Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies.
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies.
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DOI：
10.1093/molbev/msw079
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发表时间：
2016-07
影响因子：
10.7
通讯作者：
Mirarab S
中科院分区：
文献类型：
--
作者：
Sayyari E;Mirarab S
物种树重建是复杂的不完全谱系排序的影响，通常由多物种合并模型（MSC）建模。虽然已经有了很大的进展，在开发方法，估计一个物种树的基因树的集合，很少注意到已经支付了快速和准确的方法量化支持。在这篇文章中，我们提出了一个快速算法来计算一个给定的物种树的每一个分支的四分之一为基础的支持一组给定的基因树。然后，我们展示了如何在MSC的上下文中使用四重支持来计算（1）分支在物种树中的局部后验概率（PP）和（2）合并单元中的分支的长度。我们评估了一组广泛的模拟和生物数据集上的本地PP的精度和召回率，并表明它具有非常高的精度和提高召回率相比，多位点自举。当基因树估计误差较低时，估计的分支长度是高度准确的，但是当基因树估计误差增加时，估计的分支长度被低估。分支长度和局部PP的计算作为ASTRAL中的新功能被实现。
Species tree reconstruction is complicated by effects of incomplete lineage sorting, commonly modeled by the multi-species coalescent model (MSC). While there has been substantial progress in developing methods that estimate a species tree given a collection of gene trees, less attention has been paid to fast and accurate methods of quantifying support. In this article, we propose a fast algorithm to compute quartet-based support for each branch of a given species tree with regard to a given set of gene trees. We then show how the quartet support can be used in the context of the MSC to compute (1) the local posterior probability (PP) that the branch is in the species tree and (2) the length of the branch in coalescent units. We evaluate the precision and recall of the local PP on a wide set of simulated and biological datasets, and show that it has very high precision and improved recall compared with multi-locus bootstrapping. The estimated branch lengths are highly accurate when gene tree estimation error is low, but are underestimated when gene tree estimation error increases. Computation of both the branch length and local PP is implemented as new features in ASTRAL.