Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction
Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction
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DOI：
10.1093/sysbio/syw041
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发表时间：
2016-09-01
影响因子：
6.5
通讯作者：
Giribet, Gonzalo
中科院分区：
文献类型：
--
作者：
Fernandez, Rosa;Edgecombe, Gregory D.;Giribet, Gonzalo
多足类是陆生节肢动物的主要类群之一，其中包括种类繁多且为人所熟悉的蜈蚣和千足虫。虽然分子证据显示多足目是单系的，但其内部的单系发生仍然存在争议和研究不足，特别是与螯肢目和六足目相比。到目前为止，努力的重点是分类群抽样（例如，通过包括来自许多物种的少量基因）或基于最大化矩阵大小（例如，通过在几个物种中包含数百或数千个基因），但是在两个水平上最大化采样的遗传学仍然是难以捉摸的。在这项研究中，我们分析了40 Illumina转录组代表3的4个多足类（倍足类，唇足类，和综合）; 25个转录组新测序，以最大限度地提高代表性在顺序水平倍足类和在家庭水平唇足类。构建了10个超矩阵以探索几种潜在的系统发育偏差的影响（例如，进化率，异序性）在每个分类单元的3个基因占有水平（50%，75%和90%）。基于最大似然法和贝叶斯混合模型的分析恢复了各多足类的单系性，并导致2个备选的系统发育位置，综合门，作为姐妹组倍足类+唇足类，或更接近倍足类，后者的假设已被传统上支持的形态。在蜈蚣，所有的订单都得到了很好的支持，但2深节点仍然在不同的分析，尽管在家庭水平上密集的分类单元采样冲突。在所有分析中，蜈蚣目之间的关系与最完整的矩阵（90%占有率）是不一致的，不仅与稀疏，但更丰富的基因超矩阵（75%和50%超矩阵）和矩阵优化系统发育信息或最保守的基因，但也与以前的假设的基础上形态，发展，或其他分子数据集。我们的研究结果表明，高比例的核糖体蛋白质在最完整的矩阵，结合距离的根，可以采取一致行动，以妥协的估计内组的关系。我们讨论的背景下，越来越普遍的追求完整性的基因组研究，这些发现的影响。
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.