Continent-wide genomic analysis of the African buffalo (Syncerus caffer)

Talenti Andrea, Wilkinson Toby, Cook Elizabeth A., Hemmink Johanneke D., Paxton Edith A., Mutinda Matthew, Ngulu Stephen D., Jayaraman Siddharth, Bishop Richard P., Obara Isaiah, Hourlier Thibaut, Garcia Giron Carlos, Martin Fergal J., Labuschagne Michel, Atimnedi Patrick, Nanteza Anne, Keyyu Julius, Mramba Furaha, Caron Alexandre, Cornelis Daniel, Chardonnet Philippe, Fyumagwa Robert, Lembo Tiziana, Auty Harriet K., Michaux Johan, Smitz Nathalie, Toye Philip, Robert Christelle, Prendergast James G.D., Morrison Liam. 2024. Continent-wide genomic analysis of the African buffalo (Syncerus caffer). Communications Biology, 7:792, 14 p.

https://doi.org/10.1038/s42003-024-06481-2

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Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_902825105.1/ / Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/bioproject/PRJEB59220/ / Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB59220 / Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB36588 / Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB36587

Résumé : The African buffalo (Syncerus caffer) is a wild bovid with a historical distribution across much of sub-Saharan Africa. Genomic analysis can provide insights into the evolutionary history of the species, and the key selective pressures shaping populations, including assessment of population level differentiation, population fragmentation, and population genetic structure. In this study we generated the highest quality de novo genome assembly (2.65 Gb, scaffold N50 69.17 Mb) of African buffalo to date, and sequenced a further 195 genomes from across the species distribution. Principal component and admixture analyses provided little support for the currently described four subspecies. Estimating Effective Migration Surfaces analysis suggested that geographical barriers have played a significant role in shaping gene flow and the population structure. Estimated effective population sizes indicated a substantial drop occurring in all populations 5-10,000 years ago, coinciding with the increase in human populations. Finally, signatures of selection were enriched for key genes associated with the immune response, suggesting infectious disease exert a substantial selective pressure upon the African buffalo. These findings have important implications for understanding bovid evolution, buffalo conservation and population management.

Mots-clés Agrovoc : buffle africain, génétique des populations, génome, variation génétique, évolution, génomique, distribution géographique, phylogénie, savane, Syncerus caffer

Mots-clés géographiques Agrovoc : Mozambique, République-Unie de Tanzanie, Zimbabwe, Gabon, Ouganda, Kenya, Botswana, Afrique du Sud

Mots-clés libres : Genome, Population genetics

Classification Agris : L10 - Génétique et amélioration des animaux

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

Agences de financement hors UE : Bill and Melinda Gates Foundation, Foreign, Commonwealth and Development Office

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