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 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.
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dig-cirad-fr-609928 |
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Francia |
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Bibliográfico |
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Europa del Oeste |
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Biblioteca del CIRAD Francia |
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eng |
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L10 - Génétique et amélioration des animaux buffle africain génétique des populations génome variation génétique évolution génomique distribution géographique phylogénie savane Syncerus caffer http://aims.fao.org/aos/agrovoc/c_167 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_5083 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_6825 http://aims.fao.org/aos/agrovoc/c_d0debf2f http://aims.fao.org/aos/agrovoc/c_4964 http://aims.fao.org/aos/agrovoc/c_7608 http://aims.fao.org/aos/agrovoc/c_8516 http://aims.fao.org/aos/agrovoc/c_3161 http://aims.fao.org/aos/agrovoc/c_8038 http://aims.fao.org/aos/agrovoc/c_4086 http://aims.fao.org/aos/agrovoc/c_1030 http://aims.fao.org/aos/agrovoc/c_7252 L10 - Génétique et amélioration des animaux buffle africain génétique des populations génome variation génétique évolution génomique distribution géographique phylogénie savane Syncerus caffer http://aims.fao.org/aos/agrovoc/c_167 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_5083 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_6825 http://aims.fao.org/aos/agrovoc/c_d0debf2f http://aims.fao.org/aos/agrovoc/c_4964 http://aims.fao.org/aos/agrovoc/c_7608 http://aims.fao.org/aos/agrovoc/c_8516 http://aims.fao.org/aos/agrovoc/c_3161 http://aims.fao.org/aos/agrovoc/c_8038 http://aims.fao.org/aos/agrovoc/c_4086 http://aims.fao.org/aos/agrovoc/c_1030 http://aims.fao.org/aos/agrovoc/c_7252 |
spellingShingle |
L10 - Génétique et amélioration des animaux buffle africain génétique des populations génome variation génétique évolution génomique distribution géographique phylogénie savane Syncerus caffer http://aims.fao.org/aos/agrovoc/c_167 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_5083 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_6825 http://aims.fao.org/aos/agrovoc/c_d0debf2f http://aims.fao.org/aos/agrovoc/c_4964 http://aims.fao.org/aos/agrovoc/c_7608 http://aims.fao.org/aos/agrovoc/c_8516 http://aims.fao.org/aos/agrovoc/c_3161 http://aims.fao.org/aos/agrovoc/c_8038 http://aims.fao.org/aos/agrovoc/c_4086 http://aims.fao.org/aos/agrovoc/c_1030 http://aims.fao.org/aos/agrovoc/c_7252 L10 - Génétique et amélioration des animaux buffle africain génétique des populations génome variation génétique évolution génomique distribution géographique phylogénie savane Syncerus caffer http://aims.fao.org/aos/agrovoc/c_167 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_5083 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_6825 http://aims.fao.org/aos/agrovoc/c_d0debf2f http://aims.fao.org/aos/agrovoc/c_4964 http://aims.fao.org/aos/agrovoc/c_7608 http://aims.fao.org/aos/agrovoc/c_8516 http://aims.fao.org/aos/agrovoc/c_3161 http://aims.fao.org/aos/agrovoc/c_8038 http://aims.fao.org/aos/agrovoc/c_4086 http://aims.fao.org/aos/agrovoc/c_1030 http://aims.fao.org/aos/agrovoc/c_7252 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 Continent-wide genomic analysis of the African buffalo (Syncerus caffer) |
description |
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. |
format |
article |
topic_facet |
L10 - Génétique et amélioration des animaux buffle africain génétique des populations génome variation génétique évolution génomique distribution géographique phylogénie savane Syncerus caffer http://aims.fao.org/aos/agrovoc/c_167 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_5083 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_6825 http://aims.fao.org/aos/agrovoc/c_d0debf2f http://aims.fao.org/aos/agrovoc/c_4964 http://aims.fao.org/aos/agrovoc/c_7608 http://aims.fao.org/aos/agrovoc/c_8516 http://aims.fao.org/aos/agrovoc/c_3161 http://aims.fao.org/aos/agrovoc/c_8038 http://aims.fao.org/aos/agrovoc/c_4086 http://aims.fao.org/aos/agrovoc/c_1030 http://aims.fao.org/aos/agrovoc/c_7252 |
author |
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 |
author_facet |
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 |
author_sort |
Talenti, Andrea |
title |
Continent-wide genomic analysis of the African buffalo (Syncerus caffer) |
title_short |
Continent-wide genomic analysis of the African buffalo (Syncerus caffer) |
title_full |
Continent-wide genomic analysis of the African buffalo (Syncerus caffer) |
title_fullStr |
Continent-wide genomic analysis of the African buffalo (Syncerus caffer) |
title_full_unstemmed |
Continent-wide genomic analysis of the African buffalo (Syncerus caffer) |
title_sort |
continent-wide genomic analysis of the african buffalo (syncerus caffer) |
url |
http://agritrop.cirad.fr/609928/ http://agritrop.cirad.fr/609928/1/s42003-024-06481-2.pdf |
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1807170505468280832 |
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dig-cirad-fr-6099282024-08-02T13:41:59Z http://agritrop.cirad.fr/609928/ http://agritrop.cirad.fr/609928/ 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. Communications Biology, 7:792, 14 p.https://doi.org/10.1038/s42003-024-06481-2 <https://doi.org/10.1038/s42003-024-06481-2> 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 eng 2024 Communications Biology L10 - Génétique et amélioration des animaux buffle africain génétique des populations génome variation génétique évolution génomique distribution géographique phylogénie savane Syncerus caffer http://aims.fao.org/aos/agrovoc/c_167 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_2745 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_5083 http://aims.fao.org/aos/agrovoc/c_13325 http://aims.fao.org/aos/agrovoc/c_6825 http://aims.fao.org/aos/agrovoc/c_d0debf2f Mozambique République-Unie de Tanzanie Zimbabwe Gabon Ouganda Kenya Botswana Afrique du Sud http://aims.fao.org/aos/agrovoc/c_4964 http://aims.fao.org/aos/agrovoc/c_7608 http://aims.fao.org/aos/agrovoc/c_8516 http://aims.fao.org/aos/agrovoc/c_3161 http://aims.fao.org/aos/agrovoc/c_8038 http://aims.fao.org/aos/agrovoc/c_4086 http://aims.fao.org/aos/agrovoc/c_1030 http://aims.fao.org/aos/agrovoc/c_7252 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/609928/1/s42003-024-06481-2.pdf text cc_by info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ https://doi.org/10.1038/s42003-024-06481-2 10.1038/s42003-024-06481-2 info:eu-repo/semantics/altIdentifier/doi/10.1038/s42003-024-06481-2 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1038/s42003-024-06481-2 info:eu-repo/semantics/dataset/purl/https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_902825105.1/ info:eu-repo/semantics/dataset/purl/https://www.ncbi.nlm.nih.gov/bioproject/PRJEB59220/ info:eu-repo/semantics/dataset/purl/https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB59220 info:eu-repo/semantics/dataset/purl/https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB36588 info:eu-repo/semantics/dataset/purl/https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB36587 |