Surprising details about the transition of early whales from living on shore to diving down to feast on deep-dwelling prey have been revealed by Sarah Dungan and Belinda Chang. Their pivotal result shows that early whales had visual systems adapted to deep diving, firmly linking this change in behaviour to swift evolutionary adaptation.
Deep diving by marine mammals is one of the great evolutionary transitions, along with powered flight and living on land, and reveals much about how quickly life can adapt in a changing world.
Whales evolved from mammals that share a common ancestor with hippos and that were partially aquatic. The great mystery of their transition to deep sea foraging was how quickly this ability developed. Dungan and Chang looked at whale fossils on a molecular level and focused on the rhodopsin protein which absorbs light and sends a signal that travels through the retina to the brain.
“One of the most intriguing aspects of this iconic land-to-sea evolutionary transition is that the qualities of the visual environment completely changed,” says Chang. “This helped to define which genes would be the most interesting for us to target in our studies.”
Dungan applied robust data science models to rhodopsin proteins from a variety of living whales and related mammals. This computerized analysis revealed a gene sequence representing the rhodopsin found in the common ancestor of all living whales. She expressed this gene in lab-grown cells to ‘resurrect’ the predicted protein and experiment on purified samples.
The fossil record is the gold standard for understanding evolutionary biology. But despite what Jurassic Park would have you believe, extracting DNA from fossil specimens is rare because the condition tends to be poor.
"The fossil record is the gold standard for understanding evolutionary biology,” says Dungan. “But despite what Jurassic Park would have you believe, extracting DNA from fossil specimens is rare because the condition tends to be poor. So, if you’re interested in how genes and DNA are evolving, you rely on mathematical modelling and a strong sample of genes from living organisms to complement what we understand from the fossil record."
Dungan and Chang were astonished by the biochemical properties of the resurrected protein compared to land mammals. Early whale rhodopsin was more sensitive to the blue light that penetrates deepest into the ocean, to a degree that exceeded expectations. Its biochemical properties also suggested that the retinas of early whales could respond rapidly to changes in light levels.
These results mean that the common ancestor of living whales was already a deep diver, able to see in the blue twilight zone of the ocean, with eyes that swiftly adjusted to dark conditions as the whale rushed down on a deep breath of surface air.
"In the evolution of whale diving, there's been a long-standing question of when deep-sea foraging evolved," says Chang. "And it seems that based on our data, this happened before toothed and baleen whales diverged. The common ancestor of all living cetaceans was deeper diving — and then later species evolved all the diverse foraging specializations we see in modern whales and dolphins today."
Early whales eventually evolved into the many kinds of toothed whales and baleen whales we see today. As separate species of whale evolved, they established ecological niches at various levels of the sea and even in freshwater rivers. Dungan and Chang’s work shows that there were further evolutionary adaptations as members of both groups either surfaced from the early deep levels to hunt closer to the surface or specialized to become even more extreme divers.
It is amazing that now, we can have this level of insight into the lifestyle of a long-extinct organism, just from doing laboratory experiments on one protein. Ancestral protein resurrection is an incredibly powerful way for us to interrogate how ancient organisms evolved that most people don't know about.
"I’ve always been fascinated by whales. The idea that there was a land mammal like me that eventually evolved to live underwater blew my mind as a kid, even though I really didn't understand exactly what that meant at the time,” says Dungan. “It is amazing that now, we can have this level of insight into the lifestyle of a long-extinct organism, just from doing laboratory experiments on one protein. Ancestral protein resurrection is an incredibly powerful way for us to interrogate how ancient organisms evolved that most people don't know about.”
Dungan and Chang now plan to resurrect the ancestral whale proteins that transmit the rhodopsin light signal from the retina to the brain to provide insights into the neurological adaptations associated with deep diving. They will probe ancient evolutionary adaptations associated with new behaviours and hope to gain greater insight into how animals may adapt to our changing world.