Bayesian Data Analyses Research Articles

Aeschynomene chicocesariana, a Striking New Unifoliolate Legume Species from the Brazilian Chapada Diamantina and its Phylogenetic Placement in the Dalbergioid Clade

Abstract—Unifoliolate leaves are relatively rare in the species-rich dalbergioid clade of papilionoid legumes (Leguminosae, Papilionoideae). For the pantropical, diverse genus Aeschynomene (ca. 180 species), the only known record of unifoliolate species described so far is the savanna-inhabiting A. simplicifolia from Chapada dos Veadeiros in Goiás, Brazil. The current work provides a description, illustrations, and a distribution map of another unifoliolate species, Aeschynomene chicocesariana, which was newly discovered in the rupestrian grasslands of Chapada Diamantina in Bahia, Brazil. Bayesian phylogenetic analyses of DNA sequence data (nuclear ribosomal ITS/5.8S and the plastid genes matK and trnL intron) have unequivocally placed A. chicocesariana with the rest of Aeschynomene species that are traditionally placed within Aeschynomene sect. Ochopodium. This result agrees with the shared morphology of A. chicocesariana and members of that section.

Molecular phylogeny and divergence times of the genus Hedysarum (Fabaceae) with special reference to section Multicaulia in Southwest Asia

A total of 93 species of Hedysarum from diverse biogeographic regions, in particular from southwest Asia, were included in phylogenetic analyses using nuclear (ITS) and plastid DNA sequences (trnL–trnF and matK). Maximum likelihood and Bayesian analyses of combined plastid data retrieved Hedysarum as monophyletic, whereas phylogenetic analyses of the nuclear data inferred Hedysarum as non-monophyletic. In both datasets, Hedysarum comprised three distinct and well-supported clades corresponding to sections Hedysarum, Stracheya and Multicaulia. The latter section fell into two distinct lineages, taxonomically redefined as H. subsects. Multicaulia and Crinifera. Thus, our results did not support the monophyly of the three traditionally recognized subsections of Multicaulia. Furthermore, within H. subsect. Crinifera, several species groups were recognized. Bayesian divergence time estimation suggested that the initial radiation of Hedysarum and the subsequent divergence of its major clades started in the middle Miocene and extended into the Pliocene and Pleistocene. Based on the molecular phylogenetic results, an updated taxonomic treatment is provided for H. subsects. Multicaulia and Crinifera as well as for H. sect. Stracheya expanded to include H. tibeticum plus four species traditionally placed in H. subsect. Subacaulia. For species of H. sect. Stracheya, a determination key is given.

Phylogeny, character evolution and tribal classification in Crambinae and Scopariinae (Lepidoptera, Crambidae)

AbstractCrambinae (2047 spp.) and Scopariinae (577 spp.) are two major groups of pyraloid moths with a worldwide distribution. Their larvae feed predominantly on Poales and Bryophyta, with many cereal crop pests. We present the first molecular phylogeny of the two groups based on five nuclear genes and one mitochondrial gene (total = 4713 bp) sampled for 58 crambine species representing 56 genera and all tribes, 33 scopariine species representing 12 genera, and species in several other crambid lineages. Maximum likelihood and Bayesian analyses of the molecular data resolve suprageneric relationships in Crambinae and Scopariinae, whereas relationships between these and other subfamilies remain ambiguous. Crambinae and Scopariinae are each recovered as monophyletic groups, and Erupini, formerly regarded as an ingroup of Midilinae, is recovered as a possible sister group of Crambinae. The tree topology suggests the following two major changes within Crambinae: Prionapterygini Landry syn.n. of Ancylolomiini Ragonot stat. rev. and Myelobiini Minet syn.n. of Chiloini Heinemann. Argyriini Munroe is monophyletic after the transfer of Pseudocatharylla Bleszynski and Vaxi Bleszynski to Calamotrophini. Crambini, Diptychophorini and Haimbachiini are monophyletic after the exclusion of Ancylolomia Hübner, Euchromius Guenée, Micrelephas Dognin and Miyakea Marumo from Crambini, as well as Microchilo Okano from Diptychophorini. Euchromiini tribe n. is described for Euchromius. Microcramboides Bleszynski syn.n. and Tortriculladia Bleszynski syn.n. are synonymized with Microcrambus Bleszynski. In Scopariinae, Caradjaina Leraut syn.n. and Cholius Guenée syn.n. are synonymized with Scoparia Haworth, and, in addition, Dasyscopa Meyrick syn.n., Dipleurinodes Leraut syn.n. and Eudipleurina Leraut syn.n. are synonymized with Eudonia Billberg. Micraglossa melanoxantha (Turner) (Scoparia) comb.n. is proposed as a new combination. We analysed 27 morphological characters of wing venation, tympanal organs, male and female genitalia, as well as host plant data and egg‐laying behaviour. The ancestral character‐state reconstructions confirmed previous apomorphies and highlighted new apomorphies for some of the newly recovered clades. The derived, nonadhesive egg‐dropping behaviour is found to have evolved at least twice in Crambinae and is associated with the use of Pooideae as host plants.This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:1A84282D‐930A‐4C32‐8340‐D681BFF27A12.

