Scientists long assumed that new genes appear when evolution tinkers with old ones. It turns out that natural selection is much more creative.
In the depths of winter, water temperatures in the ice-covered Arctic Ocean can sink below zero. That’s cold enough to freeze many fish, but the conditions don’t trouble the cod. A protein in its blood and tissues binds to tiny ice crystals and stops them from growing.
Where codfish got this talent was a puzzle that evolutionary biologist Helle Tessand Baalsrud wanted to solve. She and her team at the University of Oslo searched the genomes of the Atlantic cod (Gadus morhua) and several of its closest relatives, thinking they would track down the cousins of the antifreeze gene. None showed up. Baalsrud, who at the time was a new parent, worried that her lack of sleep was causing her to miss something obvious.
But then she stumbled on studies suggesting that genes do not always evolve from existing ones, as biologists long supposed. Instead, some are fashioned from desolate stretches of the genome that do not code for any functional molecules. When she looked back at the fish genomes, she saw hints this might be the case: the antifreeze protein — essential to the cod’s survival — had seemingly been built from scratch1.
The cod is in good company. In the past five years, researchers have found numerous signs of these newly minted ‘de novo’ genes in every lineage they have surveyed. These include model organisms such as fruit flies and mice, important crop plants and humans; some of the genes are expressed in brain and testicular tissue, others in various cancers.
De novo genes are even prompting a rethink of some portions of evolutionary theory. Conventional wisdom was that new genes tended to arise when existing ones are accidentally duplicated, blended with others or broken up, but some researchers now think that de novo genes could be quite common: some studies suggest at least one-tenth of genes could be made in this way; others estimate that more genes could emerge de novo than from gene duplication. Their existence blurs the boundaries of what constitutes a gene, revealing that the starting material for some new genes is non-coding DNA (see ‘Birth of a gene’).
The ability of organisms to acquire new genes in this way is testament to evolution’s “plasticity to make something seemingly impossible, possible”, says Yong Zhang, a geneticist at the Chinese Academy of Sciences’ Institute of Zoology in Beijing, who has studied the role of de novo genes in the human brain.
But researchers have yet to work out how to definitively identify a gene as being de novo, and questions still remain over exactly how — and how often — they are born. Scientists also wonder why evolution would bother making genes from scratch when so much gene-ready material already exists. Such basic questions are a sign of how young the field is. “You don’t have to go back that many years before de novo gene evolution was dismissed,” Baalsrud says.
Back in the 1970s, geneticists saw evolution as a rather conservative process. When Susumu Ohno laid out the hypothesis that most genes evolved through duplication2, he wrote that “In a strict sense, nothing in evolution is created de novo. Each new gene must have arisen from an already existing gene.”
Gene duplication occurs when errors in the DNA-replication process produce multiple instances of a gene. Over generations, the versions accrue mutations and diverge, so that they eventually encode different molecules, each with their own function. Since the 1970s, researchers have found a raft of other examples of how evolution tinkers with genes — existing genes can be broken up or ‘laterally transferred’ between species. All these processes have something in common: their main ingredient is existing code from a well-oiled molecular machine.