DNA barcoding: Writing the encyclopaedia of South African biodiversity
The DNA barcoding process. All relevant data, along with a photograph, accompany DNA barcodes in an online public library, the Barcode of Life Database (BOLD). (Image: IBOL)
Collections are invaluable. Voucher specimens with known classification and relevant collection information provide the cornerstone of this DNA barcoding project. (Photo: Rutger Spies)
Rhabdomys pumilio (Four-striped mouse). DNA barcoding will shed light on the classification of South Africa's "hard-to-identify" small mammals. (Photo: Nina du Toit, Stellenbosch University)
South Africa has a wealth of plant and animal life. Although it covers a mere 2% of the global land area, it rates as one of 17 mega diverse countries which collectively contain more than two-thirds of global biodiversity.
South Africa is home to 6% of the global total of mammal species (260 species), 7% of bird species (800 species) and 5% of reptile species (363 species). It is also the 24th richest country in the world in terms of endemic fauna.
Previously, comparisons based on morphological characteristics were used by taxonomists to describe species. Currently molecular characteristics, in combination with taxonomic classifications, are employed to add leaves to the existing tree of life.
DNA barcoding is used to identify organisms at species-level by examining a small conserved region in its genetic code. It is a rapid and practical molecular method to identify an unknown biological sample, based on variation within a short universal genetic marker. This variation is unique for each species.
The use of DNA barcoding as a molecular identification tool has been assessed in several studies, and its value has been scientifically proven. Barcodes of the cytochrome oxidase subunit I gene (COI) in animals, for example, were able to identify 94% of species across taxa, from blowflies to birds. DNA barcoding has several applications, including the control of food quality, traceability of raw and processed products derived from trade species and providing valuable information in conservation biology and wildlife management.
The National Zoological Gardens of South Africa (NZG) is undertaking the barcoding of South African terrestrial vertebrate species (birds, mammals and reptiles) as part of a collaborative project with the South African National Biodiversity Institute (SANBI), the African Centre for DNA Barcoding (ACDB) at the University of Johannesburg and various natural history museums and biological repositories.
One of the aims is to barcode not only all terrestrial vertebrate species in the country, but also exotic or alien species that pose risks to endemic species, or have the potential to be invasive.
International Barcode of Life
The project forms part of a larger initiative, the International Barcode of Life (IBOL) - the largest biodiversity genomics project ever undertaken. IBOL is hosted by the Biodiversity Institute of Ontario at the University of Guelph, Canada, but the research is divided among institutions in 27 partner nations, of which South Africa is one.
The goals of this initiative are to accelerate the compilation of species barcodes (of both known and new species), to establish a public library of DNA barcodes that are linked to voucher specimens and their classification and to create a digital identification system for all species. This will provide a quick way of identifying organisms in nature simply by comparing a DNA barcode to an online reference library linked to relevant information for each species with the use of a portable "Life Barcoder" device.
In the effort to include South African fauna in the new global "encyclopaedia", the Bio-molecular Genetics Unit at the NZG's Centre for Conservation Science has collected approximately 400 voucher samples from 165 bird and 149 mammal species since September 2011. The first collection of DNA samples has been sent to the Canadian Centre for DNA Barcoding (CCDB) to be included in the International Barcode of Life (IBOL) online library.
South African reptiles are still underrepresented and the aim for the next three months is to collect voucher samples from a wide range of reptiles, with the help of taxonomists and curators of reptile collections.
The success of this project is largely dependent on collaborations with repositories of biological materials such as natural history museums, zoos and biobanks and also with taxonomical experts.
To ensure that the widest coverage of South African species are collected and documented in the online library, the Bio-molecular Genetics Unit would like to extend an invitation to anyone (curators, collectors or taxonomists) who would like to contribute to this project.