The Phylogeny of Rosoideae (Rosaceae) Based on Sequences of the Internal Transcribed Spacers (ITS) of Nuclear Ribosomal DNA and thetrnL/FRegion of Chloroplast DNA

Abstract

The phylogeny of Rosoideae was investigated using 44 species. Here we report new sequence data from the chloroplast trnL/F region as well as an increased sample of species. The analysis of these new data, along with previously used data from the nuclear ribosomal internal transcribed spacers (ITS), significantly increased resolution as well as confidence for Rosoideae phylogeny. Using both Bayesian inference and parsimony methods, we conducted analyses on the data sets separately and in combination. The resulting phylogenies are congruent with all well-supported clades of Rosoideae found in previous analyses of ITS or rbcL data. The support for these and other clades is improved, and we consider several clades to be supported well enough to be named. The following clades are given phylogenetic definitions: Sanguisorbeae and its subclades Agrimoniinae and Sanguisorbinae, Potentilleae and its subclades Fragariinae and Potentilla, Roperculina (Rosa + Sanguisorbeae + Potentilleae), and Sanpotina (Sanguisorbeae + Potentilleae). Potentilla includes the Potentilla anserina clade (Argentina) in our trnL/F and combined analyses, but this relationship is not resolved by ITS alone. The previously used genera Duchesnea (Potentilla indica), Horkelia, and Ivesia are strongly supported as nested within Potentilla. Comarum (Potentilla palustris and Potentilla salesowianum), Sibbaldiopsis (Potentilla tridentata), Dasiphora (Potentilla fruticosa), and Drymocallis (Potentilla arguta) join Alchemilla, Aphanes, Sibbaldia, Chamaerhodos, and Fragaria in the well-supported Fragariinae clade outside of Potentilla. The monophyly of both Potentilleae and Sanguisorbeae is well supported, and the clades correspond to previously named tribes with the exception of Alchemilla and its segregate Aphanes, which are nested within Potentilleae instead of in Sanguisorbeae. The position of Rubus is still not securely resolved.

Phylogeny of Rosa sections Chinenses and Synstylae (Rosaceae) based on chloroplast and nuclear markers

“…Chinenses, and three putative hybrids related to these two sections. According to previous studies (Eriksson et al, 2003;Potter et al, 2007Potter et al, , 2002, Potentilla parvifolia Fisch. and Rubus idaeopsis Focke were chosen as outgroups.…”

Range shifts of Potentilla fruticosa on the Qinghai-Tibetan Plateau during glacial and interglacial periods revealed by chloroplast DNA sequence variation

“…To determine the ancestral haplotype, Fragaria vesca was selected as an outgroup by referring to the phylogeny of the Rosaceae (Eriksson et al, 2003). Eriksson et al (2003) reported that the clade including P. fruticosa comprises a number of Potentilla species along with several other Range shifts of P. fruticosa A Shimono et al groups (namely Fragaria, Alchemilla, Chamaerhodos and Sibbaldia) and that F. vesca is the sister group of P. fruticosa. The out-group sequence for matK (Potter et al, 2002) was downloaded from GenBank (accession no.…”

Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach

“…Members of the sub-family Rosoideae, including Fragaria (strawberry) and Rubus (raspberry and blackberry), have the same base chromosome number of x = 7, similar fruit form, and are closely related based on chloroplast and nuclear DNA phylogenies (Potter et al 2007), as well as morphological data (Eriksson et al 2003). These lines of evidence suggest colinearity between the Fragaria and Rubus genomes; however, a lack of transferable markers has made genomic comparisons between these genera unachievable to date (Lewers et al 2005).…”