History Lesson

Geneticists comb DNA of ‘survivor’ fish for clues to withstanding climate change

Blue gloved hands hold a preserved beige fish about one foot long with open mouth and blank eyes
The DNA of Antarctic icefish, like this preserved specimen, could reveal how certain organisms gain and lose tolerance to changing temperatures. Image: Stephanie Dutchen

Some 25 to 30 million years ago, the Earth’s temperature fell. Ice caps grew and sea level dropped. Plants and animals died off as their environments rapidly shifted.

Some species, however, survived the upheaval. Among them were Antarctic fishes harboring genes that produced antifreeze proteins. The proteins prevented ice crystals from forming in cells, allowing the fish to avoid freezing solid in ocean waters that frequently dipped below 32 degrees Fahrenheit.

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Today, as climate change threatens life around the world, scientists are looking to the descendants of these and other fish for genetic clues about how to withstand fluctuating temperatures and other types of environmental instability.

“Evolution has already solved these problems,” said Stephen Treaster, research fellow in genetics in the lab of Matthew Harris at Harvard Medical School and Boston Children’s Hospital.

As finalists in an HMS Department of Genetics competition that challenged trainees to use their research expertise to tackle climate change, Treaster and colleagues are sequencing the genomes of 46 kinds of fish that have adapted to extreme environments. These include modern-day Antarctic icefish, cave-dwelling sculpins, and fish that thrive in some of the deepest regions of the sea, such as eelpouts, snailfish, and blobfish.

The data will allow the researchers to flesh out the fishes’ evolutionary branches, noting when genetic changes were gained or lost. Looking at these changes alongside climate records should narrow down which genes most likely helped each species survive. The team can also learn from genes that have faded over time in fish that live in unchanging waters.

“Evolution can be ‘use it or lose it,’ so once fish are in a stable environment, they may shed genes that helped them tolerate stress from changing temperature or salinity or pH,” explained co-finalist Jacob Daane, a former postdoctoral researcher in the Harris lab who has continued to work on the project at Northeastern University.

The strongest candidates of all would be any genes that were gained or lost in multiple fish species independently. Such convergent evolution can happen when organisms adapt to similar environments.

Two young men pose at a lab bench, each holding a jar with preserved fish
FILE—Treaster (left) and Daane with preserved Antarctic icefish in Jan. 2020. Image: Stephanie Dutchen
 

Treaster and Daane got into the study of unusual fish to learn about evolution and human disease. The icefish they investigate lack red blood cells, which results in enlarged hearts and intricately branched blood vessels—and offers a model for better understanding severe chronic anemia in people. These and other fish in the lab may have additional lessons to teach about kidney function, low bone density, high cholesterol, and musculoskeletal development and disease.

Now, the researchers are excited to consider new applications for their work. What they uncover could help the aquaculture industry identify, or even engineer, hardier fish stocks as waters warm. That would safeguard human health because farmed fish are an increasingly important food source for people around the world, said Treaster.

“We can use information on how species adapt to local climate change to help support other species, including vulnerable ones of economic or ecologic importance,” he said.

They have already published a paper, partially funded by the competition grant, probing the intersection of climate change, embryonic development, and genome evolution related to the loss of red blood cells in Antarctic fish. Daane led a related study in 2019 about how genetic changes that evolved before the ancient big chill primed icefish to adapt and diversify when temperatures plummeted.

Adapting their research to address climate change has been a rewarding endeavor for the team.

“It’s exciting to take the approach we were already using to understand human disease and apply it to answer questions about this pressing global problem,” said Daane.

For Treaster, the work has only underscored his belief in the value of comparative genomics.

“You don’t have to reinvent the wheel to adapt to scorching or freezing environments,” he said. “You look at a fish that knows how to do it already.”