de Jager Deon, Möller Marlo, Hoal Eileen, van Helden Paul, Glanzmann Brigitte, Harper Cindy, Bloomer Paulette
Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology University of Pretoria Pretoria South Africa.
Globe Institute University of Copenhagen Copenhagen Denmark.
Ecol Evol. 2025 Jan 9;15(1):e70640. doi: 10.1002/ece3.70640. eCollection 2025 Jan.
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 () 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 ( = 15) and Mokala National Park ( = 5) were similar to diversity levels in southern and eastern Africa. Hluhluwe-iMfolozi Park ( = 15) had low levels of genetic diversity, with only four haplotypes detected, reflecting its past bottleneck. Addo Elephant National Park ( = 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 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 or . 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.
新一代测序（NGS）成本的降低使研究人员能够生成核基因组和线粒体基因组数据，从而更深入地了解非模式物种的系统地理学、进化历史和生物学特性。在过去25年里，非洲水牛（）已通过传统遗传标记在其分布范围内得到了充分研究，研究人员正基于这些知识，通过生成全基因组、种群水平的数据集来增进对该物种遗传组成和进化历史的理解。利用公开可用的NGS数据，我们从南非的四个保护区组装了40个非洲水牛线粒体基因组（线粒体基因组），扩大了地理范围，并且使该物种可用的线粒体基因组数量几乎增加了一倍。线粒体基因组的覆盖范围从154倍到1036倍不等。克鲁格国家公园（=15）和莫卡拉国家公园（=5）的单倍型和核苷酸多样性与南部和东部非洲的多样性水平相似。伊卢赫卢韦-乌姆福洛齐公园（=15）的遗传多样性水平较低，仅检测到四种单倍型，这反映了其过去经历的瓶颈。阿多大象国家公园（=5）在非洲所有种群中具有最高的核苷酸多样性，这出人意料，因为已知其核多样性较低。这种多样性是由一个样本中高度分化的线粒体基因组驱动的，随后通过细胞色素基因的桑格测序在另一个样本中也鉴定出了该线粒体基因组。通过化石校准的系统发育分析，我们估计这个谱系大约在251万年前与所有其他非洲水牛谱系分化。我们讨论了这个线粒体基因组的几个潜在来源，但认为它很可能起源于与已灭绝的水牛物种或的渐渗杂交。最后，我们讨论了这一发现对阿多大象国家公园种群的保护意义，建议进行谨慎的遗传管理，以防止近亲繁殖衰退，同时保持这种高度独特的多样性。
