ADVANCING BIODIVERSITY INFORMATICS AND ECOLOGICAL MODELLING
Environmental scientists urgently need a unified strategy for biodiversity data management as concerns over climate change, land use change, pollution, and natural resource exploitation rise and the global crisis for biodiversity conservation continues.
The Mathematical Sciences Hub (BioMath) in the Mathematical Sciences Department at Stellenbosch University is exploring innovative new ways to synthesise and analyse vast amounts of ecological data to develop a more holistic understanding of our environment. This type of understanding is essential for park managers and scientists to design ways to halt, or ideally even reverse, biodiversity loss.
Together with the NITheCS and South African National Parks (SANParks), BioMath is working towards a future where biodiversity data is more easily accessible by designing user-friendly tools, reproducible workflows and models to consolidate biodiversity data sources and predict future dynamics of biodiversity change.
Research Programme Team Members and Collaborating Researchers
- Emmanuel Dufourq (African Institute for Mathematical Sciences)
- Cang Hui (Stellenbosch University)
- Lorène Jeantet (African Institute for Mathematical Sciences)
- Pietro Landi (Stellenbosch University)
- Sandra MacFadyen (Stellenbosch University)
- Vernon Visser (University of Cape Town)
Administrative Team Members
- Hanlie Swart
- Mathilda van der Vyver
Current projects
Workshop on Evolutionary Game Theory to Advance Ecological Science [12-15 September 2023]
Venue: Lovane Guesthouse, Stellenbosch
Hosted by: the Mathematical Biosciences Hub (BioMath), Stellenbosch University and NITheCS
DETAILS
The workshop brings together a team of mathematicians, evolutionary ecologists, theoretical ecologists, and data scientists, to tackle a list of emerging questions in the field of community ecology, invasion science, and biodiversity informatics.
The workshop will use evolutionary game theory to model open ecological communities in the face of constant invasions. The fresh insights from this approach will help us understand how some species may thrive and become invasive while others fail.
Attendees will collaborate on a research article that tackles key hurdles for estimating community evolution and transition with trait-mediated interaction kernels. The workshop will also discuss potential workflows for model testing using open-access databases, such as GBIF and TRY.
Besides the BioMath research team, the workshop also features experts in various domains:
- Thomas Koffel (Université Lyon, France): Prof Koffel is a distinguished theoretical ecologist and evolutionary biologist with a diverse background in fundamental physics and adds a unique perspective to the workshop.
- Maarten Trekels (Meise Botanic Garden, Belgium): As a Biodiversity Data Scientist, Maarten is instrumental in the development of standards and open data in biodiversity informatics.
- Fabio Dercole (Politecnico di Milano, Italy): Prof Dercole, an Associate Professor of Systems and Control Theory, brings his expertise in complex systems, nonlinear dynamics, and Citizen Science projects to the event.
- Mihaja Ramanantoanina (University of Pretoria): Dr Ramanantoanina is a Lecturer in the Department of Mathematics and Applied Mathematics. She is an expert in numerical simulations with differential equations, with a focus on eco-evolutionary modelling.
Stay tuned: Workshop outcomes will be presented after the event. Follow our group’s progress, insights, and upcoming initiatives.
Ecology Hackathon [October 2023]
We will host a hackathon in late-October to develop workflows (and/or Wiki pages) relevant to important unanswered questions in ecology. Prizes, totalling R50 000.00 up for grabs. Watch this space!
Carbon sequestration in Savanna Ecosystems [November 2023]
Assess the role of Savanna ecosystems in global carbon accounting measures. Review the current state of knowledge in this field, and assess the practical implementation using study sites in Kenya and the Kruger National Park. The carbon credit market has grown exponentially in the past few years. Savannas represent the third largest global store of carbon after tropical and temperate forests. Due to the relative difficulty in estimating carbon stores in savanna systems, which are subject to much higher environmental variability, limited research has focussed here. Despite these challenges, we will explore the use of remote sensing of savanna carbon stores, an active field of research, using different machine learning, mechanistic and traditional parametric approaches.
