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

• Published in: Communications biology Vol. 7; no. 1; pp. 792 - 14
• Main Authors: Talenti, Andrea, Wilkinson, Toby, Cook, Elizabeth A., Hemmink, Johanneke D., Paxton, Edith, 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 D., 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 J.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 29.06.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 45; 631/208/457; 631/208/726; Africa South of the Sahara; Animals; Biomedical and Life Sciences; Buffaloes - genetics; Evolutionary conservation; Evolutionary genetics; Gene Flow; Genetic structure; Genetic Variation; Genetics, Population; Genome; Genomes; Genomic analysis; Genomics - methods; Geographical distribution; Immune response; Infectious diseases; Life Sciences; Phylogeny; Population genetics; Population structure; Population studies; Syncerus caffer; Africa South of the Sahara
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-024-06481-2

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. The generation of a de novo contiguous reference genome for the African buffalo reveals that continent wide population structure is influenced by isolation by distance, and signatures of selection suggest a strong effect of infectious disease.