Baskin Fellowship Recognizes Enterprising Work of Nathan Schaefer

Tuesday, October 17, 2017
Tyler Bartholome

Nathan Schaefer, a graduate student in biomolecular engineering, is this year's recipient of the prestigious Jack Baskin and Peggy Downes-Baskin Fellowship.  

Originally from Wisconsin, Schaefer came to California four years ago after completing his undergraduate studies at the University of Wisconsin, Madison. “I had no idea what I wanted to do when I started college,” Schaefer explained, “I changed my mind a thousand times,” originally pursuing a degree in journalism.

By his junior year, however, Schaefer decided to pursue botany, reasoning that it was one of the few biology courses that didn’t have to do with medical practices. “I’ve always been interested in evolution,” he continued, eventually meeting students from the University of California, Santa Cruz who explained how they had an entire degree program for bioinformatics. At the time, he knew little about the subject as it was rarely offered as a course at UW Madison.

Soon thereafter, Schaefer spoke with professors Ed Green and Beth Shapiro who would later become his academic advisors. He became enthralled with the idea of extracting DNA from fossils. “I knew right away I wanted to come here,” Schaefer said.

 “I knew right away I wanted to come here” 

Once he arrived at UC Santa Cruz for his graduate studies, Schaefer joined the Paleogenomics Lab, working side-by-side with both Green and Shapiro on research that primarily has to do with admixture—the mixing of exclusive populations of organisms. Through this, they hope to investigate how certain species have diverged. Their recent research, for example, focused on the finding that brown bears have a surprising portion of polar bear ancestry.

Having first seen this phenomenon in isolated groups of brown bears in Alaska, Schaefer and his colleagues were intrigued to find that this also existed for every sequenced brown bear in the United States, even 1000 miles away in Montana. “Studying how ancestry is inherited could tell us something about what genes worked well together in hybrids and which ones didn’t,” Schaefer added, explaining that while these brown bears have some genes with polar bear ancestry, it is the genes that have no polar bear ancestry that indicate how the species began to diverge. These slight differences between the two started the gradual process of their becoming what we know today as the brown bear and polar bear.

He doesn’t want to stop at bears, though; specifically, Schaefer is interested in finding the genes where these same events occurred between humans and Neanderthals. “What is the full tree that shows how everyone and Neanderthals are related?” is the question Schaefer is exploring. In other words, “can we learn something about what makes us human?” Oftentimes when mapping ancestry, there is an average tree, showing humans, then Neanderthals, then bonobos, chimps, apes, on and on branching from one another. Yet Schaefer is interested in the “weird cases.” These are where admixture “violate[s] the species tree,” one being that certain human populations have been found to be more closely related to Neanderthals than other humans for particular genes.

Now, Schaefer is hoping to investigate this and more by creating new tools for use in his field. Earlier this year, he collaborated with Green and Shapiro on a tool called AD-LIBS, which allows the exploration of ancestry for genomes that are not extensively sequenced, such as brown bears.

In addition, Schaefer is developing a tool that will allow researchers to input the genetic information of over 1000 humans and Neanderthals to quickly compare differences among not only humans, but between the two species. Previously, this has been possible at only a hundredth of that scale. Yet even when involving just a mere ten subjects, the process was often slow and laborious, thus Schaefer’s tool will be a welcome innovation in the field.

 “What is the full tree that shows how everyone and Neanderthals are related?”

The journey to where he is today was made even more fruitful by those Schaefer surrounded himself with—especially those in his department. “I like how my whole department feels like a group of people who all know each other. . . it doesn’t feel competitive, it feels collaborative,” he explains. “Being in this lab has helped me learn what I’m capable of doing.” It is this very ideology that helps research prosper; to help rather than to hinder, a mantra that seems to be at the core of the Paleogenomics Lab.

With all of the ingredients he’s been searching for and now with the fellowship, Schaefer is happy to have much of his stress relieved, adding that he can see “the finish line. . . and it’s great to know that this year I’m covered and can just keep working on what I’m already focused on.” Part of that focus is devoted to his dissertation, and he doesn’t want to simply rely on an ask-and-answer format; rather, he hopes his work will inspire additional hypotheses and ideas to explore, expanding the scope of the field.

 “I like how my whole department feels like a group of people who all know each other. . . it doesn’t feel competitive, it feels collaborative”

On being selected, Schaefer said “It does feel good to be able to figure out how to put what you’re doing into context, explain it to people, and have them get it and be excited about it too. . . it makes you feel like you’re doing something for a reason,” and one glance at his dedication to the field can confirm for anyone that he is unequivocally deserving of this year’s award.