H. Van der Bank

DNA BARCODING REVEALS MICRO-EVOLUTIONARY CHANGES AND RIVER SYSTEM-LEVEL PHYLOGEOGRAPHIC RESOLUTION OF AFRICAN SILVER CATFISH, SCHILBE INTERMEDIUS (ACTINOPTERYGII: SILURIFORMES: SCHILBEIDAE) FROM SEVEN POPULATIONS ACROSS DIFFERENT AFRICAN RIVER SYSTEMS

Background. Under the tropics, less than 40% of known fishes are identified to species-level. Further, the ongo- ing global change poses unprecedented threat to biodiversity, and several taxa are likely to go extinct even before they could be described. Traditional ecological theory suggests that species would escape extinction risk posed by global threats (e.g., climate change) only by migrating to new environments. In this study, we hypothesise that micro-evolutionary changes (evolution within species and populations) are also important mechanisms for the survival of Schilbe intermedius in Africa, a continent subjected to uneven distribution of climate severity. Materials and methods. Using the mitochondrial cytochrome c oxidase subunit I (COI) gene, known as animal DNA barcode, we tested this hypothesis by analysing the genetic diversity and phylogenetic relations between seven populations of S. intermedius across different African river systems. Results. We reveal a clear geographical patterning in genetic variations, with three clear clusters (southern Africa, eastern Africa, and western Africa). In southern Africa, the South African population is distinct from that of Namibia and Botswana. In addition, within Nigerian populations of silver catfish, two sub-clusters emerged from two isolated river systems. We suggest that the phylogeographic pattern within African silver catfish pop- ulations mirror the past effects of selection and gene flow, and that the split within Nigerian silver catfish popu- lations might be the result of micro-evolutionary adaptive responses to local selection pressures. Conclusion. We suggest that the strong genetic difference in African silver catfish among geographically isolat- ed river systems might be the result of in situ micro-evolutionary adaptive responses to changing environments, and that DNA barcode has potential beyond species delimitation.

DNA Barcode Efficacy for the Identification of Economically Important Scale Insects (Hemiptera: Coccoidea) in South Africa

Scale insects (Sternorrhyncha: Coccoidea) are one of the most invasive groups of insects. They are sedentary, cryptic, and often resemble the plant parts that they feed on. This coupled with increased international trade in fresh agricultural produce, makes them a major quarantine risk. An important limitation in controlling these pests involves species identification. When scale insects are intercepted on imported produce, they must be rapidly and accurately identified, using morphology-based keys. This is time-consuming and requires extensive taxonomic experience. In addition, intercepted specimens are often immature or damaged, making identification difficult or impossible. A reliable complementary tool is needed for identification. DNA barcoding may be of great value for this purpose. In this study we investigate the suitability of the nuclear regions 18S and 28S as complementary DNA barcodes to the mitochondrial CO1 gene, across 10 scale insect families. Combining multiple criteria, our results indicate that the concatenation of CO1 and 28S greatly improves the identification success rate of scale insects to 91.5 %, demonstrating the utility of DNA barcoding in pest management.

Ten years of barcoding at the African Centre for DNA Barcoding

The African Centre for DNA Barcoding (ACDB) was established in 2005 as part of a global initiative to accurately and rapidly survey biodiversity using short DNA sequences. The mitochondrial cytochrome c oxidase 1 gene (CO1) was rapidly adopted as the de facto barcode for animals. Following the evaluation of several candidate loci for plants, the Plant Working Group of the Consortium for the Barcoding of Life in 2009 recommended that two plastid genes, rbcLa and matK, be adopted as core DNA barcodes for terrestrial plants. To date, numerous studies continue to test the discriminatory power of these markers across various plant lineages. Over the past decade, we at the ACDB have used these core DNA barcodes to generate a barcode library for southern Africa. To date, the ACDB has contributed more than 21 000 plant barcodes and over 3000 CO1 barcodes for animals to the Barcode of Life Database (BOLD). Building upon this effort, we at the ACDB have addressed questions related to community assembly, biogeography, phylogenetic diversification, and invasion biology. Collectively, our work demonstrates the diverse applications of DNA barcoding in ecology, systematics, evolutionary biology, and conservation.

