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(American Journal of Botany. 2008;95:353-366.)
© 2008 Botanical Society of America, Inc.

Systematics and Phytogeography

AFLP markers as a tool to reconstruct complex relationships: A case study in Rosa (Rosaceae)1

Wim J. M. Koopman2,9,10, Volker Wissemann3, Katrien De Cock4, Johan Van Huylenbroeck4, Jan De Riek4, Gerda J. H. Sabatino2, Dirk Visser2, Ben Vosman2, Christiane M. Ritz5, Bert Maes6, Gun Werlemark7, Hilde Nybom7, Thomas Debener8, Marcus Linde8 and Marinus J. M. Smulders2

2 Plant Research International, Wageningen UR, P.O. Box 16, 6700 AA Wageningen, The Netherlands 3 Institut fuer Allgemeine Botanik und Pflanzenphysiologie AG Spezielle Botanik, Justus-Liebig-Universitaet Giessen, Senckenbergstr. 17 35390 Giessen, Germany 4 Unit Plant, Applied Genetics and Breeding, Institute for Agricultural and Fisheries Research, Caritasstraat 21, 9090 Melle, Belgium 5 Department of Systematic Botany, Friedrich Schiller Universität Jena, Philosophenweg 16 07743 Jena, Germany 6 Ecologisch Adviesbureau Maes, Achter Clarenburg 2, 3511 JJ Utrecht, The Netherlands 7 Balsgård-Department of Plant Breeding and Biotechnology, Swedish University of Agricultural Sciences, Fjälkestadsvägen 459, 291 94 Kristianstad, Sweden 8 Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuserstrasse 2 30419 Hannover, Germany

ABSTRACT

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.

Key Words: amplified fragment length polymorphism (AFLP) • Bayesian inference • parsimony • phylogeny • Rosa • Rosaceae • roses • UPGMA






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