Davydov & al. • phylogeny TAXON 66 (6) • December 2017: 1282–1303

Umbilicariaceae (lichenized ) – Trait evolution and a new generic concept Evgeny A. Davydov,1 Derek Peršoh2 & Gerhard Rambold3 1 Altai State University, Lenin Ave. 61, Barnaul, 656049 Russia 2 Ruhr-Universität Bochum, AG Geobotanik, Gebäude ND 03/170, Universitätsstraße 150, 44801 Bochum, Germany 3 University of Bayreuth, Plant Systematics, Mycology Dept., Universitätsstraße 30, NW I, 95445 Bayreuth, Germany Author for correspondence: Evgeny A. Davydov, [email protected] ORCID EAD, http://orcid.org/0000-0002-2316-8506; DP, http://orcid.org/0000-0001-5561-0189

DOI https://doi.org/10.12705/666.2

Abstract To reconstruct hypotheses on the evolution of Umbilicariaceae, 644 sequences from three independent DNA regions were used, 433 of which were newly produced. The study includes a representative fraction (presumably about 80%) of the known diversity of the Umbilicariaceae s.str. and is based on the phylograms obtained using maximum likelihood and a Bayesian phylogenetic inference framework. The analyses resulted in the recognition of eight well-supported clades, delimited by a combination of morphological and chemical features. None of the previous classifications within Umbilicariaceae s.str. were supported by the phylogenetic analyses. The distribution of the diagnostic morphological and chemical traits against the molecular phylogenetic topology revealed the following patterns of evolution: (1) Rhizinomorphs were gained at least four times independently and are lacking in most clades grouping in the proximity of . (2) Asexual reproductive structures, i.e., thalloconidia and lichenized dispersal units, appear more or less mutually exclusive, being restricted to different clades. Two major ontogenetic types of thalloconidial development (thallobred versus rhizinobred) exist, reflecting their non-homologous origin. Both types of thalloconidial formation were gained multiple times. (3) “Gyrodisc-omphalodisc” apothecia are plesio- morphic in Umbilicariaceae. The apothecial type is a relatively variable trait, because the main types of apothecia switched at least six times in evolution. Multiple evolutionary changes from the gyrodiscs to leiodiscs, by reduction of carbonized hymenial structures, seem likely. (4) Ascospore characters, such as spore number per ascus, spore size, and septation type and degree are strongly correlated. Eight non-septate small ascospores per ascus represent a plesiomorphic trait. The results indicate parallel evolutionary trends from “gyrodisc-omphalodisc” to leiodisc apothecia, from octospory to mono- or bispory and from unicel- lular to multicellular-muriform ascospores. The other types of apothecia and ascospores evolved multiple times. This suggests that the concept of Umbilicariaceae s.str. has to be refined. The new classification includes eight subgenera in the only Umbilicaria: subg. Actinogyra (type: U. muehlenbergii), subg. Agyrophora (type: A. atropruinosa), subg. Floccularia subg. nov. (type: U. deusta), subg. Gyrophora (type: U. vellea), subg. Iwatakia subg. nov. (type: U. esculenta), subg. Lasallia (type: L. pustulata), subg. Umbilicaria (type: U. hyperborea), and subg. Umbilicariopsis subg. nov. (type: Umbilicaria polyrhiza). Furthermore, four new combinations are proposed: Umbilicaria daliensis comb. nov., U. hispanica comb. nov., U. sinorientalis comb. nov., U. xizangensis comb. nov.

Kewwords apothecia; ascospores; classification; likelihood; morphology; mtLSU; nrITS/5.8S; nrSSU nrDNA; RPB2; rhizinomorphs; thalloconidia

Supplementary Material The Electronic Supplement (Tables S1–S5; Figs. S1–S9) and DNA sequence alignments are available in the Supplementary Data section of the online version of this article (http://www.ingentaconnect.com/content/iapt/tax)

INTRODUCTION Bendiksby & Timdal and Fulgidea Bendiksby & Timdal, both composed of a few lignicolous species with squamulose growth The family Umbilicariaceae was long considered to habit (Umbilicariaceae s.l.). However, classification of species be composed of two genera, Umbilicaria Hoffm. and Lasallia belonging to Umbilicariaceae in the traditional view (i.e., Mérat, together comprising about one hundred species of mostly Umbilicariaceae s.str.) remained unclear. A previous molecular umbilicate growth habit (Savicz, 1950; Poelt, 1962; Wei & Jiang, study (Davydov & al., 2010) suggested that Lasallia represents 1993) (Fig. 1). Species of Umbilicariaceae are predominantly a well-defined genus, based on morphological and molecular saxicolous and mostly found in regions of higher latitudes or al- traits, whereas Umbilicaria appeared paraphyletic. titudes. Bendiksby & Timdal (2013) recently extended the fam- Major progress in clarifying the relationships among ily circumscription by including the two new genera Xylopsora Umbilicariaceae species was achieved by molecular phyloge-

Received: 14 Feb 2017 | returned for (first) revision: 16 Mar 2017 | (last) revision received: 29 Jun 2017 | accepted: 29 Jun 2017 || publication date(s): online fast track, n/a; in print and online issues, 22 Dec 2017 || © International Association for Plant (IAPT) 2017

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netic analyses over the last years (Niu & Wei, 1993; Ivanova & rather characteristic mitosporic dispersal units, so-called “thal- al., 1999; Romeike & al., 2002; Ott & al., 2004; Krzewicka & loconidia”, which were shown to be highly species-specific al., 2009; Davydov & al., 2010; Hestmark & al., 2011; McCune (Hasenhüttl & Poelt, 1978; Hestmark, 1991a, b). & Curtis, 2012; McCune & al., 2014). Molecular phylogenies Secondary metabolism of Umbilicariaceae s.str. has been based on multiple markers (Miadlikowska & al., 2014) sup- studied rather extensively since Nylander (1869). Most species ported the paraphyletic status of Umbilicaria. Those authors contain simple orcinol compounds such as depsides, tridep- recommended broader taxon sampling before drawing tax- sides, and β-orcinol depsidones being synthesized via the onomic conclusions with respect to the generic concept of acetyl-​polymalonyl pathway (Hale, 1983). Chemical data for Umbilicariaceae. 56 species were published by Narui & al. (1996) and geographic The presence of sterile, more or less carbonized hyphal variation in lichen substances was studied by Golubkova & or paraphysal elements within the hymenial layer, which is Shapiro (1979) and Feige & al. (1987). characteristic for the whole family, results in the formation of Evolution, distribution, and structural or functional cou- four major apothecial types (Scholander, 1934; Llano, 1950). pling of the phenotypic traits in Umbilicariaceae is clarified Most Umbilicaria species have eight-spored asci with unicel- in the present study. Extensive analyses of three independ- lular spores. Only a few taxa facultatively produce bicellular or ent DNA regions of different levels of variation, i.e., nuclear oligocellular, i.e., submuriform ascospores. Species of Lasallia ITS/5.8S and RPB2, as well as mtLSU sequences were con- are usually characterized by mono- or bispored asci, with mul- ducted. With 79 analysed taxa, the study presumably includes ticellular-muriform, i.e., eumuriform, ascospores (Davydov & about 80% of the known species of Umbilicariaceae s.str. (see al., 2010). Many species of the Umbilicariaceae s.str. develop Taxonomic treatment).

Fig. 1. Species of Umbilicariaceae s.str.: A, Umbilicaria pustulata (subg. Lasallia); B, U. esculenta (subg. Iwatakia); C, U. muehlenbergii (subg. Actinogyra); D, U. deusta (subg. Floccularia); E, U. hyperborea (subg. Umbilicaria); F, U. polyrhiza (subg. Umbilicariopsis); G, U. leiocarpa (subg. Agyrophora); H, U. vellea (subg. Gyrophora); I, U. pulvinaria (subg. Gyrophora). — Photos: E.A. Davydov.

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MATERIALS AND METHODS as outgroup, selected on the basis of the five-gene phylogeny of by Spatafora & al. (2006). One full-length Material. — We analyzed recently collected and herbarium sequence for each Pezizomycotina clade was downloaded specimens from different regions of the world (Appendix 1). from GenBank and aligned with newly produced sequences DNA was extracted from 186 specimens of Umbilicariaceae of Pertusaria alpina Hepp ex H.E.Ahles and Ochrolechia s.str. and of 6 specimens of outgroup taxa, i.e., 4 for the parella (L.) A.Massal. Nucleotide diversity and Tajima’s D RPB2 + ITS + mtLSU dataset and 2 for the nuSSU dataset were calculated for each dataset using DnaSP v.5 (Librado & (Appendix 1). Freshly collected specimens were obtained Rozas, 2009). from and deposited in the lichen herbaria ABL, ALTB, E, Optimal substitution models and partitions (Table 1) were FR, H, I NEP, KPABG, LE, M, MAF, VLA, and WSL, as inferred for the following subsets: ITS1, 5.8S, ITS2, RPB2 1st, well as the private collections of F. Fernandez-Mendosa, 2nd, and 3rd codon positions, and mtLSU, using PartitionFinder D. Masson, B. McCune, S. Pérez-Ortega, O.B. Blum and L.S. v.1.1.1 (Lanfear & al., 2012). Yakovchenko. Voucher specimens are available in the herbaria The unambiguously alignable regions of 89 specimens listed. Duplicates of specimens from private collections were (85 ingroup, 4 outgroup) for which all three marker regions deposited in ALTB (Appendix 1). were obtained were used to calculate ITS, RPB2, and mtLSU DNA extraction and amplification. — Up to twelve apoth- single-marker phylograms (not shown) with RAxML v.8.0.26 ecia were separated from the thallus under a magnifying lens, (Stamatakis, 2006, 2014). These were tested for conflicts. All washed in drops of sterile water and transferred to sterile 1.5 ml phylograms were similar regarding well-supported clades; only reaction tubes. For specimens lacking apothecia, central thal- two minor conflicts were found (Appendix 2). The analysis lus sections of up to 25 mm2 were excised. Rhizinomorphs was re-run without the incongruent species, which were later and thalloconidia were removed to avoid potential contami- added to the resulting phylogram. The combined data matrix nation with DNA from endolichenic fungi. The samples were consists of 1917 sites, 662 of which were variable, and used frozen in liquid nitrogen and powderized in the tubes using for RAxML and Bayesian analyses. In addition we present sterile pestles. The DNeasy Plant Mini Kit (Qiagen, Hilden, the combined analysis including the two conflicting species Germany) or ChargeSwitch gDNA Plant Kit (Invitrogen, (Electr. Suppl.: Fig. S1) because its topology did not deviate Carlsbad, California, U.S.A.) were used for DNA extraction from the tree topologies calculated without these species. as recommended by the manufacturers, except that 80 µl of The most likely tree and 1000 bootstrap replicates were prewarmed (60°C) distilled water was used to elute DNA from calculated using RAxML using the raxmlGUI software v.1.3.1 the Qiagen spin columns in a single step. (Silvestro & Michalak, 2012) and applying the GTRGAMMAI Four genetic markers were amplified: the ITS region model of substitution to the subsets. Bayesian inference was (ITS1, 5.8S, and ITS2 rRNA gene regions), SSU rRNA gene, carried out using Metropolis coupled Markov Chain Monte RPB2 (between six and seven conserved parts), and a partial Carlo (MCMCMC) as implemented in MrBayes, v.3.2.3 sequence of the large subunit of the mitochondrial ribosomal (Ronquist & al., 2012). Three independent analyses were run DNA (mtLSU). ITS, RPB2 and mtLSU were amplified in a sin- applying different models for partitions (Table 1), each running gle reaction, whereas SSU nrDNA was amplified in two parts. for 100 million generations (200 million for combined data- Primers and cycling conditions for amplification of all genes set) in six chains, and every 200th generation was sampled. A are listed in Table 1. Sequences were produced on Li-Cor 4200 burn-in value of 50% was specified to calculate standard devi- or Sanger ABI 37390xl sequencers. The program Geneious ation; the same value was used for the final 50% majority-rule v.6.0 (Biomatters, New Zealand) was used for assembling par- consensus tree calculated with the sumt command implemented tial and complementary sequences. Consensus sequences were in MrBayes v.3.2.3. exclusively compiled from double-stranded sequenced parts of Character evolution was reconstructed using Mesquite the sequences. Sequence alignments were complemented with v.3.2 (Maddison & Maddison, 2017). Modules “Trace Character Umbilicariaceae sequences from GenBank (http://www.ncbi. Over Trees” and “Reconstruct Ancestral States” with the pa- nlm.nih.gov; Sep 2013; Appendix 1). For the alignments, 644 rameter “maximum likelihood reconstruction of ancestrial sequences of Umbilicariaceae and outgroup taxa were used, states” were used to identify plesiomorphies and apomorphies. 433 of which were newly obtained and 211 downloaded from Phenotypic analyses. — Morphological and chemical GenBank (Appendix 1). traits were examined and compared with published data (Llano Phylogenetic analyses. — Phylogenetic trees were recon- 1950; Hestmark, 1990; Wei & Jiang, 1993; Narui & al., 1996). structed using a maximum likelihood (ML) and a Bayesian Morphology and anatomy were analysed by applying standard phylogenetic inference framework. We rooted the trees using light microscopic methods. For each species, general morphol- Boreoplaca ultrafrigida Timdal, scalaris ogy, structure of the upper and lower thallus cortex, special (Ach.) M.Choisy, ventosa (L.) Norman, and structures, occurrence and localization of thalloconidia, types Xylopsora friesii (Ach.) Bendiksby & Timdal, as outgroup. of lichenised dispersal units and apothecial morphology were This selection is based on the studies of Bendiksby & Timdal recorded. Thallus and apothecial anatomy were investigated (2013) and a five-gene analysis by Miadlikowska & al. (2014), under a light microscope, using freezing microtome sections in which these species of form sister clades to mounted in water and lactophenol-cotton-blue. Measurements Umbilicariaceae s.str. For the SSU dataset, we used 38 taxa of ascospores (n = 20 per specimen, sections mounted in water)

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were performed under a light microscope. Secondary metab- The phylogenetic distinctness of character states was cal- olites were analysed by applying standard thin-layer chroma- culated based on phylogenetic distances extracted from the tography techniques (Culberson & Kristinsson, 1970; Elix & Bayesian tree. We looked for indices reflecting phylogenetic Stocker-Wörgötter, 2008). relationship between species sharing a certain trait because Statistics. — The states of 12 diagnostic morpho-anatom- most biologically and diagnosticaly important traits appeared ical and chemical traits of Umbilicariaceae representing nom- non-monophyletic. Warwick & Clarke (1995) introduced the inal data were coded (Table 2) and analysed using MS Excel. concept of taxonomic distinctness into marine ecology, as a Associations between every character pair were tested using measure of the average degree to which species in a commu- cross tabulation. We used chi-squared tests of the null hypoth- nity are related to each other. This index has been extensively esis of no association between characters (Fienberg, 1980). used in ecology to measure phylogenetic relatedness of spe- Cramer’s V was calculated to test the strength of association cies in communities (Clarke & Gorley, 2015). We calculated of the cross tabulations; the phi coefficient was calculated in this index to measure phylogenetic distinctness among species addition when both variables were binary. sharing specific traits. By comparing the average phyloge- The minimum number of switches from one character state netic distance among all species in the phylogenetic tree with to another was counted from the resulting phylogenetic tree the average distance among species sharing a certain trait, we to compare the constancy of selected phenotypic traits in the assessed phylogenetic distinctness of the traits. The distance course of the phylogeny. matrix was calculated on the T-REX server (Boc & al., 2012),

Table 1. Summary statistics, PCR settings and substitution models used for the different datasets. Name ITS SSU RPB2 (partial) mtLSU (partial) ITS + RPB2 + mtLSU Regions ITS1-5.8S-ITS2 Between 6 and 7 ML3–ML4 – conservative regions (Zoller & al., 1999) (Liu & al., 1999) PCR Settings Primers 1203F-5′ / ITS 4-3′ AS-5′ / 1293R-3′ RPB2-980F-5′ / ML 3-A-5′ / – 1055F-5′ / ITS 4-3′ AS-5′ / 1400R-3′ fRPB2-7cR-3′ ML 4-A-3′ ITS 1F-5′ / ITS 4-3′ 819F-5′ / ITS2-3′ 1203F-5′ / ITS 2-3′ 1203F-5′ / ITS 4-3′ References White & al., 1990 Medlin & al., 1988 Liu & al., 1999 Printzen, 2002 – Gargas & Taylor, 1992 White & al., 1990 Reeb & al., 2004 Gardes & Bruns, 1993 Gargas & Taylor, 1992 Huss & al., 1999 Döring & Triebel, 1998 Denaturation 95°C (2 min) 95°C (2 min) 95°C (2 min) 95°C (2 min) – Amplification 35 cycles 35 cycles 35 cycles 35 cycles – 94°C (20 s) 94°C (20 s) 94°C (20 s) 94°C (20 s) 52°C (1 min) 52°C (1 min) 61°C (1 min) 52°C (1 min) 72°C (2 min) 72°C (2 min) 72°C (2 min) 72°C (2 min) Extension 72°C (15 min) 72°C (15 min) 72°C (15 min) 72°C (15 min) – Datasets Alignment length [bp] 442 1516 738 739 1917 Variable sites 191 77 293 174 662 Nucleotide diversity 0.06536 0.00745 0.09490 0.04930 0.07934 π Tajima’s D −1,59188 −1,7431 −0,70351 −1,33333 Number of sequences (ingroup): total/original 317/162 29/22 118/108 130/127 83/83 Number of taxa total/originally sequenced 78/69 21/19 64/64 71/70 53/53 Substitution model ITS1, 2: GTR + G; SYM + I + G pos. 1: HKY + G; HKY + I + G As for separate 5.8S: K80 + I + G pos. 2, 3: K80 + I + G markers

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averaging distances for species. Calculation of phylogenetic Major clades based on RPB2 + ITS + mtLSU dataset. — In distinctness was performed for each character state using the the Bayesian analysis of the RPB2 + ITS + mtLSU dataset, the module “Univariate Diversity Indices (DIVERSE)” imple- average standard deviation of split frequencies had fallen to mented in the Primer-E software v.7 (Clarke & Gorley, 2015). 0.11067 at termination (200 million generations). The topology For the states of each character, average taxonomic distinctness of the Bayesian 50% majority-rule consensus tree was similar (Δ+) and its variation (λ+) were calculated. Average phyloge- to that of the tree calculated by RAxML. Both phylograms are netic distinctness (Δ+) indicates the average phylogenetic dis- combined in Fig. 2. tance between all pairs of species (Clarke & Warwick 1998). Umbilicariaceae s.str. are monophyletic in each Bayesian Variation in phylogenetic distinctness (λ+) is a measure of the and RAxML analysis of nuSSU and RPB2 + ITS + mtLSU evenness of distribution in the phylogenetic tree. To analyse datasets. The phylogenetic analysis of three independent DNA trait distribution across the phylogenetic tree, these measures regions of different variability resulted in the recognition of six were compared between species possessing a certain trait and well-supported major clades of Umbilicariaceae (Fig. 2). The the entirety of species in the phylogenetic tree. names of clades correspond to the respective subgenera (see Taxonomic treatment). Species-level structure of the six major clades. — Species RESULTS not present in the concatenated analyses, but grouped with support in the corresponding clades in single-locus phylogenies Phylogenetic reconstructions. — DNA extracts from (Electr. Suppl.: Figs. S2, S3, S6–S9), were considered part of freshly collected specimens or samples stored in the herbarium these clades. for less than five years were mostly successful. The major taxon Clade 1 (subg. Lasallia). — Lasallia clade (Bayesian anal- grouping was similar in the phylogenetic reconstructions of all ysis: 1.0 PP; RAxML: 100% BS) unifies representatives of markers. ITS and nuSSU-based trees (Electr. Suppl.: Figs. S2– Lasallia in its former circumscription, including its type, S5) were highly resolved and contained a considerable num- L. pustulata (L.) Mérat (Fig. 1A). The trees calculated from ber of clades, including representatives of one to few species, different datasets were in full accordance regarding the topol- but species-rich clades were unsupported. The phylogenies ogy and the present circumscription of Lasallia. based on RPB2 and mtLSU (Electr. Suppl.: Fig. S6–S9) were Clade 2 (subg. Iwatakia, subg. Floccularia, subg. Actino­ less resolved, showing a smaller number of well-supported gyra). — Clade 2 combines Umbilicaria kisovana (Zahlbr. ex species-rich clades. A concatenated RPB2, ITS, and mtLSU Asahina) Zahlbr., U. mammulata (Ach.) Tuck., U. muehlen- sequence dataset provided phylograms with high support for bergii (Ach.) Tuck., and U. deusta (L.) Baumg. with consider- most clades (Fig. 2). It was used as the basis for reconstructing able support (1.0 PP; 73% BS) and rather long branch lengths. trait evolution. As complete SSU rRNA gene sequences could Assignment of species to clade 2 by single-locus analyses: be generated only from a few species representatives, these ITS, RPB2: U. esculenta (Miyoshi) Minks, U. yunnana (Nyl.) data were used only for testing results from the analyses based Hue. Morphological traits are heterogenous in clade 2. Single- on the concatenated RPB2 + ITS + mtLSU sequence dataset. marker analyses, however, resulted in several smaller clades,

Table 2. Coding of diagnostic morphological and chemical characters of Umbilicariaceae. Character number Character States and terminology Ch 1 Rhizinomorph (or rhizine) presence Two states: absent (0); present (1) Ch 2 Rhizinomorph (or rhizine) type Four states: simple to branched (0); thalloconidial (1); fasciculate (2); true rhizines (3) Ch 3 Thalloconidia presence Two states: absent (0); present (1) Ch 4 Thalloconidia origin Two states: thallobred (0); rhizinobred (1) Ch 5 Thalloconidia septation presence and type Three states: 0–1-septate (0); (2–)6–10-septate (1); (4–)20- to multiseptate (2) Ch 6 Lichenized propagules presence Two states: absent (0); present (1). Species occasionally possessing thallyles developed on rhizinomorphs have not been mentioned as having lichenized propagules due to inconstancy of the character Ch 7 Apothecia presence Two states: rare (0); common (1) Ch 8 Apothecia morphology Three states: gyrodisc or omphalodisc (0); actinodisc (1); leiodisc (2) Ch 9 Ascospore number per ascus Two states: 8 per ascus (0); 1–2 per ascus (1) Ch 10 Ascospore septation type Three states: unicellular to bicellular (0); unicellular to submuriform (1); eumuriform (2) Ch 11 Ascospore size class Three states: small-sized: 7–16 × 4–8 µm (0); mean-sized: 16–30 × 8–20 µm (1); large-sized: 30–100 × 20–40 µm (2) Ch 12 β-orcinol depsidones presence Two states: absent (0); present (1)

