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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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  <identifier identifierType="DOI">10.5281/zenodo.1112342</identifier>
      <creatorName>François Munoz</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0002-2885-2518</nameIdentifier>
      <affiliation>University Grenoble-Alpes, LECA, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France</affiliation>
      <creatorName>Guillaume Fried</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0002-3653-195X</nameIdentifier>
      <affiliation>Anses, Laboratoire de la Santé des Végétaux, Unité Entomologie et Plantes invasives, Montpellier, France</affiliation>
      <creatorName>Laura Armengot</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0002-9820-9667</nameIdentifier>
      <affiliation>FiBL, Research Institute of Organic Agriculture</affiliation>
      <creatorName>Bérenger Bourgeois</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0002-2885-2518</nameIdentifier>
      <affiliation>Agroécologie, AgroSup Dijon, INRA</affiliation>
      <creatorName>Vincent Bretagnolle</creatorName>
      <affiliation>Centre d'Etudes Biologiques de Chizé</affiliation>
      <creatorName>Joël Chadoeuf</creatorName>
      <creatorName>Lucie Mahaut</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0002-5825-3807</nameIdentifier>
      <affiliation>Agroécologie, AgroSup Dijon, INRA</affiliation>
      <creatorName>Christine Plumejeaud</creatorName>
      <creatorName>Jonathan Storkey</creatorName>
      <affiliation>Rothamsted Research</affiliation>
      <creatorName>Cyrille Violle</creatorName>
      <affiliation>CNRS, Centre d'Ecologie Fonctionnelle et Evolutive</affiliation>
      <creatorName>Sabrina Gaba</creatorName>
      <affiliation>Agroécologie, AgroSup Dijon, INRA</affiliation>
    <title>Database of weeds in cultivation fields of France and UK, with ecological and biogeographical information</title>
    <subject>species pool</subject>
    <subject>cultivated fields</subject>
    <subject>biodiversity decline</subject>
    <subject>sampling strategies</subject>
    <date dateType="Issued">2017-12-18</date>
  <resourceType resourceTypeGeneral="Dataset"/>
    <alternateIdentifier alternateIdentifierType="url"></alternateIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.1112341</relatedIdentifier>
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    <rights rightsURI="">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
    <description descriptionType="Abstract">&lt;p&gt;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.&lt;br&gt;
The database is a CSV file in which the columns are separated with comma, and the decimal sign is &amp;quot;.&amp;quot;.&lt;br&gt;
It can be imported in R with the command &amp;quot;tax.discoweed &amp;lt;- read.csv(&amp;quot;tax.discoweed_18Dec2017_zenodo.csv&amp;quot;, header=T, sep=&amp;quot;,&amp;quot;,&amp;nbsp; dec=&amp;quot;.&amp;quot;, stringsAsFactors = F)&amp;quot;&lt;/p&gt;

&lt;p&gt;Taxonomic information is based on TaxRef v10 (Gargominy et al. 2016),&lt;br&gt;
- &amp;#39;taxref10.CD_REF&amp;#39; = code of the accepted name of the taxon in TaxRef,&lt;br&gt;
- &amp;#39;binome.discoweed&amp;#39; = corresponding latine name,&lt;br&gt;
- &amp;#39;family&amp;#39; = family name (following APG III),&lt;br&gt;
- &amp;#39;taxo&amp;#39; = taxonomic rank of the taxon, either &amp;#39;binome&amp;#39; (species level) or &amp;#39;infra&amp;#39; (infraspecific level),&lt;br&gt;
- &amp;#39;binome.discoweed.noinfra&amp;#39; = latine name of the superior taxon at species level (different from &amp;#39;binome.discoweed&amp;#39; for infrataxa),&lt;br&gt;
- &amp;#39;taxref10.CD_REF.noinfra&amp;#39; = code of the accepted name of the superior taxon at species level.&lt;/p&gt;

