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Widespread Sampling Biases in Herbaria Revealed from Large-Scale Digitization 1656-2016
Non-random collecting practices may bias conclusions drawn from analyses of herbarium records. Recent efforts to fully digitize and mobilize regional floras offer a timely opportunity to assess commonalities and differences in herbarium sampling biases. We determined spatial, temporal, trait, phylogenetic, and collector biases in ~5 million herbarium records, representing three of the most complete digitized floras of the world: Australia (AU), South Africa (SA), and New England, USA (NE) We identified numerous shared and unique biases among these regions. Shared biases included specimens i) collected close to roads and herbaria; ii) collected more frequently during spring; iii) of threatened species collected less frequently; and iv) of close relatives collected in similar numbers. Regional differences included i) over-representation of graminoids in SA and AU and of annuals in AU; and ii) peak collection during the 1910s in NE, 1980s in SA, and 1990s in AU. Finally, in all regions, a disproportionately large percentage of specimens were collected by a few individuals. These mega-collectors, and their associated preferences and idiosyncrasies, may have shaped patterns of collection bias via ‘founder effects’. Studies using herbarium collections should account for sampling biases and future collecting efforts should avoid compounding these biases.
Resources from: Disparate patterns of genetic divergence in three widespread corals across a pan-pacific environmental gradient highlights species-specific adaptation trajectories
<p>The following files are contained in this repository:</p> <p><br> README.Hume_et_al_2022.zenodov4.txt - This document.</p> <p>scripts.Hume_et_al_2022.zenodov4.pdf - Contains the scripts, or locations of the scripts, used to conduct the data analyses detailed in the associated manuscript.</p> <p>acknowledgements_local_authorities.Hume_et_al_2022.zenodov1.pdf - Acknowledgements of local authorities for the collection of samples used in the associated study.</p> <p>TaraPacific_SST_timeseries_mean_productsV2mai2021.Hume_et_al_2022.zenodov1.csv - The historical temperature data set used for the RDA, Mantel tests and gradient Forest analysis.</p> <p>Pocillopora_meandrina_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip - The Pocillopora SNPs referred to as 'raw' in the Methods of the associated manuscript. Compressed using genozip (https://genozip.readthedocs.io/index.html).</p> <p>Pocillopora_meandrina_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip.md5 - md5 of the the Pocillopora raw SNPs.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'linked' in the Methods of the associated manuscript.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora linked SNPs.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'unlinked' in the Methods of the associated manuscript.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora unlinked SNPs.</p> <p>Porites_lobata_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip - The Pocillopora SNPs referred to as 'raw' in the Methods of the associated manuscript. Compressed using genozip (https://genozip.readthedocs.io/index.html).</p> <p>Porites_lobata_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip.md5 - md5 of the the Pocillopora raw SNPs.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'linked' in the Methods of the associated manuscript.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora linked SNPs.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'unlinked' in the Methods of the associated manuscript.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora unlinked SNPs.</p> <p>PANAMA2021.raw.Hume_et_al_2022.zenodov2.vcf.gz - The Millepora SNPs referred to as 'raw' in the Methods of the associated manuscript.</p> <p>PANAMA2021.raw.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Millepora raw SNPs.</p> <p>Millepora_REF_orthologue_genes.Hume_et_al_2022.zenodov2.csv - The Millepora gene list referred to as 'target genes' in the Methods of the associated manuscript.</p> <p>Mil_transcriptom.Hume_et_al_2022.zenodov2.fa.gz - The Millepora de novo assembled transcriptome.</p> <p>Mil_transcriptom.Hume_et_al_2022.zenodov2.fa.gz.md5 - md5 of the Millepora de novo assembled transcriptome.</p> <p> </p> <p>mtORF Phylogeny</p> <p>TP-Johnston_mtORF-Pocillo.fa = all sequences</p> <p>TP-Johnston_mtORF-Pocillo.mafft.fa = mafft alignment</p> <p>TP-Johnston_mtORF-Pocillo.mafft.ML.nwk = ML tree newick</p> <p> </p> <p>Hellberg genotype network Porites</p> <p>TP-Hellberg_MM32-Porites.nex = all aligned sequences for this locus with indels encoded</p> <p>TP-Hellberg_MM100-Porites.nex = all aligned sequences for this locus with indels encoded</p> <p>TP-Hellberg_ATPaseB.nex = all aligned sequences for this locus with indels encoded,</p> <p>TP-Hellberg_POFAD.nex = POFAD multilocus genotypic distance,</p> <p>TP-Hellberg_Splitstree.nex= Multilocus genotype network in nexus format</p> <p><br> Gradient Forest Analysis</p> <p>Poc_abund.csv - Pocillopora SSH Occurrences per Site er Island</p> <p>Por_abund.csv - Porites SSH Occurrences per Site er Island</p> <p>mean_depth_por.csv - per site per island mean depth among Porites colonies</p> <p>mean_depth_poc.csv - per site per island mean depth among Pocillopora colonies</p>
Data package supporting manuscript "Widespread Heterogeneity in Density-Dependent Mortality of Nearshore Fishes"
This repository contains the complete data synthesis and analysis pipeline for a global meta-analysis on density-dependent mortality in reef fishes. We estimated mortality parameters (α and β) from >30 ecological studies and explored how ecological traits, experimental methods, and phylogenetic history explain variation in density dependence. It comprises eight data tables in csv format, three .tre files for phylogenetic trees (see method document for data sources), and the zipped code folder (including 12 R scripts) to ensure transparent, end-to-end reproducibility of data processing, analysis, and visualization. This package supports the manuscript “Widespread Heterogeneity in Density-Dependent Mortality of Nearshore Fishes” by Stier & Osenberg (Ecology Letters).
