Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data
Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data
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DOI：
10.1186/s12862-014-0163-6
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发表时间：
2014-07-24
影响因子：
3.4
通讯作者：
Holmes, Edward C.
中科院分区：
文献类型：
--
作者：
Fourment, Mathieu;Holmes, Edward C.
背景：从基因序列数据中估计分歧时间的早期方法依赖于分子钟的假设。更复杂的方法被创建来模拟速率变化，并使用速率的自相关、本地时钟或所谓的“不相关放松时钟”，其中假设替代速率来自参数分布。在贝叶斯推理方法的情况下，先验知识对分支时间的影响还不清楚，如果数据量有限，先验知识可能会对后验产生很大影响。结果：我们开发了一种最大似然方法- Physher -该方法使用局部或离散时钟来估计进化速率和异时序列数据的发散时间。使用两个经验数据集，我们表明，我们的离散时钟估计是类似于通过其他方法获得的，Physher优于一些方法在估计流感病毒数据集的根年龄。模拟分析表明，Physher可以优于贝叶斯方法时，真实的拓扑结构包含两个长分支根节点以下，即使进化是强烈的时钟样Conclusions：这些结果表明，它是可取的，使用各种方法来估计进化速率和分歧时间从heterocyclic序列数据。此处使用的Physher和相关数据集可在http://code.google.com/p/physher/上在线获得。
Background: Early methods for estimating divergence times from gene sequence data relied on the assumption of a molecular clock. More sophisticated methods were created to model rate variation and used auto-correlation of rates, local clocks, or the so called "uncorrelated relaxed clock" where substitution rates are assumed to be drawn from a parametric distribution. In the case of Bayesian inference methods the impact of the prior on branching times is not clearly understood, and if the amount of data is limited the posterior could be strongly influenced by the prior.Results: We develop a maximum likelihood method - Physher - that uses local or discrete clocks to estimate evolutionary rates and divergence times from heterochronous sequence data. Using two empirical data sets we show that our discrete clock estimates are similar to those obtained by other methods, and that Physher outperformed some methods in the estimation of the root age of an influenza virus data set. A simulation analysis suggests that Physher can outperform a Bayesian method when the real topology contains two long branches below the root node, even when evolution is strongly clock-like.Conclusions: These results suggest it is advisable to use a variety of methods to estimate evolutionary rates and divergence times from heterochronous sequence data. Physher and the associated data sets used here are available online at http://code.google.com/p/physher/.