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SBC LTER: Reef: Seasonal Kelp Forest Community Dynamics: Taxon-specific seasonal net primary production (NPP) for macroalgae
This dataset provides estimates of seasonal net primary production (NPP) for all taxa of macroalgae sampled in fixed plots of the SBC LTER's seasonal kelp forest monitoring sites. The five reefs (Arroyo Quemada 34°28.048’N, 120°07.031’W; Carpinteria 34°23.474’N, 119°32.510’W; Isla Vista 34°23.275’N, 119°32.792’W; Mohawk 34°23.649’N, 119°43.762’W; and Naples 34° 25.342’N, 119° 57.102’W) ranged in depth from 5.8 m to 8.9 m (MLLW) and were chosen to represent a range of physical and biological characteristics known to influence subtidal macroalgal assemblages in the region. NPP of understory taxa was calculated using field measurements of irradiance and biomass (derived from abundance) and laboratory estimates of taxon-specific photosynthetic parameters. NPP for the giant kelp, Macrocystis pyrifera, was calculated using linear relationships between frond density in a given season and average NPP for that season.
SBC LTER: Reef: Long-term experiment: Taxon-specific seasonal net primary production (NPP) for macroalgae
This dataset provides estimates of seasonal net primary production (NPP) for all taxa of macroalgae sampled in fixed plots of the SBC LTER's long-term kelp removal experiment sites. The experiment was initiated in 2008 at 4 sites; a fifth site as added in 2011. Data collection is ongoing. NPP of understory taxa was calculated using field measurements of irradiance and biomass (derived from abundance) and laboratory estimates of taxon-specific photosynthetic parameters. NPP for the giant kelp, Macrocystis pyrifera, was calculated using linear relationships between frond density in a given season and average NPP for that season.
Taxon item properties
<p>Diagram showing examples of Wikidata properties that can be used on a Wikidata item for a taxon. </p>
Global Biotic Interactions: Taxon Graph hash://sha256/0b58753e4ff5519442689d866c0f1d19ffa7d97f917144df1d1cd56ea756921d hash://md5/b23bd0210c88ca10c3e3253091f4fdfa
<p>Global Biotic Interactions: Taxon Cache and Taxon Map</p> <p>Global Biotic Interactions (GloBI) provides access to existing species interaction datasets (Poelen et al. 2014, http://globalbioticinteractions.org). As part of the dataset integration and aggregation, a best effort is made to resolve, match and link taxonomic names and associated vernacular/common names, hierarchies and thumbnails. </p> <p>The data archives included in this publication contain established taxonomic links (taxonMap.tsv.gz) and taxonomic information (taxonCache.tsv.gz) that GloBI retrieved and integrated from taxonomic name sources and web services associated with http://itis.gov, http://globalnames.org, http://eol.org and others open data services. </p> <p>While GloBI is not a naming authority and the primary goal of the name matching process is to detect incorrect or outdates names, the archives may serve as an example of how to publish denormalized taxonomic records and their interrelatioships in a pragmatic way.</p> <p>For related discussion threads, see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/145 , https://github.com/globalbioticinteractions/globalbioticinteractions/issues/274 , https://github.com/globalbioticinteractions/globalbioticinteractions/issues/70 , https://github.com/EOL/tramea/issues/10 and https://github.com/globalbioticinteractions/globalbioticinteractions/issues/274 .</p> <p>Files<br> <br> README <br> this file</p> <p> taxonCache.tsv.gz <br> Taxonomic name, ids, hierarchies, common names and thumbnail associated to taxa known to GloBI. <br> <br> taxonCache.tsv.sha256<br> sha256 hash of taxonCache.tsv</p> <p> taxonCacheFirst10.tsv<br> Header and 10 following lines from taxonCache.tsv</p> <p> taxonCacheFirst10.tsv.sha256<br> sha256 hash of taxonCacheFirst10.tsv<br> <br> taxonMap.tsv.gz <br> Links between taxon name and ids across various taxon providers. </p> <p> taxonMap.tsv.sha256 <br> sha256 hash of taxonMap.tsv</p> <p> taxonMapFirst10.tsv<br> Header and 10 following lines from taxonMap.tsv<br> <br> taxonMapFirst10.tsv.sha256<br> sha256 hash of taxonMapFirst10.tsv</p> <p> prefixes.tsv<br> Term prefixes and their associated uri schemes. </p> <p> names.tsv.gz<br> Corpus of names used to resolve and link. Generated using https://github.com/globalbioticinteractions/elton .</p> <p> names.tsv.sha256<br> sha256 hash of names.tsv</p> <p> namesUnresolved.tsv.gz<br> Names that are not (yet) linked to name sources using https://github.com/globalbioticinteractions/nomer .</p> <p> namesUnresolved.tsv.sha256<br> sha256 hash of namesUnresolved.tsv </p> <p>Column Descriptions</p> <p> taxonCache.tsv.gz </p> <p> 1 | id<br> 2 | name<br> 3 | rank<br> 4 | commonNames<br> 5 | path<br> 6 | pathIds <br> 7 | pathNames<br> 8 | externalUrl<br> 9 | thumbnailUrl<br> <br> taxonMap.tsv.gz</p> <p> 1 | providedTaxonId<br> 2 | providedTaxonName<br> 3 | resolvedTaxonId<br> 4 | resolvedTaxonName</p> <p> names.tsv.gz</p> <p> 1 | providedTaxonId<br> 2 | providedTaxonName</p> <p> namesUnresolved.tsv.gz</p> <p> 1 | providedTaxonId<br> 2 | providedTaxonName</p> <p>References</p> <p>Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2014.08.005.