S. Kell and contributors April 16, 2004 pgr forum evk2-2001-00192

Fifth Framework Programme for Energy, Environment and Sustainable Development

Coordinated by The University of Birmingham, UK

WORKING DOCUMENT

NOT FOR CITATION

1.0 Workpackage 1: Primary objective

Create a European crop wild relative database, incorporating baseline biodiversity data with current conservation and threat status.

2.0 WP1 Deliverables

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  List of European crop wild relatives
  

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  Agreed taxon conservation dataset
  

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  European crop wild relative database
  

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  Web enabled database available via project web site
  

3.0 Background

PGR Forum is developing an information system providing access to European crop wild relative (CWR) data to enable the planning and implementation of comprehensive conservation and use strategies. A preliminary conceptual model for this information system was proposed at PGR Forum Workshop 3, In Situ Data Management Methodologies (Figure 1). At the core of the system is the CWR database containing: a list of European crops and their wild relatives (nomenclature provided by Euro+Med PlantBase); information on their use; and their degree of genetic and/or taxonomic relatedness. An XML schema (Extensible Markup Language) will act as a means of linking the database to other data sources.

Examples of some initial potential links are shown in green. Euro+Med PlantBase (http://www.euromed.org.uk/), for example, contains the taxonomic backbone to the CWR database. A link between the CWR database and Euro+Med via a scientific identifier for each taxon, means that a separate list of taxa is not required in the core database; thus, when Euro+Med is updated (this process is ongoing), the CWR database accesses the updated information. EURISCO (European Internet Search Catalogue of Ex Situ PGR Accessions) (http://eurisco.ecpgr.org/) and Mansfeld’s World Database of Agricultural and Horticultural Crops (http://mansfeld.ipk-gatersleben.de/) are further examples of databases that the CWR database could be linked to.
Any number of further ancillary data sources could be linked in this manner, the intention being that when a user wishes to access information on a particular CWR taxon e.g. Arnica montana, the information system provides links to as wide a range of appropriate data sources as possible for that taxon. Although the data is held in a number of different databases in various institutions, the user will view a standard interface through which the data will be accessed, negating the need to search individual databases for the different types of information required.

Figure 1: Proposed conceptual model for a European Crop wild relative information system. The European CWR taxon database is at the core of the infrastructure and linked to n external data sources. Some existing data sources are indicated in green. The two-way arrows indicate the reciprocal nature of the system.

4.0 List of European crop wild relatives
The development of a preliminary list of European crop wild relatives (CWR) is a major output from PGR Forum, and represents the breadth of the CWR conservation database. To date, a comprehensive list of European CWR has not been widely agreed on within the European PGR community, though there have been a number of preliminary lists drawn up. Most notable of these are Heywood and Zohary (1995) and Hammer and Spahillari (1999).
At PGR Forum Workshop 1 (Feb. 2003), participants discussed a methodology for creating the initial list of European CWRs, and for defining the criteria that would be used in order for a taxon to be included in the list. The results of these discussions are presented in the Workshop 1 Report (Kell and Maxted, 2003).
In summary, it was proposed that the initial list of European CWR taxa is produced through a process of data harmonisation and cross-checking between a number of databases; primarily Euro+Med PlantBase (http://www.euromed.org.uk/)and Mansfeld’s World Database of Agricultural and Horticultural Crops (Hanelt and IPK 2001; http://Mansfeld.ipk-gatersleben.de/Mansfeld/).
The first version of the list (CWR_Ver_1.0) was created during 2003 (see 4.1 for details of the procedure followed). This database contains the taxa in Euro+Med PlantBase (E+M) within genera matching genera in Mansfeld’s World Database of Agricultural and Horticultural Crops (Mansfeld). The total number of taxa recorded as present in Europe in E+M (including infraspecific taxa) is 23, 072.
A second version of the crop wild relative list is in progress (CWR_Ver_2.0) (see 4.2 for summary statistics). This database was created utilising an updated list of E+M taxa and a revised list of accepted genera from Mansfeld. Added to this is a list of ornamental genera extracted from the Community Plant Variety List and a list of forestry genera extracted from Schultze-Motel (1996).
4.1 Procedure: CWR_Ver_1.0 (H Knüpffer, S. Kell, S. Jury, T. El Atechi)
4.1.1 Stage 1: Selection of CWR taxa from Euro+Med PlantBase and Mansfeld database
University of Reading made the complete Euro+Med PlantBase dataset available to PGR Forum. This dataset was sent by Stephen Jury and Tarik El Atechi (University of Reading, UK) to Helmut Knüpffer (IPK, Germany).
Helmut Knüpffer carried out the following steps:

