研究人员介绍了CASTER，一种理论上有依据的基于位点的方法，消除了需要预先定义无重组位点的需求。CASTER具有可扩展性，能够处理数百个哺乳动物全基因组。研究人员在包含重组的模拟中展示了CASTER的准确性和可扩展性，并将CASTER应用于几个生物数据集，显示它的每位点得分能够揭示基因组中生物学和人为因素导致的不一致性模式。
据了解，基因组包含了不一致的演化历史拼接，这给生命树的准确推断带来了挑战。尽管基因组范围的数据通常用于考虑不一致性的系统基因组学分析，但由于建模和可扩展性限制，目前的做法忽略了基因组的大部分区域。随着越来越多高质量基因组的出现，人们迫切需要能够直接从多个基因组比对中推断树的考虑不一致性的方法。
附：英文原文
Title: CASTER: Direct species tree inference from whole-genome alignments
Author: Chao Zhang, Rasmus Nielsen, Siavash Mirarab
Issue&Volume: 2025-01-23
Abstract: Genomes contain mosaics of discordant evolutionary histories, challenging the accurate inference of the tree of life. While genome-wide data are routinely used for discordance-aware phylogenomic analyses, due to modeling and scalability limitations, the current practice leaves out large chunks of genomes. As more high-quality genomes become available, we urgently need discordance-aware methods to infer the tree directly from a multiple genome alignment. Here, we introduce CASTER, a theoretically justified site-based method that eliminates the need to predefine recombination-free loci. CASTER is scalable to hundreds of mammalian whole genomes. We demonstrate the accuracy and scalability of CASTER in simulations that include recombination and apply CASTER to several biological datasets, showing that its per-site scores can reveal both biological and artefactual patterns of discordance across the genome.
DOI: adk9688
Source: https://www.science.org/doi/10.1126/science.adk9688