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Sequencing Study Reveals Complex Model of Pig Domestication

NEW YORK (GenomeWeb) – In a study published today in Nature Genetics, researchers from Wageningen University and elsewhere relied on genome re-sequencing to retrace the history and trajectory of pig domestication.

Using genome sequences for more than 100 wild boars and domestic pigs, the team uncovered signals of selection that seemed to coincide with this domestication, for example.

But rather than seeing a linear domestication trajectory that included reproductive isolation and strong domestication bottlenecks, the researchers found that pig domestication was a complex process that's been frequently marked by gene swapping between pigs and their wild boar counterparts.

"[D]omestic pigs do not constitute a homogeneous genetic group, as would be expected under a simple model involving human-driven domestication," senior author Martien Groenen, an animal breeding and genomics researcher at Wageningen University, and colleagues wrote. "Instead, domestic pig breeds are a genetic mosaic of different wild boar populations."

The researchers started by using the Illumina Porcine 60K iSelect BeadChip array to genotype more than 600 animals, including 403 European domestic pigs, 103 wild boars from Europe, 23 Asian wild boars, and 92 domestic pigs from Asia.

They then focused in on a subset of the individuals for re-sequencing, generating 10-fold average coverage across the genomes of 103 individuals with the Illumina HiSeq.

To look back at the history of pig domestication and model this process, the team used an approximate Bayesian computation analysis to assess sequences from this re-sequenced group of animals — which included wild and domestic animals from Asia, European wild boars, commercial breeds from Europe, and non-commercial domestic breeds.

In particular, the researchers looked at whether the gene flow patterns they saw between wild and domestic animals fit with a prior model postulating two past pig domestication events, one in the Mekong valley in China and one in the Near East in Anatolia.

Through comparisons of several different models, the team concluded that domestic pigs have not remained reproductively isolated from wild boars since these domestication events. Rather, gene flow patterns gleaned from both the genome sequences and genotyping data pointed to gene flow between the wild and domestic animals, both in Asia and Europe.

"[O]ur model-testing approach shows that continuous gene flow from wild boars to domestic pigs is necessary to reconcile modern genetic data with the zooarcheological evidence," authors of the study explained.

Likewise, they noted that there appear to be signs of admixture involving domestic Asian and domestic European pigs, perhaps due to 19th century imports of Chinese pigs into Europe.

The team did see signs of positive selection in the domestic pigs, spanning almost 2,000 genome regions in the European pigs and more than 1,000 parts of the Asian pig genome. These selective events appear to have offset some of the gene flow effects from wild boar admixture, though more research is needed to nail down the precise mechanism behind this selection. 

"[F]uture sequencing of ancient DNA, together with more realistic modeling frameworks … will provide the necessary information not only to determine the geographical origin and time of domestication for animals and plants, but also to identify genes involved during domestication, and will ultimately substantially enhance knowledge of this fascinating evolutionary process," the study's authors concluded.

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