Student Highlight: Siyuan Feng – Integrating functional -omic technologies into evolutionary research

By Victoria Rubinetti

Siyuan Feng has had a vested interest in asking the questions humans have long contemplated the answers to: who we are, how we did we get here, and where we are going. Feng has devoted his research at the Laboratory of Genetics to addressing these exact questions.  

Originally from Ya’an, Southwestern China (where the first giant panda was discovered!), Feng came to UW-Madison after receiving his Bachelor and Master’s degrees in Animal Genetics at Sichuan Agricultural University. “I chose to join the [Genetics PhD] program because it is one of the best genetics training programs in the world and it really cares about the students,” says Feng. “The department has contributed notably to the formation of modern evolutionary biology and population genetics. Studying evolution in this department is like walking by the past and present giants.”  

His previous research investigated high-altitude acclimation mediated by small RNA regulation in farm animals. His interests eventually grew into evolutionary and population genomics, which offer powerful tools to investigate how organisms adapt to their environments. “By bridging my previous background in functional genomics with population genomics,” Feng notes, “we could address adaptive gene regulation.” 

Siyuan Feng

Feng also recently won a 2025 WID Kohler Fellowship to compose music from genomic data and has been nominated by the Genetics program for the CALS Thomsen Fellowship. 

What is the main goal of your research and what technologies do you focus on?

The main goal of my research is to reveal which levels of biological regulation were most strongly shaped by Darwinian selection, associated with nervous system adaptation to a colder climate. Using fruit fly as the model, my research addresses this question by integrating multiple layers of molecular regulation (such as chromatin accessibility, RNA expression, and protein abundance) in brains using multi-omics and population genetics. 

What are the big picture questions and significance of this work?

This project will answer an unresolved fundamental question of evolutionary biology: which levels of gene regulation exhibit the strongest evidence of adaptive evolution? Beyond the primary question, we also expect to reconstruct gene regulatory pathways involved in thermal adaptation, and to reveal how natural selection shapes gene function across different molecular layers. Such findings will significantly enhance our understanding of how molecular regulatory processes drive adaptation, accelerate the integration of functional -omic technologies into evolutionary research, and will help many other researchers decide which levels of regulation could offer better efficiency to identify potential molecular traits associated with specific adaptive events. 

Our optimized multi-omic experimental protocol will serve as a valuable tool for researchers investigating multi-layer gene regulation in model systems that can only provide a limited amount of material.  Our statistical framework will offer other studies a more powerful method for identifying traits shaped by local adaptation. In addition, our focus on nervous system evolution in the context of adaptation to a novel thermal environment will build our understanding of how ectothermic animals may respond to climate changes. Finally, insights into gene regulatory evolution may aid in developing new strategies for managing agricultural pests and enhancing beneficial insect populations 

Has there been a single person, event, or experience that most influenced your trajectory to where you are today?

My PhD advisor Dr. John Pool has been really impactful on my scientific journey. The transition from my previous background of functional genomics to population genomics as well as between cultural backgrounds was not easy, yet he has always been patient to help me grow in a new field and country, identify my strengths and weaknesses, and build a career path. He taught me how to think critically about science and how to communicate my research with all kinds of audiences. Beyond science, I learned a lot from him about how to strategically arrange my goals and get things done. 

What advice do you have for a young person interested in graduate school or research?

Before entering graduate school, I would encourage prospective students to question deeply about their fundamental motivation for doing research and whether they are in the best position to do so from real-life perspectives. It is important to realize the difference between consuming versus creating scientific knowledge, as well as the unpredictable nature of research outcomes that can be challenging. While graduate school opens up many exciting career opportunities, how well one could handle the ‘side effects’ of doing a PhD is impactful on how much one would enjoy the journey. 

Outside of science, Feng is passionate about making music on keyboard instruments. That passion led him to join the Kohler Fellows Program at Wisconsin Institute of Discovery where he says he can, “promote the fusion between arts and science with a group of excellent people.” In the future, Feng hopes to seek career opportunities as a computational biologist in either industry or academia.