</p> <p>Updates</p> <p>org.globalbioticinteractions.taxon v0.3, 2018-03-02</p> <p>This taxon archive version was created by taking GloBI taxon v0.2 (Jan 2018) and appending a semi-automatically created WikiData taxon mapping and taxon cache.</p> <p>org.globalbioticinteractions.taxon v0.3.1, 2018-04-05</p> <p>This taxon archive version was created by taking GloBI taxon v0.2 (Jan 2018) and appending an automatically created WikiData taxon mapping and taxon cache using Apache Spark scripts at https://github.com/bio-guoda/guoda-datasets/tree/master/wikidata .</p> <p>org.globalbioticinteractions.taxon v0.3.2, 2018-05-21</p> <p>This taxon archive version includes the following:</p> <p>1. all lines in taxonMap.tsv.gz v0.3.1 that passed all validate-term-link tests defined in nomer v0.0.7 (see https://doi.org/10.5281/zenodo.1249964 or https://github.com/globalbioticinteractions/nomer/releases/tag/0.0.7).</p> <p>2. all lines in taxonCache.tsv.gz. v0.3.1 that passed all validate-term tests defined in nomer v0.0.7 </p> <p>3. all lines in 1. that did *not* pass the validate-term test, were re-resolved using nomer v0.0.7 commands "append globi-enrich" and "append globi-globalnames". Only SAME_AS and SYNONYM_OF matches were used to generate new entries for taxonCache and taxonMap.</p> <p>4. in addition, elton v0.4.5 (see https://doi.org/10.5281/zenodo.1212599 or https://github.com/globalbioticinteractions/elton/releases/tag/0.4.5) was used to generate an up-to-date names list by running the "update" and "names" commands on 18-19 May 2018. Of the resulting names, only id/names pairs that were unknown to the taxon graph were resolved using the "append globi-enrich" and "append globi-globalnames" commands of nomer v0.0.7. Only matches classified as SAME_AS and SYNONYM_OF were used to generate new entries for taxonCache and taxonMap.</p> <p>5. the updated versions of taxonMap.tsv.gz and taxonCache.tsv.gz were produced by appending result of 1., 2., 3. and 4. , removing duplicate lines and sorting the result. </p> <p>6. finally, the resulting taxonMap.tsv.gz. and taxonCache.tsv.gz files were validated using the nomer v0.0.7 validate-term-link and validate-term commands, respectively. The result indicated that all lines (other than the header) passed the validation tests.</p> <p>org.globalbioticinteractions.taxon v0.3.3, 2018-06-12</p> <p>This taxon archive version includes the following:</p> <p>1. normalizing taxonomic ranks using nomer's taxon rank matcher</p> <p>2. include more manual taxonomic name mappings provided by Brian Hayden and collaborators.</p> <p>3. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023 . </p> <p>4. remove mapping to NCBI taxa with name "Small" (and associated OTT).</p> <p><br>org.globalbioticinteractions.taxon v0.3.4, 2018-06-27</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p> <p>Please note that nomer and elton rely on web accessible apis like taxonomy resolution services and data portals. This dependence on external web-only accessible services might make reproduction of the results tricky due to network outages, server failures, upgrades, downgrades, data loss and/or abandonment of informatics projects/ datasets. </p> <p>org.globalbioticinteractions.taxon v0.3.5, 2018-06-28</p> <p>1. remove dubious provided name from taxon map. Names include "no name", "unidentified".<br>2. remove dubious mappings to Pavlova (e.g., Unidentified Amoebozoa -> Pavlova). Related to 1.<br>3. remove dubious mappings to resolve taxa that include names like "unidentified" or "organic species"<br>4. removed dubious mappings to "Boiga dendrophila"<br>5. removed dubious mappings from "Chaetognatha" (arrowworm) to a suspected homonym Lepidoptera GBIF:3257692 and IRMNG:1252651<br>6. removed dubious mappings from "small sharks" to multiple NCBI/OTT terms with name "Small"</p> <p>Please note that nomer and elton rely on web accessible apis like taxonomy resolution services and data portals. This dependence on external web-only accessible services might make reproduction of the results tricky due to network outages, server failures, upgrades, downgrades, data loss and/or abandonment of informatics projects/ datasets.</p> <p>org.globalbioticinteractions.taxon v0.3.6, 2018-09-10</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p> <p>org.globalbioticinteractions.taxon v0.3.7, 2018-10-18</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023<br>2. remove dubious mapping to Vertebrata (WORMS:370321 , http://www.marinespecies.org/aphia.php?p=taxdetails&id=370321). Also see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/361 .<br>3. remove dubious mapping to NCBITaxon:1585532 (Beta vulgaris/Cercospora beticola mixed EST library). Also see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/346 and https://github.com/Planteome/samara/issues/50 </p> <p>org.globalbioticinteractions.taxon v0.3.8, 2018-11-15</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023</p> <p>org.globalbioticinteractions.taxon v0.3.9, 2018-11-23</p> <p>1. label deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.1495266 to taxonMap.tsv.gz and taxonCache.tsv.gz . Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/383 .<br>2. remove all Encyclopedia of Life thumbnail urls from taxonCache. Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/381 .<br>3. remove Encyclopedia of Life external urls associated with deprecated ids from taxonCache. </p> <p><br>org.globalbioticinteractions.taxon v0.3.10, 2018-11-26</p> <p>1. Remove suspicious name mappings related to Humpback scorpionfish (Scorpaenopsis gibbosa) by applying patch published in Poelen, Jorrit H. (2018). Global Biotic Interactions: Taxon Graph Patches (Version 0.2. [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1560662 </p> <p>org.globalbioticinteractions.taxon v0.3.11, 2018-12-21</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.1286023<br>2. remove suspicious name mappings using: ```zcat taxonMap.tsv.gz | grep -v -i -P "\tnone\t" | grep -v -P "(GBIF|IRMNG):.*\tBrachyura$" | grep -v -P "Gamarus" | grep -v -P "^EOL:1047365\ttrachurus trachurus" | grep -v -P "Loros\t.*Psittacidae" | grep -v -P "(GBIF|IRMNG).*Lucifer$" | grep -v -P "GBIF.*Diadema$" | gzip > taxonMapUpdated.tsv.gz```</p> <p>org.globalbioticinteractions.taxon v0.3.12, 2019-06-05</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.13, 2019-06-12</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.14, 2019-08-19</p> <p>1. revisit deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.3371634 to taxonMap.tsv.gz and taxonCache.tsv.gz . Related to https://github.com/jhpoelen/eol-globi-data/issues/403 .</p> <p>org.globalbioticinteractions.taxon v0.3.15, 2019-08-26</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.16, 2019-09-22</p> <p>1. revisit deprecated EOL ids by applying patches in http://doi.org/10.5281/zenodo.3457626 to taxonMap.tsv.gz and taxonCache.tsv.gz of http://doi.org/10.5281/zenodo.3378125. Related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/408 .</p> <p>org.globalbioticinteractions.taxon v0.3.17, 2019-09-27</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.18, 2019-10-30</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.19, 2019-11-07</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.20, 2020-01-17</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.21, 2020-03-11</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.22, 2020-04-14</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.23, 2020-05-22</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.24, 2020-06-23</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.25, 2020-08-19</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteraction.taxon v0.3.26, 2020-10-01</p> <p>1. adding links to Plazi treatment via nomer append plazi (see https://github.com/globalbioticinteractions/nomer/issues/23)<br>by applying patches available via https://doi.org/10.5281/zenodo.4062711 .</p> <p>org.globalbioticinteraction.taxon v0.3.27, 2020-10-22</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteraction.taxon v0.3.28, 2021-01-19</p> <p>1. update taxonCache and taxonMap using patch 20210114-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.6) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4451462 .</p> <p>org.globalbioticinteractions.taxon v0.3.29, 2021-01-26</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.30, 2021-03-10</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.31, 2021-03-31</p> <p>1. update taxonCache and taxonMap using patch 20210331-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.7) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4655153 .</p> <p>org.globalbioticinteractions.taxon v0.3.32, 2021-05-12</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558<br>2. remove suspicious mappings from Fungal to some virus name described in https://www.gbif.org/species/4904189 Fungal see https://github.com/globalbioticinteractions/mangal/issues/1#issuecomment-833956239 .</p> <p>org.globalbioticinteractions.taxon v0.3.33, 2021-06-23</p> <p>1. remove suspicious viral name mappings as reported in https://github.com/globalbioticinteractions/globalbioticinteractions/issues/672 by updating taxonMap.tsv.gz using patch 20210623-01 available via Poelen, Jorrit H. (2021). Global Biotic Interactions: Taxon Graph Patches (Version 0.8) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.5021824 .</p> <p>org.globalbioticinteractions.taxon v0.3.34, 2021-09-24</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.35, 2021-11-19</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.3240558</p> <p>org.globalbioticinteractions.taxon v0.3.36, 2022-03-29</p> <p>1. update taxonCache and taxonMap using automated scripts available at https://doi.org/10.5281/zenodo.6394931</p> <p>org.globalbioticinteractions.taxon v0.4.0, 2023-03-21</p> <p>1. update elton, nomer, and globi taxon graph versions<br>2. attempt to align all names, including those aligned previously. Replaced incremental name alignment. Incremental name alignment was a optimization needed because of web api performance. Now, no web apis are used, so the optimization is no longer needed.