Skip to main content Accessibility help
×
Home

Contents:

Information:

  • Access
  • Cited by 34

Figures:

Actions:

      • Send article to Kindle

        To send this article to your Kindle, first ensure no-reply@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle.

        Note you can select to send to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

        Find out more about the Kindle Personal Document Service.

        Extended phylogeny and a revised generic classification of the Pannariaceae (Peltigerales, Ascomycota)
        Available formats
        ×

        Send article to Dropbox

        To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Dropbox.

        Extended phylogeny and a revised generic classification of the Pannariaceae (Peltigerales, Ascomycota)
        Available formats
        ×

        Send article to Google Drive

        To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Google Drive.

        Extended phylogeny and a revised generic classification of the Pannariaceae (Peltigerales, Ascomycota)
        Available formats
        ×
Export citation

Abstract

We estimated phylogeny in the lichen-forming ascomycete family Pannariaceae. We specifically modelled spatial (across-site) heterogeneity in nucleotide frequencies, as models not incorporating this heterogeneity were found to be inadequate for our data. Model adequacy was measured here as the ability of the model to reconstruct nucleotide diversity per site in the original sequence data. A potential non-orthologue in the internal transcribed spacer region (ITS) of Degelia plumbea was observed. We propose a revised generic classification for the Pannariaceae, accepting 30 genera, based on our phylogeny, previously published phylogenies, as well as available morphological and chemical data. Four genera are established as new: Austroparmeliella (for the ‘Parmeliellalacerata group), Nebularia (for the ‘Parmeliellaincrassata group), Nevesia (for ‘Fuscopannariasampaiana), and Pectenia (for the ‘Degeliaplumbea group). Two genera are reduced to synonymy, Moelleropsis (included in Fuscopannaria) and Santessoniella (non-monophyletic; type included in Psoroma). Lepidocollema, described as monotypic, is expanded to include 23 species, most of which have been treated in the ‘Parmeliellamariana group. Homothecium and Leightoniella, previously treated in the Collemataceae, are here referred to the Pannariaceae. We propose 41 new species-level combinations in the newly described and re-circumscribed genera mentioned above, as well as in Leciophysma and Psoroma.

Introduction

Peltigerales is one out of nine named orders in the most species-rich class among the ascomycetes, the Lecanoromycetes (Schoch et al. 2009), and incorporates the majority of lichen-forming fungi with cyanobacteria as their photosynthesizing symbiotic partner. The Peltigeralean lichens play an important role in the terrestrial nitrogen cycle of many ecosystems through the fixation of atmospheric nitrogen (Cleveland et al. 1999; Belnap 2003). Current classifications of the Peltigerales include ten families (Wedin et al. 2007; Spribille & Muggia 2013), four of which include c. 90% of the total number of species in the order, that is, Lobariaceae, Pannariaceae, Collemataceae, and Peltigeraceae (Kirk et al. 2008). Several recent contributions have significantly increased knowledge about broad phylogenetic relationships in the Peltigerales (Wedin et al. 2007, 2009; Otálora et al. 2010; Muggia et al. 2011; Spribille & Muggia 2013).

