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Hypotrachyna is a speciose genus of primarily tropical and oceanic lichen-forming fungi. It includes species with distinct distribution patterns, such as pantropical, restricted and disjunct species. We used a dataset of mitochondrial SSU, nuclear ITS and LSU ribosomal DNA from 89 specimens to study the historical biogeography of the genus. We employed Bayesian and maximum likelihood approaches for phylogenetic analyses, a likelihood-based approach to ancestral area estimation, and a Bayesian approach to estimate divergence times of major lineages within the genus based on molecular evolutionary rates for ITS and a secondary calibration point at the Hypotrachyna clade – Parmeliopsis split. Our analyses suggest that the genus might have originated in the Neotropics during the Eocene and that the split of major lineages happened primarily during the Eocene and Oligocene. The major diversification within those clades is estimated to have occurred during the Miocene. Pantropical species distributions are explained by long-distance dispersal. A number of currently accepted species were found to be non-monophyletic, illustrating that the delimitation of species in the genus needs attention. [ABSTRACT FROM AUTHOR]

Accurate specimen identification is challenging in groups with subtle or scarce taxonomically diagnostic characters, and the use of DNA barcodes can provide an effective means for consistent identification. Here, we investigate the utility of DNA barcode identification of species in a cosmopolitan genus of lichen-forming fungi, Parmelia (Parmeliaceae). Two hundred and two internal transcribed spacer (ITS) sequences generated from specimens collected from all continents, including Antarctica, were analysed, and DNA barcodes of 14 species of Parmelia s.s. are reported. Almost all species show a barcode gap. Overall, intraspecific divergence values were lower than the threshold previously established for Parmeliaceae. However, the mean and range were elevated by deep barcode divergences in three species, indicating the likely occurrence of overlooked specieslevel lineages. Here, we provide a DNA barcode reference library with well-identified specimens sampled worldwide and sequences from most of the type material to enable easy and fast accurate sample identification and to assist in uncovering overlooked species in Parmelia s.s. Further, our results confirm the efficiency of the ITS region in the identification of species of Parmelia s.s. [ABSTRACT FROM AUTHOR]

We used a genetic distance approach in conjunction with molecular phylogeny to establish species boundaries and detect cryptic lineages in the Parmotrema reticulatum – P. pseudoreticulatum complex. The phylogeny of specimens from a broad geographic distribution was reconstructed from the internal transcribed spacer region. Pairwise genetic distances were calculated and compared to an intraspecific range defined for the parmelioid lichens to circumscribe species-level groups. Our results showed that P. reticulatum and P. pseudoreticulatum are polyphyletic, being comprised of at least seven well-supported lineages. In contrast, the genetic distance approach revealed ten cryptic lineages within the P. reticulatum – P. pseudoreticulatum complex. Neither morphology nor geography was conclusive in attempting to corroborate these genetic lineages. However FST indices suggest significant genetic differentiation between these lineages. Our results suggest that the morphology-based circumscriptions underestimated species in Parmotrema and that, in some cases, genetic distances may be used as an additional tool to determine species boundaries in morphologically cryptic species complexes. The most significant contribution of the present study is the application of a fast and accurate method to identify problematic groups and candidate species using the ITS locus with a genetic distances approach. [ABSTRACT FROM AUTHOR]

Recently, the number of cryptic species known has increased considerably, showing that species diversity has in many cases been underestimated in the past. Parmelia sulcata is a widely distributed species and one of the most common taxa in temperate Europe. The first intra-specific molecular studies on P. sulcata showed an unexpectedly high genetic variability. In the present work, we study the biodiversity of this taxon including specimens from four continents and using three molecular markers (nuITS, nuIGS rDNA, and partial β-tubulin gene). Two monophyletic groups of P. sulcata were encountered; one of these is epitypified as P. sulcata s. str and the other one is segregated as the new cryptic species P. encryptata sp. nov. Issues surrounding the lectotypification of Parmelia sulcata have also been elucidated. [ABSTRACT FROM AUTHOR]