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We describe 43 new lichen species in the family Graphidaceae, mainly from the Amazon basin: Fissurina bispora, F. diamantica, F. endothallina, F. lirelloreagens, F. reticulolirellina, Graphis inspersonorstictica, G. polystriatosubmuriformis, G. viridithallina, Heiomasia hypostictica, Leucodecton aurantiacum, Mangoldia thallolomoides, Myriochapsa negativa, M. triseptata, Myriotrema inspersosticticum, M. reticulatum, M. roseum, M. xanthonicum, Ocellularia coronatoverrucosa, O. griseosorediata, O. inspersomuriformis, O. inspersulascens, O. microschizidiata, O. norsorediata, O. pallidocolumellata, O. pedicellata, O. pertusella, O. pseudocyphellata, O. psorinspersa, O. psorsorediata, O. roseoisidiata, O. sorediopseudochapsa, O. verruciinspersa, O. vulcanica, O. wirthiotremoides, Phaeographis aureopruinosa, P. coccinea, P. fuscobilabiata, P. macrocephalica, P. norscalpturata, P. pallidoxanthonica, Rhabdodiscus lineatus, Stegobolus negativus, and Thalloloma xanthohypoleptum (the last species also from Puerto Rico). Relatively many are fertile but also form vegetative propagules. A few of the species contain no mature ascospores, but are so deviating from any other described species that we decided to describe them nonetheless. Also, we propose the following 22 new combinations for species of Graphidaceae that were previously described from Brazil and currently are accepted species but were so far assigned to the other genera: Allographa basaltica (≡ Graphis basaltica Kremp.), A. brevissima (≡ Graphis brevissima Fée), A. byrsonimae (≡ Graphina byrsonimae Redinger), A. heteroplaca (≡ Graphina heteroplaca Müll.Arg.), A. platypoda (≡ Phaeographina platypoda Zahlbr.), A. pseudoserpens (≡ Graphis pseudoserpens Chaves & Lücking), A. subargentata (≡ Graphis subargentata S.C.Feuerst., Dal Forno & Eliasaro), A. tricolorata (≡ Graphina tricolorata Redinger), Diorygma album (≡ Graphina alba Müll.Arg.), Fissurina adscripturiens (≡ Graphis adscripturiens Nyl.), F. egenella (≡ Graphina egenella Müll.Arg.), Graphis fasciata (≡ Ustalia fasciata Eschw.), Mangoldia lecideicarpa (≡ Graphina lecideicarpa Zahlbr.), O. endocrocea (≡ O. cinchonarum var. endocrocea Müll.Arg.), O. minarum (≡ Thelotrema minarum Vain.), Phaeographis atrolabiata (≡ Phaeographina atrolabiata Redinger), Phaeographis cheilomegas (≡ Graphis cheilomegas Fée), P. coriaria (≡ Phaeographina coriaria M.Wirth & Hale), P. crassa (≡ Platygramme crassa Fée), P. oxalifera (≡ Phaeographina oxalifera Redinger), P. scriptitata (≡ Phaeographina scriptitata C.W.Dodge), and Stegobolus trachodes (≡ Thelotrema trachodes Nyl.). Finally, we report several species new to Brazil or to one of the states: Allographa pitmanii new to Amapá, Cryptoschizotrema minus new to Alagoas, Glaucotrema glaucophaenum new to Amapá, Graphis pyrrhocheiloides new to Amapá, Graphis subserpentina new to Pará, Melanotrema astrolucens new to Brazil in Amazonas and Pará, Myriotrema hartii new to Amazonas, O. bullata new to Brazil in Pará, O. inspersipallens new to Brazil in Rondônia, O. jutaratiae new to Amapá, O. parvidisca new to Brazil in Amapá, O. rondoniana new to Alagoas, and Thelotrema wilsoniorum new to Brazil in Amapá. [ABSTRACT FROM AUTHOR]

A first integrative survey of the genus Usnea in 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 angulata Ach., U. baileyi (Stirt.) Zahlbr., U. bismolliuscula Zahlbr., U. brasiliensis (Zahlbr.) Motyka, U. confusa Asah., U. croceorubescens Stirt., U. dasaea Stirt., U. himalayana C. Bab., U. krogiana P. Clerc, U. longissima Ach., U. nidifica Taylor, U. norsticornuta A. Gerlach & P. Clerc sp. nov. (characterized by a moderately thick cortex and by the presence of norstictic acid), U. paleograndisora A. 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. pectinata Taylor, U. pygmoidea (Asahina) Y. Ohmura, U. rubicunda Stirt., U. rubrotincta (Stirt.) Zahlbr., U. spinulifera (Vain.) Motyka, U. subscabrosa Motyka and U. yoshihitoi P. Clerc & A. Gerlach sp. nov. (characterized by a lax medulla with non-conglutinated hyphae). Usnea krogiana is a new record for Asia; Usnea brasiliensis , Usnea confusa and U. croceorubescens are new records for the Philippines. This is the first phylogenetic study to include DNA sequences of Usnea from the Philippines. Molecular data from the ITS rDNA (76 newly generated sequences) are presented for most taxa except for U. himalayana , U. longissima and U. subscabrosa. At least six further taxa remain unidentified, awaiting the collection of additional specimens. [ABSTRACT FROM AUTHOR]

