Heritage Cases

We are applying for the destructive sampling of chacma baboon teeth from the archaeological sites of Schroda, Le6, Msuluzi Confluence, Mhlwazini, Rose Cottage Cave, and Heuningneskrans. The remains are to be included in a larger research project entitled, "Studying genetic potential of adaptation of chacma baboons to climate changes in South Africa to draw appropriate management and conservation recommendations". Archaeological remains represent micro-environments that can preserve sufficient ancient DNA (aDNA) molecules to reconstruct entire genome sequences from ancient populations. Purpose and scientific merit Observations and modelling reported over the last decade provide compelling evidence that the impacts of climate change on the world’s biodiversity are likely to be significant. Due to anthropogenic climate changes, the world is facing an increased mean temperature of 3°C-6°C, leading to increases in fire incidence and severity, storm activity, the length of drought and flood conditions, etc. Austral African regions are among the more impacted by climate changes and will continue to be among the most impacted regions of the world by climate changes (Scholes & Engelbrecht 2021). Indeed, reports showed that most South African biomes will likely be threatened by 2050, by increased global warming, lower rainfall, and desertification (Lawal et al. 2019). In these biomes, under the semi-arid climatic conditions, even a few degrees increase in temperature and a few millimetres decrease in rainfall could cause a decline in the biodiversity of several species. Recent climate change research has indicated that many species will become extinct by the year 2100 because of these rapid changes in climatic conditions. Facing such a situation, it is fundamental to evaluate if wild animals have the ecological, biological, and evolutionary potential to adapt. Will all populations be able to respond to these changes? And finally, how managers should integrate the information on the adaptive potential to manage the wild animal populations? Currently, there is limited knowledge on the level of the combined ecological, biological, and genetic adaptive potential of wild animals to these rapid modifications that affect their environments. The main goal of this project is to fill this as much as possible this gap by analysing the adaptive potential of a non-human primate species, the chacma baboon (Papio ursinus). This project is articulated around two main aims: Objective 1: Evolutionary history and genetic adaptation of chacma baboons in different environments Key Questions: 1. What is the evolutionary history of chacma baboons in South Africa? 2. Which genetic traits allowed the chacma baboons to adapt to different biomes, particularly warmer environments: looking to the past to understand the future. Objective 2: Identify suitable strategies to conserve and manage wild populations facing warmer climate changes. Key Questions: 1. Facing global warming, what will be chacma baboon’s distribution by 2050? 2. What is the most suitable conservation recommendation to manage chacma baboons facing climate changes? Outcomes One way to reconstruct the evolutionary history and investigate the genetic adaptation of organisms to new environments is to analyse genetic variation across the whole genomes of natural populations of a species. Through the genetic data that will be extracted from ancient and modern samples collected in different geographic zones, we will generate genomic data that will allow us to first characterise the population structure and history of chacma baboons in South Africa and then to identify genomic regions that allowed this species to adapt to different biomes. To study genetic adaptation of an organism in different and/or new environments, one pre-requisite is to characterise its population genetic structure and evolutionary history. We will thus answer the following questions: what are the relationships between populations from South Africa? What are the historical population sizes of the populations? Which populations exchanged migrants? To address these questions, we will use genetics and genomic tools, to determine how and when chacma baboons evolved through history. When an environmental change occurred, it is expected to be accompanied by adaptive evolutionary changes that allow the animal to survive and reproduce. We will identify genomic regions that played a role in chacma baboons’ adaptation in different biomes over their evolutionary history. We will perform comparative genomic analyses to identify the regions of the genome that have been under selection and that have thus been involved in the adaptation of chacma baboons to different biomes. Currently, there is no common adapted strategic planning to manage and conserve animal species considering warmer climate changes, integrating ecological, biological, and genetic data. We need to secure and mobilise all these resources now to have options for the future. To predict chacma baboon’s distribution, we will use ecological niche modelling and integrate information on genetic variability and local adaptation. WorldClim bioclimate data will be used to project current and future niches for each biome genetic data in the analyses to quantify and compare niches. Material required Archaeological and historic remains represent microenvironments that can preserve sufficient ancient DNA (aDNA) molecules to reconstruct entire genome sequences. As such, screening ancient chacma baboons’ remains from different southern African areas may unlock access to the first set of ancient genomic data on chacma baboons. These new data will be analysed with data obtained from recently collected fresh samples of chacma baboon populations. Finally, all remaining samples (DNA and remains) will be sent to the repositories at the end of the project. Extant specimens from DNMNH and archaeological specimens from Unisa, Wits, Wits ESI, KZN Museum, University of Pretoria and DNMCH have been selected for this study. These specimens have been chosen according to their availability (more than one specimen available), state (entire tooth, bone, etc.), location (different geographic locations) and dates of collection (from 1940-1970 and older archaeological specimens). To take the most of these samples, we will also conduct micro-wear analysis and CT-scans before aDNA analysis and proceed to stable isotope analysis to study the ancient diet of these chacma baboon populations. Expected scientific and societal impacts Results and conclusions from this project will be disseminated through articles in peer-reviewed journals, and through flagship journals with open access. Results will be made available through open repositories, such as the French HAL and the European PMC, in agreement with the Feuille de route des infrastructures nationales des infrastructures de recherche du Ministère (2016-2020). At least five top-level articles can be expected to result from this project. Results will also be disseminated at international conferences and workshops. Scientific team Dr Virginie Rougeron, (Nelson Mandela University) will manage the overall project. She is an evolutionary biologist and geneticist, specialising in the study of organism’s adaptation and evolutionary history. The team will mostly be based at the international research laboratory REHABS, based at Nelson Mandela University (George Campus, South Africa) and several international scientists will help in the supervision of the project. The team members include Dr Annie Antonites (DNMNH), Dr Aurore Val (Laboratoire Méditerranéen de Préhistoire Europe Afrique, CNRS), Dr Franck Prugnolle (NMU), and Locadia Dzingwena (MSc student, NMU). Prof Orlando Ludovic will conduct the aDNA analysis at the Centre for Anthropobiology and Genomics of Toulouse, France (www.cagt.cnrs.fr). Dr Paul Duru will direct the CT-scanning at the Institut of Fluid Mechanics of Toulouse, France (https://www.imft.fr/en/laboratory-2/).