Graph Data: Hydrological impact of widespread afforestation in Great Britain using a large ensemble of modelled scenarios
<p>Data used for creating the figures in the paper: Hydrological impact of widespread afforestation in Great Britain using a large ensemble of modelled scenarios.</p> <p>It contains the flow exceedances (as mm day<sup>-1</sup>), flow duration slope, median elasticity and runoff ratio for the different afforestation scenarios. Also included is the information on the changes of broadleaf afforestation. </p> <p>If you have any questions, please email marcus.buechel@ouce.ox.ac.uk.</p>
Data for "Globally widespread and increasing violations of environmental flow envelopes"
<p>Data and code for</p> <p><strong>Globally widespread and increasing violations of environmental flow envelopes</strong></p> <p>Vili Virkki*#, Elina Alanärä#, Miina Porkka, Lauri Ahopelto, Tom Gleeson, Chinchu Mohan, Lan Wang-Erlandsson, Martina Flörke, Dieter Gerten, Simon N. Gosling, Naota Hanasaki, Hannes Müller Schmied, Niko Wanders, and Matti Kummu*</p> <p># equal contribution to the article<br> * Correspondence to: Vili Virkki (vili.virkki@aalto.fi), Matti Kummu (matti.kummu@aalto.fi)</p> <p><br> link to published version: https://hess.copernicus.org/articles/26/3315/2022/</p> <p><strong>Please cite the published version of the article when using these data.</strong></p> <p><strong>See readme.txt in data for a detailed description of attached files.</strong></p>
Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing
<p>Genes in prokaryotic genomes are often arranged into clusters and co-transcribed into poly- cistronic RNAs. Isolated examples of polycistronic RNAs were also reported in some higher eukaryotes but their presence was generally considered rare. Here we developed a long- read sequencing strategy to identify polycistronic transcripts in several mushroom forming fungal species including Plicaturopsis crispa, Phanerochaete chrysosporium, Trametes ver- sicolor, and Gloeophyllum trabeum. We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, involving up to 8% of the transcribed genes. Unlike polycistronic mRNAs in prokaryotes, these co-transcribed genes are also independently transcribed. We show that polycistronic transcription may interfere with expression of the downstream tandem gene. Further comparative genomic analysis indicates that polycis- tronic transcription is conserved among a wide range of mushroom forming fungi. In sum- mary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a phylogenetic range of higher fungi. Furthermore, we systematically show that our long-read sequencing approach and combined bioinformatics pipeline is a generic powerful tool for precise characterization of complex transcriptomes that enables identifica- tion of mRNA isoforms not recovered via short-read assembly.</p>
Supplementary data for Willemsen et al., 2024 "Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts".
