Submission information
Submission Number: 22
Submission ID: 39
Submission UUID: cd466e1b-3dca-4ec6-a912-2ca5b4ec267b
Submission URI: /form/project
Created: Tue, 09/03/2019 - 13:43
Completed: Tue, 09/03/2019 - 13:45
Changed: Wed, 07/15/2020 - 13:01
Remote IP address: 130.215.55.243
Submitted by: Michael Sundue
Language: English
Is draft: No
Webform: Project
| Project Title | The foundation of terrestrial life: Inferring a total-evidence timeline of vascular plant evolution |
|---|---|
| Program | Northeast |
| Project Leader | Michael Sundue |
| sundue@gmail.com | |
| Mobile Phone | |
| Work Phone | 6462478992 |
| Mentor(s) | Adrian Del Maestro |
| Student-facilitator(s) | Jo Robertson |
| Mentee(s) | |
| Project Description | Vascular plants form the foundation of Earth's terrestrial ecosystems; understanding the timing and pattern of their origin and diversification thus underpins macroevolutionary study of all of terrestrial life. This project employs "total-evidence dating" (TED) methodologies for the simultaneous inference of the phylogenetic relationships of extant and extinct vascular plants, their divergence times, and their patterns of morphological evolution. We combine genomic data with morphological trait data from extant and extinct fossilized plants to generate a comprehensive view of land plant evolution over millions of years. Analyses are conducted using RevBayes which allows for the modular assembly of probabilistic models that use Markov chain Monte Carlo to perform inference. Our goal with the NECyberteam is to facilitate the transition from laptop to HPC in order to decrease run-times, increase efficiency, and further develop our tools, codes, and workflow on the VACC |
| Project Deliverables | |
| Project Deliverables | |
| Student Research Computing Facilitator Profile | The undergraduate researcher will be the liaison between the researchers developing the statistical analyses and the VACC. They will learn to submit jobs, manage installed packages, optimize runs, and return results. The student will also participate in the development of statistical modeling using RevBayes. |
| Mentee Research Computing Profile | |
| Student Facilitator Programming Skill Level | |
| Mentee Programming Skill Level | |
| Project Institution | University of Vermont |
| Project Address | Dept. of Plant Biology, University of Vermont 111 Jeffords Hall, 63 Carrigan Dr. Burlington, Vermont. 05405 |
| Anchor Institution | NE-University of Vermont |
| Preferred Start Date | 05/01/2019 |
| Start as soon as possible. | |
| Project Urgency | |
| Expected Project Duration (in months) | |
| Launch Presentation | |
| Launch Presentation Date | |
| Wrap Presentation | |
| Wrap Presentation Date | |
| Project Milestones | |
| Github Contributions | |
| Planned Portal Contributions (if any) | |
| Planned Publications (if any) | We intend to publish a series of papers demonstrating the utility of our statistical approach for inferring the history of life on earth. |
| What will the student learn? | How to submit jobs to the VACC, basic understanding of HPC tools, codes, and workflow. They will also interact with our collaborative team of computational biologists. |
| What will the mentee learn? | |
| What will the Cyberteam program learn from this project? | |
| HPC resources needed to complete this project? | approximately 10,000 hours on the VACC |
| Notes | |
| What is the impact on the development of the principal discipline(s) of the project? | Use of HPC varies in the discipline but is growing along with the complexity of analytical tools and models increases. This project has provided increased training and access to HPC and therefore allowed us to explore how we use it in the discipline. |
| What is the impact on other disciplines? | NA |
| Is there an impact physical resources that form infrastructure? | NA |
| Is there an impact on the development of human resources for research computing? | A major impact of this project was training for the PI and student to access and use HPC more effectively. |
| Is there an impact on institutional resources that form infrastructure? | Primarily though the networking of people using HPC resources in our institution which facilitates information exchange. |
| Is there an impact on information resources that form infrastructure? | NA |
| Is there an impact on technology transfer? | NA |
| Is there an impact on society beyond science and technology? | Results of our research are helping to improve our estimates of the timing and pace of the evolution of life on earth. Ultimately, this informs our sense of what it means to be human. |
| Lessons Learned | |
| Overall results | Training was provided to the PI and one student to improve understanding of coding skills and HPC. We successfully moved from running analyses on local machines to the institutional VACC. Our results find novel clade age estimates for Marattialean ferns and their fossil ancestors, a major group of land plants. This pilot project provides a foundation to expand our work to additional clades of land plants. |