Phylogenetic relationships among tibet Rubus (Rosaceae) species inferred from multiple chloroplast and nuclear DNA sequences

In this study, we collected 20 Tibet Rubus taxa from 4 sections, Idaeobatus, Malachobatus, Chamaebatus, and Cylactis of genus Rubus, as well as two outgroups, Fragaria vesca and Rosa banksiae. To investigate the phylogenetic relationships among Tibet Rubus species, the phylogeny was reconstructed by using chloroplast rbcL, rpl20-rps12, and trnG-trnS, nuclear ITS, GBSSI-2 and PEPC sequences. The final combined chloroplast DNA matrix consisted of 22 taxa and 2124 bp, of which 204 (9.60%) were variable and 94 (4.43%) parsimony informative. The nuclear DNA dataset included 22 accessions and 1897 aligned nucleotides that contained 374 (19.72%) variable and 146 (7.70%) parsimony informative sites. TIM1+I+G and TrN+G were selected as the best-fit models for the combined chloroplast and nuclear datasets, respectively. The Tibet Rubus is resolved as a monophyletic group and well supported through both chloroplast and nuclear datasets. Sect. Idaeobatus species have at least two independent evolutionary routes. Two sect. Malachobatus species clustered together with high support values. Then they were sister to three sect. Cylactis species in chloroplast tree, while to the subclade of major sect. Idaeobatus species in nuclear tree. This could be interpreted by frequent hybridization and genetic introgression. Rubus calycinus of sect. Chamaebatus forms a separate clade, suggesting its monophyly. To be concluded, the combined chloroplast and nuclear DNA sequences provided abundant information for the phylogenetic relationships among Tibet Rubus species.