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  Converted the Euro+Med dataset into a database under Visual FoxPro;
  

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  Split the scientific names in Euro+Med into the fields: GENUS, SPECIES, AUTHOR_OF_SPECIES, INFRA (-specific or -generic name);
  

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  Assigned 3-letter ISO country codes to the geographical regions in Euro+Med, so that the list can be sorted by “country”. Some regions included 2 countries (e.g. Austria with Liechtenstein, or Sicily with Malta), in such cases the code was assigned to the first country;
  

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  Created a list of genus names from Euro+Med, and carried out a spell-check, using Thomas Metz’s taxonomic spell-checker (http://pgrdoc.ipgri.cgiar.org/taxcheck/grin/) based on an (almost) complete list of genus names from GRIN Taxonomy). (A report of the results of this spell-check is available on request);
  

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  Selected a list of accepted genus and species names from the Mansfeld Database.
  

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  Created a list of genus names occurring both in Euro+Med and Mansfeld (accepted names only);
  

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  Selected the entries from Euro+Med and from Mansfeld, respectively, matching this genus name list;
  

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  Created the following files:
  

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  EM_Countries (list of “country” names in Euro+Med, with their translation into 3-letter ISO country codes) (91 records) (MS Excel)
  

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  EM_CWR_Genera (Crop Wild Relative genera selected from Euro+Med) (838 records) (MS Excel)
  
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  EM_CWR_Scient (Crop Wild Relative scientific names, selected from Euro+Med) (27,062 records) (DBF)
  
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  MF_CWR_Species (Species names from Mansfeld matching genus names in EM_CWR_Genera, i.e. those cultivated species that have wild relatives in Euro+Med) (4,520 records) (MS Excel)
  
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  EM_CWR_Distribution (contains, for each CWR taxon in EM_CWR_Scient, its distribution in “Europe”. It is linked with the taxon names in EM_CWR_Scient through a numerical Id_Scient.) (297,873 records) (DBF)
  

NB: Some fields containing non-ASCII characters were corrupted when imported from the Euro+Med dataset (a text file) into FoxPro. The scientific names are mostly not affected. (This requires checking)

PGR Forum is grateful to Helmut Knüpffer (IPK, Germany), Stephen Jury and Tarik El Atechi (University of Reading, UK) for their assistance in the production of the initial taxon list.
4.1.2 Stage 2: Import files into MS Access database
The (DBF or MS Excel) files provided by Helmut Knüpffer (listed above) were imported by UOB (Shelagh Kell) into an MS Access database (named “European CWR”) for sorting and refinement. The files were renamed as follows:

IPK file name	UOB file name (MS Access table)	No. records
EM_Countries	E+M Countries	91
EM_CWR_Genera	E+M CWR Genera	838
EM_CWR_Scient	E+M CWR Taxa	27,062
MF_CWR_Species	Mansfeld CWR Species	4,520
EM_CWR_Distribution	E+M CWR Distribution Data	297,873

Note:
E+M Countries includes countries and subunits within countries. The dataset includes the geographic area covered by the Euro+Med project. This includes entries such as the Canary Islands and Northern Africa. The list of countries and country subunits is shown in the table below.