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Fig. 2. Phylogenetic relation- 0.45/12 agrED213, L. pustulata 4 ships among Umbilicariaceae 0.97/82 agrED212, L. pustulata 3 1.0/98 agrED027, L. pustulata 1 based on combined RPB2, ITS, 1.0/100 agrED107, L. pustulata 2 and mtLSU sequence data. 1.0/91 agrED223, L. hispanica 2 agrED106, L. hispanica 1 Posterior probabilities of the 1.0/52 1.0/100 agrED065, L. asiae-orientalis 1 Clade 1: Lasallia MCMCMC Bayesian analysis 0.55/- agrED096, L. daliensis 1.0/ var. caeongshanensis 0.41/- and bootstrap support values 0.56/79 100 agrED052, L. rossica 1 of the best scoring tree of the 0.60/ agrED014, L. rossica 2 52 agrED419, L. papulosa1 RAxML maximum likeli- 1.0/100 agrED221, L. pertusa 2 hood analysis are given above agrED007, L. pensylvanica1 or to the left of the respec- 1.0/81 agrED311, L. caroliniana 1 1.0/82 acpED444, U. kisovana Clade 2a: Iwatakia tive branches. Lines in bold 1.0/73 agrED218, U. mammulata indicate clades with posterior 0.72/42 agrED012, U. muehlenbergii 1 Clade 2b: Actinogyra probability of 0.95 or higher agrED041, U. deusta 1 1.=/100 agrED078, U. indica Clade 2c: Floccularia and bootstrap support of 70% 1.0/100 agrED227, U. thamnodes 1 or higher. Two species showing 1.0/91 acpED462, U. badia U. badia group phylogenetic conflict between 0.87/72 agrED166, U. pseudocinerascens 1.0/100 agrED184, U. hypococcinea markers (Appendix 2) are 1.0/99 acpED016, U. formosana 1 1.0/100 agrED295, U. rhizinata marked with asterisks; the 0.98/47 U. aprina group position of these species are agrED173, U. aprina 1 acpED473, U. africana 1* 1.0/96 agrED292, U. cylindrica 1 marked by dotted lines. 1.0/13 1.0/100 agrED348, U. umbilicarioides 1 U. cylindrica group 0.63/- 1.0/91 agrED085, U. dendrophora 1 agrED291, U. altaiensis 1 1.0/100 agrED022, U. decussata 1 1.0/90 1.0/77 1.0/ agrED132, U. decussata 2 Clade 3: Umbilicaria 100 agrED174, U. decussata 3 1.0/ agrED296, U. polaris 2 U. decussata group 1.0/100 100 agrED018, U. polaris 1 agrED306, U. virginis 1 0.99/77 agrED293, U. proboscidea1 acpED472, U. havaasii 1 1.0/91 1.0/49 1.0/100 agrED112, U. polyphylla 2 1.0/100 agrED061, U. polyphylla 1 1.0/99 agrED397, U. iberica 1 1.0/83 1.0/99 U. hyperborea group agrED042, U. arctica (1) 1 0.54/- agrED013, U. hyperborea 1 agrED332, U. arctica (2) 1.0/97 agrED060, U. polyrhiza 2 agrED331, U. polyrhiza 1 Clade 4: Umbilicariopsis 0.96/- agrED024, U. rigida 1 1.0/100 agrED372, U. leiocarpa 2 1.0/80 agrED359, U. leiocarpa 1 1.0/94 1.0/100 agrED421, U. subglabra 1 Clade 5: Agyrophora agrED390, U. subglabra var. pallens acpED017, U. lambii 0.33/- agrED097, U. cinereorufescens 1 0.33/- agrED183, U. cinereorufescens 2 1.0/100 agrED074, U. cinereorufescens 3 1.0/86 1.0/ agrED333, U. cinereorufescens 6 100 agrED301, U. vellea (2) 2 1.0/100 agrED156, U. vellea (2) 1 1.0/94 agrED353, U. crustulosa var. badiofusca 1.0/76 0.67/72 agrED226, U. spodochroa (1) 2 1.0/100 agrED108, U. spodochroa (1) 1 agrED386, U. spodochroa (1) 3 1.0/00 0.38/87 agrED310, U. vellea (1) 6 0.98/90 agrED004, U. vellea (1)1 1.0/100 agrED134, U. vellea (1) 2 U. vellea group 1.0/96 agrED155, U. vellea (1) 3 1.0/95 agrED122, U. hirsuta 2 0.55/- 1.0/100 agrED044, U. hirsuta 1 agrED224, U. hirsuta 4 1.0/100 agrED358, U. josiae 1* agrED057, U. crustulosa (2) 1 Clade 6: Gyrophora agrED118, U. crustulosa (1) 1 1.0/100 1.0/100 agrED225, U. crustulosa (1) 2 0.89/- 1.0/100 agrED373, U. crustulosa (1) 3 0.57/- agrED056, U. spodochroa (2) 1.0/100 agrED211, U. freyi 1 0.66/- 1.0/91 agrED371, U. freyi 2 agrED400, U. grisea 1

1.0/99 agrED164, U. tylorhiza 1.0/100 agrED154, U. torrefacta 3 agrED016, U. torrefacta 1 1.0/97 agrED309, U. angulata1 U. angulata group agrED307, U. semitensis 1 acpED018, U. pulvinaria acpED467, Xylopsorafriesii 20.0 Version of Record 1287 Davydov & al. • Umbilicariaceae phylogeny TAXON 66 (6) • December 2017: 1282–1303

i.e., subclades 2a with taxa of more homogenous morphology, U. crustu­ losa­ var. badiofusca) group in three different well- as well as 2b and 2c containing one species each. supported clades. Despite their similar thallus morphology, Clade 3 (subg. Umbilicaria). — The Umbilicaria clade apothecial and rhizinomorph traits differ. Two individuals comprises sequences of Umbilicaria species, including the assigned to U. vellea (“U. vellea-2”) from the Khibiny Mtns generic type U. hyperborea (Ach.) Hoffm. (Fig. 1E), and com- have a morphology similar to other specimens of U. vellea bines several lineages of closely related species such as the (“U. vellea-1”), but have clearly darker rhizinomorphs and group U. hyper­borea group (U. arctica (Ach.) Nyl., U. herrei Frey, with U. crustulosa var. badiofusca Frey. The sequence of one U. hyper­borea, U. iberica Sancho & Krzewicka, U. nylan- specimen of U. spodochroa (Ehrh. ex Hoffm.) Ach. from Turkey deriana (Zahlbr.) H.Magn., U. polyphylla (L.) Baumg.), the (Izmir, V. John, H) groups apart from the other specimens. U. cylindrica group (U. altaiensis J.C.Wei & Y.M.Jiang, Taxa assigned by single-locus analyses: ITS: U. lobo­ U. cylindrica (L.) Delise ex Duby, U. dendrophora (Poelt) peripherica J.C.Wei & al.; ITS + mtLSU: U. phaea Tuck. ITS Hestmark, U. maculata Krzewicka & al., U. umbilicarioides sequences of the endemic South American species U. calves- (Stein) Krog & Swinscow), the U. decussata group (U. decus- cens Nyl., U. haplocarpa Nyl., U. dichroa Nyl., and U. leprosa sata (Vill.) Zahlbr., U. polaris (Schol.) Zahlbr.), the U. aprina (Zahlbr.) Frey were obtained from GenBank. They group in group (U. africana, U. antarctica Frey & Lamb, U. aprina, a well-supported clade (1.0 PP; 89% BS, Electr. Suppl.: Figs. U. formosana, U. kappeni Sancho & al., U. krascheninnikovii S2, S3) together with U. cf. phaea, also from South America. (Savicz) Zahlbr., U. rhizinata), and the U. badia group (U. ba- However, the relationship of U. phaea s.str. to other phyloge- dia Frey, U. indica Frey, U. thamnodes Hue). netic groups remains obscure. We assigned U. phaea and its Umbilicaria hypococcinea (Jatta) Llano and U. pseudo- relatives to the U. vellea clade based on published phylogenetic cinerascens J.C.Wei & Y.M.Jiang group together as sister to analyses of three markers (Hestmark & al., 2011; Miadlikowska the U. badia group. Umbilicaria proboscidea (L.) Schrad. & al., 2014). Three ITS sequences of U. nodulospora McCune and U. havaasii Llano form a clade sister to the remainder of & al. obtained from GenBank group together (1.0 PP; 96% clade 3 except the U. hyperborea group. The precise phyloge- BS), but their relationship to other phylogenetic groups lacked netic placement of U. virginis Schaer. remains obscure due to statistical support. Therefore, these species are not treated in its different phylogenetic positions across phylograms based detail here, even though an affiliation to clade 6 appears plau- on different datasets. Its intermediate morphology fits to more sible according to morphological traits. than one group within the Umbilicaria clade. Taxa assigned by Classification of phenotypic traits. — The phylogenetic single-locus analyses: ITS, mtLSU: U. antarctica, U. herrei, analysis of taxon and trait evolution was at first based on a U. kappeni, U. krascheninnikovii. narrow classification of traits. This provided evidence for Clade 4 (subg. Umbilicariopsis). — Umbilicaria polyrhiza multiple origins of certain phenotypic traits. For subsequent clade (Fig. 1F) is sister to clade 3 with rather strong support comparisons of morphological traits and phylogenetic rela- (1.0 PP; 83% BS), but clearly differs morphologically (see tionship, we applied a more generalized classification of the discussion). traits (Table 2). Clade 5 (subg. Agyrophora). — The Agyrophora clade com- Rhizinoid structures were classified into four different bines representatives of Umbilicaria sect. Anthracinae sensu types – “simple to branched”: non-branched to dichotomously Imshaug and U. lambii Imshaug. The Agyrophora clade is or irregularly branched, cylindrical or complanate; “thalloconi- well supported by the ITS and RPB2 analyses (Electr. Suppl.: dial”: simple to irregularly branched, dissolving into clumps of Figs. S2, S3, S6, S7). The mtLSU analysis, however, shows septate thalloconidia; ”fasciculate”: short and richly branched, that clade 5 split into three subclades (Electr. Suppl.: Figs. S8, with distal branches several times thinner than the basal branch; S9). Taxa assigned by single-locus analyses: ITS and mtLSU: and “true rhizines”: relatively long, sparsely branched, attach- U. cinerascens (Arnold) Frey, U. laevis (Schaer.) Frey, U. lyn- ing the thallus. Classification of thalloconidia septation follows gei Schol., and U. ruebeliana Du Rietz & Frey; RPB2 and Hestmark (1990). Apothecia types were classified mainly after mtLSU: U. microphilla (Laurer) A.Massal. Scholander (1934) and Llano (1950), but since omphalodisc and Clade 6 (subg. Gyrophora). — The Gyrophora clade com- gyrodisc types are morphologically highly congruent, they prises sequences of the group as well as the may reflect only successional steps of apothecial ontogeny U. angulata group (U. angulata Tuck., U. pulvinaria (Savicz) (Henssen, 1970). The “gyrodisc” and “omphalodisc” type are Frey, U. semitensis Tuck., U. torrefacta (Lightf.) Schrad.). The combined into one character state. Ascospore septation is clas- U. vellea group is monophyletic, whereas the U. angulata group sified as proposed by Davydov & al. (2010) with two types consists of paraphyletic lineages forming the sister group(s) to for multiseptate spores. “Submuriform” are spores with rela- the U. vellea group (Fig. 2). Two species groups are morpho- tively few longitudinal and transverse septa and 12(–25) cells logically distinguishable. However, analyses of single-marker in optical section, usually restricted to the distally positioned datasets do not fully support this segregation. Umbilicaria spores within the ascus. “Eumuriform” are regularly developed americana Poelt & T.H.Nash, being sister to U. angulata and multicellular-muriform spores subtype with (25–)30 or more U. semitensis in the RPB2 dataset, is morphologically more septa and exceeding 50–100 cells in optical section. similar to the U. vellea group. Co-occurrence and dependency of major phenotypic Three species appear non-monophyletic. Sequences of traits. — The cross tabulation analysis shows a strong degree U. crustulosa s.l. (U. crustulosa-1, U. crustulosa-2, and of association (Table 3) between presence of rhizinomorph and

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apothecial morphology. This is due to the absence of rhizino- Absence of thalloconidia is moderately associated with pres- morphs in most species with leiodisc apothecia. The strong ence of lichenized propagules and vice versa (Table 3). When association of rhizinomorph type with ascospore morphology species exclusively reproducing by ascospores are excluded (Cramer’s V = 0.58 for ascospore septation and 0.62 for size from the analysis, the association increases significantly (phi class) is due to the co-occurrence of absence of rhizinomorphs = −0.85; Cramer’s V = 0.60). The same degree of association with large-sized muriform ascospores in the Lasallia clade and (Table 3) is found for absence of thalloconidia and presence of rhizinomorphs of the “fasciculate” type with mean-sized sim- apothecia. Most species having thalloconidia rarely produce ple spores in the Iwatakia clade. A strong association (Cramer’s apothecia. An association between production of lichenized V = 0.71) was revealed for thalloconidia origin and septation. propagules and apothecia is not obvious due to an only mod- While thallobred thalloconidia are non-septate or have few erate association of lichenized propagules presence and rarity (6–10) septa, rhizinobred thalloconidia are always multiseptate. of apothecia (phi = −0.39; Cramer’s V = 0.28). The presence of

Fig. 3. Reconstruction of the evolution of traits, based on tree Fig. 2. A, Rhizinomorphs (presence and types); B, Thalloconidia (origin); C, Thalloconidia (presence and types); D, Lichenized propagules presence E, Apothecia morphology (type); F, Ascospores (type). — Grey, char- acter lacking.

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lichenized propagules is strongly associated with spore type, have thallobred non-septate thalloconidia. The Lasallia clade size, and number per ascus. This resulted from co-occurrence includes species lacking thalloconidia (Fig. 3B, C). of lichenized propagules with 1–2 large-sized eumuriform Most, or, if lobules are regarded as propagules, all species spores per ascus in the Lasallia clade. The strong association of clades Lasallia, Iwatakia, and Floccularia have lichenized of apothecial morphology with ascospore number, septation dispersal units, which are lacking in the clades Umbilicaria and size is due to the associated presence of gyrodisc-omph- (apart from U. kappeni), Umbilicariopsis, and Agyrophora. alodisc apothecia and octosporic asci with small non-septate Lichenized propagules are also rather common in Gyrophora spores. Associations are strong between apothecial morpholo- (Fig. 3D). gies and ascospore number, septation and size (Table 3). While Gyrodisc-omphalodisc apothecia occur in all clades, pre- the pairwise comparisons indicate strong correlations between vail in clades Iwatakia and Gyrophora, and are found in all single characters, additional multivariate interdependencies species of the Umbilicaria clade. Our maximum likelihood can not be excluded. reconstruction suggests that gyrodisc-omphalodisc apothecia Phylogenetic distribution of major phenotypic traits. — represents a plesiomorphic trait. All but one representative of Rhizinomorphs occur in all clades except Agyrophora and clades Lasallia and Agyrophora each have leiodisc apothe- Lasallia (Fig. 3A). Clades Umbilicaria, Umbilicariopsis, and cia. Three known species with actinodisc apothecia are found Gyrophora mostly include species bearing rhizinomorphs. in different clades, i.e., Actinogyra, Umbilicariopsis, and Most species of the Umbilicaria and Gyrophora clades often Gyrophora (Fig. 3E). develop rhizinomorphs of the “simple to branched” type which Unicellular (to rarely bicellular) ascospores predominate is, according to the maximum likelihood reconstruction using in all clades except Lasallia and represent a plesiomorphic Mesquite, a plesiomorphic trait (Fig. 3A). The “thalloconid- trait (Fig. 3F). Oligocellular-muriform ascospores occasion- ial” type appears in clades Umbilicaria and Gyrophora along ally occur in clades Agyrophora and Gyrophora. Multicellular- with the “simple to branched” type and exclusively in clade muriform ascospores are found in clade Lasallia. Eight-spored Umbilicariopsis. Only the “fasciculate” type occurs in Iwatakia. asci are exclusively found in all clades except Lasallia, where True rhizines appear in one species of the Lasallia clade. all but one species have mono- or bisporic asci. Maximum likelihood reconstruction using Mesquite soft- The distribution pattern of the classes of secondary metab- ware (not shown) suggests that the absence of thalloconidia olites only partly coincides with monophyletic clades within is a plesiomorphic trait. Thalloconidia in clades Gyrophora, Umbilicariaceae. β-orcinol depsidones were found in three Umbilicariopsis, and Iwatakia (except U. yunnana with different clades (Agyrophora, Gyrophora, Umbilicaria). In the non-septate thalloconidia), if present, are rhizinobred and U. cylindrica group (Umbilicaria clade) and the Agyrophora multiseptate. The Umbilicaria clade includes all thalloconidial clade species with β-orcinol depsidones co-occur with che- septation types. Only some species of the Agyrophora clade modeficient strains. In species of the remaining clades, only

Table 3. Associations of diagnostic chemical and morphological characters Ch1 to Ch12 of the investigated species on the basis of Nominal Cramer’s V and phi coefficients calculated from the cross tabulation. Ch1 Ch2 Ch3 Ch4 Ch5 Ch6 Ch7 Ch8 Ch9 Ch10 Ch11 Ch12 Ch1 – 0.21 0.47 −0.21 0.02 −0.37 −0.07 Ch2 – Ch3 0.15 0.35 – −0.30 −0.39 −0.25 −0.003 Ch4 0.34 0.45 – 0.25 −0.31 – 0.04 Ch5 0.34 0.37 – 0.71 Ch6 0.15 0.15 0.15 0.17 0.17 −0.39 0.24 −0.20 Ch7 0.02 0.25 0.28 0.22 0.26 0.28 – 0.13

Ch8 0.42 0.18 0.14 0.26 0.25 0.09 – phi coefficient Ch9 0.26 – 0.18 – – 0.17 – 0.40 −0.14 Ch10 0.25 0.58 0.25 0.19 0.15 0.17 – 0.31 0.66 Ch11 0.31 0.62 0.19 0.12 0.13 0.16 – 0.32 0.66 0.67 Ch12 0.05 0.14 0.002 0.03 0.12 0.14 0.09 0.06 0.10 0.16 0.21 Cramer’s V coefficient The statistical significance tested with Pearson’s Chi-square test (significance level 0.1% [in bold] or 1% [in bold italic]). For empty cells the format of data is not appropriate to calculate the phi-coefficient. Cramer’s V gives a value between 0 and +1 in proportion to the strength of association, whereas phi coefficient ranges from −1 to +1, where +1/−1 indicates perfect agreement or disagreement, and 0 indicates no relationship.

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orcinol depsides occur; our maximum likelihood reconstruc- Interclade and intraclade tree topology. — High statistical tion (not shown) suggests that this trait is plesiomorphic. support for the major clades and a well-resolved backbone of In summary, our results suggest that the states of all char- the phylogenetic tree (Fig. 2) enable the analysis of co-occur- acters, except for ascospore number, switched multiple times rences of phenotypic traits as well as a reconstruction of general during the evolution of the Umbilicariaceae (Table 4). evolutionary trends. The distribution of selected biological and Phylogenetic distinctness of character states. — Phylo­ diagnostically relevant features among the clades are sum- genetic distances (Δ+) between the character states rhizino- marized in Table S1 (Electr. Suppl.), whereas morphological morphs, thalloconidia, lichenized propagules and β-orcinol descriptions for the accepted groups (subgenera) are given in depsidones presence and absence, and apothecia commonness the section Taxonomic treatment below and in Table S3 (Electr. and rareness are close to the phylogenetic distance among all Suppl.). These descriptions also consider species missing in the sequences in the tree (Δ+ = 55.5; Electr. Suppl.: Table S2). These phylogenetic analyses but added to the clades based on morpho- character states also show high variation in phylogenetic dis- logical congruence. A discussion of morphological character- tinctness (λ+). This reflects a largely stochastic distribution istics and geographical distribution is presented below, based on the tree and occurrence in different phylogenetic lineages. mostly on species included in our analyses but some additional, Phylogenetic distances between types of rhizinomorphs, thallo- morphologically similar species were included as well. conidia, and apothecia are lower. Species having “thalloconid- Clade 1 (subg. Lasallia). — The circumscription of the ial” rhizinomorphs (Δ+ = 36.2; λ+ = 373.4) are more closely re- genus Lasallia based on ITS sequence data has been discussed lated than are species with “simple to branched” rhizinomorphs in detail by Davydov & al. (2010). The present study, however, (Δ+ = 50.1; λ+ = 540.3). Species with non-septate thalloconidia includes a wider spectrum of taxa. Lasallia caroliniana (Tuck.) (Δ+ = 37.2; λ+ = 261.3) are, on average, phylogenetically closer Davydov & al. – the only species in subg. Lasallia with octo- than species with oligoseptate (Δ+ = 36.9; λ+ = 418.8) and es- sporic asci – is sister to the remaining taxa of the Lasallia clade. pecially multiseptate (Δ+ = 50.3; λ+ = 502.4) thalloconidia. The clade combines several well-supported subclades of taxa Species having actinodisc (Δ+ = 38.8; λ+ = 22.3) or leiodisc with distinct geographic distributions. Both L. caroliniana apothecia (Δ+ = 39.4; λ+ = 325.9) are, on average, less distantly and L. pensylvanica (Hoffm.) Llano are found in north Asia related to each other than are species with gyrodisc-omphalo- and North America. Lasallia pertusa (Rass.) Llano propagates disc apothecia (Δ+ = 53.6; λ+ = 434.4). Phylogenetic distances only via soredia and soredial isidia and is widely distributed in and their variation are lowest in the analysis for 1–2 eumuri- Asia and East Africa. A further well-supported clade includes form large ascospores (Δ+ = 24.7; λ+ = 55.8; Δ+ = 24.8; λ+ two East Asian isidiate species – L. asiae-orientalis Asahina = 49.8; Δ+ = 24.8; λ+ = 49.8) reflecting close phylogenetic and L. daliensis J.C.Wei. Together they consistently group as relationships among clade Lasallia species sharing these traits. sister to the morphologically similar species of the following Species with submuriform ascospores (Δ+ = 28.5; λ+ = 174.6) two clades. The north Asian species L. rossica Dombr. con- are, on average, more distantly related than are species with sistently groups with the Afroamerican species L. papulosa eumuriform ascospores. (Ach.) Llano. These two species are highly similar according to their morphological traits. The ITS sequence data show some

DISCUSSION

Phylogenetic resolution. — Umbilicariaceae s.str. forms Table 4. Minimal numbers of switches of diagnostic morphological a monophyletic group, based on a nuSSU sequence dataset and chemical traits as inferred from the phylogenetic tree in Fig. 2. including 29 sequences of 22 taxa of Umbilicariaceae and 38 Minimal number taxa of Pezizomycotina (Electr. Suppl.: Figs. S4, S5), which is Character of switches in accordance with studies focusing on higher taxonomic levels Ch 1: Rhizinomorph (or rhizine) presence 7 (e.g., Peršoh & al., 2004, Hofstetter & al., 2007; Miadlikowska Ch 2: Rhizinomorph (or rhizine) type* 8 & al., 2014). The backbone of the Umbilicariaceae s.str., how- ever, was still poorly resolved in these previously published Ch 3: Thalloconidia presence 15 trees, and therefore delimitations of and relationships among Ch 4: Thalloconidia origin 6 the respective species groups largely remained unclear. A phy- Ch 5: Thalloconidia septation presence and type* 8 logram obtained from the 2–5 markers and 30 species dataset Ch 6: Lichenized propagules presence 5 (Miadlikowska & al., 2014) revealed two well-supported clades: Ch 7: Apothecia presence 2 one including representatives of the core of Umbilicaria, the Agyrophora clade, and the Gyrophora clade, and the other in- Ch 8: Apothecia morphology* 6 cluding Lasallia and Iwatakia clades. The broader taxon sam- Ch 9: Ascospore number per ascus 1 pling in the present study and the use of three markers for all Ch 10: Ascospore septation type* 4 specimens provided a better resolved backbone, whereas all Ch 11: Ascospore size class* 7 single-marker phylograms revealed an unresolved backbone but the same well-supported branches forming rather similar Ch 12: β-orcinol depsidones presence 9 topologies. * Multistate characters

