An Integrative Phylogenomic Framework Quantifies the Dominant Role of Introgression in Phylogenetic Discordance among Diploid Oryza Species

ABSTRACT Background Phylogenomic studies frequently reveal widespread gene tree discordance, primarily arising from incomplete lineage sorting (ILS) and hybridization and/or introgression. Disentangling these processes is especially challenging in rapidly radiating lineages. The genus Oryza , with its rapid diversification and multiple genome types, exemplifies this pervasive phylogenetic incongruence. We integrated multiple genomic datasets including whole-genome resequencing, transcriptomes, and published genomes from diploid Oryza species. Concatenation and multispecies coalescent analyses recovered a robust, congruent species tree, placing the FF and GG genome groups as a monophyletic basal clade, followed by successive divergence of the EE, CC, BB, and AA lineages, a topology differing from some prior hypotheses. Results To assess the sources of discordance, we employed a suite of complementary phylogenomic methods. Quantifying introgression via Branch Lengths (QuIBL)-based model comparisons suggested that ∼74.17% of gene tree-species tree discordance is better explained by post-speciation introgression, whereas only ∼15.56% is consistent with ILS alone. Phylogenetic networks (PhyloNet) and allele-sharing statistics ( D -statistics, f -branch) corroborated these results, indicating widespread historical introgression both within and between genome groups. Furthermore, genome-wide scans using the f dM statistic localized introgressed genomic regions, which showed reduced interspecific divergence and were enriched for genes involved in stress responses and metabolism. Conclusions Taken together, our results demonstrate that historical introgression, not ILS, is the dominant force shaping phylogenetic discordance in diploid Oryza . The integrative phylogenomic framework implemented here, which quantifies the contributions of introgression versus ILS and maps the genomic footprint of gene flow, provides a replicable strategy for resolving complex evolutionary histories in other rapidly radiating lineages.