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

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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.