<br>take names from https://globalbioticinteractions.org/data verbatim-interactions.tsv.gz instead of parsing verbatim names from their sources</p> <p>org.globalbioticinteractions.taxon v0.4.1, 2023-03-23</p> <p>update taxon graph build script to fit into existing taxonMap/taxonCache schema<br>fix various bugs<br>remove internal validation until a more up-to-date validation method is available</p> <p>org.globalbioticinteractions.taxon v0.4.2, 2022-10-14</p> <p>update taxonCache and taxonMap using automated scripts available at globalbioticinteractions. (2023). globalbioticinteractions/taxon-graph-builder: 0.0.7 (0.0.7). Zenodo. https://doi.org/10.5281/zenodo.10037579</p> <p>org.globalbioticinteractions.taxon v0.4.3, 2022-10-26</p> <p>apply patch 20231026-01 to address https://github.com/globalbioticinteractions/globalwebdb/issues/1 and https://discuss.eol.org/t/questionable-link-in-trophic-web-for-white-tailed-jackrabbit/2296</p> <p>org.globalbioticinteractions.taxon v0.4.4, 2022-10-26</p> <p>apply patch 20231026-02 to continue to work towards addressing https://github.com/globalbioticinteractions/globalwebdb/issues/1 and https://discuss.eol.org/t/questionable-link-in-trophic-web-for-white-tailed-jackrabbit/2296</p> <p>org.globalbioticinteractions.taxon v0.4.5, 2022-10-26</p> <p>apply patch 20231026-03 to continue to work towards addressing https://github.com/globalbioticinteractions/globalwebdb/issues/1 and https://discuss.eol.org/t/questionable-link-in-trophic-web-for-white-tailed-jackrabbit/2296</p> <p>org.globalbioticinteractions.taxon v0.4.6, 2024-06-17</p> <p>apply patch 20240617 to work towards addressing suspicious Candidatus name mapping reported in https://github.com/globalbioticinteractions/globalbioticinteractions/issues/968</p> <p>org.globalbioticinteractions.taxon v0.5.0, 2024-07-05</p> <p>1. update taxonCache and taxonMap using automated scripts available via Taxon Graph Builder v0.1.0 https://github.com/globalbioticinteractions/taxon-graph-builder/releases/tag/0.1.0 and/or https://doi.org/10.5281/zenodo.1286023 . </p> <p>org.globalbioticinteractions.taxon v0.5.1, 2024-07-08</p> <p>1. update taxonCache and taxonMap using automated scripts available via Taxon Graph Builder v0.1.1 https://github.com/globalbioticinteractions/taxon-graph-builder/releases/tag/0.1.1 and/or https://doi.org/10.5281/zenodo.12687693 . </p> <p>org.globalbioticinteractions.taxon v0.5.2, 2024-07-11</p> <p>1. update taxonCache and taxonMap using automated scripts available via Taxon Graph Builder v0.1.2 https://github.com/globalbioticinteractions/taxon-graph-builder/releases/tag/0.1.2 and/or https://doi.org/10.5281/zenodo.12687693 . </p> <p>org.globalbioticinteractions.taxon v0.5.3, 2024-07-24</p> <p>1. update taxonCache and taxonMap using automated scripts available via Taxon Graph Builder v0.1.2 https://github.com/globalbioticinteractions/taxon-graph-builder/releases/tag/0.1.2 and/or https://doi.org/10.5281/zenodo.12687693 . </p> <p><br>org.globalbioticinteractions.taxon v0.5.4, 2025-02-12</p> <p>1. update taxonCache and taxonMap using automated scripts available via Taxon Graph Builder v0.1.2 https://github.com/globalbioticinteractions/taxon-graph-builder/releases/tag/0.1.2 and/or https://doi.org/10.5281/zenodo.12687693 . </p>
EOL full taxon identifier map
<p>A mapping of taxon identifiers from EOL resources, of the form: node_id, resource_pk, resource_id, page_id, preferred_canonical_for_page</p> <ul> <li>node_id: internal to EOL; useful for some API calls</li> <li>resource_pk: identifier according to the classification provider </li> <li>resource_id: identifies the classification provider (see below) </li> <li>page_id: EOL taxon concept identifier; official, for sharing </li> <li>preferred_canonical_for_page: canonical name preferred by EOL for this taxon concept </li> </ul> <p>commas within entries are "escaped, by, quoting", and quotes-within-quotes are ""double quoted""</p> <p>resource_ids, their names and descriptions, are available at: <a href="https://eol.org/resources.json">https://eol.org/resources.json </a></p> <p>To view one at a time: https://eol.org/resources/[enter ID here] </p> <p>There is also a summary file with resources ids, links, and resource names here: <a href="https://github.com/KatjaSchulz/eolResources">https://github.com/KatjaSchulz/eolResources</a></p> <p>And there is a smaller mapping file just for the major EOL classification sources: <a href="../doi/10.5281/zenodo.13769681">EOL taxon identifier map</a></p>
Wikidata Taxon Items in JSON Lines Format hash://sha256/13ffa9679bae381aa5914d810638fb5a0c75d71f5f7d47f38b3c00d750c88b9c hash://md5/bdcc99bfedfd34abdfdd3802182f225c
