ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets
ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets
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DOI：
10.1093/jhered/esz076
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发表时间：
2020-03-01
影响因子：
3.1
通讯作者：
Gatesy, John
中科院分区：
文献类型：
--
作者：
Springer, Mark S.;Molloy, Erin K.;Gatesy, John
DNA 序列比对为通过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 序列容易受到广泛的同质性影响，尤其是生命之树中的深度分歧。逆转录元件插入已成为解释进化关系的序列的强大替代方案，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合并方法的“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学研究中通常采样的DNA位点更好地近似中性。传统上使用简约法、距离法和网络法来分析逆向元素。在这里，我们使用 2 种 ILS 感知方法分析脊椎动物进化枝（胎盘目、Laurasiatheria、Balaenopteroidea、Palaeognathae）的逆向元素数据集，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 从逆向元素二分构建物种树，第二种方法基于简约性的分裂分解。我们还开发了四重不对称测试来检测使用逆转录元件的杂交。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 物种树在异常区域内具有连续的短分支长度，而古颌动物科则在该区域之外。对于鲸鱼科数据集，其中包括须鲸科 (Balaenopteridae) 和灰鲸 (Eschrichtiidae)，两种 ILS 感知方法都将鲸鱼科解析为并系群。对该数据集应用四重不对称测试检测到 19 个不同的四重物种，可以推断其历史基因渗入。在其他数据集中未检测到基因渗入的证据。
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 2 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.