About the Author: Marisa Lim is a bioinformatics training postdoctoral scholar at the University of California at Davis. Her past research has covered a range of topics from conservation genetics and high-elevation adaptation to species identification tool optimization. Read more on her website! She currently thinks about how to improve computational biology training for researchers as part of the NIH Common Fund Data Ecosystem training team.
The journey from brainstorming a novel research project to publishing the results in a paper is often a long one. As a first year graduate student, I wanted to focus on bird evolution and population genetics. I explored ideas to study the range expansion of Anna’s hummingbirds in the western United States or genetic mechanisms for heat tolerance in desert hummingbirds after a fieldwork stint in Arizona during the spring migration. After forming critical collaborations with Dr. Chris Witt and Dr. Ke Bi, those initial ideas were reshaped into my dissertation, which aimed to investigate the genetic mechanisms that underlie high-elevation adaptation in Andean hummingbirds.
I was especially excited to investigate spatial genetic patterns and potential for local adaptation in populations of two highland hummingbird species – the sparkling violetear (Colibri coruscans) and the violet-throated starfrontlet (Coeligena violifer) – distributed across the Peruvian Andes. This idea formed the basis of our paper (Lim et al. 2021) in the June Journal of Heredity issue. Embarking on a new research project is often an exciting, but overwhelming process. The following decisions pushed this project across the finish line:
Ask for help
When I was starting this research, it was clear there were skills I could teach myself and skills I would need help to develop. My co-authors brought different theoretical and technical expertise to the project, and discussions with researchers I met at workshops, conferences, and travel abroad programs provided fresh perspectives and motivation. The collective advice helped me navigate which lab protocols and analysis approaches to try, and grounded interpretations of the sometimes abstract and complex results in biology.
Be on the lookout for opportunities
Omics projects, while decreasing in cost every year, are expensive for a graduate student budget. I applied to as many small and large grants as I was eligible for, and was fortunate to receive funding from many sources, including an AGA EECG Research Award. I also decided to use museum specimens for my study, as the species and spatial sampling were sufficient to answer my research questions, fit my experimental design, and were readily available.
Write everything down
This paper was several years in the making and I made lots of decisions along the way. I kept notebooks, many Word documents, and eventually a GitHub repository dedicated to organizing code and analysis workflows. While tedious at times, I am thankful that past me wrote nearly everything down somewhere. These notes especially helped when responding to reviewer questions, as well as those from researchers interested in reusing my sequence data for future exploration.
After several years of hard work and thanks to a team effort, I’m pleased to see this research published and honored to have my paper selected for Editor’s Choice!
Lim, M.C.W., K. Bi, C.C. Witt, C.H. Graham, and L.M. Dávalos. 2021. Pervasive genomic signatures of local adaptation to altitude across highland specialist Andean hummingbird populations. Journal of Heredity 112: 229-240.