Contrasting genomic routes to domestication in Occidental and Oriental pears

Despite their global importance, the genomic foundations of domestication in perennial fruit trees remain incompletely integrated across demography, selection, and structural variation. Pear (Pyrus spp.), domesticated in Europe and East Asia, provides a powerful system to compare alternative evolutionary trajectories within a balanced genomic framework. Using lineage-specific reference genomes, we analyzed nucleotide and transposable element (TE) polymorphisms across 396 well-documented wild and cultivated individuals spanning both regions. We uncovered weak domestication bottlenecks and extensive wild-crop gene flow, consistent with a protracted evolutionary process. In Europe, dessert and perry P. communis diverged independently based on fruit use. In East Asia, P. pyrifolia diversified geographically in China and Japan, following distinct domestication trajectories. Selection scans identify lineage- and population-specific targets associated with fruit texture, metabolism, and immunity. We find no support for the cost-of-domestication hypothesis: cultivated pears show a lower realized burden of deleterious mutations than their wild relatives. TE insertion patterns largely reflect demographic history, and are not enriched near the genes under positive selection. Together, our results support a protracted, multi-regional model of pear domestication shaped by recurrent gene flow and lineage-specific genomic architectures.