Bayesian phylogeography finds its roots.
Bayesian phylogeography finds its roots.
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DOI：
10.1371/journal.pcbi.1000520
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发表时间：
2009-09
影响因子：
4.3
通讯作者：
Suchard MA
中科院分区：
文献类型：
--
作者：
Lemey P;Rambaut A;Drummond AJ;Suchard MA
作为地方病和流行病动态的关键因素，病毒的地理分布经常根据其遗传历史来解释。不幸的是，推理的历史传播或迁移模式的病毒主要限于无模型的启发式方法，提供很少的洞察到的时间设置的空间动态。然而，概率进化模型的引入为从事这一统计奋进提供了独特的机会。在这里，我们介绍了一个贝叶斯框架的推理，可视化和假设检验的地理历史。通过在贝叶斯软件中实现特征映射，对时间尺度的遗传进行采样，我们能够重建时间病毒传播模式，同时适应系统发育的不确定性。标准的马尔可夫模型的推理扩展了随机搜索变量选择过程，确定的简约描述的扩散过程。此外，我们提出了先验，可以将地理采样分布或表征替代假设的空间动态。为了将空间和时间信息可视化，我们使用虚拟地球仪软件总结推理。我们描述了如何贝叶斯地理学比较与以前的简约分析在调查甲型流感H5N1的起源和H5N1流行病学之间的联系抽样地点。西非犬群狂犬病的分析揭示了病毒扩散如何通过连续的流行周期使地方病得以维持。从这些分析中，我们得出结论，我们的生物地理学框架将成为分子流行病学的重要资产，可以很容易地推广到从许多生物体的遗传数据中推断生物地理学。在时间和空间上传播，快速进化的病毒可以积累相当数量的遗传变异。因此，病毒基因组成为重建影响流行病或地方病动态的空间和时间过程的宝贵资源。在分子流行病学中，空间推断通常仅限于解释病原体采样位置的进化历史。为了检验关于病毒空间扩散模式的假设，需要分析技术，使我们能够重建病毒在过去的迁移方式。在这里，我们开发了一个模型来推断扩散过程中的离散位置在定时的进化历史中的统计有效的方式。应用于禽流感A H5N1和狂犬病病毒在中非和西非的狗证明了几个优势，同时推断的空间和时间过程的基因序列。
As a key factor in endemic and epidemic dynamics, the geographical distribution of viruses has been frequently interpreted in the light of their genetic histories. Unfortunately, inference of historical dispersal or migration patterns of viruses has mainly been restricted to model-free heuristic approaches that provide little insight into the temporal setting of the spatial dynamics. The introduction of probabilistic models of evolution, however, offers unique opportunities to engage in this statistical endeavor. Here we introduce a Bayesian framework for inference, visualization and hypothesis testing of phylogeographic history. By implementing character mapping in a Bayesian software that samples time-scaled phylogenies, we enable the reconstruction of timed viral dispersal patterns while accommodating phylogenetic uncertainty. Standard Markov model inference is extended with a stochastic search variable selection procedure that identifies the parsimonious descriptions of the diffusion process. In addition, we propose priors that can incorporate geographical sampling distributions or characterize alternative hypotheses about the spatial dynamics. To visualize the spatial and temporal information, we summarize inferences using virtual globe software. We describe how Bayesian phylogeography compares with previous parsimony analysis in the investigation of the influenza A H5N1 origin and H5N1 epidemiological linkage among sampling localities. Analysis of rabies in West African dog populations reveals how virus diffusion may enable endemic maintenance through continuous epidemic cycles. From these analyses, we conclude that our phylogeographic framework will make an important asset in molecular epidemiology that can be easily generalized to infer biogeogeography from genetic data for many organisms. Spreading in time and space, rapidly evolving viruses can accumulate a considerable amount of genetic variation. As a consequence, viral genomes become valuable resources to reconstruct the spatial and temporal processes that are shaping epidemic or endemic dynamics. In molecular epidemiology, spatial inference is often limited to the interpretation of evolutionary histories with respect to the sampling locations of the pathogens. To test hypotheses about the spatial diffusion patterns of viruses, analytical techniques are required that enable us to reconstruct how viruses migrated in the past. Here, we develop a model to infer diffusion processes among discrete locations in timed evolutionary histories in a statistically efficient fashion. Applications to Avian Influenza A H5N1 and Rabies virus in Central and West African dogs demonstrate several advantages of simultaneously inferring spatial and temporal processes from gene sequences.
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DOI：
10.1098/rstb.2008.0176
发表时间：
2008-12-27
影响因子：
6.3
作者：
Minin, Vladimir N.;Suchard, Marc A.
通讯作者：
Suchard, Marc A.
影响因子：
4.9
作者：
Knowles, LL;Maddison, WP
通讯作者：
Maddison, WP
影响因子：
--
作者：
KULLBACK, S;LEIBLER, RA
通讯作者：
LEIBLER, RA
影响因子：
5.4
作者：
Chen, HL;Li, YB;Kawaoka, Y
通讯作者：
Kawaoka, Y
DOI：
10.1073/pnas.0609122104
发表时间：
2007-05-01
影响因子：
11.1
作者：
Hampson, Katie;Dushoff, Jonathan;Dobson, Andy
通讯作者：
Dobson, Andy