Diachrony and Synchrony When Studying Pig Genomes

The history of livestock is sculpted in their genomes and can be recovered from either studying ancient sample genomes during a historical period (diachrony) or by comparing the extant genomes pertaining to different geographic locations and/or breeds (synchrony). An example of the latter approach is the evolution of the IGF2 regulatory mutation that increases lean content: by comparing the frequency of the favorable allele across breeds and tracing the haplotypes surrounding the mutation, we are able to recover the selective sweep. Nevertheless, resolving important issues like disentangling the effects of domestication from those of modern breeding is difficult because domestics carry signatures of modern breeding and selection. To that end, the sequencing of ancient domestic genomes predating the advent of breeds and modern artificial selection era is unavoidable. Here, we present the analysis of a 16^th century pig from Spain and we definitely prove that a large part of variability that we now observe in modern pigs breeds is due to Asian introgression; in fact, it is estimated that ca. 20-25% of some international pig breeds is of Asian origin. Furthermore, by sequencing a feral pig population from the Coco island in Costa Rica that has remained isolated since 1793, we do show that this percentage has remained stable over the last two centuries, but that is not shared across breeds, i.e., there is a large heterogeneity in the Asian haplotypes among international pig breeds.