Flight and Food

The small can be mighty. Birds no bigger than the palm of your hand can be the key to the inner workings of an ecosystem. From their feathers to their scat, they can provide useful clues on the health of an environment. 

In the summer of 2023, biology professor Justen Whittall and his bird molecular ecology class looked to uncover answers within the birds of Santa Clara County. First, they wanted to identify differences in bird species and diet by extracting plant DNA from the scat and feathers of birds. This could help contribute to other research looking into what birds are eating and the effectiveness of plant restoration. Next, Whittall and his class wanted to use feather samples to determine if there were more male or female migrating Yellow-rumped warblers. This information could contribute to a greater understanding of bird populations in the Bay Area.

Following previous iterations of the class, these studies have continued to feature birds as the link to a greater ecosystem. While Whittall’s research at SCU mainly specializes in plants and flower color, he explains that birds are a gateway to discovering biodiversity – his true passion.

“The great thing is as soon as you become interested in birds you’ll never be lonely again,” Whittall says. “There are always birds around and my job is to help open students’ eyes (and ears) and honestly, they often remind me to open myself to not only seeing the birds but also hearing the birds.”

Aside from inspiring students to see surrounding biodiversity, the class allows students to apply modern genomic and molecular tools to real-world situations. For Whittall, the class represents an intersection between a field opportunity to discover bird diversity and a molecular and genomic skills course to prepare students for careers in biotech and beyond.

In all three iterations of this class, Whittall has aimed to connect field experiences at bird banding stations with the molecular tools of genome analysis. For students, this has meant getting to work in labs comparing DNA sequences and making original discoveries about bird diversity in the San Francisco Bay Area.

“They’re learning something new about the world that nobody else has ever known, and they become the world experts on that particular data set,” Whittall says. “That’s an empowering moment for students, and that gives me great joy.”

For Avi Subramanian ’25, the class came as the perfect opportunity to get experience in conducting molecular biology research while blending in his love of birds. This has meant visiting bird banding stations to collect samples and using bioinformatic tools like Sanger Sequencing to translate the collected DNA into a code that can later be matched with organisms.

“I’ve always loved birds,” Subramanian says. “They symbolize to me a unique sense of freedom, and how they can live their lives to the best as they can with how they take flight [and] can literally go anywhere if they put their minds to it. You can take that mindset into anything that you do and I’ve always kind of related to that with birds.”

Subramanian takes this mindset into molecular biology and explains that there are many ways to approach it, from looking at how species interact to how the proteins in a cell interact with DNA. Regardless of the approach, molecular biology all starts with interactions across scales. If DNA is the recipe for every living organism on earth, then scale is the various sizes you can examine life through. For example, with the naked eye, you might see a bird eating seeds, but on a molecular scale, you could see the genetic makeup of a seed within the bird’s scat.

According to Subramanian, biology is built around scale and can start at any level, from the single-celled to the complex. This can mean starting with the type of plants and animals that live in an area and then shifting to a molecular level to examine the relationship between these living organisms. In examining the molecular scale of an ecosystem, students can develop an understanding of how each organism interacts with each other in an ecosystem. This then informs restoration projects on how to best engineer a region that may allow for life to thrive. 

For Josephine (Joey) Hernandez Mena ’25 the class allowed her to gain both “muddy boots biology” and in-lab technical experience while participating in the integration of biology across scales. Specifically, being able to catch these birds in the wild to collect samples, extract DNA, and then later amplify and isolate the specific genetic material they were looking for has helped Hernandez understand how biology travels across scales.

“It’s all trickle down and trickle up,” Hernandez says. “What’s happening on a molecular, atomic scale travels up just as much as it travels down. When we tear down large portions of native land and the flora within, it’s going to impact organismal relationships down to their trace DNA, it is our job to unlock those mysteries via molecular tools. We want to make restoration work genuinely beneficial to the animals living there.”