Human populations evolved in similar ways after we began farming

A study combining the growing number of ancient genomes from living people has given us our best picture yet of how humans have evolved over the past 10,000 years or so. It shows that people in different parts of the world evolved in similar – and sometimes even identical – ways after we adopted farming.

“Some of the same traits and the same genes are under selection in different populations,” says Laura Colbran at the University of Pennsylvania.

Evolution occurs when a genetic variant becomes more common in a population – usually, but not always, because it provides an advantage. By comparing human genomes, then, we can find signs of recent human evolution.

The genomes of long-dead people are especially helpful, says Colbran. “Ancient DNA lets us look at genetic history live, as it were, whereas a lot of other methods tend to try and infer that.”

Studies of recent evolution have focused on Europe because that’s where researchers have collected the most ancient and modern genomes. But Colbran’s team has taken advantage of the growing number of genomes from outside Europe to take a wider look, based on more than 7000 ancient and modern genomes. The ancient genomes mostly come from within the past 10,000 years, while the modern ones are from living people.

The team essentially used the ancient genomes to predict what modern genomes should be like if there were no evolution, and then looked for differences – signals of selection. They found 31 altogether, and many of them were shared – that is, peoples in different parts of the world were evolving in similar ways, most likely because of the independent adoption of farming around the world at around the same time.

For instance, less than a quarter of the most ancient people had a genetic variant that boosts the expression of the FADS1 gene. The FADS1 enzyme converts short fatty acids of a kind common in plants into the longer ones common in meat, so making more of the enzyme is thought to benefit people with more plant-based diets. The FADS1-boosting variant is now present in more than three-quarters of people in Europe, Japan and northern China. In Europe, the strength of selection has remained constant over the past 300 generations, the team found, but in East Asia it has increased over the past 100 generations.

Then there’s the enzyme alcohol dehydrogenase 1B, encoded by the gene ADH1B. It’s well known that a variant of ADH1B that rapidly turns alcohol into acetaldehyde, producing unpleasant symptoms such as facial flushing, has become common in East Asia. It is thought this variant has been selected for because it discourages drinking. “It’s the strongest signal for selection you see in East Asia,” says Colbran.

This variant didn’t exist in ancient Europeans, but her team still found evidence of strong selection involving the ADH1B enzyme. “There’s something that’s changing the amount made, or how it’s responding,” says Colbran. Further work is going to be required to pin down the precise variant involved, and what it does, but it is almost certainly an adaptation to alcohol drinking.

The team even looked at traits that are affected by multiple genetic variants, such as the ratio of a person’s waist to their hips. An increase in the waist-hip ratio is linked to higher fertility, so you might think there would be selection for this.

Instead, the team found that there appears to be strong selection that keeps the female waist-hip ratio within certain parameters. “It is a really interesting one in that we do see stabilising selection,” says Colbran.

The waist-hip ratio does vary in different populations, but the findings suggest there is an optimum value somewhere in the middle, she says. “Population to population, it might shift depending on the precise context.”

It’s an exciting study that includes a lot of ancient DNA that hasn’t been analysed before, says Alexander Gusev at Harvard University. “The authors find that variants under selection in one population are significantly enriched for being under selection in other populations,” Gusev says. “I take this to mean that selection is likely to be parallel across populations. This has been hypothesised but not shown before.”

Yassine Souilmi at the University of Adelaide, Australia, says the team’s approach was able to identify regions of the genome that weren’t known to be under selection before, in addition to previously identified regions. “Their new method takes full advantage of the large amount of ancient DNA available now,” Souilmi says.

The results are the tip of the iceberg, says Colbran. As more genomes are sequenced – especially more non-European ones – we’ll find much more evidence of recent evolution.

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