Inferring complex evolutionary history of the closely related East Asian wild roses in Rosa sect. Synstylae...

The section Synstylae in the genus Rosa (Rosaceae) comprises 25-36 species and includes several major progenitors of modern rose cultivars. East Asian Synstylae species have recently diverged and are closely related, but their phylogenetic relationships remain unclear. In the present study, we employed conserved orthologue set (COS) markers and genome-wide nuclear orthologues to elucidate their phylogenetic relationships and unravel their complex evolutionary history.

Utilizing eight Rosaceae COS (RosCOS) markers, we analysed a total of 137 accessions representing 15 East Asian Synstylae taxa to establish a robust phylogenetic framework and reconstruct ancestral areas. Furthermore, we constructed the species tree for eight representative species and estimated their divergence times based on 1683 genome-wide orthologues. The species tree-gene tree coalescence time comparison, Patterson's D, f4-ratio and f-branch statistics were analysed to identify incomplete lineage sorting (ILS), genetic introgression and reticulation events using conserved orthologue data.

RosCOS markers and genome-wide orthologues effectively resolved a robust phylogeny of East Asian Rosa sect. Synstylae. Species divergence times estimated with genome-wide orthologues indicated that East Asian Synstylae species have recently diverged, with an estimated crown age of ~2 Mya. The rampant gene tree discordance indicated the possibility of ILS and/or genetic introgression. In the section Synstylae, deeper coalescence in the gene trees compared to the species tree suggested ILS as a source of gene tree discordance. Further, Patterson's D and f-branch statistics indicated that several lineages in the section were involved in genetic introgression.

We have unravelled the complex evolutionary history of East Asian Rosa sect. Synstylae, including recent species divergences, ILS and genetic introgression. Coupled with the geographical and ecological complexity of East Asia, ILS and genetic introgression may have contributed to the rapid diversification of East Asian Synstylae species by permitting adaptation to diverse environments.