逆转掩盖了微生物组适应性进化的贡献
Paul A Torrillo1,2, Tami D Lieberman1,2,3,4
1Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, United States.
eLife
|September 6, 2024
概括
细菌基因组的进化取决于突变距离. 适应性回归模型,而不是弱净化选择,更好地解释了微生物组中的dN/dS衰变,在解释长期进化数据时建议谨慎.
科学领域:
- 进化生物学 进化生物学
- 基因组学就是基因组学.
- 微生物组研究 微生物组研究
背景情况:
- 对细菌基因组进化的解释依赖于突变距离.
- 非同义突变与同义突变的比率 (dN/dS) 是选择的一个关键指标.
- 现有的模型很难解释肠道微生物组数据中观察到的dN/dS模式.
研究的目的:
- 挑战dN/dS衰变的经典解释,将其视为弱净化选择.
- 提出和验证一个替代模型的细菌基因组进化在微生物组.
- 重新评估dN/dS比对理解细菌适应性的影响.
主要方法:
- 对细菌基因组数据的分析,重点关注突变距离.
- 开发和应用一种自适应逆转模型.
- 使用分析和模拟方法来测试模型.
- 在肠道微生物组动态的背景下检查dN/dS比率.
主要成果:
- 对于微生物组数据来说,dN/dS衰变的经典解释是有问题的.
- 一个适应逆转模型准确地解释了dN/dS衰变与波动选择.
- 由于大量的种群和快速的进化,在微生物群中可能存在适应性逆转.
- 该模型特别适用于像*Bacteroides*这样的细菌.
结论:
- 长时间内的低dN/dS值可能是由于频繁的适应性扫描而产生的,而不仅仅是弱选择.
- 突变逆转在塑造细菌基因组景观方面发挥着重要作用.
- 在较短的时间尺度上研究细菌进化对于准确的解释至关重要.
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