模拟进化谱系的速度和预测扩散模式。
Modeling the velocity of evolving lineages and predicting dispersal patterns.
机构信息
Institut Montpelliérain Alexander Grothendieck, Université de Montpellier, CNRS, Montpellier 34090, France.
Université Paris Cité, CNRS, Mathématiques appliquées 'a Paris 5, Paris F-75006, France.
出版信息
Proc Natl Acad Sci U S A. 2024 Nov 19;121(47):e2411582121. doi: 10.1073/pnas.2411582121. Epub 2024 Nov 15.
Accurate estimation of the dispersal velocity or speed of evolving organisms is no mean feat. In fact, existing probabilistic models in phylogeography or spatial population genetics generally do not provide an adequate framework to define velocity in a relevant manner. For instance, the very concept of instantaneous speed simply does not exist under one of the most popular approaches that models the evolution of spatial coordinates as Brownian trajectories running along a phylogeny. Here, we introduce a family of models-the so-called Phylogenetic Integrated Velocity (PIV) models-that use Gaussian processes to explicitly model the velocity of evolving lineages instead of focusing on the fluctuation of spatial coordinates over time. We describe the properties of these models and show an increased accuracy of velocity estimates compared to previous approaches. Analyses of West Nile virus data in the United States indicate that PIV models provide sensible predictions of the dispersal of evolving pathogens at a one-year time horizon. These results demonstrate the feasibility and relevance of predictive phylogeography in monitoring epidemics in time and space.
准确估计扩散速度或进化生物的速度并非易事。事实上,生物地理学或空间种群遗传学中的现有概率模型通常不能提供一个适当的框架以相关的方式来定义速度。例如,在最流行的方法之一中,瞬时速度的概念根本不存在,该方法将空间坐标的演化建模为沿着系统发育运行的布朗轨迹。在这里,我们引入了一系列模型,即所谓的系统发育综合速度(PIV)模型,这些模型使用高斯过程来明确地对进化谱系的速度进行建模,而不是关注时空坐标的波动。我们描述了这些模型的特性,并表明与以前的方法相比,速度估计的准确性有所提高。对美国西尼罗河病毒数据的分析表明,PIV 模型能够合理地预测进化病原体在一年时间跨度内的扩散。这些结果证明了在时间和空间上监测流行病的预测性生物地理学的可行性和相关性。
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