基于收缩的随机局部时钟,具有可扩展的推理
Alexander A Fisher1, Xiang Ji2, Akihiko Nishimura3
1Department of Statistical Science, Duke University, Durham, NC, USA.
Molecular biology and evolution
|November 11, 2023
概括
我们开发了一种新的贝叶斯模型,用于分子时钟的进化,提高了分歧时间估计的可扩展性和准确性. 这种收缩时钟方法有效地处理大型的基因树和复杂的进化速率.
科学领域:
- 计算生物学 计算生物学
- 人类遗传学 是一个学科.
- 进化生物学 进化生物学
背景情况:
- 分子时钟模型对于估计进化生物学中的分歧时间至关重要.
- 现有的局部时钟模型面临着可扩展性,模型错误规格的局限性,并且需要先前了解时钟位置.
- 有效而准确的分子时钟推断对于理解进化历史至关重要.
研究的目的:
- 提出一种新的自相关的贝叶斯模型,用于遗传时钟速率进化,克服当前方法的局限性.
- 开发一种高效的计算方法,用于将分子时钟推理扩展到大型遗传树上.
- 将新模型应用于推断哺乳动物和流感病毒系的进化速率.
主要方法:
- 开发了一个自相关的贝叶斯模型,用于遗传时钟速率进化.
- 实现了一种高效的哈密尔顿式蒙特卡洛采样器,并使用闭式梯度计算来实现可扩展性.
- 将"收缩钟"模型应用于模拟的数据集,哺乳动物类型和流感A病毒表面糖蛋白.
主要成果:
- 收缩时钟模型与随机局部时钟方法相比显示出显著的加快速度,特别是在大型数据集中.
- 该模型成功地恢复了动物和哺乳动物的已知局部时钟结构.
- 启用了对流感A病毒表面糖蛋白演变的计算密集分析,没有先前的时钟位置假设.
结论:
- 拟议的收缩时钟模型为分子时钟推断提供了一个可扩展和准确的方法.
- 这种方法推进了对分歧时间的估计和对进化速率变化的理解.
- 在BEAST公开可用的实现促进了在进化和遗传学研究中的更广泛应用.
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