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degree of polymorphism between two morphotypes of L. ros- Clade 2c (subg. Floccularia). — (Fig. sica, but specimens with lightly pigmented, more areolate and 1D) is morphologically rather similar to subg. Lasallia due less papillose lower thallus surfaces appear to be conspecific to its isidiate and often pustulate thallus, but differs by its with those of the more geographically widespread phenotype. unicellular ascospores. The lack of rhizinomorphs and thallo- The most terminal clade combines the two European species, conidia are also common traits of U. deusta and subg. Lasallia L. hispanica (Frey) Sancho & Crespo and L. pustulata. The species. However, a relationship to subg. Lasallia or to any latter species was also reported for Asia from a single locality other species group lacks evidence from molecular data. The in the Khangai Mts. (Byazrov, 1986; LE-L5923!). species habitually resembles U. kisovana, which, however, Clade 2. — The species of clade 2 are most heterogeneous does not group with U. deusta in any analysis. The species is morphologically (Fig. 1B–D; Electr. Suppl.: Table S3) and the widely distributed in the Holarctic. clade obtained the lowest bootstrap support (73%) of all major Clade 3 (subg. Umbilicaria). — Species of the Umbilicaria clades. In single-marker analyses, the monophyletic Iwatakia clade have a uniform morphology (Electr. Suppl.: Table S3); the clade, combining four species, groups close to representatives characteristic feature of this group is their elevated pruinose or of U. muehlenbergii and U. deusta, but with insufficient sup- reticulate-ridged upper thalline center, which can be prominent port and rather heterogeneous branch lengths (Electr. Suppl.: or only rarely observed for some species (e.g., U. hyper­borea, Figs. S2, S3, S6–S9), reflecting a distant relationship. Finally, U. polyphylla). Species are generally widely distributed in the geographical distribution appears also quite heterogene- high mountainous and subpolar regions in both hemispheres ous in this group. Phylograms, morphology and geographical or only in the Holarctic. Himalayan species (U. badia group, distribution therefore indicate the necessity of segregating U. hypococcinea, U. pseudocinerascens) group together with species into more homogeneous groups, as suggested in the high support (1.0 PP; 95% BS), indicating a common origin. following. The apparent non-monophyletic origin of Eurasian and North Clade 2a (subg. Iwatakia). — American U. arctica specimens should be investigated in more and U. esculenta (Fig. 1B) are sister species of east Asian detail, based on a broader and geographically more balanced and North American distribution, respectively. Their sister sampling. taxon, U. yunnana, differs by the presence of abundant angular Clade 4 (subg. Umbilicariopsis). — Umbilicaria polyrhiza apothecia and a deviating type of thalloconidiogenesis. All is sister to Umbilicaria s.str. but differs morphologically (Fig. three species have in common relatively large spores and the 1F; Electr. Suppl.: Table S3) and seems to represent an isolated same type of rhizinomorphs. Despite their similarity to the phylogenetic lineage. The species has actinodisc apothecia, “U. vellea” group in gross morphology, U. mammulata and multiseptate thalloconidia on the tips of richly branched to U. esculenta differ in the type of rhizinomorphs and thalloco- coralloid rhizinomorphs, and a rough areolated lower surface. nidia and are, in agreement with Hasenhüttl & Poelt (1978) and The species has a multiregional oceanic distribution. Poelt & Nash (1993), considered to be only distantly related to Clade 5 (subg. Agyrophora). — The species of the that group. Umbilicaria kisovana groups within the Iwatakia Agyrophora clade have rather uniform thallus morphology clade, but differs by having a small and thin lobulate thallus (Fig. 1G) and all but Umbilicaria ruebeliana have leiodisc lacking rhizinomorphs and thalloconidia and having small as- apothecia and simple ascospores. The species are distributed cospores. It is morphologically similar to U. esculenta at early in the high-mountain or subpolar regions of the Northern stages of ontogeny (both species often grow in the same hab- Hemisphere; U. subglabra (Nyl.) Llano also occurs in the itat), but U. kisovana forms patches of densely growing small Southern Hemisphere. The crustose or squamulose U. lambii thalli, whereas thalli of U. esculenta are monophyllous and is sister to the remaining species of the U. leiocarpa clade. expanded. Species of the U. esculenta group occur in regions Additional species represent pairs of morphologically similar with high humidity in forest clearings. species, each species in the pair differing in their mode of repro- and U. kisovana occur in East Asia and U. mammulata occurs duction (Electr. Suppl.: Table S1): U. leiocarpa DС.–U. rigida in eastern North America in landscapes with rock outcrops (Du Rietz) Frey and U. subglabra–U. subglabra var. pallens and boulders. Umbilicaria yunnana is a Taiwanian-Himalayan (Nyl.) Frey. Species within each of these pairs are not well endemic in mountain forests and is characterized by its corti- separated, differ in only a small number of nucleotides and colous growth, known only for this species and Lasallia maye- therefore may be conspecific. However, more extensive sam- barae (Satô) Asahina. Thus, these species are well character- pling is required to draw unambiguous taxonomic conclusions. ized by ecological and biogeographical traits. Clade 6 (subg. Gyrophora). — The diagnostic characters Clade 2b (subg. Actinogyra). — Umbilicaria muehlenber- for the species of the Umbilicaria vellea group and U. angu- gii (Fig. 1C) differs from the remaining species of clade 2 in lata group overlap. The U. angulata group is morphologically that its lower surface is covered with trabeculae (flattened fil- segregated by brown thalli and angular gyrodisc to actinodisc aments), it lacks thalloconidia and it has actinodisc apothecia. apothecia. Groupings with any other species in single-marker datasets Umbilicaria vellea group. – Taxa belonging to the mono- are insufficiently supported, reflecting its isolated position. phyletic U. vellea group s.str. are morphologically rather uni- The species occurs both in Asia and North America, is most form (Fig. 1H; Electr. Suppl.: Table S3). Poelt & Nash (1993) common on boulders in mountain forests, and is distributed considered several species to belong to the U. vellea group more widely than species of the Iwatakia clade due to their commonly occurring rhizinomorphs, multicellular

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thallo­conidia, gyrodisc apothecia, and usually simple as- of the Lasallia clade is the increase in ascospore septation cospores, which are, however, oligocellular-muriform in U. ci- (multicellular-​muriform) together with an enlargement of the nereorufescens. Our results reveal that multicellular thalloco- spores and the reduction of spore number (except for L. caro- nidia occur only in some of the species of the U. vellea group, liniana). This apomorphy appears functionally significant in and that species lacking thalloconidia (i.e., U. crustulosa (Ach.) that it increases cytoplasmal resources for single meiospores Frey, U. freyi Codogno & al., U. grisea Hoffm., U. hirsuta, and may, therefore, be advantageous in the early stage of U. josiae, U. loboperipherica, U. spodochroa) also should fungal growth. Thus, Lasallia represents a taxon within the be included. The status of non-monophyletic species requires Umbilicariaceae characterized by a derived and presumably further investigation, based on more samples. Umbilicaria functionally meaningful morphological trait (Davydov & al., vellea-2 probably belongs to the enigmatic U. tylorhiza (Nyl.) 2010). However, the clade is nested within the Umbilicaria Nyl., the holotype of which (Н-9503606!) probably represents a sequences. Therefore, Umbilicaria forms a paraphyletic group- senescent thallus. The U. vellea group combines widely distrib- ing of clades, a finding previously reported based on a smaller uted bipolar (e.g., U. cinereorufescens (Schaer.) Frey, U. gri- number of taxa (Ivanova & al., 1999; Davydov & al., 2010; sea, U. hirsuta, U. vellea (L.) Hoffm.) as well as endemic taxa Miadlikowska & al., 2014). Our analyses reveal eight well-sup- (e.g., U. crustulosa-2(?), U. crustulosa var. badiofusca, U. jo- ported main clades delimited by a combination of morphologi- siae and U. vellea-2(?) from Europe, and U. loboperipherica cal and chemical features. The taxonomic consequences of this and U. squamosa J.C.Wei & Y.M.Jiang from Southeast Asia). finding require further discussion. A subdivision of the family Umbilicaria angulata group. – This paraphyletic group Umbilicariaceae requires either the acceptance of Umbilicaria combines morphologically similar species with a smooth and as a paraphyletic genus or the establishment of several new brownish upper thalline surface and a papillate lower surface, monophyletic entities at the genus or subgenus level. simple rhizinomorphs and filaments, and lack of thallo­conidia. The first solution requires acceptance of two genera – Apothecia are angular, star-like gyrodisc or “actinodisc”. Lasallia and Umbilicaria – as they are recognized today, and Angular gyrose apothecia are similar to actinodisc apothe- segregating of the latter genus into seven subgenera. This con- cia in their radial growth, but differ in having an apothecial cept would perfectly reflect the phylogenetic situation, with margin. This subtype of apothecia links typical round gyro- one out of eight lineages, i.e., Lasallia, showing an evolution- disc apothecia with star-like actinodisc apothecia. Species of arily significant apomorphy. The problem with this scheme the U. angulata group have eight hyaline, unicellular spores is the paraphyletic status of Umbilicaria, which was either per ascus, except for U. semitensis, which has submuriform accepted (Davydov & al., 2010) or considered unacceptable ascospores. Gyrophoric and lecanoric acids occur throughout (Miadlikowska & al., 2014) earlier. the group, instead of or in addition to β-orcinol depsidones The second approach would fully solve the problem of (stictic, norstictic, α-metylsalacinic acids). The group combines paraphyly and is generally followed in modern publications in species of wide distribution in the Western Hemisphere, i.e., which authors propose separate taxa for strongly monophyletic U. phaea and U. angulata (North and South American), U. tor- (holophyletic) groups based on morphological or molecular refacta (Circumboreal), with the endemic taxa U. pulvinaria characters. Creation of a number of relatively small genera (Far East), and U. semitensis (California and southern Oregon). often follows the comprehensive molecular phylogenetic anal- Comparsion with morphology-based classification con- yses of a particular family or genus, such as cepts. — Over time, the classification of Umbilicariaceae (Thell & al., 2012), Megasporaceae (Nordin & al., 2010), s.str. was rearranged several times (see historical overviews Teloschistaceae (e.g., Arup & al., 2013; Kondratyuk & al., in Llano, 1950 and Davydov, 2007). Two major intrafamiliar 2014a, b), Collemataceae (Otálora, 2014) and many others. classification concepts exist, one proposed by Frey (1933, 1949) Unfortunately, since no fully consistent genus concept exists and modified by Imshaug (1957) and Motyka (1964), and a in mycology, the differences between genera and other species second by Scholander (1934) and Llano (1950), modified by Wei groups (series, sections, subgenera, or non-taxonomical group- (1966) and Wei & Jiang (1993). However, most of the suggested ings) have been treated on a subjective basis by the experts genera, subgenera or sections are non-monophyletic in the phy- (authors, reviewers, and editors). The fact that the generic name logeny of the present study (Electr. Suppl.: Table S4). Frey’s is a part of the binary scientific name assigns high impor- sect. Anthracinae, sect. Glabrae, sect. Polymorphae, and sect. tance to the generic level classification. Some well-established Velleae appear in several clades each. Imshaug (1957) split sect. species-rich genera as Cladonia Hill ex P.Browne, Peltigera Anthracinae sensu Frey into sect. Anthracinae sensu Imshaug Willd., and Usnea Dill. ex Adans. so far remain as taxonomic (grouping only in the Agyrophora clade of the present phylog- units (Truong & al., 2013; Athukorala & al., 2016; Magain & al., eny) and sect. Decussatae (Schol. ex Llano) Imshaug (grouping 2017), but still include phylogenetically distinct smaller entities. in the Umbilicaria clade). Subgenera according to Wei & Jiang A natural, i.e., phylogenetically defined, classification of (1993) are also not congruent with the tree topology (Electr. Umbilicariaceae s.str. may be achieved by rearrangements at Suppl.: Table S4). The results therefore do not support any of the generic or subgeneric level. The finding that most major the previously proposed intrafamilar classifications. phylogenetic lineages are supported by morphological traits All algorithms applied resulted in the recognition of a would favour a rearrangement at the generic level. The diag- monophyletic origin of the sequences included of the genus nostic characters and character combinations identified for Lasallia. The most prominent distinctive trait of the species every clade allow for placing new species into one of the eight

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clades with high certainty and without the help of DNA data. (Table 3) largely support the view of replacement of functional However, several uncertainties would remain. First, the pheno- structures and functional coupling. The association between typic characterization of clades 2 and 6 still remains ambigu- producing apothecia, thalloconidia and lichenized propagules ous, due to the high homoplasy of characters in the phylogeny. (Table 3) may be the result of a functional coupling of traits. Second, some species groups, e.g., endemic Southeast Asian For species having thalloconidia or lichenized propagules, and New Zealand species, have not yet been included in phy- the significance of propagation by ascospores is decreased logenetic analyses or are represented only by ITS sequences (Hestmark, 1991b, c). Functional coupling also concerns sex- (Appendix 1). New species and possibly new markers to the ual reproductive structures. Ascospore traits, such as number analyses may result in re-consideration of clades 2 and 6. per ascus, size and septation are strongly associated (Table 3). The erection of new genera, therefore, appears to be prema- Moreover, reduction to mono- or bispory is associated with ture, while separating a single genus (i.e., Lasallia) also appears increase in spore septation and size. This is also associated implausible. We propose to combine Lasallia and Umbilicaria with reduction of carbonized hymenial structures, mainly in into one genus Umbilicaria s.l., and to segregate eight sub- the Lasallia clade. While multicellular-​muriform ascospores genera to obtain units for naming phylogenetic lineages for (both in eight- and one-spored asci) are always large, the size future discussions. While the concept of Umbilicaria as the of oligocellular-muriform spores classified as “small-sized” only genus in Umbilicariaceae s.str. appears to be broad in (Umbilicaria ruebeliana) or “mean-sized” (subg. Gyrophora) comparison to other (cf. Parmelia s.l.), this are similar to unicellular spores of some species of subg. new phylogenetic classification of Umbilicariaceae s.str. is a Iwatakia and subg. Floccularia (Electr. Suppl.: Table S1). first step towards a consistent phylogeny of Umbilicariaceae, In parallel, an evolutionary progression towards reduction of based on monophyletic taxa. If the current trend of splitting spore number per ascus and an increase of septa number per as- continues and further phylogenetic and anatomical results pro- cospore is observed, as had also been shown for Rhizocarpon vide further support for the clades obtained here, subgenera Ramond ex DC. (Rambold & al., 1998). Increased cellularity could easily be raised to genus level. entails the gain of additional compartments with secondary Names are available for some well-delimited clades sug- nuclei and additional cytoplasmic resources. Ascospore num- gested as subgenera here, such as Actinogyra for Umbilicaria ber reduction results in a decrease of the relative number of in- muehlenbergii, Gyrophora for the Umbilicaria vellea and dependent meiospore units in favour of additional cytoplasmic U. angulata groups, and Agyrophora for species of clade 5. resources per meiospore. In addition, a reduction of carbonized New subgeneric names are required for species of clade 2a, for hymenial hyphal and paraphysal structures, i.e., a shift towards U. deusta, and U. polyrhiza. leiodisc apothecia, is observed. This apothecial type in subg. Co-occurrence, dependency and functional coupling of Lasallia is likely the result of outbreeding due to presence of major phenotypic traits. — As a result of our phylogenetic large ascospores, since the reduction of carbonized structures analysis, functional coupling for the rhizinoid, asexual re- at the hymenial surface enables a free passage of the epihy- productive structures and lichenized dispersal units became menial zone of large-sized spores when released. evident. The gain of rhizinomorphs gave rise to the production Evolution of major phenotypic traits. — The distribution of rhizinobred thalloconidia. Rhizinomorphs are therefore of biologically and diagnostically important traits against the considered a precondition for the development of this different background of the molecular phylogenetic tree can help to de- kind of thalloconidia. Our statistical analysis of trait associ- fine the phylogenetic (plesiomorphic vs. apomorphic) status of ations (Table 3) revealed not only such primary dependen- the various character states. The maximum likelihood recon- cies, but also the structural or functional interdependencies struction (Fig. 3A) as well as morphology of the taxa positioned of traits that are not connected directly, i.e., phylogenetic de- closest to the root of the main phylogenetic lineages suggest that pendency. For example, rhizinomorph presence is associated rhizinomorphs represent a plesiomorphic trait. Umbilicaria with apothecial and ascospore morphology and the occur- caroliniana, U. lambii and U. pulvinaria are attached by the rence of lichenized propagules is strongly associated with umbilicus and a lamellar-trabecular net of the underthallus or ascospore characteristics. The strong degree of association of rhizines. Rhizinomorphs therefore may represent a reduced thalloconidia origin and septation was considered by Hestmark form of this underthalline structure. There are no parallelisms (1990, 1991a) as structural dependence, due to the existence in rhizinomorph appearance in the different clades. Switching of “architectural” (space conditional) constraints determin- between presence and absence of the rhizinomorphs apparently ing the degree of septation. Species possessing multiseptate occurred at least seven times, and at least eight times between rhizinobred thalloconidia or lichenized dispersal units, i.e., the rhizinomorph types (Table 3). These results suggest that parasoredia and schizidia, occur in the clade which forms the rhizinomorphs were lost and gained more than once during sister group to all other Umbilicariaceae (Gyrophora clade). the evolution of Umbilicariaceae and evidently led to differ- In Umbilicariaceae clades of the sister group to the Lasallia ent morphological types, which consequently represent non-​ clade (Iwatakia plus Floccularia clades), thalloconidia combine homologous structures. with schizidia, lobules or isidia, and in the Lasallia clade, taxa The plesiomorphic status of thalloconidia absence looks completely shift from non-lichenized to lichenized asexual plausible in Umbilicariaceae because they are lacking in taxa dispersal units (Fig. 3B–D). Correlation analyses of these four positioned close to the root of the Umbilicariceae and phy- types of rhizinomorph and asexual reproductive structures logenetically related outgroup taxa (Boreoplaca, Xylopsora,

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etc.) lack them. Species with thalloconidia are dispersed over Table S2) because of its presence in phylogenetically distant the tree with the exception of the Lasallia clade, always along lineages. Similarly, as with thalloconidia, some evolutionary with other propagation types. The number of assumed gains trends are evident within certain species groups. Several clades and losses of thalloconidia (15) is the highest for any trait combine two closely related species reproducing sexually and (Table 4). The production of thalloconidia requires no addi- by lichenized propagules, respectively, such as Umbilicaria tional morphological structures, as they are produced by the hirsuta–U. josiae, U. freyi–U. crustulosa-2, U. spodochroa-1–​ lower cortex, parathecium or rhizinomorphs. Thalloconidia U. grisea, and U. pustulata–U. hispanica. The possession of may not always develop during ontogenesis of some spe- lichenized propagules therefore initiates species divergence by cies (Umbilicaria aprina, U. krascheninnikovii, U. subgla- alteration of the reproduction mode. Only a few species repro- bra, U. umbilicarioides). It is likely that some species pairs duce exclusively by vegetative propagules (Electr. Suppl.: Table (e.g., U. decussata–U. polaris, U. leiocarpa–U. rigida, S1). The lack of ascomata therefore is an apomorphy. U. subglabra–U. subglabra var. pallens) represent two mor- All clades except the monospecific subgenera include photypes of one biological species, individuals of which ex- at least one species having gyrodisc-omphalodisc ascomata. hibit a sexual and asexual life habit, respectively, which was Moreover, this trait is also predominant in taxa of Xylopsora. possibly induced in the early stages of ontogenesis. Divergence Therefore, it appears plausible that the gyrodisc-omphalodisc by alternation of the reproduction mode, as shown for several apothecium is plesiomorphic in Umbilicariaceae. Apothecia species pairs (Poelt, 1970; Hestmark, 1991b), may be a result of types accordingly switched during phylogeny at least six times fixation of such shifts during evolution and isolation of popula- (Table 4). Any of three representatives of Umbilicariaceae tions. The genetic potential for producing thalloconidia appears having actinodisc apothecia, i.e., Umbilicaria pulvinaria, prevalent in Umbilicariaceae because this trait has evolved U. polyrhiza, and U. muehlenbergii, group separately and in separate clades of morphologically homogenous species represent apomorphies in different phylogenetic lineages. The (Iwatakia, Umbilicaria, Agyrophora, Gyrophora). Phylogenetic phylogenetic distinctness of the trait actinodisc apothecia (Δ+ distinctness of the character states thalloconidia presence and = 38.8) is similar to the leiodisc (Δ+ = 39.4), which also appears absence (Δ+ = 55.5; 49.2; Electr. Suppl.: Table S2) is close to in different clades. Based on the previously applied categories, the phylogenetic distance among all sequences in the tree (Δ+ apothecial morphology appeared to be diagnostically useful at = 55.5). This reflects a distant relationship of species having the genus level only to some extent. This conclusion by earlier thalloconidia. Within clades, however, the types of thalloco- authors (e.g., Frey, 1931, 1933; Henssen, 1970; Hestmark & nidia are uniform and seem to have evolved once. Species with al., 2011) could be supported by the present results. Whereas thallobred (or similar rhizobred) thalloconidia from different gyrodisc-omphalodisc apothecia contain octosporic asci, leio- clades differ in details of thalloconidiogenesis, indicating mul- disc apothecia may contain asci either with eight unicellular tiple evolution of thalloconidia. The presence of thalloconidia small spores (Agyrophora and Gyrophora clades, Umbilicaria would then represent a synapomorphic trait. These findings are sholanderii) or with 1–2 eumuriform large spores (Lasallia in agreement with the conclusion of Hestmark (1990, 1991a) clade), which supports the recognition of their independent that the thallobred and rhizinobred thalloconidia are not ho- evolution and non-homologous relation. mologous and that the corresponding two types of thalloco- Ascospore numbers and types are mostly consist- nidiogenesis emerged more than once during the evolution of ent within clades but vary little outside the Lasallia clade. Umbilicariaceae. While the presence of thalloconidia is highly Unicellular (to rarely bicellular) ascospores predominate in variable, thalloconidia septation type is more conserved (eight all clades except Lasallia, as well as in outgroup taxa, and switches, despite being a multistate character) and phyloge- represent the symplesiomorphic trait. Ascospore number per netically distinct. Species with non-​septate thalloconidia are, ascus changed only once (Table 4), and one additional switch on average, phylogenetically closer than species with septate is most likely a reversal (Davydov & al., 2010). Ascospore thalloconidia. Species with a certain septation type often group characters are the phylogenetically most distinct ones in the with non-thaloconidial species, but rarely with species having analysis (Electr. Suppl.: Table S2). All species with large eu- other types of thalloconidia septation. The traits thallobred muriform ascospores belong to the monophyletic Lasallia thalloconidia, non-septate and oligoseptate thalloconidia are clade, combining all mono- or bisporic species. An exception more phylogenetically distinct. is U. caroliniana with eight spores per ascus, which is nev- Thus, the specification of the trait is more conserved than ertheless strongly supported as belonging to Lasallia by its its presence, due to structural dependencies from the thallo- eumuriform ascospores. However, species with submuriform conidial formation type, which is a relatively constant trait in spores appear in subg. Gyrophora and subg. Agyrophora. the phylogeny (six switches) (Table 4). These differ by size class (Electr. Suppl.: Table S1) and are Most of the clades (except those containing one species) non-monophyletic. Due to such homoplasies, the traits “as- combine representatives with sexual reproduction and asexual cospore type” and “ascospore number” do not fully reflect reproduction by thalloconidia or lichenized dispersal units. evolutionary relationships in Umbilicariaceae. A compara- The presence of lichenized propagules in Umbilicariaceae has ble combination of ascospore traits is given in Rhizocarpon, evolved at least five times and is predominant only in the Lasallia where nuRNA ITS and mtRNA SSU gene sequences analyses clade. The phylogenetic distinctness of lichenized propagula (Ihlen & Ekman, 2002) revealed that ascospore septation types presence and absence is low (Δ+ = 49.2; 50.5; Electr. Suppl.: did not correspond to monophyletic groups.