Current estimates indicate that the Pannariaceae is the second most species-rich family of the Peltigerales, and includes more than 300 known species (Kirk et al. 2008). In its original description (Tuckerman 1872), however, the Pannariaceae included only two genera, Pannaria and Heppia. It was not until the treatment by Zahlbruckner (1926) that the familial circumscription was stabilized and came to include large and well-known genera such as Psoroma and Parmeliella, which are still treated in the Pannariaceae. Zahlbruckner included eleven genera altogether, although he excluded Heppia. Some genera included by Zahlbruckner, Hydrothyrea, Massalongia, Placynthium and Coccocarpia, have later been excluded from the Pannariaceae (see, e.g. Wedin et al. 2007, 2009). Jørgensen (1978, 1994) pointed out that Zahlbruckner's generic classification had paid too much attention to the photobiont (green-algal or cyanobacterial) and presence or absence of a thalline margin in the apothecia. In the survey by Henssen & Jahns (1973), only four genera were included in the Pannariaceae: Lepidocollema, Pannaria, Parmeliella, and Psoroma. A preliminary single-gene phylogeny of the family (Ekman & Jørgensen 2002) confirmed that Protopannaria is distinct from Pannaria (in which it had previously been included), that Pannaria included a mixture of species with a green-algal and cyanobacterial photobiont, and excluded the Fuscopannaria leucophaea group, later described as Vahliella (Jørgensen 2008), from the Pannariaceae. Continued revision of familial and generic boundaries led Jørgensen (2003) to recognize 17 genera altogether, although some with doubt. Later investigations demonstrated that all studied genera with non-septate ascospores (Leciophysma, Physma, Ramalodium, and Staurolemma), traditionally referred to the Collemataceae because of their gelatinous thallus, should be transferred to the Pannariaceae (Wedin et al. 2009; Otálora et al. 2010; Muggia et al. 2011). In addition, Vahliella was shown to belong in a family of its own, Vahliellaceae (Wedin et al. 2009, 2011), whereas species with a Scytonema photobiont previously treated in Polychidium belong in a genus of Pannariaceae, Leptogidium (Muggia et al. 2011).

Despite previous efforts, phylogenetic relationships within the Pannariaceae remain insufficiently known. Our aim was to estimate phylogenetic relationships in the Pannariaceae based on an expanded sampling of taxa, and provide a revised taxonomic overview of the family in light of the phylogenetic estimate, previous phylogenetic estimates, as well as morphological data.

Material and Methods

Taxonomy and nomenclature

We studied the type species of most described genera in the Pannariaceae, located in the herbaria cited in the taxonomic section below. The morphology and anatomy of the specimens were examined, and chemistry was investigated by thin-layer chromatography (Culberson & Kristinsson 1970).

Taxon selection for molecular studies

We selected representatives of all genera included in the Pannariaceae as circumscribed by Jørgensen (2003), Wedin et al. (2009), Muggia et al. (2011), and Spribille & Muggia (2013) except Kroswia (Jørgensen & Gjerde 2012), Leptogidium (Muggia et al. 2011), Psoromidium (Galloway & James 1985), and Steineropsis (Spribille et al. 2010; Spribille & Muggia 2013). We were unable to obtain fresh enough material of Lepidocollema and Psoromidium, whereas repeated attempts to generate PCR products from Kroswia were unsuccessful. Leptogidium and Steineropsis were not included because they were recognized as members of the Pannariaceae only after the initiation of this study (Muggia et al. 2011; Spribille & Muggia 2013). Altogether, the data matrix included 110 ingroup terminals representing 88 species (see Supplementary Materials , available online). Vahliella leucophaea, a member of the Vahliellaceae (Wedin et al. 2011), was used as outgroup.

DNA extraction, PCR amplification and sequence editing

We obtained DNA sequences from three different genes, the largest subunit of the RNA polymerase II gene (RPB1), the internal transcribed spacer (ITS) region (including ITS1, 5.8S, and ITS2) of the nuclear ribosomal RNA gene, and the small subunit of the mitochondrial ribosomal RNA gene (mrSSU). Laboratory methods followed Lindblom & Ekman (2005), Ekman et al. (2008), Wedin et al. (2009), and Ekman & Blaalid (2011).

