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Maps of the diversity and distribution of Raunkiær's life forms in European vegetation
<p>This repository contains raster files (TIF format) with a 50 km × 50 km resolution (over UTM grid EPSG:32633), showcasing the diversity and distribution of Raunkiær’s life forms in European vegetation. The maps are based on two key metrics: (i) the proportion (%) of species within each life form and (ii) the diversity of life forms, including richness and evenness.</p> <p>To generate these maps, we averaged plot-level metric values across a comprehensive dataset comprising 546,501 vegetation plots sourced from the European Vegetation Archive (EVA; Project 163; <a href="https://euroveg.org" target="_new">https://euroveg.org</a>). These plots cover diverse habitats, including 173,190 forests, 260,884 grasslands, 52,517 scrubs, and 59,910 wetlands.</p> <p>The maps encompass the entire dataset, offering a visualization of the geographical distribution patterns of life forms across Europe. Additionally, we created habitat-specific maps by subsetting the dataset to explore unique patterns within each habitat type (forest, grassland, scrub, and wetland).</p> <p>Furthermore, we generated additional maps based on standardised effect sizes (SES) of diversity metrics. Through 500 species identity shuffles without replacement, specific to each habitat type, we examined the deviations from random expectations. SES values outside the range of -1.96 to 1.96 indicate significantly lower or higher metric values than expected at random, respectively. </p> <p> </p> <table> <tbody> <tr> <td><strong>Folder name</strong></td> <td><strong>Description of TIF raster values</strong></td> </tr> <tr> <td>full.div</td> <td>Mean richness and evenness of life forms across all habitat types</td> </tr> <tr> <td>full.mean.rel.prop</td> <td>Mean proportion of each life form across all habitat types</td> </tr> <tr> <td>habitat.div</td> <td>Mean richness and evenness of life forms across separate habitat types (forest, grassland, scrub, and wetland)</td> </tr> <tr> <td>habitat.mean.rel.prop</td> <td>Mean proportion of each life form across separate habitat types (forest, grassland, scrub, and wetland)</td> </tr> <tr> <td>SES.full.div</td> <td>Mean richness and evenness of life forms across all habitat types measured with standardized effect sizes (SES)</td> </tr> <tr> <td>SES.full.mean.rel.prop</td> <td>Mean proportion of each life form across all habitat types measured with standardized effect sizes (SES)</td> </tr> <tr> <td>SES.habitat.div</td> <td>Mean richness and evenness of life forms across separate habitat types (forest, grassland, scrub, and wetland) measured with standardized effect sizes (SES)</td> </tr> <tr> <td>SES.habitat.mean.rel.prop</td> <td>Mean proportion of each life form across separate habitat types (forest, grassland, scrub, and wetland) measured with standardized effect sizes (SES)</td> </tr> </tbody> </table> <p><br>Additional information is available in our publication:<br><br>Midolo, G., Axmanová, I., Divíšek, J., Dřevojan, P., Lososová, Z., Večeřa, M., Karger, D. N., Thuiller, W., Bruelheide, H., Aćić, S., Attorre, F., Biurrun, I., Boch, S., Bonari, G., Čarni, A., Chiarucci, A., Ćušterevska, R., Dengler, J., Dziuba, T., Garbolino, E., Jandt, U., Lenoir, J., Marcenò, C., Rūsiņa, S., Šibík, J., Škvorc, Ž., Stančić, Z., Stanišić-Vujačić, M., Svenning, J. C., Swacha, G., Vassilev, K., & Chytrý, M. (2024) Diversity and distribution of Raunkiær’s life forms in European vegetation.<em> Journal of Vegetation Science. </em>Accepted on the 10th of December 2023</p>
Figure 1 in New record and revised list of Megalops atlanticus (Elopiformes: Megalopidae) from Atlantic European waters
Figure 1. – Specimen of Megalops atlanticus of 1885 mm TL and location of records in the European Atlantic waters. The black dots constitute the historical captures and the red triangle represents the present record in the Gulf of Cádiz in 2018.
