Details
| Original language | English |
|---|---|
| Pages (from-to) | 353-366 |
| Number of pages | 14 |
| Journal | American journal of botany |
| Volume | 95 |
| Issue number | 3 |
| Publication status | Published - Mar 2008 |
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.
Keywords
- Amplified fragment length polymorphism (AFLP), Bayesian inference, Parsimony, Phylogeny, Rosa, Rosaceae, Roses, UPGMA
ASJC Scopus subject areas
- Agricultural and Biological Sciences(all)
- Ecology, Evolution, Behavior and Systematics
- Biochemistry, Genetics and Molecular Biology(all)
- Genetics
- Agricultural and Biological Sciences(all)
- Plant Science
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In: American journal of botany, Vol. 95, No. 3, 03.2008, p. 353-366.
Research output: Contribution to journal › Article › Research › peer review
}
TY - JOUR
T1 - AFLP markers as a tool to reconstruct complex relationships
T2 - A case study in Rosa (Rosaceae)
AU - Koopman, Wim J.M.
AU - Wissemann, Volker
AU - De Cock, Katrien
AU - Van Huylenbroeck, Johan
AU - De Riek, Jan
AU - Sabatino, Gerda J.H.
AU - Visser, Dirk
AU - Vosman, Ben
AU - Ritz, Christiane M.
AU - Maes, Bert
AU - Werlemark, Gun
AU - Nybom, Hilde
AU - Debener, Thomas
AU - Linde, Marcus
AU - Smulders, Marinus J.M.
PY - 2008/3
Y1 - 2008/3
N2 - 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.
AB - 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.
KW - Amplified fragment length polymorphism (AFLP)
KW - Bayesian inference
KW - Parsimony
KW - Phylogeny
KW - Rosa
KW - Rosaceae
KW - Roses
KW - UPGMA
UR - http://www.scopus.com/inward/record.url?scp=41149149173&partnerID=8YFLogxK
U2 - 10.3732/ajb.95.3.353
DO - 10.3732/ajb.95.3.353
M3 - Article
AN - SCOPUS:41149149173
VL - 95
SP - 353
EP - 366
JO - American journal of botany
JF - American journal of botany
SN - 0002-9122
IS - 3
ER -