Alignment of ITS

The ITS1 region was assumed to start immediately after the GATCATTA pattern at the end of the small subunit of the nuclear ribosomal RNA gene region. The ITS2 region was assumed to end after the 9th nucleotide preceding the TCGGATCA pattern at the beginning of the large subunit of the nuclear ribosomal RNA gene region. Borders between ITS1 and 5.8S and between 5.8S and ITS2 were defined using the Rfam 5.8S seed alignment (Gardner et al. 2009). A preliminary alignment was created using the G-INS-I algorithm of MAFFT version 6.820 (Katoh & Toh 2008). The ITS region was subsequently split into separate data sets. The 5.8S region was considered unambiguously and finally aligned, whereas the ITS1 and ITS2 regions were prepared for downstream structural alignment by stripping all gaps introduced by the preliminary alignment procedure. The two gene regions were subsequently aligned separately using three different structural aligners, viz. Murlet version 0.1 (Kiryu et al. 2007), CentroidAlign version 1.0 (Hamada et al. 2009), and MAFFT with the X-INS-i algorithm using MXSCARNA pairwise structural alignments and Contrafold base-pairing probabilities (Katoh & Toh 2008). The three structural alignments (for each gene region) were combined into a single alignment for each gene region using T-Coffee version 8.93 (Notredame et al. 2000). Subsequently, we filtered out ambiguously aligned regions as well as sites with a nucleotide in a single terminal and a gap in all other terminals. We defined ambiguous alignment as sites with a local consistency score (described by Notredame & Abergel 2003) less than 5. Scores from 5 to 9 (the highest) are, according to the documentation, considered to be correctly aligned with a probability exceeding 90%, given the underlying separate alignments. In other words, we kept alignment for which the three structural aligners generally agreed and excluded the rest.

Alignment of mrSSU

We downloaded the structural euascomycete mitochondrial 16S rRNA gene reference alignment from the Comparative RNA Web Site (http://www.rna.ccbb.utexas.edu; Cannone et al. 2002). We added our unaligned sequences to this profile using the L-INS-i algorithm of MAFFT and subsequently removed the profile and resulting gap-only columns. Ambiguously aligned sites were removed using Aliscore version 1.0 (Misof & Misof 2009). All possible pairs of taxa were used to infer the consensus profile. The window size was set to 4 and gaps were treated as ambiguities.

Alignment of RPB1

Initial alignment was performed using the L-INS-i algorithm of MAFFT. Introns were identified and excised in accordance with the GenBank records submitted by James et al. (2006). Finally, we trimmed the alignment to start with the first complete codon after the first intron reported by James et al. (2006). The end of the alignment was trimmed to end after a third codon position and to keep the amount of missing data in the final alignment position below 50%.

Selection of partitioning scheme

The data were tentatively partitioned into seven initial subsets: ITS1, 5.8S, ITS2, mrSSU, and RPB1 first, second, and third codon positions, respectively. These subsets were subsequently input into PartitionFinder version 1.0.1 (Lanfear et al. 2012) for an exhaustive search for the best-fitting partitioning scheme. We used the Bayesian Information Criterion (BIC) to select among models and partitioning schemes. We only considered proportional models (“branchlengths=linked”) across subsets (Pupko et al. 2002). The BIC has been shown to more accurately identify the generating model than the commonly used Akaike Information Criterion (AIC), assuming that the true generating model is included in the set of candidate models (Darriba et al. 2012).

Model selection

Although PartitionFinder reports a selected model for each of the partitions suggested, we performed a more thorough model selection from among the GTR family of likelihood models, including rate heterogeneity across sites and a proportion of invariable sites, on each of the final five subsets suggested by PartitionFinder. Model selection was performed using the Perl script MrAIC version 1.4.4 (Nylander 2004) in combination with PhyML version 20110919 (Guindon et al. 2010). As before, the BIC, with alignment length taken as sample size, was used to select among models. We included the number of branches in the number of free model parameters but we did not add an extra parameter for the topology. We selected among a reduced set of models with one, two, or six substitution rate categories, that is the ones available in frequently used software such as MrBayes version 3 (Ronquist & Huelsenbeck 2003). We consistently used six discrete gamma categories for modelling rate heterogeneity across sites. We modified MrAIC to improve PhyML search intensity by performing both NNI and SPR branch swapping and choosing the best outcome (the default is to perform only NNI branch swapping).

