A Highly Divergent Mitochondrial Genome in Extant Cape Buffalo From Addo Elephant National Park, South Africa
ABSTRACT The reduced cost of next‐generation sequencing (NGS) has allowed researchers to generate nuclear and mitochondrial genome data to gain deeper insights into the phylogeography, evolutionary history and biology of non‐model species. While the Cape buffalo (Syncerus caffer caffer) has been wel...
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Wiley
2025-01-01
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| Series: | Ecology and Evolution |
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| Online Access: | https://doi.org/10.1002/ece3.70640 |
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| author | Deon deJager Marlo Möller Eileen Hoal Paul vanHelden Brigitte Glanzmann Cindy Harper Paulette Bloomer |
| author_facet | Deon deJager Marlo Möller Eileen Hoal Paul vanHelden Brigitte Glanzmann Cindy Harper Paulette Bloomer |
| author_sort | Deon deJager |
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| description | ABSTRACT The reduced cost of next‐generation sequencing (NGS) has allowed researchers to generate nuclear and mitochondrial genome data to gain deeper insights into the phylogeography, evolutionary history and biology of non‐model species. While the Cape buffalo (Syncerus caffer caffer) has been well‐studied across its range with traditional genetic markers over the last 25 years, researchers are building on this knowledge by generating whole genome, population‐level data sets to improve understanding of the genetic composition and evolutionary history of the species. Using publicly available NGS data, we assembled 40 Cape buffalo mitochondrial genomes (mitogenomes) from four protected areas in South Africa, expanding the geographical range and almost doubling the number of mitogenomes available for this species. Coverage of the mitogenomes ranged from 154 to 1036X. Haplotype and nucleotide diversity for Kruger National Park (n = 15) and Mokala National Park (n = 5) were similar to diversity levels in southern and eastern Africa. Hluhluwe–iMfolozi Park (n = 15) had low levels of genetic diversity, with only four haplotypes detected, reflecting its past bottleneck. Addo Elephant National Park (n = 5) had the highest nucleotide diversity of all populations across Africa, which was unexpected, as it is known to have low nuclear diversity. This diversity was driven by a highly divergent mitogenome from one sample, which was subsequently identified in another sample via Sanger sequencing of the cytochrome b gene. Using a fossil‐calibrated phylogenetic analysis, we estimated that this lineage diverged from all other Cape buffalo lineages approximately 2.51 million years ago. We discuss several potential sources of this mitogenome but propose that it most likely originated through introgressive hybridisation with an extinct buffalo species, either S. acoelotus or S. antiquus. We conclude by discussing the conservation consequences of this finding for the Addo Elephant National Park population, proposing careful genetic management to prevent inbreeding depression while maintaining this highly unique diversity. |
| format | Article |
| id | doaj-art-d0739331c87f4c099bbcfa858ac7b4db |
| institution | Kabale University |
| issn | 2045-7758 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Wiley |
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| series | Ecology and Evolution |
| spelling | doaj-art-d0739331c87f4c099bbcfa858ac7b4db2025-01-29T05:08:41ZengWileyEcology and Evolution2045-77582025-01-01151n/an/a10.1002/ece3.70640A Highly Divergent Mitochondrial Genome in Extant Cape Buffalo From Addo Elephant National Park, South AfricaDeon deJager0Marlo Möller1Eileen Hoal2Paul vanHelden3Brigitte Glanzmann4Cindy Harper5Paulette Bloomer6Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology University of Pretoria Pretoria South AfricaDSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South AfricaDSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South AfricaDSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South AfricaDSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South AfricaVeterinary Genetics Laboratory, Faculty of Veterinary Science University of Pretoria Pretoria South AfricaMolecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology University of Pretoria Pretoria South AfricaABSTRACT The reduced cost of next‐generation sequencing (NGS) has allowed researchers to generate nuclear and mitochondrial genome data to gain deeper insights into the phylogeography, evolutionary history and biology of non‐model species. While the Cape buffalo (Syncerus caffer caffer) has been well‐studied across its range with traditional genetic markers over the last 25 years, researchers are building on this knowledge by generating whole genome, population‐level data sets to improve understanding of the genetic composition and evolutionary history of the species. Using publicly available NGS data, we assembled 40 Cape buffalo mitochondrial genomes (mitogenomes) from four protected areas in South Africa, expanding the geographical range and almost doubling the number of mitogenomes available for this species. Coverage of the mitogenomes ranged from 154 to 1036X. Haplotype and nucleotide diversity for Kruger National Park (n = 15) and Mokala National Park (n = 5) were similar to diversity levels in southern and eastern Africa. Hluhluwe–iMfolozi Park (n = 15) had low levels of genetic diversity, with only four haplotypes detected, reflecting its past bottleneck. Addo Elephant National Park (n = 5) had the highest nucleotide diversity of all populations across Africa, which was unexpected, as it is known to have low nuclear diversity. This diversity was driven by a highly divergent mitogenome from one sample, which was subsequently identified in another sample via Sanger sequencing of the cytochrome b gene. Using a fossil‐calibrated phylogenetic analysis, we estimated that this lineage diverged from all other Cape buffalo lineages approximately 2.51 million years ago. We discuss several potential sources of this mitogenome but propose that it most likely originated through introgressive hybridisation with an extinct buffalo species, either S. acoelotus or S. antiquus. We conclude by discussing the conservation consequences of this finding for the Addo Elephant National Park population, proposing careful genetic management to prevent inbreeding depression while maintaining this highly unique diversity.https://doi.org/10.1002/ece3.70640Africaconservation geneticshybridisationintrogressionlong‐horned buffalopalaeontology |
| spellingShingle | Deon deJager Marlo Möller Eileen Hoal Paul vanHelden Brigitte Glanzmann Cindy Harper Paulette Bloomer A Highly Divergent Mitochondrial Genome in Extant Cape Buffalo From Addo Elephant National Park, South Africa Ecology and Evolution Africa conservation genetics hybridisation introgression long‐horned buffalo palaeontology |
| title | A Highly Divergent Mitochondrial Genome in Extant Cape Buffalo From Addo Elephant National Park, South Africa |
| title_full | A Highly Divergent Mitochondrial Genome in Extant Cape Buffalo From Addo Elephant National Park, South Africa |
| title_fullStr | A Highly Divergent Mitochondrial Genome in Extant Cape Buffalo From Addo Elephant National Park, South Africa |
| title_full_unstemmed | A Highly Divergent Mitochondrial Genome in Extant Cape Buffalo From Addo Elephant National Park, South Africa |
| title_short | A Highly Divergent Mitochondrial Genome in Extant Cape Buffalo From Addo Elephant National Park, South Africa |
| title_sort | highly divergent mitochondrial genome in extant cape buffalo from addo elephant national park south africa |
| topic | Africa conservation genetics hybridisation introgression long‐horned buffalo palaeontology |
| url | https://doi.org/10.1002/ece3.70640 |
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