1. Phylogenetic signal quantifies the degree to which resemblance in continuously valued traits reflects phylogenetic relatedness. Measures of phylogenetic signal are widely used in ecological and evolutionary research and are recently gaining traction in viral evolutionary studies. Standard estimators of phylogenetic signal frequently condition on data summary statistics of the repeated trait observations and fixed phylogenetics trees, resulting in information loss and potential bias.
2. To incorporate the observation process and phylogenetic uncertainty in a model‐based approach, we develop a novel Bayesian inference method to simultaneously estimate the evolutionary history and phylogenetic signal from molecular sequence data and repeated multivariate traits. Our approach builds upon a phylogenetic diffusion framework that models continuous trait evolution as a Brownian motion process and incorporates Pagel's λ transformation parameter to estimate dependence among traits. We provide a computationally efficient inference implementation in the BEAST software package.
3. We evaluate the synthetic performance of the Bayesian estimator of phylogenetic signal against standard estimators and demonstrate the use of our coherent framework to address several virus‐host evolutionary questions, including virulence heritability for HIV, antigenic evolution in influenza and HIV, and Drosophila sensitivity to sigma virus infection. Finally, we discuss model extensions that will make useful contributions to our flexible framework for simultaneously studying sequence and trait evolution.

中文翻译：

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同时估计进化历史和重复性状系统发育信号：在病毒和宿主表型进化中的应用。

1. 
   系统发育信号量化了连续有价值的性状的相似性反映系统发育相关性的程度。系统发育信号的测量广泛应用于生态和进化研究，并且最近在病毒进化研究中受到关注。系统发育信号的标准估计器经常以重复性状观察和固定系统发育树的数据汇总统计为条件，导致信息丢失和潜在偏差。
2. 
   为了将观察过程和系统发育不确定性纳入基于模型的方法中，我们开发了一种新颖的贝叶斯推理方法，可以根据分子序列数据和重复的多变量特征同时估计进化历史和系统发育信号。我们的方法建立在系统发育扩散框架的基础上，该框架将连续性状进化建模为布朗运动过程，并结合 Pagel 的 λ 变换参数来估计性状之间的依赖性。我们在 BEAST 软件包中提供了计算高效的推理实现。
3. 
   我们评估了系统发生信号的贝叶斯估计器与标准估计器的综合性能，并证明了使用我们的连贯框架来解决几个病毒宿主进化问题，包括 HIV 的毒力遗传力、流感和 HIV 的抗原进化以及果蝇对 sigma 的敏感性病毒感染。最后，我们讨论模型扩展，这将为我们同时研究序列和性状进化的灵活框架做出有用的贡献。