Model adequacy assessment

We assessed model adequacy (Goldman 1993; Bollback 2002), that is, the adequacy of the model selected to generate patterns similar to the sequence data observed. Model adequacy was assessed with PhyloBayes, using posterior predictive simulation from the GTR+Γ and F81+Γ+CAT models for each of the five subsets in the phylogenetic analysis. Simulations were performed across a random subset of 1000 trees drawn from the posterior distribution. We used the mean number of states per site ('site diversity') as the test statistic. Reported posterior predictive probabilities correspond to the fraction of times that the value from the posterior simulation exceeded the value observed from the data. Note that these are not probabilities in the classical sense, but rather describe the position of the test statistic derived from the observed data relative to the simulated data. The match to the model is perfect when the observed data fall in the centre of the simulated data, that is, when P is close to 0·5. Both extremely high and extremely low values of P signal poor adequacy of the model to reproduce the observed data. We considered P=<0·025 or P=>0·975 (i.e. the extreme 5%) as a significant departure from the model. We deliberately avoided the unconstrained (multinomial) likelihood as the test statistic (e.g. Bollback 2002) as all current implementations, unlike site diversity, require that all sites with gaps be excluded.

Phylogenetic analyses

PhyloBayes version 3.3b (Lartillot et al. 2009) was used to infer phylogeny under a baseline GTR+Γ model as well as under a F81+Γ+CAT and GTR+Γ+CAT model, using data from each of the five subsets separately as well as the concatenated data. Gamma distributed rate heterogeneity across sites was approximated as six discrete categories in all cases. Note that PhyloBayes does not implement a proportion of invariable sites. For concatenated data, we explored models with and without proportional branch lengths across subsets suggested by PartitionFinder. Under the CAT model (Lartillot & Philippe 2004), substitution rates are constant across sites and trees, whereas state frequencies are treated as a Dirichlet process with an infinite number of mixtures across sites, unobserved states at each site being united into a single state (Lartillot et al. 2007). We used default priors, except that the prior on branch lengths was set to an exponential with a mean seeded by an exponential hyperprior with mean 0·1. We chose an exponential prior because empirical data suggest that true branch lengths are often exponentially distributed (Venditti et al. 2010). Single-subset analyses were performed with three parallel runs, which were set to terminate automatically when the effective sample size of all model parameters exceeded 100 and the maximum discrepancy between runs of the likelihood and all diagnosed parameters descended below 0·1, discrepancy being measured as twice the difference in mean divided by the sum of standard deviations. The burn-in was set to a fifth of the chain length and is fixed by the software. In the end, however, we accepted only runs as converged if, in addition, the discrepancy of all parameters in the second half of the run was below 0·3. Concatenated analyses were performed in a similar manner, except that the three runs, for reasons of computational time, were treated as separate processes for a fixed number of cycles, 60 000. We subsequently applied the same convergence criteria as in the analyses of the individual partitions, except that we discarded the first half of the runs as burn-in and used every 10th tree from the second half of the runs to calculate a majority-rule consensus tree.

We also used MrBayes version 3.2.1 (Ronquist & Huelsenbeck 2003; Ronquist et al. 2012) to infer phylogenies under a model with five partitions, each subset with the model favoured by MrAIC. Prior distributions included treating all tree topologies as equally likely, and (when applicable) a uniform (0·001, 200) distribution for the gamma shape parameter, a uniform (0, 1) distribution for the proportion of invariable sites, a (1, 1, 1, 1, 1, 1) Dirichlet for the rate matrix, independent beta (1, 1) distributions for the transition and transversion rates, and a (1, 1, 1, 1) Dirichlet for the state frequencies. The number of discrete categories used to approximate the gamma distribution was set to six in all analyses. We assumed an exponentially distributed branch length prior. The exponential distribution was parameterized with an empirical Bayes' approach (Ekman & Blaalid 2011), whereby the inverted branch length average calculated from a phylogeny generated with PhyML 3.0 online (Guindon et al. 2005, 2010) was used as the exponential distribution rate parameter (d). This phylogeny was generated with a heuristic search involving NNI and SPR branch swapping from 10 random and one BIONJ tree under a GTR+I+Γ model. Three parallel Markov chain Monte Carlo (MCMC) runs were performed, each with four parallel chains and the temperature increment parameter set to 0·10 (Altekar et al. 2004). The appropriate degree of heating was determined by observing swap rates between chains in preliminary runs. Every 1000th tree was sampled. Analyses were diagnosed for convergence every 106 generations in the last 50% of the tree sample and automatically halted when convergence was reached. Convergence was defined as an average standard deviation of splits (with frequency 0·1) between runs below 0·01. Finally, the potential scale reduction factor (PSRF) was monitored manually, and we only accepted runs with PSRF values smaller than 1·1 for all model parameters and all bipartitions.

