Lee Hui-Jie, Kishino Hirohisa, Rodrigue Nicolas, Thorne Jeffrey L
Department of Statistics, North Carolina State University, Raleigh, NC 27695, USA
Laboratory of Biometrics and Bioinformatics, University of Tokyo, Tokyo, Japan.
Philos Trans R Soc Lond B Biol Sci. 2016 Jul 19;371(1699). doi: 10.1098/rstb.2015.0141.
Different types of nucleotide substitutions experience different patterns of rate change over time. We propose clustering context-dependent (or context-independent) nucleotide substitution types according to how their rates change and then using the grouping for divergence time estimation. With our models, relative rates among types that are in the same group are fixed, whereas absolute rates of the types within a group change over time according to a shared relaxed molecular clock. We illustrate our procedure by analysing a 0.15 Mb intergenic region to infer divergence times relating eight primates. The different groupings of substitution types that we explore have little effect on the posterior means of divergence times, but the widths of the credibility intervals decrease as the number of groups increases.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
不同类型的核苷酸替换随时间经历不同的速率变化模式。我们建议根据其速率变化方式对上下文相关（或上下文无关）的核苷酸替换类型进行聚类，然后使用该分组来估计分歧时间。在我们的模型中，同一组内类型之间的相对速率是固定的，而组内各类型的绝对速率则根据共享的宽松分子钟随时间变化。我们通过分析一个0.15 Mb的基因间区域来推断八种灵长类动物的分歧时间，以此阐述我们的方法。我们探索的替换类型的不同分组对分歧时间的后验均值影响不大，但可信区间的宽度会随着组数的增加而减小。本文是主题为“利用岩石和时钟确定物种分歧时间”的特刊的一部分。
