American Journal of Botany, (95): 353-366. (2008)
AFLP markers as a tool to reconstruct complex relationships: A case study in Rosa (Rosaceae).
Koopman WJM, Wissemann V, De Cock K, Van Huylenbroeck J, De Riek J, Sabatino GJ,
Visser D, Vosman B, Ritz CM, Maes B, Werlemark G, Nybom H, Debener T, Linde M, Smulders MJ.

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.

p. 357
In accordance with the phenogram, the sect. Pimpinellifoliae species form distinct clades in various positions in the tree, making this section polyphyletic. Rosa foetida, R. sericea var. omeiensis (both sect. Pimpinellifoliae), and R. persica (subgenus Hulthemia) are early derived groups in the MPT. A clade with R. roxburghii (subgenus Platyrhodon and R. hugonis (sect. Pimpinellifoliae) is slightly more derived. The R. spinosissima accessions occupy a much more derived position in the MPT as a sister group to sect. Caninae (clade 1 in Fig. 2 ).

pp. 357, 359
In the sect. Rosa cluster (2a), R. x damascena ‘Ispahan’ and R. gallica ‘Boule de Nanteuil’ cluster with the other cultivars, while a cluster of species including a wild R. gallica provenance (2b) is sister to this group. Therefore, we propose that the Rosa cluster has a mainly European genetic background. In line with this view, the cultivars in cluster 2a belong to the Damask, Centifolia, Gallica, Alba, Moss, and Portland cultivar groups (online Appendix S1). According to Wylie (1954) , these cultivar groups all have their main ancestry in the old European garden roses of the sect. Gallicanae (=Rosa), notwithstanding the fact that many of the groups also include hybrid influences of the China roses. The principal involvement of European roses in cluster 2a is further corroborated by the (more distant) affinity with sect. Caninae (cluster 1 in Fig. 1). Rosa canina was suggested as the female parent of the Alba roses (Wylie, 1954). Given their positions in clusters 2a/b, we propose that R. x damascena was the most important direct ancestor of the cultivars in the Northwest-European (Rosa) cluster, while R. gallica was a slightly more distant ancestor.