CAREER: Identifying the Role of Tandem Repeats in Great Ape Adaptation through Undergraduate Team Research Using a Novel Statistical Framework

University Of Oregon Eugene, Eugene OR

Investigators

Abstract

This award is funded in whole or in part under the American Rescue Plan Act of 2021 (Public Law 117-2). This project will substantially expand our ability to study rapid trait evolution. Rapid trait evolution results in dramatic differences between closely related species, such as chimpanzees and humans. The way genes are used (gene expression) has been implicated in such differences, but the genetic basis for altered gene expression is poorly understood. Until recently, because of limits in DNA sequencing techniques, a major source of genetic variation (tandem repeats) has been difficult to study. While sequencing technology has advanced so that we can produce these data, we still lack a way to analyze it. This project will create a new analysis tool and will demonstrate its use by studying great ape evolution, addressing longstanding biological problems such brain evolution. Further, this project will support the professional development of undergraduate and masters student scientists, mostly persons excluded due to ethnicity, race, and gender, improving the diversity, rigor, and relevance of science in the long term. Specifically, this project will complete the following objectives: (1) create TREVA, a statistical tool that uses tandem repeat (TR) variation data between and within species to test evolutionary hypotheses, in particular to identify TRs under balancing or directional selection; (2) apply TREVA to empirical data to determine how TR variation underlies adaptation in great apes; (3) identify genes impacted by TRs under selection and determine the downstream biological processes and traits under selection. This project will integrate education into research using three mechanisms. (1) The research will primarily be carried out by San Francisco State University (SFSU) undergraduates and master’s students. (2) The project will create the Computational Research Introductory Summer Program where SFSU masters students will be supported to mentor teams of novice SFSU undergraduates to learn computer science skills and apply them to original research projects. (3) Students performing the research will create video abstracts describing their work, which will be used in science classes nationally to engage students with diverse scientists. This project is co-funded by the Biological Anthropology program in the Division of Behavioral and Cognitive Sciences. 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.