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The production of orcinol depsides as secondary metab- which are outlined in the following, but which require verifi- olites is common in Umbilicariaceae (Table 1). Both depsides cation in future studies. Lichenization and the umbrella-like, and β-orcinol depsidones are synthesized via the acetyl-poly- umbilicate growth habit may have enabled Umbilicariaceae malonyl pathway from orcellinic acid with different numbers to occupy extreme ecological niches, in which they may have of biosynthesis steps; 1 to 4 steps for depsides and 4 to 5 steps rapidly radiated since the early stages of their evolution. Within for β-orcinol depsidones (Electr. Suppl.: Table S5). The syn- epilithic microbial and lichen communities, their growth habit is thesis of β-orcinol depsidones differs from the very first step highly effective with regard to competition for light, space, and on and requires a number of fermentation reactions (Chooi & water (Degelius, 1940; Larson, 1984; Harris, 1996; Hestmark, al., 2008). 1997), mainly because umbilicate thalli with their horizontally The presence of secondary compounds is very variable, expanding unattached margins do not overgrow, but overlap with a minimum of nine switches between traits (Table 4). neighbouring thalli. Moreover, overlapping and shadowing of Fungal secondary metabolites are encoded by clusters of se- less active distal parts of umbilicate thalli, which grow from quentially arranged genes (Keller & Hohn, 1997). The presence their centres, is less invasive compared to the growth of crustose or absence of a compound in the phenotype cannot fully ad- and foliose (Hestmark & al., 1997). The production of dress evolutionary questions, because a chemical phenotype is thalloconidia provides additional advantages in competition for determined not only by the presence of genes required for the substrate colonization, particularily within-habitat colonization production of a compound, but by the expression of the entire (Hestmark, 1991c), and may therefore have been advantageous pathway leading to the compound. It is not clear to what extent since the early stages of the evolution of this family. expression patterns are determined genetically, or whether an It is remarkable that subg. Gyrophora, being sister to the entire pathway or parts of it can evolve or degenerate repeatedly remaining taxa in the present phylogeny, combines species with (Grube & Blaha, 2003). As a consequence, it is impossible to a wide range of ascoma and ascospores traits, i.e., all apoth- say which character state is plesiomorphic in Umbilicariaceae. ecial morphology types as well as both simple and muriform Several species of subg. Umbilicaria and subg. Gyrophora ascospore types. Species of subg. Gyrophora may or may not (e.g., U. proboscidea, U. virginis, U. torrefacta) may contain have a trabeculate network or rhizinomorphs, the latter with either orcinol depsides or additional β-orcinol depsidones. This or without non-septate to multiseptate thalloconidia. Both or- fact of multiple switches from one type of polyketide to another, cinol depsides and β-orcinol depsidones can be produced by according to the present phylogeny, suggests that a change in species of subg. Gyrophora. Other taxa appear to be more the control of gene expression (e.g., Calo & al., 2014) may be specialized regarding these traits. Thus, subg. Gyrophora may more likely than functionally relevant nucleotide substitutions represent an unspecialized ancestral group in Umbilicariaceae in the coding genes. Additional knowledge of polyketide syn- s.str., in which most diagnostic characters have been realized thase genes and their regulation will be necessary to identify already. Umbilicaria pulvinaria (Fig. 1I) and U. semitensis the course of evolution of secondary metabolism. Regarding are sister to the remaining taxa within subg. Gyrophora. These the occurrence of β-orcinol depsidones in a few species pres- species as well as the related U. angulata share the rare trait ent in different clades, there is no direct evidence for overall of a dense mat of trabeculae and tangled black cylindrical to phylogenetic and chemotaxonomic congruency. The presence flattened rhizines. This loose ‘underthallus’ may also be useful of β-orcinol depsidones was not found to be significantly asso- for attaching the polyphyllous crustose-like thallus of U. pul- ciated with any analysed morphological trait (Table 3). vinaria and U. angulata var. compacta Krog (Krog, 1968) to Most conservative are character states of ascospores and their substrates. Moreover, U. pulvinaria and U. semitensis apothecia (1 to 7 switches), while those concerning asexual have a rather restricted distribution: Kamchatka Peninsula propagation and secondary metabolism are most variable (up and Sakhalin Island (Davydov & al., 2011), and California and to 5 to 15 switches). The ascospore septation type, postulated southern Oregon (McCune & Curtis, 2012), respectively. They as most suitable for distinguishing the subg. Lasallia, is quite are therefore likely to represent paleoendemics. The fact that conserved (4 gains and losses, despite being a multistate char- both species inhabit the territories of recent volcanism and acter). However, other generic markers, such as the predomi- geologically young rocks (2000 to 100,000 years old) might nant number of spores per ascus, the presence and predominant just underline their high degree of adaptability. It is remarkable type of apothecia, rhizinomorphs or thalloconidia, may have that the species sister to the remaining taxa in the Agyrophora few or many gains and losses. High number of gains and losses, clade, Umbilicaria lambii, is also polyphyllous and thickly especially within the same clade, may reflect that changes of crustose to squamulose. Imshaug (1957) treated this species character states require just minor genetic changes. as most basal in Umbilicariaceae and placed it in sect. Vellea, Macroevolutionary trends. — Umbilicariales have the which, however, obtained no support in the present analyses. shortest branches to the base of Lecanoromycetes in the nuSSU The species has a restricted likely paleoendemic distribution phylogram (Electr. Suppl. Fig. S4, S5). This indicates a relatively in the Pacific Northwest of North America, including British old phylogenetic age of the order. This hypothesis is supported Columbia, Alberta, south to Montana and northern California by a recent molecular clock analysis (Prieto & Wedin, 2013) (McCune & Geiser, 2009). If the umbilicate habit is synapo- where Umbilicariales branched off from the main lineages of morphic in Umbilicariaceae s.str., the presence of species Lecanoromycetes prior to the major diversification of the latter. with a similar crustose-like thalline habit in monotypic or low Our results indicate some possible macroevolutionary trends, diverse clades sister to all remaining taxa of the respective

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group in different phylogenetic lineages may indicate their Rietz & Frey) Frey, U. lyngei Schol., U. rigida (Du Rietz) Frey, plesiomorphic status. Consequently such a habit was present in U. subglabra (Nyl.) Harm., U. zahlbrucknerii Frey. the common ancestor of Umbilicariaceae s.str. The species of subg. Lasallia, which groups least distant to subg. Umbilicaria, Umbilicaria subg. Floccularia Davydov, Peršoh & Rambold, i.e., U. caroliniana, produces big cushion-like thalli. It is also subg. nov. [MB 821406] – Type: Umbilicaria deusta (L.) not clearly umbilicate but attached to the substrate by a small Baumg. umbilicus and true rhizines. In North America, U. caroliniana Clade 2c has a relictual disjunct distribution, occurring in Alaska and Diagnostic characters. – Thallus small to medium, thin, the Yukon Territory (Llano, 1950; Brodo & al., 2001). In East weakly pustulate, curled and lobed, margins often downwardly Asia, the species is known from Kamchatka and Japan to east- recurved; upper thallus brownish-black, matt, and smooth, ern Siberia. The traits named for U. caroliniana also converge with isidiose to subsquamulose structures concolorous with with the ancestral traits. No taxon or group of taxa converging the upper cortex; lower surface brighter in colour, smooth, with with the ancestral traits can be identified in the Umbilicaria deep depressions, lacking rhizinomorphs and thalloconidia. s.str. clade. Umbilicaria kisovana stands out sharing plesio- Apothecia sessile, gyrodisc, with asci containing hyaline uni- morphic traits with subg. Umbilicaria and therefore appears cellular spores. Secondary metabolites: gyrophoric, lecanoric, to be ancestral within the subg. Iwatakia. and umbilicaric acids. Etymology. – The name refers to the typical habit of Floccularia deusta with abundant granular to flattened-squa- TAXONOMIC TREATMENT mulose isidia. The epithet “flocculosa” had priority over “deusta” until the type of Lichen deustus L. had been con- New system of the family Umbilicariaceae: served (Jørgensen & al., 1994; Gams, 1996). Included species. – Umbilicaria deusta (L.) Baumg. Fulgidea Bendiksby & Timdal in Taxon 62: 952. 2013 – Type: Fulgidea oligospora (Timdal) Bendiksby & Timdal. Umbilicaria subg. Gyrophora (Ach.) Frey in Rabenh. Krypt.-Fl. 9(4, 1): 209. 1933 ≡ Gyrophora Ach., Methodus: 100. 1803 Umbilicaria Hoffm., Descr. Pl. Cl. Crypt. 1: 8. 1789 – Type: – Type (designated here): Umbilicaria vellea (L.) Ach. (Ach.) Hoffm. [typ. cons. ICBN Clade 6 1999]. Diagnostic characters. – Thallus medium to large, rigid, never pustulate or reticulate; upper thallus surface smooth, Umbilicaria subg. Actinogyra (Schol.) Savicz in Bot. Mater. granulose to parasorediate or schizidiate, occasionally areolate, Otd. Sporov. Rast. Bot. Inst. Akad. Nauk. S.S.S.R. 4: 107. centrally never reticulate; lower surface and rhizinomorphs 1950 ≡ Actinogyra Schol. in Nyt. Mag. Naturvidensk. 75: papillose or areolate, trabeculae emerging from the umbilicus 28. 1934 – Type: Umbilicaria muehlenbergii (Ach.) Tuck. often present; rhizinomorphs with or without 6–50-septate thal- Clade 2b loconidia, sometimes with thallyles. Apothecia sub­immersed Diagnostic characters. – Thallus medium to large, never to sessile, gyrodisc or omphalodisc, occasionally leiodisc or pustulate, upper surface smooth and brownish; lower surface actinodisc. Asci containing eight hyaline unicellular or brown papillate, grey-brown, lacking rhizinomorphs and thallo­ oligocellular-muriform spores. Secondary metabolites: gy- conidia, covered by a thick lamellate-trabeculate network. rophoric, lecanoric, and umbilicaric acids, sometimes also Apothecia subimmersed, actinodisc with asci containing eight β-orcinol depsidones. Mostly Holarctic with European and simple, small hyaline spores. North American – Asian. South American endemic elements. Included species. – Umbilicaria muehlenbergii (Ach.) Included species. – Poelt & Tuck. T.H.Nash, U. angulata Tuck., U. calvescens Nyl., U. cinereo­ rufescens (Schaer.) Frey, U. crustulosa (Ach.) Frey, U. crustu- Umbilicaria subg. Agyrophora Nyl. in Flora 61: 247. 1878 – losa var. badiofusca Frey, U. dichroa Nyl., U. freyi Codogno Type: Agyrophora atropruinosa (Schaer.) Nyl. [= Umbi­ & al., U. grisea Ach., U. haplocarpa Nyl., U. hirsuta (Sw.) licaria­ leiocarpa DC.]. Ach., U. josiae Frey, U. koidzumii Yasuda ex Satô, U. leprosa Clade 5 (Zahlbr.) Fray, U. loboperipherica J.C.Wei & al., U. murihi- Diagnostic characters. – Thallus small to medium, never kuana D.J.Galloway & Sancho, U. nodulospora McCune & al., pustulate, without lichenized propagules; upper surface areo- U. phaea Tuck., U. pulvinaria (Savicz) Frey, U. semitensis Tuck., late, rarely reticulate, matt, grey; lower surface smooth to areo- U. soralifera (Frey) Krog & Swinscow, U. spodochroa Ehrh. ex late, lacking rhizinomorphs, often with thallobred non-septate Hoffm., U. squamosa J.C.Wei & Y.M.Jiang, U. tylorhiza Nyl., thalloconidia. Apothecia sessile to stipitate subimmersed to U. torrefacta (Lightf.) Schrad., U. vellea (L.) Ach. sessile, leiodisc, rare omphalodisc, containing asci with eight small simple or rare submuriform spores. Umbilicaria subg. Iwatakia Davydov, Peršoh & Rambold, Included species. – Umbilicaria cinerascens (Arnold) subg. nov. [MB 821405] – Type: Umbilicaria esculenta Frey, U. leiocarpa DC., U. laevis (Schaer.) Frey, U. lambii (Miyoshi) Minks. Imshaug, U. microphylla (Laur.) A.Massal., U. ruebeliana (Du Clade 2a

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Diagnostic characters. – Thallus medium to large or rarely orcinol depsides gyrophoric, lecanoric, and umbilicaric acids small, never pustulate or reticulate, often bearing schizidia; regularly present; β-orcinol depsidone occasionally present. upper surface smooth to finely areolate, greyish to brownish; Bipolar or holarctic with endemic elements. lower surface brown to black, verrucose to areolate, usually Included species. – Umbilicaria africana (Jatta) Krog with short and richly branched rhizinomorphs with relatively & Swinscow, U. altaiensis J.C.Wei & Y.M.Jiang, U. antarc- wide base and thin distal branches, possessing multicellular tica Frey & Lamb, U. aprina Nyl., U. arctica (Ach.) Nyl., thalloconidia, or thalloconidia thallobred and non-septate. U. badia Frey, U. cristata C.W.Dodge & G.E.Baker, U. cylin- Apothecia subimmersed to sessile, gyrodisc, containing asci drica (L.) Delise ex Duby, U. decussata (Vill.) Zahlbr., U. den- with eight simple small to mean-size spores. drophora (Poelt) Hestmark, U. durietzii Frey, U. formosana Etymology. – The name refers to “iwatake”, the Japanese Frey, U. havaasii Llano, U. herrei Frey, U. hyperborea (Ach.) name for the edible lichen Umbilicaria esculenta. Hoffm., U. hypococcinea (Jatta) Llano, U. iberica Sancho & Included species. – Umbilicaria esculenta (Miyoshi) Krzewicka, U. indica Frey, U. isidiosa Krzewicka, U. kap- Minks, U. kisovana (Zahlbr. ex Asahina) Zahlbr., U. mam- peni Sancho & al., U. krascheninnikovii (Savicz) Zahlbr., mulata (Ach.) Tuck., U. yunnana (Nyl.) Hue. U. maculata Krzewicka & al., U. minuta J.C.Wei & Y.M.Jiang, U. nanella Frey & Poelt, U. nepalensis Poelt, U. nylanderi- Umbilicaria subg. Lasallia (Mérat) Frey in Rabenh. Krypt.-Fl. ana (Zahlbr.) H.Magn., U. polaris (Schol.) Zahlbr., U. poly- 9(4/1): 208. 1933 ≡ Lasallia Mérat, Nouv. Fl. Env. Paris, phylla (L.) Baumg., U. proboscidea (L.) Schrad., U. pseu- ed. 2, 1: 202. 1821 – Type: (L.) Mérat. docinerascens J.C.Wei & Y.M.Jiang, U. rhizinata (Frey & Clade 1 Poelt) Krzewicka, U. robusta (Llano) D.J.​Galloway & Sancho, Diagnostic characters. – Thallus medium to large, pus- U. scholanderii (Llano) Krog, U. subaprina Frey, U. subum- tulate; upper surface smooth to areolate or echinose, brown bilicarioides J.C.Wei & Y.M.Jiang, U. taibaiensis J.C.Wei & to grey, with lobules or isidia; lower surface papillose or are- Y.M.Jiang, U. thamnodes Hue, U. umbilicarioides (Stein) olate, lacking rhizinomorphs, but with true rhizines, lacking Krog & Swinscow, U. virginis Schaer. thalloconidia; apothecia sessile to stipitate, leiodisc or rarely gyrodisc, containing asci with 1–2, rarely 8 large eumuriform Umbilicaria subg. Umbilicariopsis Davydov, Peršoh & spores. Mostly Holarctic with European, North American, Rambold, subg. nov. [MB 821407] – Type: Umbilicaria South African and East Asian endemic elements. polyrhiza (L.) Ach. Included species. – Umbilicaria asiae-orientalis Clade 4 (Asahina) Satô, U. brigantium Zschacke, U. caroliniana Diagnostic characters. – Thallus medium to large; upper Tuck., U. chiriquiensis (Llano) Llano, U. daliensis (J.C.Wei) surface smooth, non-pustulate or pustulate, red-brown with Davydov, Peršoh & Rambold, comb. nov. ≡ Lasallia daliensis abundant, erect, marginal rhizinomorphs; lower surface black, J.C.Wei in Acta Mycol. Sin 1(1): 21. 1982, U. hispanica (Frey) areolate, densely felted with richly branched rhizinomorphs; Davydov, Peršoh & Rambold, comb. nov. ≡ Lasallia brigan- thalloconidia on the tips of the rhizinomorphs, multicellular. tium var. hispanica Frey in Ber. Schweiz. Bot. Ges. 59: 443. Apothecia adnate, actinodisc, containing asci with eight small 1949, U. mayebarae Satô, U. membranacea Laurer, U. pap- simple hyaline spores. ulosa (Ach.) Nyl., U. pensylvanica Hoffm., U. pertusa Rass., Etymology. – The name reflects the close phylogenetic U. pustulata (L.) Hoffm., U. rossica (Dombr.) N.S.Golubk., relationship to subg. Umbilicaria. U. sin­orientalis (J.C.Wei) Davydov, Peršoh & Rambold, comb. Included species. – Umbilicaria polyrhiza (L.) Ach. nov. ≡ Lasallia sinorientalis J.C.Wei in Acta Mycol. Sin. 1(1): 23. 1982, U. xizangensis (J.C.Wei & Y.M.Jiang) Davydov, Xylopsora Bendiksby & Timdal in Taxon 62: 952. 2013 – Type: Peršoh & Rambold, comb. nov. ≡ Lasallia xizangensis J.C.Wei Xylopsora friesii (Ach.) Bendiksby & Timdal. & Y.M.Jiang in Acta Phytotax. Sin. 20: 500. 1982.

Umbilicaria subg. Umbilicaria ACKNOWLEDGEMENTS Clade 3 Diagnostic characters. – Thallus small to medium, We appreciate Prof. B. McCune for his valuable comments and non-pustulate; upper surface smooth to areolate with elevated improving of the text and to anonymous reviewers for helpful feedback pruinose or reticulate ridged center (only rarely observed for on an earlier version of this work. The curators of the herbaria cited some species), brown or grey to blackish; lower surface smooth above as well as Prof. B. McCune, Dr D. Masson, Dr F. Fernandez- to areolate; rhizinomorphs frequently present, simple or mod- Mendosa, Dr S. Pérez-Ortega, Dr O.B. Blum and Dr L.S. Yakovchenko erately dichotomously or irregularly branched, cylindrical or are thanked for the loan of herbarium specimens. We are also indebted complanate, with smooth surface; thalloconidia thallobred or in to Christina Leistner for technical assistance and to Prof. Patricia addition rhizinobred, non-septate to oligoseptate or rarely rhiz- S. Muir for improving the English. The first author was supported inobred and multicellular. Apothecia sessile to stipitate, gyro- by Russian Foundation for Basic Research (no. 14-04-00067). The disc and omphalodisc, occasionally leiodisc, with 8-spored asci, work in Bayreuth University was supported by the DAAD (German containing uni- to bicellular spores. Secondary metabolites: Academic Exchange Service) and by the DFG (no. RA 731/13-1).

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Appendix 1. Voucher data and GenBank accession numbers for samples included in this study. Taxon, voucher (given for newly generated sequences), accession number of ITS, RPB2, mtLSU, and nrSSU. *, newly generated sequence; –, missing informa- tion. ED, collector E.A. Davydov. Boreoplaca ultrafrigida Timdal, Korea, Mt. Sorak, L.S. Yakovchenko 1265 (ALTB), KY947736*, KY972584*, KY947872*, –. Hypocenomyce scalaris (Ach. ex Lilj.) M.Choisy, Germany, Bavaria, B., P. & T. Dornes s.n. (M-0166177), KY947864*, KY972691*, KY947994*, –. Lasallia asiae-orientalis Asahina 1, China, Yunnan, A.A. Zavarzin s.n. (ALTB-L174), EU909470, KY972612*, KY947908*, –. 2, Nepal, A. Cross AC9 (E), –, KY972588*, KY947875*, –. Lasallia caroliniana (Tuck.) Davydov & al. 1, U.S.A., Alaska, B. McCune 30743 (OSC), KY947836*, KY972665*, KY947962*, –. 2, Russia, Khabarovsk Territory, I.F. Skirina s.n. (VLA-L13502), EU909475, –, –, –. 3, Russia, Irkutsk Region, S.E. Voronyuk (ALTB-L5632), –, KY972640*, –, –. 4, Russia, Sokhondinsky Reserve, I.A. Galanina s.n. (VLA-L86), EU909464, KY972641*, KY947936*, –. Lasallia daliensis var. caeongshanensis (J.C.Wei) J.C.Wei, China, Yunnan, A.A. Zavarzin s.n. (ALTB-L172), EU909471, KY972617*, KY947912*, –. Lasallia hispanica (Frey) Sancho & Crespo 1, Spain, Madrid, L.G. Sancho & S. Pannewitz s.n. (M-0082659), EU909473, KY972619*, KY947914*, –. 2, Spain, Madrid, A. Crespo s.n. (MAF-10313), KY947821*, KY972649*, KY947945*, –. 3, Spain, Madrid, A. Crespo s.n. (MAF-10315), –, KY972645*, KY947941*, –. (Ach.) Llano 1, South Africa, Cape Town, S.I. Tschabanenko s.n. (ALTB-L186), KY947860*, KY972688*, KY947990*, –. 2, South Africa, Cape Town, M.P. Andreev 041101 (ALTB-L159), –, KY972633*, –, –. 3, same collection (ALTB-L160), –, KY972634*, –, –. 4, same collection (ALTB-L161), –, KY972635*, –, –. Lasallia pensylvanica (Hoffm.) Llano 1, Russia, Tigireksky Reserve, ED 5310 (ALTB), EU909462, KY972594*, KY947882*, –. 2, Turkey, Anatolia, V. John s.n. (M-0082754), EU909472, –, –, –. 3, AF096202, –, –, –. 4, HM161513, –, –, –. Lasallia pertusa (Rass.) Llano 1, Russia, Altai, ED 5311 (ALTB), KY948000, –, KY947889*, KY948000*. 2, China, Tibet, W. Obermayer 08338 (M-0082746), KY947820*, KY972648*, KY947944*, –. 3, AF096203, –, –, –. Lasallia pustulata (L.) Mérat 1, Finland, Uusimaa, T. Ahti & ED 5037 (ALTB), EU909467, KY972602*, KY947893*, –. 2, Portugal, G.B. & I. Feige s.n. (M-0083314), EU909474, KY972620*, KY947915*, –. 3, Spain, Madrid, A. Crespo s.n. (MAF-10320), KY947816*, KY972643*, KY947939*, –. 4, same locality, A. Crespo s.n. (MAF-10303), KY947817*, KY972644*, KY947940*, –. 5, same locality, A. Crespo s.n. (MAF-10303), KY947818*, –, –, –. Lasallia rossica Dombr. 1, Russia, Laplandsky Reserve, I.N. Urbanavichene & G.P. Urbanavichus s.n. (ALTB-L155), EU909469, KY972607*, KY947903*, –. 2, Russia, Altai, ED 5267 (ALTB), KY947999*, KY972597*, KY947887*, KY947999*. 3, Russia, Tigireksky Reserve, ED 5263 (ALTB), EU909461, –, –, –. 4, Russia, Altai, ED 5270 (ALTB), KY948003*, –, KY947895*, KY948003*. 5, Russia, Sokhondinsky Reserve, I.A. Galanina s.n. (ALTB), EU909463, –, –, –. 6, Russia, Tigireksky Reserve, ED 7537 (ALTB), KY947826*, KY972654*, KY947950*, –. 7, AF096201, –, –, –. Ochrolechia parella (L.) A.Massal., Russia, Tigireksky Reserve, ED 5537, KY948009*, –, – KY948009*. (L.) Norman, Norway, Spitsbergen, L.A. Konoreva s.n. (ALTB), KY947741*, KY972590*, KY947877*, –. Pertusaria alpina Hepp ex Ahles., Russia, Tigireksky Reserve, ED 5540 (ALTB), KY948010*, –, –, KY948010*. Umbilicaria africana (Jatta) Krog & Swinscow 1, Ethiopia, Simien Mts. National Park, T. Lutsak s.n. (FR-220099), KY947743*, KY972592*, KY947879*, –. 2, Chile, XII Region, S. Perez-Ortega & F. Fernandez-Mendoza 1774 (Herb. Perez-Ortega), KY947844*, –, KY947971*, –. 3, HM161482, –, –, –. Umbilicaria altaiensis J.C.Wei & Y.M.Jiang 1, Russia, Altai, ED 7230 (ALTB), KY947827*, KY972655*, KY947951*, –. 2, Russia, Altai, ED 5357 (ALTB), KY947757*, –, KY947900*, –. 3, Russia, Altai, ED 5366 (ALTB), KY947764*, –, –, –. 4, Mongolia, Altai, ED 5363 (ALTB), KY947768*, –, –, –. 5, Austria, Tirol, R. Guderley & al. s.n. (M-0083187), KY947786*, –, –, –. 6, Austria, Tirol, H. Wittmann & al. s.n. (M-0083186), KY947787*, –, –, –. 7, Russia, Altai, ED 5307 (ALTB), KY947787*, –, –, –. Umbilicaria americana Poelt & Nash 1, U.S.A., Katmai National Park, J. K. Walton 13054 (KATM 492), –, KY972671*, KY947968*, –. 2, AF096218, –, –, –. Umbilicaria angulata Tuck. 1, U.S.A., Oregon, B. McCune 30050 (OSC), KY947834*, KY972663*, KY947960*, –. 2, JQ764746, –, –, –. 3, JQ764734, –, –, –. 4, JQ764738, –, –, –. Umbilicaria antarctica Frey & Lamb 1, Antarctica, Barton, M.P. Andreev L03951 (ALTB), KY947849*, –, KY947978*, –. 2, AF096213, –, –, –. 3, AJ431604, –, –, –. 4, FN185922, –, –, –. 5, AY603123,

