The mutation for milk-drinking evolved independently in different parts of the world over the last 10,000 years as a result of strong natural selection, but why was it so advantageous?

Among the more momentous developments in human evolution was the ability to digest milk beyond early childhood.

Mutations that enabled lifelong milk drinking appeared independently in several parts of the world over the last 7,500 years, according to growing evidence. And those genes spread rapidly. Today, about a third of adults around the world can drink milk without stomach problems, a trait known as lactase persistence.

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But why was milk drinking so advantageous to humankind?

A new study debunks one leading theory: that milk provided a valuable source of vitamin D, which would’ve helped people absorb its calcium.

Newly analyzed human skeletons from an ancient site in Spain show that the milk-drinking gene spread just as rapidly in that sun-drenched climate as it did in other places, suggesting that milk must have been beneficial there for some reason other than its vitamin D content.

“Throughout the years, I have heard so many evolutionary hypotheses about lactase persistence because they are so fun to coin,” said Oddný Sverrisdóttir, an evolutionary biologist at the University of Uppsala in Sweden. “For decades now, people have hypothesized that it was because of lack of sunlight in the north of Europe that people would have had to supplement the lack of calcium and vitamin D by drinking milk.”

“Now, looking at this picture from Spain,” she said, “the calcium-assimilation hypothesis either didn’t affect the evolution of lactase persistence at all, or other forces were there as well.”

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Sverrisdóttir has long been interested in how and why Europe’s early farmers began drinking milk, so she was excited when she got her hands on well-preserved samples of skeletal remains from eight people who lived in northeastern Spain about 5,000 years ago. That was well after the milk-drinking mutation had appeared in northern Europe, and she was eager to find out if those ancient Spaniards were drinking milk, too. So the first thing she did was test their DNA for lactase persistence.

“I thought at least one would have the mutation,” since so many of today’s Spanish adults can drink milk without health consequences, Sverrisdóttir said. “None did.”

To figure out whether the recent and rapid spread of lactase persistence in Spain was a fluke or if natural selection was at play, Sverrisdóttir and colleagues compared the mitochondrial DNA of modern Spaniards with the ancient samples. Mitochondrial DNA changes very slowly, making it ideal for tracing family trees over time.

And, the researchers report today in the journal Molecular Biology and Evolution, analyses showed that the ancient cave dwellers were indeed ancestors of people who live and frequently drink milk in Spain today.

Peter-John Freeman

Then, the team used computer simulations to see what kind of genetic shifts were necessary to get from a population where no one could digest milk past childhood to one where about a third of adults could drink it over the course of just 5,000 years.

Those simulations ruled out the possibility that the mutation reached its current level just by chance and instead showed that there was strong selection for it: Something gave people who had the milk-drinking gene a big advantage over people who didn’t.

But if it wasn’t the vitamin D that made milk so beneficial in sunny Spain, then what was it?

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The new findings can’t answer that question, but Sverrisdóttir has a favorite theory. Early farmers were eating cheese and yogurt long before they could drink milk because fermented dairy products are easier to digest. But in times of famine, when crops failed and all of the processed dairy foods had been consumed, people would have turned to milk out of desperation.

Those who happened to have a lurking mutation that helped them digest it would’ve thrived while those who were lactose intolerant would’ve ended up with life-threatening diarrhea.

“During normal times, if you were well-fed and you had diarrhea for days, it wouldn’t matter much,” Sverrisdóttir said. “But if you were already starving, this would mean the difference between life and death. People would have not lived long enough to get their genes into the next generation. This was the new super-food for people who could tolerate it.”

It’s still possible that milk got its value from vitamin D’s calcium-absorbing powers in some places, said Pascale Gerbault, an evolutionary geneticist at University College London.

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But the new study suggests that there may have been multiple reasons why milk was so pivotal in changing the course of human evolution and that those reasons varied through location and time.

“It makes sense that milk was a good food resource at different points in our evolution,” Gerbault said. “But what were the situations that triggered these pressures? They’re not quite known yet.”