Data from: Only rare classical MHC-I alleles are highly expressed in the European house sparrow
<p>The exceptional polymorphism observed within genes of the major histocompatibility complex (MHC), a core component of the vertebrate immune system, has long fascinated biologists. The highly polymorphic <em>classical</em> MHC class-I (MHC-I) genes are maintained by pathogen-mediated balancing selection (PMBS), as shown by many sites subject to positive selection, while the more monomorphic MHC-I genes show signatures of purifying selection. In line with PMBS, at any point in time, rare classical MHC alleles are more likely than common classical MHC alleles to confer a selective advantage in host-pathogen interactions. Combining genomic and expression data from the blood of wild house sparrows <em>Passer domesticus</em>, we found that only rare classical MHC-I alleles were highly expressed, while common classical MHC-I alleles were lowly expressed or not expressed. Moreover, highly expressed rare classical MHC-I alleles had more positively selected sites, indicating exposure to stronger PMBS, compared with lowly expressed classical alleles. As predicted, the level of expression was unrelated to allele frequency in the monomorphic non-classical MHC-I alleles. Going beyond previous studies, we offer a fine-scale view of selection on classical MHC-I genes in a wild population by revealing differences in the strength of PMBS according to allele frequency and expression level.</p>
European Ivies (Hedera L., Araliaceae) Point Occurrence Database with Taxonomic Certainty
<p>We present two databases and six spatial layers recording biodiversity information of the six species of ivies (<em>Hedera </em>L., Araliaceae) native to W Europe (<em>Hedera azorica, H. canariensis, H. helix, H. hiberncia, H. iberica, H. maderensis)</em>. Each database covers the entire native distribution of each species. Therefore, the databases document the distribution and occurrence of all the European <em>Hedera </em>taxa except for <em>H. pastuchovii </em>subsp.<em> cypria</em> which is a restricted endemic of the south-west of the island of Cyprus. </p> <ul> <li>The first database (TaxRev) includes taxonomic, geographic and habitat information from the morphological revision of 2,276 individuals from 1,280 populations. 866 of the records also included point-occurrence data. This database represents the entire native distribution and the morphological variation of each species.</li> <li>The second database (MixOcc) includes the spatial-point occurrence of the six species across their entire native distribution ranges. This database was compiled with the 880 records from the TaxRev database (records with high taxonomic certainty, as they all were examined by the taxonomist of the genus) plus 2,372 records from curated online databases selected from the European regions with low expected taxonomic uncertainty (C and E Europe and the Macaronesian Islands). As a result the database have high taxonomic quality (certainty and coverage) and good geographical coverage for Europe at a large-scale except for France and Ireland.</li> <li>The uploaded files related to the TaxRev database are as follows:</li> </ul> <p>Hedera_TaxRevDatabase_Field description: a cvs file with the description of the 71 variables included in the database</p> <p>Hedera_TaxRevDatabase_Records: a cvs file with the database (71 variables, 1,280 records)</p> <ul> <li>The uploaded files related to the MixOcc database are as follows:</li> </ul> <p>Hedera_MixOccDatabase_Field description: a cvs file with the description of the 11 variables included in the database</p> <p>Hedera_MixDatabase_Records: a cvs file with the database (11 variables, 3,252 records)</p> <p>Finally, we also upload 20 layers including the point-occurrence maps obtained from the MixOcc database. Six