Independently assessing seed-plant molecular phylogenies: does the cordaite fossil record support close relationships between Gnetales and conifers

对生物体中DNA的研究彻底改变了我们如何概念化和分析生物群体的进化历史，这是一门被称为遗传重建的科学学科。早期的方法依赖于对生物体的形态和解剖特征的分析，称为形态分支分析，但最近这些方法仅用于补充基于DNA序列的分析，称为分子分支分析。在某些情况下，从形态学和分子分析中获得的结果相互之间存在强烈的对比，产生了破坏性的不确定性，即哪一组证据更正确地推断了所研究的生物体的进化历史，并且不仅破坏了正式分类的信心，而且破坏了任何后续进化解释的信心。一个这样的关键群体，种子植物，起源于CA。3.63亿年前的泥盆纪晚期;它们有广泛的化石记录，并主导着现代陆地生态系统。活的种子植物代表五个主要的分类群：苏铁、银杏、针叶树、买麻藤和被子植物（开花植物）。化石记录中其他几个主要的种子植物类群早已灭绝，因此无法提供分子信息。它们包括一个复合体的植物，结合了联合收割机蕨类植物样的叶子和种子，被称为蕨类植物，这是牵连在进化起源的所有五个现存的种子植物群。这些化石是弥合将现存的五个种子植物群分开的巨大形态差距的唯一手段，这些差距无法直接使用分子系统学方法来解决。在现存的五个类群中，买麻藤目包括三个不同的现存谱系（以Welwitschia属、买麻藤属和麻黄属为代表），它们显示出形态特征的显著组合。大多数形态学分支研究将买麻藤目置于被子植物旁边，紧挨着化石群，如高级蕨类植物Pentoxylon和Bennettitales（种子植物关系的花植物假说）。然而，数据丰富（如果分类贫乏）的分子系统发育研究越来越多地将买麻藤目置于针叶树的基部（买麻藤假说）或紧邻松树的针叶树内（买麻藤假说）。该项目旨在（a）利用保存异常完好的植物的新化石数据独立评估当前的分子结果，（B）将结果与当前发育研究的形态学数据和支持发育的关键基因以及分子遗传学相结合。因此，我们的目标是采用全证据的方法来重建种子植物的进化历史。Gnepine，Gnetifer和Anthophyte的关系假设将通过仔细有针对性的化石记录分析进行测试，重点是详细的形态特征，可能会或可能不会，将Gnetales与针叶树结合起来。最近对现存买麻藤目植物的形态学重新分析表明，植物遗传学家以前误解了它们的雄性器官，它们与一些灭绝的针叶树和一个密切相关的灭绝类群科达亚针叶植物相似。这将是第一个详细的研究，旨在确定是否cordaites有基本的相似之处买麻藤。任何基本的相似之处都将支持格涅派恩假说，尤其是格奈蒂弗假说。任何根本的差异可能返回的重点gnetalean的关系固有的被子植物的花植物假说，但也可能需要大量的修订推断的主要群体之间的关系在针叶植物。因此，我们相信，这个项目将有助于阐明种子植物的争议历史。

The study of DNA in living organisms has revolutionised how we conceptualise and analyse the evolutionary history of biological groups, a scientific discipline known as phylogeny reconstruction. Earlier methods relied on the analysis of morphological and anatomical features of organisms in what are termed morphological cladistic analyses, but more recently these have been used only to supplement analyses based on DNA sequences, which are termed molecular cladistic analyses. In some cases the results gained from morphological and molecular analyses contrast strongly with each other, generating damaging uncertainties regarding which set of evidence more correctly infers the evolutionary history of the organisms studied, and undermining the confidence not only of formal classifications but also of any following evolutionary interpretations. One such critical group, the seed plants, originated ca. 363 million years ago in the late Devonian period; they have an extensive fossil record and dominate modern terrestrial ecosystems. Living seed plants represent five major taxonomic groups: cycads, Ginkgo, conifers, Gnetales and angiosperms (flowering plants). Several other major seed-plant groups evident in the fossil record are long extinct, and so cannot yield molecular information. They include a complex of plants that combine fern-like foliage and seeds, termed the pteridosperms, that are implicated in the evolutionary origins of all five extant groups of seed-plants. Such fossils are the only means of bridging the vast morphological gaps that separate the five extant seed-plants groups, which cannot be addressed directly using molecular systematic methods. Of the five extant groups, the Gnetales includes three distinct extant lineages (represented by the genera Welwitschia, Gnetum and Ephedra) that show remarkable combinations of morphological features. Most morphological cladistic studies place Gnetales next to angiosperms, immediately above fossil groups such as the advanced pteridosperm Pentoxylon and the Bennettitales (the Anthophyte hypothesis of seed-plant relationships). However, data-rich (if taxon-poor) molecular phylogenetic studies increasingly place Gnetales either at the base of the conifers (the Gnetifers hypothesis) or within conifers immediately adjacent to pines (the Gnepines hypothesis). This project seeks to (a) independently assess current molecular results with new fossil data from exceptionally well-preserved plants, and (b) integrate the results with morphological data from current investigations of development and the key genes that underpin development, together with molecular phylogenies. Thus, we aim to employ a whole-evidence approach to reconstruct the evolutionary history of seed plants. The Gnepine, Gnetifer and Anthophyte hypotheses of relationships will be tested by carefully targeted analysis of the fossil record, focusing on detailed morphological features that may, or may not, unite Gnetales with conifers. Recent morphological reanalysis of living Gnetales shows that phylogeneticists have previously been misinterpreting their male organs, which are similar to some extinct conifers and to a closely allied extinct group called the cordaitean coniferophytes. This will be the first detailed study designed to determine whether the cordaites have fundamental similarities with Gnetales. Any fundamental similarities will support the Gnepine and especially the Gnetifer hypotheses. Any fundamental dissimilarities may return the focus of gnetalean relationships to the angiosperms inherent in the Anthophyte hypothesis, but may also require substantial revision of inferred relationships among major groups within the coniferophytes. We are therefore confident that this project will help to elucidate the controversial history of seed plants.