Genome‐wide analysis of hybridization in wild boar populations reveals adaptive introgression from domestic pig

Abstract

The admixture of domestic pig into French wild boar populations has been monitored since the 1980s thanks to the existence of a cytogenetic difference between the two sub-species. The number of chromosomes is 2n = 36 in wild boar and 2n = 38 in pig, respectively. This difference makes it possible to assign the "hybrid" status to wild boar individuals controlled with 37 or 38 chromosomes. However, it does not make it possible to determine the timing of the hybridization(s), nor to guarantee the absence of domestic admixture in an animal with 2n = 36 chromosomes. In order to analyze hybridization in greater detail and to avoid the inherent limitations of the cytogenetic approach, 362 wild boars (WB) recently collected in different French geographical areas and in different environments (farms, free ranging in protected or unprotected areas, animals with 2n = 36, 37 or 38 chromosomes) were genotyped on a 70K SNP chip. Principal component analyses allowed the identification of 13 "outliers" (3.6%), for which the proportion of the genome of "domestic" origin was greater than 40% (Admixture analyses). These animals were probably recent hybrids, having Asian domestic pig ancestry for most of them. For the remaining 349 animals studied, the proportion of the genome of "wild" origin varied between 83% and 100% (median: 94%).This proportion varied significantly depending on how the wild boar populations were managed. Local ancestry analyses revealed adaptive introgression from domestic pig, suggesting a critical role of genetic admixture in improving the fitness and population growth of WB. Overall, our results show that the methods used to monitor the domestic genetic contributions to wild boar populations should evolve in order to limit the level of admixture between the two gene pools.

Genetic diversity and population structure analysis of Philippine native pigs highlight five priority populations for conservation

“…In addition to the benefits of having high Ne , hybridization is known to introduce novel adaptive variations and further increase fitness (Adavoudi & Pilot, 2022 ). In fact, hybridization in French wild boar revealed adaptive introgression from domestic pigs (Mary et al., 2022 ). Our study suggests that a high Ne in native pigs can be achieved by hybridization with wild pigs, thus necessitating the comanagement of PhNPs and Philippine wild pigs.…”

Current Analytical Methods and Research Trends Are Used to Identify Domestic Pig and Wild Boar DNA in Meat and Meat Products

“…It is highly likely that domestic pigs sporadically crossed with wild boars [ 10 ]. The frequent hybridisation of these two breeds was found in the studies on the European population [ 10 , 11 , 12 , 13 ]. Studies of the MC1R (melanocortin 1 receptor) gene in the Polish population of wild boars also proved the existence of admixed genotypes [ 14 , 15 ].…”

“…As pigs and wild boars are closely related, and genetic introgression from domestic pigs into European wild boar has been proved [ 74 , 76 ], phylogenetically close taxa distinguishing requires introduction of high-throughput, SNP-based (SNP, Single Nucleotide Polymorphism) molecular techniques. A 70K SNP chip was used in a French study [ 13 ] to determine the timing of the hybridisation (s) and to check the domestic pig admixture in the wild boar population. The study revealed that among wild boars, 83% to 100% of animals had a genome of “wild” origin and local ancestry analyses showed adaptive introgression from a domestic pig.…”

Genomic evidence of genuine wild versus admixed olive populations evolving in the same natural environments in western Mediterranean Basin

“…Gene flows between domesticated species and their wild relatives have been identified in several studies in animals [ 1 – 3 ] and plant species [ 4 , 5 ]. This phenomenon is noted when cultivated genomic variants occur in unmanaged naturally occurring populations in natural environments.…”