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

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...

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Published inCommunications 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
LanguageEnglish
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
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Abstract 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.
AbstractList 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.
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.
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 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 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.
Abstract 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.
ArticleNumber 792
Author Nanteza, Anne
Auty, Harriet K.
Obara, Isaiah
Fyumagwa, Robert
Robert, Christelle
Paxton, Edith
Mutinda, Matthew
Cornelis, Daniel
Michaux, Johan
Hourlier, Thibaut
Ngulu, Stephen D.
Wilkinson, Toby
Labuschagne, Michel
Smitz, Nathalie
Caron, Alexandre
Lembo, Tiziana
Atimnedi, Patrick
Bishop, Richard P.
Mramba, Furaha
Cook, Elizabeth A.
Chardonnet, Philippe
Talenti, Andrea
Toye, Philip
Hemmink, Johanneke D.
Garcia Giron, Carlos
Keyyu, Julius D.
Martin, Fergal J.
Morrison, Liam J.
Jayaraman, Siddharth
Prendergast, James G. D.
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Snippet The African buffalo ( Syncerus caffer ) is a wild bovid with a historical distribution across much of sub-Saharan Africa. Genomic analysis can provide insights...
The African buffalo (Syncerus caffer) is a wild bovid with a historical distribution across much of sub-Saharan Africa. Genomic analysis can provide insights...
Abstract The African buffalo ( Syncerus caffer ) is a wild bovid with a historical distribution across much of sub-Saharan Africa. Genomic analysis can provide...
Abstract The African buffalo (Syncerus caffer) is a wild bovid with a historical distribution across much of sub-Saharan Africa. Genomic analysis can provide...
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SubjectTerms 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
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Title Continent-wide genomic analysis of the African buffalo (Syncerus caffer)
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