<p>Wikidata contains information about taxonomic names, and these taxonomic names are key to integrating biodiversity datasets across different platforms, datasets and institutions. </p> <h2>Content</h2> <table> <tbody> <tr> <td><strong>filename/alias</strong></td> <td><strong>content ids</strong></td> </tr> <tr> <td>wikidata-taxon.json.bz2</td> <td> <p><a href="https://linker.bio/hash://sha256/a7592b72c9013d67d655b6ea5d1f4f67f2057dc5b5ee52578a07f58fea835580">hash://sha256/</a><a href="https://zenodo.org/api/records/13920038/draft/files/701a1382e304a6b1bb38fe828d82f7b8b562c77f918f33097966e38bacf0b2e7/content" target="_blank" rel="noopener noreferrer">701a1382e304a6b1bb38fe828d82f7b8b562c77f918f33097966e38bacf0b2e7</a></p> <p><a href="https://linker.bio/hash://md5/d5bad3553470506f3bde383566a5dea3">hash://md5/d5bad3553470506f3bde383566a5dea3</a></p> </td> </tr> <tr> <td>wikidata-taxa.sh</td> <td> <p><a href="https://linker.bio/hash://sha256/6f4fac44054d54ec3006d091ba702f872b3f4d013628add98fcca08a3b768962">hash://sha256/6f4fac44054d54ec3006d091ba702f872b3f4d013628add98fcca08a3b768962</a></p> <p><a href="https://linker.bio/hash://md5/1d80083d498d61c8b63fbd46d51f7c5c">hash://md5/1d80083d498d61c8b63fbd46d51f7c5c</a></p> </td> </tr> <tr> <td>Q140.json (example)</td> <td> <p><a href="https://linker.bio/hash://md5/44ab0031091fb96caa063e3fe41a85f2">hash://md5/44ab0031091fb96caa063e3fe41a85f2</a></p> </td> </tr> </tbody> </table> <h2>Provenance</h2> <h3>for humans</h3> <p>This dataset contains a subset of Wikidata items referencing the taxonomic name concept https://www.wikidata.org/wiki/Q16521 and is expressed in JSON Lines format. </p> <p>An example of such item is https://wikidata.org/wiki/Q140, an item that describes the taxonomic name associated with <em>Panthera leo</em>, commonly known as Lion (English), León (Spanish), or 狮子 (Chinese). You can find a "pretty" printed example of Q140 in the file "Q140.json" included in this publication. The first 10 lines of "Q140.json" are shown below: </p> <pre><code>{ "type": "item", "id": "Q140", "labels": { "fr": { "language": "fr", "value": "lion" }, "it": { "language": "it", ...</code></pre> <p> </p> <p>The reason for creating a wikidata subset is because all of wikidata (~85G) didn't fit in Zenodo. </p> <h3>for machines</h3> <p>This dataset was generated using the script below with content id <a href="https://linker.bio/hash://sha256/6f4fac44054d54ec3006d091ba702f872b3f4d013628add98fcca08a3b768962">hash://sha256/6f4fac44054d54ec3006d091ba702f872b3f4d013628add98fcca08a3b768962</a> or <a href="https://linker.bio/hash://md5/1d80083d498d61c8b63fbd46d51f7c5c">hash://md5/1d80083d498d61c8b63fbd46d51f7c5c</a></p> <pre><code> 1 #!/bin/bash 2 # 3 # streams Wikidata taxon items (or items containing https://www.wikidata.org/wiki/Q16521) 4 # from latest data dump in line json (one json object per line) 5 # 6 curl --silent "https://dumps.wikimedia.org/wikidatawiki/entities/latest-all.json.bz2"\ 7 | bunzip2\ 8 | grep -E "Q16521[^0-9]"\ 9 | sed 's/,$//g'\ 10 | bzip2 </code></pre> <p>The script first downloads a recent copy of all wikidata entities in bzip2 compressed format (line 6), decompresses them (line 7), selects only lines containing "Q16521" (line 8), removes any trailing commas (line 9), and recompresses the output. With this, the output contains wikidata items/entities as described earlier.</p> <p>Preston, a biodiversity data tracker, was used to (a) track the script, as well as (b) recording a script execution and (c) tracking the outcome by running :</p> <pre><code>#!/bin/bash # # run the script with id hash://sha256/13ff... # preston bash\ --remote https://linker.bio\ -c "hash://sha256/13ffa9679bae381aa5914d810638fb5a0c75d71f5f7d47f38b3c00d750c88b9c" </code></pre> <p>The recording of this process is identified with hash://sha256/13ffa9679bae381aa5914d810638fb5a0c75d71f5f7d47f38b3c00d750c88b9c and hash://md5/bdcc99bfedfd34abdfdd3802182f225c , and can be reconstructed using </p> <pre><code>preston ls\ --remote https://linker.bio/,https://zenodo.org/records/13920038/files\ --anchor hash://sha256/13ffa9679bae381aa5914d810638fb5a0c75d71f5f7d47f38b3c00d750c88b9c</code></pre> <p>Which is expected to produce:</p> <pre><code><https://preston.guoda.bio> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#SoftwareAgent> <urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> .<br><https://preston.guoda.bio> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Agent> <urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> .<br><https://preston.guoda.bio> <http://purl.org/dc/terms/description> "Preston is a software program that finds, archives and provides access to biodiversity datasets."@en <urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> .<br><urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> <urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> .<br><urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> <http://purl.org/dc/terms/description> "Executes script and captures stdout"@en <urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> .<br><urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> <http://www.w3.org/ns/prov#startedAtTime> "2024-10-10T16:37:36.659Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> <urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> .<br><urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> <http://www.w3.org/ns/prov#wasStartedBy> <https://preston.guoda.bio> <urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> .<br><https://doi.org/10.5281/zenodo.1410543> <http://www.w3.org/ns/prov#usedBy> <urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> <urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> .