Pervasive selection pressure in wild and domestic pigs

Abstract

ABSTRACTAnimal domestication typically affected numerous polygenic quantitative traits, such as behavior, development and reproduction. However, uncovering the genetic basis of quantitative trait variation is challenging, since they are caused by small allele-frequency changes. To date, only a few causative mutations related to domestication processes have been reported, strengthening the hypothesis that small effect variants have a prominent role. So far, approaches on domestication have been limited to the detection of the global effect of domestication on deleterious mutations and on strong beneficial variants, ignoring the importance of variants with small selective effects. To overcome these difficulties, here we propose to estimate the proportion of beneficial variants based on the asymptotic MacDonald Kreitman (MK) method, according to estimates of variability based on frequency spectrum. We applied this approach to the pig species, analyzing 46 complete genome sequences from 20 European wild boars, 6 Iberian and 20 Large White pigs at different molecular scales: gene, metabolic pathway and whole-genome.Descriptive variability analyses on pig populations indicate that domestic and wild pig populations do not differ in nonsynonymous fixed mutations. Instead, most variants are shared among them, despite that the phenotypes of wild and domestic individuals are clearly divergent. Additionally, asymptotic MK plots based on summary statistics show that small effects variants may affect the final calculation ofα, the proportion of beneficial mutations. The distribution of fitness effects inferred with Approximate Bayesian Computation analysis indicates that both wild and domestic pigs display an important quantity of deleterious mutations at low frequency (~83% of total mutations) and a high number of nearly-neutral mutations (~17%) that may have a significant effect on the evolution of domestic and wild populations. Exclusive mutations show that recent demographic changes have severely affected the fitness of populations, especially of the local Iberian breed. Finally, the median proportion of the strong favorable mutations are very scarce in all cases (≤ 0.2%). The median estimated alpha values (weak and strong favorable) are 0.9% for wild and domestic pigs.