"This gene variant is present in billions of people, and it's likely responsible for millions of cases of arthritis around the globe. " said Dr David Kingsley, Professor of developmental biology at Stanford University.
"Many people think of osteoarthritis as a kind of wear-and-tear disease, but there's clearly a genetic component at work here as well.
"It's possible that climbing around in cold environments was enough of a risk factor to select for a protective variant even if it brought along an increased likelihood of an age-related disease like arthritis, which typically doesn't develop until late in life."
Researchers first linked a mutated form of GDF5 to arthritis and height in the 1990s. They also discovered it was being controlled by a key piece of genetic machinery which they labelled GROW1, and which signals to the gene to turn off bone growth.
In the new study they looked at the genomes of people from across the world who had submitted their DNA for the 1,000 Genomes project and noticed that the gene variant and its bone-limiting switch were far more common in European populations. In contrast the gene variant is extremely rare in African populations.
The also discovered the variant was common in Neanderthals and Denisovans - hominids who moved north in Europe and Asia around 600,000 years ago ahead of modern humans, but eventually became extinct.
"It's clear that the genetic machinery around a gene can have a dramatic impact on how it works," added Capellini.
"It's clear that the genetic machinery around a gene can have a dramatic impact on how it works," said Dr Terence Capellini, associate professor of human evolutionary biology at Harvard University.
"The variant that decreases height is lowering the activity of GDF5 in the growth plates of the bone. Interestingly, the region that harbors this variant is closely linked to other mutations that affect GDF5 activity in the joints, increasing the risk of osteoarthritis in the knee and hip."
The research was published in the journal Nature Genetics.