Incongruence between the three genes (not the five partitions) was assessed by identifying conflicts between majority-rule consensus trees obtained by 1) maximum likelihood (ML) bootstrap analyses with PhyML 3.0 online and 2) Bayesian MCMC using PhyloBayes under a F81+Γ+CAT model. Each bootstrap analysis included 1000 bootstrap replicates and was performed under a GTR+I+Γ model. PhyloBayes analyses were performed in the same way as other analyses with the software described above. Majority-rule consensus trees were subsequently passed to Compat.py (Kauff & Lutzoni 2002) for identification of conflicts. Tests were performed between all three pairs of genes. The cut-off for conflict identification was set to 0·7 in the ML analysis and 0·95 in the Bayesian analysis.

Branch attachment frequencies were calculated for selected taxa using Phyutility version 2.2.5 (Smith & Dunn 2008).

Marginal likelihoods of the data were calculated with Tracer version 1.5 (Rambaut & Drummond 2009) using importance sampling as suggested by Newton & Raftery (1994) and modified by Suchard et al. (2003).

Results

Resources

The concatenated data, individual gene data used for assessing congruence, as well as all majority-rule consensus trees estimated from these data (including branch lengths and support values) are permanently filed in the TreeBASE repository (http://www.treebase.org) under study number 14978.

Partitioning and model selection

The selection of a partitioning scheme using PartitionFinder on the concatenated data indicated a preference for five subsets, viz. ITS1+ITS2, 5.8S, mrSSU, RPB1 first and second codon positions, and RPB1 third codon positions. The following models were selected by MrAIC under the Bayesian Information Criterion: HKY+Γ for the ITS1+ITS2, K80+I+Γ for the 5.8S, HKY+I+Γ for the mrSSU, GTR+Γ for the RPB1 1st+2nd positions, and HKY+I+Γ for the RPB1 3rd positions. Descriptive statistics for the five subsets, as well as the concatenated data, are found in Supplementary (see Supplementary Material , available online).

Gene tree incongruence

We identified two conflicts between gene trees. The very different placement of Degelia plumbea caused a deep conflict between the ITS on the one hand, and the mrSSU and RPB1 trees on the other hand in the ML bootstrap consensus but not in the Bayesian consensus. However, branch attachment frequencies reveal that in the Bayesian posterior tree sample obtained from ITS data, the three samples of D. plumbea cluster together with 100% posterior probability, and as sister group to Staurolemma omphalarioides with 98% posterior probability, a relationship that does not at all make sense from a morphological perspective. In the mrSSU and RPB1 trees, D. plumbea clusters, as expected from morphology, with D. atlantica and D. cyanoloma. Because of this deep incongruence, we excluded three specimens of D. plumbea (1–111) represented by ITS data. The second conflict, supported by both the ML and Bayesian consensus trees, occurred between the ITS and RPB1 and concerned the branching order among five closely related species of Pannaria. We did not exclude any taxa on account of this shallow incongruence.

Model adequacy

A GTR+Γ model was deemed significantly inadequate (P=1·000) in the case of the mrSSU and the RPB1 third codon positions, with poor performance also in the subsets consisting of ITS1 and ITS2 (P=0·970), 5.8S (P=0·844), and the RPB1 first and second codon positions (P=0·943). The F81+Γ+CAT model was not rejected for any of the five subsets (0·118≤P≤0·711).