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Appendix 1. Continued. –, AY603135, –. 6, AY603124, –, AY603136, –. 7, AY603125, –, AY603137, –. Umbilicaria aprina Nyl. 1, Antarctica, Queen Mod Land, M.P. Andreev 42501 (ALTB-L158), KY947808*, KY972636*, KY947931*, –. 2, Russia, Baikalsky Reserve, Urbanavichus G.P. s.n. (ALTB), KY947810*, –, KY947933*, –. 3, Norway, Svalbard, S. Perez-Ortega & S. Domaschke 1796 (ALTB), KY948014*, –, KY947976*, KY948014*. 4, same collection, S. Perez-Ortega & S. Domaschke 1796 (ALTB), KY947859*, –, KY947989*, –. 5, HM161483, –, –, –. 6, HM161502, –, –, –. 7, FN185930, –, –, –. 8, FN185931, –, –, –. Umbilicaria arctica (Ach.) Nyl. (1) 1, Russia, Kola Penins., ED 5351 (ALTB), KY947754*, KY972604*, KY947898*, –. 2, Russia, Kola Peninsula, A.A. Zavarzin s.n. (ALTB-L149), KY947996*, –, KY947884*, KY947996*. 3, HM161454, –, –, –. Umbilicaria arctica (Ach.) Nyl. (2), U.S.A., Alaska, B. McCune 30832 (OSC), KY947839*, KY972669*, KY947966*, –. Umbilicaria badia Frey, Nepal, Sharma & al. s.n. (E00321836), KY947738*, KY972586*, KY947874*, –. Umbilicaria calvescens Nyl. 1, HM161506, –, –, –. 2, HM161507, –, –, –. 3, HM161508, –, –, –. 4, HM161458, –, –, –. 5, HM161459, –, –, –. 6, HM161484, –, –, –. 7, HM161485, –, –, –. 8, HM161460, –, –, –. 9, HM161461, –, –, –. 10, HM161462, –, –, –. 11, HM161463, –, –, –. 12, HM161486, –, –, –. Umbilicaria cinerascens (Arnold) Frey 1, Russia, Altai, ED 5361 (ALTB), KY947758*, –, KY947902*, –. 2, Russia, Altai, ED 5446 (ALTB), KY947779*, –, –, –. Umbilicaria cinereorufescens (Schaer.) Frey 1, Russia, Baikalsky Reserve, G.P. Urbanavichus s.n. (ALTB), KY947778*, KY972618*, KY947913*, –. 2, Russia, Baikalsky Reserve, G.P. Urbanavichus s.n. (ALTB), KY947811*, KY972638*, KY947934*, –. 3, Russia, Altai, ED 651 (ALTB), KY947766*, KY972613*, KY947909*, –. 4, Russia, Altai, ED 5275 (ALTB), KY948002*, –, KY947894*, KY948002*. 5, Mongolia, Altai, ED 5283 (ALTB), KY947765*, –, –, –. 6, U.S.A., Alaska, B. McCune 31407 (OSC), KY947840*, KY972670*, KY947967*, –. 7, Nepal, Ch. Sheidegger s.n. (WSL), –, –, KY947992*, –. 8, HM161503, –, –, –. 9, HM161511, –, –, –. (Ach.) Frey (1) 1, Norway, Hordaland, T. Tønsberg 28870 (M-0083255), KY948007*, KY972623*, KY947918*, KY948007*. 2, Spain, Madrid, A. Crespo s.n. (MAF-10294), KY947823*, KY972651*, KY947947*, –. 3, France, D.M. Masson 83.4189 (ALTB), KY948016*, KY972680*, KY947981*, KY948016*. 4, AF096215, –, –, –. 5, HM161497, –, –, –. Umbilicaria crustulosa (Ach.) Frey (2) 1, Austria, W. Obermayer 7104 (H), KY947761*, KY972609*, KY947905*, –. 2, France, D.M. Masson 31.3651 (ALTB), –, KY972687*, –, –. 3, HM161498, –, –, –. 4, HM161499, –, –, –. Umbilicaria crustulosa var. badio- fusca Frey, France, D.M. Masson 2B.3733 (ALTB), KY948012*, KY972675*, KY947972*, KY948012*. Umbilicaria cylindrica (L.) Delise ex Duby 1, Russia, Tigireksky Reserve, ED 7255 (ALTB), KY947828*, KY972656*, KY947952*, –. 2, Russia, Laplandsky Reserve, I.N. Urbanavichene 03-0109 (ALTB), KY947773*, –, –, –. 3, Russia, Teberdinsky Reserve, O.V. Blinkova 200700104 (ALTB), KY947776*, –, –, –. 4, Russia, Altai, ED 5427 (ALTB), KY947802*, –, –, –. 5, Russia, Altai, ED 5376 (ALTB), KY947803*, –, –, –. 6, Russia, Tigireksky Reserve, ED 7255 (ALTB), KY947828*, KY972656*, KY947952*, –. 7, Russia, Tigireksky Reserve, ED 7257 (ALTB), –, KY972684*,–, –. 8, Ukraine, Carpaty Mts. Blum O.B. s.n. (ALTB) –, –, KY947869*, –. 9, AF096199, –, –, –. 10, AF096209, –, –, –. 11, FN185933, –, –, –. 12, FN185934, –, –, –. 13, FN185938, –, –, –. 14, FN185982, –, –, –. 15, FN185942, –, –, –. Umbilicaria decussata (Vill.) Zahlbr. 1, Kazakhstan, Altai, D.A. German s.n. (ALTB-L153), KY948001*, KY972600*, KY947891*, KY948001*. 2, Russia, Altai, ED 5468 (ALTB), KY947795*, KY972626*, KY947922*, –. 3, Antarctica, Hasuell Is., M.P. Andreev 41601 (ALTB-L157), KY947809*, KY972637*, KY947932*, –. 4, Russia, Altai, ED 5464 (ALTB), KY947790*, –, –, –. 5, Turkey, Anatolia, O. Beeuss & al. s.n. (M-0083214), KY947785*, –, –, –. 6, AF096214, –, –, –. 7, HM161501, –, –, –. 8, HM161510, –, –, –. Umbilicaria dendrophora (Poelt) Hestmark 1, Finland, H. Väre L 1777 (H), KY947772*, KY972616*, KY947911*, –. 2, France, D.M. Masson 65.3254 (ALTB), KY947847*, –, –, –. 3, HM161504, –, –, –. 4, HM161509, –, –, –. 5, HM161505, –, –, –. Umbilicaria deusta (L.) Baumg. 1, Russia, Altai, ED 5353 (ALTB), KY947753*, KY972603*, KY947897*, –. 2, Russia, Baikalsky Reserve, G.P. Urbanavichus s.n. (ALTB), KY947774*, –, –, –. 3, Russia, Laplandsky Reserve, I.N. Urbanavichene 03-0107 (ALTB), KY947775*, –, –, –. 4, AF096206, –, –, –. Umbilicaria dichroa Nyl. 1, HM161464, –, –, –. 2, HM161465, –, –, –. Umbilicaria esculenta (Miyoshi) Minks, Korea, K.H. Moon 10001 (H), KY947856*, KY972583*, –, –. Umbilicaria formosana Frey 1, Russia, Primorye, I.S. Zhdanov s.n. (LE-L6823), KY947733*, KY972580*, KY947865*, –. 2, China, Yunnan, A. Aptroot 55680 (ALTB), KY947806*, –, KY947929*, –. Umbilicaria freyi Codogno & al. 1, Spain, Madrid, A. Pintado & A. Argueello (MAF-10307), KY947815*, KY972642*, KY947938*, –. 2, France, D.M. Masson 2B.3815 (ALTB), KY948015*, KY972678*, KY947979*, KY948015*. Umbilicaria grisea Ach. 1, France, D.M. Masson 2B.3813 (ALTB), KY948018*, KY972686*, KY947986*, KY948018*. 2, Ukraine, O.B. Blum (ALTB-L197), –, KY972666*, –, –. 3, Ukraine, O.B. Blum (ALTB), KY947848*, –, KY947977*, –. 4, HM161491, –, –, –. 5, HM161493, –, –, –. 6, HM161500, –, –, –. Umbilicaria haplocarpa Nyl. 1, HM161466, –, –, –. 2, HM161467, –, –, –. 3, HM161468, –, –, –. 4, HM161469, –, –, –. 5, HM161470, –, –, –. 6, HM161471, –, –, –. 7, HM161472, –, –, –. 8, HM161474, –, –, –. 9, HM161475, –, –, –. 10, HM161476, –, –, –. 11, HM161487, –, –, –. 12, HM161477, –, –, –. Umbilicaria havaasii Llano 1, Russia, Lapland Reserve, A.V. Melekhin s.n. (KPABG-L11690), KY947742*, KY972591*, KY947878*, –. 2, U.S.A., Oregon, B. McCune 27067 (H), KY947858*, –, –, –. 3, JQ764739, –, –, –. Umbilicaria herrei Frey, U.S.A., Washington, B. McCune 32307 (OSC), KY947837*, –, KY947963*, –. Umbilicaria hirsuta (Sw.) Ach. 1, Russia, Altai, ED 5354 (ALTB), KY948004*, KY972605*, KY947899*, KY948004*. 2, Russia, Altai, ED 5449 (ALTB), KY947788*, KY972624*, KY947919*, –. 3, Russia, Altai, ED 5449 (ALTB), KY947789*, –, –, –. 4, Spain, Madrid, A. Crespo (MAF-L10300), KY947822*, KY972650*, KY947946*, –. 5, HM161494, –, –, –. 6, HM161495, –, –, –. Umbilicaria hyperborea (Ach.) Hoffm. 1, Russia, Karelia, A.A. Zavarzin s.n. (ALTB-L148), KY947998*, KY972596*, KY947886*, KY947998*. 2, Russia, Altai, ED 5309 (ALTB), KY947744*, –, –, –. 3, U.S.A., Washington, B. McCune 32306 (OSC), –, KY972667*, KY947964*, –. 4, Russia, Altai, ED 7444 (ALTB), –, –, KY947871*, –. 5, AF096216, –, –, –. Umbilicaria hypococcinea (Jatta) Llano, China, Yunnan, A. Aptroot 55687 (ALTB-L165), KY947812*, KY972639*, KY947935*, –. Umbilicaria iberica Sancho & Krzewicka 1, France, D.M. Masson 2B.3791 (ALTB), KY948017*, KY972685*, KY947985*, KY948017*. 2, FN185964, –, –, –. 3, FN185965, –, –, –. 4, FN185966, –, –, –. Umbilicaria indica Frey, China, Yunnan, A.A. Zavarzin s.n. (ALTB-L170), KY948006*, KY972614*, KY947910*, KY948006*. Umbilicaria josiae Frey 1, France, D.M. Masson 31.3650 (ALTB), KY948013*, KY972676*, KY947974*, KY948013*. 2, France, D.M. Masson 09.3803 (ALTB), KY947852*, KY972681*, –, –. Umbilicaria kappeni Sancho & al. 1, AY603129, –, AY603142, –. 2, AY603131, –, –, –. Umbilicaria kisovana (Zahlbr. ex Asahina) Zahlbr., Russia, Primorye Territory, I.S. Zhdanov s.n. (ALTB-L190), KY947737*, KY972585*, KY947873*, –. Umbilicaria krascheninnikovii (Savicz) Zahlbr. 1, Russia, Kamchatka, D.E. Himelbrant s.n. (ALTB), KY947752*, –, KY947896*, –. 2, Russia, Kamchatka, D.E. Himelbrant & I.S. Stepanchikova K-226-06 (H), KY947857*, –, KY947988*, –. 3, same region and collectors (LE-L7461), –, –, KY947957*, –. Umbilicaria laevis (Schaer.) Frey, France, D.M. Masson 65.3580 (ALTB), KY947845*, –, KY947973*, –. Umbilicaria lambii Imshaug, Canada, M. Zhurbenko 02238 (ALTB-L193), KY947734*, KY972581*, KY947866*, –. Umbilicaria leiocarpa DC. 1, France, D.M. Masson 2B.4194 (ALTB), KY947846*, KY972677*, KY947975*, –. 2, France, D.M. Masson 65.3593 (ALTB), KY947850*, KY972679*, KY947980*, –. 3, AF096211, –, –, –. Umbilicaria leprosa (Zahlbr.) Frey 1, HM161478, –, –, –. 2, HM161479, –, –, –. Umbilicaria lyngei Schol. 1, N. Greenland, E.S. Hansen s.n. (H), KY947771*, –, –, –. 2, Russia, Altai, ED 5465 (ALTB), KY948008*, –, KY947920*, KY948008*. 3, Russia, Altai, ED 5466 (ALTB), KY947792*, –, –, –. 4, AF096217, –, –, –. Umbilicaria maculata Krzewicka & al. 1, Russia, Altai, ED 653 (ALTB), KY947793*, –, –, –. 2, Russia, Altai, ED 1008 (ALTB), KY947794*, –, –, –. 3, Russia, Altai, ED 5656 (ALTB), KY947813*, –, KY947868*, –. 4, Russia, Altai, ED 5656 (ALTB), KY947814*, –, –, –. 5, France, D.M. Masson 04.4199 (ALTB), KY947863*, KY972690*, –, –. Umbilicaria mammulata (Ach.) Tuck., U.S.A., Minnesota, C.M. Wetmore 82463 (M-0083027), KY947819*, KY972647*, KY947943*, –. Umbilicaria microphylla (Laurer) A.Massal., Austria, R. Turk & R. Reiter s.n. (M-0083177), –, KY972646*, KY947942*, –. Umbilicaria muehlenbergii (Ach.) Tuck. 1, Russia, Primorye Territory, S.V. Smirnov s.n. (ALTB-L154), KY947997*, KY972595*, KY947885*, KY947997*. 2, Russia, Altai, ED 5360 (ALTB), KY948005*, –, KY947901*, KY948005*. 3, AF096204, –, –, –. Umbilicaria nodulospora McCune & al. 1, KJ740718, –, –, –. 2, KJ740719, –, –, –. 3, KJ740720, –, –, –. Umbilicaria nylanderiana (Zahlbr.) H. Magn. 1, –, –, KY947880*, –. 2, Mongolia, Altai, ED 5657 (ALTB), –, –, KY947937*, –. 3, Russia, Altai, ED 5295 (ALTB), KY947855*, –, KY947987*, –. 4, Russia, Tigireksky Reserve, ED 5456 (ALTB), KY947796*, –, KY947923*, –. 5, Argentina, Rio Negro, S. Perez- Ortega & F. Fernandez-Mendoza 1788 (Herb. Perez-Ortega), KY947841*, –, KY947969*, –. 6, AY603133, –, –, –. 7, AF096205, –, –, –. 8, HM161488, –, –, –. 9, HM161489, –, –, –. 10, FN185974, –, –, –. Umbilicaria cf. phaea Tuck., Chile, VII Region, S. Perez-Ortega & F. Fernandez-Mendoza 1789 (Herb. Perez-Ortega), KY947843*, KY972674*, –, –. Tuck. 1, U.S.A., California, J.C. Lendemer & K. Knudsen 14858 (H), KY947862*, –, KY947993*, –. 2, JQ764736, –, –, –. 3, JQ764741, –, –, –. 4, JQ764733, –, –, –. Umbilicaria polaris (Schol.) Zahlbr. 1, Russia, Tigireksky Reserve, ED 5306 (ALTB), KY947747*, KY972599*, KY947890*, –. 2, Russia, Tigireksky Reserve, ED 7251 (ALTB), KY947830*, KY972659*, KY947955*, –. 3, Russia, Altai, ED 5298 (ALTB), KY947759*, –, –, –. 4, U.S.A., Montana, B. McCune 32070 (OSC), –, KY972672*, –, –. 5, Russia, Tigireksky Reserve, ED 7301 (ALTB),–,

1302 Version of Record TAXON 66 (6) • December 2017: 1282–1303 Davydov & al. • Umbilicariaceae phylogeny

Appendix 1. Continued. –, KY947870*, –. 6, AY603131, –, –, –. (L.) Baumg. 1, Finland, V. Haikonen 21060 (H), KY947763*, KY972611*, KY947907*, –. 2, Canada, British Columbia, T. Spribille s.n. (M-0083126), KY947784*, KY972622*, KY947917*, –. 3, Great Britain, Scotland, F. Bungartz s.n. (M-0083113), KY947782*, –, –, –. 4, Norway, ED 5470 (ALTB), KY947798*, –, –, –. 5, FN185975, –, –, –. 6, FN185976, –, –, –. 7, FN185977, –, –, –. 8, FN185978, –, –, –. 9, FN185979, –, –, –. Umbilicaria polyrhiza (L.) Ach. 1, U.S.A., California, B. McCune 30433 (OSC), KY947838*, KY972668*, KY947965*, –. 2, Finland, V. Haikonen 20887 (H), KY947762*, KY972610*, KY947906*, –. 3, Norway, T. Tønsberg 28871 (M-0082944), KY947783*, –, –, –. 4, JQ764737, –, –, –. Umbilicaria proboscidea (L.) Schrad. 1, Russia, Tigireksky Reserve, ED 7253 (ALTB), KY947829*, KY972657*, KY947953*, –. Umbilicaria pseudocin- erascens J.C.Wei & Y.M.Jiang, China, Yunnan, A. Aptroot 55686 (ALTB), KY947807*, KY972632*, KY947930*, –. Umbilicaria pulvinaria (Savicz) Frey, Russia, Sakhalin I., S.I. Chabanenko s.n. (LE-L7943), KY947735*, KY972582*, KY947867*, –. Umbilicaria rhizinata (Frey & Poelt) Krzewicka, Russia, Tigireksky Reserve, ED 7258 (ALTB), KY948011*, KY972658*, KY947954*, KY948011*. Umbilicaria rigida (Du Rietz) Frey 1, Norway, ED 5367 (ALTB), KY947749*, KY972601*, KY947892*, –. 2, AF096212, –, –, –. 3, HM161455, –, –, –. Umbilicaria ruebeliana (Du Rietz & Frey) Frey 1, France, D.M. Masson 04.4198 (ALTB), KY947851*, –, KY947982*, –. 2, AF096219, –, –, –. Umbilicaria semitensis Tuck. 1, U.S.A., Oregon, B. McCune 30048 (OSC), KY947833*, KY972662*, KY947959*, –. 2, JQ764742, –, –, –. 3, JQ764735, –, –, –. 4, JQ764745, –, –, –. 5, JQ764743, –, –, –. Umbilicaria spodochroa Ehrh. ex Hoffm. (1) 1, Norway, T. Tønsberg (M-0082898), KY947780*, KY972621*, KY947916*, –. 2, Spain, Madrid, A. Crespo s.n. (MAF-10297), KY947824*, KY972652*, KY947948*, –. 3, France, D.M. Masson 2A.3739 (ALTB), KY947853*, KY972682*, KY947983*, –. 4, AF096207, –, –, –. Umbilicaria spodochroa Ehrh. ex Hoffm. (2), Turkey, Izmir, V. John s.n. (H), KY947760*, KY972608*, KY947904*, –. Umbilicaria subglabra (Nyl.) Harm. 1, France, Ph. Clerk 2215 (ALTB-L205), KY947861*, KY972689*, KY947991*, –. 2, Russia, Altai, ED 5313 (ALTB), KY947750*, –, –, –. 3, Mongolia, Altai, ED 5355 (ALTB), KY947755*, KY972606*, –, –. 4, Russia, Altai, ED 1210 (ALTB), KY947756*, –, –, –. 5, AF096200, –, –, –. Umbilicaria subglabra var. pallens (Nyl.) Frey, France, D.M. Masson 09.4191 (ALTB), KY947854*, KY972683*, KY947984*, –. Umbilicaria thamnodes Hue 1, China, Yunnan, A. Aptroot 55697 (ALTB-166), KY947825*, KY972653*, KY947949*, –. 2, China, Yunnan, A.A. Zavarzin s.n. (ALTB-L173), KY947769*, KY972615*, –, –. Umbilicaria torrefacta (Lightf.) Schrad. 1, Russia, Altai, ED 5314 (ALTB), KY947746*, KY972598*, KY947888*, –. 2, Russia, Laplandsky Reserve, I. N. Urbanavichene 03-0111 (ALTB), KY947777*, –, –, –. 3, Norway, ED 5352 (ALTB), KY947799*, KY972628*, KY947925*, –. 4, JQ764744, –, –, –. Umbilicaria tylorhiza Nyl., China, Yunnan, A. Aptroot 56888a (ALTB), KY947805*, KY972631*, KY947928*, –. Umbilicaria umbilicarioides (Stein) Krog & Swinscow 1, Chile, XII Region, S. Perez-Ortega & F. Fernandez-Mendoza 1773 (Herb. Perez-Ortega), KY947842*, KY972673*, KY947970*, –. 2, South Africa, F. Brusse s.n. (M-0082846), KY947781*, –, –, –. 3, AY603121, –, –, –. 4, AF096210, –, –, –. 5, FN185980, –, –, –. 6, FN185981, –, –, –. 7, FN185941, –, –, –. Umbilicaria vellea (L.) Ach. (1) 1, Russia, Altai, ED 5305 (ALTB), KY947995*, KY972593*, KY947881*, KY947995*. 2, Russia, Altai ED 5469 (ALTB), KY947797*, KY972627*, KY947924*, –. 3, Russia, Teberdinsky Reserve, O.V. Blinkova 240700106 (ALTB), KY947800*, KY972629*, KY947926*, –. 4, Russia, Altai, ED 5294 (ALTB), KY947751*, –, –, –. 5, Russia, Tigireksky Reserve, ED 5453 (ALTB), KY947791*, KY972625*, KY947921*, –. 6, U.S.A., Flathead, B. McCune 32390 (OSC), KY947835*, KY972664*, KY947961*, –. 7, AF096208, –, –, –. 8, HM161490, –, –, –. Umbilicaria vellea (L.) Ach. (2) 1, Russia, Laplandsky Reserve, I.N. Urbanavichene (ALTB-5163), KY947801*, KY972630*, KY947927*, –. 2, Russia, Laplandsky Reserve, I.S. Zhdanov s.n. (ALTB-196), KY947831*, KY972660*, KY947956*, –. 3, FN185983, –, –, –. 4, FN185984, –, –, –. Umbilicaria virginis Schaer. 1, U.S.A., Montana, B. McCune 32089 (OSC), KY947832*, KY972661*, KY947958*, –. 2, Russia, Altai, ED 5541 (ALTB), KY947804*, –, –, –. 3, Russia, Altai, ED 5422 (ALTB), KY947767*, –, –, –. Umbilicaria yunnana (Nyl.) Hue 1, China, Yunnan, A.A. Zavarzin s.n. (ALTB-L169), KY947770*, –, –, –. 2, KY947739*, KY972587*, –, –. Xylopsora friesii (Ach.) Bendiksby & Timdal, Russia, Murmansk Region, G.P. Urbanavichus s.n. (INEP-48), KY947740*, KY972589*, KY947876*, –.

Appendix 2. Conflicts between ITS, RPB2, and mtLSU single-marker phylograms. Two conflicts were found: (1) Umbilicaria hirsuta is monophyletic in RPB2 and mtLSU analyses (99% and 92% BS, respectively) and U. josiae groups as a sister group (97% and 98% BS). However, in the ITS phylogram, KY947822 U. hirsuta groups with U. josiae (95% BS) and with a clade of two remaining sequences of U. hirsuta (99% BS). (2) All phylograms include well-supported clade U. formosana–U. rhizinata (BS ITS: 81%; RPB2: 85%; mtLSU: 99%). In the ITS analysis this clade groups with U. africana (86% BS) and with KY947808 U. aprina (43% BS), whereas in the mtLSU phylogram with U. aprina and U. africana. In the RPB2 analysis, the interactions between these three branches are unresolved due to low bootstrap support. Mentioned conflicts were considered as minor, because they appeared in the grouping of distal branches among sequences of taxa belonging to closely related species, and often have bootstrap support less then 90%.

