Fourment Mathieu, Darling Aaron E
ithree institute, University of Technology Sydney, Sydney, Australia.
PeerJ. 2018 Jul 3;6:e5140. doi: 10.7717/peerj.5140. eCollection 2018.
Time-resolved phylogenetic methods use information about the time of sample collection to estimate the rate of evolution. Originally, the models used to estimate evolutionary rates were quite simple, assuming that all lineages evolve at the same rate, an assumption commonly known as the molecular clock. Richer and more complex models have since been introduced to capture the phenomenon of substitution rate variation among lineages. Two well known model extensions are the local clock, wherein all lineages in a clade share a common substitution rate, and the uncorrelated relaxed clock, wherein the substitution rate on each lineage is independent from other lineages while being constrained to fit some parametric distribution. We introduce a further model extension, called the flexible local clock (FLC), which provides a flexible framework to combine relaxed clock models with local clock models. We evaluate the flexible local clock on simulated and real datasets and show that it provides substantially improved fit to an influenza dataset. An implementation of the model is available for download from https://www.github.com/4ment/flc.
时间分辨系统发育方法利用样本采集时间的信息来估计进化速率。最初，用于估计进化速率的模型相当简单，假设所有谱系以相同速率进化，这一假设通常被称为分子钟。此后引入了更丰富、更复杂的模型来捕捉谱系间替代率变化的现象。两个著名的模型扩展是局部时钟，其中一个分支中的所有谱系共享一个共同的替代率，以及不相关的宽松时钟，其中每个谱系上的替代率与其他谱系独立，同时受限于符合某种参数分布。我们引入了另一种模型扩展，称为灵活局部时钟（FLC），它提供了一个灵活的框架，用于将宽松时钟模型与局部时钟模型相结合。我们在模拟和真实数据集上评估了灵活局部时钟，并表明它对流感数据集的拟合有显著改善。该模型的一个实现可从https://www.github.com/4ment/flc下载。
