Xenacoelomorpha are mostly microscopic, morphologically simple worms, lacking many structures typical of other bilaterians. Xenacoelomorphs –which include three main groups: Acoela, Nemertodermatida, and Xenoturbella– have been proposed to be an early diverging Bilateria, sister to protostomes and deuterostomes, but other phylogenomic analyses have recovered this clade nested within the deuterostomes, as sister to Ambulacraria. The position of Xenacoelomorpha within the metazoan tree has understandably attracted a lot of attention, overshadowing the study of phylogenetic relationships within this group. Given that Xenoturbella includes only six species whose relationships are well understood, we decided to focus on the most speciose Acoelomorpha (Acoela + Nemertodermatida). Here, we have sequenced 29 transcriptomes, doubling the number of sequenced species, to infer a backbone tree for Acoelomorpha based on genomic data. The recovered topology is mostly congruent with previous studies. The most important difference is the recovery of Paratomella as the first off-shoot within Acoela, dramatically changing the reconstruction of the ancestral acoel. Besides, we have detected incongruence between the gene trees and the species tree, likely linked to incomplete lineage sorting, and some signal of introgression between the families Dakuidae and Mecynostomidae, which hampers inferring the correct placement of this family and, particularly, of the genus Notocelis. We have also used this dataset to infer for the first time diversification times within Acoelomorpha, which coincide with known bilaterian diversification and extinction events. Given the importance of morphological data in acoelomorph phylogenetics, we tested several partitions and models. Although morphological data failed to recover a robust phylogeny, phylogenetic placement has proven to be a suitable alternative when a reference phylogeny is available.

中文翻译：

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从转录组数据推断的 Acoelomorpha 的系统发育骨架


Xenacoelomorpha 大多是微观的、形态简单的蠕虫，缺乏其他双侧动物的许多典型结构。Xenacoelomorphs - 包括三个主要组：Acoela、Nemertodermatida 和 Xenoturbella——被认为是早期分化的双侧目，是原口和后口的姐妹，但其他系统发育分析发现这个分支嵌套在后口内，是 Ambulacraria的姐妹。可以理解的是，Xenacoelomorpha 在后生动物树中的位置引起了很多关注，使该组内系统发育关系的研究黯然失色。鉴于 Xenoturbella 只包括六个关系很好理解的物种，我们决定专注于最特殊的 Acoelomorpha （Acoela + Nemertodermatida）。在这里，我们对 29 个转录组进行了测序，将测序物种的数量增加了一倍，以根据基因组数据推断出 Acoelomorpha 的主干树。恢复的拓扑结构与以前的研究基本一致。最重要的区别是 Paratomella 作为 Acoela 内的第一个分支的恢复，极大地改变了祖先 acoel 的重建。此外，我们还检测到基因树和物种树之间的不一致，这可能与不完整的谱系排序有关，以及 Dakuidae 和 Mecynostomidae 科之间的一些渗入信号，这阻碍了推断该科的正确位置，特别是 Notocelis 属。我们还使用这个数据集首次推断了 Acoelomorpha 内的多元化时间，这与已知的双侧多元化和灭绝事件相吻合。鉴于形态学数据在 acoelomorph 系统发育学中的重要性，我们测试了几个分区和模型。 尽管形态学数据未能恢复稳健的系统发育，但当参考系统发育可用时，系统发育位置已被证明是一个合适的选择。