对古代犬类基因组的推算揭示了过去1万年内在繁殖的历史
Katia Bougiouri1, Sabhrina Gita Aninta2,3, Sophy Charlton4
1Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
bioRxiv : the preprint server for biology
|June 21, 2024
概括
基因型归算增强了古老的狗和狼基因组分析,揭示了过去1万年来较低的近亲繁殖水平. 这种方法提高了我们对狗的进化历史和品种多样性的理解.
科学领域:
- 古遗传学是古遗传学的一部分.
- 狗的遗传学 狗的遗传学
- 进化生物学是进化的生物学.
背景情况:
- 狗的养历史涉及与人类的复杂互动,留下了许多关于它们的起源和品种多样化的问题.
- 古代基因组提供了洞察力,但通常受到低覆盖率和DNA损伤的限制,阻碍了准确的基因型调用.
- 使用参考面板进行基因型归因可能可以克服古代DNA研究中的这些局限性.
研究的目的:
- 评估基因型归算对改善古代狗和狼基因组分辨率的有效性.
- 评估归算对种群遗传分析的影响,包括主要成分分析和同卵性运行.
- 调查近亲繁殖水平的变化,并确定与古代犬的特定特征相关的基因组区域.
主要方法:
- 将高覆盖率的狗和狼基因组向低覆盖率 (0.05-2x) 下降采样,以模拟古代数据.
- 评估基因型归算准确性,通过将归算的基因型与高覆盖率数据进行比较.
- 对90个古老的狗和狼基因组的数据集进行归算.
- 在推算前后分析主要组件结构和同卵性性 (ROH) 运行.
- 关联ROH密度与基因功能,特别关注嗅觉和免疫反应.
主要成果:
- 在0.5倍覆盖率的狗和1.0倍覆盖率的狼中,实现了高的归算精度 (R2 > 0.9).
- 推算改善了主要成分分析的分辨率和古代犬类的同卵性运行.
- 古代的狗和狼种群与今天的个人相比,通常表现出较低的近亲繁殖水平.
- 保持低ROH密度的区域与参与嗅觉和免疫反应的基因显著相关.
结论:
- 基因型归因是一种可行的和强大的策略,用于分析低覆盖率的古老犬类基因组.
- 这种方法使得先进的分析方法可以应用于古代DNA数据集,以前仅限于高质量的数据.
- 这项研究为狗的微观进化历史提供了新的见解,包括近亲繁殖的模式和重要的特征的遗传基础.
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