An ecologist’s data pipeline toolkit [December 2023]
Develop a biodiversity data pipeline that is locally relevant and globally integrative. The pipeline aims to improve the management, presentation, discovery, exploration, integration, and analysis of biodiversity data. We aim to develop reproducible workflows that ecologists (non-data or computer scientists) can to use as a toolkit for local biodiversity data pipeline design and implementation. The programme will also focus on identifying challenges facing biodiversity informatics in South Africa, with an emphasis on developing solutions for national biodiversity monitoring bodies and protected area managers, like those in SANParks.
Behavioural analysis of the endangered African penguin [December 2023]
Discover novel insights into the behaviours of the Endangered African penguin (Spheniscus demersus). Not enough behavioural insights are known about this species with respect to different contexts. We will develop automated machine learning algorithms that can learn about penguin behaviours – from video and acoustic recordings – within a colony setting and within an individual or smaller group setting. Different contexts will be analysed such as penguins in captivity as opposed to in the wild, seasonality and how the presence of humans or other species impact their individual and social behaviours. Video and acoustic data will be collected at key sites such as Stony Point, Simon’s Town, Algoa Bay, St Croix (Port Elizabeth) and the Two Oceans Aquarium.
World cloud of all presentations given at Biodiversity Informatics Symposium from 28 to 30 November 2022. Top words include: data, biodiversity, research and analysis, learning, communication, quality, collaborative, access and sharing, conservation and innovation.
Past projects
The first Biodiversity Informatics Symposium at the Stellenbosch Institute for Advanced Study (STIAS) took place from 28-30 November 2022. The symposium brought together researchers, managers and practitioners from across South Africa and abroad, with expertise in a wide range of fields including conservation, ecology, information science, information technology, mathematics and statistics.
Overall, the symposium was an important first step in moving the field of biodiversity informatics in South Africa forward. It allowed many important role-players the first opportunity to meet one another and to start building a community of practice around biodiversity informatics. Participants felt that future engagements of this type should be encouraged. They are eager to participate in these, as well as projects and collaborations that address some of the issues raised at the workshop. Condensing all symposium presentations into a word cloud (left), illustrates the urgent need to build capacity, encourage data sharing, support monitoring and biodiversity conservation programmes, centralise data access and services for integrative reporting.
News
PhD Position: Modelling community turnover, invasibility and impacts to safeguard biodiversity. Apply by 5 June 2023.
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Papers
2024
Basel AM, Simaika JP, Samways MJ, Midgley GF, Latombe G, MacFadyen S, Hui C. 2024. Drivers of compositional turnover in narrow-ranged and widespread dragonflies and damselflies in Africa. Insect Conservation and Diversity 17:501-511. https://doi.org/10.1111/icad.12718.
Batist CH, Dufourq E, Jeantet L, Razafindraibe MN, Randriamanantena F, Baden AL. 2024. An integrated passive acoustic monitoring and deep learning pipeline for black-and-white ruffed lemurs (Varecia variegata) in Ranomafana National Park, Madagascar. American Journal of Primatology. 86:e23599. https://doi.org/10.1002/ajp.23599.
Čuda K, Pyšková K, Hejda M, Foxcroft LC, MacFadyen S, Storch D, Tropek R, Zambatis G, Pyšek P. 2024. Habitat modifies the relationship between grass and herbivore species richness in a South African savanna. Ecology and Evolution. 14:e11167. https://doi.org/10.1002/ece3.11167.
Gibbs R, Landi P, Hui C. 2024. Heterogeneity in the resource landscape encourages increased cognitive and perceptive capabilities in foragers. Ecological Modelling. 492:110693. https://doi.org/10.1016/j.ecolmodel.2023.110693.
Hui C, MacFadyen S, Visser V, Groom Q, Isaac NJB. 2024. Editorial: Biodiversity informatics: building a lifeboat for high functionality data to decision pipeline. Frontiers in Ecology and Evolution 12:1386917. https://doi.org/10.3389/fevo.2024.1386917.
