Ancestry and diversity of American village pigs.

Abstract

Advances in high throughput genetic technologies are revolutionizing the understanding of domestic animal genomes, including their history and how demography and selective processes have shaped the variation of individuals’ genomes. Here we studied for the first time a large survey of village pig populations from America and estimate their relatedness with worldwide pig populations. In complement, we also analysed an ancient pig genome of 16th century to provide new evidence on important historical and genetic events like domestication and admixture. These studies showed the high differentiation between European and Asian pig populations, being particularly pronounced for the non-pseudoautosomal region of chromosome X. Despite the Iberian origin of pigs firstly introduced to America, a substantial reduction of this ancestry was observed in almost all American village pig populations. The actual ancestry observed in America is likely the result of admixing Iberian pigs in 15th century and recent introgression of commercial pig breeds. Additionally, some Asian ancestry also was observed probably due to introgression of commercial breeds carrying Asian haplotype, although direct admixture with Chinese breeds cannot be ruled out. Because the large diversity of environmental condition in the American continent, we compared the allele frequencies observed between populations to estimate signatures of selection in the genome, detecting some genes related with cardiovascular system and limbs conformation. Ancient DNA provides valuable information about the historical events that have modelled the genome of modern individuals. In chapter 5 we performed the analysis of the partial genome of a pig that lived in 16th century at North eastern Spain together three new modern genomes from Iberian pig, Spanish wild boar and a Guatemalan Creole pig obtained by whole genome shotgun sequencing. Archaeological and genomic data suggested that ancient pig was domestic, closely related to extant Iberian pigs and to European wild boar with some genetic signals of admixture with wild boar. Surprisingly, the comparison of ancient pig and modern Iberian pig to American sample from Guatemala, showed that they are equally close to American Creole pigs, and could support the hypothesis of reduction of Iberian origin in American village pigs driven by introgression of other breeds. Finally, among the highly differentiated genes we found those involved in coat colour and an increase the reproductive performance, both known functions associated with early domestication process. One of the analytical strategies to describe the population relationships of pigs used in this thesis, and widely used in similar studies is the principal component analysis (PCA). Nonetheless, PCA projections are sensitive to unequal sample size. In Chapter 6 we evaluated a correction in PCA that consider either sample size of evaluated populations or their FST estimates to correct bias in individual projections. Simulations suggest that the proposed method improves the two-dimensional projections of PCA data and, in some cases, entirely recovers population relationships patterns, even when sample size is as low as n=1. The weighted PCA can recover a more realistic structure than inferred with traditional PCA in well-structured populations.

Date of Award	7 Jul 2014
Original language	English
Supervisor	Sebastián Ernesto Ramos Onsins (Director) & Miguel Pérez Enciso (Director)