Many people consider human evolution to be a done deal, something that happened in our distant, wild past. But as Nicholas Wade wrote last week in the New York Times, there is increasing scientific evidence that natural selection has continued to act upon humans, producing observable evolutionary changes as recently as 3,000 years ago. Studies have found that everything from high altitude tolerance in Tibet to dry earwax may have evolved in relatively recent human history, producing subtle but significant population differences in the frequency of certain rare gene variants.
One of the genetic approaches cited by Wade in his article is the work of Anna Di Rienzo, professor of human genetics at the University of Chicago. In a paper published earlier this year in the Proceedings of the National Academy of Sciences, a group from Di Rienzo’s laboratory led by graduate student Angela Hancock went looking for recently evolved human genes in an unusual way. Their results uncovered new ways humans evolved in the recent past, with consequences still felt in our modern age of obesity.
Many genetic studies take an intentionally “naive” approach to such a genetic hunt, comparing gene variants between regional populations with no preconceptions so as not to bias the data. But sometimes a little bias doesn’t hurt; in fact, it may help find differences that fall through the cracks of a broad, unbiased sweep. Hancock and colleagues hit upon the idea of filtering their comparisons by predictable selective pressures expected to drive evolution, such as ecology and diet.
“A lot of the studies done before have been done in a way that was sort of agnostic to the selective pressure,” Di Rienzo said. “We are using aspects of human environments to learn about natural selection and the way humans adapted specifically at genetic level. We use genetic as well as ecological data, and we think that this combination allows us to tap into a set of genetic adaptations that are not accessible by other studies.”
To do this, the team took a particular variable expected to drive evolution, such as polar ecoregion. Because modern humans first arose in the tropical temperatures of Africa, those populations who migrated to a colder environment would be expected to need dramatic genetic changes to survive. So the researchers (using data from the Human Genome Diversity Project, the International HapMap Project, and their own original sequencing) compared the genomes of polar populations against non-polar populations, to see if it revealed specific gene variant differences.
Indeed it did. Several genes were found to appear at different frequencies in the polar populations, and most were found to have the kind of function one would expect to be selected for in a cold environment. Genes that helped people regulate body temperature, for instance, were more likely to have changed in a polar population. Energy metabolism also appeared to have been selected for, with the genes for enzymes that degrade sugars showing differences. The results lined up nicely with a 2008 paper by Hancock and colleagues that used a different analysis method to detect a relationship between climate and genes associated with metabolic disorders.
In addition to environment, a population’s diet was also found to be a valid selective pressure in human evolution. Humans that historically subsisted on roots and tubers – “survival foods,” as Di Rienzo described them – exhibited a high frequency of variants in genes for metabolizing the starches and sucrose found in foods such as sweet potatoes and yams. While these changes took place thousands or tens of thousands of years ago, their significance is still felt on humans today.
“We ended up finding, at least for the variables related to subsistence and diet, that most of the variants previously associated with phenotypes are related to energy metabolism, cholesterol, and type 2 diabetes-related traits,” Hancock said.
Genes that may have evolved in early humans to cope with scarce crops may have enabled the body to absorb maximum energy from food (a theory known as the “thrifty gene hypothesis“). But in the modern world, where a wide variety of food is abundant at the local supermarket, those genes could cause more harm than good, leading to obesity and other metabolic disorders. On the other hand, locating those genes via evolutionary analysis can help partially explain modern health disparities, and potentially point the way to new therapies. One such gene uncovered by this paper – and previously unidentified by genome-wide association studies – may be the focus of future diabetes research, Hancock said.
“This kind of approach can also try to tell you about the evolutionary origin of human diseases, and the origin to some extent of the different prevalence of diseases between populations,” Di Rienzo said. “Disparities are certainly due to socioeconomic and environmental factors before they’re due to any genetic factors, but there is a growing idea that there may be also a genetic contribution. It’s something that is interesting, but it’s going to take a few years before we really understand.”
Hancock, A., Witonsky, D., Ehler, E., Alkorta-Aranburu, G., Beall, C., Gebremedhin, A., Sukernik, R., Utermann, G., Pritchard, J., Coop, G., & Di Rienzo, A. (2010). Colloquium Paper: Human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency Proceedings of the National Academy of Sciences, 107 (Supplement_2), 8924-8930 DOI: 10.1073/pnas.0914625107