An overview of DNA barcoding of biodiversity in South Africa

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.

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PLoS ONE
Published
2026-04-21
DOI
https://doi.org/10.1371/journal.pone.0345173
Primary Topic
Environmental DNA in Biodiversity Studies
Type
article
Field-Weighted Citation Impact
0.00

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article

An overview of DNA barcoding of biodiversity in South Africa

Kagiso Mashego, Monica Mwale, Peter G. Hawkes, Shane Murray et al.
PLoS ONE
Environmental DNA in Biodiversity Studies
article

An overview of DNA barcoding of biodiversity in South Africa

Kagiso Mashego, Monica Mwale, Peter G. Hawkes, Shane Murray, Michael Cherry, Tendekai Mahlanza, Carol Anne Simon, Buyisile G. Makhubo, Sandi Willows‐Munro, Bárbara van Asch, Cassandra Barker, Bettine Jansen van Vuuren, Conrad A. Matthee, Charlene Janion‐Scheepers, Mamohale Chaisi, Genevieve Theron, Adriaana Jacobs, Albert Chakona, Toufiek Samaai, R.M. Kabongo, Veronica Phetla, Thierry B. Hoareau, Martin H. Villet, Kirstin A. Williams, Jessica M. da Silva, Gwynneth F. Matcher, Aletta E. Bester‐van der Merwe, Mduduzi Ndlovu, Musa C. Mlambo, Karin Jacobs, J. R. Baxter, Daniela M. Monsanto, Samantha Mynhardt, Thembile T. Khoza, Mahlatse Kgatla, Nozipho Khumalo, Mudzuli Mavhunga, Michelle van der Bank, Chris Ho, Lindiwe Makapela, Gavin W. Maneveldt, John M. Midgley, Catherine L. Sole, Kerry Sink, Clarke J.M. van Steenderen, Louis H. Du Preez, Charles R. Haddad, Metlholo Phukuntsi, Savel R. Daniels, Brielle-Jennifer Nang-Mba, Cobus M. Visagie, Tristan R. Pitcher, Rungula Mthombeni, Shilpa P. Parbhu, Mamadi T. Sethusa
article en

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.

PLoS ONEVol. 21(4)
Department of Agriculture, Land Reform and Rural Development (ZA), African Institute for Mathematical Sciences (ZA), University of Cape Town (ZA), South African Reserve Bank (ZA), Rhodes University (ZA), University of Johannesburg (ZA), Stellenbosch University (ZA), University of the Free State (ZA), North-West University (ZA), Iziko Museums of South Africa (ZA), University of Mpumalanga (ZA), South African National Biodiversity Institute (ZA), National Museum (ZA), Museum of Literature (HU), International Wildlife Consultants (United Kingdom) (GB), South African Environmental Observation Network (ZA), Reneco (United Arab Emirates) (AE), Umkhuseli Innovation and Research Management (ZA), South African Institute for Aquatic Biodiversity (ZA), University of Pretoria (ZA), University of Guelph (CA), University of Venda (ZA), University of the Western Cape (ZA), University of KwaZulu-Natal (ZA), Nelson Mandela University (ZA)
Canada Foundation for Innovation
Openalex Percentile: Top 16%
Environmental DNA in Biodiversity Studies
DOIOpen Access PDFOpenAlex
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