论文标题
贝叶斯加权三胞胎和物种树的四重奏方法
Bayesian Weighted Triplet and Quartet Methods for Species Tree Inference
论文作者
论文摘要
通常由物种树代表的物种进化史的推论使基因组不同部位的不同进化史变得复杂。基因组上的不同基因座与基础物种树（以及彼此）的历史不同，诸如谱系分类（ILS），基因的重复和损失以及水平基因转移等过程。多物种合并是在IL存在下对物种和基因树进行推断的常用模型。本文介绍了Lily-T和Lily-Q，这是多种物种合并下的两种新方法。然后，我们使用模拟和经验数据将它们与两种常用的方法：SVDQuartets和Astral进行比较。两种方法通常均表现出比SVDQuartets的改进，而Lily-Q对于大多数仿真设置都优于Lily-T。当无重组基因座的长度短，合并群体参数θ很小或内部分支长度更长时，与星体的比较更混合 - 百合-Q趋于比星体更好。
Inference of the evolutionary histories of species, commonly represented by a species tree, is complicated by the divergent evolutionary history of different parts of the genome. Different loci on the genome can have different histories from the underlying species tree (and each other) due to processes such as incomplete lineage sorting (ILS), gene duplication and loss, and horizontal gene transfer. The multispecies coalescent is a commonly used model for performing inference on species and gene trees in the presence of ILS. This paper introduces Lily-T and Lily-Q, two new methods for species tree inference under the multispecies coalescent. We then compare them to two frequently used methods, SVDQuartets and ASTRAL, using simulated and empirical data. Both methods generally showed improvement over SVDQuartets, and Lily-Q was superior to Lily-T for most simulation settings. The comparison to ASTRAL was more mixed - Lily-Q tended to be better than ASTRAL when the length of recombination-free loci was short, when the coalescent population parameter θ was small, or when the internal branch lengths were longer.
