Assessing support for Blaberoidea phylogeny suggests optimal locus quality,Systematic Entomology

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Assessing support for Blaberoidea phylogeny suggests optimal locus quality
Systematic Entomology ( IF 4.7 ) Pub Date : 2020-09-15 , DOI: 10.1111/syen.12454
Dominic Evangelista _{1,

2,

3} , Sabrina Simon ₄ , Megan M. Wilson ₅ , Akito Y. Kawahara ₆ , Manpreet K. Kohli ₇ , Jessica L. Ware ₇ , Benjamin Wipfler ₈ , Olivier Béthoux ₉ , Philippe Grandcolas ₁ , Frédéric Legendre ₁

Affiliation

Phylogenomics seeks to use next‐generation data to robustly infer an organism's evolutionary history. Yet, the practical caveats of phylogenomics motivate investigation of improved efficiency, particularly when quality of phylogenies are questionable. To achieve improvements, one goal is to maintain or enhance the quality of phylogenetic inference while severely reducing dataset size. We approach this by assessing which kinds of loci in phylogenomic alignments provide the majority of support for a phylogenetic inference of cockroaches in Blaberoidea. We examine locus substitution rate, saturation, evolutionary divergence, rate heterogeneity, stabilizing selection, and a priori information content as traits that may determine optimality. Our controlled experimental design is based on 265 loci for 102 blaberoidean taxa and 22 outgroup species. Loci with high substitution rate, low saturation, low sequence distance, low rate heterogeneity, and strong stabilizing selection derive more support for phylogenetic relationships. We found that some phylogenetic information content estimators may not be meaningful for assessing information content a priori. We use these findings to design concatenated datasets with an optimized subsample of 100 loci. The tree inferred from the optimized subsample alignment was largely identical to that inferred from all 265 loci but with less evidence of long branch attraction, improved statistical support, and potential 4‐6x improvements to computation time. Supported by phylogenetic and morphological evidence, we erect three newly named clades (Anallactinae Evangelista & Wipfler subfam. nov., Orkrasomeria tax. nov. Evangelista, Wipfler, & Béthoux and Hemithyrsocerini Evangelista tribe nov.) and propose other taxonomic modifications. The diagnosis of Pseudophyllodromiidae Grandcolas, 1996 is modified to accommodate Anallactinae and Pseudophyllodromiinae Vickery & Kevan, 1983. The diagnosis of Ectobiidae Brunner von Wattenwyl, 1865 is modified to add novel morphological characters.

中文翻译：

评估对 Blaberoidea 系统发育的支持表明最佳基因座质量

系统基因组学试图使用下一代数据来可靠地推断生物体的进化历史。然而，系统基因组学的实际警告激发了对提高效率的研究，特别是当系统发育的质量有问题时。为了实现改进，一个目标是保持或提高系统发育推断的质量，同时大幅减少数据集大小。我们通过评估系统基因组比对中哪种基因座为 Blaberoidea 中蟑螂的系统发育推断提供了大部分支持来解决这个问题。我们检查基因座替换率、饱和度、进化分歧、速率异质性、稳定选择和先验信息内容作为可能决定最优性的特征。我们的受控实验设计基于 102 个 blaberoidean 分类群和 22 个外群物种的 265 个基因座。具有高取代率、低饱和度、低序列距离、低速率异质性和强稳定选择的位点为系统发育关系提供了更多支持。我们发现一些系统发育信息内容估计器对于先验地评估信息内容可能没有意义。我们使用这些发现来设计具有 100 个基因座的优化子样本的串联数据集。从优化的子样本对齐推断的树与从所有 265 个基因座推断的树基本相同，但长分支吸引的证据较少，统计支持得到改善，计算时间可能提高 4-6 倍。在系统发育和形态学证据的支持下，我们建立了三个新命名的进化枝（Anallactinae Evangelista & Wipfler subfam. nov., Orkrasomeria tax. nov. Evangelista, Wipfler, & Béthoux 和 Hemithyrsocerini Evangelista 部落 11 月）并提出其他分类学修改。Pseudophyllodromiidae Grandcolas, 1996 的诊断被修改以适应 Anallactinae 和 Pseudophyllodromiinae Vickery & Kevan, 1983。Ectobiidae Brunner von Wattenwyl, 1865 的诊断被修改以添加新的形态特征。

更新日期：2020-09-15

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