Data from: Genome-wide SNP data unveils the globalization of domesticated pigs

Background: Pigs were domesticated independently in Eastern and Western
Eurasia early during the agricultural revolution, and have since been
transported and traded across the globe. Here, we present a worldwide
survey on 60K genome-wide single nucleotide polymorphism (SNP) data for
2093 pigs, including 1839 domestic pigs representing 122 local and
commercial breeds, 215 wild boars, and 39 out-group suids, from Asia,
Europe, America, Oceania and Africa. The aim of this study was to infer
global patterns in pig domestication and diversity related to demography,
migration, and selection. Results: A deep phylogeographic division
reflects the dichotomy between early domestication centers. In the core
Eastern and Western domestication regions, Chinese pigs show
differentiation between breeds due to geographic isolation, whereas this
is less pronounced in European pigs. The inferred European origin of pigs
in the Americas, Africa, and Australia reflects European expansion during
the sixteenth to nineteenth centuries. Human-mediated introgression, which
is due, in particular, to importing Chinese pigs into the UK during the
eighteenth and nineteenth centuries, played an important role in the
formation of modern pig breeds. Inbreeding levels vary markedly between
populations, from almost no runs of homozygosity (ROH) in a number of
Asian wild boar populations, to up to 20% of the genome covered by ROH in
a number of Southern European breeds. Commercial populations show moderate
ROH statistics. For domesticated pigs and wild boars in Asia and Europe,
we identified highly differentiated loci that include candidate genes
related to muscle and body development, central nervous system,
reproduction, and energy balance, which are putatively under artificial
selection. Conclusions: Key events related to domestication, dispersal,
and mixing of pigs from different regions are reflected in the 60K SNP
data, including the globalization that has recently become full circle
since Chinese pig breeders in the past decades started selecting Western
breeds to improve local Chinese pigs. Furthermore, signatures of ongoing
and past selection, acting at different times and on different genetic
backgrounds, enhance our insight in the mechanism of domestication and
selection. The global diversity statistics presented here highlight
concerns for maintaining agrodiversity, but also provide a necessary
framework for directing genetic conservation.