ISO	Country
0	Albania
AND	Andorra
AUT	Austria
AUT	Austria with Liechtenstein
PRT	Azores
ESP	Baleares
BLR	Belarus
BEL	Belgium
BEL	Belgium with Luxembourg
BIH	Bosnia-Herzegovina
BGR	Bulgaria
ESP	Canary Is.
RUS	Central European Russia
FRA	Corse
PRT	Corvo
HRV	Croatia
CZE	Czech Republic
DNK	Denmark including Bornholm
GRC	East Aegean Islands
*EU	East Europe
RUS	Eastern European Russia
EST	Estonia
FRO	Faeroe Islands
PRT	Faial
FIN	Finland including Ahvenanmaa
PRT	Flores
CSK	Former Czechoslovakia
YUG	Former Jugoslavia
*SU	Former USSR
FRA	France
ESP	Fuerteventura including Lobos
GER	Germany
GBR	Great Britain
GRC	Greece
GRC	Greek East Aegean Islands
HUN	Hungary
ESP	Ibiza including Formentera
ISL	Iceland
IRL	Ireland
ITA	Italy
RUS	Kaliningrad
GRC	Kriti with Karpathos, Kasos & Gavdhos
UKR	Krym
ESP	Lanzarote including Graciosa
LVA	Latvia
LIE	Liechtenstein
LTU	Lithuania
LUX	Luxembourg
ESP	Macaronesia
ESP	Mallorca
MLT	Malta
ESP	Menorca
MDA	Moldova
YUG	Montenegro
NLD	Netherlands
RUS	North Caucasus
*AF	Northern Africa
RUS	Northern European Russia
RUS	Northwest European Russia
NOR	Norway
RUS	Novaya Zemlya & Franz-Joseph Land
PRT	Pico
POL	Poland
PRT	Portugal
ROM	Romania
RUS	Russia Baltic
RUS	Russia Central
RUS	Russia Northern
RUS	Russia Southeast
RUS	Russia Southwest
PRT	Sa$Ho Jorge
PRT	Sa$Ho Miguel
PRT	Santa Maria
ITA	Sardegna
YUG	Serbia & Montenegro
YUG	Serbia including Kosovo and Vojvodina
ITA	Sicilia
ITA	Sicily with Malta
SVK	Slovakia
SVN	Slovenia
RUS	South European Russia
ESP	Spain
NOR	Svalbard
SWE	Sweden
CHE	Switzerland
PRT	Terceira
MKD	The former Jugoslav Republic of Makedonija
RUS	The Russian Federation
TUR	Turkey
TUR	Turkey-in-Europe
UKR	Ukraine

Query name	Output	No. records
E+M CWR Names	Genus, Species, Species author, Infra-specific name (Euro+Med list)	27,062
Mansfeld CWR Names	Genus, species (Mansfeld list)	4,520
Mansfeld CWR Species Not In E+M List	Genus + species in Mansfeld list but not in Euro+Med	1,530
E+M CWR Genera Not In Mansfeld List	Genera in 1. that are not 2.	26
E+M CWR taxa + scient ID	As 1. + Scientific ID	27,062
E+M CWR Distribution + status	As 5. + Country, Country ISO, Occurrence, + (Native, Introduced, Endemic, Cultivated)	297,873
ECWR + distrib (not A + not F)	As 6. without occurrence “A” and “F”	164, 463
ECWR taxa (not A + not F)	Genus, Species, Infra-specific name (without occurrence “A” and “F”)	23,072
ECWR Genera + Species (not A + not F)	Genus + Species (without occurrence “A” and “F”)	15,031
ECWR Genera (not A + not F)	Genus (without occurrence “A” and “F”)	813

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  Occurrence is recorded in Euro+Med using POSS (Plant Occurrence and Status Scheme)
  

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  “A” = “absent”; “F” = “Recorded as present in error”
  

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  Euro+Med data standards can be viewed at: http://www.euromed.org.uk/d_ocuments/Data_Standards_Version2-8.pdf
  

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  E+M CWR Distribution Data: records of uncertainty (i.e. more than one code in the field for one record) were updated according to instructions from Euro+Med PlantBase Secretariat (Tarik El Atechi):
  

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  All uncertainty records beginning with “P”, present, changed to “P” where native status is “N”, except “P+E” (uncertainty about extinct status).
  
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  All other uncertainty records remain unchanged.
  