Bayesian Extraction of Jet Energy Loss Distributions in Heavy-Ion Collisions.

Based on the factorization in perturbative QCD, a jet cross section in heavy-ion collisions can be expressed as a convolution of the jet cross section in p+p collisions and a jet energy loss distribution. Using this simple expression and the Markov Chain MonteCarlo method, we carry out Bayesian analyses of experimental data on jet spectra to extract energy loss distributions for both single inclusive and γ-triggered jets in Pb+Pb collisions with different centralities at two colliding energies at the Large Hadron Collider. The average jet energy loss has a dependence on the initial jet energy that is slightly stronger than a logarithmic form and decreases from central to peripheral collisions. The extracted jet energy loss distributions with a scaling behavior in x=Δp_{T}/⟨Δp_{T}⟩ have a large width. These are consistent with the linear Boltzmann transport model simulations, in which the observed jet quenching is caused on the average by only a few out-of-cone scatterings.

Multi-gene phylogeny and morphotaxonomy of Phaeosphaeria ampeli sp. nov. from Ficus ampelas and a new record of P. musae from Roystonea regia

Phaeosphaeria ampeli is a new species collected from dead leaves of Ficus ampelas in Fanlu Township area, Dahu forest, Chiayi, Taiwan. Phaeosphaeria musae is a new record from dead leaves of Roystonea regia. Both species are described, illustrated and compared with similar species. Phaeosphaeria ampeli is distinguished from other Phaeosphaeria species based on distinct size differences of the ascomata, asci, ascospores and analyses of DNA sequence data. Maximum parsimony, maximum likelihood and Bayesian inference analyses of combined ITS, LSU, SSU and tef1-α sequence data are used to clarify the phylogenetic affinities of the species.

Genetic data of museum specimens allow for inferring evolutionary history of the cosmopolitan genus Sirthenea (Heteroptera: Reduviidae).

Among the 30 known genera within subfamily Peiratinae, only the genus Sirthenea has a cosmopolitan distribution. The results of our studies are the first comprehensive analysis concerning one of the representatives of mentioned subfamily based on joint phylogenetic analyses of molecular and morphological data as well as molecular dating. A total of 32 species were included into the dataset with all known species of the genus Sirthenea. Material of over 400 dry specimens was examined for the morphological part of this study. The cosmopolitan distribution of Sirthenea and the inaccessibility of specimens preserved in alcohol required the extraction of DNA from the dried skeletal muscles of specimens deposited in 24 entomological collections. The oldest specimens used for the successful extraction and sequencing were collected more than 120 years ago in India. We performed Bayesian Inference analyses of molecular and morphological data separately, as well as combined analysis. The molecular and morphological data obtained during our research verify the correlation of the divergence dates of all known Sirthenea species. Results of the relaxed molecular clock analysis of the molecular data show that, the genus Sirthenea started diverging in the Late Cretaceous into two clades, which subsequently began to branch off in the Paleocene. Our results of phylogenetic analyses suggest that the fossula spongiosa and its development could be one of the most important morphological characters in the evolution of the genus, most likely associated with the ecological niche inhabited by Sirthenea representatives. Confirmation of the results obtained in our studies is the reconciliation of the evolutionary history of Sirthenea with the biogeographical processes that have shaped current global distribution of the genus.

