Phylogenomics and evolution of the Acer section Lithocarpa

• Chloroplast genome and nuclear SNP datasets clarified Acer section Lithocarpa should be divided into three clades (series Lithocarpa , series Macrophylla, and Leipo group). • Series Macrophylla should be treated as a distinct section. • Introgression and ILS are key factors contributed to reticulate evolution in Acer series Lithocarpa. Maple trees are known for their graceful appearance and high ornamental value, thanks to their attractive leaf shapes and vibrant autumn foliage. However, the Acer phylogenetic relationships remain unclear, particularly the circumscription of the sections and the relationships between species within those sections. Section Lithocarpa is a typical group with an inconsistent circumscription, containing Lithocarpa and Macrophylla series and about nine species. Here, we used whole chloroplast genomes and nuclear SNP datasets to determine the circumscription of Acer section Lithocarpa infer the phylogenetic relationships, and explore the reticulate evolution in this section. The whole chloroplast genome data suggest that section Lithocarpa is not a monophyletic group, and includes three independent clades, such as series Lithocarpa , series Macrophylla, and the Leipo group including A. yangbiense and A. leipoense . These results support that series Macrophylla should be treated as a distinct section and the taxonomic status of A. yangbiense and A. leipoense in the Leipo group needs to be re-evaluated. We found significant incongruence among the nuclear and chloroplast phylogenies in the series Lithocarpa . The introgression signal detected by the d -statistic in the series Lithocarpa species indicated that introgression was the main cause of cytonuclear discordances. Incomplete lineage sorting (ILS) also contributed to phylogenetic discordance among A. sinopurpurascens, A. tsinglingense , and A. diabolicum . Our results highlight that introgression and ILS are key factors, resulting in the reticulate evolution in Acer .