Sus scrofa domesticus reveals the genetic evolution of adaptive traits during early divergence

This is the authors' abstract. We don't add key points for this paper.

Domestication has generated extensive phenotypic diversity within Sus scrofa, producing marked divergence from wild boars in morphology, behavior, and metabolic physiology across numerous distinct breeds. Yet domestic pigs and wild boars remain interfertile, as effective reproductive barriers have not emerged. This condition, phenotypic divergence without reproductive isolation, makes domestic pigs an informative model for studying genetic processes during the earliest phases of speciation, capturing the tension between selection-driven innovation and gene flow–maintained continuity. Here, we categorize domestic pig breeds by historical gene flow intensity with wild boars (high vs. low) and examine their contrasting genetic architectures, assessing how environmental adaptation and artificial selection shape genomic homogeneity and heterogeneity. Using bile acid (BA) metabolism as an illustrative example, we show that domestic pigs experienced a functional shift in which cytochrome P450 family 8 subfamily B member 1 (CYP8B1) silencing and 4 subfamily A member 21 (CYP4A21) neofunctionalization replaced cholic acid (CA) with hyocholic acid (HCA) as the primary BA. This transition suggests that phenotypic diversification can precede reproductive isolation and that evolutionary changes in regulatory regions may occur before alterations in coding sequences.