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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. [ABSTRACT FROM AUTHOR]

Water scarcity has directly influenced food security across the world. Water scarcity issues remain a major crisis in South Africa which derives the bulk of its food from the local agricultural sector. Likewise, water scarcity is a major challenge to agriculture crop productivity among under-resourced farmers in Limpopo Province which is also the country's economic hub. The current study was undertaken to explore the challenges of water scarcity and the subsequent threat posed to food security at the Luvhada Irrigation Scheme in Limpopo Province and possible solutions thereof. An explorative case study design was utilised. Respondents were selected using the random sampling technique. Data were collected using open and close-ended questionnaires. Quantitative data were analysed using the IBM Statistical Package for the Social Sciences (SPSS) version 25 (descriptive statistics) while the Atlas ti version 8 software (network diagram technique) was used to analyse qualitative data from the open-ended questions. The major agricultural water challenges in the area were mainly broken canal challenge (35.7%), blocked furrows (16.67%), damaged furrows (26.19%), lack of alternative water sources (11.90%), inadequate water sources and competition for water (9.52%). Thus, major recommendations to improve water access at the scheme encompasses the construction of water storage facilities; construction of pipe lines and technically sound irrigation systems; drilling of boreholes; and full utilisation of water from the Nzhelele River. The recommendations are critical to improving water access and improving water conservation particularly at current times where water scarcity is rapidly increasing in Limpopo and South Africa at large. [ABSTRACT FROM AUTHOR]

In South Africa, small-scale farmers in rural areas are likely to suffer most from water scarcity, as they do not have adequate resources to deal with the threat. Yet, there is little understanding of farm-level resilience mechanisms against water scarcity in Vhembe District, a typical rural setting in the country. The current study was undertaken to identify and explain small-scale farmers' resilience factors to water scarcity at the farm level. The study was conducted at the Luvhada Irrigation Scheme in Limpopo Province. An explorative case study design was adopted. Eighteen respondents were purposively sampled and data were collected using semi-structured interview guides. The ATLAS.ti version 8 software (network and primary document table tools) was utilised to analyse data. Results illustrated water access challenges that encompassed dilapidated canal infrastructure, low water pressure and irregular water access. Management challenges such as insensitiveness of schedules to crop variety, limited irrigation time and disproportionate water distribution were further highlighted. To address these challenges, mechanisms such as regular canal maintenance, reduction of farming area and irrigation scheduling are applied to retain resilience. However, these mechanisms are survivalist in nature, as they did not translate to increased crop production. Thus, small-scale farmers need to be capacitated on modern water management mechanisms and be provided with resource to build on the existing water management mechanisms in the area. [ABSTRACT FROM AUTHOR]

The Asian green musselPerna viridisis an invasive Indo-Pacific species recently reported from South African harbours. To verify the invasion, a phylogenetic (and morphological) analysis of green-shelled mussels (n= 39), found in six South African harbours, was conducted using the mitochondrial cytochromecoxidase subunit I gene (COI). Estimates of genetic distances using the neighbour-joining analysis identifiedP. viridisonly from Durban Harbour. All other green mussels were more than 3.2% divergent fromP. viridisand were identified as green-shelled variants of indigenousP. perna. The only reliable morphological differences distinguishing the two species were the poorly developed mantle papillae and the wavy pallial line inP. viridis. The confirmed occurrence ofP. viridisin a South African harbour suggests that there is a possible threat of the species becoming established and then spreading onto the open coast and competing with indigenousP. perna. [ABSTRACT FROM AUTHOR]

Genetic studies on South African marine fishes have shown that many species exist as single, well-mixed stocks throughout their core distribution. The black musselcracker or poenskopCymatoceps nasutusis a slow-growing, late-maturing and long-lived sparid (Perciformes: Sparidae) that is endemic to South African coastal waters. Conventional tagging studies suggest that it is resident, with limited connectivity between different regions along the coast. Mitochondrial and nuclear DNA were used to investigate the genetic structure ofC. nasutusalong the South African coastline and showed evidence of at least two populations. Samples collected from the Tsitsikamma Marine Protected Area on the South Coast to KwaZulu-Natal on the East Coast showed no significant population structure over much of the distribution. Gene flow forC. nasutuswithin this region is not limited by geographic distance and appears to be unaffected by various oceanographic barriers and biogeographical boundaries. Samples from the Western Cape to the west of Tsitsikamma, however, showed moderate to substantial differentiation for both markers, which may be influenced by a temperature barrier – a coldwater ridge – along the South Coast. These data provide the first genetic assessment of this South African sparid, and suggest that a two-stock management strategy would be appropriate for the species. [ABSTRACT FROM AUTHOR]