Phylogeny from concatenated data

The ln marginal likelihoods calculated from the posterior samples produced by MrBayes (under a partitioned model, each subset with model selected by MrAIC) and PhyloBayes (under a F81+Γ+CAT model) were −19754·560 and −18454·879, respectively. The superiority of the F81+Γ+CAT model in this case, despite its very simple underlying substitution rate model, is not caused by differences in priors or the MCMC machinery across software, as analyses of each of the five subsets with MrBayes and PhyloBayes under a single GTR+Γ model produce closely matching marginal likelihoods (results not shown). The median posterior number of nucleotide frequency categories (‘profiles’) in the CAT model was 42. Apparently, there are substantial differences in nucleotide frequencies across our sequence data, leading to vastly different local instantaneous rates of substitution. We take the results from the F81+Γ+CAT model as our phylogenetic estimate, because this model clearly outperforms standard GTR family models with respect to model adequacy and likelihood. A majority-rule consensus tree with all compatible groups obtained with PhyloBayes under a F81+Γ+CAT model without subset-specific rate multipliers is shown in Fig. 1. Convergence statistics for this analysis translated to MrBayes standards (by feeding reformatted tree samples to ‘sumt’ of MrBayes) correspond to an average standard deviation of splits of 0·004 and a maximum topology PSRF of 1·003. We experienced severe convergence issues under the GTR+Γ+CAT (with and without subset-specific rate multipliers), as well as the F81+Γ+CAT with subset-specific rate multipliers despite very long runs, leading us to discard the results from these analyses.

Fig. 1. Majority-rule consensus tree with all compatible groups and average branch lengths resulting from Bayesian MCMC with PhyloBayes under an F81+Γ+CAT model on concatenated data from ITS, mrSSU, and RPB1. Bayesian posterior probabilities are indicated. Vahliella leucophaea in the Vahliellaceae is the outgroup. Names generally follow Jørgensen (2003), although our interpretation of generic affinities (resulting from this phylogeny, other published phylogenies cited in the text, as well as morphological data) is indicated with white text against a black background. Four main clades (1, 2a, 2b, and 2c) are indicated in colour. Roman numerals are used to distinguish specimens of the same taxon. Coloured dots after taxon names indicate the type of primary photobiont (blue=cyanobacterial, green=green-algal photobiont). In colour online.

Discussion

Model adequacy, robustness, and branch support

Spuriously high branch support in Bayesian phylogenetics as sometimes reported (summarized by Alfaro & Holder 2006) can have two explanations, disregarding MCMC machinery failure: mis-specified priors and/or under-parameterized models (Yang 2006: 178–179). We safeguarded against the bias from a mis-specified prior on branch lengths by use of a hyperprior (in PhyloBayes) or an empirical Bayes prior (in MrBayes) (Kolaczkowski & Thornton 2007; Ekman & Blaalid 2011). Bayesian branch support estimates seem to be particularly sensitive to model under-parameterization (Buckley 2002; Huelsenbeck & Rannala 2004; Lemmon & Moriarty 2004; Brown & Lemmon 2007). Therefore, we conducted an assessment of model adequacy in an attempt to identify a model that was capable of reproducing patterns of the observed data. We found that ordinary GTR family models, including rate heterogeneity across sites, were inadequate as long as spatial heterogeneity in nucleotide frequency, and consequently local differences in the instantaneous rates of substitution, were not included in the model. A model incorporating this process, in this case CAT (Lartillot & Philippe 2004), was found to be adequate for all our data subsets as measured by nucleotide site diversity. Branch support generated from an adequate model is unlikely to be overestimated. Indeed, average support for internal branches in the consensus tree estimated by MrBayes (not shown here but included in the TreeBASE submission) was on average 2·1% higher than the corresponding tree obtained with PhyloBayes (87·7% vs. 85·6%), and three branches in the MrBayes consensus had distinctly higher support to the point where it would affect conclusions drawn from the analysis.