species maps (one per species), five additional maps of <em>H. canariensis</em> (one per island), eight additional maps of <em>H. azorica</em> (one per island) and a combined map including the six species. In all of them, we distinguish the records from individuals morphologically reviewed by the taxonomist of the genus and those obtained from online repositories and not reviewed by the taxonomist:</p> <ul> <li>Hedera azorica_MixOccDatabase_Map</li> <li>Hedera_azorica_map_Corvo</li> <li>Hedera_azorica_map_Faial</li> <li>Hedera_azorica_map_Flores</li> <li>Hedera_azorica_map_Graciosa</li> <li>Hedera_azorica_map_Pico</li> <li>Hedera_azorica_map_Santa Maria</li> <li>Hedera_azorica_map_Sao Jorge</li> <li>Hedera_azorica_map_Sao Miguel</li> <li>Hedera_azorica_map_Terceira</li> <li>Hedera canariensis_MixOccDatabase_Map</li> <li>Hedera_canariensis_map_El Hierro</li> <li>Hedera_canariensis_map_Gran Canaria</li> <li>Hedera_canariensis_map_La Gomera</li> <li>Hedera_canariensis_map_La Palma</li> <li>Hedera_canariensis_map_Tenerife</li> <li>Hedera helix_MixOccDatabase_Map</li> <li>Hedera hibernica_TaxRevDatabase_Map</li> <li>Hedera iberica_TaxRevDatabase_Map</li> <li>Hedera maderensis_MixOccDatabase_Map</li> <li>Hedera_MixOccDatabase_Map</li> </ul> <p>The records which allow us to improve geographic coverage without compromising taxonomic certainty. The databases and the resulting spatial layers have high taxonomic and geographic certainty and a good geographic coverage for ivies in Europe.</p>
European Olfactory Knowledge Graph
<p>The European Olfactory Knowledge Graph (EOKG) includes information about smell from (digital) text and image collections from the European history (1600-1920), extracted in the context of the <a title="Odeuropa" href="https://odeuropa.eu/" target="_blank" rel="noopener">Odeuropa project</a> in a cultural heritage preservation perspective.</p> <p>It contains over 2,500,000 olfactory reference coming from over 43,000 images and 2,400,000 texts in six languages, organised according to the <a href="https://data.odeuropa.eu/ontology" target="_blank" rel="noopener">Odeuropa Ontology</a> and leveraging machine learning to recognise and categorise olfactory elements.</p> <h3>Additional Links</h3> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div>EOKG Vocabularies: <a href="https://vocab.odeuropa.eu/" target="_blank" rel="noopener noreferrer">https://vocab.odeuropa.eu/</a> (vocabulary browser)<br>Odeuropa Ontology: <a href="https://data.odeuropa.eu/ontology/" target="_blank" rel="noopener noreferrer">https://data.odeuropa.eu/ontology/</a> (data model)<br>EOKG API: <a href="https://grlc.eurecom.fr/api/Odeuropa/kg-api/" target="_blank" rel="noopener noreferrer">https://grlc.eurecom.fr/api/Odeuropa/kg-api/</a> (API)<br>EOKG technical report: <a href="https://odeuropa.eu/wp-content/uploads/2024/10/D4_3_European_Olfactory_Knowledge_Graph_v2_final.pdf">https://odeuropa.eu/wp-content/uploads/2024/10/D4_3_European_Olfactory_Knowledge_Graph_v2_final.pdf</a> (documentation)<br>Odeuropa Smell Explorer: <a href="https://explorer.odeuropa.eu/" target="_blank" rel="noopener noreferrer">https://explorer.odeuropa.eu/</a> (demonstrator)</div> </div> </div> </div> </div> </div> </div> </div> <div> </div> </div> </div> </div> </div>
Shared mobility provision in European cities
<p>This dataset includes different types of shared mobility schemes (i.e. including service provider, type of modality, type of operational model and type of public/private involvement) across European cities (having a population of more than 100.000).</p>
Figure 3 in Diet of the European eel Anguilla anguilla (Linnaeus, 1758) in two transitional waters of Southwestern Mediterranean
Figure 3. – Comparison of the IRI of major items ingested by Anguilla anguilla from Mellah lagoon (in black) and Wadi El Kebir (in gray).
