Passage IV

NATURAL SCIENCE: This passage is adapted from the article “How We Are Evolving” by Jonathan K. Pritchard (©2010 byScientific American, a division of Nature America, Inc.).

A few years ago it was extremely difficult for scientists to trace our species' genetic responses to our environment; the needed tools just did not exist. All that changed with the completion of the human genome sequence and the subsequent cataloguing of genetic variation. To understand exactly what we did, it helps to know a bit about how DNA is structured and how small changes can affect its function. The human genome sequence consists of about three billion pairs of DNA nucleotides, or “letters,” that serve as an instruction manual for how to assemble a human. The manual is now known to contain a parts list of about 20,000 genes—strings of DNA letters that spell out the information required to build proteins. (Proteins, which include enzymes, do much of the work in cells.) About 2 percent of the human genome encodes proteins, and a roughly similar amount seems to be involved in gene regulation. Most of the rest of the genome has no known role.

Overall the genomes of any two people are extremely similar, differing in only about one out of every 1,000 nucleotide pairs. Sites where one nucleotide pair substitutes for another are referred to as single-nucleotide polymorphisms, or SNPs (pronounced “snips”), and the alternative versions of the DNA at each SNP are called alleles. Because most of the genome does not encode proteins or regulate genes, most SNPs probably have no measurable effect on the individual. But if a SNP occurs in a region of the genome that does have a coding or regulating function, it may affect the structure or function of a protein or where and how much of the protein is made. In this way, SNPs can conceivably modify almost any trait, be it height, eye color, ability to digest milk, or susceptibility to diseases.

When natural selection strongly favors a particular allele, it becomes more common in the population with each generation, while the disfavored allele becomes less common. Eventually, if the environment remains stable, the beneficial allele will spread until everyone in the population carries it, at which point it has become fixed in that group. This process typically takes many generations. In theory, a helpful allele could become fixed in as little as a few hundred years if it conferred an extraordinarily large advantage. Conversely, a less advantageous allele could take many thousands of years to spread.

It would be great if in our efforts to understand recent human evolution, we could obtain DNA samples from ancient remains and actually track the changes of favored alleles over time. But DNA usually degrades quickly in ancient samples, thereby hindering this approach. Research groups around the world have developed methods of examining genetic variation in modern-day humans for signs of natural selection that has happened in the past.

One such tactic is to comb DNA data from many different people for stretches that show few differences in SNP alleles within a population. The spread of selected alleles by natural selection can leave distinctive patterns in the SNP data: if an existing allele suddenly proves particularly helpful when a population finds itself in new circumstances, that allele can reach high frequency (while remaining rare in other populations).

Over the past few years multiple studies have identified several hundred genome signals of apparent natural selection that occurred within the past 60,000 years or so. In a few of these cases, scientists have a pretty good grasp on the selective pressures and the adaptive benefit of the favored allele. For example, among dairy-farming populations in Europe, the Middle East and East Africa, the region of the genome that houses the gene for the lactase enzyme that digests lactose (the sugar in milk) shows clear signs of having been the target of strong selection. In most populations, babies are born with the ability to digest lactose, but the lactase gene turns off after weaning, leaving people unable to digest lactose as adults. Writing in the American Journal of Human Genetics in 2004, a team at the Massachusetts Institute of Technology estimated that variants of the lactase gene that remain active into adulthood achieved high frequency in European dairy-farming groups in just 5,000 to 10,000 years. In 2006 a group led by Sarah Tishkoff, who is now at the University of Pennsylvania, reported in Nature Genetics that they had found rapid evolution of the lactase gene in East African dairy-farming populations. These changes were surely an adaptive response to a new subsistence practice.