Abstract
This study aimed to reveal the evolutionary timescale and processes underlying the diversity of Rubus in the Japanese Archipelago. We conducted molecular phylogenetic analyses of most native species (35 species), along with previously published data from 116 foreign species, based on nuclear ribosomal internal transcribed spacer (ITS) and chloroplast DNA sequences. Most of the northern species of Japan, that is, Rubus chamaemorus, R. pedatus, R. vernus, R. pseudojaponicus, and R. ikenoensis, were found to belong to anciently diverged lineages; in particular, R. ikenoensis formed a unique lineage distinct from other species. The other species diverged into two evolutionary groups. One included subg. Malachobatus, Chamaebatus, and sects. Pungentes, Idaeanthi, and Parvifolii (subg. Idaeobatus), which was further divided into two clades in the chloroplast phylogenies. Although the phylogenetic structures within this group were unresolved, R. sieboldii has been proven to be recently derived. The second group represented a well-supported clade, comprising sects. Microphylli, Corchorifolii, Peltati, and Rosifolii (subg. Idaeobatus) and suggested early Miocene diversification of this Asian lineage associated with character specialization in vegetative reproduction and leaf shape. This clade was further resolved into lower clades primarily representing the sectional classifications, although the placement of the earliest diverged species, R. sumatranus, R. peltatus, R. corchorifolius, and R. chingii, was incongruent among gene trees. At the lower taxonomic levels, R. illecebrosus, R. grayanus, and the thornless species of sect. Microphylli showed earlier divergence.
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Acknowledgements
We are grateful to Dr. Goro Kokubugata, Dr. Nobuyuki Tanaka, Mitsuru Ayabe, and Takahito Ideno for their help with the collection of leaf samples from botanical gardens, and to Dr. Hisato Kunitake, Dr. Yoichiro Hoshino, Michiharu Kato, and Dr. Shuri Kato for providing samples for this study. We also thank Ayana Okada and Akiko Hisamatsu for their support and contribution to the laboratory work. Dr. Hiroshi Yoshimaru, Kensuke Yoshimura, Yasuko Kawamata, and Chisako Furusawa are gratefully acknowledged for providing DNA samples and sequence data from the DNA-barcoding project. Our colleague, Dr. James Worth, kindly provided valuable comments that greatly improved the manuscript. We would like to thank Editage (www.editage.com) for English language editing.
Funding
This study received financial support from the Japanese Society for the Promotion of Science (JSPS KAKENHI Grant Numbers 20248017, 25292098, and 17K07571).
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Online Resource 1. List of samples.
Online Resource 2. Primers used in this study.
Online Resource 3. List of data from published studies.
Online Resource 4. Best-fit models of substitution.
Online Resource 5. ITS phylogenies based on BI and ML methods.
Online Resource 6. Chloroplast phylogenies based on BI and ML methods.
Online Resource 7. Partial chloroplast phylogenies based on BI and ML methods.
Online Resource 8. Marginal likelihood estimates of each molecular clock model.
Online Resource 9. The results of ancestral trait reconstruction.
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Kikuchi, S., Mimura, M., Naruhashi, N. et al. Phylogenetic inferences using nuclear ribosomal ITS and chloroplast sequences provide insights into the biogeographic origins, diversification timescales and trait evolution of Rubus in the Japanese Archipelago. Plant Syst Evol 308, 20 (2022). https://doi.org/10.1007/s00606-022-01810-6
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DOI: https://doi.org/10.1007/s00606-022-01810-6