Using genomewide polymorphisms to explore demography and feralization in the pig species

The advent of next generation sequencing technologies has revolutionized the study of livestock genomics, such as in pigs. For instance, using genomic data it is possible to better understand wild boars demography and its impact on domestication. Moreover, the analysis of feral pigs improves the knowledge on the dynamics of feralization, and serves as yardstick against which to compare modern breeds. In this thesis we provide insights about the demography and the feralization process in the pig species using genomewide polymorphisms. In the first part of this work, we analyzed 128 complete pig and 5 outgroup genomes, in order to obtain the first genomewide and worldwide catalog of SNPs of the pig. We were able to assess the ancestral allele of ~39M out of the ~48M variants found. The number of unique derived variants in European breeds (>6M) is smaller than in Asian breeds (>13M), in agreement with the Asiatic origin of Sus scrofa. Moreover, we found a marked correlation in allele frequencies between domestics and wild boar within Asia and within Europe. This correlation was absent across continents, due to the large evolutive distance between pigs in both continents (~1 MYA). In the second part of this work, we tried to disentangle the demographic history of wild boars using the polymorphisms found in the previous study. We analyzed the joint site frequency spectrum of ~2M SNPs of 9 European and 8 Asian wild boars using coalescence and the analytical approach of ∂a∂i. Using coalescence we evaluated whether a split between the two populations was enough to explain the observed spectrum, but only when migration was included in the model, we found a joint spectrum coherent with the observed data. Using ∂a∂i, we analyzed 6 models that differed in the number of bottlenecks and migration events. Only the simplest model seemed to converge, whereas this was not clear for more complex scenarios. Despite this convergence issue, both methods pointed to migration events after the split as a demographic factor shaping wild boars variability. Further analyses are needed to improve wild boars' demographic history inference. Finally, in the third part of this thesis, we focused on the analysis of the dynamics of feralization. We analyzed the genome of the feral population of Isla del Coco (Costa Rica), which have been isolated since its foundation in 1793, and is therefore an excellent model to study feralization dynamics. We confirm that English domestic pigs were already hybrids between Asian and European breeds in late 17th century. Interestingly, despite the bottleneck suffered, Cocos pigs average variability is comparable to those of current commercial pig breeds such Large White or Duroc. Yet, we also found a 10-Mb region with a marked decrease in variability across all sampled tested, which was previously identified as highly differentiated between wild boars and domestic breeds. Domestication and feralization are symmetric events of pig history. The analysis of wild boars demography will serve as null model to study the dynamics before domestication. On the other side, the analysis of the feral pigs of Isla del Coco improved the knowledge on the last 200 years of breeding managements on domestic breeds. Moreover it will help to understand the dynamics after domestication when a hybrid animal becomes feral. All these studies are now possible only thanks to the evolution of sequencing techniques, which resulted in an increasing number of public worldwide whole genome sequence data.