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AFLP markers as a tool to reconstruct complex relationships: A case study in Rosa (Rosaceae)
Author(s) -
Koopman Wim J. M.,
Wissemann Volker,
De Cock Katrien,
Van Huylenbroeck Johan,
De Riek Jan,
Sabatino Gerda J. H.,
Visser Dirk,
Vosman Ben,
Ritz Christiane M.,
Maes Bert,
Werlemark Gun,
Nybom Hilde,
Debener Thomas,
Linde Marcus,
Smulders Marinus J. M.
Publication year - 2008
Publication title -
american journal of botany
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.218
H-Index - 151
eISSN - 1537-2197
pISSN - 0002-9122
DOI - 10.3732/ajb.95.3.353
Subject(s) - biology , paraphyly , monophyly , subgenus , maximum parsimony , upgma , amplified fragment length polymorphism , phylogenetic tree , evolutionary biology , lineage (genetic) , coalescent theory , genus , zoology , botany , clade , genetics , genetic variation , genetic diversity , population , demography , sociology , gene
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.