祖先序列重建的稳定性,使其达到现场间的进化异质性和表观性
Ricardo Muñiz-Trejo1, Yeonwoo Park2,3, Joseph W Thornton1,4
1Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
bioRxiv : the preprint server for biology
|January 7, 2025
概括
祖先序列重建 (ASR) 是对进化异质性的强大. 通过密集采样的对齐来最大化基因信号,而不是复杂的模型,是提高ASR准确性的关键.
科学领域:
- 进化生物学是进化的生物学.
- 生物信息学是一种生物信息学.
- 计算生物学是一种计算生物学.
背景情况:
- 在祖先序列重建 (ASR) 中,均质的进化模型假定所有地点和谱系的替代率均.
- 真正的生物系统表现出特定于地点和谱系的约束,由于结构,功能和表观相互作用,违反了这种同质性假设.
研究的目的:
- 调查现实的进化异质性对祖先序列重建 (ASR) 的影响.
- 评估与同质模型相比,是否结合特定地点的模型可以提高ASR准确性.
主要方法:
- 开发了特定站点的替代模型,通过三种蛋白质家族的深度突变扫描数据进行参数化.
- 在同质和异质进化条件下对实证和模拟对齐进行ASR.
- 通过在不同的建模方法中比较重建的序列来评估ASR准确性.
主要成果:
- 在数据集中观察到广泛的位点和谱系异质性.
- 当应用到经验数据时,ASR结果在同质和异质模型之间在很大程度上是一致.
- 重建差异很少见,主要发生在快速发展的部位或基因信号较弱的节点.
- 模拟数据显示,较长的分支长度增加了错误,但异质模型没有提高准确性.
结论:
- 祖先序列重建 (ASR) 对于现实的进化异质性是强大的.
- 基因信号,而不是模型复杂性,是ASR准确性的主要驱动因素.
- 提高ASR准确性取决于使用密集的样本对齐来最大限度地提高家族遗传信号,而不是开发更复杂的替代模型.
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