Conservation & local programs

PigARGs and gene flow between worldwide pig populations

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Abstract

The evolutionary history of domestic pigs is complex. Following their expansion from Southeast Asian islands across the Eurasian continent, wild boar populations were domesticated independently in multiple geographic regions. Around 200 years ago, the process of globalisation facilitated the intentional introgression of Chinese pig breeds into local European populations, significantly improving modern breeds such as Yorkshire and Landrace. However, the extent and structure of gene flow - both between wild and domestic pigs and among domestic breeds - remains unclear. This study aimed to reconstruct detailed demographic and admixture histories of global pig populations using Ancestral Recombination Graphs (ARGs). Whole-genome data from 1,241 pigs across 18 autosomal chromosomes were analyzed, encompassing approximately 34 million variants (8.3 GB compressed VCF; 166 GB uncompressed VCF). Tree sequences encoding of an ARG were inferred and dated using tsinfer and tsdate, generating an ARG containing 28.7 M local trees, 58.9 M nodes, 731.8 M edges, and 160.4 M mutations, occupying 5.33 GB (37.3 GB before compression). Genealogical nearest-neighbour (GNN) analyses were used to quantify ancestry composition, and cross-coalescent rate (CCR) analysis was applied to evaluate divergence and gene flow. The tree-sequence required 78% less storage than the VCF format, and its compressed storage was 36% lower than that of compressed VCF. GNN analysis revealed a primary split between Asian and European lineages and clear evidence of historical introgression in the sampled genomes. Asian ancestry in European samples ranges from ~6% in Yorkshire to higher levels of 14-16% in Berkshire and Hampshire. In the reverse direction, Chinese samples contained up to approximately 20% European ancestry (e.g., 13% in Meishan). Some wild boar samples had reduced shared ancestry with their reference populations, suggesting recent admixture with domestic pigs, although the Japanese wild boar remained genetically distinct. CCR profiles indicated that wild-boar divergence patterns were consistent with prior studies, while slower declines between domestic and wild lineages suggested frequent historical gene exchange. ARG-based approach provides an unprecedented detail of pig evolution and the formation of pig breeds, demonstrating how waves of gene exchange have shaped the genetic landscape of a key domesticated species.

Keywords: 2026

How to Cite:

Zhang, Y., Becher, H., Fortuna, G. & Gorjanc, G., (2026) “PigARGs and gene flow between worldwide pig populations”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286096. doi: https://doi.org/10.31274/wcgalp.23852

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