DNA Bank

Ecology and Evolution | African Centre for DNA Barcoding – ACDB

Contact: Prof. Kowiyou Yessoufou

1. Background – Vision and Mission

The African Centre for DNA Barcoding (ACDB) was formally established within the department of botany and plant biotechnology, University of Johannesburg, in 2010-2011. The vision of ACDB is to be the first African reference in i) DNA data generation for continental flora/fauna/fungi, and ii) translation of generated DNA data into research and development.

Four specific missions were set to accomplish this vision:

• Documentation of African flora, fauna and macro-fungi in the form of DNA bank, including a reference database of DNA barcode in BOLD,
• Rendering DNA sequencing services to universities, governments, or organizations,
• Training of students and professionals in DNA barcoding/genomics and its applications in taxonomy, ecology and conservation,
• Contribution to global debate on biodiversity and conservation from an evolutionary perspective in the form of scientific publications, seminars and conferences

2. Research Focus at ACDB

• General focus – At ACDB, our general focus is conservation biology. Specifically, we aim to understand the evolutionary and ecological forces that create species/lineages and structure communities across space and time, bearing in mind how this understanding can guide conservation decisions at local and global scales. Our research address conservation issues from various angles with phylogenetic tools as the common denominator of our research.

Specific focus:

DNA barcoding, Genomics and Taxonomy – How many species are out there on Earth? Nobody knows with certainty. What we do know is that it is not possible to appropriately conserve biodiversity if we have a biased knowledge of its extent. Interestingly, several studies used statistical techniques to predict the extent of biodiversity and quantify the remaining efforts to accelerate the discovery and description of new species. The difference in the outcomes of their predictions is striking ranging from ~2 million to ~1 trillion species. Clearly, the predictions reveal that the size of biodiversity is far greater than the 1.5 million species we currently know of. This is an important knowledge gap that needs to be addressed, especially in megadiverse countries, e.g., South Africa, which is home to ~10% of the world’s plant species richness with more than 50% being endemic plant species.

In light of the alarming statistics around the ongoing biodiversity crisis, pre-emptive and urgent actions are required to prevent species loss at all costs. However, how can such actions take place in an effective way if we have limited knowledge of the extent of existing species diversity? More concerning is that several unknown species are undoubtedly sliding into extinction simply because they are unknown to science. There is therefore a need to accelerate biodiversity assessment to unveil the extent of species richness and make informed decisions. This calls for strong commitments to estimate the potential number of currently unknown species so that appropriate efforts (number of taxonomists, funds, time, and resources required) can be estimated, planned and deployed.

At the same time, not only the number of taxonomists is declining rapidly worldwide with dire consequences on conservation but so too is the species description rate. In such context (exponential decline of biodiversity, poor knowledge of the extent of biodiversity, unaffordability of traditional taxonomy in the developing world, rarity of taxonomists), DNA barcoding and molecular taxonomy become an imperative.

At ACDB, we host the state-of-the-art equipment for DNA barcoding, molecular taxonomy to accelerate biodiversity assessment and evolutionary studies.

Extinction risk, Biodiversity and Conservation – We are witnessing an unprecedented biodiversity crisis largely driven by anthropogenic pressures. Some even refer to this crisis as the 6^th mass extinction.

This global crisis requires robust, quick and urgent actions targeting various facets of biodiversity if we are to bend the curve of biodiversity loss and meet the ambitious targets set to accelerate recovery. Conservation planning has traditionally focused on species richness and endemism, but the protection of evolutionary processes is now a priority, especially in the context of the ongoing biodiversity crisis.

At ACDB, we contribute, using modern statistics and AI tools, to accelerate extinction risk assessment and analyse risk patterns and impacts on the tree of life.

Ecology of alien invasive species – Alien species are found outside their native geographic ranges due to accidental or intentional introduction by humans. Their intentional introductions are motivated by the services these plants provide to humans, including plantation, medicinal or horticulture, restoration, recreation and ornamentals. Species introductions are further aided by domestic and global travels and trades, as well as global climate change. Once introduced into the recipient ecosystem and overcome ecological and anthropogenic barriers, they naturalize and become invasive and threaten the ecological integrity of the recipient ecosystems. For example, several studies reported that Invasive Alien Species (IAS) may drive local extinction, disrupt pollination and ecological networks, alter ecosystem functioning, lead to economic losses and impact negatively on human well-being. Although efforts are deployed towards biological controls of IASs, the main control strategy used is physical removal of IASs from the invaded ecosystems. Unfortunately, the success of this strategy is very limited, and this limitation is undoubtedly linked to the strategies used which do not account for the population dynamic strategies of the IASs. Understanding the population dynamic strategies of IASs is key to reveal which life stages (seedling, juveniles, sapling, adults) contribute significantly and in a unique way to the dynamics of the populations of IASs. The benefit of such knowledge is that it allows targeted efforts in the control of the invasion process. At ACDB, we aim to fill our knowledge gaps in this area.

Population dynamics – Plant resources are variously harvested to meet human needs. While some plants are lethally harvested (e.g., for roots or timber through logging), others are non-lethally harvested in search of non-timber forest products (e.g., fruits, leaves, resin and barks), and this practice is observed worldwide. Plant harvesting may bear heavy ecological and biological consequences, e.g., delayed reproduction, plant vulnerability to insect attacks reduced intraspecific competition, decreased flower visitation and pollination rates, limitation of various facilitative biotic interactions, negatively affecting population dynamics, and local extinction. As such, harvesting plant products in a sustainable manner becomes an imperative. To this end, classic forest management theory assumes that a high seedling density of a given species would ensure the sustainability of its population as long as forest management strategy accounts for it. However, this systematic use of seedling density as a silver bullet has been increasingly questioned both from theoretical and practical perspectives. Therefore, it is imperative to model population dynamics of each species to understand which life stage is more sensitive to perturbations. In other words, forest management strategies must be informed of elasticity analysis of both long- and short-term population dynamics if they are to develop more realistic management plans. At ACDB, we are working towards the development of mathematical models of population dynamics at least for our threatened species in Africa to understand how these species respond to environmental changes.