Introgression shapes the genomic conflict landscape of Malus, revealing a reticulate backbone in a woody crop lineage

In woody lineages in particular, incomplete lineage sorting (ILS), introgression, and genome duplication can interact over long timescales to produce complex genomic histories that are not adequately summarized by a strictly bifurcating tree.

Here, we use Malus as a model woody genus to investigate how these processes structure conflict across a genus-scale phylogenomic framework. Using dense taxon sampling, hundreds of nuclear loci, plastid genomes, and genome-wide SNP summaries, we reconstruct a robust nuclear backbone for Malus and evaluate where discordance is concentrated and which processes best explain it. Nuclear analyses resolve eight major clades, whereas conflict is non-random and localized to recurrent hotspots rather than evenly distributed across the tree.