Continent-wide genomic analysis of the African buffalo ( Syncerus caffer )
Continent-wide genomic analysis of the African buffalo ( Syncerus caffer )
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非洲水牛（Syncerus caffer）的全大陆基因组分析
DOI：
10.1101/2023.11.12.566748
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Talenti A
中科院分区：
文献类型：
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作者：
Talenti A
非洲水牛(Syncerus Caffer)是一种野生水牛，历史上分布在撒哈拉以南非洲的大部分地区。基因组分析可以洞察物种的进化史，以及形成种群的关键选择压力，包括种群水平分化、种群碎片化和种群遗传结构的评估。在这项研究中，我们生成了迄今为止质量最高的非洲水牛新基因组组装(2.65 GB，支架N50 69.17 Mb)，并对来自物种分布的195个基因组进行了测序。主成分分析和混合分析对目前描述的四个亚种提供的支持少得令人惊讶，但表明了三个主要谱系，分别位于非洲西部/中部、东部和南部。估计有效迁移面的分析表明，地理障碍在塑造基因流动和种群结构方面发挥了重要作用。估计的有效人口规模表明，在5-10000年前，所有人口都出现了大幅下降，而与此同时，人口却在增加。最后，与免疫反应相关的关键基因的选择特征得到了丰富，这表明传染病对非洲水牛施加了很大的选择压力。这些发现对理解水牛进化、水牛保护和种群管理具有重要意义。
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 qualityde novogenome 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 surprisingly little support for the currently described four subspecies, but indicated three main lineages, in Western/Central, Eastern and Southern Africa, respectively. 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.