Phylogenomics of Parasitic and Nonparasitic Lice (Insecta: Psocodea): Combining Sequence Data and Exploring Compositional Bias Solutions in Next Generation Data Sets
Phylogenomics of Parasitic and Nonparasitic Lice (Insecta: Psocodea): Combining Sequence Data and Exploring Compositional Bias Solutions in Next Generation Data Sets
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DOI：
10.1093/sysbio/syaa075
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发表时间：
2021-07-01
影响因子：
6.5
通讯作者：
Kevin, Johnson P.
中科院分区：
文献类型：
--
作者：
de Moya, Robert S.;Yoshizawa, Kazunori;Kevin, Johnson P.
Psocodea是一个由寄生性（Phthiraptera）和非寄生性（Psocoptera）组成的多样性谱系。极端的年龄和生态多样性的组可能与主要的基因组变化，如基地组成的偏见，预计会影响系统发育的推断。寄生和非寄生的成员之间的分歧形态也掩盖了内的顺序寄生的起源。我们利用转录组和基因组测序对Psocodea目进行了基因组分析，获得了2370个直链基因的数据集。所有的基因组分析，包括连接和合并的方法表明，一个单一的起源内的寄生Psocodea，解决以前的研究结果相矛盾。这一系统发生学使我们能够提出一个稳定的序数水平分类方案，保留了历史科学文献中存在的重要分类名称，并反映了整个群体的演变。一个测年分析，与内部节点校准化石证据，表明寄生的起源，早于K-Pg边界。在第三和第一个密码子位置检测到核苷酸组成的偏见，并导致在异常放置的双齿纲作为姐妹的Pamphiorpha时，所有的核苷酸位点进行分析。可能性映射和四重抽样方法表明，基础组成偏差也会对基于四重的方法产生影响。
The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and nonparasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and nonparasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2370 orthologous genes. All phylogenomic analyses, including both concatenated and coalescent methods suggest a single origin of parasitism within the order Psocodea, resolving conflicting results from previous studies. This phylogeny allows us to propose a stable ordinal level classification scheme that retains significant taxonomic names present in historical scientific literature and reflects the evolution of the group as a whole. A dating analysis, with internal nodes calibrated by fossil evidence, suggests an origin of parasitism that predates the K-Pg boundary. Nucleotide compositional biases are detected in third and first codon positions and result in the anomalous placement of the Amphientometae as sister to Psocomorpha when all nucleotide sites are analyzed. Likelihood-mapping and quartet sampling methods demonstrate that base compositional biases can also have an effect on quartet-based methods.