Building a cattle pan-genome using more de novo assemblies

Abstract

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 × 10−9 per site 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 ∼ 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 suggested that Sus speciation occurred ∼ 1.36 million years ago (Mya); European pigs split from Asian pigs only ∼ 219 Kya; South and north Chinese wild pigs split ∼ 25 Kya. Meanwhile, our results showed that the most recent divergence event between Chinese wild and domesticated pigs occurred in the Hetao plain, north China, approximately 20 Kya, supporting the possibly independent domestication in north China along the middle Yellow River. We also found the maximum effective population size of pigs was ∼ 6 times larger than the previous estimate. An archaic migration from other Sus species originating ∼ 2 Mya to European pigs was detected during western colonization of pigs; this interfered with the 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.