SNPs genotypes of Italian wild boar (Sus scrofa) populations

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.

人类活动可在全球范围内改造自然生态系统，进而对多种动物的生态、种群动态及分布范围造成扰动。此类变化会以多种方式危及本土基因库，要么导致遗传均质化，反之则会引发种群分化为遗传趋异的同类群（deme）。

过去数十年间，多数欧洲野猪（Sus scrofa）种群都受到了人类的高强度管控。人为干预同样对意大利野猪种群造成了强烈影响——高强度狩猎、种群易位与重新引入行为，可能已极大改变了其原始基因库。

本研究依托已完成精细图谱绘制的猪基因组，运用基因组学工具探究意大利野猪种群的全基因组变异特征，解析其遗传结构，并检测来自家猪与非本土野猪的潜在基因渐渗信号。研究采集了意大利半岛6个区域及撒丁岛的134份野猪样本，通过Illumina猪60K SNP芯片（60k单核苷酸多态性，SNPs）获取基因组数据，并结合多元统计与最大似然法，将所得数据与欧洲野猪标本及家猪（包括商业品种与意大利地方品种）的参考基因型进行比对分析。

两两FST值、多元分析及种群归属分析结果均显示，意大利野猪种群与所有其他纳入分析的欧洲野猪种群存在显著遗传分化。

整体而言，意大利野猪种群的杂合度低于其他欧洲区域种群。卡斯泰尔波尔齐亚诺总统庄园与马雷马区域公园的种群分化程度最高，这可能源于长期的地理隔离、种群规模缩减及遗传漂变。与之相反，亚平宁山脉的野猪种群即便分布距离较远，却呈现出意料之外的遗传相似性。来自非意大利本土野猪与家猪品种的基因渐渗信号均极为有限。

综上，本研究首次运用全基因组学方法系统探究了意大利野猪的基因组多样性，结果表明其种群是由具有不同种群动态与人为干预历史的同类群构成的高度异质集合。不过，研究结果同时显示，在多数意大利野猪种群中，本土基因组变异成分相较于外源性成分仍占据主导地位。