Exploring phylogeny and genomic vulnerability of Melastoma (Melastomataceae) endemic to a World Natural Heritage site, the Bonin Islands

Melastoma (Melastomataceae) includes ca. 100 species across tropical to subtropical regions of Asia and Oceania. The Bonin Islands harbor three endemic taxa: M. tetramerum, M. tetramerum var. pentapetalum, and M. candidum var. alessandrense. Of these, M. tetramerum is critically endangered and faces near extinction in the wild. This study investigates the phylogenetic relationships among these endemic Melastoma species in the Bonin Islands based on the whole chloroplast genome and nuclear SNPs. The results revealed that M. candidum var. alessandrense was placed in the clade of the widespread East Asian M. candidum and has a distinct evolutionary origin from the other two taxa. The population genomics analyses (heterozygosity, rates of deleterious mutations, and numbers and lengths of runs of homozygosity) indicated lower genetic diversity and more vulnerable genomes of endemic Melastoma, especially M. tetramerum var. pentapetalum. M. tetramerum var. pentapetalum is not a target of any protection programs, however, conservation plans might be required for this variety because M. tetramerum var. pentapetalum would have a more vulnerable genome than M. tetramerum, which faces near extinction in the wild. This information can facilitate the development of effective conservation strategies in a precautionary way that anticipates imminent threats to the survival of the species.