Genomic footprints of historical introgression between ancient lineages of wild Oryza AA-genome species with widely separated contemporary distributions

Phylogenetic incongruence is increasingly recognized as pervasive, yet the extent to which reticulate evolution occurs between groups separated by substantial geographical distances and deep phylogenetic divergence remains poorly characterized. In the Oryza AA-genome group--a model for plant speciation and domestication--the traditional bifurcation model posits that Australian Oryza meridionalis and African Oryza longistaminata occupy basal branches, distinct from the more recently diversified monophyletic clade comprising Asian and other African lineages, including major cultivars. However, recent evidence from endogenous viral sequences has hinted at unexpected genetic relatedness between African O. longistaminata and Asian Oryza sativa, which are geographically and phylogenetically distant. Here, we conducted a genome-wide survey across 11 Oryza species to systematically identify genomic regions exhibiting phylogenetic incongruence. Widespread phylogenetic discordance was observed, notably involving genomic segments in which O. longistaminata showed phylogenetic proximity to Asian species, contradicting their established deep divergence. To distinguish between introgression and incomplete lineage sorting, we performed four-taxon ABBA-BABA tests, which provided statistical support for introgression. Furthermore, divergence time estimates for these incongruent regions were younger than the species divergence times, suggesting historical introgression between the ancestors of lineages that are currently separated by vast geographical distances. Systematic assessments indicated that potential analytical artifacts, such as compositional bias and substitution saturation, were unlikely to explain the observations. These convergent lines of evidence suggest that ancient introgression had occurred between currently geographically separated and evolutionarily divergent Oryza lineages, leaving detectable footprints across their modern genomes.