Retroviruses shows that human-specific variety developed when humans, chimps diverged

Scientists in the past decade have discovered that remnants of ancient germ line infections called human endogenous retroviruses make up a substantial part of the human genome. Once thought to be merely “junk” DNA and inactive, many of these elements, in fact, perform functions in human cells.

Now, a new study by John McDonald of the University of Georgia and King Jordan at the National Center for Biotechnology Information at the National Institutes of Health, suggests for the first time that a burst of transpositional activity occurred at the same time humans and chimps are believed to have diverged from a common ancestor – 6 million years ago. These new results implicate retroelements, a particular type of transposable elements that are abundant in the human genome, in the actual shift from more rudimentary primates to modern human beings. The research was just published in the journal Genome Letters.

“There is a growing body of evidence that transposable elements have contributed to the evolution of genome structure and function in many species,” said McDonald, a molecular evolutionist and head of the genetics department at UGA. “Our results suggest that a bust of transposable element activity may well have contributed to the genetic changes that led to the emergence of the human species.” Jordan received his doctoral degree at UGA working with McDonald.

There has been a molecular arms race going on between transposable elements and their host genomes for millions of years. Host genomes are continually evolving new regulatory mechanisms to silence the mutagenic effects associated with the replication of these elements which, in turn, place selective pressure on the elements to evolve mechanisms to escape these controls. The result is an internal drive mechanism to increase biological complexity.

Just as new technologies generated by the military arms races between rival countries get spun off and used for non-military purposes, so the new regulatory mechanisms resulting from the arms race between transposable elements and host genomes generate new molecular mechanisms that can be used to accelerate evolution on the organismic level.

The idea of a relatively sudden genetic change that alters evolution isn’t new. Scientists, such as the late Stephen Jay Gould, proposed a mechanism called “punctuated equilibrium” more than two decades ago. This idea, not yet completely accepted by scientists, proposes that evolution has depended more often on sudden and unexpected changes in genomes rather than a simple Darwinian paradigm of gradual evolutionary change due to extremely long-term natural selection.

While Darwin’s theories have been around for more than a century, it took analyses of DNA using modern tools to find that human and chimpanzee DNA are more than 95 percent identical, a clue to a mutual origin.

Finding real evidence for sudden genetic changes, however, has been slow. By using phylogenetic surveys, however, McDonald and King were able to distinguish between the youngest HERVs (human endogenous retroviruses) and more ancient lineages.

The discovery that human-specific retroviruses emerged at the same time other researchers believe humans and chimps diverged was startling. Equally interesting, however was the discovery that the oldest subfamily of HERV elements is closely related and gave rise to the youngest and most recently active group of these elements. This suggests, the authors say, that “ancient families of HERVs may be capable of retaining the potential for biological activity over long spans of evolutionary time.”

Interest in retroelements, which McDonald has been studying for more than a decade, has been growing recently. In a paper published last December in Nature Genetics, two researchers from Tufts University, Jennifer Hughes and John Coffin, identified 23 new members of the HERV-K group – the assemblage thought to contain the most recently active members. They found that at least 16 percent of those elements had undergone rearrangements that resulted in large-scale “deletions, duplications, and chromosome reshuffling during the evolution of the human genome.”

The widespread presence of these viral elements led Coffin to tell one science magazine that humans probably have “more viruses in our genes than genes in our genes.”

Just how these retroviral elements have moved around in the human genome and possibly changed organisms at the morphological level remains speculative. But there is increasing evidence that they may have been – and may still be – a driving force between evolution at the cellular and organismal levels.

The research of Jordan and McDonald is intriguing because it suggests that rather than simply playing a role in human evolution, retroviral elements may actually be implicated in the leap from chimpanzees to humans. Until a mere 50 years ago, scientists thought all genes worked from a stable position along a chromosome. That idea, however, began to change dramatically in the 1970s, when it became clear that the elements are pervasive in plant and animal genomes and that it simply made no sense that such elements would be conserved over thousands of millennia if they had no real function.

McDonald said it is increasingly clear that organisms need the viral elements and that their apparent continual backdoor assaults on normal genes may, in truth, be more like a vast, sophisticated chess game on an enormously complex board.

This is the first evidence, however, that suggests they may have made humans what they are today.