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


MARC21 XML Export

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    <subfield code="x">Cambecèdes, J., Largier, G. &amp; Lombard, A. (2012) Plan national d'actions en faveur des plantes messicoles 2012-2017. Conservatoire botanique national des Pyrénées et de Midi-Pyrénées – Fédération des Conservatoires botaniques nationaux – Ministère de l'Écologie, du Développement durable.</subfield>
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    <subfield code="x">Carboni, M., Münkemüller, 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.</subfield>
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    <subfield code="x">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.</subfield>
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    <subfield code="x">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.</subfield>
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    <subfield code="x">Gargominy, O., Tercerie, S., Régnier, C., Ramage, T., Dupont, P., Vandel, E., Daszkiewicz, P., Lévêque, A., Leblond, S., De Massary, J.-C., Horellou, A., Noël, P., Noblecourt, T., Comolet, J., Touroult, J., Barbut, J., Rome, Q., Bernard, J.-F., Bock, B., Malécot, V., Boullet, V., Robbert Gradstein, S., Lavocat Bernard, E., &amp; Ah-Peng, C. (2016) TAXREF v10.0, référentiel taxonomique pour la France. Muséum national d'Histoire naturelle, Paris.</subfield>
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    <subfield code="x">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.</subfield>
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    <subfield code="x">Jauzein, P. (1995) Flore des champs cultivés. Editions Quae.</subfield>
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    <subfield code="x">UICN  France, FCBN &amp; MNHN (2012) La  Liste  Rouge  des  espèces  menacées  en  France.  Chapitre  Flore  vasculaire de  France  métropolitaine  :  premiers  résultats  pour  1  000  espèces,  sous-espèces  et  variétés.</subfield>
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    <subfield code="x">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.</subfield>
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    <subfield code="u">Anses, Laboratoire de la Santé des Végétaux, Unité Entomologie et Plantes invasives, Montpellier, France</subfield>
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    <subfield code="a">Guillaume Fried</subfield>
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    <subfield code="a">Laura Armengot</subfield>
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    <subfield code="a">Bérenger Bourgeois</subfield>
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    <subfield code="a">Vincent Bretagnolle</subfield>
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    <subfield code="a">Lucie Mahaut</subfield>
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    <subfield code="a">Christine Plumejeaud</subfield>
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    <subfield code="a">François Munoz</subfield>
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    <subfield code="a">Database of weeds in cultivation fields of France and UK, with ecological and biogeographical information</subfield>
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    <subfield code="a">&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;</subfield>
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