Fish had the genes to adapt to life on land – while they were still swimming in the seas | Science

By Elizabeth PennisiFeb. 10, 2021 at 3:30 p.m.

Nearly 700 years ago, Jacob van Maerlant, a Dutch poet, imagined a fish ready to live on land: it had pushed out its arms to hoist itself ashore. Now three genetic studies make her fantasy look remarkably premonitory. Together, the studies suggest that in terms of genes, the aquatic precursors of the four-limbed land animals, or tetrapods, were as well prepared as the Dutch fantasy fish. They were pre-equipped with genes that could be used to build limbs, efficient respiratory lungs, and nervous systems to tune in to the challenges of life on earth.

“All of these studies tell us that the origin of the tetrapods was something that was waiting to happen,” says Borja Esteve-Altava, an evolutionary biologist at Pompeu Fabra University in Barcelona, ​​Spain. Genetically, “everything we needed was already there” before the arrival of vertebrates, nearly 400 million years ago.

Fossils reveal the outlines of history. Fish with fleshy fins supported at their base by a single bone, known as lobed finfish, moved through shallow water around 375 million years ago. About 5 million years later, some of these lobed fins crawled on dry land. The first fish to put its fins on land must already have at least some of the physical traits and genetic modifications needed to do so, but the researchers had not determined how and when they equipped for the change. “The big question of how such a large morphological change actually occurred remains very much at stake,” says Peter Currie, evolutionary developmental biologist at Monash University.

In the trio of studies published last week in Cell, the genes of living fish have replaced fossils as a way to go back in time. A set of clues have come from studies of mutagenized zebrafish, a preferred model for studying development. Mr. Brent Hawkins, then a graduate student of Harvard University and now a post-doctoral fellow, was shocked to discover zebrafish mutants with two bones resembling the bones of the forelimbs of land animals in their front fins, with muscles, joints and blood vessels. The result is “quite spectacular,” says Marie-Andrée Akimenko, a developmental biologist at the University of Ottawa.

Two mutated genes, vav2 and waslb, were responsible for the transformation. The two genes code for proteins that are part of a pathway controlling the activity of Hox11 proteins, regulatory molecules that guide the formation of the two forearm bones in mammals, among other functions. In fish, other proteins normally suppress Hox11 and prevent the formation of these bones. But the mutations, which Hawkins recreated using the CRISPR gene editor, reactivate the pathway. The ‘landmark’ discovery is ‘to change the paradigm of development and evolution of limbs,’ says Renata Freitas, development biologist at the University of Porto in Portugal.

Other genetic clues come from living representatives of ancient lines of fish. Only two groups of lobed finfish are alive today: the lungs and the coelacanths. About 400 million years ago, they diverged from the line of lobed finfish that gave birth to tetrapods 30 million years later. Today’s oceans are mostly populated by species of another group that originated around 420 million years ago: ray-finned fish, so named because their fins are supported by thin spines.

Evolutionary geneticists Guojie Zhang of the University of Copenhagen and Wen Wang of Northwest Polytechnic University in Xi’an, China, and their colleagues sequenced the genomes of the African lungfish, which detached early other lobed finfish. The researchers also sequenced the bichir, an elongated, air-breathing, ray-finned fish that lives in the shallows of tropical Africa’s rivers, as well as the American paddlefish, bowfin and gar alligator. All of them are ray-finned fish that evolved much earlier than Teleosts, the group that dominates the waters of the world today (see diagram below). Knowing when each of these lines branched out from the others, the researchers were able to deduce when and where certain genes first appeared on the fish family tree.

The long swim to land

Cartilaginous fishes Nonteleost ray-finned fish Teleosts Tetrapods Lung fish Common ancestor jawed vertebrates (460 million years ago) Common ancestor of ray-finned fish (420 ma) Common ancestor of lobed finfish (420 mya) Common ancestor of bony fish (425 mya)

None of the sequenced fish are on the precise branch that led to the tetrapods. Yet all of them have much of the genetic material necessary for life on earth, including most of the genes and regulatory DNA needed to build limbs. For example, all sequenced fish have a regulatory element that helps form synovial joints, which make fins and limbs flexible, and are essential for terrestrial locomotion. Fish also have 11 genes that are needed to build lungs and that work the same in bichir lungs as they do in humans. The first involves a pulmonary surfactant, a lubricating secretion that helps the lungs expand and contract. Ray-finned fish and lobed-fin lungfish also apparently have a regulatory element that helps shape the heart’s right ventricle to deliver oxygen more efficiently.

The results show that “a lot of things that we think are only in terrestrial animals are also present in fish,” says Gage Crump, a developmental biologist at the University of Southern California. The discovery of all of these genes in lobed and radiated fin fish means that these genetic pathways must have been present in their common ancestor, around 425 million years ago. “It’s surprising that some of these elements are so preserved over such a long period of evolution,” says Zhang. (Teleosts, on the other hand, lost much of the DNA that prepared the first fish for life on earth, except for the Hox11 pathway, the team reported.)

The genome of the lungfish offers insight into subsequent adaptations on the path of terrestrial life. It includes additional lung surfactant genes that ray-finned fish lack, as well as DNA to specify five toes, connect nerves to limb muscles, and sensitize the brain to a rapid reaction. All of these genes were previously thought to be unique to tetrapods.

Putting it all together, Wang and Zhang believe that the transition to land involved three key stages. The ability to breathe air sometimes first appeared in the common ancestor of the striped-finned and lobed fishes, around 425 million years ago. Then, surfactant genes, new nervous system genes, and other innovations allowed lobed finfish to temporarily leave the water. Finally, after the African lungfish separated from the lobe fins, the common ancestor of terrestrial vertebrates acquired other respiratory and locomotor refinements necessary to live out of water.

Rather than building new genetic structures and pathways just as vertebrates moved on land, evolution was apparently thrifty, using existing genes to adapt to the opportunities offered by terrestrial habitats. “[The studies] show how well the fish-tetrapod transition has been achieved by modifying existing molecular systems, rather than creating new ones, ”explains Per Ahlberg, paleontologist at Uppsala University.

Gaps remain in understanding how the fish reached the coast, but the new studies “bring us closer to the living biology of the fish-tetrapod transition,” Ahlberg adds. Van Maerlant would be delighted.

* Update, February 10, 12:30 p.m .: This story, first published on February 4, has been updated to include information on two more articles using genomics to understand how vertebrates have adapted to life on earth.