School of Biological Sciences, University of Bristol, Bristol, UK.
School of Biological Sciences, University of Aberdeen, Aberdeen, UK.
Methods Mol Biol. 2022;2569:189-211. doi: 10.1007/978-1-0716-2691-7_9.
Interpreting phylogenetic trees requires a root, which provides the direction of evolution and polarizes ancestor-descendant relationships. But inferring the root using genetic data is difficult, particularly in cases where the closest available outgroup is only distantly related, which are common for microbes. In this chapter, we present a workflow for estimating rooted species trees and the evolutionary history of the gene families that evolve within them using probabilistic gene tree-species tree reconciliation. We illustrate the pipeline using a small dataset of prokaryotic genomes, for which the example scripts can be run using modest computer resources. We describe the rooting method used in this work in the context or other rooting strategies and discuss some of the limitations and opportunities presented by probabilistic gene tree-species tree reconciliation methods.
解析系统发育树需要一个根，它提供了进化的方向，并使祖先-后代关系两极分化。但是，使用遗传数据推断根是困难的，特别是在最接近的可用外群只有远亲关系的情况下，这种情况在微生物中很常见。在本章中，我们提出了一种使用概率基因树-物种树协调来估计有根物种树和在其中进化的基因家族的进化历史的工作流程。我们使用一个小型原核基因组数据集来说明该管道，对于该数据集，可以使用适度的计算机资源运行示例脚本。我们将在其他根策略的上下文中描述本工作中使用的根方法，并讨论概率基因树-物种树协调方法所带来的一些限制和机遇。
