The genus Rosa has a complex evolutionary history caused by several factors, often in conjunction: extensive hybridization, recent radiation, incomplete lineage sorting, and multiple events of polyploidy. We examined the applicability of AFLP markers for reconstructing (species) relationships in Rosa, using UPGMA clustering, Wagner parsimony, and Bayesian inference. All trees were well resolved, but many of the deeper branches were weakly supported. The cluster analysis showed that the rose cultivars can be separated into a European and an Oriental cluster, each being related to different wild species. The phylogenetic analyses showed that (1) two of the four subgenera (Hulthemia and Platyrhodon) do not deserve subgeneric status; (2) section Carolinae should be merged with sect. Cinnamomeae; (3) subsection Rubigineae is a monophyletic group within sect. Caninae, making sect. Caninae paraphyletic; and (4) there is little support for the distinction of the five other subsections within sect. Caninae. Comparison of the trees with morphological classifications and with previous molecular studies showed that all methods yielded reliable trees. Bayesian inference proved to be a useful alternative to parsimony analysis of AFLP data. Because of their genome-wide sampling, AFLPs are the markers of choice to reconstruct (species) relationships in evolutionary complex groups.

The genus Rosa (Rosoideae, Rosaceae) revisited: molecular analysis of nrITS-1 and atp B-rbc L intergenic spacer (IGS) versus conventional taxonomy Sequences of the nrDNA internal transcribed spacer 1 (nrITS-1) and atp B-rbc L intergenic spacer (IGS) of the cpDNA were analysed for all sections of the genus Rosa L. (Rosoideae, Rosaceae) to study molecular infrageneric taxonomy and relationships of Rosa with respect to conventional taxonomy based upon morphological and anatomical data as well as phytochemical characters. The results suggest that Rosa in its traditional infrageneric circumscription is not reflected by molecular data. Cinnamomeae , Carolinae and Pimpinellifoliae are not monophyletic based on the molecular data and this is mirrored in conventional taxonomy that separates these sections by weak morphological characters such as sepal performance, existence of bracts, and number of flowers per inflorescence. Section Pimpinellifoliae is split by the monotypic sections Laevigatae , Platyrhodon , Bracteatae and Hesperhodos . Section Caninae is a natural allopolyploid group characterized by its autapomorphic ITS C-type and Canina-meiosis. CpDNA subdivides sect. Caninae into two natural clusters of eglandular and glandular species. NrITS shows sect. Synstylae / Indicae to be the direct sister group to sect. Caninae , not Rosa ( Gallicanae ) although both groups are morphologically characterized by pinnate sepals. From our molecular data sect. Indicae and sect. Synstylae are consectional. The highest taxonomic rank below the generic level should be the sectional status.

The European dogroses (Rosa sect. Caninae (DC.) Ser.) are characterized by a unique meiosis system ("canina-meiosis"), which controls the heterogamous development of tetraploid egg cells and haploid pollen grains resulting in a pentaploid somatic status. This permanent anorthoploidy is supposed to have originated by a hybridization event in the postglacial period. In this study we present molecular evidence by an analysis of nuclear ribosomal DNA data that dogroses are complex allopolyploids resulting from multiple hybridization events. As previously described, the nrITS-1 region does not undergo concerted evolution in dogroses. Thus, different ITS-1 sequences persist within single individuals. Secondary structure predictions do not point to the existence of pseudogenes within these ITS-1 types. Our data suggest that the pentaploid Caninae genome originated from different members of nondogroses and the now extinct Protocaninae.

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