Figure 1 in Diet of the European eel Anguilla anguilla (Linnaeus, 1758) in two transitional waters of Southwestern Mediterranean
Figure 1. – Geographical location of sampling sites (*) of Anguilla anguilla in Mellah lagoon (ML) and Wadi El Kebir (WEK).
Figure 1 in Evidence of trilobed testes in European sardine (Sardina pilchardus)
Figure 1. – Map of the sampling locations. Numbers refer to the Geographical Subareas (GSAs) of the Mediterranean in which samples were collected. The darker shade corresponds to the distributional range of the European sardine (Sardina pilchardus).
FIGURE 2 in Environmental correlates of the European common toad hybrid zone
FIGURE 2 Two-species 'global' distribution model for Bufo toads in western Europe. The colour scale runs from deep red for B. spinosus (Pb is zero) to deep blue for B. bufo (Pb at unity). The interrupted black line represents the center of the species' hybrid zone from molecular data, as in fig. 1. Outlined circular windows are those for which model fit is less than good (AUC <0.8, windows 1, 6–8 and 14–16).
FIGURE 3 in Environmental correlates of the European common toad hybrid zone
FIGURE 3 Two regions in the common–spined toad hybrid zone where the mutual species border appears to coincide with rivers. Coloured dots indicate toad populations with nuclear genetic species identifications as Bufo bufo (Q = Pb> 0.5, blue symbols) and B. spinosus (Q = Pb <0.5, red symbols). Open dots have Q-values in the 0.2–0.8 range. For numerical detail see supplementary table S1. Base map figure credits as in fig. 1. A) central France where the species border appears to coincide with the northern- most sections of the Loire (windows 5 and 6) and the upper stretches of the Cher (windows 7 and 8). B) southeastern France where the species border coincides with the Rhône and the lower Isère river at window 13. Note the paucity of data for the high Alps at windows 15 and 16 (see also Lescure and de Downloaded from Brill.com 12/12/2023 03:07:30PM Massary, 2012; Arntzen et al., via2017Open). Access. This is an open access article distributed under the terms of the CC-BY 4.0 License. https://creativecommons.org/licenses/by/4.0/
FIGURE 1 in Environmental correlates of the European common toad hybrid zone
FIGURE 1 Western Europe with France and adjacent countries in Mercator projection. Colours from green to brown indicate increasing altitudes. The Bufo bufo versus B. spinosus mutual range delineation is based upon molecular genetic data, in which the smooth interrupted line is derived by linear interpolation whereas the more angular line is based upon Dirichlet cells (for details see text). The small bodied common toad B. bufo occurs to the northeast and the large bodied spined toad B. spinosus to the southwest of the mutual range border. Environmental data were gathered for 17 overlapping and adjoining circular windows positioned over the mutual range border. Here shown are window 1 in the northwest of France, window 17 in the northwest of Italy and windows 5, 9 and 13 in between. The two boxed areas are highlighted in fig. 3. The base map was downloaded from MapsLand at https://www.mapsland.com, under a Creative Commons Attribution-ShareAlike 3.0 Licence. The animal drawings are by Bas Blankevoort, Naturalis Biodiversity Center.
FIGURE 4 Average values for eight environmental variables over 17 windows that follow the Bufo bufo – B in Environmental correlates of the European common toad hybrid zone
FIGURE 4 Average values for eight environmental variables over 17 windows that follow the Bufo bufo – B. spinosus hybrid zone from the Atlantic coast (window 1) to the Mediterranean (window 17). Variables shown are those selected by a logistic regression analysis, with 'species' as dependent variable and explanatory variables available for selection as in table 1. Units are as in table 1; see also Hijmans et al. (2005). Values for B. bufo and B. spinosus are shown by small and large dots, respectively. Grey areas indicate that values for B. bufo are lower than for B. spinosus. The graph at the top left provides AUC model fit values along with major topographical references. Rectangles indicate stretches of the species contact for which the environmental models have good fit (AUC> 0.8), with consistent results indicated by green shadings. For the other windows with less than good model fit, signals are likely to be absent or void, either from poor sampling (window 1), the presence of rivers (windows 5–9, 13–14), or a thin or absent species' contact (windows 16–17) (see fig. 3).
