Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography.
Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography.
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DOI：
10.1093/sysbio/syu015
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发表时间：
2014-07
影响因子：
6.5
通讯作者：
Suchard MA
中科院分区：
文献类型：
--
作者：
Bielejec F;Lemey P;Baele G;Rambaut A;Suchard MA
分子系统发育和地理分布的重建通常假设时间上的同质替换过程。受计算便利性的影响，这种假设牺牲了生物现实主义，几乎没有机会揭示进化历史中的时间动态。在这里，我们提出了一个进化的方法，明确放宽时间均匀性假设，允许规范不同的无穷小替代率矩阵在不同的时间间隔，称为时代，沿着进化的历史。我们专注于一个时代的模型实现贝叶斯推理框架，提供了很大的建模灵活性，在绘制任何离散数据类型的特征为一个连续时间马尔可夫链，包括地理特征的推断。为了减轻额外的时间异质性施加的计算负担，我们采用了大规模并行的方法，实现了细粒度和粗粒度的并行计算跨分支，适应时代的过渡，广泛使用的图形处理单元。通过合成的例子，我们评估模型的性能，从根据不同的进化方案，包括不同数量的时代的核苷酸和密码子取代过程中产生的数据恢复进化参数。我们说明了我们的推理框架在两个不同的应用经验数据集的有用性：在整个感染和全球流感流行的季节性的宿主内艾滋病毒种群的选择动态。在这两种情况下，我们的历元模型捕捉到了时间异质性的关键特征，这些特征仍然难以使用特设程序进行测试。[贝叶斯推理; BEAGLE; BEAST;时代模型;地理学;系统发生学。]
Molecular phylogenetic and phylogeographic reconstructions generally assume time-homogeneous substitution processes. Motivated by computational convenience, this assumption sacrifices biological realism and offers little opportunity to uncover the temporal dynamics in evolutionary histories. Here, we propose an evolutionary approach that explicitly relaxes the time-homogeneity assumption by allowing the specification of different infinitesimal substitution rate matrices across different time intervals, called epochs, along the evolutionary history. We focus on an epoch model implementation in a Bayesian inference framework that offers great modeling flexibility in drawing inference about any discrete data type characterized as a continuous-time Markov chain, including phylogeographic traits. To alleviate the computational burden that the additional temporal heterogeneity imposes, we adopt a massively parallel approach that achieves both fine- and coarse-grain parallelization of the computations across branches that accommodate epoch transitions, making extensive use of graphics processing units. Through synthetic examples, we assess model performance in recovering evolutionary parameters from data generated according to different evolutionary scenarios that comprise different numbers of epochs for both nucleotide and codon substitution processes. We illustrate the usefulness of our inference framework in two different applications to empirical data sets: the selection dynamics on within-host HIV populations throughout infection and the seasonality of global influenza circulation. In both cases, our epoch model captures key features of temporal heterogeneity that remained difficult to test using ad hoc procedures. [Bayesian inference; BEAGLE; BEAST; Epoch Model; phylogeography; Phylogenetics.]
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影响因子：
4.3
作者：
Lee, Ha Youn;Perelson, Alan S.;Park, Su-Chan;Leitner, Thomas
通讯作者：
Leitner, Thomas
DOI：
10.1098/rstb.2012.0196
发表时间：
2013-03-19
期刊：
Philosophical transactions of the Royal Society of London. Series B, Biological sciences
影响因子：
--
作者：
Faria NR;Suchard MA;Rambaut A;Streicker DG;Lemey P
通讯作者：
Lemey P
影响因子：
9.8
作者：
Drummond AJ;Ho SY;Phillips MJ;Rambaut A
通讯作者：
Rambaut A
影响因子：
10.7
作者：
Edo-Matas, Diana;Lemey, Philippe;Suchard, Marc A.
通讯作者：
Suchard, Marc A.
影响因子：
4.3
作者：
Lemey P;Rambaut A;Drummond AJ;Suchard MA
通讯作者：
Suchard MA