Molecular phylogenetic relationships reveal taxonomic and biogeographic clades in Dianella (flax lilies; Asphodelaceae, Hemerocallidoideae)

A phylogeny of Dianella is presented based on Bayesian and maximum parsimony analyses of a combined molecular data set using three chloroplast markers (trnQUUG–5'rps16, 3'rps16–5'trnK(UUU) and rpl14–rps8–infA–rpl36) and two nuclear markers (ITS and ETS). Accessions included most Dianella species, including all species from Australia, the centre of diversity for the genus, and related outgroup genera Eccremis, Stypandra, Thelionema and Herpolirion. The phylogeny showed Stypandra sister to Herpolirion + Thelionema, and confirmed the monophyly of Dianella. Within Dianella, a number of clades were resolved that revealed biogeographic relationships. Accessions from south-western Australia (extending into South Australia) formed the earliest diverging clade, followed by D. serrulata from New Guinea, sister to all other clades of Dianella from Australia and other regions. Tropical North Queensland species, including the D. pavopennacea complex, were related to a clade of accessions from New Caledonia and the Hawaiian Islands in the Pacific, and a clade that included samples of D. carolinensis (Caroline Islands) and the widespread D. ensifolia from South-East Asia and across the Indian Ocean to Mauritius and Madagascar. However, D. ensifolia is not monophyletic, with accessions from Japan and Taiwan related to a clade of Queensland samples that are part of the D. revoluta complex. Three New Zealand species (diploid, 2n = 16) were found to be related to Norfolk Island D. intermedia (type locality; octoploid, 2n = 64). In contrast ‘D. intermedia’ from Lord Howe Island was resolved as sister to the eastern Australian D. caerulea complex. The phylogenetic results indicate the need for taxonomic revision, particularly revision of the species ‘complexes’ D. longifolia and D. caerulea in Australia, and recognition of more than one species within D. ensifolia and within D. sandwicensis on the Hawaiian Islands.

Molecular taxonomy reveals the sexual morph of Nodulosphaeria digitalis in Phaeosphaeriaceae from Campanula trachelium in Italy

The fungal genus Nodulosphaeria is one of the oldest phaeosphaeriaceous genera that comprises saprobic, endophytic and pathogenic species associated with a wide variety of substrates. There are 71 species epithets listed under Nodulosphaeria in Index Fungorum and most of these published records lack illustrations and descriptions, or DNA sequence data and thus it is challenging to confirm their names or investigate taxonomic relationships. In this study, we report the sexual morph of Nodulosphaeria digitalis, a terrestrial saprobe belonging to the genus Nodulosphaeria (Phaeosphaeriaceae, Pleosporales), on stems of Campanula trachelium from Arezzo Province, Italy. This is the first record of a Nodulosphaeria taxon on Campanulaceae. Maximum likelihood, Maximum parsimony and Bayesian inference analyses of combined ITS, LSU, SSU and TEF1-α sequence data reveal that the novel isolate belongs to the family Phaeosphaeriaceae and nests with Nodulosphaeria digitalis with strong bootstrap support. The detailed descriptions and illustrations of the sexual morph of N. digitalis, an updated phylogenetic tree for the genus Nodulosphaeria are provided.

BsamGP: An R Package for Bayesian Spectral Analysis Models Using Gaussian Process Priors

The Bayesian spectral analysis model (BSAM) is a powerful tool to deal with semiparametric methods in regression and density estimation based on the spectral representation of Gaussian process priors. The bsamGP package for R provides a comprehensive set of programs for the implementation of fully Bayesian semiparametric methods based on BSAM. Currently, bsamGP includes semiparametric additive models for regression, generalized models and density estimation. In particular, bsamGP deals with constrained regression models with monotone, convex/concave, S-shaped and U-shaped functions by modeling derivatives of regression functions as squared Gaussian processes. bsamGP also contains Bayesian model selection procedures for testing the adequacy of a parametric model relative to a non-specific semiparametric alternative and the existence of the shape restriction. To maximize computational efficiency, we carry out posterior sampling algorithms of all models using compiled Fortran code. The package is illustrated through Bayesian semiparametric analyses of synthetic data and benchmark data.

Selecting the Best Method among Several: Bayesian and Classical Data Analyses Comparison in a Complex Microbiological Validation Setting

