Final Report Summary - SELSWEEP (Molecular characterization of genetic factors in the pig under selection during speciation, domestication and breeding)
Ever since Darwin’s first description of the theory of evolution, the forces that act during speciation and, to a lesser extent, domestication have attracted much attention. To further address these questions in detail at the molecular level, the pig is of particular interest. Domestication and selection have resulted in a large number of distinct breeds worldwide with very distinct characteristics. Unique for pigs are the availability of 12 closely related species that have diverged over a time span of 1 to 10 million years. The SelSweep project addressed these questions in detail by analysing the complete genome sequences of over 300 individual pigs representing wild boar populations, domestic breeds and the different Suids across the world.
We were able to unequivocally reconstruct the phylogeny of the 12 species of the Suidae superfamily (a group of species representing pig species from Africa, Europe and Asia) and to estimate the time at which these different species diverged. For the family Sus (pig species found in Eurasia and on the islands of South-East Asia), we showed that contrary to the expectation of simple models of speciation, the evolutionary history of these species involved alternating periods of gene-flow and genetic differentiation that are tightly linked to past climatic fluctuations that took place over the last 4 million years. An unexpected finding was the deep divergence of European and Asian wild boar, which we estimate at about 1 million years ago. As a result, due to the independent domestication of pigs in Anatolia (European pig) and Asia (Chinese pigs) this has resulted in very distinct divergent breeds in these two parts of the world. While it is well documented that European breeders imported Chinese pigs in the late 18th and early19th century to improve their breeds, our findings show that the percentage of Asian genetic variants in current commercial European breeds is surprisingly high (25-35%). The deep divergence of European and Asian genomes allowed us to identify specific Asian variants that have been strongly selected for after their introgression in the European breeds. Many of the selected Asian variants affect traits like fertility and fatness in pigs.
Many of the pig species, in particular the pygmy hog, which inhabited the grasslands of the foothill plain south of the Himalayas but is now only restricted to a few areas in Northern India, and the different pig species found on the islands of South-East Asia (Indonesia and the Philippines), are highly endangered. Furthermore, also many local pig breeds found in Europe and Asia are under threat of becoming extinct, resulting in loss of genetic diversity. Our analysis of the genomes of individual pigs from these species and domestic breeds provided insight to help conservation and breeding programmes to maintain most of this diversity and avoid the deleterious effects of inbreeding. This will help to keep these populations genetically healthy and ensure maintaining this important genetic variation for the future.
We were able to unequivocally reconstruct the phylogeny of the 12 species of the Suidae superfamily (a group of species representing pig species from Africa, Europe and Asia) and to estimate the time at which these different species diverged. For the family Sus (pig species found in Eurasia and on the islands of South-East Asia), we showed that contrary to the expectation of simple models of speciation, the evolutionary history of these species involved alternating periods of gene-flow and genetic differentiation that are tightly linked to past climatic fluctuations that took place over the last 4 million years. An unexpected finding was the deep divergence of European and Asian wild boar, which we estimate at about 1 million years ago. As a result, due to the independent domestication of pigs in Anatolia (European pig) and Asia (Chinese pigs) this has resulted in very distinct divergent breeds in these two parts of the world. While it is well documented that European breeders imported Chinese pigs in the late 18th and early19th century to improve their breeds, our findings show that the percentage of Asian genetic variants in current commercial European breeds is surprisingly high (25-35%). The deep divergence of European and Asian genomes allowed us to identify specific Asian variants that have been strongly selected for after their introgression in the European breeds. Many of the selected Asian variants affect traits like fertility and fatness in pigs.
Many of the pig species, in particular the pygmy hog, which inhabited the grasslands of the foothill plain south of the Himalayas but is now only restricted to a few areas in Northern India, and the different pig species found on the islands of South-East Asia (Indonesia and the Philippines), are highly endangered. Furthermore, also many local pig breeds found in Europe and Asia are under threat of becoming extinct, resulting in loss of genetic diversity. Our analysis of the genomes of individual pigs from these species and domestic breeds provided insight to help conservation and breeding programmes to maintain most of this diversity and avoid the deleterious effects of inbreeding. This will help to keep these populations genetically healthy and ensure maintaining this important genetic variation for the future.