A flood of new genetic variation


Jason Collins


December 7, 2012

A new Nature paper by Fu and colleagues has been the subject of a few good write-ups. First, from Brandon Keim at Wired:

In the most massive study of genetic variation yet, researchers estimated the age of more than one million variants, or changes to our DNA code, found across human populations. The vast majority proved to be quite young. The chronologies tell a story of evolutionary dynamics in recent human history, a period characterized by both narrow reproductive bottlenecks and sudden, enormous population growth.

The evolutionary dynamics of these features resulted in a flood of new genetic variation, accumulating so fast that natural selection hasn’t caught up yet. As a species, we are freshly bursting with the raw material of evolution.

“Most of the mutations that we found arose in the last 200 generations or so. There hasn’t been much time for random change or deterministic change through natural selection,” said geneticist Joshua Akey of the University of Washington, co-author of the Nov. 28 Nature study. “We have a repository of all this new variation for humanity to use as a substrate. In a way, we’re more evolvable now than at any time in our history.” …

Put simply, more people means more mutations, and in a growing population, there is less chance that those mutations will be lost through drift.

Despite their young age, these new variants are relevant for our recent evolutionary history. If you couple this explosion in new variants with the large changes in selection pressures associated with the shift to agriculture, you would see adaptive evolution in humans speed up.

The different population dynamics associated with African and European populations is also interesting. More from Keim:

Also playing a role are the dynamics of bottlenecks, or periods when populations are reduced to a small number. The out-of-Africa migration represents one such bottleneck, and others have occurred during times of geographic and cultural isolation. Scientists have shown that when populations are small, natural selection actually becomes weaker, and the effects of randomness grow more powerful. …

The result, calculated Akey, is that people of European descent have five times as many gene variants as they would if population growth had been slow and steady. People of African descent, whose ancestors didn’t go through that original bottleneck, have somewhat less new variation, but it’s still a large amount: three times more variation than would have accumulated under slow-growth conditions.

This finding is an interesting fit with the argument of Ashraf and Galor linking genetic diversity and economic development. As genetic diversity results in a wider spectrum of traits in the population, it is more likely that there will be traits complementary to technological advance. The measure of diversity used by Ashraf and Galor, expected heterozygosity, is based on the probability that two randomly selected people will differ with respect to a certain gene, averaged over all measured genes. As people migrated from Africa through Europe and beyond, they migrated out with only a subset of the available genetic variation in the population, and therefore, expected heterozygosity declines with distance from Africa. But as the paper by Fu and colleagues shows, the prevalence rare variants does not decline with distance from Africa. Could these additional rare variants in some populations increase the probability that there will be traits complementary to technological advance?

Also worth reading is the post from John Hawks. Hawks raises some questions around the estimated age of the variants (are they older than they seem?) and asks whether some of these rare variants came from Neanderthals.