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

对生物体内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史，这是一门被称为系统发育重建的科学学科。早期的方法在所谓的形态分支分析中依赖于生物的形态和解剖特征的分析，但最近这些方法仅用于补充基于DNA序列的分析，这被称为分子分支分析。在某些情况下，从形态和分子分析获得的结果相互强烈反差，产生了关于哪一组证据更正确地推断所研究生物的进化史的破坏性不确定性，并不仅破坏了正式分类的信心，也破坏了任何后续进化解释的信心。种子植物是这样一个关键的类群，起源于约3.63亿年前的泥盆纪晚期；它们拥有广泛的化石记录，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类群：苏铁、银杏、针叶树、龙须菜和被子植物(开花植物)。化石记录中明显的其他几个主要种子植物类群早已灭绝，因此无法提供分子信息。它们包括一种将蕨类植物的叶子和种子结合在一起的植物复合体，被称为蕨类植物，与现存的所有五类种子植物的进化起源有关。这样的化石是弥合巨大的形态鸿沟的唯一手段，这些鸿沟将现存的五个种子植物群分开，而这些鸿沟不能用分子系统学方法直接解决。在五个现存的类群中，Gnetales包括三个不同的现存谱系(以Welwitschia属、Gnetum属和Ephedra属为代表)，它们表现出显著的形态特征组合。大多数形态分支学研究将Gnetales放在被子植物旁边，紧挨着化石类群，如高级蕨类五倍体和Bennettitales(种子-植物关系的植物群假说)。然而，数据丰富(如果缺乏分类单元)的分子系统学研究越来越多地将Gnetale置于针叶树的底部(Gnetifers假说)或紧邻松树的针叶树内(Gnepines假说)。该项目寻求(A)利用保存极为完好的植物的新化石数据独立评估当前的分子结果，以及(B)将结果与当前发育调查的形态数据和支撑发育的关键基因以及分子系统学结合起来。因此，我们的目标是使用全证据方法来重建种子植物的进化史。将通过对化石记录的仔细有针对性的分析，重点研究可能会或可能不会将Gnetale和针叶树结合在一起的详细的形态特征，来检验Gneine、Gnetifer和Anthophyte之间的关系假说。最近对活着的Gnetales进行的形态重新分析表明，系统发育学家此前错误地解释了它们的雄性器官，这些雄性器官类似于一些已灭绝的针叶树，以及与之密切相关的已灭绝的类群，称为Cordaitean针叶植物。这将是第一项详细的研究，旨在确定科尔多瓦人是否与格内塔莱斯人有根本上的相似之处。任何基本的相似之处都将支持麻雀说，尤其是格涅蒂费假说。任何根本性的不同之处都可能使被子植物与被子植物之间关系的焦点回归到被子植物中，但也可能需要对针叶植物内主要类群之间的关系进行实质性的修正。因此，我们有信心这个项目将有助于阐明有争议的种子植物的历史。

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.