Align or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study.

The Caloplaca saxicola group is the main group of saxicolous, lobed-effigurate species within genus Caloplaca (Teloschistaceae, lichen-forming Ascomycota). A recent monographic revision by the first author detected a wide range of morphological variation. To confront the phenotypically based circumscription of these taxa and to resolve their relationships morphological and ITS rDNA data were obtained for 56 individuals representing eight Caloplaca species 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 (with and without a priori alignments). Restricting phylogenetic analyses to unambiguously aligned portions of ITS was sufficient to resolve, with high bootstrap support, five of the eight previously recognized species within the C. saxicola group. However, phylogenetic resolution of all or most of the eight species currently included as two distinct subgroups within the C. saxicola group was possible only by combining morphological characters and signal from ambiguously aligned regions with the unambiguously aligned ITS sites or when the entire ITS1 and 2 regions were not aligned a priori and included as an integral component of a Bayesian analysis (BAli-Phy). The C. arnoldii subgroup includes C. arnoldii, comprising four subspecies, and the C. saxicola subgroup encompasses seven species. Contrary to the C. saxicola subgroup, monophyly of taxa included within the C. arnoldii subgroup and their relationships could not be resolved with combined ITS and morphological data. Unequivocal morphological synapomorphies for all species except C. arnoldii and C. pusilla are recognized and presented.

Phylogenetic reassessment of the Teloschistaceae (lichen-forming Ascomycota, Lecanoromycetes).

The Teloschistaceae is a widespread family with considerable morphological and ecological heterogeneity across genera and species groups. In order to provide a comprehensive molecular phylogeny for this family, phylogenetic analyses were carried out on sequences from the nuclear ribosomal ITS region obtained from 114 individuals that represent virtually all main lineages of Teloschistaceae. Our study confirmed the polyphyly of Caloplaca, Fulgensia and Xanthoria, and revealed that Teloschistes is probably non-monophyletic. We also confirm here that species traditionally included in Caloplaca subgenus Gasparrinia do not form a monophyletic entity. Caloplaca aurantia, C. carphinea and C. saxicola s. str. groups were recovered as monophyletic. The subgenera Caloplaca and Pyrenodesmia were also polyphyletic. In the subgenus Caloplaca, the traditionally recognized C. cerina group was recovered as monophyletic. Because this study is based solely on ITS, to maximize taxon sampling, the inclusion of phylogenetic signal from ambiguously aligned regions in MP (recoded INAASE and arc characters) resulted in the most highly supported phylogenetic reconstruction, compared with Bayesian inference restricted to alignable sites.

Phylogenetic study of Fulgensia and allied Caloplaca and Xanthoria species (Teloschistaceae, lichen-forming ascomycota).

Fulgensia Massal. & De Not. is a widespread genus with considerable morphological and ecological heterogeneity across species. For this reason, the taxonomic delimitation of this genus has been controversial. Relationships among species of Fulgensia, Caloplaca Th. Fr., and Xanthoria (Fr.) Th. Fr. (Lecanorales) were investigated based on a comprehensive phylogenetic analysis of 62 DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) region using maximum parsimony (MP) and likelihood (ML). Ambiguously aligned (INAASE coded characters) and unambiguous regions were analyzed separately and combined when using MP as the optimization criterion. All our analyses confirm the polyphyly of this genus as three distinct lineages: Fulgensia sensu stricto, F. australis, and F. schistidii. We report here that Caloplaca, Fulgensia, and Xanthoria together form two main sister lineages. One lineage includes Fulgensia schistidii (part of the C. saxicola group), Xanthoria, and most of the lobed Caloplaca species belonging to the Gasparrinia group. A second main lineage comprises the remaining Caloplaca species, Fulgensia sensu stricto, and F. australis. Therefore, the traditional generic level classification schemes for the family Teloschistaceae appear to be highly artificial. All three genera were found to be nonmonophyletic. We demonstrate here that the ITS is appropriate to resolve relationships across the Teloschistaceae. However, a combination of an MP analysis, in which ambiguously aligned regions are accommodated using INAASE, with an ML analysis, in which phylogenetic confidence is estimated using a Bayesian approach, is needed.