DNA Barcoding

DNA Barcoding the flora of the Kruger National Park

Senior researchers: Michelle van der Bank and Vincent Savolainen

Post-doctoral positions: Sylvie Duthoit and Renaud Lahaye

PhD: Olivier Maurin

MSc: Matlou Jerminah Moeaha

Collaborator: Yanis Bouchenak-Khelladi

What is DNA barcoding —In 2004 the Consortium of Barcode of Life (www.barcodinglife.com) has launched an initiative to promote DNA barcoding, a process enabling the rapid and inexpensive identification of the estimated 10 million species on Earth. It is a diagnostic technique in which short gene sequence(s) can be used for species identification. In animals, the mitochondrial cox1 gene (CO1) has been identified as a suitable DNA barcode, however, in plants it is still unclear which marker(s) could be used as a DNA barcode. Scientists from 11 institutions all over the world, supported by the Plant Working Group (http:/kew.org.uk/barcoding/index.html), are searching for this short fragment(s) of DNA. Once the potential “barcode” is identified, all 300.000 species of plants on Earth will have to be barcoded.

Benefits of DNA barcoding — (i) enabling species identification, including any life stage or fragment, (ii) facilitating species discoveries based on cluster analyses of gene sequences, (iii, and providing insight into the diversity of life (iv) promoting development of handheld DNA “barcoder” that can be applied in the field for biodiversity inventories. When this technology becomes available it will help many non-scientists to quickly and inexpensively identify known species and retrieve information about them.

The KNP and its flora — The KNP was established in 1898 to protect the wildlife of the South African Lowveld. It provides an ideal environment for a plant barcoding study since it is one of the largest protected areas in Africa. This large protected area of 20 000 km² is roughly the same size as Wales. It now forms part of the Great Limpopo Transfrontier Park, which links the KNP with Gonarezhou National Park in Zimbabwe and the Limpopo National Park in Mozambique. UNESCO has designated this new Transfrontier Park as a World Heritage Site. Since its creation in 2000, fences between the Parks have started to come down allowing the animals to take up their old migratory routes that had previously been blocked due to political boundaries. Various habitats and ecological regions exist within the boundary of the Kruger, with at least 16 recognized ‘ecozones’, each one characterize by specific vegetation, geology, soils, rainfall rate, and temperature. For example the vegetation and plant diversity found in the Malelane Bushveld Mountain is very distinctive of what can be found in the Lebombo Mountains located on the border with Mozambique. In the northern part of the Park the Sandveld is divided in several fragments and represent a particularly interesting area in term of plant diversity. This area has many highly localized species, which just enter from Mozambique or the Limpopo valley. Large rivers like the Limpopo, the Elephant and the Crocodile as well as rocky outcrops spreading all over the Park also represents places of botanical interest. Surprisingly, no comprehensive botanical inventory has recently been done in the KNP.

Collecting in the KNP — Since the beginning of this project in September 2005, we have collected more than 2 000 plant specimens. This represents the most complete and recent inventory of the Parks flora, which will be useful to update datasets of the Scientific Services of the KNP. This is also the largest and most diverse sampling ever made for barcoding purposes in a protected area.

Producing a DNA barcode for the flora of the KNP — Results based on eight plastid DNA markers (coding and non-coding) were evaluated, across a phylogenetically diverse set of taxa, which include 19 families, 22 genera and 38 species. The results suggest that a combination of genes is recommended as a barcode for the flora of the KNP, although matK alone correctly identified >90% of the species. The first data from this study has recently been presented at the Second barcode of life conference in Taipei and a scientific paper was submitted to PNAS entitled “DNA barcoding the floras of biodiversity hotspots”.

This study will improve the knowledge of plant biodiversity of the KNP, as well as conservation management, by providing exact localities of native, alien, rare and endangered plants. DNA-barcoding will also facilitate the future monitoring of botanical plots throughout the park by providing DNA-based taxonomic identification tools. Lastly this study will also reduce plant bio-prospecting in the KNP because herbarium specimens and DNA samples will be made available to the scientific community.

DNA barcoding of all trees and shrubs species is now nearly completed (300 spp) and the DNA barcoding program of herbs, grasses and bulbs is also well on its way.

DNA Bank for the Flora of the KNP at UJ — A DNA bank was set up at the University of Johannesburg where DNA extracts for the flora of KNP will be held centrally and made available for the scientific community. DNA extracts will also be duplicated and transferred to the DNA bank of the South African Biodiversity Institute (SANBI) in Kirstenbosch near Cape Town, South Africa, and the Royal Botanic Gardens, Kew in the United Kingdom.