Conclusion
Our study on the Callicarpa genus in the Bonin Islands provides
crucial insights into phylogenetic relationships, divergence patterns,
and speciation drivers. The ancestral ecotype ST of C.
subpubescens was over twofold older than the other species/ecotypes,
followed by ecotype SD, species P and G, ecotype S, and finally ecotype
SG, all diverging simultaneously. The concurrent diversification of
species/ecotypes adapted to different environments suggests a connection
to island aridification. Shifts from tall forests to lower forests with
increased forest edges and an increase in dry environments likely
triggered rapid phenotypic and genetic changes for adaptation, as
observed in other organisms. Future research will focus on identifying
genes associated with drought adaptation. Cryptic species were found
within C. subpubescens , with ecotypes SD and ST considered
distinct species based on leaf morphology, flowering phenology, and
genetic divergence patterns. Although genetically distinct, ecotypes S
and SG show no significant phenotypic differences and can be treated as
the same species. Ecotype SH, presumed to be a hybrid between ecotypes
ST and SG and found only on Hahajima Island, exhibited different
characteristics from its parent ecotypes. Long-distance seed dispersal
events likely contributed to the presence of the same ecotypes in
different island groups. Certain birds, such as the brown-eared bulbul,
Japanese wood pigeon, and jungle crow, are potential seed dispersers,
with estimated dispersal distances aligning with the longer distances
between islands. However, genetic differentiation among the same
ecotypes in different island groups suggests rare long-distance
dispersal. Our study provides a comprehensive understanding of
phylogenetic relationships, divergence patterns, and speciation
processes in Callicarpa in the Bonin Islands. Moreover, it
emphasizes the importance of hybridization, adaptive radiation in
response to changing environments, and long-distance seed dispersal in
shaping the evolutionary history of plants in oceanic islands.
ACKNOWLEDGEMENTS
The authors are grateful to K. Hayama for assistance in the field
survey; Drs. H. Kudo, M. Yasugi, A. Tezuka for their experimental
support; Drs. K. Uchiyama, A. Izuno, J.R.P. Worth and H. Mori for their
valuable advice in SNP analysis. We also thank Metropolis of Tokyo, the
Ministry of the Environmental Government of Japan, and Forestry Agency
of Japan for allowing this study. This research was conducted using the
Ogasawara Field Research Station of Tokyo Metropolitan University. This
work was funded by Grants-in-Aid for Science Research from the Japanese
Society for Promotion of Science (JP26290073, JP15K07203, JP21K05694),
the Environment Research and Technology Development Fund of the Ministry
of the Environment, Japan (4-1402, 4MF-2202).
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DATA ACCESSIBILITY AND BENEFIT-SHARING
Genotype data has been deposited at FigShare:
https://figshare.com/account/articles/24356665. The PacBio Sequel raw
reads are available at NCBI Sequence Reads Archive (DRA017215), and the
reference genome sequence of C. subpubescence has been deposited
at DDBJ/EMBL/GenBank under the accessions BTTA01000001–BTTA0106011.
AUTHOR CONTRIBUTIONS
SS, SN, IY and HK designed the research. SS, SN, KS and HK sampled
materials. SN and AJN performed the laboratory work. TUI performed de
novo genome assembly. SS and IT performed data analysis. All co-authors
discussed the results. SS and IT wrote the paper.
Table 1 Population characteristics of the three Callicarpaspecies in the Bonin Islands examined in this study.