Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree

The mutation rate used in the previous analyses of pig evolution and demographics was cursory and hence invited potential bias in inferring evolutionary history. Herein, we estimated the de novo mutation rate of pigs as 3.6 x 10(9) per base per generation using high-quality whole-genome sequencing data from nine individuals in a three-generation pedigree through stringent filtering and validation. Using this mutation rate, we re-investigated the evolutionary history of pigs. The estimated divergence time of similar to 10 kiloyears ago (KYA) between European wild and domesticated pigs was consistent with the domestication time of European pigs based on archaeological evidence. However, other divergence events inferred here were not as ancient as previously described. Our estimates suggest that Sus speciation occurred similar to 1.36 million years ago (MYA); European wild pigs split from Asian wild pigs only similar to 219 KYA; and south and north Chinese wild pigs split similar to 25 KYA. Meanwhile, our results showed that the most recent divergence event between Chinese wild and domesticated pigs occurred in the Hetao Plain, northern China, approximately 20 KYA, supporting the possibly independent domestication in northern China along the middle Yellow River. We also found that the maximum effective population size of pigs was similar to 6 times larger than estimated before. An archaic migration from other Sus species originating similar to 2 MYA to European pigs was detected during western colonization of pigs, which may affect the accuracy of previous demographic inference. Our de novo mutation rate estimation and its consequences for demographic history inference reasonably provide a new vision regarding the evolutionary history of pigs.

Automated summary

This study estimated the de novo mutation rate of pigs and reinvestigated their evolutionary history. The results showed that the divergence events in pig evolution were not as ancient as previously thought, and the most recent divergence between Chinese wild and domesticated pigs occurred in northern China.