Version of Record 1303 Vol. 66 (6) • December 2017

International Journal of Taxonomy, Phylogeny and Evolution

Electronic Supplement to

Umbilicariaceae (lichenized Ascomycota) – Trait evolution and a new generic concept Evgeny A. Davydov, Derek Peršoh & Gerhard Rambold

Taxon 66: 1282–1303 TAXON 66 (6) • December 2017 Electr. Suppl. to: Davydov & al. • Umbilicariaceae phylogney

Table S1. Distribution of the diagnostic morphological and chemical traits to the investigated species and clades recognized by the phylogenetic analyses. Clade Taxon no. Ch1 Ch2 Ch3 Ch4 Ch5 Ch6 Ch7 Ch8 Ch9 Ch 10 Ch 11 Ch 12 L. asiae-orientalis C1 0 – 0 – – 1 0 2 1 2 2 0 L. caroliniana 1 3 0 – – 0 1 0 0 2 2 0 L. daliensis var. caeongshanensis 0 – 0 – – 1 1 2 1 2 2 0 L. hispanica 0 – 0 – – 0 1 2 1 2 2 0 L. papulosa 0 – 0 – – 0 1 2 1 2 2 0 L. pennsylvanica 0 – 0 – – 0 1 2 1 2 2 0 L. pertusa 0 – 0 – – 1 0* – – – – 0 L. pustulata 0 – 0 – – 1 0 2 1 2 2 0 L. rossica 0 – 0 – – 0 1 2 1 2 2 0 U. esculenta C2a 1 2 1 1 2 1 0 0 0 0 1 0 U. mammulata 1 2 1 1 2 0 0 0 0 0 1 0 U. yunnana 1 2 1 0 0 0 1 0 0 0 1 0 U. kisovana 0 – 0 – – 1 0 0 0 0 0 0 U. muehlenbergii C2b 0 – 0 – – 0 1 1 0 0 0 0 U. deusta C2c 0 – 0 – – 1 1 0 0 0 1 0 U. africana 1 0 1 0 1 0 0 0 0 0 0 0 U. altaiensis 1 0 0 – – 0 0 0 0 0 0 0 U. antarctica 1 0 1 0 0 0 1 0 0 0 0 0 U. aprina 1 0 1 0 0 0 0 0 0 0 0 0 U. arctica-1 0 – 0 – – 0 1 0 0 0 0 1 U. arctica-2 0 – 0 – – 0 1 0 0 0 0 1 U. badia 1 0 1 0 0 0 1 0 0 0 0 0 U. cylindrica 1 0 0 – – 0 1 0 0 0 0 1 U. decussata 0 – 1 0 0 0 0 0 0 0 0 1 U. dendrophora 1 0 1 1 2 0 0 0 0 0 0 1 U. formosana 1 0 1 0 0 0 1 0 0 0 0 0 U. havaasii 1 0&1 1 1 2 0 0 0 0 0 0 0 U. herrei 1 0 1 0 0 0 1 0 0 0 0 0 U. hyperborea 0 – 0 – – 0 1 0 0 0 0 0 U. hypococcinea 1 0 0 – – 0 1 0 0 0 0 0 U. iberica 0 – 1 0 1 0 0 0 0 0 0 0 U. indica 1 0 1 0 0 0 1 0 0 0 1 0 U. kappenii 1 0 0 – – 1 0* – – – – 0 U. krascheninnikovii 1 0 1 0 0 0 1 0 0 0 0 0 U. maculata 1 0 0 – – 0 1 0 0 0 0 0 U. nylanderiana 0 – 1 0 0 0 0 0 0 0 0 0 U. polaris 0&1 0 0 – – 0 1 0 0 0 0 1 U. polyphylla 0 – 1 0 1 0 0 0 0 0 0 0 U. proboscidea 1 0 0 – – 0 1 0 0 0 0 1 U. pseudocinerascens 0 – 1 0 0 0 1 0 0 0 – 0 U. rhizinata 1 0 1 0 1 0 1 0 0 0 0 0 U. thamnodes 1 0 1 0 0 0 0 0 0 0 1 0 U. umbilicarioides 1 0 1 1 2 0 1 0 0 0 0 1

S1 TAXON 66 (6) • December 2017 Electr. Suppl. to: Davydov & al. • Umbilicariaceae phylogney

Table S1. Continued. Clade Taxon no. Ch1 Ch2 Ch3 Ch4 Ch5 Ch6 Ch7 Ch8 Ch9 Ch 10 Ch 11 Ch 12 U. virginis C3 1 0 0 – – 0 1 0 0 0 0 1 U. polyrhiza C4 1 1 1 1 2 0 1 1 0 0 0 0 U. cinerascens C5 0 – 1 0 0 0 0 2 0 0 0 0 U. laevis 0 – 0 – – 0 1 2 0 0 0 0 U. lambii 0 – 0 – – 0 1 2 0 0 0 0 U. leiocarpa 0 – 1 0 0 0 1 2 0 0 0 1 U. lyngei 0 – 1 0 0 0 0 2 0 0 0 1 U. microphylla 0 – 0 – – 0 1 2 0 0 0 0 U. rigida 0 – 0 – – 0 1 2 0 0 0 1 U. ruebeliana 0 – 0 – – 0 1 0 0 1 0 0 U. subglabra 0 – 1 0 0 0 0 2 0 0 0 0 U. subglabra var. pallens 0 – 0 – – 0 1 2 0 0 0 0 U. americana C6 1 0 1 1 2 0 0 0 0 0 0 0 U. angulata 1 0 0 – – 0 1 0 0 0 1 0 U. cinereorufescens 1 1 1 1 2 0 0 0 0 1 1 0 U. crustulosa var. badiofusca 1 0 0 – – 0 1 0 0 1 1 0 U. crustulosa-1 1 0 0 – – 0 1 0 0 1 1 0 U. crustulosa-2 1 0 0 – – 0 1 0 0 1 1 0 U. freyi 1 0 0 – – 1 0 0 0 0 0 0 U. grisea 0 – 0 – – 1 0 0 0 0 0 0 U. hirsuta 1 0 0 – – 1 0 0 0 0 0 0 U. josiae 1 0 0 – – 0 1 0 0 0 0 0 U. loboperipherica 1 0 0 – – 1 0 0 0 0 – 0 U. phaea 0 – 0 – – 0 1 0 0 0 0 0 U. pulvinaria 1 0 0 – – 0 1 1 0 0 0 0 U. semitensis 1 0 0 – – 0 1 0 0 1 1 0 U. spodochroa-1 1 0 0 – – 0 1 0 0 1 1 0 U. spodochroa-2 1 0 0 – – 0 1 0 0 1 1 0 U. torrefacta 1 0 0 – – 0 1 0 0 0 0 1 U. tylorhiza 1 1 1 1 2 0 0 0 0 0 0 0 U. vellea-1 1 0&1 1 1 2 0 0 0 0 0 0 0 U. vellea-2 1 0&1 1 1 2 0 0* – – – – 0 U. calvescens C6 (?) 1 0 0 – – 0 1 0 0 0 0 0 U. dichroa 0 – 0 – – 1 1 2 0 0 0 0 U. haplocarpa 1 0 0 – – 0 1 2 0 0 0 0 U. leprosa 0 – 0 – – 1 0 0 0 0 0 0 U. nodulospora 1 0 0 – – 0 1 0 0 0 0 0 The classification of characters follows the scheme as given in Tables 2 and S2. * apothecia unknown

S2 TAXON 66 (6) • December 2017 Electr. Suppl. to: Davydov & al. • Umbilicariaceae phylogney

Table S2. Phylogenetic distinctness of traits. Phylogenetic distances (Δ+) and variation in taxonomic distinctness (λ+) are indicated. Character state Number of taxa Δ+ λ+ ALL 59 55.5 372.3 Ch 1: Rhizinomorph (or rhizine) presence 0 25 50.9 289.2 1 34 50.2 513.0 Ch 2: Rhizinomorph (or rhizine) type 0 30 50.1 540.3 1 6 36.2 373.4 2 1 0 0 3 1 0 0 Ch 3: Thalloconidia presence 0 37 55.5 331.7 1 22 49.2 410.0 Ch 4: Thalloconidia origin 0 13 39.0 295.9 1 9 50.3 502.4 Ch 5: Thalloconidia septation presence and type 0 9 37.2 261.3 1 4 36.9 418.8 2 9 50.3 502.4 Ch 6: Lichenized propagules presence 0 45 50.5 357.9 1 14 49.2 551.2 Ch 7: Apothecia presence 0 21 57.5 446.0 1 38 54.9 329.8 Ch 8: Apothecia morphology 0 42 53.6 434.4 1 3 38.8 22.3 2 13 39.4 325.9 Ch 9: Ascospore number per ascus 0 50 51.8 344.7 1 8 24.7 55.8 Ch 10: Ascospore septation type 0 42 49.4 316.2 1 7 28.4 174.6 2 9 24.8 49.8 Ch 11: Ascospore size class 0 36 47.0 299.7 1 12 55.8 625.1 2 9 24.8 49.8 Ch 12: β-orcinol depsidones presence 0 47 58.3 411.2 1 12 36.3 250.0 The classification of characters follows the scheme as given in Table 2.

S3 TAXON 66 (6) • December 2017 Electr. Suppl. to: Electr. Suppl. to: Davydov & al. • Umbilicariaceae phylogney

Table S3. Characteristics of subgenera in Umbilicariaceae. subg. Actinogyra subg. Agyrophora subg. Floccularia subg. Gyrophora subg. Iwatakia subg. Lasallia subg. Umbilicaria subg. Umbilicariopsis

Type Umbilicaria Agyrophora Umbilicaria deusta Umbilicaria vellea Umbilicaria Lasallia pustulata Umbilicaria Umbilicaria polyrhiza muehlenbergii atropruinosa esculenta hyperborea

Character Thalline morphology thallus size medium to large small to medium small to medium medium to large medium to large medium to large small to medium medium to large thallus structure never pustulate never pustulate pustulate never pustulate never pustulate pustulate never pustulate non-pustulate or pustulate upper surface smooth, brownish areolate, matt, gray smooth, smooth to finely smooth to finely smooth to areolate smooth to areolate smooth, red-brown structure and brownish-black areolate, whitish to areolate, greyish to or echinose, brown with elevated pru- colour brownish brownish to grey inose or reticulately ridged center brown or grey to blackish lower surface papillose, covered smooth or areolate smooth, lacunose papillose or areolate; verrucose to papillose or areolate smooth to areolate areolate structure by lamellate- trabeculae going from areolate trabeculate network the umbilicus often present rhizinomorphs or absent absent absent simple to branched fasciculate or absent except one simple to branched richly branched rhizines presence and/or thalloconidial absent species (U. caro- and/or thalloconidial to coralloid and type or absent liniana) with true or absent rhisinae lichenized propa- absent, occasionally absent laminal isidia thallyles, soredia, schizidia isidia, lobulae absent (or marginal absent gula presence and shizidia parasoredia, shizidia isidia) type Thalloconidia thalloconidia absent present or absent absent present or absent present or absent absent present or absent present presence thalloconidia ori- – thallobred – rhizinobred rhizinobred – thallobred or rhizinobred gin and septation non-septate multicelullar multicelullar thallobred and multicelullar rhizinobred non-septate to oligoseptate, but U. umbilicarioi- des – multiseptate rhizinobred

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Table S3. Continued. subg. Actinogyra subg. Agyrophora subg. Floccularia subg. Gyrophora subg. Iwatakia subg. Lasallia subg. Umbilicaria subg. Umbilicariopsis Apothecial morphology Apothecial disc actinodisc leiodisc, but gyrodisc omphalodisc and gy- gyrodisc leiodisc (but omphalodisc and actinodisc type A. ruebeliana rodisc (but U. dichroa U. caroliniana gyrodisc (but – omphalodisc and U. haplocarpa – and U. sinensis U. scholanderii leiodisc; U. pulvinaria – gyrodisc) – leiodisc) – actinodisc) Apothecia attach- subimmersed sessile to stipitate sessile subimmersed to sessile subimmersed to sessile to stipitate sessile to stipitate apothecia adnate ing type sessile Spore number 8 8 8 8 8 1, 2, 8 8 8 Spore septation simple, small simple (but U. rue- simple, mean-size simple small to simple, mean-size eumuriform, large simple to one- simple, small and size beliana – submuri- submuriform, to small septate, small form), small mean-size Secondary orcinol depsides orcinol depsides, orcinol depsides orcinol depsides, orcinol depsides orcinol depsides orcinol depsides, orcinol depsides methabolites sometimes also sometimes also sometimes also β-orcinol depsidones β-orcinol depsidones β-orcinol depsidones Distribution North American– mostly Holarctic bipolar mostly Holarctic with mostly East Asian mostly Holarctic bipolar or Holarctic Holarctic Asian with European and European, East Asian with European, with East Asian, North American and South American South African and New Zealand, South endemic elements endemic elements East Asian endemic and North American elements and Antarctic endemic elements

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Table S4. Correspondence of the phylogenetic tree topology of Umbilicariaceae to previous intrafamiliar classifications. Frey (1949) with modifications of Clades 1Imshaug (1957) or ²Motyka (1964) Llano (1950), modifyed by Wei & Jiang (1993) Clade 1 Lasallia subg. Lasallia Lasallia subg. Lasallia Umbilicaria subg. Gyrophoropsis p. pte Umbilicaria sect. Gyrophoropsis p. pte Clade 2a Umbilicaria Umbilicaria Subg. Umbilicaria, sect. Glabrae p. pte Subg. Umbilicaria, sect. Umbilicaria p. pte Subg. Umbilicaria, sect. Vellea p. pte Clade 2b Subg. Umbilicaria, sect. Vellea p. pte Subg. Actinogyra p. pte Clade 2c Subg. Umbilicaria, sect. Glabrae p. pte Subg. Umbilicaria, sect. Umbilicaria p. pte Clade 3 Umbilicaria Umbilicaria Subg. Umbilicaria, sect. Anthracinae p. pte Subg. Omphalodiscus, sect. Omphalodiscus (= Subg. Umbilicaria, sect. Decussatae1) Subg. Umbilicaria, sect. Umbilicaria p. pte Subg. Umbilicaria, sect. Glabrae p. pte Subg. Polymorphae (= subg. Umbilicaria2) Subg. Umbilicaria, sect. Vellea p. pte Clade 4 Umbilicaria Umbilicaria Subg. Umbilicaria, sect. Vellea p. pte Subg. Actinogyra p. pte Subg. Actinogyra p. pte2 Clade 5 Umbilicaria Umbilicaria Subg. Umbilicaria, sect. Anthracinae p. pte Subg. Agyrophora Subg. Umbilicaria, sect. Anthracinae1 Subg. Omphalodiscus sect. Spodochroae p. pte Subg. Gyrophoropsis p. pte Clade 6 Umbilicaria Umbilicaria Subg. Gyrophoropsis p. pte Subg. Actinogyra p. pte Subg. Umbilicaria, sect. Vellea p. pte Subg. Agyrophora Subg. Umbilicaria, sect. Glabrae p. pte Subg. Umbilicaria sect. Gyrophoropsis p. pte Subg. Omphalodiscus sect. Spodochroae p. pte Subg. Umbilicaria sect. Umbilicaria p. pte

Literature cited Imshaug, H.A. 1957. Alpine lichens of western United States and adjacent Canada. I. The Macrolichens. Bryologist 60: 177–272. https://doi.org/10.2307/3240365 Motyka, J. 1964. Flora Polska, vol. 3(2), Porosty (Lichenes). Warsaw: Panstwowe Wydawnictwo Naukowe. Wei, J.C. & Jiang, Y.M. 1993. The Asian Umbilicariaceae (Ascomycota). Mycosystema Monographicum Series, No. 1. Beijing: International Academic Publishers.

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Table S5. Number of biosynthetical steps for secondary compounds synthesis from orcellinic acid. Number of biosynthesis steps for Compound Additional compound Process Resulting compound synthesis from orcellinic acid Orcellinic acid Orcellinic a. dehydration Lecanoric a. 1 Lecanoric a. Orcellinic a. dehydration Gyrophoric a. 2 Gyrophoric a. methylation Umbilicaric a. 3 Gyrophoric a. methylation Ovoic a. 3 Gyrophoric a. hydroxylation Hiasic a. 3 Gyrophoric a. 5-hydroxylation, smiles rearrangement Crustinic a. 4 Gyrophoric a. 3-hydroxylation, smiles rearrangement Lasallic a. 4 Orcellinic a. C-methylation β-Orcellinic a. 1 β-Orsellinic a. O-methylation Methyl β-Orsellinate 2 Methyl β-Orsellinate Methyl β-Orsellinate dehydration Methyl 4-O-Demethylbarbatate 3 Methyl 4-O-Demethylbarbatate oxidation Atranorin 4 β-Orcellinic a. β-Orcellinic a. dehydration 4-O-demethylbarbatic 2 4-O-demethylbarbatic oxidation Hypoprotocetraric 3 Hypoprotocetraric oxidation Norstictic a. 4 Norstictic a. O-methylation Stictic a. 5

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1.0/93 U. hispanica 2 1.0/100 U. hispanica 1 1.0/97 U. pustulata 2 U. pustulata 1 0.97/72 0.82/72 U. pustulata 4 1.0/99 U. pustulata 3 1.0/100 1.0/ U. asiae-orientalis 1 100 U. daliensis var. caeongshanensis 1.0/ Clade 1: Lasallia 0.84/79 100 U. rossica 1 0.52/32 U. rossica 2 0.91/58 U. papulosa 1 1.0/100 U. pensylvanica 1 U. pertusa 2 1.0/83 U. caroliniana 1 1.0/82 U. kisovana Clade 2a: Iwatakia 1.0/76 U. mammulata 0.90/37 U. muehlenbergii 1 Clade 2b: Actinogyra U. deusta 1 1.0/99 U. arctica (1) 1 Clade 2c: Floccularia 1.0/100 U. iberica 1 1.0/99 U. polyphylla 2 1.0/100 U. hyperborea group 0.58/- U. polyphylla 1 U. hyperborea 1 U. arctica (2) 1.0/100 U. indica 1.0/100 U. thamnodes 1 0.91/45 U. badia group 1.0/90 U. badia 0.92/64 U. pseudocinerascens 1.0/100 U. hypococcinea 1.0/99 U. formosana 1 Clade 3: Umbilicaria 0.92/63 U. rhizinata 1.0/100 1.0/93 0.98/- U. africana 1* U. aprina group U. aprina 1 1.0/95 U. cylindrica 1 1.0/100 U. umbilicarioides 1 Fig. S1. Phylogenetic relationships 0.79/- 1.0/91 U. dendrophora 1 U. cylindrica group U. altaiensis 1 among Umbilicariaceae based on 1.0/41 1.0/94 U. decussata 1 combined RPB2, ITS, and mtLSU 1.0/100 1.0/83 1.0/71 U. decussata 2 1.0/100 U. decussata 3 sequence data. Posterior prob- 1.0/ U. polaris 2 U. decussata group abilities of MCMCMC Bayesian 1.0/100 100 U. polaris 1 analysis and bootstrap support U. virginis 1 0.98/79 U. proboscidea 1 values of best scoring tree found U. havaasii 1 by the RAxML are noted above 1.0/98 U. polyrhiza 2 or to the left of the respective U. polyrhiza 1 Clade 4: Umbilicariopsis 1.0/100 U. subglabra 1 branches; Lines in bold indicate 0.99/76 U. subglabra var. pallens clades with posterior probability 0.79/- U. rigida 1 0.95 or higher and bootstrap sup- 1.0/93 1.0/100 U. leiocarpa 2 Clade 5: Agyrophora U. leiocarpa 1 port 70% or higher. Two species U. lambii showing phylogenetic conflict 0.64/66 U. spodochroa (1) 2 1.0/100 U. spodochroa (1) 1 between markers (Appendix 2) U. spodochroa (1) 3 marked with asterix; includ- U. cinereorufescens 1 1.0/93 1.0/ ing those species had no impact 100 U. cinereorufescens 6 U. cinereorufescens 3 overall tree topology. 1.0/72 0.75/75 U. cinereorufescens 2 0.63/- 1.0/100 U. vellea (2) 2 1.0/100 U. vellea (2) 1 U. crustulosa var. badiofusca 1.0/95 U. crustulosa (2) 1 U. vellea (1) 3 1.0/100 U. vellea (1) 2 U. vellea group 0.97/98 U. vellea (1) 6 1.0/97 U. vellea (1) 1 U. josiae 1* 1.0/84 1.0/100 U. hirsuta 2 1.0/97 Clade 6: Gyrophora 1.0/95 U. hirsuta 1 1.0/100 U. hirsuta 4 U. spodochroa (2) 0.65/- U. crustulosa (1) 3 1.0/100 1.0/100 U. crustulosa (1) 2 0.66/- U. crustulosa (1) 1 1.0/100 U. freyi 1 1.0/90 U. freyi 2 U. grisea 1 1.0/99 U. tylorhiza 1.0/100 U. torrefacta 3 U. torrefacta 1 1.0/95 U. angulata 1 U. angulata group U. semitensis 1 U. pulvinaria Xylopsora friesii 20.0 S8 TAXON 66 (6) • December 2017 Electr. Suppl. to: Davydov & al. • Umbilicariaceae phylogney

