# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz These observations would suggest the possibility of using analyses of branch lengths on a DNA tree for explicit tests of species boundaries, based on the difference in branching rates at the level of species and populations. Branch lengths between species are determined by speciation and extinction rates (macroevolution) (Nee et al., 1994), whereas branch lengths within a species reflect coalescence processes at the level of populations (microevolution) (Hudson, 1991; Rosenberg and Nordborg, 2002; Wakeley, 2006). Well-developed approaches exist for analyzing branching rates in either framework. Combining equations that describe processes of lineage birth at the species level with coalescence models within species, it is possible to develop a statistical framework for estimating the predicted shift in dynamics of branching associated with the species boundary. Here we develop a method that determines the locations of ancestral nodes that define putative species and applies a likelihood ratio test to assess the fit of the branch lengths to a mixed lineage birth-population coalescence model. 这些观察结果表明，根据物种和种群水平上的分支速率差异，可以利用 DNA 树上的分支长度分析来明确探测物种边界。物种间的分支长度由物种形成和灭绝率（宏观进化）决定（ Nee et al., 1994 ），而物种内的分支长度反映了种群水平上的溯祖过程（微观进化）（ Hudson, 1991; Rosenberg and Nordborg, 2002; Wakeley, 2006 ）。在这两个框架中，都存在分析分支率的成熟方法。将描述物种层次上谱系产生过程的方程与物种内部的溯祖模型相结合，可以建立一个统计框架来估计与物种边界相关的分支动态变化。在这里，我们开发了一种方法，确定祖先节点的位置以定义推定物种，并应用似然率测试来评估分支长度匹配混合的谱系发生 - 种群溯祖模型的程度。 Pons J, Barraclough T G, Gomez-Zurita J, et al. Sequence-based species delimitation for the DNA taxonomy of undescribed insects . Systematic biology, 2006, 55(4): 595-609.
# 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.
标签: 溯祖