<br><https://doi.org/10.5281/zenodo.1410543> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/dc/dcmitype/Software> <urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> .<br><https://doi.org/10.5281/zenodo.1410543> <http://purl.org/dc/terms/bibliographicCitation> "Jorrit Poelen, Icaro Alzuru, & Michael Elliott. 2018-2024. Preston: a biodiversity dataset tracker (Version 0.9.9-SNAPSHOT) [Software]. Zenodo. https://doi.org/10.5281/zenodo.1410543"@en <urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> .<br><urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Entity> <urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> .<br><urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/dc/terms/description> "A biodiversity dataset graph archive."@en <urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> .<br><hash://sha256/e76276c283090381fc4b3efe28fc61c28f5bf03db0f3743f7178b999ebccada2> <http://www.w3.org/ns/prov#usedBy> <urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> <urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> .<br><hash://sha256/6f4fac44054d54ec3006d091ba702f872b3f4d013628add98fcca08a3b768962> <http://purl.org/dc/elements/1.1/format> "text/x-shellscript" .<br><urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> <http://www.w3.org/ns/prov#used> <hash://sha256/6f4fac44054d54ec3006d091ba702f872b3f4d013628add98fcca08a3b768962> .<br><urn:uuid:7ecf1c84-0438-4224-8909-0804028cf3f6> <http://www.w3.org/ns/prov#wasGeneratedBy> <urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440> .<br><hash://sha256/701a1382e304a6b1bb38fe828d82f7b8b562c77f918f33097966e38bacf0b2e7> <http://www.w3.org/ns/prov#wasGeneratedBy> <urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b> <urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b> .<br><hash://sha256/701a1382e304a6b1bb38fe828d82f7b8b562c77f918f33097966e38bacf0b2e7> <http://www.w3.org/ns/prov#qualifiedGeneration> <urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b> <urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b> .<br><urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b> <http://www.w3.org/ns/prov#generatedAtTime> "2024-10-11T02:08:03.739Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> <urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b> .<br><urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Generation> <urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b> .<br><urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b> <http://www.w3.org/ns/prov#used> <urn:uuid:7ecf1c84-0438-4224-8909-0804028cf3f6> <urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b> .<br><urn:uuid:7ecf1c84-0438-4224-8909-0804028cf3f6> <http://purl.org/pav/hasVersion> <hash://sha256/701a1382e304a6b1bb38fe828d82f7b8b562c77f918f33097966e38bacf0b2e7> <urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b> .<br><https://preston.guoda.bio> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#SoftwareAgent> <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> . <https://preston.guoda.bio> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Agent> <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> . <https://preston.guoda.bio> <http://purl.org/dc/terms/description> "Preston is a software program that finds, archives and provides access to biodiversity datasets."@en <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> . <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> . <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> <http://purl.org/dc/terms/description> "Executes script and captures stdout"@en <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> . <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> <http://www.w3.org/ns/prov#startedAtTime> "2024-06-22T10:40:12.016Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> . <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> <http://www.w3.org/ns/prov#wasStartedBy> <https://preston.guoda.bio> <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> . <https://doi.org/10.5281/zenodo.1410543> <http://www.w3.org/ns/prov#usedBy> <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> . <https://doi.org/10.5281/zenodo.1410543> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/dc/dcmitype/Software> <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> . <https://doi.org/10.5281/zenodo.1410543> <http://purl.org/dc/terms/bibliographicCitation> "Jorrit Poelen, Icaro Alzuru, & Michael Elliott. 2021. Preston: a biodiversity dataset tracker (Version 0.8.4) [Software]. Zenodo. https://doi.org/10.5281/zenodo.1410543"@en <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> . <urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Entity> <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> . <urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/dc/terms/description> "A biodiversity dataset graph archive."