摘要
      在存在重组的情况下，个体可能从不同的祖先那里继承其基因组的不同区域，从而导致整个基因组的系统发育历史马赛克。祖先重组图（ARGs）可以捕捉到由于重组而导致的基因组系统发育关系的变化，但从基因组序列数据中重建ARGs是出了名的困难。在这里，我们提出了一种调和不一致的系统发育树并使用最大一致森林（MAFs）重建ARG的方法。给定两个不一致的树，MAF识别两个树中存在的一组拓扑一致的子树。我们展示了如何通过它们的MAF来协调不一致的树，以保持序列数据有力支持的不一致，同时消除可能归因于系统发育噪声的冲突。我们进一步展示了MAF和我们的协调方法如何结合起来，以选择整个基因组的局部树路径，从而最大限度地提高基因组序列数据的可能性，最大限度地减少相邻局部树之间的不一致，并确定解释剩余不一致所需的重组事件，以获得完全连接的ARG。虽然是启发式的，但我们的ARG重建方法通常与更精确的方法一样准确，同时计算效率更高。此外，重要的人口统计学参数，如重组率，可以从重建的ARG中准确估计。最后，我们将我们的方法应用于感染Potyvirus属植物的RNA病毒，以证明如何使用我们的ARG重建方法将真正的重组事件从系统发育噪声中分离出来。
Abstract
In the presence of recombination individuals may inherit different regions of their genome from different ancestors, resulting in a mosaic of phylogenetic histories across their genome. Ancestral recombination graphs (ARGs) can capture how phylogenetic relationships vary across the genome due to recombination, but reconstructing ARGs from genomic sequence data is notoriously difficult. Here we present a method for reconciling discordant phylogenetic trees and reconstructing ARGs using maximum agreement forests (MAFs). Given two discordant trees, a MAF identifies a set of topologically concordant subtrees present in both trees. We show how discordant trees can be reconciled through their MAF in a way that retains discordances strongly supported by sequence data while eliminating conflicts likely attributable to phylogenetic noise. We further show how MAFs and our reconciliation approach can be combined to select a path of local trees across the genome that maximizes the likelihood of the genomic sequence data, minimizes discordance between neighboring local trees, and identifies the recombination events necessary to explain remaining discordances to obtain a fully connected ARG. While heuristic, our ARG reconstruction approach is often as accurate as more exact methods while being much more computationally efficient. Moreover, important demographic parameters such as recombination rates can be accurately estimated from reconstructed ARGs. Finally, we apply our approach to plant infecting RNA viruses in the genus Potyvirus to demonstrate how true recombination events can be disentangled from phylogenetic noise using our ARG reconstruction methods.

https://www.biorxiv.org/content/10.1101/2022.01.17.476639v2.abstract