Lemarcis Thomas, Fedosov Alexander E, Kantor Yuri I, Abdelkrim Jawad, Zaharias Paul, Puillandre Nicolas
Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, EPHE Sorbonne Université, Université des Antilles Paris France.
A. N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia.
Zool Scr. 2022 Sep;51(5):550-561. doi: 10.1111/zsc.12552. Epub 2022 Jun 29.
The Neogastropoda (Mollusca, Gastropoda) encompass more than 15,000 described species of marine predators, including several model organisms in toxinology, embryology and physiology. However, their phylogenetic relationships remain mostly unresolved and their classification unstable. We took advantage of the many mitogenomes published in GenBank to produce a new molecular phylogeny of the neogastropods. We completed the taxon sampling by using an in-house bioinformatic pipeline to retrieve mitochondrial genes from 13 transcriptomes, corresponding to five families not represented in GenBank, for a final dataset of 113 taxa. Because mitogenomic data are prone to reconstruction artefacts, eight different evolutionary models were applied to reconstruct phylogenetic trees with IQTREE, RAxML and MrBayes. If the over-parametrization of some models produced trees with aberrant internal long branches, the global topology of the trees remained stable over models and softwares, and several relationships were revealed or found supported here for the first time. However, even if our dataset encompasses 60% of the valid families of neogastropods, some key taxa are missing and should be added in the future before proposing a revision of the classification of the neogastropods. Our study also demonstrates that even complex models struggle to satisfactorily handle the evolutionary history of mitogenomes, still leading to long-branch attractions in phylogenetic trees. Other approaches, such as reduced-genome strategies, must be envisaged to fully resolve the neogastropod phylogeny.
新腹足目(软体动物门,腹足纲)包含超过15000种已描述的海洋捕食者物种,其中包括毒理学、胚胎学和生理学领域的几种模式生物。然而,它们的系统发育关系大多仍未解决,其分类也不稳定。我们利用GenBank中公布的众多线粒体基因组来构建新腹足目的新分子系统发育树。我们通过使用内部生物信息学管道从13个转录组中检索线粒体基因来完成分类群采样,这些转录组对应于GenBank中未涵盖的五个科,最终数据集包含113个分类群。由于线粒体基因组数据容易出现重建假象,我们应用了八种不同的进化模型,使用IQ-TREE、RAxML和MrBayes来重建系统发育树。如果某些模型的过度参数化产生了具有异常内部长枝的树,那么树的整体拓扑结构在不同模型和软件之间保持稳定,并且首次揭示或发现了几种关系得到支持。然而,即使我们的数据集涵盖了新腹足目60%的有效科,一些关键分类群仍然缺失,在提出新腹足目分类修订之前,未来应将其补充进来。我们的研究还表明,即使是复杂的模型也难以令人满意地处理线粒体基因组的进化历史,仍然会导致系统发育树中的长枝吸引现象。必须设想其他方法,如简化基因组策略,以完全解决新腹足目的系统发育问题。