Kubyana MS, Landi P, Hui C. 2024. Adaptive rock-paper-scissors game enhances eco-evolutionary performance at cost of dynamic stability. Applied Mathematics and Computation. 468:128535. https://doi.org/10.1016/j.amc.2023.128535.
Lelong P, Besnard A, Girondot M, Habold C, Priam F, Giraudeau M, Le Loc’h G, Le Loc’h A, Fournier P, Fournier-Chambrillon C, Bustamante P, Dupont SM, Vincze O, Gros-Desormeaux J-R, Martin J, Bourgeois O, Lepori M, Régis S, Lecerf N, Lefebvre F, Aubert N, Frouin C, Flora F, Pimentel E, Pimentel M, Siegwalt F, Jeantet L, Chambault P, Hielard G, Arqué A, Arthus M, Louis-Jean L, Brador A, Giannasi P, Etienne D, Lecerf N, Chevallier P, Chevallier T, Meslier S, Landreau A, Maceno M, Larcher E, Le Maho Y, Chevallier D. 2024. Demography of endangered juvenile green turtles in face of environmental changes: 10 years of capture-mark-recapture efforts in Martinique. Biological Conservation. 291:110471. https://doi.org/10.1016/j.biocon.2024.110471.
Riccardi T, Wigley BJ, Kleyn L, Coetsee C, MacFadyen S, Attorre F, Malatesta L. 2024. First woody cover vegetation map of Kruger National Park in 1939–1944: Evidence from historical black and white aerial photography. Ecological Informatics. 81:102590. https://doi.org/10.1016/j.ecoinf.2024.102590.
Roy HE, Pauchard A, Stoett PJ, Truong TR, Meyerson LA, Bacher S, Galil BS, Hulme PE, Ikeda T, Kavileveettil S, McGeoch MA, Nuñez MA, Ordonez A, Rahlao SJ, Schwindt E, Seebens H, Sheppard AW, Vandvik V, Aleksanyan A, Kwame MA, August T, Blanchard R, Brugnoli E, Bukombe JK, Bwalya B, Byun C, Camacho-Cervantes M, Cassey P, Castillo ML, Courchamp F, Dehnen-Schmutz K, Dudeque Zenni R, Egawa C, Essl F, Fayvush G, Fernandez RD, Fernandez M, Foxcroft LC, Genovesi P, González Martínez AI, Groom QJ, Helm A, Herrera I, Hiremath AJ, Howard PL, Hui C, Ikegami M, Keskin E, Koyama A, Ksenofontov S, Lenzner B, Lipinskaya T, Lockwood JL, Mangwa DC, Martinou AF, McDermott SM, Morales CL, Müllerová J, Mungi NA, Munishi LK, Ojaveer H, Pagad SN, Pallewatta PKN, Peacock LR, Per E, Pergl J, Preda C, Pyšek P, Rai RK, Ricciardi A, Richardson DM, Riley S, Rono BJ, Ryan-Colton E, Saeedi H, Shrestha BB, Simberloff D, Tawake A, Tricarico E, Vanderhoeven S, Vicente J, Vilà M, Wanzala W, Werenkraut V, Weyl OLF, Wilson JRU, Xavier RO, Ziller SR. 2024. Curbing the major and growing threats from invasive alien species is urgent and achievable. Nature Ecology and Evolution 8:1216-1223. https://doi.org/10.1038/s41559-024-02412-w.
Sikazwe G, Yocgo REE, Landi P, Richardson DM, Hui C. 2024. Current and future scenarios of suitability and expansion of cassava brown streak disease, Bemisia tabaci species complex, and cassava planting in Africa. PeerJ. 12:e17386. https://doi.org/10.7717/peerj.17386.
Sikazwe G, Yocgo REE, Landi P, Richardson DM, Hui C. 2024. Managing whitefly development to control cassava brown streak virus coinfections. Ecological Modelling. 493:110753. https://doi.org/10.1016/j.ecolmodel.2023.110753.