Statistical procedures to compare new methods to gold standards, after validation of microbiological food methods, exist. However, evaluation of the best microbiological detection method among several is more challenging; there is little precedent in scientific literature. Our work compares Bayesian hierarchical (BH), Bayesian logistic Anova-like (BL-AL) and Classical logistic (CL) models using an original validation study, based on Health Canada’s Microbiological Methods Committee guidelines.The validation study design includes 6 microbiological methods, 13 food panels of 20 samples each, and 10 laboratories, and theoretically generates 780 sub-groups, reduced to 198 after quality review. In classical statistics this would lead to 231 null hypothesis tests, requiring significance level (α) correction for multiple comparisons. Assuming non-informative priors, BH and BL-AL estimations include meaningful parameters (e.g. method detection rate (DR), DR differences between methods, etc.), reallocate their credibility based on observed data, and provide posterior distributions and 95% high credibility intervals (HCI). Joining HCI with pre-defined Regions of Practical Equivalence (ROPEs) allows for null hypotheses decision making: rejection, acceptance, or no decision.BH and BL-AL give similar results and posteriors. Posteriors’ modes are nearly identical to best-estimates computed with CL. Statistical conclusions will be similar between BH, BL-AL and CL if, and only if, significance level (α) is corrected for multiple comparisons. Nevertheless only Bayesian allows null hypotheses acceptance and a clean ranking of the 6 microbiological methods using posterior densities within, below, and above ROPE limits.Using flat priors, it isn’t surprising to find similarities between Bayesian and Classical methods. However, while avoiding classical paradigm misinterpretation issues, the Bayesian framework provides informative and meaningful results with no multiple comparison issues.

Studies on Parmulariaceae I. A phylogeny based on available sequence data; introducing Parmulariales ord. nov., and Hemigraphaceae, Melaspileellaceae and Stictographaceae fam. nov.

The family Parmulariaceae comprises three polyphyletic genera, but with very little data in GenBank and is presently placed in the order Asterinales. In this study, we re-analyze the available sequence data for taxa of the family and re-examine the type species of Hemigrapha, Inocyclus and Parmularia. The phylogenetic tree generated from maximum likelihood and Bayesian analyses of combined LSU-SSU sequence data demonstrate the relationships among Hemigrapha, Inocyclus and Parmularia species, and the relations of Buelliella, Karschia, Labrocarpon, Lembosia, Melaspileella, Melaspileopsis and Stictographa. We introduce Parmulariales ord. nov. to accommodate Parmulariaceae and the order Asterinales accommodates Asterinaceae, Asterotexaceae, Hemigraphaceae fam. nov., Melaspileellaceae fam. nov. and Stictographaceae fam. nov. Notes for each new order and families are provided. We confirm that Asterinaceae sensu lato is distant from Asterinaceae sensu stricto in the phylogenic analysis. The classification presented here is provisional, as more species are needed to re-collected and sequenced. We expect further support for our ordinal and familial lineages, as well as further novel lineages.

The African timber tree Entandrophragma congoense (Pierre ex De Wild.) A.Chev. is morphologically and genetically distinct from Entandrophragma angolense (Welw.) C.DC

Interpreting morphological variability in terms of species delimitation can be challenging. However, correcting species delineation can have strong implications for the sustainable management of exploited species. Up to now, species delimitation between two putative timber species from African forests, Entandrophragma congoense and E. angolense, remained unclear. To investigate their differences, we applied an integrated approach which combines morphological traits and genetic markers. We defined 13 morphological characters from 81 herbarium specimens and developed 15 new polymorphic microsatellite markers to genotype 305 samples (herbarium samples and specimens collected in the field across the species distribution ranges). Principal component analysis (PCA) of morphological data and the Bayesian clustering analyses of genetic data were used to assess differentiation between putative species. These analyses support two well-differentiated groups (FST = 0.30) occurring locally in sympatry. Moreover, these two groups present distinct morphological characters at the level of the trunk, leaflets, and seeds. Our genetic markers identified few individuals (4%) that seem to be hybrids, though there is no evidence of genetic introgression from geographic patterns of genetic variation. Hence, our results provide clear support to recognize E. congoense as a species distinct from E. angolense, with a much lower genetic diversity than the latter, and that should be managed accordingly. This work highlights the power of microsatellite markers in resolving species boundaries.

Saprobic Lophiostomataceae (Dothideomycetes): Pseudolophiostoma mangiferae sp. nov. and Neovaginatispora fuckelii, a new record from Mangifera indica

Pseudolophiostoma mangiferae, isolated from a dead stem of Mangifera indica, collected in Fanlu Township area, Dahu village in Chiayi, Taiwan (Elevation 634 m) and is introduced as a new species based on morphological data and DNA sequence analyses. Maximum parsimony, Maximum likelihood and Bayesian analyses of combined ITS, LSU, SSU and tef1-α sequence data were performed to clarify the phylogenetic affinities of the species. Pseudolophiostoma mangiferae is distinguished from the other Pseudolophiostoma species based on distinct size differences in ascomata, asci, ascospores and DNA sequence data. In addition, Neovaginatispora fuckelii is described as a new record from Taiwan. Both species are compared with other similar species and comprehensive descriptions and micrographs are provided.

