European pigs shook off their ancestry

When ancient Near Eastern farmers migrated westward into Europe about 8500 years ago, they brought their pigs with them – along with their sheep, goats, cattle and grains.

But you wouldn’t know that by looking at the genes of modern European pigs, which are more similar to European wild boars.

That’s because the genetic traces of those original domestic pigs were almost entirely erased over a period of 3000 years, according to an analysis of ancient and modern pig and wild boar genomes.

Such a drastic genomic turnover is unusual. It could be because pigs were less isolated from their wild counterparts compared with other domestic animals, such as cattle and dogs.

Domestic pigs – more petite and with smaller teeth than wild boars – first crop up in the archaeological record around 10,500 years ago in the Near East, a region that covers the Middle Eastern countries of today.

In Europe, domestic pigs only make an appearance around 8500 years ago, which coincides with a migration of Neolithic people from the Near East into Europe. 

But questions have lingered over whether European domestic pigs were domesticated not in the Near East, but instead from wild boars in Europe.

To work out what happened, a team led by Greger Larson from Oxford University, UK, looked at mitochondrial genomes, which are inherited through the female line, from over 2000 pigs and wild boars across Europe and the Middle East. 

The samples span 14,000 years, from before pigs were domesticated until present times, and over half of those samples utilise ancient DNA.

Early European domestic pigs have mitochondrial genomes that originated in the Near East. The earliest occurs in Bulgaria around 8000 year ago. But by 5000 years ago, Near Eastern mitochondrial types have disappeared from European pigs.

A smattering of Near Eastern genetic signatures persisted in Mediterranean islands off Greece, but the ancestral trace was essentially eliminated across the mainland.

Instead, all of the mitochondrial types came from European wild boars, indicating that female wild boars interbred with European domestic pigs.

To get a better handle on whether the European wild boar genes were the result of deliberate breeding, the team sequenced 63 ancient nuclear DNA genomes, which are inherited through both the male and female lines.

Most modern domestic pigs had next to no Near Eastern ancestry, and overall, Near Eastern ancestry accounted for just 4% of European pig ancestry.

“We are all taught that the big change was the initial process of domestication, but our data suggests that almost none of the human-selection over the first 2500 years of pig domestication has been important in the development of modern European commercial pigs,” says lead author Laurent Frantz, from Queen Mary University, UK.

While most Near Eastern genes were replaced, the team identified a notable exception. Black coat colour, which is the result of a mutation in the a Melanocortin 1 Receptor (MC1R) gene, originated in ancient Anatolia, and has persisted to the present day in some European breeds.

“Having access to ancient genomes over such a large space and time has allowed us to see the slow-motion replacement of the entire genome of domestic pigs,” Larson says.

“This suggests that pig management in Europe over millennia was extensive, and that though swine herders maintained selection for some coat colours, domestic pigs interacted with wild boar frequently enough that they lost the ancestral signature of the wild boar from which they were derived,” he says.