Post-Doc Andrew Thompson First Author on Report Detailing Bowfin Fish Genome

Ingo Braasch and Andrew Thompson are leading a project that included more than two dozen researchers spanning three continents to assemble the most complete picture of the bowfin genome to date.

Ingo said, "For the first time, we have what's called a chromosome-level genome assembly for the bowfin. If you think of the genome like a book, what we had in the past was like having all the pages ripped out in pieces. Now, we've put them back in the book."

"And in order," added Andrew, a postdoctoral researcher in Ingo's lab and the first author of the new research report, published Aug. 30 in the journal Nature Genetics.

This is really important information for a few reasons, the duo said, and it starts with the bowfin being what Charles Darwin referred to as a "living fossil." The bowfin, or dogfish, looks like an ancient fish. This doesn't mean that the bowfin hasn't evolved since ancient times, but it has evolved more slowly than most fishes. 

One particularly interesting gene is one that's used in developing the bowfin's gas bladder, an organ the fish uses to breathe and store air. Scientists believe that the last common ancestor shared by fish and humans had air-filled organs like these that were evolutionary predecessors to human lungs. In their new study, Ingo and Andrew could see that a certain genetic process in the bowfin's gas bladder development bore striking similarities to what's known about human lung development. A similar process is also present in the modern teleost fishes, but it's been obscured by eons of evolution.

Andrew said, "When you looked for the human genetic elements of this organ development in zebrafish, you couldn't find it because teleost fishes have higher rates of evolution. It's there in modern fishes, but it's hidden from view until you see it in bowfin and gar." The gar is another air-breathing fish with "living fossil" status that's studied by Ingo and his team. With both the gar and bowfin genomes, the team was able to show where these genetic elements linked to gas bladder and lung formation were hiding out in the modern teleost fishes. The ancient fish enable researchers to build a better bridge between the established modern fish model organisms and human biology.

Ingo said, You don't want to base that bridge on one species," adding that this finding also strengthens the implications for evolutionary history. "This is another piece of the puzzle that suggests the common ancestor of fish and humans had an air-filled organ and used it for breathing at the water surface, quite similar to what you see in bowfin and gar."

Bowfins are native to Michigan. They could be in the Red Cedar River on MSU's campus now, according to Andrew, but they also can be quite elusive and, sometimes, very aggressive. This made collaborations essential for securing specimens. With colleagues at Nicholls State University in Louisiana, the team caught bowfins for genome sequencing. Amy McCune, a collaborator and professor at Cornell University, knew where to find bowfin eggs in upstate New York and had a graduate student gifted at securing these unique samples for investigating bowfin development.

Ingo and Andrew also had connections at other universities and institutions with experts in bowfin biology, chromosome evolution and more. All told, the team included researchers from six states as well as France, Japan and Switzerland. Back in East Lansing, graduate students Mauricio Losilla and Olivia Fitch, research technologist Brett Racicot, and Kevin Childs, director of the MSU Genomics Core facility, also contributed to the study, which comes with an interesting twist at the end.

Almost all vertebrate creatures that grow paired limbs or fins share a common gene. "Humans use it, mice use it. All fishes that have been studied so far use it," Ingo said. "The naïve expectation would be that bowfin do, too."

But that's not what the team found. The bowfin, the "living fossil," has evolved a different way of growing its paired fins.

"For whatever reason, it changed its genetic programming. Even '€˜living fossils' keep evolving. They're not frozen in time," Ingo said. "It's sort of a cautionary tale that we shouldn't take these things for granted. You have to look trait by trait, gene by gene and across many different species to paint the complete picture."