Resilience to Historical Human Manipulations in the Genomic Variation of Italian Wild Boar Populations

Abstract

Human activities can globally modify natural ecosystems determining ecological, demographic and range perturbations for several animal species. These changes can jeopardize native gene pools in different ways, leading either to genetic homogenization, or conversely, to the split into genetically divergent demes. In the past decades, most European wild boar (Sus scrofa) populations were heavily managed by humans. Anthropic manipulations have strongly affected also Italian populations through heavy hunting, translocations and reintroductions that might have deeply modified their original gene pools. In this study, exploiting the availability of the well-mapped porcine genome, we applied genomic tools to explore genome-wide variability in Italian wild boar populations, investigate their genetic structure and detect signatures of possible introgression from domestic pigs and non-native wild boar. Genomic data from 134 wild boar sampled in six areas of peninsular Italy and in Sardinia were gathered using the Illumina Porcine SNP60 BeadChip (60k Single Nucleotide Polymorphisms – SNPs) and compared with reference genotypes from European specimens and from domestic pigs (both commercial and Italian local breeds), using multivariate and maximum-likelihood approaches. Pairwise FST values, multivariate analysis and assignment procedures indicated that Italian populations were highly differentiated from all the other analyzed European wild boar populations. Overall, a lower heterozygosity was found in the Italian population than in the other European regions. The most diverging populations in Castelporziano Presidential Estate and Maremma Regional Park can be the result of long-lasting isolation, reduced population size and genetic drift. Conversely, an unexpected similarity was found among Apennine populations, even at high distances. Signatures of introgression from both non-Italian wild boar and domestic breeds were very limited. To summarize, we successfully applied genome-wide procedures to explore, for the first time, the genomic diversity of Italian wild boar, demonstrating that they represent a strongly heterogeneous assemblage of demes with different demographic and manipulation histories. Nonetheless, our results suggest that a native component of genomic variation is predominant over exogenous ones in most populations.

Spatial genetic structure of European wild boar, with inferences on late-Pleistocene and Holocene demographic history

“…S2) was difficult to ascertain through detection of introgressed haplotypes. Either the signal is a type-I error and pig hybridization is infrequent (in line with findings for Italian wild boar by Scandura et al 2022) or pig hybridization has been so frequent and long-lasting that introgressed segments are too short to detect with medium density SNP data. Both Iberia and Italy share a long tradition of extensive pig herding for regional ham production, up to the present, that possibly has led to a prolonged gene-flow between the wild boar and domestic pigs (Herrero-Medrano et al 2013;Canu et al 2014;Iacolina et al 2016;Maselli et al 2016).…”

Anthropogenic hybridization and its influence on the adaptive potential of the Sardinian wild boar (Sus scrofa meridionalis)

“…The dataset we analyzed here was taken from publicly available data (Iacolina et al 2016 ; Yang et al 2017 ; Scandura et al 2022 ), comprising various WB, DP, and outgroup species, all genotyped with the Illumina Porcine SNP60 Beadchip (Ramos et al 2009 ), that is mapped onto the pig reference genome Sscrofa10.2 (Groenen et al 2012 ). In particular, we selected the SarWB samples, together with a reference set of commercial European pig breeds (Berkshire (BK), Duroc (DU), Large White (LW), Pietrain (PI), Yorkshire (YO), Sardinian local pigs (SarDP)), and Italian WB that are assumed to be free of recent domestic introgression (ItaWB), and finally an outgroup — here represented by S. barbatus (SB; Bornean bearded pig).…”

The Boar War: Five Hot Factors Unleashing Boar Expansion and Related Emergency

“…Moving the individuals into non-native range distributions, potentially alarming situations could arise for both the environment and the indigenous fauna and flora, where boar are invasive [17,43,67,[211][212][213][214][215][216]. Indeed, allochthonous individuals more easily could invade ecological niches unattended by indigenous populations.…”