Chloroplast genome and haplotype relationships unravel the genetic introgression and complex evolutionary history of East Asian Rosa section Synstylae roses (Rosaceae)

The chloroplast genomes of Sino-Japanese Synstylae species may have diverged along geographic gradients, influenced by the geographical and ecological complexity of East Asia and the climate oscillations during the Pleistocene. The recurring cycles of fragmentation and rejoining in Sino-Japanese Synstylae populations have allowed founder effects and genetic drift to drive divergence and diversification of their chloroplast genomes along these geographic gradients. The substantial incongruence between the chloroplast and nuclear phylogenies evidenced the prevalent genetic introgression within the Sino-Japanese Synstylae lineage. Additionally, two putative hybrid speciation events highlighted the role of genetic introgression in species diversification of the East Asian Synstylae lineage. This study substantiates the value of chloroplast genomes in elucidating genetic introgression and the unique evolutionary history of recently diverged and closely related East Asian Synstylae species.