) parallel-sided, basal two-thirds without sclerotization except laterally; (1) apically broadened with "ears"; (2) basally divided into two discs, apical arms lobe-like; (3) deeply divided into two arms; (4) midline deeply furrowed, apically square or bilobed (dorsolateral view); (5) short, broad, usually rounded; (6) T-shaped; (7) Y-shaped; (8) broad, triangular with anterior angles elongate; (9) broad, apically broadly bilobed.
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.