Common Physical Properties Improve Metaphor Effect Even in the Context of Multiple Examples

A previous experimental analog study by Sierra et al. International Journal of Psychology and Psychological Therapy, 16, 265–279 (2016) showed that including common physical properties of participants’ pain in the metaphor content improved its effect in promoting pain tolerance. Using a 2x2 factorial design, this study analyzed the effect of common physical properties in the context of multiple examples of functionally equivalent metaphors. Eighty-four participants responded to a measure of experiential avoidance. They were subsequently exposed to a cold-pressor task at pretest. Participants were then randomly assigned to four experimental protocols: (a) three functionally equivalent metaphors with common physical properties of participants’ pain, (b) three functionally equivalent metaphors without common physical properties, (c) a metaphor with common physical properties that was repeated three times, and (d) a metaphor without common physical properties that was repeated three times. Participants were then reexposed to the cold-pressor task (posttest). Bayesian data analyses showed that the presence of common physical properties was the only variable associated with an increase of the metaphor effect, and this was independent of the number of metaphors proposed. The update of evidence by means of a Bayes factor meta-analysis showed that data very strongly support the hypothesis of common physical properties being an effective component of metaphors. These results highlight the relevance of training therapists in designing metaphors with common physical properties of the clients’ discomfort.

Genetic Characterization of Some Neoponera (Hymenoptera: Formicidae) Populations Within the foetida Species Complex.

The foetida species complex comprises 13 Neotropical species in the ant genus Neoponera. Neoponera villosa Fabricius (1804) , Neoponera inversa Smith (1858), Neoponera bactronica Fernandes, Oliveira & Delabie (2013), and Neoponera curvinodis (Forel, 1899) have had an ambiguous taxonomic status for more than two decades. In southern Bahia, Brazil, these four species are frequently found in sympatry. Here we used Bayesian Inference and maximum likelihood analyses of COI and 16S mtDNA sequence data and conventional cytogenetic data together with observations on morphology to characterize sympatric populations of N. villosa, N. inversa, N. bactronica, and N. curvinodis. Our results showed marked differences in the karyotype of these ants. Both N. curvinodis and N. inversa have chromosome number of 2n = 30. Their chromosome composition, however, is distinct, which indicates that N. curvinodis is more closely related to N. bactronica. These four species clustered into three distinct groups. The close relationship between N. bactronica and N. curvinodis deserves further investigation since it has not been fully resolved here. Our results confirm that N. inversa, N. villosa, N. bactronica + N. curvinodis indeed represent four distinct taxa within the foetida species complex.

New molecular markers resolve the phylogenetic position of the enigmatic wood-boring weevils Platypodinae (Coleoptera: Curculionidae)

The precise phylogenetic position of the weevil subfamily Platypodinae continues to be one of the more contentious issues in weevil systematics. Morphological features of adult beetles and similar ecological adaptations point towards a close relationship with the wood boring Scolytinae, while some recent molecular studies and larval morphology have indicated a closer relationship to Dryophthorinae. To test these opposing hypotheses, a molecular phylogeny was reconstructed using 5,966 nucleotides from ten gene fragments. Five of these genes are used for the first time to explore beetle phylogeny, i.e. the nuclear protein coding genes PABP1, UBA5, Arr2, TPI, and Iap2, while five markers have been used in earlier studies (28S, COI, CAD, ArgK, and EF-1α). Bayesian, maximum likelihood and parsimony analyses of the combined data strongly support a monophyletic Curculionidae (the advanced weevils with geniculate antennae), where Brachycerinae, Platypodinae, and Dryophthorinae formed the earliest diverging groups. Dryophthorinae and core Platypodinae were sister groups with high support, with the contentious genera Mecopelmus Blackman, 1944 and Coptonotus Chapuis, 1873 placed elsewhere. Other lineages of wood boring weevils such as Scolytinae, Cossoninae, and Conoderinae were part of a derived, but less resolved, clade forming the sister group to Entiminae. Resolution among major curculionid subfamilies was ambiguous, emphasizing the need for large volumes of data to further improve resolution in this most diverse section of the weevil tree.

The Efficacy of Consensus Tree Methods for Summarizing Phylogenetic Relationships from a Posterior Sample of Trees Estimated from Morphological Data.

