Why Did Europeans Evolve Into Becoming Lactose Tolerant?

Just 5,000 years ago, even though it was a part of their diet, virtually no adult humans could properly digest milk. But in the blink of an evolutionary eye northern Europeans began inheriting a genetic mutation that enabled them to do so. The trait became common in just a few thousand years, and today it’s found in up to 95 percent of the population. By piecing together Neolithic pottery fragments and ancient human genomes, scientists may have solved the riddle of how European lactose tolerance evolved.

In a study published today in Nature, researchers compared archaeological evidence for 9,000 years of European milk use with genetics, and found an unusually rapid, evolution of lactose tolerance among Europeans well after they first started consuming the beverage. The authors suggest that something more extreme than regular milk consumption drove the genetic change. Exceptional stressors like famines and pathogens may have exacerbated milk’s typically mild gastrointestinal effects on the lactose intolerant, creating deadly bouts of diarrhea and dehydration while making the ability to digest milk extra valuable.

“It rewrites the textbooks on why drinking milk was an advantage,” says lead author Richard Evershed, director of the Biogeochemistry Research Center at the University of Bristol. “In order to evolve a genetic mutation so quickly, something has to kill off the people that don’t carry it.”

The wide-ranging study, led by Evershed and colleagues from the University of Bristol and University College London, included contributions from experts in 20 other countries.

Almost all babies around the world are born with the ability to digest lactose—after all, it’s found in breast milk. But about two-thirds of adults can no longer digest the natural milk sugar because the production of a milk-digesting enzyme called lactase switches off after they’ve finished weaning. That’s why the majority of the world’s adult population is lactase non-persistent, otherwise known as lactose intolerant.

The other third of the world’s adult population has evolved lactose tolerance, meaning they keep producing lactase, and that’s particularly true among groups like those of northern European descent.

Shevan Wilkin, a biological anthropologist at the Max Planck Institute for the Science of Human History, says that until perhaps five years ago, the lactose tolerance story seemed simple. Once groups of humans began herding animals and drinking their milk the health benefits of milk favored those who could digest it, while digestive ailments worked against the success of the intolerant, so the genetic mutation that helped humans digest milk eventually spread through those populations.

“Then we realized some crazy trends,” says Wilkin, who wasn’t involved in the study. “When you look at the ancient genomes no one has lactose tolerance until recently, the past few thousand years.” For a genetic trait to become widespread that quickly, there should be a very important reason why people who have it survive and reproduce, while others die off.

“We also realized that huge populations throughout the steppe, people in modern day Kazakstan, Russia, Mongolia, people who are drinking a ton of milk, aren’t lactase persistent at all.” If the simple benefits of drinking a lot of milk produced and propagated a mutation for lactase persistence, the steppe dwellers surely should have evolved the trait just as Europeans did.

What’s more, studies of ancient human DNA have shown that the genetic mutation that enabled European lactase persistence doesn’t look like something that conferred a marginal nutritional advantage. In European genomes it is the single trait most favored by positive natural selection over the past 10,000 years.

The authors used several different lines of inquiry to delve into the murky past of European milk.

Richard Evershed and colleagues mapped human milk use during the past 9,000 years, creating an enormous database from 6,899 animal fat residues derived from 13,181 fragments of pottery from 554 archaeological sites around Europe. Over the past three decades scientists, with experts like Evershed at the fore, have developed methods to analyze ancient pottery and reveal evidence of what it contained.

As luck, or science, would have it, milk fat is absorbed into ancient pottery and preserved at a remarkable level. Studying carbon isotope compositions of the two major fatty acids that exist and persist in degraded animal fats in pots reveals that milk leaves a distinctive signature because it’s made in a different way than carcass fat in ruminant animals.

Evershed found plentiful evidence that humans were drinking milk widely, across Europe, from around 9,000 years ago.

