Massive Ancient-DNA Study Reveals Natural Selection Has Accelerated in Recent Human Evolution

Amazing stuff!

"At a glance

• Applying new analytic methods to nearly 16,000 ancient genomes reveals natural selection has acted on hundreds, not dozens, of genes in West Eurasia over the last 10,000 years.
• More than half of the genes have known links to disease risk and other traits today, although it’s not yet clear what made each gene advantageous in prehistoric contexts.
• The work demonstrates the power of ancient DNA to illuminate human biology and medicine in addition to history.

A massive study of ancient DNA from nearly 16,000 people across more than 10,000 years in West Eurasia reveals that natural selection has shaped modern human genomes far more than previously thought. ...

Combining an unprecedented amount of ancient genomic data with novel computational methods, the new analysis shows instead that directional selection has driven the spread or decline of hundreds of gene variants in West Eurasia since the end of the Ice Age and that selection has actually accelerated since people transitioned from hunting and gathering to farming. ...

Since 2010, when the first genome-wide data was recovered from ancient human remains, ancient-DNA research has expanded understanding of the relationships among people living in different time periods and regions of the world.

But geneticists struggled to realize the technology’s promise to illuminate how natural selection has shaped human genetic variation even over the last 10,000 years, when there is enough well-preserved genetic material to support large-scale studies.

The new study broke through that barrier using two innovations.

First, the Reich Lab spent seven years building a collection of DNA sequences from ancient people living in West Eurasia — what is now Europe and parts of the Middle East — that would be comprehensive enough in size and time span to support the work. ...

The lab collaborated with more than 250 archeologists and anthropologists to report new DNA data from 10,016 ancient individuals from West Eurasia. They added those to another 5,820 published ancient sequences and 6,438 modern ones.

“This single paper doubles the size of the ancient human DNA literature,” ...

The second innovation — and even more important to the success of the study, ...  development of computational methods to isolate the signal of directional selection from other causes of gene frequency changes, such as human migration, population mixing, and random genetic fluctuations that occur in small populations. ..."

From the abstract:

"Ancient DNA has transformed our understanding of population history, but its potential to reveal as much about human evolutionary biology has not been realized because of limited sample sizes and the difficulty of distinguishing sustained rises in allele frequency increasing fitness—directional selection—from shifts due to migrations, population structure, or non-adaptive purifying or stabilizing selection.

Here we present a method for detecting directional selection in ancient DNA time-series data that tests for consistent trends in allele frequency change over time, and apply it to 15,836 West Eurasians (10,016 with new data).

Previous work has shown that classic hard sweeps driving advantageous mutations to fixation have been rare over the broad span of human evolution.

By contrast, in the past ten millennia, we find that many hundreds of alleles have been affected by strong directional selection.

We also document one-standard-deviation changes on the scale of modern variation in combinations of alleles that today predict complex traits. This includes decreases in predicted body fat and schizophrenia, and increases in measures of cognitive performance. These effects were measured in industrialized societies, and it remains unclear how these relate to phenotypes that were adaptive in the past. We estimate selection coefficients at 9.7 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits."

Massive Ancient-DNA Study Reveals Natural Selection Has Accelerated in Recent Human Evolution | Harvard Medical School (Caveat: I did not read the entire, long article) "Hundreds of genes selected in West Eurasia since farming began, many linked to health"

Ancient DNA reveals pervasive directional selection across West Eurasia (no public access)