@en <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> . <hash://sha256/6f4fac44054d54ec3006d091ba702f872b3f4d013628add98fcca08a3b768962> <http://purl.org/dc/elements/1.1/format> "text/x-shellscript" . <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> <http://www.w3.org/ns/prov#used> <hash://sha256/6f4fac44054d54ec3006d091ba702f872b3f4d013628add98fcca08a3b768962> . <urn:uuid:6fa51a99-a137-4387-90b1-23589d7b60ae> <http://www.w3.org/ns/prov#wasGeneratedBy> <urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758> . <hash://sha256/a7592b72c9013d67d655b6ea5d1f4f67f2057dc5b5ee52578a07f58fea835580> <http://www.w3.org/ns/prov#wasGeneratedBy> <urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e> <urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e> . <hash://sha256/a7592b72c9013d67d655b6ea5d1f4f67f2057dc5b5ee52578a07f58fea835580> <http://www.w3.org/ns/prov#qualifiedGeneration> <urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e> <urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e> . <urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e> <http://www.w3.org/ns/prov#generatedAtTime> "2024-06-22T19:01:55.863Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> <urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e> . <urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Generation> <urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e> . <urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e> <http://www.w3.org/ns/prov#used> <urn:uuid:6fa51a99-a137-4387-90b1-23589d7b60ae> <urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e> . <urn:uuid:6fa51a99-a137-4387-90b1-23589d7b60ae> <http://purl.org/pav/hasVersion> <hash://sha256/a7592b72c9013d67d655b6ea5d1f4f67f2057dc5b5ee52578a07f58fea835580> <urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e> . </code></pre>
Generated Wikidata Subset for Taxons based on dump: 20201102-all
<p>Source file: GeneTaxon_wikidata-20201102-all.ttl.gz</p> <p>ShEx: https://github.com/kg-subsetting/paper-wikidata-subsetting-2023/blob/master/flexibility-experiments/genes%2Btaxons/GeneTaxon.shex</p> <p>More information: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation</p>
Generated Wikidata Subset for Taxons based on dump: GeneTaxon_wikidata-20190121-all
<p>Source file: GeneTaxon_wikidata-20190121-all.ttl.gz</p> <p>ShEx: https://github.com/kg-subsetting/paper-wikidata-subsetting-2023/blob/master/flexibility-experiments/genes%2Btaxons/GeneTaxon.shex</p> <p>More information: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation</p>
Generated Wikidata Subset for Taxons based on dump: GeneTaxon_wikidata-20180115-all
<p>Source file: GeneTaxon_wikidata-20180115-all.ttl.gz</p> <p>ShEx: https://github.com/kg-subsetting/paper-wikidata-subsetting-2023/blob/master/flexibility-experiments/genes%2Btaxons/GeneTaxon.shex</p> <p>More information: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation</p>
Generated Wikidata Subset for Taxons based on dump: 20170821-all
<p>Source file: GeneTaxon_wikidata-20170821-all.ttl.gz</p> <p>ShEx: https://github.com/kg-subsetting/paper-wikidata-subsetting-2023/blob/master/flexibility-experiments/genes%2Btaxons/GeneTaxon.shex</p> <p>More information: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation</p>
Generated Wikidata Subset for Taxons based on dump: wikidata-20150601-all
<p>Source file: GeneTaxon_wikidata-20150601-all.ttl.gz</p> <p>ShEx: https://github.com/kg-subsetting/paper-wikidata-subsetting-2023/blob/master/flexibility-experiments/genes%2Btaxons/GeneTaxon.shex</p> <p>More information: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation</p>
Generated Wikidata Subset for Taxons based on dump: 20160613-all
<p>Source file: GeneTaxon_wikidata-20160613-all.ttl.gz</p> <p>ShEx: https://github.com/kg-subsetting/paper-wikidata-subsetting-2023/blob/master/flexibility-experiments/genes%2Btaxons/GeneTaxon.shex</p> <p>More information: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation</p>
Generated Wikidata Subset for Taxons based on dump: 20220630-all
<p>Source file: GeneTaxon_wikidata-20220630-all.ttl.gz</p> <p>ShEx: https://github.com/kg-subsetting/paper-wikidata-subsetting-2023/blob/master/flexibility-experiments/genes%2Btaxons/GeneTaxon.shex</p> <p>More information: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation</p>
Generated Wikidata Subset for Taxons based on dump: 20210531-all
<p>Source file: GeneTaxon_wikidata-20210531-all.ttl.gz</p> <p>ShEx: https://github.com/kg-subsetting/paper-wikidata-subsetting-2023/blob/master/flexibility-experiments/genes%2Btaxons/GeneTaxon.shex</p> <p>More information: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation</p>
Figure 18 in Expanded concept and revised taxonomy of the milliped family Xystodesmidae Cook, 1895 (Polydesmida: Leptodesmidea: Xystodesmoidea): incorporations of Euryuridae Pocock, 1909 and Eurymerodesmidae Causey, 1951, taxon revivals/proposals/ transferrals, and a distributional update
Figure 18. The East-Nearctic Region of Xystodesmidae. The eastern- and northernmost dots denote localities of the two Appalachian species of Rhysodesmus; the dot in Texas within the black line signifies the northernmost locality of R. texicolens (Chamberlin), San Diego, Duval Co. The arrow indicates Bald Head Island, NC, occupied by Apheloria (Xystodesminae: Apheloriini).
