Coelacanth DNA analysis illuminates a time when fish crawled

If you look back far enough, humans evolved from fish. Anyone doubting this aspect of our ancestry must contend with a growing wealth of DNA evidence. Among the fish living today, we share a particularly close relationship to a rare deep-sea dweller known as the coelacanth, which is more closely related to us than it is to other fish.

Coelacanths can grow to more than 5 feet long and live at great depths off the coast of South Africa. They were so elusive and rare that the scientific community long assumed they’d been extinct for at least 70 million years — until one turned up in a fishermen’s catch in the 1930s.

Earlier this month, scientists released an analysis of coelacanth DNA that not only backs up our evolutionary relationship but sheds light on how our ancestral fish became equipped to crawl out of the water and give rise to amphibians, reptiles, birds and mammals.

One of the scientists on the DNA team is Neil Shubin of the University of Chicago, who has been on a long quest to understand how fish evolved into the first land vertebrates some 370 million years ago.

For years, he’s been collaborating with paleontologist Ted Daeschler of Philadelphia’s Academy of Natural Sciences, the two of them travelling around the world seeking the fossilized remains of animals part way through the transition. On an expedition to the Canadian Arctic in 2004 they came across their most famous discovery — a creature called a tiktaalik, which looks like a blend between a fish, a salamander and a crocodile.

These land pioneers share a common feature with the coelacanth — both have a humerus and other bones analogous to those in our limbs. “The anatomy would suggest coelacanths are close living cousins and the genome confirms that,” Shubin said. “They are more closely related to us than they are to ray finned fish or sharks.”

We share an even closer relationship with a creature called a lungfish, but it carries an unmanageable abundance of DNA — more than 30 times the amount in either the human or coelacanth genomes. The challenge with the coelacanth was in getting a DNA sample in the first place. The scientists went about it by enlisting the help of fishermen — giving them test kits and asking them to get samples if they caught a coelacanth by accident.

The coelacanth’s DNA turned out to have some stretches in common with other fish and some in common with mammals but not fish. Shubin said one particularly interesting segment of DNA guides the development of limbs in mice. What it does for the coelacanth is not yet clear, but it seems to have been repurposed for limb development.

The Academy’s Ted Daeschler, who was not part of the DNA team, said this kind of analysis is allowing people to ask questions about evolutionary relationships they couldn’t have dreamed of asking even 10 years ago. “It’s fun and interesting,” he said. “They showed we’re into a new world in terms of the amount of data we can gather from DNA.”

Neither Daeschler nor Shubin care much for the term “living fossil.” A handful of plants and animals look relatively unchanged from their fossil predecessors — most notably the horseshoe crab, crocodile, salamander and coelacanth. But the term is a bit of a misnomer, said Daeschler. Evolution hasn’t stopped for any of them. The similarities these organisms share with their predecessors are mostly skin deep, he said. They’ve undoubtedly changed physiological mechanisms, immunity and other less visible aspects of their biology.

The coelacanth has been evolving from the time we split off from a common ancestor more than 300 million years ago. Like everything else that’s alive, it evolves.

Read the original scientific paper on the coelacanth genome here.