@ARTICLE{TreeBASE2Ref16218, author = {Dirk Kr?ger and Andrea Gargas}, title = {Secondary structure of ITS2 ribosomal RNA provides taxonomic characters for systematic studies ?? a case in Lycoperdaceae (Basidiomycota)}, year = {2008}, keywords = {}, doi = {}, url = {}, pmid = {}, journal = {Mycological Research}, volume = {}, number = {}, pages = {}, abstract = {The secondary structure of the ITS2 rDNA transcript (pre-rRNA) could provide information for identifying homologous nucleotide characters useful for cladistic inference of relationships and for selecting identifying taxonomic characters whose evolutionary past may be studied. This work compares the effect of several modern nucleotide alignment strategies, including those making use of structure data, on phylogenetic inference. From both the phylogenetic analyses and comparative secondary structure, implications for taxonomy and evolution of puffball fungi are discussed. Lycoperdaceae remain insufficiently resolved with present taxon and data sampling. Neither alignment allows statistically robust phylogenetic hypotheses under any current optimality criterion. The secondary structure data at this time are best used as accessory taxonomic characters as their phylogenetic resolving power and confidence in validity is limited compared to underlying nucleotide characters. We introduce a preliminary nomenclature convention to describe secondary structure for defining consensus features. These consensus structures are illustrated for the clades /Calvatia, /Handkea-Echinatum, /Vascellum, /Morganella, and /Plumbea-Paludosa (Bovista).} }

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