Junk DNA and evolution

Murdoch University scientists have developed an improved theory of evolution with a hypothesis that reconciles evolutionary theory with the fossil record.

Developed by PhD student Keith Oliver and Program Chair of Biomedical Sciences Dr Wayne Greene, the Genomic Drive hypothesis potentially represents one of the biggest advances in evolutionary theory since the 1930s.

In a co-authored report, due to be published in the journal BioEssays,  the researchers argue that transposable elements (TEs) — or what is colloquially termed jumping genes, selfish or junk DNA, have a critical role in ensuring the survival of biological lineages.

Without this DNA junk, a species is effectively frozen and faces eventual extinction.

On the other hand, species with genomes with high TE activity or strong presence of identical TEs possess a greater ability to evolve, diversify and survive.

Take, for example, humans, rodents and bats.

As primates some 46% of the human genome is comprised of TEs while other mammals such as rodents and bats are known to possess around 40%.

These TEs are generally suppressed in the ordinary body cells of most species but are allowed to reactivate in reproductive cells for the potential benefit of the next generation.

Their activity can also be triggered when they suddenly hop between species or by stress.

TEs do their survival work by reformatting and rearranging DNA genomes to sometimes create significant adaptive mutations that undergo natural selection.

Dr Greene, a Senior Lecturer in Molecular Genetics, said current evolutionary theory, which assumed biological lineages evolved by the slow accumulation of adaptive mutations, did not tally with the fossil record.

However, the Genomic Drive theory provided a significant explanation for the way new species arose abruptly and periodically.

The theory also fitted with fossil records which showed intermittent and long periods of stasis — where many species stood still or remained the same.

Oliver said the hypothesis argued that significant evolution could not take place without the activity of TEs.

“Although we are standing on the shoulders of others that have worked on TEs, we believe this is the strongest and most comprehensive case ever put forward on the role of TEs in evolution,” Oliver said.

“If our theory proves correct it would be one of the biggest advances in evolution since the 1930s when Darwinism and Mendelism were reconciled in NeoDarwinism.”

Dr Greene said species that were devoid of TEs were more at risk of extinction because they simply lacked the capacity to adapt, change and diversify.

“If you don’t have this junk in your genome then you can’t evolve and are stuck, thereby remaining in what is termed evolutionary stasis,” Dr Greene said.

“This would explain why almost all species control their TEs rather than eliminate them.

“And of course having these TEs in a genome doesn’t mean a lineage will necessarily diversify. What it does mean is that it has a much greater potential to do so.”

Oliver said an example of evolutionary stasis occurring in species without TE activity could be seen in the living fossil, the coelacanth, once thought to be extinct for 63 million years.

The coelacanth, which had been found off the coast of South Africa and Indonesia, had inactive or low levels of TEs and had been in stasis for 400 million years.

In another example he referred to the tuatara, where just two species had been found off the coast of New Zealand.

Like the coelacanth, the tuatara was characterised by very few jumping genes and has been unchanged for 220 million years.

Dr Greene said Genomic Drive theory provided an explanation for many unanswered questions such as why species suddenly appeared in the fossil record, why some groups of organisms were species rich and others species poor, and why some species changed little over millions of years.

Successive waves of TE activity in a lineage potentially explained alternations of rapid evolution and stasis.

He said some species — such as bats which “came out of nowhere” in the Eocene Period — suddenly appeared in the fossil record.

This was in keeping with evidence that TE or jumping gene activity occurred in sudden episodic bursts.

Dr Greene said an example of how TE activity affected the richness of a lineage was seen in rodents and bats.

These were species-rich orders of mammals and, unusually for modern mammals, both harboured highly active TEs.

Although there wasn’t enough data yet, the presence of TEs could also help to explain why one order of birds, commonly known as the songbirds (the Passeriformes), accounted for over half of all bird species and why the Perciformes accounted for 40% of fish species.

While jumping gene activity in the 235 species of primates had quietened down a lot since its peak about 40 million years ago, the high presence of identical TEs in the primate genome pointed to an improved ability to diversify, adapt and survive.

By comparison, a cousin of the primate, the Flying Lemur, lacked a key TE that primates had in abundance and only two species of it remained.