&lt;p&gt;The presence of each taxon in one or several of the following data sources is reported:&lt;br&gt;
- Species list from a reference flora (observations in cultivated fields over the long term, without sampling protocol),&lt;br&gt;
* &amp;#39;jauzein&amp;#39; =&amp;nbsp; national and comprehensive flora in France (Jauzein 1995),&lt;br&gt;
- Species lists from plot-based inventories in cultivated fields,&lt;br&gt;
* &amp;#39;za&amp;#39; = regional survey in &amp;#39;Zone Atelier Plaine &amp;amp; Val de S&amp;egrave;vre&amp;#39; in SW France (Gaba et al. 2010),&lt;br&gt;
* &amp;#39;biovigilance&amp;#39; = national survey of cultivated fields in France (Biovigilance, Fried et al. 2008),&lt;br&gt;
* &amp;#39;fse&amp;#39; = Farm Scale Evaluations in England and Scotland, UK (Perry, Rothery, Clark et al., 2003),&lt;br&gt;
* &amp;#39;farmbio&amp;#39; = Farm4Bio survey, farms in south east and south west of England, UK (Holland et al., 2013)&lt;br&gt;
- Reference list of segetal species (species specialist of arable fields),&lt;br&gt;
* &amp;#39;cambacedes&amp;#39; = reference list in France (Cambacedes et al. 2002)&lt;/p&gt;

&lt;p&gt;Life form information is extracted from Julve (2014) and provided in the column &amp;#39;lifeform&amp;#39;.&lt;br&gt;
The 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.&lt;/p&gt;

&lt;p&gt;Biogeographic zones are also extracted from Julve (2014) and provided in the column &amp;#39;biogeo&amp;#39;.&lt;br&gt;
The main categories are &amp;#39;atlantic&amp;#39;, &amp;#39;circumboreal&amp;#39;, &amp;#39;cosmopolitan, &amp;#39;Eurasian&amp;#39;, &amp;#39;European&amp;#39;, &amp;#39;holarctic&amp;#39;, &amp;#39;introduced&amp;#39;, &amp;#39;Mediterranean&amp;#39;, &amp;#39;orophyte&amp;#39; and &amp;#39;subtropical&amp;#39;.&lt;br&gt;
In some cases, a precision is included within brackets after the category name. For instance, &amp;#39;introduced(North America)&amp;#39; indicates that the taxon is introduced from North America.&lt;br&gt;
In addition, some taxa are local endemics (&amp;#39;Aquitanian&amp;#39;, &amp;#39;Catalan&amp;#39;, &amp;#39;Corsican&amp;#39;, &amp;#39;corso-sard&amp;#39;, &amp;#39;ligure&amp;#39;, &amp;#39;Provencal&amp;#39;).&lt;br&gt;
A single taxon is classified &amp;#39;arctic-alpine&amp;#39;.&lt;/p&gt;

&lt;p&gt;Red list status of weed taxa is derived for France and UK:&lt;br&gt;
- &amp;#39;red.FR&amp;#39; is the status following the assessment of the French National Museum of Natural History (2012),&lt;br&gt;
- &amp;#39;red.UK&amp;#39; is based on the Red List of vascular plants of Cheffings and Farrell (2005), last updated in 2006.&lt;br&gt;
The categories are coded following the IUCN nomenclature.&lt;/p&gt;

&lt;p&gt;A habitat index is provided in column &amp;#39;module&amp;#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).&lt;br&gt;
The main habitat categories of weeds are coded following the Divgrass classification,&lt;br&gt;
- 1 = Dry calcareous grasslands&lt;br&gt;
- 3 = Mesic grasslands&lt;br&gt;
- 5 = Ruderal and trampled grasslands&lt;br&gt;
- 9 = Mesophilous and nitrophilous fringes (hedgerows, forest edges...)&lt;br&gt;
Taxa belonging to other habitats in Divgrass are coded 99, while the taxa absent from Divgrass have a &amp;#39;NA&amp;#39; value.&lt;/p&gt;

