# Graduate student studies oyster genomics to preserve biodiversity > Source: > Published: 2026-08-26 19:03:04+00:00 # Graduate student studies oyster genomics to preserve biodiversity Graduate student Megha Prasad tapped into the power of AI when studying Eastern oyster genomics to uncover patterns that show what makes them thrive. As it turns out, you don’t need a boat or waders to help oysters survive. While a colleague traveled along the East Coast from Canada to the Gulf of Mexico collecting oysters, Northeastern University bioinformatics graduate student Megha Prasad worked away at her computer. She zeroed in on DNA, the molecule containing instructions for making proteins that shape the critters’ traits. It also holds the key to their adaptation to the changing climate. A senior with just one semester to go, Prasad was working as a co-op at Northeastern’s [Center for Marine Ecological Genomics](https://sites.google.com/view/c-meg/home) (CMEG). Her mission? Helping conservationists restore dwindling oyster populations by identifying the genes behind the traits that give them a better shot at survival. Despite the task at hand, Prasad herself rarely came face-to-face with the mollusks during her workday. Instead, she put her computational skills to use by developing new code that brought AI on board. It made the task of combing through genetic data of oysters easier than ever by directing the AI to spot promising mutations related to adaptations in vast stretches of DNA. She also discovered that some genetic changes scientists previously overlooked actually played an important role in adaptations. “People might be thinking marine biology is about being outdoors, collecting samples in a boat somewhere,” she said. “But for me, as a bioinformatician, it was mainly about majorly working on computers. Just staring at the screen and trying to write the code and debug a lot of it.” Established in 2025, CMEG is dedicated to tracking biodiversity. Not the large-scale kind that accounts for the Great Barrier Reef having more than 1,600 species of fish and over 400 types of coral. Instead, CMEG’s scientists zoom into the vast amount of mutations, or variations in marine animals’ genes. They pay special attention to ones that equip them with coping mechanisms for environmental challenges. And oysters, for one, have quite a few to grapple with. There was a time when oyster reefs in the Chesapeake Bay grew so tall they became a navigational hazard for incoming ships, according to the National Oceanic and Atmospheric Administration. Those days are long gone — and not just in the mid-Atlantic. Native oysters have all but disappeared from Massachusetts waters due to overharvesting and habitat loss, and the few survivors [struggle in the warming climate](https://news.northeastern.edu/2023/06/27/antarctic-fish-extreme-cold/). According to NOAA, [Eastern oysters thrive](https://www.fisheries.noaa.gov/national/habitat-conservation/oyster-reef-habitat) in shallow bays and estuaries, where salt and fresh water mix. They cling to hard surfaces in brackish water with optimal temperatures ranging from about 68 to 86 degrees Fahrenheit. “Oysters matter a lot, since they support the entire coastal ecosystem. They also play a major part in the seafood industry,” Prasad said. As a result, their decline is bad news for gourmands who enjoy a good half-shell spread, as well as for the entire habitat. Known for their water filtration abilities, each one clearing roughly 50 gallons per day — more than an average Brita water filter designed to process 40 gallons in two months. Oyster reefs also provide foundational support to marine life. They shelter small fish, crabs and shrimp, prevent soil erosion and serve as natural breakwaters during storms. Luckily, as their genetic diversity shows, oysters are quick to develop a variety of traits that help them adapt to global warming relatively quickly, [CMEG director Kathleen Lotterhos](https://sites.google.com/site/katielotterhos/people) explained in an interview. One trait might help them make more heat shock proteins, which protect cells from various types of external stressors. Another might improve disease resistance or tolerance to changing salinity. ## Editor’s Picks Prasad was helping to uncover the mechanisms behind these adaptations by looking at genetic mutations that give rise to new traits that aid in the survival of the species. Mutations are glitches in the DNA sequence. They get introduced into the genome when genes are passed down from parent to offspring. Most don’t matter, some can be harmful and an occasional few hit the evolutionary jackpot by resulting in traits that boost the organism’s chances of survival. Over time, mutations leading to beneficial traits spread through the population and add to the species’ overall diversity. Prasad set out to figure out which mutations were behind the adaptations. This knowledge could allow conservationists to harness the benefits of the protective traits for oyster restoration. But this would not prove to be an easy task. Identifying mutations involves processing long stretches of the oyster’s genetic sequence. Oysters have more genes than humans — 28,000 compared to 21,000. Each consists of about 1,000 to 5,000 pairs of building blocks. A mutation, in turn, often involves a change in just one of them. The genetic sequence also contains lots of duplications, which are thought to drive adaptations and survival. Combing through all that data is time-consuming, which is where AI comes to the rescue. Prasad developed computer code that instructed the AI model to look for patterns in the sequence and spot mutations that might be connected to useful adaptations. There were also some unexpected surprises along the way. Prasad mentioned that certain mutations in the organism’s messenger RNA — the single-stranded version of the DNA code used to create proteins in the cell — were always thought to be biologically inconsequential. But as it turns out, they might actually play a role in the adaptations. However, scientists have yet to explore just how they work their magic. The significance of the other findings is still coming into focus as well. For now, the team has been tagging promising mutations with scores that represent how likely they are to contribute to adaptations. In the end, the diverse traits serve as clues for conservation scientists looking for ways to help oysters. Knowing what conditions the organisms have learned to cope with, they can foster an oyster-friendly environment. A clear map of beneficial traits also lets conservationists use selective breeding methods to make the most of the adaptations. For example, Lotterhos said that breeding oysters that have evolved to thrive in unusually warm weather can give the next generation better odds of weathering the heat. It can also help oyster restoration by making them more resilient to salinity changes and disease. Lotterhos was impressed with Prasad’s knack for making complex material clear and engaging and praised her capacity for innovation. “She’s really helped steer our research in a new direction,” she said, referring to Prasad’s research accomplishments. “It’s really cutting edge and a new approach that we haven’t seen taken before in the scientific literature,” she added. What’s next for Prasad? She is looking for jobs and research positions that will let her build on her co-op experience. “I’m really interested in working in the industry, and applying what I’ve learned so far into something practical,” she said.