Phylogenomics reveals distinct evolutionary lineages of Japanese Cinnamomum species in the Nansei Islands

Cinnamomum, a genus encompassing essential spices and medicinal plants, has undergone limited genome-scale exploration for Japanese species. The Nansei Islands, a sprawling 1,200-kilometer chain of islands situated between the Pacific Ocean and the East China Sea, serve as a crucial biogeographic region characterized by deep-sea barriers like the Tokara and Kerama Gaps.

To elucidate the phylogenetic connections among four native Nansei Island Cinnamomum species and ten related species, researchers combined chloroplast and nuclear genome data from this study with public datasets. Chloroplast genomes exhibited negligible structural variation among the four island species. However, nuclear genome data unveiled two separate evolutionary lineages in the Nansei Islands: C. yabunikkei, C. x durifruticeticola, and C. daphnoides constituted a unique lineage distinct from Sri Lankan, Indonesian, and Taiwanese lineages, while C. sieboldii was affiliated with a Taiwanese lineage.

By estimating ancestry, researchers discovered that C. x durifruticeticola and C. daphnoides inherited a shared ancestral component, whereas C. sieboldii possessed a singular, homogeneous ancestral component, implying a diminished ancestral diversity following divergence from the Taiwanese lineage. These discoveries illuminate previously unnoticed genomic differentiation among Japanese Cinnamomum species and imply that deep-sea barriers, dispersal, and prolonged isolation have sculpted their evolutionary trajectories.