<p>Supplementary data for Willemsen et al., 2024 "Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts". The data set consists of five folders: “Codon_usage_amoebae_and_viruses”, "Genome_annotations_amoebae", "Phylogenetic_trees_18S_amoebae", “Phylogenomic_trees_amoebae”, and "Viral_integration_detection_amoebae". The “Codon_usage_amoebae_and_viruses” folder contains for each amoeba host the calculated codon usage tables in the subfolder "codon_usage_table_host", the calculated codon usage preferences using different scores in the subfolder "codon_usage_scores_host", and the calculated codon usage preferences of giant viruses versus each host in the subfolder "codon_usage_scores_viruses_vs_host". The giant viruses in the subfolder "codon_usage_scores_viruses_vs_host" are organised by viral family and genus in separate sub-subfolders. The "Genome_annotations_amoebae" folder contains the generated genome annotations in different formats and the manually curated mitochondrial genome annotations for each amoeba host. The "Phylogenetic_trees_18S_amoebae" contains for the eukaryotic phyla <em>Discosea</em>, <em>Heterolobosea</em>, and <em>Tubulinea, </em>the 18S rRNA nucleotide alignments, distance matrices, and computed phylogenetic trees. The folder "Phylogenomic_trees_amoebae" contains for the eukaryotic clades <em>Amoebozoa</em> and <em>Discoba, </em>the protein alignment matrices and computed phylogenomic trees. The folder "Viral_integration_detection_amoebae" contains the MCP databases used (fasta file, alignment file, HMM profile and DIAMOND BLASTX database) and the MCP sequences detected in this study and the blast results of these. </p>
Exploiting the Greenland volcanic ash repository to date caldera-forming eruptions and widespread isochrons during the Holocene
<p>Polar ice-cores have long been recognised as unrivalled repositories of past volcanic events. Although tephra products from local eruptions tend to dominate these records, improvements in micro-sampling and analytical techniques are uncovering a growing number of cryptotephras erupted from exceptionally distant volcanoes. We present a series of nine Middle Holocene cryptotephra deposits detected within the NGRIP ice-core that originate from five different volcanic regions across the Northern Hemisphere (Alaska, Cascades, Iceland, Japan, Kamchatka). Unique compositional signatures are employed to identify ash from three large caldera-forming events in Kamchatka (KS<sub>2 </sub>from Ksudach), the Cascades (Mazama) and North East Japan (Mashu), along with ash from the Hekla 4 eruption in Iceland. High-precision ice-core ages (adopting a 1950 datum for the GICC05 timescale assigned to the Greenland ice cores) are derived for each eruption: Hekla 4 (4325 ± 8 a b1.95k), KS<sub>2</sub> (7089 ± 26 a b1.95k), Mashu (i-f) (7473 ± 33 a b1.95k) and Mazama (7562 ± 35 a b1.95k), all of which can be employed as chronological fix-points in other proxy records where these deposits are also preserved. Four further cryptotephra deposits and one macro-deposit (in the GRIP ice core) are also identified and traced to sources in Iceland and Alaska. The cryptotephra originating from Alaska is correlated to a deposit identified in lake records from the Kenai Peninsula, thought to originate from Redoubt Volcano. The remaining four deposits are typical of the products of Katla, Grímsvötn and Veiðivötn in Iceland. This ensemble of mid-Holocene tephra deposits highlights the pivotal position of the Greenland ice-sheet and its ice-cores to capture deposition from the convergence of several far-travelled ash clouds. Precise age estimates derived from the annually resolved ice-core record greatly enhances the value of these tephra isochrons.</p> <p> </p>
Meta-analysis results of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight
<p>Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from -183 to 178 grams per 10% increase in methylation (P<sub>Bonferroni</sub><1.06x10<sup>-7</sup>).</p>
Supplementary material for "High turn-over rates at the upper range limit and elevational source-sink dynamics in a widespread songbird"
<p><strong>Abstract</strong></p> <p>The formation of an upper distributional range limit for species breeding along mountain slopes is often based on environmental gradients resulting in changing demographic rates towards high elevations. However, we still lack an empirical understanding of how the interplay of demographic parameters forms the upper range limit in highly mobile species. Here, we study apparent survival and within-study area dispersal over a 700 m elevational gradient in barn swallows (<em>Hirundo rustica</em>) by using 15 years of capture-mark-recapture data. Annual apparent survival of adult breeding birds decreased while breeding dispersal probability of adult females, but not males increased towards the upper range limit. Individuals at high elevations dispersed to farms situated at elevations lower than would be expected by random dispersal. These results suggest higher turn-over rates of breeding individuals at high elevations, an elevational increase in immigration and thus, within-population source-sink dynamics between low and high elevations. The formation of the upper range limit therefore is based on preference for low-elevation breeding sites and immigration to high elevations. Thus, shifts of the upper range limit are not only affected by changes in the quality of high-elevation habitats but also by factors affecting the number of immigrants produced at low elevations.</p>
Sources of Environmental risks from artificial nighttime lighting widespread and increasing across Europe
<p>Sources of the article Environmental risks from artificial nighttime lighting widespread and<br> increasing across Europe. Calibrated ISS images using Sánchez de Miguel, A., Zamorano, J., Aubé, M., Bennie, J., Gallego, J., Ocaña, F., ... & Gaston, K. J. (2021). Colour remote sensing of the impact of artificial light at night (II): Calibration of DSLR-based images from the International Space Station. <em>Remote Sensing of Environment</em>, <em>264</em>, 112611.</p>
Widespread deoxygenation of temperate lakes: companion dataset 1980 - 2017
Lake surface temperatures are steadily increasing. DO responds to temperature through multiple mechanisms, suggesting that DO in lakes should be responding to changing water temperatures. To determine whether and how DO is changing in temperate lakes, we collected and analyzed 22,983 temperature and dissolved oxygen profiles from approximately 400 mostly temperate zone lakes. Here, we present resulting derived statistics from this analysis. These statistics include mean summer epilimnetic temperature and DO, hypolimnetic temperature and DO, Secchi depth, chlorophyll a, as well as select meteorological variables such as mean summer air temperature and wind speed.
