Data from: Exploring phylogenetic relationships within Myriapoda and the effects of matrix composition and occupancy on phylogenomic reconstruction

Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed 40 Illumina transcriptomes representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and Symphyla); 25 transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at 3 levels of gene occupancy per taxon (50%, 75%, and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in 2 alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but 2 deep nodes remained in conflict in the different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses conducted with the most complete matrix (90% occupancy) are at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also with previous hypotheses based on morphology, development, or other molecular data sets. Our results indicate that a high percentage of ribosomal proteins in the most complete matrices, in conjunction with distance from the root, can act in concert to compromise the estimated relationships within the ingroup. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.多足类（Myriapoda）包含种类繁多且为人熟知的唇足纲（Chilopoda，俗称蜈蚣）与倍足纲（Diplopoda，俗称马陆），是陆地节肢动物的主要类群之一。尽管分子证据已证实多足类（Myriapoda）为单系群，但其内部系统发育关系仍存在争议且研究不足，相较于螯肢亚门（Chelicerata）与六足亚门（Hexapoda）的相关研究尤为如此。迄今为止，相关研究多聚焦于类群采样（例如从众多物种中选取少量基因），或是最大化矩阵规模（例如仅在少数物种中纳入数百乃至数千个基因），但同时兼顾两类采样最大化的系统发育研究仍难以实现。本研究共分析了40个基于Illumina平台的转录组数据，涵盖多足类4个纲中的3个：倍足纲（Diplopoda）、唇足纲（Chilopoda）与综合纲（Symphyla）；其中25个转录组为新测序获得，旨在最大化倍足纲的目级类群覆盖度以及唇足纲的科级类群覆盖度。本研究构建了10个超级矩阵，以探究3个基因占用率水平（50%、75%与90%）下，多种潜在系统发育偏差（例如进化速率、异速进化（heterotachy））对分析结果的影响。基于最大似然法与贝叶斯混合模型的分析结果均证实各多足类纲均为单系群，同时得到综合纲（Symphyla）的两种系统发育位置假说：其一为倍足纲+唇足纲的姊妹群，其二为与倍足纲亲缘关系更近，其中后者为传统形态学研究所支持的假说。在唇足纲（蜈蚣类）内部，所有目级类群均得到良好支持，但尽管已实现科级类群的高密度采样，不同分析中仍有2个深层节点存在冲突。在使用最完整矩阵（基因占用率90%）开展的所有分析中，蜈蚣类各目之间的系统发育关系，不仅与基因占比更低但基因数量更多的超级矩阵（75%与50%基因占用率矩阵）、以及优化系统发育信息度或选取高度保守基因构建的矩阵结果相悖，同时也与此前基于形态学、发育学或其他分子数据集提出的假说不符。本研究结果表明，在最完整的矩阵中，高占比的核糖体蛋白与类群距根节点的距离共同作用，会干扰内群类群系统发育关系的估算结果。最后，我们结合当前系统发育组学研究中日益普遍的"追求完整性"趋势，讨论了本研究结果的学术启示。