Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen 1352, Denmark.
Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen 1352, Denmark.
Genome Biol Evol. 2024 Apr 2;16(4). doi: 10.1093/gbe/evae064.
Phylogenomic data provide valuable opportunities for studying evolutionary rates and timescales. These analyses require theoretical and statistical tools based on molecular clocks. We present ClockstaRX, a flexible platform for exploring and testing evolutionary rate signals in phylogenomic data. Here, information about evolutionary rates in branches across gene trees is placed in Euclidean space, allowing data transformation, visualization, and hypothesis testing. ClockstaRX implements formal tests for identifying groups of loci and branches that make a large contribution to patterns of rate variation. This information can then be used to test for drivers of genomic evolutionary rates or to inform models for molecular dating. Drawing on the results of a simulation study, we recommend forms of data exploration and filtering that might be useful prior to molecular-clock analyses.
系统发育基因组学数据为研究进化速率和时间尺度提供了有价值的机会。这些分析需要基于分子钟的理论和统计工具。我们提出了 ClockstaRX，这是一个用于探索和测试系统发育基因组学数据中进化速率信号的灵活平台。在这里，基因树中各分支的进化速率信息被放置在欧几里得空间中，允许数据转换、可视化和假设检验。ClockstaRX 实现了正式的测试，以识别对速率变化模式有较大贡献的基因座和分支组。然后，可以使用这些信息来测试基因组进化速率的驱动因素，或为分子定年模型提供信息。基于模拟研究的结果，我们建议在进行分子钟分析之前，可以采用某些形式的数据探索和过滤方法。
