Animals; Gene Flow; Africa South of the Sahara; Genetics, Population; Phylogeny; Genetic Variation; Buffaloes/genetics; Genomics/methods; Genome; Buffaloes; Genomics; Medicine (miscellaneous); Biochemistry, Genetics and Molecular Biology (all); Agricultural and Biological Sciences (all)
Abstract :
[en] 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.
Disciplines :
Zoology
Author, co-author :
Talenti, Andrea ; The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom ; Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, EH25 9RG, United Kingdom
Wilkinson, Toby ; The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom ; Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, EH25 9RG, United Kingdom
Cook, Elizabeth A; International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya ; Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, P.O. Box 30709, Nairobi, 00100, Kenya
Hemmink, Johanneke D ; The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom ; Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, EH25 9RG, United Kingdom ; International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya ; Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, P.O. Box 30709, Nairobi, 00100, Kenya
Paxton, Edith; The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom
Mutinda, Matthew; Kenya Wildlife Service, P.O. Box 40241, Nairobi, 00100, Kenya
Ngulu, Stephen D; Ol Pejeta Conservancy, Private Bag, Nanyuki, 10400, Kenya
Jayaraman, Siddharth ; The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom
Bishop, Richard P; International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
Obara, Isaiah; Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany
Hourlier, Thibaut ; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
Garcia Giron, Carlos; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
Martin, Fergal J ; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
Labuschagne, Michel; Clinomics, Uitzich Road, Bainsvlei, Bloemfontein, 9338, South Africa
Nanteza, Anne; College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
Keyyu, Julius D; Tanzania Wildlife Research Institute, Box 661, Arusha, Tanzania
Mramba, Furaha; Vector and Vector-Borne Diseases Institute, Tanga, Tanzania
Caron, Alexandre ; ASTRE, University of Montpellier (UMR), CIRAD, 34090, Montpellier, France ; CIRAD, UMR ASTRE, RP-PCP, Maputo, 01009, Mozambique ; Faculdade Veterinaria, Universidade Eduardo Mondlan, Maputo, Mozambique
Cornelis, Daniel; CIRAD, Forêts et Sociétés, 34398, Montpellier, France ; Forêts et Sociétés, University of Montpellier, CIRAD, 34090, Montpellier, France
Chardonnet, Philippe; IUCN SSC Antelope Specialist Group co-chair, 92100, Boulogne, France
Fyumagwa, Robert; Tanzania Wildlife Research Institute, Box 661, Arusha, Tanzania
Lembo, Tiziana ; School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
Auty, Harriet K; School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
Michaux, Johan ; Université de Liège - ULiège > Integrative Biological Sciences (InBioS)
Smitz, Nathalie ; Royal Museum for Central Africa (BopCo), Leuvensesteenweg 13, 3080, Tervuren, Belgium
Toye, Philip; International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya ; Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, P.O. Box 30709, Nairobi, 00100, Kenya
Robert, Christelle; The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom ; Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, EH25 9RG, United Kingdom ; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, United Kingdom
Prendergast, James G D; The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom ; Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, EH25 9RG, United Kingdom
Morrison, Liam J ; The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom. liam.morrison@roslin.ed.ac.uk ; Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, EH25 9RG, United Kingdom. liam.morrison@roslin.ed.ac.uk
FCDO - Foreign, Commonwealth and Development Office BBSRC - Biotechnology and Biological Sciences Research Council BMGF - Bill and Melinda Gates Foundation Wellcome Trust
Funding text :
This research was funded in part by the Bill & Melinda Gates Foundation (USA) and with UK aid from the UK Foreign, Commonwealth and Development Office (Grant Agreement OPP1127286) under the auspices of the Centre for Tropical Livestock Genetics and Health (CTLGH), established jointly by the University of Edinburgh (UK), Scotland\u2019s Rural College (SRUC, UK), and the International Livestock Research Institute (UK). The findings and conclusions contained within are those of the authors and do not necessarily reflect positions or policies of the Bill & Melinda Gates Foundation nor the UK Government. The work was also supported by grants BBS/OS/GC/000012C, BBS/E/D/10002070, BBS/E/D/20002172 and BBS/E/D/20002174 from the Biotechnology and Biological Sciences Research Council (BBSRC, UK), and\u00A0grant OB 490/2\u20131 from\u00A0Deutsche Forschungsgemeinschaft (DFG, Germany). This research was conducted as part of the Consultative Group on International Agricultural Research (CGIAR) Program on Livestock (Kenya). International Livestock Research Institute (ILRI), Kenya, is supported by contributors to the CGIAR Trust Fund. CGIAR is a global research partnership for a food-secure future. Its science is carried out by 15 Research Centres in close collaboration with hundreds of partners across the globe (www.cgiar.org). Work carried out at EMBL, EBI was supported by the Wellcome Trust (WT222155/Z/20/Z) and BBSRC (BB/S020152/1).This research was funded in part by the Bill & Melinda Gates Foundation (USA) and with UK aid from the UK Foreign, Commonwealth and Development Office (Grant Agreement OPP1127286) under the auspices of the Centre for Tropical Livestock Genetics and Health (CTLGH), established jointly by the University of Edinburgh (UK), Scotland\u2019s Rural College (SRUC, UK), and the International Livestock Research Institute (UK). The findings and conclusions contained within are those of the authors and do not necessarily reflect positions or policies of the Bill & Melinda Gates Foundation nor the UK Government. The work was also supported by grants BBS/OS/GC/000012C, BBS/E/D/10002070, BBS/E/D/20002172 and BBS/E/D/20002174 from the Biotechnology and Biological Sciences Research Council (BBSRC, UK), and grant OB 490/2\u20131 from Deutsche Forschungsgemeinschaft (DFG, Germany). This research was conducted as part of the Consultative Group on International Agricultural Research (CGIAR) Program on Livestock (Kenya). International Livestock Research Institute (ILRI), Kenya, is supported by contributors to the CGIAR Trust Fund. CGIAR is a global research partnership for a food-secure future. Its science is carried out by 15 Research Centres in close collaboration with hundreds of partners across the globe ( www.cgiar.org ). Work carried out at EMBL, EBI was supported by the Wellcome Trust (WT222155/Z/20/Z) and BBSRC (BB/S020152/1).
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