Epinephelus andersoni is a range-restricted species that is endemic to the south-east coast of Africa from Quissico in Mozambique to Knysna in South Africa. The species is an important commercial and recreational linefish species that is currently considered to be optimally exploited although there have been some signs of depletion within its range. This is likely because of its complex life-history including diandric protogyny and high residency, which make it potentially vulnerable to over-exploitation. This study analysed the genetic structure and diversity of E. andersoni using nuclear (intron 1 S7) and mitochondrial (cyt b) DNA genes for 240 and 269 individuals,respectively, to provide information for fisheries conservation and management. S7-1 allelic diversity was high (0.801) with the AMOVA showing significantly high among group variation (Φ CT = 0.204, p < 0.05) between five groups: 1. Quissico to Inhaca; 2. Cape Vidal to Port Edward; 3 Port St Johns to Coffee Bay; 4. Mbhashe; 5. Port Alfred. This geographic structuring could be attributed to low gene flow across barriers such as the Port Alfred upwelling cell, the Mozambique Channel eddies and smaller more localised upwelling cells such as the Port St Johns cell. Contrastingly, the cytochrome b (cyt b) results indicate low haplotype diversity (0.309) and no differentiation (Φ CT = 0.265, p = 0.074) between groups, supporting the hypothesis of a historical population bottleneck. This may be due to an unusually slower mutation rate of the cyt b region than the S7-1 gene region suggesting more recent diversification. Complex patterns of diversity revealed by this study highlight that a precautionary approach is required for the management of this species that takes into account some regional differentiation, while some connectivity still exists, making it practical to continue to manage E. andersoni as a single stock. [ABSTRACT FROM AUTHOR]

Ticks transmit pathogens of veterinary and public health importance. Understanding their diversity is critical as infestations lead to significant economic losses globally. To date, over 90 species across three families have been identified in South Africa. However, the taxonomy of most species has not been resolved due to morphological identification challenges. DNA barcoding through the Barcode of Life Data Systems (BOLD) is therefore a valuable tool for species verifications for biodiversity assessments. This study conducted an analysis of South African tick COI barcodes on BOLD by verifying species on checklists, literature, and other sequence databases. The compiled list represented 97 species, including indigenous (59), endemics (27), introduced (2), invasives (1), and eight that could not be classified. Analyses indicated that 31 species (32%) from 11 genera have verified COI barcodes. These are distributed across all nine provinces with the Eastern Cape having the highest species diversity, followed by Limpopo, with KwaZulu-Natal having the least diversity. Rhipicephalus, Hyalomma , and Argas species had multiple barcode index numbers, suggesting cryptic diversity or unresolved taxonomy. We identified 21 species of veterinary or zoonotic importance from the Argasidae and Ixodidae families that should be prioritised for barcoding. Coordinating studies and defining barcoding targets is necessary to ensure that tick checklists are updated to support decision-making for the control of vector-borne diseases and alien invasives., Competing Interests: The authors declare there are no competing interests.

