School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; School of Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK.
Curr Biol. 2018 Mar 5;28(5):733-745.e2. doi: 10.1016/j.cub.2018.01.063. Epub 2018 Feb 15.
The evolutionary emergence of land plant body plans transformed the planet. However, our understanding of this formative episode is mired in the uncertainty associated with the phylogenetic relationships among bryophytes (hornworts, liverworts, and mosses) and tracheophytes (vascular plants). Here we attempt to clarify this problem by analyzing a large transcriptomic dataset with models that allow for compositional heterogeneity between sites. Zygnematophyceae is resolved as sister to land plants, but we obtain several distinct relationships between bryophytes and tracheophytes. Concatenated sequence analyses that can explicitly accommodate site-specific compositional heterogeneity give more support for a mosses-liverworts clade, "Setaphyta," as the sister to all other land plants, and weak support for hornworts as the sister to all other land plants. Bryophyte monophyly is supported by gene concatenation analyses using models explicitly accommodating lineage-specific compositional heterogeneity and analyses of gene trees. Both maximum-likelihood analyses that compare the fit of each gene tree to proposed species trees and Bayesian supertree estimation based on gene trees support bryophyte monophyly. Of the 15 distinct rooted relationships for embryophytes, we reject all but three hypotheses, which differ only in the position of hornworts. Our results imply that the ancestral embryophyte was more complex than has been envisaged based on topologies recognizing liverworts as the sister lineage to all other embryophytes. This requires many phenotypic character losses and transformations in the liverwort lineage, diminishes inconsistency between phylogeny and the fossil record, and prompts re-evaluation of the phylogenetic affinity of early land plant fossils, the majority of which are considered stem tracheophytes.
陆地植物体型的进化出现改变了地球。然而，我们对这一形成阶段的理解受到了与苔藓植物（角苔、地钱和藓类植物）和维管植物（有胚植物）之间系统发育关系相关不确定性的困扰。在这里，我们试图通过分析一个允许站点之间组成异质性的大型转录组数据集来解决这个问题。Zygnetophyceae 被解析为陆地植物的姐妹群，但我们得到了苔藓植物和维管植物之间的几种不同关系。可以明确容纳站点特异性组成异质性的串联序列分析为藓类植物-地钱类群“Setaphyta”作为所有其他陆地植物的姐妹群提供了更多支持，而对hornworts 作为所有其他陆地植物的姐妹群的支持较弱。基于明确容纳谱系特异性组成异质性的基因串联分析和基因树分析，支持苔藓植物的单系性。比较每个基因树与提出的物种树的拟合的最大似然分析以及基于基因树的贝叶斯超树估计都支持苔藓植物的单系性。在 15 个不同的有胚植物有根关系中，我们拒绝了除三个假说以外的所有假说，这三个假说仅在角苔的位置上有所不同。我们的结果表明，与承认地钱为所有其他有胚植物姐妹群的拓扑相比，祖先有胚植物更为复杂。这需要在地钱谱系中丢失和转化许多表型特征，减少系统发育与化石记录之间的不一致，并促使重新评估大多数被认为是茎维管植物的早期陆地植物化石的系统发育亲缘关系。
