# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz Examples Figure 2 presents a reconstruction of the gene tree relating 13 species of Darwin’s fnches from a 2,065-bp partial nucleotide alignment of the mitochondrial control region and cytochrome b genes (Sato et al. 1999) and fve continuously measured phenotypic traits of the corresponding species (Sulloway 1982). In performing this simultaneous inference, we exploit the RLC model (Drummond and Suchard 2010) and find evidence for one suggestive rate change (Bayes factor in favor of the RLC over a strict clock = 2.3) in the lineage leading to the Cocos Island Finch, Pinaroloxias inornata. Multivariate Brownian trait diffusion shows strong correlation between wing and tarsus length and between bill depth and gonys length. Posterior trait prediction at any point along the history is possible and, currently unique to BEAST, comparative method inference is performed jointly with phylogenetic inference. 举例说明 图 2 展示了 13 个达尔文雀的基因树情况，该树是基于 2065 bp 线粒体控制区和细胞色素 b 基因（ Sato et al. 1999 ）比对序列以及相关物种 5 个表型量化特征构建的（ Sulloway 1982 ）。在进行这一同步推断的过程中，我们采用了 RLC 模型（ Drummond and Suchard 2010 ）且在科科斯岛雀（ Pinaroloxias Inornata ）的谱系中找到一个提示性速率变化的证据（ strict clock = 2.3 时， Bayes 因子对 RLC 最优）。多变异的布朗性状扩散显示翼长与跗骨长度之间以及 嘴高 与下喙长度之间的存在强相关性。对于 BEAST 来说，进化树上任何一点的后验特性预测都是可能且唯一，（特征）比较推理与系统发育推理相可以结合起来。 Drummond A J , Suchard M A , Xie D , et al. Bayesian Phylogenetics with BEAUti and the BEAST 1.7 . Molecular Biology and Evolution, 2012, 29(8):1969-1973.
# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz Performance Finally, to exploit high-performance computing, BEAST 1.7 integrates with and provides a GUI interface to confgure the BEAGLE library (Ayres et al. 2011) that utilizes multicore processors, vectorization, and massively parallel graphics processors to substantially decrease BEAST runtimes (Suchard and Rambaut 2009) 性能 最后，为了利用高性能计算， BEAST 1.7 集成并提供了一个 GUI 接口来配置 BEAGLE 库（ Ayres et al. 2011 ），它利用多核处理器、矢量化和大规模并行图形处理器大幅减少 BEAST 运行时间（ Suchard and Rambaut 2009 ） Drummond A J , Suchard M A , Xie D , et al. Bayesian Phylogenetics with BEAUti and the BEAST 1.7 . Molecular Biology and Evolution, 2012, 29(8):1969-1973.
# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz Molecular Clocks We have refned the relaxed clock models to allow more than one branch to have the same rate value to remove anticorrelation. In practice, this will only have any appreciable impact on trees that have a small number of branches (15 taxa). An effcient implementation of the relaxed clock models that facilitates calculation of Bayes Factors for model selection and model averaging of several clock models has also be developed (Li and Drummond, 2012). Further, we provide a new random local clock (RLC) model (Drummond and Suchard 2010), in which all possible local clock confgurations and a strict clock are nested, providing a convenient model to test for a strict clock. Heled and Drummond (2011) begins to investigate alternative approaches to the calibration of tree priors with fossil and geological evidence, and this area of research is still in its infancy. Often, uncertainty exists in the age of viral RNA/DNA or ancient DNA samples and these can now be incorporated (Shapiro et al. 2011), along with models for sequence damage and error (Rambaut et al. 2009). 分子钟 我们重新定义了松散的时钟模型，以允许多个分支具有相同的速率值来消除反相关。在实践中，这只会对枝条数量很少（ 15 个分类群）的树产生明显的影响。此外，还开发了实施有效的简化时钟模型，该模型有助于计算模型选择的贝叶斯因子和几个时钟模型的模型平均（ Li and Drummond, 2012 ）。此外，我们还提供了一个新的随机局部时钟（ RLC ）模型（ Drummond and Suchard 2010 ），其中嵌套了所有可能的局部时钟配置和严格的时钟，为测试严格的时钟提供了一个方便的模型。 Heled 和 Drummond （ 2011 ）开始研究用化石和地质证据来校准树先验值，这一研究领域仍处于起步阶段。通常，病毒 RNA/DNA 或古代 DNA 样本的年龄存在不确定性，现在可以整合（ Shapiro et al. 2011 ）到序列损伤和误差模型（ Rambaut et al. 2009 ）。 Drummond A J , Suchard M A , Xie D , et al. Bayesian Phylogenetics with BEAUti and the BEAST 1.7 . Molecular Biology and Evolution, 2012, 29(8):1969-1973.
# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz Phenotypic Trait Analysis For trait inference including phylogeography, we now provide several tools for mapping posterior distributions of trees onto higher dimensional or geographics maps for both interactive exploration and better visualization (Bielejec et al. 2011). These tools interface with GoogleEarth via keyhole markup language and enable users to generate animations of evolutionary processes through time and real space; see http://www.phylogeography.org for several examples. 表型性状分析 对于包括系统地理学在内的特征推断，我们现在提供了几种工具，用于将系统树的后验分布映射到更高维度或地理地图上，以便进行交互式探索和更佳可视化（ Bielejec et al. 2011 ）。这些工具通过 keyhole 标记语言与 GoogleEarth 交互，使用户能够通过时间和真实空间生成进化过程的动画；有关几个示例，请参见 http://www.phylography.org 。 Drummond A J , Suchard M A , Xie D , et al. Bayesian Phylogenetics with BEAUti and the BEAST 1.7 . Molecular Biology and Evolution, 2012, 29(8):1969-1973.
# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz Multispecies Coalescent Discordance between individual gene trees that share a phylogenetic history results from incomplete lineage sorting and becomes increasingly likely when times between speciation events are short compared with species’ population sizes. We provide a fully Bayesian implementation of the multispecies coalescent that improves the accuracy and precision of species tree reconstruction (Heled and Drummond 2010) and divergence time estimation (McCormack et al. 2011). 多物种溯祖 共享一个系统发育史的多个单基因树之间的不一致性是由于不完全的谱系分类造成的，并且与物种的种群规模相比，当物种形成事件之间的时间较短时，这种不一致性变得越来越可能。我们提供了多物种联合溯祖的全贝叶斯实现，提高了物种树重建（ Heled and Drummond 2010 ）和分化时间估计（ McCormack et al. 2011 ）的精准度。 Drummond A J , Suchard M A , Xie D , et al. Bayesian Phylogenetics with BEAUti and the BEAST 1.7 . Molecular Biology and Evolution, 2012, 29(8):1969-1973.
# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz Heterogeneous Data Multiple data partitions may reflect separate loci for simultaneous inference of genealogies and species trees (Heled and Drummond 2010) and stochastic ancestral recombination graph reconstruction (Bloomquist and Suchard 2010) or the growing wealth of nonsequence data and their respective substitution models. These latter data and models include microsatellite markers (Wu and Drummond 2011), phenotypic traits under a multistate stochastic Dollo process (Alekseyenko et al. 2008), discretized geographic diffusion (Lemey et al. 2009), and multivariate continuous relaxed random walks (Lemey et al. 2010). We also ease the use of a growing number of tree prior specifcations. These include the extended Bayesian skyline model (Heled and Drummond 2008) for multilocus data, the flexible Gaussian Markov random field skyride model (Minin et al. 2008), and birth–death models of speciation (Stadler 2010) . 异质数据 多重数据分区可能反映了使用不同的基因座同时推断系谱和物种树（ Heled and Drummond 2010 ）和随机祖先重组图重建（ Bloomquist and Suchard 2010 ）或日益丰富的非序列数据及其自身的替代模型。后一种数据和模型包括微卫星标记（ Wu and Drummond 2011 ），多状态随机 Dollo 过程下的表型特征（ Alekseyenko et al. 2008 ），离散地理扩散（ Lemey et al. 2009 ），以及多变量连续松弛随机行走（ Lemey et al. 2010 ）。我们还可以轻松使用越来越多的系统发育树的先验设置。包括针对多基因片段数据的扩展贝叶斯天际线模型（ Heled and Drummond 2008 ），弹性高斯马尔可夫随机场天桥模型（ Minin et al. 2008 ），以及物种形成的出生 - 死亡模型（ Stadler 2010 ）。 Drummond A J , Suchard M A , Xie D , et al. Bayesian Phylogenetics with BEAUti and the BEAST 1.7 . Molecular Biology and Evolution, 2012, 29(8):1969-1973.
# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz Here, we present a major new version of the molecular evolutionary software package Bayesian Evolutionary Analysis by Sampling Trees (BEAST), updated to version 1.7, and representing a signifcant software advance over that previously described (Drummond and Rambaut 2007). Alongside the primary analysis engine in BEAST, this package also includes a suite of utilities for specifying the analysis design, processing output files, and summarizing and visualizing the results. Taken together, these programs enable Bayesian inference of molecular sequences with an emphasis on time-structured evolutionary models including phylodynamic models, divergence time estimates, multiloci demographic models, gene–/species–tree inference, a range of spatial phylogeographic analyses, and discrete and continuous trait evolution. Implementing Markov chain Monte Carlo (MCMC) algorithms to perform these inferences, the package is intended and used for rigorous statistical inference and hypothesis testing of evolutionary models with joint inference of phylogeny. It is also possible to constrain portions of the phylogenetic model space to known values, including the tree topology, and perform conditional inference if required. 在这里，我们提出了 BEAST 一个重要更新版本（ 1.7 版），相较先前介绍的版本（ Drummond and Rambaut 2007 ）它代表了一个显著的软件进步。除了 BEAST 中的主要分析核心要件外，此软件包还包括一套用于指定分析设置、处理输出文件以及汇总和可视化结果的实用程序。综合起来，这些程序使分子序列的贝叶斯推断成为可能，重点是时间结构进化模型，包括系统动力学模型、分化时间估计、多基因座种群模型、基因 / 物种树推断、空间分布范围系统地理分析，以及离散和连续的特征进化。利用马尔可夫蒙特卡罗（ MCMC ）算法实现这些推断，并将其应用于系统发育联合推论的进化模型的严格统计推断和假设检验。还可以将系统发育模型空间的一部分限制为已知值，包括树拓扑结构，并在需要时执行条件推断。 Drummond A J , Suchard M A , Xie D , et al. Bayesian Phylogenetics with BEAUti and the BEAST 1.7 . Molecular Biology and Evolution, 2012, 29(8):1969-1973.
标签: beast
