Population genomic, olfactory, dietary, and gut microbiota analyses demonstrate the unique evolutionary trajectory of feral pigs

Abstract

Domestication is an intriguing evolutionary process. Many domestic populations are subjected to strong human-mediated selection, and when some individuals return to the wild, they are again subjected to selective forces associated with new environments. Generally, these feral populations evolve into something different from their wild predecessors and their members typically possess a combination of both wild and human selected traits. Feralisation can manifest in different forms on a spectrum from a wild to a domestic phenotype. This depends on how the rewilded domesticated populations can readapt to natural environments based on how much potential and flexibility the ancestral genome retains after its domestication signature. Whether feralisation leads to the evolution of new traits that do not exist in the wild or to convergence with wild forms, however, remains unclear. To address this question, we performed population genomic, olfactory, dietary, and gut microbiota analyses on different populations of Sus scrofa (wild boar, hybrid, feral and several domestic pig breeds). Porcine single nucleotide polymorphisms (SNPs) analysis shows that the feral population represents a cluster distinctly separate from all others. Its members display signatures of past artificial selection, as demonstrated by values of F_ST in specific regions of the genome and bottleneck signature, such as the number and length of runs of homozygosity. Generalised F_ST values, reacquired olfactory abilities, diet, and gut microbiota variation show current responses to natural selection. Our results suggest that feral pigs are an independent evolutionary unit which can persist so long as levels of human intervention remain unchanged.

Keywords: Sus scrofa; diet; feralisation; gut microbiota; olfaction; population genomics.

FIGURE 1

Some feral phenotypes of individuals included in this study

FIGURE 2

Sampling. (a) Study areas. (b) Corsican area. (c) Sardinian area. (d) Southern Italy area. (e) Principal component analysis based on 15,531 SNPs. Each point represents a genotyped individual coloured according to geographic origin and category. The star‐shaped symbols represent the different Italian pig breeds: cyan, Calabrese breed; pink, Cinta Senese breed; grey, Casertana breed; and yellow, Nero siciliano breed. Blue squares: Italian Wild Boar, with black border individuals from Northern‐Central Italy and without black border individuals from Southern Italy

FIGURE 3

Runs of homozygosity. (a) Box plots showing the distribution of the total ROH lengths (Kb). (b) Number of ROHs per animal by population. (*): p < .05; (**): p < .01. The box plots indicate the median, 25th and 75th percentiles, the lowest datum of the lower quartile and the highest datum of the upper quartile

FIGURE 4

F _ST (a) Genome wide plots of smoothed F _ST (red line) for three swine forms (wild boar, domestic pig and feral pig). Notice how the smoothed F _ST highlights at least five regions under potential selection for pig populations. The horizontal line shows the significance threshold. (b) Manhattan plots of F _ST for genic and nongenic regions. F _ST values above the threshold line (black horizontal line) show SNPs under potential selection. The different SNP classes (y‐axis) ‐ nonsynonymous, cis‐regulatory, nongenic and intronic – are examined across the 18 autosomal chromosomes and X chromosome, shown in different colours on the x‐axis (the X chromosome represented in green on the far right)

FIGURE 5

(a) Differential gene expression analysis of the odorant binding protein (OBP) gene. Blue, wild boar; orange, domestic pig; green, feral pig. (*), statistically significant differences compared to pig levels (ANOVA one‐way test; p < .05). Error bars represent standard deviation. (b–c) Plant component of diet. Frequency of sequence occurrence (log10) for each plant family in the diet of wild boar (b) and feral pigs (c). (d–e) Animal component of diet. Frequency of sequence occurrence (log10) for each animal family in the diet of wild boar (d) and feral pigs (e)

FIGURE 6

Microbiota composition. (a) Venn diagram illustrates the overlap of bacteria genera in gut microbiota among 25 individuals (wild boar, N = 7, feral pigs, N = 10, domestic pigs, N = 8). (b) PCoA plot of gut microbiota in all groups based on Bray‐Curtis dissimilarity. Each point represents the intestinal microbiota of an individual, coloured according to its geographic origin and category