FIG. 4 in Dryopithecins, Darwin, de Bonis, and the European origin of the African apes and human clade
FIG. 4. — Views of the Çorakyerler hominine: A, palatal; B, lateral; C, medial; D, frontal. Scale bar: 1cm.
FIG. 1 in Dryopithecins, Darwin, de Bonis, and the European origin of the African apes and human clade
FIG. 1. — Comparisons between Pierolapithecus Moyà-Solà, KÖhler, Alba, Casanovas-Villar & Galindo, 2004 and D. fontani Lartet, 1856: A, Pierolapithecus I1; B, La Grive I1, NMB g. a. 9; C, Pierolapithecus M3, NMB; D, la Grive M3; E, left M from Can Vila; F, left M 3 3 from D. fontani. Images of the Pierolapithecus specimens are modified from Moyà-Solà et al. (2004). Scale bars: 1 cm.
FIG. 3 in Dryopithecins, Darwin, de Bonis, and the European origin of the African apes and human clade
FIG. 3. — Views of IPS 18000 from Can Llobateres: A, frontal view of the periorbital region with the right side reconstructed based on a mirror image of the better preserved left side; B, view from below of the interorbital space of IPS 18000 showing the extensive frontal sinus, outlined on the right side; C, lateral view of the frontal fragment showing the frontal's joint surface of the frontozygomatic suture; D, view from superiorly and medially showing the zygomatic's joint surface of the frontozygomatic suture. Scale bar: 1 cm.
FIG. 2 in Dryopithecins, Darwin, de Bonis, and the European origin of the African apes and human clade
FIG. 2. — Cladograms depicting alternative hypotheses discussed in the text. Modified from Begun et al. (1997) and Begun (2001, 2002, 2007). Griphopithecus alpani Tekkaya, 1974 and Kenyapithecus kizili Kelley, Andrews & Alpagut, 2008 are thickly enameled middle Miocene hominoids from Paşalar (Turkey). Griphopithecus darwini Abel, 1902 is the type species, from Dĕvínská Nová Ves (Slovakia). Neopithecus brancoi Schlosser, 1901 is an isolated M3 that is most similar to Rudapithecus Kretzoi, 1969 but with insufficient anatomy preserved to justify synonomy. Other taxa are discussed in the text. In A, Ouranopithecus is a hominin; in B, it is a dryopithecin.
Ecosystem Services Potential Dynamics of European Capital Metropolitan Areas
<p>These are the Supplementary Dataset of the article "Ecosystem Services Potential is Declining across European Capital Metropolitan Areas". These results rely on the Urban Atlas (UA) data. In our study, we first used the UA data 2018 to compare all ECMA by their current ESP. While the UA change products enabled us to reveal the ESP dynamics across three different periods. Consequently, we could differentiate between metropolitan areas that have faced high rates of ESP reduction and ECMA that have slightly improved. </p> <p>The data presented here include the following files:</p> <ol> <li>UAch_12_18_ALL.gpkg: Includes all altered LULC patches within the European capital metropolitan areas.</li> <li>FINAL_corr_Table.xlsx: Is the cumulative table which feeds the correlation analysis between ESP and ESPD results to socio-economic and other variables.</li> <li>WB_Urban_Population_Growth_Europe.xlsx: Delivers the population change metrics based on World Bank data.</li> <li>ESPD__Experts_Matrix_Revision: Including the revision procedure of the expert matrox evaluation criteria.</li> <li>ESPD_1806_ALL_City_level: Results of Ecosystem Services Potential Dynamics between 12 year period for 27 European metropolitan regions.</li> <li>ESPD_1812_ALL_City_level: Results of Ecosystem Services Potential Dynamics between 6 year period for 38 European metropolitan regions.</li> <li>ESPD_1812_ALL_Patch_level: Detailed table including all changed patches within 38 European metropolitan regions.</li> <li>ESPD_1812_UD_Pop_correlation: cumulative table incuding the urban expansion ratio and population growth, which feed our correlation analysis in our article.</li> </ol> <p> </p>
Data from: European green crab predation in a Washington State estuary revealed with DNA metabarcoding
