The development and safeguarding of the vast arachnid specimen collections and associated biological information reference sources held in the National Collection of Arachnida (NCA) are of importance to agriculture and biodiversity conservation in South Africa. Through this reference source we renders invaluable biosystematic support to a wide range of scientific disciplines within the ARC, and the research community as a whole. The NCA consist of:

a) Arachnida collections (excluding the mites and ticks)

b) Mite collection

NATIONAL COLLECTION OF ARACNIDA (non-ACARI)

The National Collection of Arachnida (non-Acari) (NCA), is the most comprehensive and fastest growing collection of arachnids in South Africa. It contains 43,000 accessions represented by approximately 180,000 alcohol preserved specimens sampled mainly in South Africa. It serves as an invaluable scientific reference source and research tool as well as an archive of South Africa’s arachnid biodiversity.

The collection was established in 1976. A large part of the collection contains specimens collected within agro-ecosystems through surveys that span periods of a year or more, as well as surveys undertaken during the South African National Survey of Arachnida (SANSA)

Six orders of arachnida are housed in the collection:

  1. Araneae (Spiders)
    1. 40 525 accessions representing 75 families, 484 genera and 1 363 species
    2. 562 accessions are type specimens representing 217 species
  2. Amblypygi (Whipspiders)
    1. 40 accessions representing 1 family, 2 genera and 4 species
  3. Opiliones (Harvestman)
    1. 248 accessions representing 10 families, 14 genera and 44 species
  4. Pseudoscorpiones
    1. 295 accessions representing 15 families, 11 genera and 10 species
  5. Scorpiones
    1. 859 accessions representing 4 families, 9 genera and 68 species
  6. Solifugae (Sunspiders)
    1. 505 accessions representing 6 families, 15 genera and 30 species.

NCA DATABASE:

Computerization of the NCA (non-Acari) started in 1991 using a relational database for collected specimens, article library and loan registry.

In 2000 the database was migrated to a Microsoft Access database and a new module, the African Arachnida Database (AFRAD) was added. AFRAD consists of a taxon dataset (including descriptive and behavioural data, distribution per country, photographs and line drawings) for all 6000 spider species of the Afrotropical Region. Synonym and taxonomic name changes could now also be accommodated.

In 2005 all the modules were migrated to a MySQL database written in PHP, housed on a special server at ARC-Central Office. During this migration extensive data cleaning and geo-referencing of all locality data were done.

In 2006 the South African National Survey of Arachnida (SANSA) module was added. This module focuses only on published records of South African species and incorporates information on species records from both taxonomic and ecological papers from more than 17 institutions world-wide.

Activities:

  • During 2009 the entire collection was inspected and upgraded
  • On average 6,000 bottles containing approximately 20,000 specimens are newly accessioned annually. The specimens come from surveys undertaken by teams under the auspices of the South African National Survey of Arachnida (SANSA) as well as conservation agents, student and other projects and citizen scientists
  • From 2010 a new dimension was added to the collection when the DNA barcoding of new specimens through the International Barcode of Life Project (iBOL) started


Contact: Petro Marais (Collection Manager) at MaraisP@arc.agric.za

 

 

DNA BARCODING

BACKGROUND

In 2003 Paul Herbert and his research group at the University of Guelph in Canada published a paper “Biological identifications through DNA barcodes”. The paper proposed a new system for identifying and discovering species using a very short sequence from a standard part of the genome. This new molecular identification system is called “DNA barcoding”.

In June 2007 delegates from 25 countries came together in Guelph, Canada to discuss a proposed global collaboration of biodiversity scientists that would create a DNA barcode reference library for all multi-cellular life.

Positive response and rapid progress led to work beginning on establishing the administrative structures and finalizing the research plans of the International Barcode of Life project (iBOL) in July 2009. Formal activation of iBOL will take place in October 2010.

WHAT IS DNA BARCODING?

DNA barcoding is similar to the way a supermarket scanner distinguishes products using the black stripes of the Universal Product Code (UPC).

A standard 648 base-pair gene region (“CO1”) is being used for almost all animal groups. Using CO1 has the advantage that it is short enough to be sequenced quickly and cheaply yet long enough to identify variations among species.

THE BARCODE PRODUCTION PIPELINE

DNA barcoding starts with a specimen. The specimen may come from the field, a collection, zoo, botanical garden, seed bank, etc.

In the laboratory a tiny piece of tissue from the specimen is used by technicians to extract its DNA. They isolate the barcode region, replicate it using PCR amplification and then sequence the barcode. The sequence is represented by a series of the letters CATG.

After obtaining the barcode sequence, it is placed in the Barcode of Life Data Systems (BOLD) database.

BOLD is a sophisticated bioinformatics platform that incorporates a repository for DNA barcode records made up out of stored specimen data and images as well as sequences and trace files. It serves as a reference library of DNA barcodes used to assign identities to unknown species, and monitors the number of barcode sequence records and species coverage.

PURPOSE OF iBOL

Hundreds of scientists and technicians from 26 countries involved in this largest biodiversity genomics initiative ever is using DNA barcode technology to create and extend the geographic and taxonomic coverage of the barcode reference library, BOLD, for all multi-cellular life. Over the next five years, iBOL collaborators will gather DNA barcodes from five million specimens representing 500,000 species.

Once implemented, this DNA based identification system will have wide-ranging impacts in areas such as pest and disease control, food production and safety, resource management, conservation, research, education and recreation. These impacts will translate into economic benefits.

A number of DNA barcoding campaigns have already started collecting and registering DNA barcodes focusing on species endangered by human activity, species that are of particular socio-economic importance or species that are used in environmental assessment.