一种用于确定蓝藻进化时间的计算方案。

A Computational Protocol for Dating the Evolution of Cyanobacteria.

机构信息

Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.

Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China.

出版信息

Methods Mol Biol. 2022;2569:23-40. doi: 10.1007/978-1-0716-2691-7_2.

DOI:10.1007/978-1-0716-2691-7_2

PMID:36083442

Abstract

Cyanobacteria are known to play important roles in driving biological and geochemical innovations in ancient Earth. The origin of Cyanobacteria is the key to understanding these evolutionary events and thus has gained much interest to biologists and geobiologists. Recent development of the molecular dating approaches provides us an opportunity to assess the timeline of Cyanobacteria evolution based on relaxed clock models. The implementation of Bayesian phylogenetic approaches accommodates the uncertainties from different sources, such as fossil calibrations and topological structure of the phylogenomic tree, and provides us converged estimates of posterior mean ages. In this chapter, by taking Cyanobacteria as an example, we introduce a refined strategy to perform molecular dating analysis, as well as a practical method to evaluate the precision of dating analysis.

摘要

蓝藻在驱动古代地球的生物和地球化学创新方面起着重要作用。蓝藻的起源是理解这些进化事件的关键，因此引起了生物学家和地球生物学家的极大兴趣。分子定年方法的最新发展为我们提供了一个机会，使我们能够基于松弛时钟模型评估蓝藻进化的时间线。贝叶斯系统发育方法的实施考虑了来自不同来源的不确定性，例如化石校准和系统基因组树的拓扑结构，并为我们提供了后验均值年龄的收敛估计。在本章中，我们以蓝藻为例，介绍了一种执行分子定年分析的改进策略，以及一种评估定年分析精度的实用方法。