Yahaya M, Rodger J, Landi P, Hui C. 2024. Emergence of structure in plant–pollinator networks: low floral resource constrains network specialisation. Oikos. e10533. https://doi.org/10.1111/oik.10533.
2023
Bell, W, Hoffman, MT, Visser, V, Kirsten T. 2023. Modelling land condition to augment Land Degradation Neutrality assessments – The succulent Karoo biome of South Africa as a case study. Journal of Arid Environments, 219, p.105086.
De Beer IW, Hui C, Botella C, Richardson DM. 2023. Drivers of compositional turnover of narrow-ranged versus widespread naturalised woody plants in South Africa. Frontiers in Ecology and Evolution 11:1106197. https://doi.org/10.3389/fevo.2023.1106197.
Frainer G, Dufourq E, Fearey J, Dines S, Probert R, Elwen S, Gridley T. 2023. Automatic detection and taxonomic identification of dolphin vocalisations using convolutional neural networks for passive acoustic monitoring. Ecological Informatics. 78:102291. https://doi.org/10.1016/j.ecoinf.2023.102291.
Hui C, Pyšek P, Richardson DM. 2023 Disentangling the relationships among abundance, invasiveness and invasibility in trait space. npj Biodiversity 2:13. https://doi.org/10.1038/s44185-023-00019-1.
Hui C, Richardson DM, Basel AM, Lagat VK, Latombe G. 2023. The macroecology of Acacia in Australia. In: Richardson DM, Le Roux JJ, Marchante E (eds.) Wattles: Australian Acacia species around the world. CAB International, Wallingford, UK, pages 41-57. https://doi.org/10.1079/9781800622197.0003.
Jeantet L, Dufourq E. 2023. Improving deep learning acoustic classifiers with contextual information for wildlife monitoring. Ecological Informatics. 77:102256. https://doi.org/10.1016/j.ecoinf.2023.102256.
Keet JH, Ellis AG, Hui C, Le Roux JJ. 2023. Responses of soil bacterial communities to invasive Australian acacias over large spatial scales. In: Richardson DM, Le Roux JJ, Marchante E (eds.) Wattles: Australian Acacia species around the world. CAB International, Wallingford, UK, pages 382-398. https://doi.org/10.1079/9781800622197.0024.
Kirsten, T, Hoffman, MT, Bell, WD and Visser, V. 2023. A regional, remote sensing-based approach to mapping land degradation in the Little Karoo, South Africa. Journal of Arid Environments, 219, p.105066.
2022
Bell, WD, Visser V, Kirsten T, Hoffman MT. 2022. An evaluation of different approaches which use Google Street View imagery to ground truth land degradation assessments. Environmental Monitoring and Assessment, 194(10), p.732.
Dufourq E, Batist C, Foquet R, Durbach I. 2022. Passive acoustic monitoring of animal populations with transfer learning. Ecological Informatics. 70:101688. https://doi.org/10.1016/j.ecoinf.2022.101688.
MacFadyen S, Altwegg R, Archibald S, Botha J, Bradshaw K, Carruthers J, De Klerk H, de Vos A, Distiller G, Gibbs R, Landi P, Midgley G, Moncrieff G, Munch Z, Mutanga O, Naidoo S, Ngwenya Z, Pretorius J, Robertson M, Skowno A, Slingsby J, Visser V, Van Wageningen G, Hui C. 2022. Drowning in data, thirsty for information and starved for understanding: Biodiversity informatics lifeboat for high functionality data to decision pipeline. Biological Conservation 274: 109736. doi: https://doi.org/10.1016/j.biocon.2022.109736.
Matthys, C, Jubase, N, Visser, V and Geerts, S. 2022. Distribution of Melaleuca rugulosa (Schlechtendal ex Link) Craven (Myrtaceae) in South Africa: assessment of invasiveness and feasibility of eradication. South African Journal of Botany, 148, pp.228-237.
Mirugwe A, Nyirenda J, Dufourq E. 2022. Automating bird detection based on webcam captured images using deep learning. Proceedings of the 43rd Conference of the South African Institute. 85. https://easychair.org/publications/paper/8gh7.