Exposing the illegal trade in cycad species (Cycadophyta: Encephalartos) at two traditional medicine markets in South Africa using DNA barcoding.

Species in the cycad genus Encephalartos are listed in CITES Appendix I and as Threatened or Protected Species in terms of South Africas National Environmental Management: Biodiversity Act (NEM:BA) of 2004. Despite regulations, illegal plant harvesting for medicinal trade has continued in South Africa and resulted in declines in cycad populations and even complete loss of sub-populations. Encephalartos is traded at traditional medicine markets in South Africa in the form of bark strips and stem sections; thus, determining the species traded presents a major challenge due to a lack of characteristic plant parts. Here, a case study is presented on the use of DNA barcoding to identify cycads sold at the Faraday and Warwick traditional medicine markets in Johannesburg and Durban, respectively. Market samples were sequenced for the core DNA barcodes (rbcLa and matK) as well as two additional regions: nrITS and trnH-psbA. The barcoding database for cycads at the University of Johannesburg was utilized to assign query samples to known species. Three approaches were followed: tree-based, similarity-based, and character-based (BRONX) methods. Market samples identified were Encephalartos ferox (Near Threatened), Encephalartos lebomboensis (Endangered), Encephalartos natalensis (Near Threatened), Encephalartos senticosus (Vulnerable), and Encephalartos villosus (Least Concern). Results from this study are crucial for making appropriate assessments and decisions on how to manage these markets.

Systematic reinstatement of Schilbe depressirostris (Peters, 1852), based on differences in DNA barcoding and morphology, from Schilbe intermedius Rüppell, 1832 (Siluriformes, Schilbeidae)

Climate change poses an unprecedented threat to biodiversity worldwide. Consequently, unrecognised taxa may not receive adequate conservation attention to survive. We used molecular and morphological data to address the challenge of species delimitation within the genus Schilbe. The presence or absence of an adipose fin and distribution based on east-flowing, conceivably faster-flowing, or west-flowing, probably more slow-flowing, river systems were considered. Distinctive geographic patterns in genetic variation within southern, eastern, and western African populations were revealed. Particularly, the South African population is distinct from those of Namibia, Botswana and Nigeria. No individuals with rudimentary adipose fins were found at any locality, but specimens from three localities either had or did not have adipose fins. These mixed occurrences are suspected to be a result of human interventions, and that the presence of rudimentary adipose fins in the east African species could be an adaptive feature that serves to stabilise these fish in faster currents. In addition, the genetic divergence observed among African silver catfish from geographically isolated river systems is conceivably the result of micro-evolutionary adaptive responses to different environmental conditions. Collectively, these results distinguish S. depressirostris from S. intermedius.

Low allozyme variation in tigerfish Hydrocynus vittatus (Teleostei: Alestidae) from the Okavango panhandle, with notes on the selection of candidates for artificial breeding

To ensure the utilisation of optimal tigerfish gene pools for artificial propagation, the hypothesis that tigerfish from the Okavango system should have greater heterozygosity than those from smaller river systems was tested. This electrophoretic analysis provides the first report of the quantity and pattern of genetic variation for tigerfish of the Okavango Delta to be considered for artificial propagation and as candidates for an evolutionary significant unit. Mean heterozygosity was 1% in the Okavango, as compared to 1.9% in the Upper Zambezi and 5.6% in the Olifants River systems. Possible reasons for this anomaly, in terms of the Hardy-Weinberg principle, include the founder effect caused when the Okavango and Zambezi rivers became separated, and/or that the Okavango is a more stable system and therefore that a large variation might not be required in its individuals for survival. Significant differences of genotypes were found among all populations previously studied. The selection of potential candidates for artificial breeding is discussed.