TY - JOUR
T1 - 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
AU - Kikuchi, Satoshi
AU - Mimura, Makiko
AU - Naruhashi, Naohiro
AU - Setsuko, Suzuki
AU - Suzuki, Wajiro
N1 - Funding Information:
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 Information:
This study received financial support from the Japanese Society for the Promotion of Science (JSPS KAKENHI Grant Numbers 20248017, 25292098, and 17K07571).
Publisher Copyright:
© 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.
PY - 2022/6
Y1 - 2022/6
N2 - 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.
AB - 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.
KW - Ancestral trait
KW - Chloroplast gene
KW - Japanese Archipelago
KW - Phylogeny
KW - Ribosomal internal transcribed spacer
KW - Rubus
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UR - http://www.scopus.com/inward/citedby.url?scp=85128895725&partnerID=8YFLogxK
U2 - 10.1007/s00606-022-01810-6
DO - 10.1007/s00606-022-01810-6
M3 - Article
AN - SCOPUS:85128895725
VL - 308
JO - Plant Systematics and Evolution
JF - Plant Systematics and Evolution
SN - 0378-2697
IS - 3
M1 - 20
ER -