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  E+M CWR Genera Not In Mansfeld List: Some of these genera do not have separate entries in the Mansfeld Book (and therefore in the database), but they are mentioned in the text of some other entries, under another name. For nomenclatural completeness, scientific names mentioned only in the text (without separate entries in the book), have got separate entries in the Mansfeld database. So the first SELECT statement for accepted genus names would yield these 26 names, whereas the next SELECT statement requesting the complete list of accepted species names will not yield any species of these 26 genera. By checking the Mansfeld DB on the web for these 26 genera, one could find out whether the text information indicates that these genera have cultivated members or not.
  

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  Euro+Med PlantBase data has been updated since dataset was made available to PGR Forum for initial selection of taxa matching Mansfeld genera. UoB to meet with Euro+Med Plant Base Secretariat to discuss update of dataset.
  

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  Mansfeld CWR Species Not In E+M List: these may include
  

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  Taxa that do not occur as wild species in Europe
  
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  Cultivated species that do not have known wild ancestors
  
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  Taxa with different accepted names.
  

Cross-checking between Mansfeld and E+M is required.

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  The MS Excel file was imported into “European CWR” and named “Ornamental taxa”;
  

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  The scientific names were split into the fields: Genus, Gen_author, Species, Sp_author, Infra, Infra_author;
  

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  The following tables and queries relate to the ornamental taxa:
  

Table name	Query name	Output	No. records
Ornamental taxa		Genus, Genus author, Species, Species author, Infra-specific name, Infra-specific name author	548
	Ornamental genera	Genera occurring in “Ornamental taxa”	366
	Ornamental genera Not In E+M CWR Genera	Genera occurring in “Ornamental taxa”, but not in E+M CWR Genera	198

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  The ornamental list requires cross-checking with the Euro+Med PlantBase complete dataset, in order to match those ornamental genera occurring in Europe. (Some of the 198 genera listed in query “Ornamental genera Not In E+M CWR Genera” are not European taxa.) (See 4.2)
  

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  If fields in addition to the genus field in “Ornamental taxa” are required for incorporation into the database, this data requires checking as regards nomenclature and authorities.
  

2. 
   CWR_Ver_2.0: Summary statistics
   

CWR_Ver_2.0 has been created utilising an updated list of E+M taxa and a revised list of accepted genera from Mansfeld. Added to this, is the list of ornamental genera obtained from the CPVO (see 4.1.4) and a list of forestry genera extracted from Schultze-Motel (1996), provided by Helmut Knüpffer, IPK. Summary statistics are provided in the table below.

Table/Query name	Output	No. records
Mansfeld_CWR_Genera_E+M_V2	Genera in Mansfeld matching genera in E+M	816
Mansfeld_CWR_Taxa_E+M_V2	Genus, Species, Species author, Infra-specific name, Infra-specific name author (Mansfeld/E+M Match)	23,508
Ornamental_CWR_Genera_E+M_V2	Genera in ornamental list matching genera in E+M	226
Ornamental_CWR_Taxa_E+M_V2	Genus, Species, Species author, Infra-specific name, Infra-specific name author (Ornamental/E+M Match))	9,433
Forestry_CWR_Genera_E+M_V2	Genera in forestry list matching genera in E+M	138
Foresty_CWR_Taxa_E+M_V2	Genus, Species, Species author, Infra-specific name, Infra-specific name author (Forestry/E+M Match))	3,652
Mansfeld+Ornamental+Forestry_Genera	Genera in Mansfeld, ornamental and forestry lists combined, matching genera in E+M	896

Table/Query name	Output	No. records
E+M_CWR_Taxa_V2	Genus, Species, Species author, Infra-specific name, Infra-specific name author (Mansfeld, ornamental + forestry taxa in E+M)	25,095
E+M_CWR_Distribution_+_Status_V2	As 8. + Country, Country ISO, Occurrence, + (Native, Introduced, Endemic, Cultivated)	307,981
ECWR+Distrib_(not A + not F)_V2	As 9. without occurrence “A” and “F”	172,691
ECWR_Taxa_(not A + not F)_V2	Genus, Species, Species author, Infra-specific name, Infra-specific name author (without occurrence “A” and “F”)	21,347
ECWR_Genera+Species (not A + not F)_V2	Genus + Species (without occurrence “A” and “F”)	13,711
ECWR_Genera (not A + not F)_V2	Genus (without occurrence “A” and “F”)	870