&lt;p&gt;Two indexes of ecological specialization are provided based on the frequency of weed taxa in different habitats of the Divgrass database.&lt;br&gt;
The indexes are network-based metrics proposed by Guimera and Amaral (2005),&lt;br&gt;
- 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),&lt;br&gt;
- 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.&lt;/p&gt;</description>
    <description descriptionType="Other">{"references": ["Cambec\u00e8des, J., Largier, G. &amp; Lombard, A. (2012) Plan national d'actions en faveur des plantes messicoles 2012-2017. Conservatoire botanique national des Pyr\u00e9n\u00e9es et de Midi-Pyr\u00e9n\u00e9es \u2013 F\u00e9d\u00e9ration des Conservatoires botaniques nationaux \u2013 Minist\u00e8re de l'\u00c9cologie, du D\u00e9veloppement durable.", "Carboni, M., M\u00fcnkem\u00fcller, T., Lavergne, S., Choler, P., Borgy, B., Violle, C., Essl, F., Roquet, C., Munoz, F., Consortium, T.D. &amp; Thuiller, W. (2016) What it takes to invade grassland ecosystems: traits, introduction history and filtering processes. Ecology Letters 19, 219-229.", "Cheffings, C.M. &amp; Farrell, L. (Eds), Dines, T.D., Jones, R.A., Leach, S.J., McKean, D.R., Pearman, D.A., Preston, C.D., Rumsey, F.J., Taylor, I. 2005. The Vascular Plant Red Data List for Great Britain. Species Status 7: 1-116. Joint Nature Conservation Committee, Peterborough.", "Fried, G., Norton, L.R. &amp; Reboud, X. (2008) Environmental and management factors determining weed species composition and diversity in France. Agriculture, Ecosystems &amp; Environment 128, 68-76.", "Gaba, S., Chauvel, B., Dessaint, F., Bretagnolle, V. &amp; Petit, S. (2010) Weed species richness in winter wheat increases with landscape heterogeneity. Agriculture, Ecosystems &amp; Environment 138, 318-323.", "Gargominy, O., Tercerie, S., R\u00e9gnier, C., Ramage, T., Dupont, P., Vandel, E., Daszkiewicz, P., L\u00e9v\u00eaque, A., Leblond, S., De Massary, J.-C., Horellou, A., No\u00ebl, P., Noblecourt, T., Comolet, J., Touroult, J., Barbut, J., Rome, Q., Bernard, J.-F., Bock, B., Mal\u00e9cot, V., Boullet, V., Robbert Gradstein, S., Lavocat Bernard, E., &amp; Ah-Peng, C. (2016) TAXREF v10.0, r\u00e9f\u00e9rentiel taxonomique pour la France. Mus\u00e9um national d'Histoire naturelle, Paris.", "Guimera, R. &amp; Amaral, L.A.N. (2005) Cartography of complex networks: modules and universal roles. Journal of Statistical Mechanics: Theory and Experiment 2005, P02001.", "Holland, J.M., Storkey, J., Lutman, P.J.W., Henderson, I. &amp; Orson, J. (2013) The Farm4Bio project: managing uncropped land for biodiversity. Aspects of Applied Biology 118, 89-99.", "Jauzein, P. (1995) Flore des champs cultiv\u00e9s. Editions Quae.", "Julve, P. (2014) Baseflor. Index botanique, \u00e9cologique et chorologique de la flore de France. Version: 2014.", "Perry, J.N., Rothery, P., Clark, S.J., Heard, M.S. &amp; Hawes, C. (2003) Design, analysis and statistical power of the Farm\u2010Scale Evaluations of genetically modified herbicide\u2010tolerant crops. Journal of Applied Ecology 40, 17-31.", "UICN  France, FCBN &amp; MNHN (2012) La  Liste  Rouge  des  esp\u00e8ces  menac\u00e9es  en  France.  Chapitre  Flore  vasculaire de  France  m\u00e9tropolitaine  :  premiers  r\u00e9sultats  pour  1  000  esp\u00e8ces,  sous-esp\u00e8ces  et  vari\u00e9t\u00e9s.", "Violle, C., Choler, P., Borgy, B., Garnier, E., Amiaud, B., Debarros, G., Diquelou, S., Gachet, S., Joliver, C., Kattge, J., Lavorel, S., Lemauviel-Lavenant, S., Loranger, J., Mikolajczak, A., Munoz, F., Olivier, J. &amp; Viovy, N. (2015) Vegetation Ecology meets Ecosystem Science: permanent grasslands as a functional biogeography case study. Science of the Total Environment 534, 43-51."]}</description>
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