Human populations evolved in similar ways after we started farming

A study combining the growing number of ancient genomes from living humans 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 agriculture.

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

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

The genomes of long-dead people are particularly useful, says Colbran. “Ancient DNA allows us to look at genetic history live, as it were, whereas many other methods tend to try to infer it.”

Studies of recent evolution have focused on Europe because that is where scientists have collected the oldest and most modern genomes. But Colbran’s team has taken advantage of the growing number of genomes from outside Europe to look more broadly, based on more than 7,000 ancient and modern genomes. The ancient genomes mostly come from the last 10,000 years, while the modern ones are from living people.

The team essentially used the ancient genomes to predict what modern genomes would be like if there was no evolution, and then looked for differences – signals of selection. They found 31 in all, and many of them were shared—that is, people in different parts of the world evolved in similar ways, most likely due to the independent adoption of agriculture around the world at about the same time.

For example, less than a quarter of the oldest people had a genetic variant that increases the expression of FADS1 the gene. The FADS1 enzyme converts short fatty acids of a type common in plants to the longer ones common in meat, so making more of the enzyme is thought to benefit people with more plant-based diets. The FADS1-amplifying 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 is the enzyme alcohol dehydrogenase 1B, encoded by the gene ADH1B. It is well known that a variant of ADH1B which quickly transforms alcohol into acetaldehyde, causing unpleasant symptoms such as facial redness, has become common in East Asia. It is believed that this variant was chosen because it discourages drinking. “It’s the strongest signal of selection you see in East Asia,” says Colbran.

This variant did not exist in ancient Europeans, but her team still found evidence of strong selection involving the ADH1B enzyme. “It’s something that changes the amount of the layer, or how it reacts,” says Colbran. Further work will be required to determine the exact 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 hips. An increase in waist-to-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 a strong selection that keeps the female waist-to-hip ratio within certain parameters. “It’s very interesting in that we see stabilizing selection,” says Colbran.

The waist-hip ratio varies in different populations, but the findings suggest that there is an optimal value somewhere in the middle, she says. “Population to population, it can change depending on the exact context.”

It is an exciting study that includes a lot of old DNA that has not been analyzed 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,” says Gusev. “I take this to mean that selection is likely to be parallel across populations. This has been hypothesized but not shown before.”

Yassine Souilmi of the University of Adelaide, Australia, says the team’s approach was able to identify regions of the genome not 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,” says Souilmi.

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

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