We attempted to include a basal and a terminal representative from each clade to determine if the morphological characters used to distinguish taxonomic groups were synapomorphic. We also use independent four-gene analyses of Hygrophorus s.s. presented by Larsson (2010, and unpublished data). In this paper, we selleck compound used four gene regions: nuclear ribosomal ITS (ITS 1–2 and 5.8S), LSU (25S), and SSU (18S), and added the nuclear rpb2 6F to 7.1R region to as many of the backbone representatives as possible. We augmented the dataset used for the backbone with additional species and specimens that had at least an LSU sequence and performed a supermatrix analysis. In addition, we present paired
ITS-LSU phylogenies that have greater species representation for four overlapping segments of the Hygrophoraceae. We have included more species and genera than previous analyses, though not all of the species or GDC-0941 order collections that we sequenced are presented. Our initial analyses revealed many cases where the same name has been applied to multiple, molecularly distinguishable species. We therefore sought collections from the same region as the type location to serve as reference taxa. We have retained some unknown taxa with misapplied names, however, to show the depth of the taxonomic problems that exist. We have resolved some previously known issues, while others have been raised or are in need of further
work. The ITS analyses in Dentinger et
al. (unpublished data) has been especially helpful in resolving species complexes and misapplied names in Hygrocybe s.l. We use this paper to establish Carnitine palmitoyltransferase II a higher-level taxonomic framework for the Hygrophoraceae and to show where the remaining issues lie. Methods Species selection Lodge and Cantrell targeted several species per clade using previous unpublished preliminary analyses by Moncalvo, Vilgalys, Hughes and Matheny together with published molecular phylogenies by Moncalvo et al. (2000, 2002), Matheny et al. (2006), Lawrey et al. (2009) and Binder et al. (2010). Preference was for one basal and one distal taxon per clade and for types of genera and sections. In clades comprising difficult species complexes, we selected at least one named species known from a restricted geographic range (e.g., Hygrocybe graminicolor, Humidicutis lewellianae). The sequences that were learn more generated in this study together with those from GenBank and UNITE are given in Online Resource 1. We generated 306 sequences for this work: 90 ITS, 109 LSU, 65 SSU and 42 RPB2. The rpb2 sequences we analyzed contain indels that caused reading frame shifts so they are not accessible in GenBank using the BLASTx protocol. The taxa for the backbone analysis were winnowed to two (rarely three) per clade based on whether all or most of the four gene regions could be sequenced, preferably from the same collection.