欧洲生物信息学研究所Nick Goldman课题组取得一项新突破。他们提出了在大流行规模上评估系统发育置信度。该项研究成果发表在2025年11月5日出版的《自然》上。

在此，该课题组研究人员提出了基于子树修剪和重新嫁接的树评估（SPRTA），这是一种有效且可解释的评估系统发育树置信度的方法。SPRTA将系统发育支持测量的范式从评估支系的信心转变为进化历史和系统发育定位，例如，评估一个谱系是否从另一个被认为的谱系进化而来，这在基因组流行病学中特别有价值。研究小组利用SPRTA研究了涉及200多万个基因组的全球公开SARS-CoV-2系统发育树，突出了许多SARS-CoV-2变体的可替代进化起源，评估了Pango暴发谱系分类系统的可靠性，并证明了系统发育不确定性对推断突变率的影响。他们的结果表明，SPRTA能够对传播和突变历史进行大流行规模和详细的概率评估。他们的方法引入了一种评估系统发育置信度的新方法，增强了大流行规模系统发育分析的可解释性，并提高了它们准备和应对未来大流行的能力。

据了解，系统发育学在进化生物学和基因组流行病学中起着核心作用。因此，评估系统发育的可信度和可靠性是至关重要的，而用于评估系统发育的方法，比如从Felsenstein的bootstrap中衍生出来的方法，是现代科学中最广泛的主题之一。然而，这些方法需要巨大的计算能力，并且不适合大型数据集。此外，这些方法大多集中在分支（分类群的分组）的成员关系上，这使得它们的结果很难在基因组流行病学的背景下解释。

附：英文原文

Title: Assessing phylogenetic confidence at pandemic scales

Author: De Maio, Nicola, Ly-Trong, Nhan, Martin, Samuel, Minh, Bui Quang, Goldman, Nick

Issue&Volume: 2025-11-05

Abstract: Phylogenetics has a central role in evolutionary biology and genomic epidemiology1. Assessing phylogenetic confidence and reliability is therefore crucial and the methods that do this, such as those derived from Felsenstein’s bootstrap2, are among the most widely used in modern science. However, these methods require enormous computational capacity, and are unsuitable for large datasets. Furthermore, most of these methods emerge from a focus on the membership of clades (groupings of taxa), which makes their results difficult to interpret in the context of genomic epidemiology. Here we propose subtree pruning and regrafting-based tree assessment (SPRTA), an efficient and interpretable approach to assess confidence in phylogenetic trees. SPRTA shifts the paradigm of phylogenetic support measurement from evaluating the confidence in clades to evolution histories and phylogenetic placement—for example, assessing whether a lineage evolved from another considered lineage, which is particularly valuable in genomic epidemiology. We use SPRTA to investigate a global public SARS-CoV-2 phylogenetic tree relating more than two million genomes, highlighting plausible alternative evolutionary origins of many SARS-CoV-2 variants, assessing reliability in the Pango outbreak lineage classification system3, and demonstrating the effect of phylogenetic uncertainty on inferred mutation rates. Our results show that SPRTA enables pandemic-scale and detailed probabilistic assessment of transmission and mutational histories. Our method introduces a new approach to assessing phylogenetic confidence, enhancing the interpretability of pandemic-scale phylogenetic analyses and improving our ability to prepare for and respond to future pandemics.

DOI: 10.1038/s41586-025-09567-x

Source: https://www.nature.com/articles/s41586-025-09567-x