Phylogenomics reveal extensive phylogenetic discordances in Diospyros (Ebenaceae) of China.
The pantropical genus Diospyros L. (Ebenaceae) includes many economically valuable species prized for ebony timber and edible fruits. However, its high species diversity and morphological similarity pose significant challenges for understanding its evolutionary history. Previous phylogenetic studies have suggested a rapid adaptive radiation in Diospyros, but relationships among major lineages remain poorly resolved. Here, we reconstruct a comprehensive species-level phylogeny for Chinese Diospyros using whole genome sequencing data from 69 individuals representing 65 species. Phylogenomic analyses of a concatenated nuclear SNP matrix recovered six strongly supported major clades. Notably, we found substantial cytonuclear discordance between nuclear and plastid phylogenies. To investigate this conflict, we conducted extensive gene-tree concordance analyses (Phytop, MSCquartets) and quantified introgression and incomplete lineage sorting (ILS) using Dsuite, QuIB, and PhyloNet. These analyses revealed widespread, statistically significant gene-tree conflict, particularly at deep nodes. Our results demonstrate that the evolutionary history of Chinese Diospyros has been likely shaped by deep ILS-a probable genomic signature of rapid early radiation-alongside localized ancient hybridization, most prominently within the morphologically diverse Asian clade F. Recent gene flow appears to have played a limited role, although the relative contributions of ILS and introgression remain challenging to fully disentangle. These findings provide insights into the drivers of cytonuclear discordance and offer a robust phylogenetic framework for understanding the mechanistic role of ILS in diversification, with implications for adaptive radiation dynamics in species-rich tropical lineages.