<p><strong>Fisher, MC, Grason, EW, Stote, A, Kelly, RP, Litle, K, & PS McDonald. (in review). <em>Invasive European green crab (</em>Carcinus maenas<em>) predation in a Washington State estuary revealed with DNA metabarcoding. </em></strong></p> <p>Sequencing data files produced for Fisher et al. (in review) on an Illumina MiSeq (2x300bp) targeting a 418bp DNA sequence in the mitochondrial cytochrome C oxidase subunit I gene (cox1 or COI) Folmer region. Data are demultiplexed but otherwise un-processed. Sample data sheets used to load each sequencing run are included as excel spreadsheets in the appropriate zipped folder. The metadata file contains sample (green crab stomach / mock community) metadata and corresponding MiSeq run number(s). </p> <p>Associated lab protocols are available on Github (<a href="https://github.com/mfisher5/Green-crab-dDNA/tree/main/doc" target="_blank" rel="noopener">Green-Crab-dDNA</a>)</p> <p>---</p> <p>Abstract: Predation by invasive species can threaten local ecosystems and economies. The European green crab (<em>Carcinus maenas</em>), one of the most widespread marine invasive species, is an effective predator associated with clam and crab population declines outside of its native range. In the U.S. Pacific Northwest, green crab has recently increased in abundance and expanded its distribution, generating concern for estuarine ecosystems and associated aquaculture production. However, regionally-specific information on the trophic impacts of invasive green crab is very limited. We compared the stomach contents of green crabs collected on shellfish aquaculture beds versus natural intertidal sloughs in Willapa Bay, Washington, to provide the first in-depth description of European green crab diet at a particularly crucial time for regional management. We first identified putative prey items using DNA metabarcoding of stomach content samples. We compared diet composition across sites using prey presence/absence and an index of species-specific relative abundance. For eight prey species, we also calibrated metabarcoding data to quantitatively compare DNA abundance between prey items, and to describe an ‘average’ green crab diet at an intertidal slough and an actively cultivated Manila clam bed. From the stomach contents of 61 green crabs, we identified 54 unique taxa belonging to nine phyla. The stomach contents of crabs collected from cultivated Manila clam beds were significantly different from the stomach contents of crabs collected at natural intertidal sloughs. Across all sites, arthropods were the most frequently detected prey, with the native hairy shore crab (<em>Hemigrapsus oregonensis</em>) the single most common prey item. Of the eight species included in the quantitative model, two ecologically-important native species – the sand shrimp (<em>Crangon franciscorum</em>) and the Pacific staghorn sculpin (<em>Leptocottus armatus</em>) – were the most abundant in crab stomach contents, when present. In addition to providing timely information on green crab diet, our research demonstrates the novel application of a recently developed model for more quantitative DNA metabarcoding. This represents another step in the ongoing evolution of DNA-based diet analysis towards producing the quantitative data necessary for modeling invasive species impacts.</p>
F I G U R E 3 in The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches
F I G U R E 3 Comparison of trait-based metrics expressed in relative number of individuals computed from eDNA () and traditional electro-fishing (TEF;) samples in the five river stretches (RS), A, B, C, D and E. Trait categories: BEN, benthic; EUR, eurytopic; INS, insectivorous; OMN, omnivorous; PHY, phytophilic; POT, potamodromous; RHE, rheophilic; TOL, tolerant; PEL pelagic. Significance of the differences between eDNA and TEF metrics are shown: ns, not significant (P> 0.05)
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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.