Genomic diversity and differentiation of a managed island wild boar population

Abstract

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.

Mixed ancestry from wild and domestic lineages contributes to the rapid expansion of invasive feral swine

“…We assembled our reference set by compiling domestic pig and native wild boar HD SNP genotypes from previously published data sets ( n = 2,450; Alexandri et al, 2017; Burgos‐Paz et al, 2013; Goedbloed, Megens, et al, 2013; Iacolina et al, 2016; Roberts & Lamberson, 2015; Yang et al, 2017), which we augmented with novel genotypes produced by our research group ( n = 566; produced with extraction methods described above and genotyped with the Genomic Profiler for Porcine HD [GeneSeek]). To align with feral swine genotypes, we restricted our reference set to data sets similarly produced with either the PorcineSNP60 (versions 1 and 2; Illumina) or Genomic Profiler for Porcine HD (GeneSeek) BeadChip microarrays (Ramos et al, 2009).…”

Novel Graphical Analyses of Runs of Homozygosity among Species and Livestock Breeds

“…Additionally, fixed ROH in all the individuals in a population could indicate past selective events. Clearly, the presence of long ROH at relatively high frequency in a population could also indicate the presence of genetic substructure, with consanguineous mating occurring only within some subpopulations [13]. ROH are also affected by demographic events [8] and further investigation should examine issues such as skewed reproductive success.…”

Landscape-Scale Genetic Structure of Wild Rice Zizania latifolia: The Roles of Rivers, Mountains and Fragmentation

“…In the present study, the 2MOD analysis suggested that genetic drift may have an important impact on the present genetic patterns. Additionally, the evident population differentiation may be associated with different environmental adaptations of the populations (Hufford and Mazer, 2003;Iacolina et al, 2016), and common-garden experiments should be carried out to test this assumption.…”