Figure 1 in Expanded concept and revised taxonomy of the milliped family Xystodesmidae Cook, 1895 (Polydesmida: Leptodesmidea: Xystodesmoidea): incorporations of Euryuridae Pocock, 1909 and Eurymerodesmidae Causey, 1951, taxon revivals/proposals/ transferrals, and a distributional update
Figure 1. Distribution of Euryurinae plotted against the maximal extent of the Cretaceous Western Inland Sea. Euryurina (Euryurini, red), Eurymerodesmina (Eurymerodesmini, black), Nannariina (Eurymerodesmini, green). The red line, Euryurina, in eastern North Carolina and southcentral Virginia connects disparate peripheral localities; the area of greatest euryurinan concentration is circumscribed by the red dots.
Figures 8–15 in Expanded concept and revised taxonomy of the milliped family Xystodesmidae Cook, 1895 (Polydesmida: Leptodesmidea: Xystodesmoidea): incorporations of Euryuridae Pocock, 1909 and Eurymerodesmidae Causey, 1951, taxon revivals/proposals/ transferrals, and a distributional update
Figures 8–15. Eurymerodesmini gonopodal tel-/acropodites; 8–11, Nannariina. 8) telopodite of Nannaria cayugae Chamberlin, Tompkins Co., NY. 9) acropodite of the same. 10) telopodite of Mimuloria castanea (McNeill), Monroe Co., IN. 11) the same of M. d. dilatata Hennen and Shelley, Marshall Co., TN. 12–15, Eurymerodesmina. 12) Eurymerodesmus varius louisianae Chamberlin, Natchitoches Par., LA. 13) acropodite of a second individual from the same locality. 14) the same, Columbia Co., AR. 15) E. v. varius (McNeill), Escambia Co., FL. Figures 8–9 reprinted from Chamberlin (1949) with permission from the Biological Society of Washington. Figures 10–11 reprinted from Hennen and Shelley (2015) with permission of the Center for Systematic Entomology. Figures 12–15 reprinted from Shelley (1990a) with permission of the American Entomological Society.
Data from: Multi-taxon inventory reveals highly consistent biodiversity responses to ecospace variation
Amidst the global biodiversity crisis, identifying general principles for variation in biodiversity remains a key challenge. Scientific consensus is limited to a few macroecological rules, such as species richness increasing with area, which provide limited guidance for conservation. In fact, few agreed ecological principles apply at the scale of sites or reserve management, partly because most community-level studies are restricted to single habitat types and species groups. We used the recently proposed ecospace framework and a comprehensive data set for aggregating environmental variation to predict multi-taxon diversity. We studied richness of plants, fungi, and arthropods in 130 sites representing the major terrestrial habitat types in Denmark. We found the abiotic environment (ecospace position) to be pivotal for the richness of primary producers (vascular plants, mosses, and lichens) and, more surprisingly, little support for ecospace continuity as a driver. A peak in richness at intermediate productivity adds new empirical evidence to a long-standing debate over biodiversity responses to productivity. Finally, we discovered a dominant and positive response of fungi and insect richness to organic matter accumulation and diversification (ecospace expansion). Two simple models of producer and consumer richness accounted for 77 % of the variation in multi-taxon species richness suggesting a significant potential for generalization beyond individual species responses. Our study widens the traditional conservation focus on vegetation and vertebrate populations unravelling the importance of diversification of carbon resources for diverse heterotrophs, such as fungi and insects.
Data from: Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics
1. The amount and patterns of phylodiversity in a community are often used to draw inferences about the local and historical factors affecting community assembly and can be used to prioritize communities and locations for conservation. Because measures of phylodiversity are based on the topology and branch lengths of phylogenetic trees, which are affected by the number and diversity of taxa in the tree, these analyses may be sensitive to changes in taxon sampling and tree reconstruction methods. 2. To investigate the effects of taxon sampling and tree reconstruction methods on measures of phylodiversity, we investigated the community phylogenetics of the Ordway-Swisher Biological Station (Florida), which is home to over 600 species of vascular plants. We studied the effects of 1) the number of taxa included in the regional phylogeny; 2) random vs. targeted sampling of species to assemble the regional species pool; 3) including only species from specific clades rather than broad sampling; 4) using trees reconstructed directly for the taxa under study compared to trees pruned from a larger reconstructed tree; and 5) using phylograms compared to chronograms. 3. We found that including more taxa in a study increases the likelihood of observing significantly non-random phylogenetic patterns. However, there were no consistent trends in the phylodiversity patterns based on random taxon sampling compared to targeted sampling, or within individual clades compared to the complete dataset. Using pruned and reconstructed phylogenies resulted in similar patterns of phylodiversity, while chronograms in some cases led to significantly different results from phylograms. 4. The methods commonly used in community phylogenetic studies can significantly impact the results, potentially influencing both inferences of community assembly and conservation decisions. We highlight the need for both careful selection of methods in community phylogenetic studies and appropriate interpretation of results, depending on the specific questions to be addressed.
Figure 7 in New eriophyoid mites (Acari: Prostigmata: Eriophyoidea) from cultivated plants from northeastern Brazil, including the second taxon in the Prothricinae
Figure 7. Tegolophus indica. CGM, coxigenital region, male; D, dorsal habitus, female; DS, detail of prodorsal shield; em, empodium, leg I, female; IG,. internal genital structures, female; L1, leg I, female; L2, leg II, female; V, ventral habitus, female.
ScienceDex guides
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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.