Collaborative proposal: The foundation of terrestrial life: Inferring a total-evidence timeline of vascular plant evolution

该项目将确定维管植物何时进化以及它们之间的关系。维管植物包括石松类、蕨类及其同属植物，以及针叶树和开花植物。它们构成了几乎所有陆地生态系统和我们食物供应的基础，但科学家们对它们何时以及如何进化存在分歧。目前估计这些物种进化时间表的方法导致了相互矛盾的答案，因为它们依赖于研究人员将灭绝的化石物种正确地分配到生命之树的特定分支点的能力。这项任务是具有挑战性的，因为灭绝的物种可能有不同的形态可以解释。研究人员将改进一种新的数据分析方法来解决这一限制。他们将比较现存维管植物的DNA序列，并结合现存和灭绝物种的形态数据来重建它们的进化关系。在这个过程中，研究人员将应用新的计算机算法来估计物种的进化时间表。研究人员将培训本科生和研究生，包括代表性不足的群体的成员，并支持早期职业研究人员的专业发展。他们将在加州大学伯克利分校举办一个解释性展览，并为高中生和教育工作者制作一系列在线视频课程，向公众宣传植物进化。该项目将开发一种新的全证据测年方法，以重建包括灭绝和现存物种在内的下一代时间校准系统发育假说。研究人员将利用现有NSF奖励收集的DNA序列数据，利用核基因组数据重建约300种现存维管植物的骨干系统发育。他们还将收集这些物种的大约300个特征以及大约200个已灭绝的化石物种的形态学数据。这些数据将同时被RevBayes软件程序整合，以推断出一个经过时间校准的系统发育。这个程序结合了复杂的树形先验，强大的形态进化模型，以及最近开发的放松分子钟的方法。项目成果将包括对维管植物分化时间和形态进化模式的可靠估计，并明确测量该估计的全部相关不确定性。该项目将通过在在线开放访问的PROTEUS数据库中共享新的和遗留的形态学数据集，并举办一个培训研讨会，重点是改进发散时间测年的理论和实践，从而支持研究。研究将加强美国和国际科学家之间的合作。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This project will determine when vascular plants evolved and how they are related. Vascular plants include lycopods, ferns and their allies, as well as conifers and flowering plants. They form the foundation of nearly all terrestrial ecosystems and our food supply, yet scientists disagree about when and how they evolved. Current methods for estimating evolutionary timelines for these species have led to conflicting answers, as they rely on the ability of researchers to assign extinct fossil species correctly to particular branch points in the tree of life. This assignment is challenging to do because extinct species may have morphology that can be interpreted differently. Researchers will refine a new data analysis method to address this limitation. They will compare the DNA sequences of living vascular plants and incorporate morphological data from both living and extinct species to reconstruct their evolutionary relationships. During this process, researchers will apply new computer algorithms to estimate the evolutionary timeline for the species. Researchers will train undergraduate and graduate students, including members of under-represented groups, and support the professional development of an early-career researcher. They will educate the public about plant evolution by creating an interpretive exhibit at the University of California Berkeley and by producing a series of online video lessons for high school students and educators.This project will develop a new total-evidence dating method to reconstruct the next-generation of time-calibrated phylogenetic hypotheses that incorporate both extinct and extant species. Researchers will leverage DNA sequence data collected by an existing NSF award to reconstruct a backbone phylogeny of ca. 300 extant vascular plants using nuclear genomic data. They will also collect morphological data for ca. 300 traits from these species as well as ca. 200 extinct fossil species. These data will be simultaneously integrated by the software program RevBayes to infer a time-calibrated phylogeny. This program combines sophisticated tree-shape priors, powerful models of morphological evolution, and recently developed methods for relaxing the molecular clock. Project outcomes will include a robust estimate of vascular plant divergence times and patterns of morphological evolution with an explicit measure of the full associated uncertainty of that estimate. The project will support research by sharing new and legacy morphological datasets in the online, open-access PROTEUS database and by hosting a training workshop focused on refining the theory and practice of divergence-time dating. Research will strengthen collaborations among US and international scientists.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.