The blue crane (Anthropoides paradiseus), wattled crane (Bugeranus carunculatus), and grey-crowned crane (Balearica regulorum) are species of concern as their populations are declining and they face several threats including habitat loss, disturbance and illegal trade. In South Africa, these species are bred in captivity for trade purposes which is permitted and regulated globally under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Legal sustainable trade through captive breeding of endangered wildlife species such as cranes has been promoted to counteract the illegal trade of individuals from the wild. Captive breeding independent of wild populations may reduce the harvest pressures on wild bird populations which in turn benefit the recovery of exploited species. This approach is considered to be controversial by some individuals. Although captive breeding of endangered species, for both population sustainability and commercial purposes, is promoted to aid in conserving species, concerns have been raised with regards to breeding facilities being used for laundering of animals. To monitor the legal trade of cranes in South Africa a short tandem repeat (STR) assay following recommendations of the International Society for Forensic Genetics (ISFG) was developed and validated. An STR assay comprising of four multiplexes that include 16 STR markers and two gender determination markers was proven to be highly informative with average polymorphic information content (PIC) values of 0.806, 0.646 and 0.725 for A. paradiseus, B. regulorum and B. carunculatus respectively. In addition, the assay showed sufficient discriminatory power for parentage assignment of closely related individuals in all three species (A. paradiseus: PI = 1.7×10 -24 , PIsibs = 4.7×10 -08 , and B. carunculatus: PI = 1.4×10 -19 , PIsibs = 2.9×10 -07 and B. regulorum: PI = 1.7×10 -12 , PIsibs = 5.0×10 -05 ). Analysis of 251 samples suggested that the validated multiplex assay ensures reliability, reproducibility, and repeatability for applications in forensic case work where illegal trade of offspring is suspected through verifying parentage of captive birds in breeding facilities., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Ticks are arachnid blood-feeding parasites, which infest livestock, wildlife, and humans, transmitting medically and veterinary significant pathogens. Their biodiversity and distribution in wild animals remains complex. This study analysed archived tick samples (n = 48) from the South African Biodiversity Institute (SANBI) Wildlife Biobank utilizing morphology and genetic analyses of the 16S rRNA and COI (DNA barcoding) mitochondrial genes to identify ticks collected among 13 vertebratesavian, reptilian, and mammalian host species. The specimens came from nine localities including nature reserves and captive facilities (zoological garden) in South Africa, Namibia, and Botswana. These ticks were also assessed for associated pathogens with the reverse line blot (RLB) hybridization assay. Seven tick genera, Amblyomma, Hyalomma, Haemaphysalis, Ixodes, Rhipicephalus, Rhipicentor, and Otobius were identified, with Amblyomma being the most prevalent (22.9 %) in our sample set. Obtained sequences were 95-100 % similar to published records of tick species collected from wild and domestic animals, as well as those collected from vegetation, from different southern African areas. However, tick specimens (n = 3) identified morphologically as Hyalomma truncatum, Rhipicephalus e. evertsi, and R. simus, were, on a molecularly level, more closely related to their sister taxa (H. glabrum, R. e. mimeticus, and R. gertrudae, respectively) suggesting a need for taxonomic verification. With the RLB hybridization assay, six samples reacted with the Ehrlichia/Anaplasma genus-specific probe, while two reacted with the Theileria/Babesia genus-specific probe. Sequencing of the RLB amplicons targeting the 18S rRNA gene (n = 2) indicated 100 % similarity to Hepatozoon fitzsimonsi, while one was closely related to He. ingwe with 99.39 % similarity. The results show that wildlife harbour different tick species, and pathogen detection identified novel genotypes, indicating wildlife as potential pathogens reservoirs. This study enhances our understanding of tick biodiversity, distribution and highlights wildlife's role in harbouring diverse tick species and novel pathogens., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024. Published by Elsevier B.V.)

Mwale and Masika 2009 Ethno-veterinary control of parasites, management and role of village chickens in rural households of Centane district in the Eastern Cape, South Africa. Tropical Animal Health and Production. Village chickens contribute significantly towards rural livelihood in the African continent through the provision of animal protein, income and socio-cultural uses. However, village chickens are susceptible to parasite infestation. Due to limitations of using western drugs to control these parasites, farmers resort to the use of ethno-veterinary medicine (EVM). However, there is dearth of information on EVM use in chickens. Therefore, the objective of the current study was to document various EVM practices used in controlling gastro-intestinal parasites in village chickens. Stratified random sampling was used to select 62 chicken farmers that were interviewed using a structured questionnaire About 70 and 96.7% of farmers provided housing and water for their chickens respectively whereas the rest did not. The chief role of chickens was meat provision (91.7%). Most households (86%) reported parasite problems in chickens, particularly gastro-intestinal parasites. Eighty-three percent of the interviewed respondents use medicinal plants to control both internal and external parasites in chickens. Use of plants increased with parasite incidences (r=0.347; P<0.01). Mainly gastro-intestinal parasites were problematic and were largely controlled by medicinal plants. Further research on pharmacological properties, safety and efficacy of these plants is important for improved chicken productivity and hence rural livelihood.