We present a novel identification tool called PhyloKey , based on the method of morphology-based, phylogenetic binning developed within the software package RAxML. This method takes a reference data set of species for which both molecular and morphological data are available, computes a molecular reference tree, maps the morphological characters on the tree, and computes weights based on their level of consistency versus homoplasy using maximum likelihood (ML) and maximum parsimony (MP). Additional units for which only morphological data are known are then binned onto the reference tree, calculating bootstrap support values for alternative placements. This approach is modified here to work as an identification tool which uses the same character coding approach as interactive keys. However, rather than identifying individual samples through a progressive filtering process when entering or selecting characters, query samples are binned in batch mode to all possible alternative species in the tree, with each placement receiving a bootstrap support adding to 100% for all alternative placements. In addition to the fact that, after scoring a character matrix, a large number of specimens can be identified at once in short time, all possible alternative identifications are immediately apparent and can be evaluated based on their bootstrap support values. We illustrate this approach using the basidiolichen genus Cora , which was recently shown to contain hundreds of species. We also demonstrate how the PhyloKey approach can aid the restudying of herbarium samples, adding further value to these collections and contributing with large quantitative data matrices to 'non-molecular museomics'. Our analysis showed that PhyloKey identifies species correctly with as low as 50% of the characters sampled, depending on the nature of the reference tree and the character weighting scheme. Overall, a molecular reference tree worked best, but a randomized reference tree gave more consistent results, whereas a morphological reference tree performed less well. Surprisingly, even character weighting gave the best results, followed by parsimony weighting and then maximum likelihood weighting. [ABSTRACT FROM AUTHOR]

A survey of the lichen family Graphidaceae in Macaronesia (Madeira, the Canary Islands, and the Azores) is presented, with detailed treatments for the genera Allographa, Fissurina, and Graphis. All other species are listed and new records provided. A key to all Graphicacy known from Macaronesia, except the thelotremoid species, is presented. The following species are newly described: Fissurina azorica, Fissurina elaiocarpoides, Fissurina nigrolabiata, and Topeliopsis juniperina. Many species are newly recorded for one or more islands of the three archipelagos. [ABSTRACT FROM AUTHOR]

[Display omitted] • The eco-evolutionary history of insular Caribbean Sticta was explored. • Species assemblages date back to the early Miocene and show strong biogeographic links to South America. • Colonization of the islands did not increase diversification rates. • Environmental variation most strongly explains taxonomic and phylogenetic turnover between island-level communities. Phylogenetic approaches to macroevolution have provided unique insight into evolutionary relationships, ancestral ranges, and diversification patterns for many taxa. Similar frameworks have also been developed to assess how environmental and/or spatial variables shape species diversity and distribution patterns at different spatial/temporal scales, but studies implementing these are still scarce for many groups, including lichens. Here, we combine phylogeny-based ancestral range reconstruction and diversification analysis with community phylogenetics to reconstruct evolutionary origins and assess patterns of taxonomic and phylogenetic relatedness between island communities of the lichenized fungal genus Sticta in the Caribbean. Sampling was carried out in the Greater Antilles (Cuba, Jamaica, Dominican Republic, and Puerto Rico) and Lesser Antilles (Dominica, Guadeloupe, and Martinique). Data for six molecular loci were obtained for 64 candidate Caribbean species and used to perform both macroevolutionary phylogenetics, which also included worldwide taxa, and phylobetadiversity analyses, which emphasized island-level communities. Our work uncovered high levels of island endemism (∼59%) in Caribbean Sticta. We estimate initial colonization of the region occurred about 19 Mya from a South American ancestor. Reverse migration events by Caribbean lineages to South America were also inferred. We found no evidence for increased diversification rates associated with range expansion into the Caribbean. Taxonomic and phylogenetic turnover between island-level communities was most strongly correlated with environmental variation rather than with geographic distance. We observed less dissimilarity among communities from the Dominican Republic and Jamaica than between these islands and the Lesser Antilles/Puerto Rico. High levels of hidden diversity and endemism in Caribbean Sticta reaffirm that islands are crucial for the maintenance of global biodiversity of lichenized fungi. Altogether, our findings suggest that strong evolutionary links exist between Caribbean and South American biotas but at regional scales, species assemblages exhibit complex taxonomic and phylogenetic relationships that are determined by local environments and shared evolutionary histories. [ABSTRACT FROM AUTHOR]

Thirty-one taxa of Gyalideopsis and its recent segregates (Ferraroa, Jamesiella, Lithogyalideopsis) are reported in a first assessment of the group from Costa Rica. Six species are described as new, all originating from perhumid montane rainforest: Gyalideopsis altamirensis Lücking & Umaña, with broadly sessile, brown apothecia and single-spored asci with muriform ascospores (hyphophores unknown); G. macarthurii Lücking, Umaña & Aptroot, with dark greyish brown apothecia having their margin covered by triangular thalline lobules and shortly bristle-shaped hyphophores producing moniliform diahyphae; G. pseudoactinoplaca Lücking & Chaves, with sessile, globose diahyphal bunches similar to those of Actinoplaca and resembling isidia (apothecia unknown), G. wesselsii Lücking, Sipman & Chaves, with verrucose thallus, dark greyish brown, applanate apothecia with single-spored asci producing muriform ascospores, and minutely spathulate, dark brown hyphophores with moniliform diahyphae, and Jamesiella chaverriae Chaves, Umaña & Lucking, with isidioid hyphophores (‘thlasidia’) which are flask-shaped and apically thinly ciliate (apothecia unknown). A further species, Gyalideopsis sp., with distinctly stipitate, umbelliform hyphophores, is not formally described due to the lack of apothecia and hyphophores. A further nine species are reported as new to Costa Rica: G. buckei, G. capitata, G. confluens, G. giganteoides, G. megalospora, G. napoensis, G. nepalensis, G. palmata, and Lithogyalideopsis zeylandica. A world-wide key to all presently known 94 taxa of Gyalideopsis and its recent segregates is presented, as well as a checklist. [ABSTRACT FROM AUTHOR]