@ARTICLE{TreeBASE2Ref19104, author = {Ester Gaya and Benjamin D. Redelings and Pere Navarro-Rosines and Xavier Llimona and Miquel de Caceres and Francois M. Lutzoni}, title = {Align, or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study}, year = {2010}, keywords = {Alignment, Caloplaca, Gasparrinia, lichens, molecular phylogeny, morphological phylogeny, morphospecies, species complex, Teloschistaceae}, doi = {}, url = {http://www.mycologia.org/}, pmid = {}, journal = {Mycologia}, volume = {}, number = {}, pages = {}, abstract = {The Caloplaca saxicola group is the main group of saxicolous lobed-effigurate species within the genus Caloplaca (Teloschistaceae, Lecanoromycetideae, lichen-forming Ascomycota). A recent monographic revision by the first author detected a wide range of morphological variation at both intra- and interspecific levels within this group. To confront the phenotypically-based circumscription of these taxa and to resolve their relationships, morphological and internal-transcribed spacer (ITS rDNA) data were obtained for 56 individuals representing eight Caloplaca species (11 taxa) belonging to the C. saxicola group. We tested the monophyly of these eight morphospecies by performing maximum parsimony, maximum likelihood, and two different types of Bayesian analyses (i.e., with and without a priori alignments). Restricting phylogenetic analyses to non-ambiguously aligned portions of ITS was sufficient to resolve, with high bootstrap support, five of the eight previously recognized species of Caloplaca within the C. saxicola group. However, only when morphological characters and signal from ambiguously aligned regions was recovered with coded characters (INAASE) and added to the non-ambiguously aligned ITS sites, or when the entire ITS 1 and 2 regions were not aligned a priori but rather were an integral component of a Bayesian analysis (BAli-Phy) was it possible to reach the level of phylogenetic resolution and support necessary to disentangle all or most of the eight species, currently included as two distinct subgroups within the C. saxicola group. The C. arnoldii subgroup includes the C. arnoldii species comprising four subspecies. The C. saxicola subgroup includes two well-supported main clades. Clade A encompasses C. arnoldiiconfusa, C. rouxii, and C. saxicola s. str. Clade B includes C. biatorina, C. decipiens, C. pusilla, and C. schistidii. Contrary to the C. saxicola subgroup, monophyly of taxa included within the C. arnoldii subgroup (C. arnoldii ssp. arnoldii, C. arnoldii ssp. clauzadeana, C. arnoldii ssp. nana, and C. arnoldii ssp. obliterata) and their relationships cannot be resolved with ITS and morphological data. Unequivocal morphological synapomorphies for all species except for C. arnoldii and C. pusilla are recognized and presented. } }

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