Efficient Bayesian inference under the structured coalescent.
Efficient Bayesian inference under the structured coalescent.
复制标题
DOI：
10.1093/bioinformatics/btu201
复制
发表时间：
2014-08-15
期刊：
影响因子：
--
通讯作者：
Drummond AJ
中科院分区：
文献类型：
--
作者：
Vaughan TG;Kühnert D;Popinga A;Welch D;Drummond AJ
动机：种群结构显著影响进化动力学。这样的结构可能是由于空间分离，但也可能反映任何其他基因流限制模型的方面。结合结构化聚结，这一事实可以用于告知系统发育树重建，以及推断参数，如迁移率和亚群大小从注释的序列数据。然而，进行贝叶斯推理下的结构化合并是阻碍了困难的马尔可夫链蒙特卡罗（MCMC）采样算法（采样器）能够有效地探索状态空间。结果如下：在这篇文章中，我们提出了一个新的MCMC采样器能够从结构树的后验分布采样：定时系统发育树中的血统与不同的亚群，他们躺在。采样器包括一组MCMC建议函数，与以前发布的方法相比，这些函数提供了显着的混合改进。此外，它作为BEAST 2包的实现确保了模型和先前规范的最大灵活性。我们证明了这种新的采样器的有用性，用它来推断新西兰，纽约和香港之间的H3N2流感的迁移率和有效的人口规模从公开可用的血凝素（HA）基因序列下的结构化结合。可用性和实施：该采样器已作为公开可用的BEAST 2软件包实现，该软件包在GNU通用公共许可证第3版下发布，网址为http://compevol.github.io/MultiTypeTree。联系方式：tgvaughan@gmail.com补充信息：补充数据可从生物信息学在线网站获得。
Motivation: Population structure significantly affects evolutionary dynamics. Such structure may be due to spatial segregation, but may also reflect any other gene-flow-limiting aspect of a model. In combination with the structured coalescent, this fact can be used to inform phylogenetic tree reconstruction, as well as to infer parameters such as migration rates and subpopulation sizes from annotated sequence data. However, conducting Bayesian inference under the structured coalescent is impeded by the difficulty of constructing Markov Chain Monte Carlo (MCMC) sampling algorithms (samplers) capable of efficiently exploring the state space. Results: In this article, we present a new MCMC sampler capable of sampling from posterior distributions over structured trees: timed phylogenetic trees in which lineages are associated with the distinct subpopulation in which they lie. The sampler includes a set of MCMC proposal functions that offer significant mixing improvements over a previously published method. Furthermore, its implementation as a BEAST 2 package ensures maximum flexibility with respect to model and prior specification. We demonstrate the usefulness of this new sampler by using it to infer migration rates and effective population sizes of H3N2 influenza between New Zealand, New York and Hong Kong from publicly available hemagglutinin (HA) gene sequences under the structured coalescent. Availability and implementation: The sampler has been implemented as a publicly available BEAST 2 package that is distributed under version 3 of the GNU General Public License at http://compevol.github.io/MultiTypeTree. Contact: tgvaughan@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
登录
查看更多内容
DOI：
10.1016/j.meegid.2011.08.005
发表时间：
2011-12
期刊：
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
影响因子：
--
作者：
Kühnert D;Wu CH;Drummond AJ
通讯作者：
Drummond AJ
影响因子：
64.8
作者：
Rambaut, Andrew;Pybus, Oliver G.;Holmes, Edward C.
通讯作者：
Holmes, Edward C.
影响因子：
56.9
作者：
Russell, Colin A.;Jones, Terry C.;Smith, Derek J.
通讯作者：
Smith, Derek J.
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：
4.3
作者：
Lemey P;Rambaut A;Drummond AJ;Suchard MA
通讯作者：
Suchard MA