Faster Accumulation of Nonsynonymous Mutations in Domestic Pigs from Europe than from Asia

Although the period since thedomestication of pigs is relatively short (~ 9,000 years) on the evolutionary time-scale, it has drastically influenced pig genomes. Previous studies have suggested that domestication has led to a faster accumulation of slightly deleterious (nonsynonymous) mitochondrial mutations in domestic pigs. However, uncertainty remains as to whether European and Asian domestic pigs accumulate mutations at different paces, since they were domesticated independently.Here we analyzed the nonsynonymous/synonymous rate ratios (ω) of mitochondrial and nuclear genomes of Eurasian wild and domestic pigs by model selection and likelihood-ratio test. The best model revealed significant evidence of slower accumulation of functional mutations in Asian domestic pigs than in European domestic pigs, but both of these exhibit a faster accumulation of functional mutations than Eurasian wild boars. Surprisingly, no difference was detected between ω ratios ofwild boars from Europe and Asia, despite strikingly different effective population sizes (N_e) suggested by previous studies. Additionally, Asian domestic pigs showed higher radical to conservative substitutions ratio than European domestic pigs. Thegenome-wide differences between European and Asian domestic pigsmight aid our understanding of the joint effects of different selection pressures and objectives, as well as genetic drift on genome evolution.