@ARTICLE{TreeBASE2Ref16114, author = {Matthew G. King and Eric H. Roalson}, title = {Exploring evolutionary dynamics of nrDNA in Carex subgenus Vignea (Cyperaceae)}, year = {2008}, keywords = {}, doi = {}, url = {}, pmid = {}, journal = {Systematic Botany}, volume = {}, number = {}, pages = {}, abstract = {Nuclear ribosomal DNA (nrDNA) has been used for more than a decade in species level phylogenetic analyses. While this marker can often be a powerful phylogenetic marker, intra-individual polymorphisms of the internal and external transcribed spacers (ITS, ETS) can lead to problems in their use for phylogeny reconstruction. Incomplete concerted evolution coupled with hybridization and incomplete lineage sorting can further exacerbate these problems. Previous phylogenetic analyses using nrDNA of Carex subgenus Vignea suggest that the current sectional classifications maybe artificial. We endeavored to identify whether those issues of sectional limits were due to poor classification, or whether the issues of polyphyletic sections were an artifact of using ITS and ETS for phylogenetic studies within Vignea. Through comprehensive cloning we identified severe intra-individual polymorphisms and in many cases this led to the polyphyly of individuals. Furthermore, individuals identified with mutations in the 5.8S ribosomal subunit did not show a significant deviation in G-C percentage and free energy. Based on these results we suggest that nrDNA has undergone a complex evolutionary history within Carex subgenus Vignea. We also suggest that the use of nrDNA markers be abandoned in species level phylogenetic reconstructions in Vignea.} }

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