The origin of plants: genomes, rocks, and biochemical cycles

毫无疑问，早期陆地植物的进化改变了地球，但我们对这一过程的了解却很混乱。陆生植物化石的首次出现与大气中氧气和二氧化碳的形成变化的明显巧合是缺乏早期陆生岩石的人工产物，解开陆生植物体形组装的时间及其对全球生物地球化学循环的影响需要对早期陆生植物进化及其影响的时间尺度有新的认识。陆地上的早期生命主要是微生物，但在大约7亿到4.2亿年前的某个时候，植物从水中搬到了陆地上。这个时间框架是有争议的，目前的理解是非常广泛的，但对这些事件的更精确的了解是将植物生命的早期进化与主要环境变化联系起来的关键。歧义和不确定性的产生是因为主要证据线的冲突。化石，特别是植物微化石（孢子），指向大约4.7 Ma（百万年前）开始的殖民，但是早期孢子生产者的亲和力是有争议的。大型化石（植物茎，多细胞器官系统等）表明晚于大约430 Ma开始的殖民。校准的分子系统发育学——基于分子序列数据对现存植物谱系分化时间的研究，其中突变率是根据化石校准的时间——指出陆地上生命的起源和早期进化可能始于新元古代晚期，远早于化石证据。最近的研究已经确定了分子系统发育和古生物学方法的困难，我们提出的研究计划将解决这些问题。我们已经组建了一个多学科团队来进行研究，以弥补这些缺点。我们将基于基因组规模的分子序列数据（约1,000个基因，因此约1,000,000个核苷酸）建立一个强大的植物谱系。家谱将通过包括重要的和特别保存的化石物种与时间联系起来。这些将通过使用最先进的同步加速器计算机断层扫描对其解剖结构进行详细描述来正确放置，这是一种新颖的方法，我们最近在最近的概念验证研究中展示了有价值的新数据。已知沉积制度会影响化石给出的年龄估计，因此我们也将应用我们开发的新方法来评估和纠正这一点。总之，这些方法将使我们能够以更高的精度开发一个强大的系统发育，我们将使用它来研究陆地植物关键器官和组织系统（如根、气孔、维管组织、叶片）的进化组装及其对主要生物地球化学循环的影响。最后，我们将在全球生物地球化学循环（GENIE）的领先计算机模型中探索我们的植物进化时间尺度的含义。这将使我们能够对大气二氧化碳水平和有机碳产量进行预测，我们将根据地质观测结果进行测试。最终，我们将为早期陆地植物进化的时间和速度、陆地植物体计划的集合建立一个新的情景，并对这一事件对地球系统进化的影响有一个新的认识。

There can be no doubt that early land plant evolution transformed the planet but how our knowledge of how this happened is in disarray. The clear coincidence in the first appearance of land plant fossils and formative shifts in atmospheric oxygen and CO2 is an artefact of the absence of earlier terrestrial rocks, and disentangling the timing of land plant bodyplan assembly and its impact on global biogeochemical cycles requires a new understanding of early land plant evolution and the timescale over which it was effected. Early life on land was mostly microbial, but sometime between about 700 million and 420 million years ago plants moved from water onto land. The timeframe is controversial and as currently understood it is very broad, but a more precise knowledge of the events is key to linking the early evolution of plant life to major environmental change. Ambiguity and uncertainty arise because the principal lines of evidence conflict. Fossils, notably plant microfossils (spores), point to colonization beginning about 470 Ma (million years ago), but the affinities of the early spore producers are controversial. Macrofossils (plant stems, multicellular organ systems, etc) indicate a later colonization, beginning about 430 Ma. Calibrated molecular phylogenies - studies of the timing of divergence of living plant lineages based on molecular sequence data, where the rate of mutation is calibrated to time using fossils - point to an origin and early evolution of life on land that may have begun during the Late Neoproterozoic, long predating the fossil evidence. Recent research has identified difficulties with both molecular phylogenetic and palaeontological approaches, which our proposed research program will address. We have assembled a multidisciplinary team to conduct research to remedy these shortcomings. We will establish a robust genealogy for living plant lineages based on a genome-scale amount of molecular sequence data (~1,000s genes and, therefore, ~1,000,000s nucleotides). The genealogy will be linked to time by including important and exceptionally preserved fossil species. These will be correctly placed through detailed characterization of their anatomy using state of the art Synchrotron Computed Tomography, a novel approach that we have recently shown to provide valuable new data in a recent proof of concept study. Sedimentary regime is known to affect the age estimate given by fossils, so we will also apply new methods develop by us to assess and to correct for this. Together, these approaches will enable us to develop a robust phylogeny calibrated with greater precision to time, which we will use to investigate the evolutionary assembly of key land plant organs and tissue systems (e.g., roots, stomata, vascular tissue, leaves) and their impact on major biogeochemical cycles. Finally, we will we will explore the implications of our plant evolutionary timescale within a leading computer model of global biogeochemical cycling (GENIE). This will enable us to generate predictions for levels of atmospheric carbon dioxide levels and of organic carbon productivity that we will test against geological observations. Ultimately, we will establish a new scenario for the timing and tempo of early land plant evolution, the assembly of land plant bodyplans, and a new understanding of the effect of this episode upon the evolution of the Earth System.