1. Evolutionary forces affect the distribution of phenotypes both within and among species. Yet, at the macro‐evolutionary scale, the evolution of intraspecific variance is rarely considered. Here, we present an r and a BEAST 2 implementation that extends the JIVE (Joint inter‐ and Intraspecific Variance Evolution) model aimed at the analysis of continuous trait evolution at both inter‐ and intraspecific level.
2. Using a hierarchical Bayesian approach, we implemented a range of models for continuous trait evolution that operate independently on species means and variances along a phylogeny. The package uses Markov chain Monte Carlo for the inference of parameters and the evaluation of model fit. JIVE is available in the bite (Bayesian Integrative models of Trait Evolution) r package, as well as in BEAST 2. The two implementations offer the same continuous trait evolutionary models, but differ in their use and types of analyses. The r implementation allows for faster analyses by taking the phylogeny as data, while providing graphical and statistical functions as part of tools for model comparison, result parsing and summary, and plotting. In the BEAST 2 implementation, the species tree is a parameter, and both its topology and divergence times are jointly estimated with trait model parameters.
3. The bite package and the BEAST 2 implementation introduce new frameworks within comparative phylogenetics that explicitly model intraspecific variance. These tools allow users to tackle long‐standing questions in evolutionary biology, such as the identification of key evolutionary processes determining niche conservatism, niche partitioning, and life‐history strategies.

中文翻译：

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用于分析种内和种间性状进化的多平台软件包

1. 进化力影响物种内部和物种之间的表型分布。然而，在宏观进化尺度上，很少考虑种内变异的演变。在这里，我们提出了r和BEAST 2实现，它扩展了JIVE（种间和种内联合变异）模型，旨在分析种间和种内水平的连续性状进化。
2. 使用分级贝叶斯方法，我们实现了一系列连续性状演化模型，这些模型独立地作用于物种均值和系统发育变异。该软件包使用马尔可夫链Monte Carlo进行参数推断和模型拟合评估。JIVE处于可用咬合（性状演进一体化贝叶斯模型）- [R包，以及在BEAST 2.两种实现提供相同的连续性状演化模型，但在它们的使用和类型的分析的不同。在[R实施通过将系统发育树作为数据来进行更快的分析，同时提供图形和统计功能作为模型比较，结果解析和汇总以及绘图工具的一部分。在BEAST 2实施中，物种树是一个参数，并且其拓扑和发散时间均与特征模型参数共同估算。
3. 该咬包和BEAST 2实施引进系统发育比较明确地模拟种内变异中的新框架。这些工具使用户能够解决进化生物学中长期存在的问题，例如确定关键生态过程，确定生态位保守性，生态位分配和生命历史策略。