Fig. 4 in The Leiobunum rupestre species group: resolving the taxonomy of four widespread European taxa (Opiliones: Sclerosomatidae)
Fig. 4. Pedipalps of the Leiobunum rupestre group, whole pedipalps in lateral view, single femora in medial view. — A–F. ♁♁. A–B. Leiobunum rupestre Herbst, 1799, Germany, Baden-Württemberg, CJM1954. A. Pedipalpus lateral. B. Femur medial. C–D. L. gracile Thorell, 1876, Denmark, Asp, CJM3531. C. Pedipalpus lateral. D. Femur medial. — E–F. Leiobunum apenninicum (Martens, 1969), France, Alpes- Maritimes, CJM2747. E. Pedipalpus lateral. F. Femur medial. — G–M. ♀♀. G–H. Leiobunum rupestre Herbst, 1799, Germany, Mt. Arber, CJM136. G. Pedipalpus lateral. H. Femur medial. J–K. L. gracile Thorell, 1876, Denmark, Asp, CJM3531. J. Pedipalpus lateral. K. Femur medial. L–M. L. apenninicum (Martens, 1969), France, Alpes-Maritimes, CJM2747. L. Pedipalpus lateral. M. Femur medial. Arrows indicate characters mentioned in the descriptions.
Fig. 1 in The Leiobunum rupestre species group: resolving the taxonomy of four widespread European taxa (Opiliones: Sclerosomatidae)
Fig. 1. Habit of Leiobunum rupestre species group. A–B. Leiobunum rupestre Herbst, 1799, Slovenia, Pohorje Mountains, resting at rock faces. A. ♁. B. ♀. C–D. Leiobunum apenninicum (Martens, 1969), Italy, Monesi di Triora, at night. C. ♁. D. ♀. E–F. Leiobunum gracile Thorell, 1876, Denmark. E. ♁. F. ♀. Photographs: A–D by A.L.Schönhofer; E–F by S. Toft, all taken in the field.
Fig. 3 in The Leiobunum rupestre species group: resolving the taxonomy of four widespread European taxa (Opiliones: Sclerosomatidae)
Fig. 3. Body of Leiobunum C.L. Koch, 1839, dorsal view. A–B. Leiobunum rupestre Herbst, 1799, Germany, Mt. Arber, CJM136. A. ♁. B. ♀. — C–D. Leiobunum gracile Thorell, 1876, Denmark. C. ♁, 2 km N of Skaerbaek, CJM3530. D. ♀, Asp, CJM3531. — E–F. Leiobunum apenninicum (Martens, 1969), France, Alpes-Maritimes. E. ♁, CJM1508. F. ♀, CJM2747. Drawings by K. Rehbinder.
Fig. 5. Leiobunum, male genitalia. A–C. L. rupestre Herbst, 1799 in The Leiobunum rupestre species group: resolving the taxonomy of four widespread European taxa (Opiliones: Sclerosomatidae)
Fig. 5. Leiobunum, male genitalia. A–C. L. rupestre Herbst, 1799, Germany, Baden-Württemberg, CJM1954. A. Ventral view. B. Lateral view. C. Cross-section. — D–F. L. gracile Thorell, 1876, Denmark, 2 km N of Skaerbaek, CJM3530. D. Ventral view. E. Lateral view. F. Cross-section. — G–J. L. apenninicum (Martens, 1969), France, Alpes-Maritimes, CJM1508. G. Ventral view. H. Lateral view. J. Cross-section. Arrows indicate the area of the respective cross-sections.
