A review of over a decade of DNA barcoding in South Africa: a faunal perspective

DNA barcoding of southern African mammal species and construction of a reference library for forensic application

Combating wildlife crimes in South Africa requires accurate identification of traded species and their products. Diagnostic morphological characteristics needed to identify species are often lost when specimens are processed and customs officials lack the expertise to identify species. As a potential solution, DNA barcoding can be used to identify morphologically indistinguishable specimens in forensic cases. However, barcoding is hindered by the reliance on comprehensive, validated DNA barcode reference databases, which are currently limited. To overcome this limitation, we constructed a barcode library of cytochrome c oxidase subunit 1 and cytochrome b sequences for threatened and protected mammals exploited in southern Africa. Additionally, we included closely related or morphologically similar species and assessed the database's ability to identify species accurately. Published southern African sequences were incorporated to estimate intraspecific and interspecific variation. Neighbor-joining trees successfully discriminated 94%-95% of the taxa. However, some widespread species exhibited high intraspecific distances (>2%), suggesting geographic sub-structuring or cryptic speciation. Lack of reliable published data prevented the unambiguous discrimination of certain species. This study highlights the efficacy of DNA barcoding in species identification, particularly for forensic applications. It also highlights the need for a taxonomic re-evaluation of certain widespread species and challenging genera.

Towards global insect biomonitoring with frugal methods

None of the global targets for protecting nature are currently met, although humanity is critically dependent on biodiversity. A significant issue is the lack of data for most biodiverse regions of the planet where the use of frugal methods for biomonitoring would be particularly important because the available funding for monitoring is insufficient, especially in low-income countries. We here discuss how three approaches to insect biomonitoring (computer vision, lidar, DNA sequences) could be made more frugal and urge that all biomonitoring techniques should be evaluated for global suitability before becoming the default in high-income countries. This requires that techniques popular in high-income countries should undergo a phase of 'innovation through simplification' before they are implemented more broadly. We predict that techniques that acquire raw data at low cost and are suitable for analysis with AI (e.g. images, lidar-signals) will be particularly suitable for global biomonitoring, while techniques that rely heavily on patented technologies may be less promising (e.g. DNA sequences). We conclude the opinion piece by pointing out that the widespread use of AI for data analysis will require a global strategy for providing the necessary computational resources and training. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

DNA barcoding allows identification of undescribed crab megalopas from the open sea

Megalopas of 15 brachyuran crab species collected in the open sea plankton, and unknown until now, were identified using DNA barcodes (COI and 16S rRNA). Specimens belonging to the families Portunidae, Pseudorhombilidae and Xanthidae (Crustacea, Decapoda, Brachyura), and corresponding to the species Achelous floridanus, Arenaeus mexicanus, Callinectes amnicola, C. arcuatus, C. ornatus, C. toxones, Charybdis (Charybdis) hellerii, Portunus hastatus, Thalamita admete, Scopolius nuttingi, Etisus odhneri, Liomera cinctimanus, Neoliomera cerasinus, Pseudoliomera variolosa, and Williamstimpsonia stimpsoni, are described and illustrated, and compared with other congeneric species previously described. We also provide a new geographical record for N. cerasinus and the most remarkable features for each species.

South Africa's contribution of insect records on the BOLD system

South Africa is the third most biodiverse country in the world and insects represent a large part of its faunal diversity, as is seen globally. With more than 65,000 described animal species in South Africa, insects represent 44,088 species. While there are still a lot of species yet to be identified, progress may be hindered by the few insect taxonomists available in South Africa and subsequently, the time-consuming nature and costs of the methods used during species identification. DNA barcoding, on the other hand, has become a valuable tool for documenting biodiversity with the use of a small DNA fragment such as cytochrome oxidase subunit 1 (COI). This paper aims to assess South Africa's contribution to the Barcode of Life Database (BOLD) as well as highlight the regions that are under-represented on BOLD. From the 4,984,215 Insecta records on BOLD, South Africa contributed 56,392 insect records, with only 16.85% of that total identified to species level. The Gauteng Province had the most represented insect samples submitted to BOLD with 63.57% followed by Kwazulu-Natal (15.74%), and Mpumalanga (5.73%). However, the Free State, Limpopo, and the Northern Cape provinces are all under-represented on BOLD. This is evident as both the Northern Cape and Limpopo provinces contain one or more biodiversity hotspots which in turn displays the high levels of biodiversity that could still be recorded on BOLD. Improving our understanding with regards to DNA barcoding data linked to geographical regions, as well as specific insect groups, can highlight the areas in need of more research.

Coastal management – working towards the UN’s Decade of Ocean Science for Sustainable Development (2021–2030)

The UN declared 2021-2030 as the Decade of Ocean Science and identified research and technology priority areas to achieve the 2030 Sustainable Development Goals. We reviewed the current status of scientific support for coastal management in South Africa within the context of these priorities and found promising development. However, challenges for the next decade remain, such as rolling out pilot projects into sustainable, national-scale programmes, facilitating greater collaboration and coordination among scientific role players, and achieving long-term commitment and political will for dedicated financial support. Through our lens as natural scientists we focused on the ecological system and coupling with the social system; however scientific support on better characterisation and understanding of the dynamics within the social system is also critical as sustainable development relies heavily on the willingness of the social system to embrace and execute related policies.

Floral hosts of leaf-cutter bees (Megachilidae) in a biodiversity hotspot revealed by pollen DNA metabarcoding of historic specimens

South Africa is a megadiverse country with three globally recognised biodiversity hotspots within its borders. Bees in particular show high diversity and endemism in the western part of the country. Not much is currently known about the floral host preferences of indigenous bees in South Africa, with data only available from observational studies. Pollen metabarcoding provides provenance information by utilising DNA analyses instead of floral visitation and traditional microscopic identification to identify pollinator food plants, which can be time consuming and imprecise. In this study, we sampled pollen from leaf-cutter bees (Megachilidae) specimens maintained in a historic insect collection (National Collection of Insects, South Africa) that were originally collected from two florally important areas in South Africa (Succulent Karoo and Savanna) and used metabarcoding to determine pollen provenance. We also sampled pollen from leafcutter bee species with wider distributions, that extend across many different biomes, to determine if these 'generalist' species show relaxed floral host specificity in some biomes. Metabarcoding involved sequencing of the nuclear internal transcribed spacer 2 (ITS2) region. Amplicons were compared to a sequence reference database to assign taxonomic classifications to family level. Sequence reads were also clustered to OTUs based on 97% sequence similarity to estimate numbers of plant species visited. We found no significant difference in the mean number of plant taxa visited in the Succulent Karoo and Savanna regions, but the widespread group visited significantly more floral hosts. Bees from the widespread group were also characterised by a significantly different composition in pollen assemblage. The time since specimens were collected did not have an effect on the mean number of taxa visited by any of the bee species studied. This study highlights national history collections as valuable sources of temporal and spatial biodiversity data.

Checklist of acanthocephalan parasites of South Africa

Twenty-one species of acanthocephalans, representative of thirteen genera from ten families of seven orders and three classes, are included in this updated checklist of acanthocephalans in South Africa.

Although South Africa appears to have a less diverse acanthocephalan fauna compared to some other countries such as Iran in Asia, or Brazil in South America, this is probably an artefact of fewer parasitological surveys.