Consensus trees are required to summarize trees obtained through MCMC sampling of a posterior distribution, providing an overview of the distribution of estimated parameters such as topology, branch lengths, and divergence times. Numerous consensus tree construction methods are available, each presenting a different interpretation of the tree sample. The rise of morphological clock and sampled-ancestor methods of divergence time estimation, in which times and topology are coestimated, has increased the popularity of the maximum clade credibility (MCC) consensus tree method. The MCC method assumes that the sampled, fully resolved topology with the highest clade credibility is an adequate summary of the most probable clades, with parameter estimates from compatible sampled trees used to obtain the marginal distributions of parameters such as clade ages and branch lengths. Using both simulated and empirical data, we demonstrate that MCC trees, and trees constructed using the similar maximum a posteriori (MAP) method, often include poorly supported and incorrect clades when summarizing diffuse posterior samples of trees. We demonstrate that the paucity of information in morphological data sets contributes to the inability of MCC and MAP trees to accurately summarise of the posterior distribution. Conversely, majority-rule consensus (MRC) trees represent a lower proportion of incorrect nodes when summarizing the same posterior samples of trees. Thus, we advocate the use of MRC trees, in place of MCC or MAP trees, in attempts to summarize the results of Bayesian phylogenetic analyses of morphological data.

Position of enigmatic miniature trichomycterid catfishes inferred from molecular data (Siluriformes)

Trichomycteridae is a well‐corroborated catfish family that comprises about 300 valid species distributed in eight subfamilies. The phyletic status of the Trichomycterinae is uncertain, with different hypothesis regarding the position of the miniaturized Trichomycterus hasemani group. This group comprises four valid species, and neither its monophyly nor its positioning among the Trichomycteridae was tested in a phylogenetic framework. Bayesian Inference and Maximum Likelihood analyses of a molecular data set comprising the mitochondrial genes 12S and 16S and the nuclear genes H3, MYH6 and RAG2 (2983 bp) for 26 taxa highly supported the miniature catfish T. hasemani group as monophyletic and sister to the Tridentinae, consequently recognized as a new genus of this subfamily. Potamoglanis gen. nov. is diagnosed by seven character states: an angle of 35–40° between the main longitudinal axis of the head and the main axis of the autopalatine; thin tubular shape of the second ceratobranchial; presence of six or seven anal‐fin rays; eyes dorsally placed on head; opercular and interopercular odontodes patches not juxtaposed; absence of a distal process on the hyomandibula and presence of a long process on the anterior region of the hyomandibula. Potamoglanis gen. nov is similar to the Tridentinae genera by the presence of a wide cranial fontanelle; presence of a short ventral process in the opercular bone and by the origin of the dorsal fin placed in a vertical through the anal‐fin origin.

Morphological and phylogenetic insights resolve Plenodomus sinensis (Leptosphaeriaceae) as a new species

Plenodomus species were collected from Tamarindus indica L. (Fabaceae) and Plukenetia volubilis L. (Euphorbiaceae) in Yunnan Province, China and subjected to morphological and molecular analysis. Morphologically novel collections comprise unique characters in having mucilaginous globoid-shaped apical and basal appendages (1.5–1.8 μm) and wider third cell from the apex in ascospores. Phylogenetic analysis (Maximum-likelihood, maximum-parsimony and Bayesian analyses) of combined LSU, SSU and ITS sequence data reveal that these collections differ from all other species in the genus. Therefore, a novel species, Plenodomus sinensis is introduced in this study. The new species is compared with other Plenodomus species and a comprehensive description and micrographs are provided.

Arthonia incarnata (Arthoniaceae), a rare and poorly known old‐growth forest lichen new to Asia

The rare and poorly known Northern Hemisphere old‐growth forest lichen Arthonia incarnata is reported for the first time for Asia from Japan and Korea. A detailed description and illustration is provided for the species based on the collections from Japan and South Korea. Bayesian and RAxML analyses of mtSSU, nLSU and RPB2 sequence data show A. incarnata to be only distantly related to the other Arthonia species hitherto sequenced and in particular to superficially similar species occurring in the same type of habitat such as A. didyma, A. spadicea and A. vinosa. For the analysis we generated new sequence data of A. incarnata for the mtSSU (5 specimens) and RPB2 (5) gene loci. Slight variation was observed in sequence data of the RPB2 gene between collections from eastern Asia and Sweden, but this is not substantiated by differences in morphology or ecological behaviour. Arthonia incarnata is confined to humid forests and only grows on parts of tree trunks shaded from precipitation and running water such as the lower side of leaning trunks or cavities at the base of trees. The species is found on trees with acidic bark, in eastern Asia mainly on Betula but also on coniferous trees and on dead wood. It was not found on bark of Salix (caprea), a common substrate for the species in Europe.