Dataset Open Access

Database of weeds in cultivation fields of France and UK, with ecological and biogeographical information

François Munoz; Guillaume Fried; Laura Armengot; Bérenger Bourgeois; Vincent Bretagnolle; Joël Chadoeuf; Lucie Mahaut; Christine Plumejeaud; Jonathan Storkey; Cyrille Violle; Sabrina Gaba


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{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.1112342", 
  "language": "eng", 
  "title": "Database of weeds in cultivation fields of France and UK, with ecological and biogeographical information", 
  "issued": {
    "date-parts": [
      [
        2017, 
        12, 
        18
      ]
    ]
  }, 
  "abstract": "<p>The database includes a list of 1577 weed plant taxa found in cultivated fields of France and UK, along with basic ecological and biogeographical information.<br>\nThe database is a CSV file in which the columns are separated with comma, and the decimal sign is &quot;.&quot;.<br>\nIt can be imported in R with the command &quot;tax.discoweed &lt;- read.csv(&quot;tax.discoweed_18Dec2017_zenodo.csv&quot;, header=T, sep=&quot;,&quot;,&nbsp; dec=&quot;.&quot;, stringsAsFactors = F)&quot;</p>\n\n<p>Taxonomic information is based on TaxRef v10 (Gargominy et al. 2016),<br>\n- &#39;taxref10.CD_REF&#39; = code of the accepted name of the taxon in TaxRef,<br>\n- &#39;binome.discoweed&#39; = corresponding latine name,<br>\n- &#39;family&#39; = family name (following APG III),<br>\n- &#39;taxo&#39; = taxonomic rank of the taxon, either &#39;binome&#39; (species level) or &#39;infra&#39; (infraspecific level),<br>\n- &#39;binome.discoweed.noinfra&#39; = latine name of the superior taxon at species level (different from &#39;binome.discoweed&#39; for infrataxa),<br>\n- &#39;taxref10.CD_REF.noinfra&#39; = code of the accepted name of the superior taxon at species level.</p>\n\n<p>The presence of each taxon in one or several of the following data sources is reported:<br>\n- Species list from a reference flora (observations in cultivated fields over the long term, without sampling protocol),<br>\n* &#39;jauzein&#39; =&nbsp; national and comprehensive flora in France (Jauzein 1995),<br>\n- Species lists from plot-based inventories in cultivated fields,<br>\n* &#39;za&#39; = regional survey in &#39;Zone Atelier Plaine &amp; Val de S&egrave;vre&#39; in SW France (Gaba et al. 2010),<br>\n* &#39;biovigilance&#39; = national survey of cultivated fields in France (Biovigilance, Fried et al. 2008),<br>\n* &#39;fse&#39; = Farm Scale Evaluations in England and Scotland, UK (Perry, Rothery, Clark et al., 2003),<br>\n* &#39;farmbio&#39; = Farm4Bio survey, farms in south east and south west of England, UK (Holland et al., 2013)<br>\n- Reference list of segetal species (species specialist of arable fields),<br>\n* &#39;cambacedes&#39; = reference list in France (Cambacedes et al. 2002)</p>\n\n<p>Life form information is extracted from Julve (2014) and provided in the column &#39;lifeform&#39;.<br>\nThe classification follows a simplified Raunkiaer classification (therophyte, hemicryptophyte, geophyte, phanerophyte-chamaephyte and liana). Regularly biannual plants are included in hemicryptophytes, while plants that can be both annual and biannual are assigned to therophytes.</p>\n\n<p>Biogeographic zones are also extracted from Julve (2014) and provided in the column &#39;biogeo&#39;.<br>\nThe main categories are &#39;atlantic&#39;, &#39;circumboreal&#39;, &#39;cosmopolitan, &#39;Eurasian&#39;, &#39;European&#39;, &#39;holarctic&#39;, &#39;introduced&#39;, &#39;Mediterranean&#39;, &#39;orophyte&#39; and &#39;subtropical&#39;.<br>\nIn some cases, a precision is included within brackets after the category name. For instance, &#39;introduced(North America)&#39; indicates that the taxon is introduced from North America.<br>\nIn addition, some taxa are local endemics (&#39;Aquitanian&#39;, &#39;Catalan&#39;, &#39;Corsican&#39;, &#39;corso-sard&#39;, &#39;ligure&#39;, &#39;Provencal&#39;).<br>\nA single taxon is classified &#39;arctic-alpine&#39;.</p>\n\n<p>Red list status of weed taxa is derived for France and UK:<br>\n- &#39;red.FR&#39; is the status following the assessment of the French National Museum of Natural History (2012),<br>\n- &#39;red.UK&#39; is based on the Red List of vascular plants of Cheffings and Farrell (2005), last updated in 2006.<br>\nThe categories are coded following the IUCN nomenclature.</p>\n\n<p>A habitat index is provided in column &#39;module&#39;, derived from a network-based analysis of plant communities in open herbaceous vegetation in France (Divgrass database, Violle et al. 2015, Carboni et al. 2016).<br>\nThe main habitat categories of weeds are coded following the Divgrass classification,<br>\n- 1 = Dry calcareous grasslands<br>\n- 3 = Mesic grasslands<br>\n- 5 = Ruderal and trampled grasslands<br>\n- 9 = Mesophilous and nitrophilous fringes (hedgerows, forest edges...)<br>\nTaxa belonging to other habitats in Divgrass are coded 99, while the taxa absent from Divgrass have a &#39;NA&#39; value.</p>\n\n<p>Two indexes of ecological specialization are provided based on the frequency of weed taxa in different habitats of the Divgrass database.<br>\nThe indexes are network-based metrics proposed by Guimera and Amaral (2005),<br>\n- c = coefficient of participation, i.e., the propensity of taxa to be present in diverse habitats, from 0 (specialist, present in a single habitat) to 1 (generalist equally represented in all habitats),<br>\n- z = within-module degree, i.e., a standardized measure of the frequency of a taxon in its habitat; it is negatve when the taxon is less frequent than average in this habitat, and positive otherwise; the index scales as a number of standard deviations from the mean.</p>", 
  "author": [
    {
      "family": "Fran\u00e7ois Munoz"
    }, 
    {
      "family": "Guillaume Fried"
    }, 
    {
      "family": "Laura Armengot"
    }, 
    {
      "family": "B\u00e9renger Bourgeois"
    }, 
    {
      "family": "Vincent Bretagnolle"
    }, 
    {
      "family": "Jo\u00ebl Chadoeuf"
    }, 
    {
      "family": "Lucie Mahaut"
    }, 
    {
      "family": "Christine Plumejeaud"
    }, 
    {
      "family": "Jonathan Storkey"
    }, 
    {
      "family": "Cyrille Violle"
    }, 
    {
      "family": "Sabrina Gaba"
    }
  ], 
  "version": "1.0.0", 
  "type": "dataset", 
  "id": "1112342"
}
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