1 0.13 1HM161474_U_haplocarpa 0.1 1 HM161475_U_haplocarpa 0.13 0.64 1 HM161479_U_leprosa Fig. S2. 1 HM161487_U_haplocarpa Consensus phylogram from 1 0.73 1 HM161476_U_haplocarpa HM161477_U_haplocarpa 0.23 1 1 HM161472_U_haplocarpa 0.91 1 HM161464_U_dichroa 1 HM161466_U_haplocarpa a Bayesian analysis of a matrix with 0.36 0.99 HM161470_U_haplocarpa 0.2 1 0.21 1 HM161471_U_haplocarpa 0.79 1 1 HM161468_U_haplocarpa 1 HM161469_U_haplocarpa 1 HM161467_U_haplocarpa 321 accessions and 442 basepairs from HM161465_U_dichroa 1 0.59 1 HM161459_U_calvescens 0.37 HM161484_U_calvescens1 1 HM161506_U_calvescens 0.58 0.92 1 1 HM161507_U_calvescens 0.45 nuclear ITS region. The Bayesian pos- 1 1 HM161458_U_calvescens 1 HM161508_U_calvescens 0.67 0.96 1 HM161460_U_calvescens HM161485_U_calvescens 1 0.81 1 1 HM161486_U_calvescens 0.96 HM161461_U_calvescens terior probability values are reported 1 1 1 1 HM161462_U_calvescens 1 HM161478_U_leprosa 0.89 1 HM161463_U_calvescens agrED350_U_phaea 1 1 1 AF096207_U_spodochroa above branches, the species names 1 agrED108_1 U_spodochroa1 0.64 0.49 1 agrED226_U_spodochroa1 0.57 1 agrED386_U_spodochroa1 AF096218_U_americana1 1 1 agrED307_U_semitensis 1 corresponding to the sequences are 1 JQ764742_U_semitensis 1 0.87 1 JQ764735_U_semitensis 1 JQ764743_U_semitensis 0.62 JQ764745_U_semitensis 1 0.99 JQ764738_U_angulata 1 1 1 JQ764746_U_angulata preceded by the GenBank accession 0.41 1 JQ764734_U_angulata 0.14 1 agrED012_U_muehlenbergii 0.11 1 JF796694_U_muehlenbergii 0.14 0.72 1 agrED050_U_muehlenbergii JQ036210_U_muehlenbergii number. 1 1 AF096204_1 U_muehlenbergii 0.34 1 AF297666_U_muehlenbergii 1 HQ455534_U_muehlenbergii 0.12 0.3 1 AF096206_U_deusta 0.06 1 agrED041_U_deusta 0.11 0.18 1 agrED090_U_deusta 1 JQ036205_U_deusta 1 0.97 1 AF297670_U_deusta 1JQ036207_U_deusta agrED087_U_deusta 1 0.56 0.36 1 JF796686_U_esculenta 1 JQ004672_U_esculenta 0.13 1 1 JQ036197_U_esculenta 0.82 JQ004640_1 U_esculenta 0.97 1 JQ004668_U_esculenta 0.11 1 agrED411_U_esculenta 0.05 0.94 1 JQ009373_U_esculenta 0.11 1 JQ004664_U_esculenta 0.99 1 JQ004686_U_esculenta 1 JQ004669_U_esculenta 1 0.89 1JQ009375_U_esculenta 1 JQ061245_U_esculenta 0.99 1 AF284448_1 U_mammulata 1 agrED218_U_mammulata 0.51 1 1 acpED463_U_yunnana 0.37 0.78 1 agrED080_U_yunnana 1 acpED444_U_kisovana acpED467_Xylopsora_friesii1 0.19 1 AF096200_U_subglabra 0.89 1 agrED028_U_subglabra 0.19 1 1 agrED045_U_subglabra 1agrED046_U_subglabra 0.68 0.85 1 agrED390_U_pallens 0.99 1 agrED421_U_subglabra 1 agrED356_U_laevis 0.58 0.92 1agrED051_U_cinerascens agrED099_U_cinerascens1 1 1 AF096219_U_ruebeliana 1 agrED379_U_ruebeliana 0.33 AF096212_U_rigida 1 0.93 1 0.93 1 HM161455_U_rigida agrED024_U_rigida 1 1 1AF096211_U_leiocarpa 1 agrED359_1 U_leiocarpa 0.47 1 agrED372_U_leiocarpa 0.58 1 AF096217_U_lyngei 0.95 agrED084_U_lyngei 1 1 1 AF297669_U_lyngei 0.99 1agrED124_U_lyngei agrED128_U_lyngei 1 0.11 1 agrED030_U_cinereorufescens 0.05 agrED073_1 U_cinereorufescens 0.11 0.94 1 agrED097_U_cinereorufescens 1 agrED183_U_cinereorufescens 0.12 0.97 1 agrED074_U_cinereorufescens agrED333_1 U_cinereorufescens 0.34 HM161490_U_vellea 0.99 1 1 1 HM161511_U_cinereorufescens 1 HM161503_U_cinereorufescens 1 agrED423_U_phaea 1 0.15 1 agrED094_U_vellea2 0.14 1 agrED301_U_vellea2 0.14 0.93 1 agrED156_U_vellea2 0.76 1 FN185984_U_vellea 1 FN185983_U_vellea 0.17 agrED353_U_badiofusca1 0.15 0.14 1 agrED118_U_crustulosa1 0.15 1 HM161497_U_crustulosa 0.15 1 1 agrED225_U_crustulosa1 0.68 1 agrED373_U_crustulosa1 1 AF096215_U_crustulosa 1 AF297671_U_loboperipherica 0.13 0.34 agrED057_U_crustulosa2 1 1 1 HM161499_U_crustulosa 0.57 1 HM161498_U_crustulosa 0.35 agrED211_U_freyi 1 1 1 HM161500_U_grisea 0.29 agrED371_1 U_freyi 0.34 1 agrED044_U_hirsuta 1 agrED122_U_hirsuta 0.19 1 1 agrED123_U_hirsuta 0.2 0.85 1 HM161491_U_grisea 1 HM161495_U_hirsuta 1 1 HM161494_U_hirsuta 0.21 agrED224_U_hirsuta 1 1 0.23 agrED380_U_josiae 0.87 1 1 agrED358_U_josiae HM161493_U_grisea 1 0.11 0.89 0.98 1 AF096208_U_vellea 0.04 1 agrED032_U_vellea1 0.11 0.79 1 agrED127_U_vellea1 0.31 1 agrED134_U_vellea1 1 0.11 1 agrED004_U_vellea1 1 agrED310_U_vellea1 1 agrED155_U_vellea1 agrED164_1 U_tylorhiza 0.31 1 agrED365_1 U_grisea agrED400_1 U_grisea 0.96 1 agrED154_U_torrefacta 1 DQ660906_U_torrefacta 1 1 1 agrED095_U_torrefacta 0.55 0.3 0.61 1 agrED016_U_torrefacta 1 JQ764744_U_torrefacta 1 agrED056_U_spodochroa2 0.77 JQ764733_U_phaea 0.58 1 0.35 1 1 JQ764741_U_phaea 0.84 1 agrED184_U_hypococcinea 1 JQ764736_U_phaea 1 acpED017_U_lambii 1 KJ740718_U_nodulospora 1 1 1 KJ740719_U_nodulospora 1 KJ740720_U_nodulospora acpED018_U_pulvinaria 1 0.15 1 agrED212_L_pustulata 0.16 1 HM161456_L_pustulata 0.15 0.87 1 agrED213_L_pustulata 0.66 1 agrED214_L_pustulata 1 1 agrED107_L_pustulata agrED027_L_pustulata1 1 1 agrED106_L_hispanica1 1 agrED223_L_hispanica 0.94 1 1 agrED065_L_asiae-orientalis 1 agrED096_L_daliensis_caeongshanensis acpED419_1 L_papulosa 0.91 0.85 AF096201_L_rossica 1 1 0.54 1 agrED033_L_rossica agrED014_L_rossica 1 1 agrED008_1L_rossica 0.96 1 1 agrED006_L_rossica 1 agrED052_L_rossica 0.33 agrED017_L_pertusa 0.98 1 1 1 EU909466_L_pertusa 1 AF096203_L_pertusa 1 1 agrED221_L_pertusa 0.19 1 AF096202_L_pensylvanica 0.79 1 agrED102_L_pensylvanica 0.18 1 1 AF297674_L_pensylvanica agrED007_1 L_pensylvanica 1 0.73 1 AF297675_L_pensylvanica 1 HM161513_L_pensylvanica 0.56 agrED010_L_caroliniana 1 1 1 agrED163_L_caroliniana 1 agrED311_L_caroliniana 0.2 FN185976_U_polyphylla 0.2 1 1 1 FN185978_U_polyphylla 0.51 1 FN185979_U_polyphylla 1 FN185977_U_polyphylla 0.49 1 agrED135_U_polyphylla 0.33 0.2 agrED110_U_polyphylla 0.21 1 1 1 FN185975_U_polyphylla 1 1 agrED112_U_polyphylla 1 agrED061_U_polyphylla 0.34 FN185964_U_iberica 1 1 0.16 0.97 1 FN185965_U_iberica 1 FN185966_U_iberica 1 agrED397_U_iberica 0.32 1 1 AF096205_U_nylanderiana 0.87 FN185974_1 U_nyladeriana 0.76 1 agrED133_U_nylanderiana 1 1 agrED401_U_nylanderiana 0.2 0.16 1 agrED345_U_nylanderiana 0.9 1 HM161489_U_nyladeriana 0.2 0.96 0.52 1 AY603133_U_nyladeriana 1HM161488_U_nyladeriana 0.99 agrED011_U_proboscidea 0.99 1 0.43 HM161454_1 U_arctica 1 agrED042_U_arctica 1 agrED320_U_radicicula 0.99 AF096216_U_hyperborea 1 1 1 agrED013_U_hyperborea 1 agrED003_U_hyperborea 1 FN185930_U_aprina 0.44 1 1 FN185931_U_aprina 0.17 agrED075_1U_virginis 1 agrED415_U_havaasii 0.49 1 1 JQ764739_U_havaasii agrED306_U_virginis 1 0.34 1 FN185941_U_cf_umbilicarioides 1 FN186102_"U_vellea" 0.69 1 1 agrED086_U_cylindrica 0.61 AF096209_U_cylindrica 0.65 1 1agrED092_U_cylindrica 0.34 1 agrED157_U_cylindrica 0.86 1 1 agrED158_U_cylindrica 1 agrED009_U_cylindrica 0.2 0.97 1 FN185980_U_cf_umbilicarioides 1 FN185981_U_cf_umbilicarioides 0.56 0.35 1 agrED362_U_dendrophora 0.34 1 agrED426_U_maculata 0.21 1 AF096210_U_umbilicarioides 1 1 1 AY603121_U_umbilicarioides 0.2 1agrED109_U_umbilicarioides 1 agrED348_U_umbilicarioides agrED292_U_cylindrica1 0.32 agrED070_U_altaiensis 0.91 1 1 1 agrED077_U_altaiensis 0.94 agrED048_U_altaiensis 0.66 1 agrED020_1 U_altaiensis 1 1 1 agrED205_U_maculata 1 agrED206_U_maculata 0.78 1 agrED291_U_altaiensis 0.99 0.97 HM161504_U_dendrophora 0.34 1 0.35 1 1 HM161509_U_dendrophora HM161505_1 U_dendrophora 1 agrED085_U_dendrophora 1 agrED116_U_altaiensis agrED115_U_altaiensis 1 0.86 0.36 1 FN185967_U_maculata 0.16 FN185968_U_maculata 1 0.64 1 1agrED130_U_maculata 0.17 0.94 1 agrED129_U_maculata 0.93 1 FN185969_U_maculata 1 AF096199_U_cylindrica 1 FN185970_U_sp1 0.66 FN185971_U_maculata 1 1 0.13 1FN185972_U_sp 0.4 1 FN185973_U_maculata 0.97 1FN185933_U_cylindrica 0.32 FN185942_U_cylindrica 0.22 0.92 1 1 1 FN185982_U_cylindrica 1 FN185938_U_cylindrica 1 FN185934_U_cylindrica 1 AF297673_1 U_virginis agrED160_U_virginis 1 0.11 1 AF096213_U_antarctica 0.05 1 AJ431604_U_antarctica 0.11 0.91 1 AY603123_U_antarctica 1 FN185922_U_antarctica 0.11 1 1agrED367_U_antarctica 1 AY603125_U_antarctica 0.2 AY603129_U_kappenii 0.49 0.21 1 1 AY603131_U_kappenii 1 AY603124_U_antarctica 0.4 0.82 1 acpED016_U_formosana 1 agrED295_U_rhizinata 0.91 agrED360_U_aprina1 0.34 1 acpED473_U_africana 0.93 1 0.78 0.99 1 HM161483_U_aprina 1 HM161502_U_aprina 0.67 1 agrED165_U_formosana agrED417_U_aprina1 1 agrED040_U_krascheninnikovii 0.94 1 1 agrED414_U_krascheninnikovii 0.7 agrED182_U_aprina 1 0.39 agrED078_U_indica 0.97 1 1 1 agrED227_U_thamnodes agrED079_1 U_thamnodes 0.27 0.52 1 acpED462_U_badia 1 agrED173_U_aprina 0.63 1 0.36 1 agrED352_U_africana 1 HM161482_U_africana acpED472_U_havaasii1 0.32 0.86 1 agrED166_U_pseudocinerascens 1 agrED293_U_proboscidea 0.3 AF096214_U_decussata 0.79 1 1 1 agrED022_U_decussata agrED132_U_decussata 0.92 1 1 HM161501_U_decussata 0.34 0.85 1agrED053_U_polaris 1 agrED125_U_decussata 1 1 agrED018_U_polaris 1 0.85 agrED296_1 U_polaris 1 1 AY603134_U_polaris 0.34 HM161510_U_decussata 1 1 1 agrED114_U_decussata 1 1 agrED174_U_decussata 0.78 1 AY603122_U_decussata 1 agrED332_U_arctica 1 1 agrED060_U_polyrhiza 1 1 agrED111_U_polyrhiza 0.71 1agrED331_U_polyrhiza 1 JQ764737_U_polyrrhiza 1 K_OA2732_Hypocenomyce_scalaris 1 acpED469_Ophioparma_ventosa acpED443_Boreoplaca_ultrafrigida

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S9 TAXON 66 (6) • December 2017 Electr. Suppl. to: Electr. Suppl. to: Davydov & al. • Umbilicariaceae phylogney

12 HM161479_U_leprosa 8 30HM161476_U_haplocarpa 62 HM161487_U_haplocarpa 82 HM161474_U_haplocarpa 58 HM161475_U_haplocarpa HM161477_U_haplocarpa HM161472_U_haplocarpa 15 82 HM161470_U_haplocarpa 26 HM161471_U_haplocarpa 19 Fig. S3. Best scoring tree found by the RAxML analysis of a matrix 42 83 HM161467_U_haplocarpa HM161469_U_haplocarpa 44 HM161468_U_haplocarpa 68 HM161464_U_dichroa HM161466_U_haplocarpa HM161465_U_dichroa 69 HM161459_U_calvescens with 321 accessions and 442 basepairs from nuclear ITS region. The 37 HM161484_U_calvescens 88 65 HM161507_U_calvescens 71 HM161506_U_calvescens 74 42 HM161508_U_calvescens HM161458_U_calvescens 46 67 HM161460_U_calvescens HM161485_U_calvescens maximum likelihood bootstrap support values are noted above the 89 39 HM161486_U_calvescens 90 HM161462_U_calvescens 100 83 HM161461_U_calvescens HM161478_U_leprosa 20 HM161463_U_calvescens agrED350_U_phaea 100 agrED108_U_spodochroa1 respective branches, the species names corresponding to the sequences 100 AF096207_U_spodochroa 22 65 2 agrED386_U_spodochroa1 agrED226_U_spodochroa1 AF096218_U_americana 100 JQ764742_U_semitensis 99 agrED307_U_semitensis 3 51 100 JQ764743_U_semitensis are preceded by the GenBank accession number. JQ764735_U_semitensis JQ764745_U_semitensis 100 JQ764746_U_angulata 100 JQ764738_U_angulata 1 JQ764734_U_angulata 21JQ036210_U_muehlenbergii 21 8 AF096204_U_muehlenbergii 82 JF796694_U_muehlenbergii 29 agrED050_U_muehlenbergii 100 agrED012_U_muehlenbergii 3 HQ455534_U_muehlenbergii AF297666_U_muehlenbergii 15AF096206_U_deusta 27 37JQ036205_U_deusta agrED041_U_deusta 70 agrED090_U_deusta 95 87 JQ036207_U_deusta AF297670_U_deusta agrED087_U_deusta 15agrED411_U_esculenta 2 19JQ009373_U_esculenta JQ004686_U_esculenta 3 29JQ004664_U_esculenta 46 JQ004668_U_esculenta 53 JQ004640_U_esculenta 67 62 JF796686_U_esculenta 86 JQ004672_U_esculenta 87 JQ036197_U_esculenta JQ004669_U_esculenta 100 72 JQ009375_U_esculenta JQ061245_U_esculenta 82 69 agrED218_U_mammulata AF284448_U_mammulata 27 100 agrED080_U_yunnana 26 acpED463_U_yunnana acpED444_U_kisovana acpED467_Xylopsora_friesii 1 41AF096200_U_subglabra 84 agrED028_U_subglabra 72 100 agrED045_U_subglabra agrED046_U_subglabra 52 85 agrED421_U_subglabra 87 agrED390_U_pallens agrED356_U_laevis 78 90 agrED099_U_cinerascens agrED051_U_cinerascens 100 AF096219_U_ruebeliana 21 agrED379_U_ruebeliana 0 71 AF096217_U_lyngei 69 agrED084_U_lyngei 91 AF297669_U_lyngei 93 62 agrED124_U_lyngei agrED128_U_lyngei 65HM161455_U_rigida 63 81 AF096212_U_rigida 0 agrED024_U_rigida 81 AF096211_U_leiocarpa 97 agrED372_U_leiocarpa agrED359_U_leiocarpa 99 KJ740719_U_nodulospora 96 KJ740718_U_nodulospora KJ740720_U_nodulospora acpED018_U_pulvinaria 39HM161491_U_grisea 50HM161494_U_hirsuta 62 HM161495_U_hirsuta 29agrED044_U_hirsuta 89 92 agrED122_U_hirsuta agrED123_U_hirsuta 25 92 agrED380_U_josiae 32agrED224_U_hirsuta agrED358_U_josiae HM161493_U_grisea 11agrED032_U_vellea1 60 7 28agrED127_U_vellea1 30agrED310_U_vellea1 81 agrED004_U_vellea1 12 100 agrED134_U_vellea1 AF096208_U_vellea agrED155_U_vellea1 72 5 HM161498_U_crustulosa 100 HM161499_U_crustulosa agrED057_U_crustulosa2 74agrED211_U_freyi 100 24 HM161500_U_grisea 3 agrED371_U_freyi 23agrED118_U_crustulosa1 47 48agrED225_U_crustulosa1 100 agrED373_U_crustulosa1 28 HM161497_U_crustulosa AF096215_U_crustulosa AF297671_U_loboperipherica 82 agrED073_U_cinereorufescens 30 agrED074_U_cinereorufescens 21 agrED097_U_cinereorufescens 15 76 51agrED333_U_cinereorufescens agrED183_U_cinereorufescens 71 agrED030_U_cinereorufescens 80HM161490_U_vellea 66 81 HM161503_U_cinereorufescens HM161511_U_cinereorufescens agrED423_U_phaea 4 81 22agrED156_U_vellea2 8 66agrED301_U_vellea2 FN185983_U_vellea 12 95 65 FN185984_U_vellea agrED094_U_vellea2 agrED353_U_badiofusca 1 agrED164_U_tylorhiza 100 agrED400_U_grisea agrED365_U_grisea 97 DQ660906_U_torrefacta 89 agrED154_U_torrefacta 94 agrED095_U_torrefacta 2 21 62 agrED016_U_torrefacta JQ764744_U_torrefacta agrED056_U_spodochroa2 84 JQ764733_U_phaea 59 93 JQ764741_U_phaea 32 agrED184_U_hypococcinea JQ764736_U_phaea 0 acpED017_U_lambii 33FN185941_U_cf_umbilicarioides 95 agrED086_U_cylindrica 52 FN186102_U_vellea 52 AF096209_U_cylindrica 47 agrED092_U_cylindrica 35agrED158_U_cylindrica 63 98 agrED009_U_cylindrica agrED157_U_cylindrica 80 FN185980_U_cf_umbilicarioides 10 FN185981_U_cf_umbilicarioides 33agrED109_U_umbilicarioides 60 26 99 AY603121_U_umbilicarioides AF096210_U_umbilicarioides 89 agrED348_U_umbilicarioides 55 agrED362_U_dendrophora 26 agrED426_U_maculata agrED292_U_cylindrica agrED116_U_altaiensis 32agrED048_U_altaiensis 84 agrED077_U_altaiensis 54 97 agrED070_U_altaiensis 90 agrED020_U_altaiensis 98 99 agrED205_U_maculata agrED206_U_maculata 80 62 agrED291_U_altaiensis 74 HM161509_U_dendrophora 73 95 HM161504_U_dendrophora HM161505_U_dendrophora agrED085_U_dendrophora agrED115_U_altaiensis 33 11 agrED129_U_maculata 18 FN185969_U_maculata 71 agrED130_U_maculata 79 66 FN185967_U_maculata 75 FN185968_U_sp AF096199_U_cylindrica 61 93 FN185970_U_maculata 74 FN185972_U_maculata 97 FN185971_U_maculata FN185973_U_maculata 77 FN185942_U_cylindrica 24 63 FN185933_U_cylindrica 100 FN185982_U_cylindrica FN185938_U_cylindrica FN185934_U_cylindrica 13agrED214_L_pustulata 6 12 agrED107_L_pustulata 50 agrED212_L_pustulata 59 HM161456_L_pustulata agrED213_L_pustulata 100 agrED027_L_pustulata 97 81 agrED106_L_hispanica agrED223_L_hispanica 71 100 agrED065_L_asiae-orientalis agrED096_L_daliensis_caeongshanensis acpED419_L_papulosa 87 AF096201_L_rossica 66 97 88 agrED033_L_rossica agrED014_L_rossica 99 agrED008_L_rossica 98 agrED006_L_rossica 48 agrED052_L_rossica 65agrED017_L_pertusa 94 100 EU909466_L_pertusa 100 AF096203_L_pertusa 2 agrED221_L_pertusa 27agrED007_L_pensylvanica 16 87 AF297674_L_pensylvanica AF096202_L_pensylvanica 100 11 agrED102_L_pensylvanica 95 AF297675_L_pensylvanica 63 HM161513_L_pensylvanica 47 agrED163_L_caroliniana 98 agrED311_L_caroliniana 0 agrED010_L_caroliniana agrED306_U_virginis 89 FN185930_U_aprina 26 FN185931_U_aprina 0 agrED075_U_virginis 100 agrED415_U_havaasii 21 JQ764739_U_havaasii agrED166_U_pseudocinerascens 20FN185977_U_polyphylla 31 99 FN185978_U_polyphylla 51 FN185979_U_polyphylla FN185976_U_polyphylla 67 agrED135_U_polyphylla 66agrED112_U_polyphylla 49 100 FN185975_U_polyphylla 98 agrED110_U_polyphylla 1 agrED061_U_polyphylla 35FN185965_U_iberica 100 66 FN185966_U_iberica FN185964_U_iberica agrED397_U_iberica 55 agrED133_U_nylanderiana 14 92 72 agrED401_U_nylanderiana FN185974_U_nylanderiana 96 AF096205_U_nylanderiana 21HM161489_U_nyladeriana 16 89 HM161488_U_nyladeriana 39 agrED345_U_nylanderiana 56 AY603133_U_nyladeriana 61 100 HM161454_U_arctica 87 agrED011_U_proboscidea agrED042_U_arctica 7 agrED320_U_radicicula 13 97 AF096216_U_hyperborea 94 agrED013_U_hyperborea agrED003_U_hyperborea 42 agrED227_U_thamnodes 91 0 92 agrED078_U_indica agrED079_U_thamnodes acpED462_U_badia 3 FN185922_U_antarctica 2 AY603123_U_antarctica 94 AF096213_U_antarctica 65 AJ431604_U_antarctica agrED367_U_antarctica 98 AY603125_U_antarctica 23AY603131_U_kappenii 25 30AY603124_U_antarctica AY603129_U_kappenii 1 agrED360_U_aprina 0 35 HM161483_U_aprina 96 41 71 acpED473_U_africana HM161502_U_aprina 33 agrED165_U_formosana 75 agrED295_U_rhizinata 36 acpED016_U_formosana 34 agrED417_U_aprina 2 99 agrED040_U_krascheninnikovii 60 47 agrED414_U_krascheninnikovii agrED182_U_aprina 100 agrED352_U_africana 68 agrED173_U_aprina HM161482_U_africana acpED472_U_havaasii agrED293_U_proboscidea 33agrED022_U_decussata 87 76 agrED132_U_decussata AF096214_U_decussata 42 39 HM161501_U_decussata 66 48 agrED125_U_decussata agrED053_U_polaris 1 95 agrED296_U_polaris agrED018_U_polaris 97 agrED160_U_virginis 19 AF297673_U_virginis 87 AY603122_U_decussata 99 31 agrED174_U_decussata 79 89 HM161510_U_decussata AY603134_U_polaris agrED114_U_decussata 49 agrED332_U_arctica 87 agrED111_U_polyrhiza agrED060_U_polyrhiza 99 JQ764737_U_polyrrhiza agrED331_U_polyrhiza K_OA2732_Hypocenomyce_scalaris acpED443_Boreoplaca_ultrafrigida acpED469_Ophioparma_ventosa

0.06

S10 TAXON 66 (6) • December 2017 Electr. Suppl. to: Electr. Suppl. to: Davydov & al. • Umbilicariaceae phylogney

1 0.81 Fig. S4. Consensus phylogram from a Bayesian analy- 1 agrED013_Umbilicaria_hyperborea 0.99 agrED397_Umbilicaria_iberica sis of a matrix with 67 accessions and 1516 basepairs 0.75 1 1 agrED011_Umbilicaria_proboscidea from nuclear SSU region. The Bayesian posterior 0.71 1 agrED022_Umbilicaria_decussata 0.92 agrED295_Umbilicaria_rhizinata probability values are reported above branches, the 0.98 1 0.43 1agrED360_Umbilicaria_aprina species names corresponding to the sequences are 1 agrED078_Umbilicaria_indica 0.99 JQ004727_Umbilicaria_deusta preceded by the GenBank accession number. 0.26 1 0.32 1 JQ004728_Umbilicaria_deusta agrED353_1 Umbilicaria_crustulosa_badiofusca 0.14 1 agrED030_Umbilicaria_cinereorufescens 0.28 1 agrED400_Umbilicaria_grisea 0.16 1 agrED044_Umbilicaria_hirsuta agrED358_Umbilicaria_josiae1 0.98 0.18 1 agrED014_Lasallia_rossica 0.76 agrED033_Lasallia_rossica 1 1 0.96 1 AF088238_Lasallia_rossica 0.19 1 agrED017_Lasallia_pertusa AY648108_Lasallia_pensylvanica 0.94 1 0.16 1 agrED012_Umbilicaria_muehlenbergii 0.19 0.81 1 agrED050_Umbilicaria_muehlenbergii 1AY648115_Umbilicaria_muehlenbergii 0.96 agrED124_Umbilicaria_lyngei 0.49 1 1 AY648118_Umbilicaria_yunnana 0.42 agrED371_1 Umbilicaria_freyi 1 1 AY648117_Umbilicaria_vellea 0.16 1 agrED118_Umbilicaria_crustulosa 0.62 1 agrED373_Umbilicaria_crustulosa agrED004_Umbilicaria_vellea 1 1 AF274112_Diploschistes_thunbergianus 0.53 1 1 agrED150_Pertusaria_alpina 1agrED147_Ochrolechia_parella 0.28 1 AM495015_Teloschistes_chrysophthalmus 1 1 JQ301630_1 Teloschistes_exilis 0.74 1 AF091585_Bacidia_rosella 1 0.41 0.98 1 AF515608_Lecanora_allophana 0.56 1 AY584658_Canoparmelia_caroliniana AY584679_1 Lobaria_scrobiculata 0.99 1 AF085473_Dibaeis_baeomyces AY552543_Acarospora_smaragdula_lesdainii 1 1 AF242260_Caliciopsis_pinea 1 1 1 DQ678043_Caliciopsis_pinea 0.55 1 EF689834_Dermatocarpon_miniatum 1 1 AJ421686_Physcia_adscendens 0.92 DQ470993_1 Leptosphaeria_maculans 1 0.68 AY548809_Schismatomma_decolorans1 0.67 1 DQ883706_Opegrapha_dolomitica DQ479933_1 Dothiora_cannabinae AF282913_Peltula_obscurans 1 0.85 1 AB003950_Bionectria_ochroleuca 0.81 1 AB079125_Cordyceps_bassiana 0.98 1 1 PSU43908_Petriella_setifera 0.82 1 DQ470989_Camarops_ustulinoides 1 1 DQ470996_Lanspora_coronata 1 1 1 HQ634835_Graphium_sp 0.92 EDORGEAA_Endothia_gyrosa 1 1 1 AY544719_Xylaria_acuta 0.67 1 AY544687_Leotia_lubrica 0.99 1 AY544695_Botryotinia_fuckeliana 0.85 0.5 DQ471005_Lanspora_coronata 0.36 1 1 EU107259_Bulgaria_inquinans 0.54 1 AY544688_Lachnum_virgineum AY544694_1 Geoglossum_nigritum 1 1 DQ646542_Peziza_badiofusca 1 AY544717_Gyromitra_californica 1 DQ247813_Pyronema_domesticum AF006307_Orbilia_fimicola

