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- Title
Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK.
- Authors
Neubig, Kurt M.; Whitten, W. Mark; Carlsward, Barbara S.; Blanco, Mario A.; Endara, Lorena; Williams, Norris H.; Moore, Michael
- Abstract
Plastid DNA sequences have been widely used by systematists for reconstructing plant phylogenies. The utility of any DNA region for phylogenetic analysis is determined by ease of amplification and sequencing, confidence of assessment in phylogenetic character alignment, and by variability across broad taxon sampling. Often, a compromise must be made between using relatively highly conserved coding regions or highly variable introns and intergenic spacers. Analyses of a combination of these types of DNA regions yield phylogenetic structure at various levels of a tree (i.e., along the spine and at the tips of the branches). Here, we demonstrate the phylogenetic utility of a heretofore unused portion of a plastid protein-coding gene, hypothetical chloroplast open reading frame 1 ( ycf1), in orchids. All portions of ycf1 examined are highly variable, yet alignable across Orchidaceae, and are phylogenetically informative at the level of species. In Orchidaceae, ycf1 is more variable than matK both in total number of parsimony informative characters and in percent variability. The nrITS region is more variable than ycf1, but is more difficult to align. Although we only demonstrate the phylogenetic utility of ycf1 in orchids, it is likely to be similarly useful among other plant taxa.
- Subjects
PLANT molecular systematics; PLANT classification; PLANT evolution; ORCHIDS; CHLOROPLASTS; PHYLOGENY
- Publication
Plant Systematics & Evolution, 2009, Vol 277, Issue 1/2, p75
- ISSN
0378-2697
- Publication type
Article
- DOI
10.1007/s00606-008-0105-0