Co-author Mark Thomas, an evolutionary geneticist at University College London, launched his own mapping project, this one charting where and when the genetic variant appeared that enabled lactase persistence in Europeans. Combing through DNA sequences of more than 1,700 prehistoric humans he found that its first appearance was not till some 5,000 years ago, or some 4,000 years after regular milk consumption began. The mutation has become commonplace in the short time since then but its late appearance means humans were drinking milk for thousands of years before they could digest it.

Thomas and colleagues compared Evershed’s datasets for historic European milk use with the genetic evidence for the rise of lactose tolerance. They found no relationship between changes in milk use over time and the rise of humans’ ability to tolerate lactose.

That’s puzzling, because for humans who don’t digest lactose the sugary milk component can cause intestinal problems ranging from flatulence to diarrhea. For this reason, the lactose intolerant don’t drink much milk—or at least that’s what many had erroneously assumed.

In fact, the work of co-author George Davey Smith shows that they do drink milk, according to his study of the UK Biobank’s data, which includes over 500,000 living individuals. His analysis found virtually no difference between the milk consumption of persistent and non persistent adults. He also found that most non persistent milk drinkers reported no long-term health impacts, nothing that would shorten their lifespans or reduce their ability to reproduce. “So how could people possibly have been dairy farmers when they were lactase non-persistent?” Evershed asks. “Because they can happily consume milk and get health benefits from it.”

George Davey Smith’s finding created another question for researchers; if lactose intolerant individuals can drink milk with no major ill effects, what drove the dramatic genetic shift that caused so many Europeans to quickly develop lactose tolerance?

Some factor or factors must have fast-forwarded the evolution of lactose tolerance, likely by making it critically important and even a matter of life and death.

“That’s where we started imagining scenarios where this would be the case,” Evershed explains.

Mark Thomas theorizes that famine may have played a major role. Typically, most non-tolerant adults won’t fare too poorly after drinking milk, he notes. “You get flatulence, diarrhea, it’s not nice, it might be unpleasant and embarrassing, but nobody ever died of lactose intolerance.”

“But if you have diarrhea when you are severely malnourished then you’ve got real problems,” he continues. “That’s a major cause of death in the world even today.” If foods like grain run out during a famine, non-persistent humans may resort to consuming a lot more dairy, exactly when they shouldn’t, which could have the biggest detrimental impact on their health.

Davey Smith, the director of the MRC Integrative Epidemiology Unit at the University of Bristol has a different idea with a similar concept; he theorizes that pathogens played a major role. Though his work shows drinking milk isn’t hurting the health of non-tolerant adults today, it’s potentially a major problem among those suffering from gut disturbances, dehydration and other ailments. During times when humans were living close together, amongst domestic animals and lacking proper hygiene, disease likely became widespread and may have severely weakened many individuals for whom lactose driven diarrhea and dehydration proved fatal. On the other hand, those who could drink and digest milk had a resource to help them pull through.

The team put these ideas to a test using models which suggested that the gene variant for lactase persistence did increase in populations when they were impacted by famine or pathogens.

The environmental stressors that drove lactose tolerance could have worked in tandem, and they might have been very different during each of the five different times it is known to have evolved in Europe, the Middle East and Africa.

“In Europe it could be about settlements and famine, while in Africa for example, it could be much more about droughts and higher disease loads,” Thomas says.

The group’s methods might also be employed to find out what happened where humans never did develop the ability to digest milk when common sense suggests they might have.

“Because across the [Eurasian] steppe people who are not lactase persistent are drinking a ton of milk,” says Shevan Wilkin. “What was happening where that didn’t evolve, when it did evolve in Europe?”

Wilkin adds that scientists have been floating various ideas to explain the mysteries of milk digestion, including how lactose tolerance evolved so late and so quickly, and why heavy milk consumers like the steppe dwellers remain lactose intolerant. Now, she says, a framework exists that can further investigate those questions.

“It’s such an impressive undertaking. And through that they’ve come up with some ideas that make a lot of sense.”