9.0 S11 TAXON 66 (6) • December 2017 Electr. Suppl. to: Electr. Suppl. to: Davydov & al. • Umbilicariaceae phylogney

Fig. S5. Best scoring tree found by the RAxML analysis 77 agrED014_Lasallia_rossica 81 agrED033_Lasallia_rossica of a matrix with 67 accessions and 1516 basepairs from 97 AF088238_Lasallia_rossica 67 nuclear SSU region. The maximum likelihood bootstrap agrED017_Lasallia_pertusa support values are noted above the respective branches, 59 AY648108_Lasallia_pensylvanica 54agrED012_Umbilicaria_muehlenbergii 82 the species names corresponding to the sequences are 23 AY648115_Umbilicaria_muehlenbergii preceded by the GenBank accession number. agrED050_Umbilicaria_muehlenbergii 3 61 AY648118_Umbilicaria_yunnana agrED124_Umbilicaria_lyngei 47 AY648117_Umbilicaria_vellea agrED371_Umbilicaria_freyi 1 72 agrED013_Umbilicaria_hyperborea 55 agrED397_Umbilicaria_iberica 17 agrED011_Umbilicaria_proboscidea 113 agrED022_Umbilicaria_decussata 96 agrED295_Umbilicaria_rhizinata 56 agrED360_Umbilicaria_aprina 14 agrED078_Umbilicaria_indica 75 JQ004727_Umbilicaria_deusta 4 JQ004728_Umbilicaria_deusta 1 agrED353_Umbilicaria_crustulosa_badiofusca agrED030_Umbilicaria_cinereorufescens 1349agrED044_Umbilicaria_hirsuta

47 agrED358_Umbilicaria_josiae agrED400_Umbilicaria_grisea 74 28 agrED118_Umbilicaria_crustulosa agrED373_Umbilicaria_crustulosa 23 agrED004_Umbilicaria_vellea 81 agrED150_Pertusaria_alpina 15 AF274112_Diploschistes_thunbergianus agrED147_Ochrolechia_parella 11 100 AM495015_Teloschistes_chrysophthalmus 61 JQ301630_Teloschistes_exilis 42 AF091585_Bacidia_rosella 24 51 84 AY584658_Canoparmelia_caroliniana 32 AF515608_Lecanora_allophana AY584679_Lobaria_scrobiculata 43 AF085473_Dibaeis_baeomyces AY552543_Acarospora_smaragdula_lesdainii 100 AF242260_Caliciopsis_pinea 83 DQ678043_Caliciopsis_pinea 11 EF689834_Dermatocarpon_miniatum 100 AY548809_Schismatomma_decolorans 53 DQ883706_Opegrapha_dolomitica 33 98 DQ470993_Leptosphaeria_maculans 23 AJ421686_Physcia_adscendens DQ479933_Dothiora_cannabinae AF282913_Peltula_obscurans 88 AB079125_Cordyceps_bassiana 100 AB003950_Bionectria_ochroleuca 29 56 PSU43908_Petriella_setifera 46 DQ470989_Camarops_ustulinoides 73 HQ634835_Graphium_sp 100 61 DQ470996_Lanspora_coronata 34 EDORGEAA_Endothia_gyrosa 71 9 AY544719_Xylaria_acuta AY544687_Leotia_lubrica 3 AY544688_Lachnum_virgineum 43 22 74 DQ471005_Lanspora_coronata AY544695_Botryotinia_fuckeliana 35 EU107259_Bulgaria_inquinans AY544694_Geoglossum_nigritum DQ646542_Peziza_badiofusca AY544717_Gyromitra_californica DQ247813_Pyronema_domesticum AF006307_Orbilia_fimicola

0.03 S12 TAXON 66 (6) • December 2017 Electr. Suppl. to: Davydov & al. • Umbilicariaceae phylogney

1 0.2 1 agrED212_L_pustulata 0.2 agrED213_L_pustulata Fig. S6. Consensus phylogram from a Bayesian analysis of a matrix 1 1 0.99 1 agrED027_L_pustulata with 122 accessions and 738 basepairs from RPB2 region. The 1 DQ883707_L_pustulata 1 1 agrED107_L_pustulata 0.95 agrED215_L_hispanica Bayesian posterior probability values are reported above branches, 0.97 1 1 agrED223_L_hispanica 1 agrED106_L_hispanica the species names corresponding to the sequences are preceded by 1 0.34 1 agrED171_L_papulosa 0.66 agrED419_L_papulosa the GenBank accession number. 1 1 1 agrED167_L_papulosa 0.45 1 agrED169_L_papulosa 0.87 0.97 agrED052_L_rossica 1 1 1 agrED290_L_rossica 1agrED014_L_rossica 0.98 0.99 1 agrED065_L_asiae-orientalis 1 1acpED464_L_freyana 0.94 1 agrED096_L_daliensis_caeongshanensis 0.98 1 DQ883708_L_papulosa 1 1 agrED007_L_pensylvanica 1 1 AY641048_L_pensylvanica 1 agrED221_L_pertusa 0.34agrED204_L_caroliniana 1 1 1 agrED311_L_caroliniana agrED203_L_caroliniana 1 0.33agrED122_U_hirsuta 1 1 1 agrED224_U_hirsuta 1 1agrED044_U_hirsuta 1 agrED358_U_josiae 0.7 1 1 agrED380_U_josiae 0.95 agrED156_U_vellea2 0.11 1 1 1 agrED301_U_vellea2 1 agrED353_U_badiofusca 0.04 1agrED164_U_tylorhiza 1 1 agrED108_U_spodochroa1 0.71 agrED226_1 U_spodochroa1 1 0.84 1 agrED386_U_spodochroa1 1 DQ992462_U_spodochroa 1 agrED056_U_spodochroa2 0.11 1 agrED074_U_cinereorufescens 0.06 0.09 1 agrED097_U_cinereorufescens 0.12 0.181 agrED183_U_cinereorufescens agrED333_1 U_cinereorufescens 1 1 agrED314_U_grisea 0.72 1agrED400_U_grisea 0.17 1 agrED127_U_vellea1 0.54 1 agrED134_U_vellea1 0.84 1 0.17 0.12 1 1 agrED310_U_vellea1 1 agrED004_U_vellea1 1 agrED155_U_vellea1 1 1 agrED211_U_freyi 1 agrED371_U_freyi 1 0.9 agrED225_U_crustulosa1 1 1 1 agrED373_U_crustulosa1 0.89 agrED118_1 U_crustulosa1 0.62 1 1 agrED057_U_crustulosa2 1 agrED406_U_crustulosa2 0.4 1 agrED350_U_phaea 1 agrED016_U_torrefacta 1 1 1 agrED154_U_torrefacta 0.97 1 agrED335_U_americana 0.81 1 agrED309_U_angulata 0.89 1 acpED018_U_pulvinaria 0.59 agrED307_1U_semitensis 1 acpED467_Xylopsora_friesii agrED041_1 U_deusta 0.21agrED012_U_muehlenbergii 0.77 0.251 1 FJ854405_U_muehlenbergii 1 1 FJ854408_U_muehlenbergii 0.95 1 AY641088_U_muehlenbergii 0.72 FJ854399_U_muehlenbergii1 1 1 agrED218_U_mammulata 1 acpED479_U_esculenta 1 1 0.66 acpED463_U_yunnana 0.65 1 1 acpED444_U_kisovana 0.34 1 agrED390_U_pallens 1 agrED421_U_subglabra 0.91 1 1 agrED045_U_subglabra 1 1 agrED216_U_microphylla 1 agrED024_U_rigida 1 1 1 1 agrED372_U_leiocarpa 1 agrED359_U_leiocarpa acpED017_1U_lambii 0.95 1 agrED079_U_thamnodes 1 agrED227_U_thamnodes 1 1 agrED078_U_indica 0.99 1 1 acpED462_U_badia 0.98 1 agrED184_U_hypococcinea 1 agrED166_U_pseudocinerascens 0.99 0.9 1 agrED295_U_rhizinata 1 acpED016_U_formosana 0.341 0.33 0.56 1 1 DQ992459_U_aprina 1 acpED473_U_africana 1 agrED173_U_aprina agrED306_1 U_virginis 0.83 0.89 agrED022_U_decussata 1 1 1 agrED132_U_decussata 1 1 agrED174_U_decussata 1 0.51 1 agrED018_U_polaris 0.8 1 agrED296_U_polaris 1 agrED336_U_polaris 1 0.84 0.31 1 acpED472_U_havaasii 1 agrED293_U_proboscidea 0.6 agrED292_U_cylindrica 0.94 1 1 agrED426_U_maculata 0.99 1 agrED348_U_umbilicarioides 0.97 0.63 1 agrED085_U_dendrophora 0.82 1 agrED291_U_altaiensis 1 agrED394_U_cylindrica 1 1 agrED042_U_arctica 1 DQ992460_U_arctica 1 0.71 1 agrED013_U_hyperborea agrED328_1 U_hyperborea 1 agrED060_U_polyrhiza 0.47 1 1 1 agrED331_U_polyrhiza 1 agrED332_U_arctica 1 agrED397_U_iberica 0.73 1 agrED061_U_polyphylla 1 agrED112_U_polyphylla 1 1 acpED443_Boreoplaca_ultrafrigida 1 K_OA2732_Hypocenomyce_scalaris acpED469_Ophioparma_ventosa

30.0

S13 TAXON 66 (6) • December 2017 Electr. Suppl. to: Davydov & al. • Umbilicariaceae phylogney

23 KY972602_L_pustulata Fig. S7. Best scoring tree found by the RAxML analysis of a matrix 51 KY972643_L_pustulata 89 KY972644_L_pustulata 96 with 122 accessions and 738 basepairs from RPB2 region. The maxi- DQ883707_L_pustulata 100 KY972620_L_pustulata mum likelihood bootstrap support values are noted above the respec- 92 KY972645_L_hispanica 75 KY972649_L_hispanica tive branches, the species names corresponding to the sequences are KY972619_L_hispanica 81 73 KY972688_L_papulosa preceded by the GenBank accession number. 53 KY972635_L_papulosa 100 KY972633_L_papulosa 41 KY972634_L_papulosa 77 70 KY972607_L_rossica 99 KY972654_L_rossica KY972597_L_rossica 100 KY972612_L_asiae-orientalis 87 100 KY972588_L_freyana 68 DQ883708_L_papulosa 75 KY972617_L_daliensis_caeongshanensis 100 AY641048_L_pennsylvanica KY972594_L_pennsylvanica 90 KY972648_L_pertusa 31KY972641_L_caroliniana 100 KY972665_L_caroliniana KY972640_L_caroliniana 81 KY972651_U_crustulosa1 94 KY972680_U_crustulosa1 58 KY972623_U_crustulosa1 94 KY972609_U_crustulosa2 34 KY972687_U_crustulosa2 100 KY972678_U_freyi KY972642_U_freyi 96 KY972652_U_spodochroa1 61 KY972621_U_spodochroa1

74 100 DQ992462_U_spodochroa KY972682_U_spodochroa1 KY972608_U_spodochroa2 32 KY972624_U_hirsuta 99 KY972605_U_hirsuta 97 KY972650_U_hirsuta 100 KY972681_U_josiae 45 KY972676_U_josiae 95 KY972660_U_vellea2 97 KY972630_U_vellea2 KY972675_U_badiofusca 87 KY972631_U_tylorhiza 19 KY972625_U_vellea1 15 KY972664_U_vellea1 40 88 KY972627_U_vellea1 100 KY972593_U_vellea1 27 KY972629_U_vellea1 89 100 KY972666_U_grisea

41 KY972686_U_grisea 24 KY972618_U_cinereorufescens 18 KY972613_U_cinereorufescens 30 54 KY972638_U_cinereorufescens KY972670_U_cinereorufescens KY972674_U_phaea 71 93 KY972598_U_torrefacta 40 KY972628_U_torrefacta 70 KY972663_U_angulata 56 KY972671_U_americana

52 KY972582_U_pulvinaria KY972662_U_semitensis 24 KY972589_Xylopsora_friesii KY972603_U_deusta 13 68 AY641088_U_muehlenbergii 47 FJ854399_U_muehlenbergii

100 45 FJ854405_U_muehlenbergii 30 KY972595_U_muehlenbergii FJ854408_U_muehlenbergii 100 KY972647_U_mammulata 100 KY972583_U_esculenta 82 KY972587_U_yunnana KY972585_U_kisovana 12 36 18 KY972683_U_pallens 82 KY972606_U_subglabra 57 KY972689_U_subglabra 72 KY972646_U_microphylla 100 KY972679_U_leiocarpa 75 99 KY972601_U_rigida KY972677_U_leiocarpa KY972581_U_lambii 60 KY972615_U_thamnodes 92 KY972653_U_thamnodes 100 KY972614_U_indica 73 KY972586_U_badia 78 KY972632_U_pseudocinerascens KY972639_U_hypococcinea 63 59 KY972658_U_rhizinata 78 KY972580_U_formosana 46 DQ992459_U_aprina 99 9 KY972592_U_africana KY972636_U_aprina 7 93 KY972600_U_decussata 92 KY972626_U_decussata 86 KY972637_U_decussata 67 100KY972659_U_polaris 59 KY972599_U_polaris 33 KY972672_U_polaris 55 KY972657_U_proboscidea KY972591_U_havaasii 9 96 KY972661_U_virginis 38 KY972656_U_cylindrica 72 KY972690_U_maculata 74 KY972673_U_umbilicarioides 75 80 KY972616_U_dendrophora 15 KY972655_U_altaiensis KY972684_U_cylindrica 91 KY972604_U_arctica DQ992460_U_arctica 30 100 KY972667_U_hyperborea KY972596_U_hyperborea 26 100 KY972610_U_polyrhiza KY972668_U_polyrhiza 100 KY972669_U_arctica KY972685_U_iberica 100 KY972622_U_polyphylla KY972611_U_polyphylla 87 KY972691_Hypocenomyce_scalaris KY972584_Boreoplaca_ultrafrigida KY972590_Ophioparma_ventosa

0.08

S14 TAXON 66 (6) • December 2017 Electr. Suppl. to: Davydov & al. • Umbilicariaceae phylogney

0.99 agrED052_L_rossica Fig. S8. Consensus phylogram from a Bayesian analysis of a matrix 1 agrED290_L_rossica 0.920.33 agrED014_L_rossica with 134 accessions and 739 basepairs from mitochondrial LSU agrED033_L_rossica 1 agrED419_L_papulosa region. The Bayesian posterior probability values are reported above 1 agrED065_L_asiae-orientalis 1 acpED464_L_freyana agrED096_L_daliensis_caeongshanensis branches, the species names corresponding to the sequences are pre- 0.39 0.2 agrED027_L_pustulata 0.2 agrED213_L_pustulata ceded by the GenBank accession number. 1 agrED107_L_pustulata 0.92 agrED212_L_pustulata 0.58 0.2 agrED106_L_hispanica 0.2 agrED223_L_hispanica agrED215_1 L_hispanica 0.98 0.33 agrED204_L_caroliniana 1 agrED010_L_caroliniana 1 agrED311_L_caroliniana 1 agrED221_L_pertusa 0.87 agrED017_L_pertusa agrED007_L_pensylvanica 0.98 1 acpED444_U_kisovana agrED218_U_mammulata 1 agrED012_U_muehlenbergii 0.96 agrED050_U_muehlenbergii agrED041_U_deusta 0.99 AY603142_U_kappenii 0.98 AY603136_U_antarctica 0.97 AY603135_U_antarctica 0.72 agrED367_U_antarctica 0.68 1 agrED173_U_aprina agrED352_U_africana 0.96 agrED182_U_aprina 0.25 agrED417_U_aprina 0.49 agrED360_U_aprina 0.94 1 agrED295_U_rhizinata acpED016_U_formosana 0.34 1 agrED304_U_krascheninnikovii 1 agrED040_U_krascheninnikovii agrED414_U_krascheninnikovii 0.96 0.33 acpED473_U_africana 1 agrED165_U_formosana 0.9 agrED078_U_indica 1 agrED227_U_thamnodes 0.54 1 acpED462_U_badia 1 agrED166_U_pseudocinerascens agrED184_U_hypococcinea 1 acpED027_U_altaiensis 0.44 altbED282_U_maculata 0.99 agrED292_U_cylindrica 1 agrED348_U_umbilicarioides 0.64 acpED029_U_cylindrica 0.88 0.88 agrED085_U_dendrophora 1 agrED048_U_altaiensis agrED291_U_altaiensis 0.17 agrED018_U_polaris 0.47 agrED296_U_polaris 0.98 0.16 0.63 agrED127_U_vellea1 acpED038_U_polaris 0.72 0.99 agrED022_U_decussata 1 0.3 agrED132_U_decussata agrED174_U_decussata agrED306_U_virginis agrED332_U_arctica 0.14 agrED345_U_nylanderiana 0.14 agrED133_U_nylanderiana 0.14 0.99 agrED401_U_nylanderiana agrED001_U_nylanderiana 0.88 agrED207_U_nylanderiana 1 0.32 agrED011_U_proboscidea 1 agrED042_U_arctica 1 agrED061_U_polyphylla 1 agrED112_U_polyphylla 1 agrED397_U_iberica 1 agrED328_U_hyperborea 0.9 1 agrED013_U_hyperborea 1 acpED049_U_hyperborea 1 0.64 1 agrED320_U_radicicula acpED472_U_havaasii agrED293_U_proboscidea agrED024_1 U_rigida 0.97 agrED390_U_pallens 0.92 agrED421_U_subglabra 0.47 1 1 agrED356_U_laevis 1 agrED051_U_cinerascens 0.91 agrED216_U_microphylla agrED379_U_ruebeliana 0.54 1 acpED017_U_lambii 0.33 agrED359_U_leiocarpa 0.94 agrED372_U_leiocarpa agrED124_U_lyngei 1 agrED331_U_polyrhiza agrED060_U_polyrhiza 0.11 agrED183_U_cinereorufescens 0.05 agrED074_U_cinereorufescens 0.11 agrED333_U_cinereorufescens 0.96 agrED422_U_tylorhiza 0.11 agrED030_U_cinereorufescens 0.57 agrED097_U_cinereorufescens 0.99 agrED156_U_vellea2 0.85 1 agrED301_U_vellea2 agrED353_U_badiofusca 0.43 0.9 agrED108_U_spodochroa1 1 agrED386_U_spodochroa1 agrED226_U_spodochroa1 agrED057_U_crustulosa2 1 0.2 0.82 agrED310_U_vellea1 0.2 agrED004_U_vellea1 1 agrED155_U_vellea1 agrED134_U_vellea1 1 0.32 0.48 agrED044_U_hirsuta 0.89 agrED224_U_hirsuta 1 agrED122_U_hirsuta agrED358_U_josiae 0.33 agrED118_U_crustulosa1 1 1 agrED373_U_crustulosa1 agrED225_U_crustulosa1 1 agrED211_U_freyi 1 1 0.99 agrED371_U_freyi 0.61 agrED056_U_spodochroa2 1 agrED365_U_grisea 0.66 agrED400_U_grisea agrED164_U_tylorhiza 1 agrED016_U_torrefacta 1 0.61 0.38 agrED154_U_torrefacta 0.49 agrED309_U_angulata 0.99 agrED335_U_americana agrED423_U_phaea 1 0.81 agrED307_U_semitensis acpED018_U_pulvinaria acpED467_Xylopsora_friesii K_OA2732_Hypocenomyce_scalaris acpED443_Boreoplaca_ultrafrigida acpED469_Ophioparma_ventosa

20.0 S15 TAXON 66 (6) • December 2017 Electr. Suppl. to: Davydov & al. • Umbilicariaceae phylogney

68agrED014_L_rossica Fig. S9. Best scoring tree found by the RAxML analysis of a matrix 86 agrED033_L_rossica 95 71 agrED052_L_rossica with 134 accessions and 739 basepairs from mitochondrial LSU agrED290_L_rossica 99 agrED419_L_papulosa 98 acpED464_L_asiae-orientalis region. The maximum likelihood bootstrap support values are noted 99 agrED065_L_asiae-orientalis agrED096_L_daliensis_caeongshanensis 40 above the respective branches, the species names corresponding to the 81agrED107_L_pustulata 65agrED027_L_pustulata 95 sequences are preceded by the GenBank accession number. agrED213_L_pustulata 70 agrED212_L_pustulata 49 47agrED106_L_hispanica 74agrED223_L_hispanica agrED215_L_hispanica 77 71agrED204_L_caroliniana 100 agrED010_L_caroliniana 100 agrED311_L_caroliniana 100 agrED017_L_pertusa 46 agrED221_L_pertusa agrED007_L_pensylvanica 64 86 agrED218_U_mammulata acpED444_U_kisovana 100 agrED050_U_muehlenbergii 64 agrED012_U_muehlenbergii agrED041_U_deusta 64 AY603136_U_antarctica 44 AY603142_U_kappenii 59 AY603135_U_antarctica 40 agrED367_U_antarctica 42 93 agrED352_U_africana agrED173_U_aprina 16 agrED182_U_aprina 6957agrED360_U_aprina agrED417_U_aprina 93 72 agrED295_U_rhizinata acpED016_U_formosana 97agrED304_U_krascheninnikovii 99 97 agrED040_U_krascheninnikovii agrED414_U_krascheninnikovii 98 13 acpED473_U_africana 100 agrED165_U_formosana 71 agrED078_U_indica 100 agrED227_U_thamnodes 35 88 acpED462_U_badia agrED166_U_pseudocinerascens 64 agrED184_U_hypococcinea 99 altbED282_U_maculata 35 acpED027_U_altaiensis 68 agrED292_U_cylindrica 99 agrED348_U_umbilicarioides 39 agrED085_U_dendrophora 42 50 acpED029_U_cylindrica 99 agrED048_U_altaiensis agrED291_U_altaiensis 9 agrED018_U_polaris 65 agrED127_U_vellea1 60 5833agrED296_U_polaris acpED038_U_polaris 39 96 agrED022_U_decussata 61 83 agrED174_U_decussata agrED132_U_decussata agrED306_U_virginis agrED332_U_arctica 38agrED401_U_nylanderiana 32agrED133_U_nylanderiana 44 94 agrED207_U_nylanderiana 9 agrED001_U_nylanderiana 86 agrED345_U_nylanderiana 56 agrED011_U_proboscidea 100 agrED042_U_arctica 100 agrED061_U_polyphylla 100 agrED112_U_polyphylla 96 agrED397_U_iberica 95 agrED013_U_hyperborea 100 56 agrED328_U_hyperborea 97 acpED049_U_hyperborea 81 35 agrED320_U_radicicula acpED472_U_havaasii agrED293_U_proboscidea agrED024_U_rigida 96 agrED356_U_laevis 92 agrED051_U_cinerascens 88 21 97 agrED421_U_subglabra 89 agrED390_U_pallens 50 agrED216_U_microphylla agrED379_U_ruebeliana acpED017_U_lambii 41 87 agrED372_U_leiocarpa 73 agrED359_U_leiocarpa 35 agrED124_U_lyngei acpED467_Xylopsora_friesii 100 agrED060_U_polyrhiza agrED331_U_polyrhiza 27agrED097_U_cinereorufescens 13agrED422_U_tylorhiza 57 agrED030_U_cinereorufescens 64 agrED333_U_cinereorufescens 30 agrED183_U_cinereorufescens 55 agrED074_U_cinereorufescens 94 agrED156_U_vellea2 66 89 agrED301_U_vellea2 agrED353_U_badiofusca 58 agrED386_U_spodochroa1 99 agrED108_U_spodochroa1 33 agrED226_U_spodochroa1 47agrED004_U_vellea1 78agrED155_U_vellea1 100 92 agrED310_U_vellea1 agrED134_U_vellea1 98 94 64agrED224_U_hirsuta 91 agrED122_U_hirsuta 98 agrED044_U_hirsuta 36 agrED358_U_josiae agrED057_U_crustulosa2 34agrED225_U_crustulosa1 100 90 agrED118_U_crustulosa1 agrED373_U_crustulosa1 100 agrED371_U_freyi 77 93 agrED211_U_freyi 47 agrED056_U_spodochroa2 100 agrED400_U_grisea 48 agrED365_U_grisea agrED164_U_tylorhiza 39 agrED335_U_americana 92 32 agrED309_U_angulata 100 agrED154_U_torrefacta 71 agrED016_U_torrefacta agrED423_U_phaea 60 agrED307_U_semitensis acpED018_U_pulvinaria 58 K_OA2732_Hypocenomyce_scalaris acpED443_Boreoplaca_ultrafrigida acpED469_Ophioparma_ventosa

0.06

S16