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European Crop Wild Relative Diversity Assessment and Conservation Forum


Workshop 4:

Population Management Methodologies

Workpackage 1: European crop wild relative assessment
Progress report

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NOT FOR CITATION





Contents


1.0 Workpackage 1: Primary objective

1







2.0 WP1 Deliverables

1







3.0 Background

1







4.0 List of European crop wild relatives




4.1 Procedure: CWR_Ver_1.0

3

4.1.1 Stage 1: Selection of CWR taxa from Euro+Med PlantBase and Mansfeld

3

4.1.2 Stage 2: Import files into MS Access database

4

4.1.3 Stage 3: Euro+Med/Mansfeld preliminary data refinement

6

4.1.4 Stage 4: Incorporate ornamental taxa

7

4.1.5 Stage 5: Incorporate forestry taxa

7

4.2 CWR_Ver_2.0: Summary statistics

7

5.0 Taxon conservation dataset




5.1 Development of data standards

9

5.2 Production of trial taxon conservation datasets

9

5.3 PGR Forum participant expertise questionnaire

9

5.4 Example datasets

17







6.0 User requirement survey




6.1 Aims

18

6.2 Results of the preliminary survey (Phase 1)

18

6.3 Phase 2 questionnaire and test results

20

6.3.1 Section A: Research interests

20

6.3.2 Section B: Information of interest

21

6.3.3 Section C: Information availability

24






Fig. 1 Proposed conceptual model for a European Crop wild relative information system

2







Table 1 Taxa and geographical areas of expertise

10

Table 2 Inventory of selected species (for in-depth data gathering) and data availability

11

Table 3 Example taxon datasets

17

Table 4 Example questions for the CWR information system (Phase 1 survey)

18

Table 5 Information categories identified from an initial analysis of the questions provided in Phase 1

19








Literature cited

25







Annex 1 Case study taxa listed by country and participant

26

Annex 2 User requirement survey

36


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

  • List of European crop wild relatives




  • Agreed taxon conservation dataset




  • European crop wild relative database





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:


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




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




  • 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;




  • 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);




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




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







  • Created the following files:




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

  • EM_CWR_Genera (Crop Wild Relative genera selected from Euro+Med) (838 records) (MS Excel)

  • EM_CWR_Scient (Crop Wild Relative scientific names, selected from Euro+Med) (27,062 records) (DBF)

  • 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)

  • 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


4.1.3 Stage 3: Euro+Med/Mansfeld preliminary data refinement
A number of database queries were performed as follows:


Query name

Output

No. records










  1. E+M CWR Names

Genus, Species, Species author, Infra-specific name (Euro+Med list)

27,062

  1. Mansfeld CWR Names

Genus, species (Mansfeld list)

4,520

  1. Mansfeld CWR Species Not In E+M List

Genus + species in Mansfeld list but not in Euro+Med

1,530

  1. E+M CWR Genera Not In Mansfeld List

Genera in 1. that are not 2.

26

  1. E+M CWR taxa + scient ID

As 1. + Scientific ID

27,062

  1. E+M CWR Distribution + status

As 5. + Country, Country ISO, Occurrence, + (Native, Introduced, Endemic, Cultivated)

297,873

  1. ECWR + distrib (not A + not F)

As 6. without occurrence “A” and “F”

164, 463

  1. ECWR taxa (not A + not F)

Genus, Species, Infra-specific name (without occurrence “A” and “F”)

23,072

  1. ECWR Genera + Species (not A + not F)

Genus + Species (without occurrence “A” and “F”)

15,031

  1. ECWR Genera (not A + not F)

Genus (without occurrence “A” and “F”)

813


Notes:


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




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




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




  • 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):

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

  • All other uncertainty records remain unchanged.




  • 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.



  • 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.




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

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




4.1.4 Stage 4: Incorporate ornamental taxa
A list of ornamental taxa (MS Excel) was obtained from Community Plant Variety Office (www.cpvo.eu.int). The list contains taxa for which the title has been granted and all active applications (as of 18th July 2003). PGR Forum is grateful to Ton Kwakkenbos and colleagues at the CPVO for providing this data. The following steps were performed with this data:


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




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




  • 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


Notes:


  • 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)




  • 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.


4.1.5 Stage 5: Incorporate forestry taxa
A list of forestry genera was produced by Helmut Knüpffer from Schultze-Motel (1996). These genera have been incorporated in CWR_Ver_2.0.



    1. 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

  1. Mansfeld_CWR_Genera_E+M_V2

Genera in Mansfeld matching genera in E+M

816

  1. Mansfeld_CWR_Taxa_E+M_V2

Genus, Species, Species author, Infra-specific name, Infra-specific name author (Mansfeld/E+M Match)

23,508

  1. Ornamental_CWR_Genera_E+M_V2

Genera in ornamental list matching genera in E+M

226

  1. Ornamental_CWR_Taxa_E+M_V2

Genus, Species, Species author, Infra-specific name, Infra-specific name author (Ornamental/E+M Match))

9,433

  1. Forestry_CWR_Genera_E+M_V2

Genera in forestry list matching genera in E+M

138

  1. Foresty_CWR_Taxa_E+M_V2

Genus, Species, Species author, Infra-specific name, Infra-specific name author (Forestry/E+M Match))

3,652

  1. Mansfeld+Ornamental+Forestry_Genera

Genera in Mansfeld, ornamental and forestry lists combined, matching genera in E+M

896




Table/Query name

Output

No. records

  1. 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

  1. E+M_CWR_Distribution_+_Status_V2

As 8. + Country, Country ISO, Occurrence, + (Native, Introduced, Endemic, Cultivated)

307,981

  1. ECWR+Distrib_(not A + not F)_V2

As 9. without occurrence “A” and “F”

172,691

  1. 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

  1. ECWR_Genera+Species (not A + not F)_V2

Genus + Species (without occurrence “A” and “F”)

13,711

  1. ECWR_Genera (not A + not F)_V2

Genus (without occurrence “A” and “F”)

870
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