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Abstract A first integrative survey of the genusUsneain the southern Philippines, taking into account morphological, anatomical, chemical and molecular characters, resulted in the recognition of 20 taxa, including three species new to science:Usnea angulataAch.,U. baileyi(Stirt.) Zahlbr.,U. bismolliusculaZahlbr.,U. brasiliensis(Zahlbr.) Motyka,U. confusaAsah.,U. croceorubescensStirt.,U. dasaeaStirt.,U. himalayanaC. Bab.,U. krogianaP. Clerc,U. longissimaAch.,U. nidificaTaylor,U. norsticornutaA. Gerlach & P. Clerc sp. nov. (characterized by a moderately thick cortex and by the presence of norstictic acid),U. paleograndisoraA. Gerlach & P. Clerc sp. nov. (characterized by an orange subcortical pigmentation in the medulla, with enlarging soralia and a moderately thick and shiny cortex),U. pectinataTaylor,U. pygmoidea(Asahina) Y. Ohmura,U. rubicundaStirt.,U. rubrotincta(Stirt.) Zahlbr.,U. spinulifera(Vain.) Motyka,U. subscabrosaMotyka andU. yoshihitoiP. Clerc & A. Gerlach sp. nov. (characterized by a lax medulla with non-conglutinated hyphae).Usnea krogianais a new record for Asia;Usnea brasiliensis,Usnea confusaandU. croceorubescensare new records for the Philippines. This is the first phylogenetic study to include DNA sequences ofUsneafrom the Philippines. Molecular data from the ITS rDNA (76 newly generated sequences) are presented for most taxa except forU. himalayana,U. longissimaandU. subscabrosa. At least six further taxa remain unidentified, awaiting the collection of additional specimens. 

Lichens collected worldwide for centuries have resulted in millions of specimens deposited in herbaria that offer the potential to assess species boundaries, phenotypic diversification, ecology, and distribution. The application of molecular approaches to historical collections has been limited due to DNA fragmentation, but high-throughput sequencing offers an opportunity to overcome this barrier. Here, we combined a large dataset of ITS sequences from recently collected material and historical collections, obtained through Sanger, 454, or Illumina Sequencing, to test the performance of ITS barcoding in two genera of lichenized Basidiomycota: Cora and Corella. We attempted to generate new sequence data for 62 fresh specimens (from 2016) and 274 historical collections (collected between 1888 and 1998), for a final dataset of 1325 sequences. We compared various quantitative approaches to delimit species (GMYC, bPTP, ASAP, ABGD) and tested the resolution and accuracy of the ITS fungal barcoding marker by comparison with a six-marker dataset. Finally, we quantitatively compared phylogenetic and phenotypic species delimitation for 87 selected Cora species that have been formally described. Our HTS approach successfully generated ITS sequences for 76% of the historical collections, and our results show that an integrative approach is the gold-standard for understanding diversity in this group. 

Abstract Three species of lichenized basidiomycetes in the Dictyonema clade from southeastern North America are described as new to science: Cyphellostereum georgianum , C. jamesianum and Dictyonema lawreyi , all with a crustose-filamentous growth form. Based on ITS sequences, the species form well-supported monophyletic clades in a phylogeny and are represented by at least two specimens each. They are also distinguishable by morphological and anatomical characters. These new findings emphasize the importance of lichenological studies in North America, especially in historically understudied taxonomic groups, such as basidiolichens. This study is dedicated to James D. Lawrey on the occasion of his 70 th birthday. 

ABSTRACT True fungi (Fungi) and fungus-like organisms (e.g.Mycetozoa,Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses. 

Abstract Recent studies have uncovered remarkable diversity inDictyonemas.lat. basidiolichens, here recognized as subtribe Dictyonemateae. This group includes five genera and 148 species, but hundreds more await description. The photobionts of these lichens belong toRhizonema, a recently resurrected cyanobacterial genus known by a single species. To further investigate photobiont diversity within Dictyonemateae, we generated 765 new cyanobacterial sequences from 635 specimens collected from 18 countries. The ITS barcoding locus supported the recognition of 200 mycobiont (fungal) species among these samples, but the photobiont diversity was comparatively low. Our analyses revealed three main divisions ofRhizonema, with two repeatedly recovered as monophyletic (proposed as new species), and the third mostly paraphyletic. The paraphyletic lineage corresponds toR. interruptumand partnered with mycobionts from all five genera in Dictyonemateae. There was no evidence of photobiont‐mycobiont co‐speciation, but one of the monophyletic lineages ofRhizonemaappears to partner predominantly with one of the two major clades ofCora(mycobiont) with samples collected largely from the northern Andes. Molecular clock estimations indicate theRhizonemaspecies are much older than the fungal species in the Dictyonemateae, suggesting that these basidiolichens obtained their photobionts from older ascolichen lineages and the photobiont variation in extant lineages of Dictyonemateae is the result of multiple photobiont switches. These results support the hypothesis of lichens representing fungal farmers, in which diverse mycobiont lineages associate with a substantially lower diversity of photobionts by sharing those photobionts best suited for the lichen symbiosis among multiple and often unrelated mycobiont lineages.