Data from: 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

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,
R. 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.