Deep phylogeny involving arthropod lineages is difficult to recover because the erosion of phylogenetic signals over time leads to unreliable multiple sequence alignment (MSA) and subsequent phylogenetic reconstruction. One way to alleviate the problem is to assemble a large number of gene sequences to compensate for the weakness in each individual gene. Such an approach has led to many robustly supported but contradictory phylogenies. A close examination shows that the supermatrix approach often suffers from two shortcomings. The first is that MSA is rarely checked for reliability and, as will be illustrated, can be poor. The second is that, to alleviate the problem of homoplasy at the third codon position of protein-coding genes due to convergent evolution of nucleotide frequencies, phylogeneticists may remove or degenerate the third codon position but may do it improperly and introduce new biases. We performed extensive reanalysis of one of such “big data” sets to highlight these two problems, and demonstrated the power and benefits of correcting or alleviating these problems. Our results support a new group with Xiphosura and Arachnopulmonata (Tetrapulmonata + Scorpiones) as sister taxa. This favors a new hypothesis in which the ancestor of Xiphosura and the extinct Eurypterida (sea scorpions, of which many later forms lived in brackish or freshwater) returned to the sea after the initial chelicerate invasion of land. Our phylogeny is supported even with the original data but processed with a new “principled” codon degeneration. We also show that removing the 1673 codon sites with both AGN and UCN codons (encoding serine) in our alignment can partially reconcile discrepancies between nucleotide-based and AA-based tree, partly because two sequences, one with AGN and the other with UCN, would be identical at the amino acid level but quite different at the nucleotide level.

涉及节肢动物谱系的深层系统发育很难恢复，因为随着时间的流逝，系统发生信号的侵蚀会导致不可靠的多序列比对（MSA）和后续的系统发生重建。减轻问题的一种方法是组装大量的基因序列，以补偿每个单独基因的弱点。这种方法导致了许多强有力的支持但相互矛盾的系统发育。仔细检查表明，超级矩阵方法通常有两个缺点。首先是，很少会检查MSA的可靠性，并且可能会很差。第二个是，为了缓解由于核苷酸频率的趋同进化而导致的蛋白质编码基因第三个密码子位置的同质性问题，系统发育学家可能会删除或简并第三个密码子位置，但可能做错了并引入了新的偏见。我们对其中一个“大数据”集进行了广泛的重新分析，以突出显示这两个问题，并展示了纠正或缓解这些问题的能力和好处。我们的结果支持了一个以Xiphosura和Arachnopulmonata（Tetrapulmonata + Scorpiones）作为姊妹类群的新小组。这支持了一种新的假设，在这种假设中，Xiphosura的祖先和灭绝的Eurypterida（海蝎，其中许多后来的形态都生活在微咸的或淡水中）在最初的螯合物入侵土地后又返回了大海。即使有原始数据，我们的系统发育也得到支持，但通过新的“原理”密码子变性处理了系统发育。