An overview of DNA barcoding of biodiversity in South Africa
Abstract
The global decline in biodiversity, driven by habitat loss, overexploitation, climate change, biological invasions, and illegal trade, poses significant challenges for conservation management. Although many South African ecosystems and species are under threat, effective conservation efforts are hindered by incomplete foundational biodiversity data and assessments, caused by taxonomic gaps and unverified distributions. DNA barcoding has emerged as an invaluable tool for species identification and classification of biodiversity. While substantial barcoding progress has been made, for many taxa, others remain underrepresented in sequence databases. This study evaluates the status and progress of DNA barcoding in South Africa through a gap analysis, comparing verified species checklists with barcoded sequences from the Barcode of Life Database (BOLD) and GenBank to assess taxonomic and geographic representation. A literature review (2003–2023) highlights applications across terrestrial, freshwater, and marine habitats. Of the 931,476 South African species barcode records, 52% were publicly available. Although the insects dominated with the highest number of records and BINs, reptiles had the highest taxonomic representation. Plants and fungi were underrepresented (16.1% and 2.8%, respectively). Regionally, Mpumalanga and Limpopo provinces showed the highest BIN counts, while North-West and Free State provinces had the lowest. The majority of barcode records were for mtDNA genes such as cytochrome c oxidase subunit I ( COI ) and were contributed by both local and international institutions. Discrepancies between GenBank records and those mined by BOLD indicated that many GenBank sequences for South Africa have poor quality metadata, including geographic sampling locality information. While significant progress has been made across taxa, further efforts are needed to expand species and geographic coverage, enhance sequence quality, improve species metadata, and resolve inconsistencies in BIN assignments, particularly for underrepresented groups such as plants and fungi. These advances would strengthen biodiversity assessments and support conservation efforts in South Africa.
Article Details
Authors (55)
Mahlatse M. Kgatla
Cassandra Barker
Janine R. Baxter
Aletta E. Bester-van der Merwe
Mamohale Chaisi
Albert Chakona
Michael I. Cherry
Savel R. Daniels
Louis H. Du Preez
Charles R. Haddad
Peter G. Hawkes
Chris Ho
Thierry B. Hoareau
Adriaana Jacobs
Karin Jacobs
Charlene Janion-Scheepers
Bettine Jansen van Vuuren
Ronny M. Kabongo
Thembile T. Khoza
Nozipho L. Khumalo
Tendekai Mahlanza
Lindiwe Makapela
Buyisile G. Makhubo
Gavin W. Maneveldt
Kagiso Mashego
Gwynneth Matcher
Conrad A. Matthee
Mudzuli Mavhunga
John M. Midgley
Musa Mlambo
Daniela M. Monsanto
Rungula Mthombeni
Shane L. Murray
Samantha Mynhardt
Brielle-Jennifer Nang-Mba
Mduduzi Ndlovu
Shilpa P. Parbhu
Veronica Phetla
Metlholo Phukuntsi
Tristan R. Pitcher
Toufiek Samaai
Carol A. Simon
Kerry Sink
Catherine L. Sole
Genevieve L. Theron
Barbara van Asch
Michelle van der Bank
Clarke J.M. van Steenderen
Martin H. Villet
Cobus M. Visagie
Kirstin A. Williams
Sandi Willows-Munro
Mamadi T. Sethusa
Jessica M. Da Silva
Monica Mwale