Uncovering the Nanozostera japonica species complex suggests cryptic speciation and underestimated seagrass diversity.

The importance of marine angiosperms, or seagrasses, as foundation species for marine coastal ecosystems is in marked contrast to their low species number of only 70 described taxa. Seagrass species tend to have very similar overall morphologies dictated by hydrodynamic forces of the ocean environment. Moreover, they have inconspicuous and simple flowers, probably due to the absence of flower-pollinator interactions in the sea. We hypothesized that the seagrass species Nanozostera japonica, distributed from tropical to temperate latitudes in the North-Western Pacific, contains cryptic species. To test this, we assembled two chromosome-level reference genomes and conducted whole-genome resequencing at 17 locations throughout its native distribution. We identified two genetically divergent clades in the north and south of its range (hereafter Nj_N and Nj_S) that diverged some 4.16 million years ago. Hybrid individuals at a contact zone were either diploid F1-crosses or featured triploidy, indicating reproductive isolation. A large (42 Mb) reciprocally fixed chromosomal inversion between Nj_N and Nj_S possibly contributed to the formation of the reproductive isolation. We conclude that the N. japonica species complex is actually consisting of two different species. Further population genomic studies may reveal additional cryptic species, solving the conundrum why there are so few described seagrass species today.