Interaction of hydric and thermal conditions drive geographic variation in thermoregulation in a widespread lizard
<p>Raw data and scripts of the article "Interaction of hydric and thermal conditions drive geographic variation in thermoregulation in a widespread lizard" by Rozen-Rechels D. et al., in Ecological Monographs. These data are freely available in csv format. See the readme file for metadata explanation.</p> <p>Data were formatted by the first author David Rozen-Rechels and collected according to standards and procedures described in the companion journal article.</p> <p> </p> <p>Abstract of the paper:</p> <p>Behavioral thermoregulation is an efficient mechanism to buffer the physiological effects of climate change. Thermal ecology studies have traditionally tested how thermal constraints shape thermoregulatory behaviors without accounting for the potential major effects of landscape structure and water availability. Thus, we lack a general understanding of the multifactorial determinants of thermoregulatory behaviors in natural populations. In this study, we quantified the relative contribution of elevation, thermal gradient, moisture gradient and landscape structure in explaining geographic variation in thermoregulation strategies of a terrestrial ectotherm species. We measured field active body temperature, thermal preferences and operative environmental temperatures to calculate thermoregulation indices, including thermal quality of the habitat and thermoregulation efficiency for a very large sample of common lizards (<em>Zootoca vivipara</em>) from 21 populations over 3 years across the Massif Central mountain range in France. We used an information-theoretic approach to compare eight <em>a priori</em> thermo-hydroregulation hypotheses predicting how behavioral thermoregulation should respond to environmental conditions. Environmental characteristics exerted little influence on thermal preference with the exception that females from habitats with permanent access to water had lower thermal preferences. Field body temperatures and accuracy of thermoregulation were best predicted by the interaction between air temperature and a moisture index. In mesic environments, field body temperature and thermoregulation inaccuracy increased with air temperature, but they decreased in drier habitats. Thermoregulation efficiency (difference between thermoregulation inaccuracy and the thermal quality of the habitat) was maximized in cooler and more humid environments and was mostly influenced by the thermal quality of the habitat. Our study highlights complex patterns of variation in thermoregulation strategies, which are mostly explained by the interaction between temperature and water availability, independent of the elevation gradient or thermal heterogeneity. Although changes in landscape structure were expected to be the main driver of extinction rate of temperate zone ectotherms with ongoing global change, we conclude that changes in water availability coupled with rising temperatures might have a drastic impact on the population dynamics of some ectotherm species.</p>
Figs 199‒204 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)
Figs 199‒204. Morphology of the male genitalia for species of the subgenus Melanobombus von Dalla Torre, 1880 from the dorsal aspect, anterior at the bottom of the image, posterior at the top. 199. Bombus alagesianus Reinig, 1930 stat. rev., Georgia. 200. B. tibeticus sp. nov., China-Qinghai. 201. B. incertoides Vogt, 1911 stat. rev., Mongolia. 202. B. qilianensis sp. nov., China-Qinghai. 203. B. keriensis Morawitz, 1887, India-Kashmir. 204. B. separandus Vogt, 1909 stat. rev., Kyrgyzstan. Scale bars = 1 mm.
Figs 209–210 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)
Figs 209–210. Images of queens of two cryptic species from around the western Qinghai-Tibetan plateau. 209. Bombus keriensis Morawitz, 1887 from Mt Apharwat (4000 m a.s.l.) in the Pir Panjal mountains (ML405). 210. B. separandus Vogt, 1909 stat. rev. from Nimaling plain (4800 m a.s.l.) in the Zanskar mountains (ML311). Viewed from the left lateral aspect.
Figs 12‒13 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)
Figs 12‒13. Maps of sequenced samples. 12. The rufipes-group and festivus-group. 13. The rufofasciatus- group as recognised as species from the UHF-PTP analysis in Fig. 10. Keys to the coloured symbols are shown on the left (in some cases symbols on the map for one species may overlie symbols for another). Maps projected onto a sphere in ArcGIS using World_Shaded_Relief basemap © 2014 ESRI and showing boundaries between countries as recognised by the UN.
ScienceDex guides
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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.