Data for: Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone

A potential shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting. Coalescent methods address this problem but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescent methods, retroelement insertions (RIs) have emerged as powerful phylogenomic markers for species tree estimation. Here, we show that two recently proposed quartet-based methods, SDPquartets and ASTRAL_BP, are statistically consistent estimators of the unrooted species tree topology under the coalescent when RIs follow a neutral infinite-sites model of mutation and the expected number of new RIs per generation is constant across the species tree. The accuracy of these (and other) methods for inferring species trees from RIs has yet to be assessed on simulated data sets, where the true species tree topology is known. Therefore, we ...

用于物种树估计的串联法（concatenation methods）存在一项固有局限，即无法考量不完全谱系分选（incomplete lineage sorting）现象。溯祖法（coalescent methods）虽可解决该问题，但需满足多项假设；若这些假设被违反，其性能甚至可能劣于串联法。鉴于同时采用串联法与溯祖法分析DNA序列存在诸多挑战，逆转录转座子插入序列（retroelement insertions, RIs）已成为物种树估计领域极具潜力的系统基因组学标记物。本研究表明，当逆转录转座子插入序列遵循中性无限位点突变模型，且每一代新增RI的期望数量在物种树各分支间保持恒定时，两种新近提出的基于四分体的方法——SDPquartets与ASTRAL_BP——可作为溯祖模型下无根物种树拓扑结构的统计一致估计量。目前，针对基于RI推断物种树的此类（及其他）方法，尚未在已知真实物种树拓扑结构的模拟数据集上开展性能评估。因此，我们……