DNA sequence alignments have provided the majority of data for inferring phylogenetic relationships with both concatenation and coalescent methods. However, DNA sequences are susceptible to extensive homoplasy, especially for deep divergences in the Tree of Life. Retroelement insertions have emerged as a powerful alternative to sequences for deciphering evolutionary relationships because these data are nearly homoplasy-free. In addition, retroelement insertions satisfy the 'no intralocus-recombination' assumption of summary coalescent methods because they are singular events and better approximate neutrality relative to DNA loci commonly sampled in phylogenomic studies. Retroelements have traditionally been analyzed with parsimony, distance, and network methods. Here, we analyze retroelement data sets for vertebrate clades (Placentalia, Laurasiatheria, Balaenopteroidea, Palaeognathae) with two ILS-aware methods that operate by extracting, weighting, and then assembling unrooted quartets into a species tree. The first approach constructs a species tree from retroelement bipartitions with ASTRAL, and the second method is based on split-decomposition with parsimony. We also develop a Quartet-Asymmetry test to detect hybridization using retroelements. Both ILS-aware methods recovered the same species-tree topology for each data set. The ASTRAL species trees for Laurasiatheria have consecutive short branch lengths in the anomaly zone whereas Palaeognathae is outside of this zone. For the Balaenopteroidea data set, which includes rorquals (Balaenopteridae) and gray whale (Eschrichtiidae), both ILS-aware methods resolved balaeonopterids as paraphyletic. Application of the Quartet-Asymmetry test to this data set detected 19 different quartets of species for which historical introgression may be inferred. Evidence for introgression was not detected in the other data sets.

中文翻译：

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低同质性逆向元素插入的 ILS 感知分析：使用四重奏推断物种树和基因渗入

DNA 序列比对为使用串联和合并方法推断系统发育关系提供了大部分数据。然而，DNA 序列易受广泛同质性的影响，特别是对于生命之树中的深度分歧。Retroelement 插入已成为破译进化关系的序列的有力替代品，因为这些数据几乎没有同质性。此外，逆向元件插入满足总结聚结方法的“无位点内重组”假设，因为它们是单一事件，并且相对于系统发育研究中常见的 DNA 位点具有更好的近似中性。传统上使用简约、距离和网络方法来分析复古元素。在这里，我们分析了脊椎动物进化枝（胎盘属，Laurasiatheria、Balaenopteroidea、Palaeognathae）使用两种 ILS 感知方法进行操作，这些方法通过提取、加权然后将无根四重奏组装成物种树来进行操作。第一种方法使用 ASTRAL 从逆元素二分法构建物种树，第二种方法基于简约分解。我们还开发了 Quartet-Asymmetry 测试来检测使用逆向元件的杂交。两种 ILS 感知方法都为每个数据集恢复了相同的物种树拓扑。Laurasiatheria 的 ASTRAL 种树在异常区具有连续的短分支长度，而古颌在该区之外。对于 Balaenopteroidea 数据集，其中包括 rorquals (Balaenopteridae) 和灰鲸 (Eschrichtiidae)，两种 ILS 感知方法都将 balaeonopterids 解析为并系群。对该数据集应用 Quartet-Asymmetry 测试检测了 19 种不同的物种，可以推断出历史基因渗入。在其他数据集中没有检测到基因渗入的证据。