Assessing confidence in root placement on phylogenies: an empirical study using non-reversible models for Mammals

Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny. In order to compensate for the inability of these models to root the tree, many researchers use external information such as using outgroup taxa or additional assumptions such as molecular-clocks. In this study, we investigate the utility of non-reversible models to root empirical phylogenies and introduce a new bootstrap measure, the rootstrap, which provides information on the statistical support for any given root position. Availability and implementation: rootstrap support is implemented in IQ-TREE 2 and a tutorial is available at the iqtree webpage http://www.iqtree.org/doc/Rootstrap. In addition, a python script is available at https://github.com/suhanaser/Rootstrap在系统发育分析研究中，采用时间可逆马尔可夫模型是极为普遍的做法。尽管我们预期经验数据往往会违反这类模型的诸多假设，但这类模型具备极高的计算效率。然而，这类模型无法对所推断得到的系统发育树进行根位置的确定。为弥补这类模型无法确定系统发育树树根的不足，众多研究者会借助外类群（outgroup taxa）等外部信息，或是引入分子钟（molecular clocks）等额外假设。本研究探讨了非可逆模型用于确定经验系统发育树树根的应用价值，并引入了一种全新的自助法测度——rootstrap（根自助测度），该测度可为任意给定的树根位置提供统计支持度信息。 可用性与实现：rootstrap支持度已在IQ-TREE 2中实现，相关教程可在IQ-TREE官方网站http://www.iqtree.org/doc/Rootstrap获取。此外，相关Python脚本可在https://github.com/suhanaser/Rootstrap获取。