Data from: Genomic diversity and differentiation of a managed island wild boar population

The evolution of island populations in natural systems is driven by local
adaptation and genetic drift. However, evolutionary pathways may be
altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an
iconic game species occurring in several islands, where it has been
strongly managed since prehistoric times. We examined genomic diversity at
49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared
them with 196 wild specimens from mainland Europe and 105 domestic pigs
(DP; 11 breeds). High levels of genetic variation were observed in
Sardinia (80.9% of the total number of polymorphisms), which can be only
in part associated to recent genetic introgression. Both Principal
Component Analysis and Bayesian clustering approach revealed that the
Sardinian WB population is highly differentiated from the other European
populations (FST=0.126–0.138), and from DP (FST=0.169). Such evidences
were mostly unaffected by an uneven sample size, although clustering
results in reference populations changed when the number of individuals
was standardized. Runs of homozygosity (ROHs) pattern and distribution in
Sardinian WB are consistent with a past expansion following a bottleneck
(small ROHs) and recent population substructuring (highly homozygous
individuals). The observed effect of a non-random selection of Sardinian
individuals on diversity, FST and ROH estimates, stressed the importance
of sampling design in the study of structured or introgressed populations.
Our results support the heterogeneity and distinctiveness of the Sardinian
population and prompt further investigations on its origins and
conservation status.