Gene tree conflicts

The ML phylogeny based on the ITS data conflicted with the corresponding mrSSU and RPB1 ML phylogenies regarding the position of Degelia plumbea, which is represented in the ITS tree by three different samples, all from western Norway. During the course of this investigation, identical ITS sequences were recovered from several more specimens, also from Norway, that are not reported here. The lack of apparent conflict regarding the position of D. plumbea between the Bayesian gene consensus trees is ostensibly caused by poor backbone support in the ITS consensus tree. The poor support is not caused by rogue behaviour of D. plumbea, as branch attachment frequencies indicate that D. plumbea clusters on a long branch as sister group to Staurolemma with 98% posterior probability. This association cannot be reconciled with morphology. In the mrSSU and RPB1 Bayesian as well as ML phylogenies, D. plumbea clusters, as expected from morphology, with D. atlantica and D. cyanoloma.

The ITS sequences we have recovered from Degelia plumbea may ultimately prove to be non-orthologous. The same potential non-orthologue was captured by Ekman & Jørgensen (2002) and fell outside the Pannariaceae in their phylogeny. Interestingly, what seems to be the orthologue was recently reported by Otálora et al. (2013), who used different PCR primers and sampled from a different geographical area, southern and central Spain. There are, however, no reported cases of ascomycetes containing a non-orthologous rDNA sequence that was transformed extensively by processes not handled well by current phylogenetic likelihood models. We do not claim the ITS sequences observed in D. plumbea to be the first such case, because crucial experimental evidence of intragenomic variation is still lacking. However, our observations call for further scrutiny.

A second gene tree conflict involved the branching order between Pannaria rubiginosa, P. rubiginella, P. tavaresii, P. subfusca, and P. hookeri in the ITS and RPB1 trees. These taxa form a group of closely related species (Jørgensen 1978). Shallow conflicts like these may represent incomplete lineage sorting (a.k.a. deep coalescence). In such instances, concatenation of data from several genes has been shown to be a poor method for estimating the species tree (Edwards et al. 2007; Kubatko & Degnan 2007). Unlike in the case of Degelia plumbea, pointing out a single culprit offending congruence is not possible. We did not proceed to exclude any data from the concatenated analysis, as we were primarily interested in inferring boundaries and relationships at the genus level. We note, however, that inferred relationships from the concatenated data between taxa involved in this conflict must be interpreted with caution.

Overview of the Pannariaceae

The Pannariaceae, as currently circumscribed, has previously been shown to be monophyletic (Wedin & Wiklund 2004; Wedin et al. 2007, 2009; Muggia et al. 2011; Spribille & Muggia 2013), and falls into two major clades (Clade 1 and 2 in Fig. 1); to some extent these coincide with the formation of a secondarily developed margin of thalline origin in the apothecia of the second clade and the corresponding absence of such a margin in the first clade. There are several exceptions to this rule, however, Joergensenia having a well-developed secondary thalline margin, as well as species scattered in the second clade lacking a thalline margin, mainly in gelatinous taxa with a cyanobacterial photobiont. Clade 1 includes Parmeliella, Degelia, Degeliella, Siphulastrum, Joergensenia, Leioderma, and Erioderma. According to Muggia et al. (2011), the genus Leptogidium, not included in our study, also belongs here. Clade 2 consists of three subclades (2a, b, c) and Xanthopsoroma. Clade 2a includes Fuscopannaria s. lat. (incl. Moelleropsis), Leciophysma, Protopannaria and some species referred to Santessoniella. The recently described Steineropsis (Spribille et al. 2010), although not included in our study, also belongs here (Spribille & Muggia 2013). Clade 2b contains Pannaria, Ramalodium, and Staurolemma, and Clade 2c includes Psoroma s. lat., Fuscoderma, Austrella, Santessoniella , Psorophorus, and Physma. The genus Xanthopsoroma falls outside these clades in our phylogeny. Support for its monophyly is very weak, but support for branches on either side of the genus is high, indicating that Xanthopsoroma, as currently understood, is either monophyletic or a paraphyletic grade.

Generic taxonomy and biogeography

We recognize 30 genera altogether in the Pannariaceae, although some are provisional. The two largest genera, Pannaria and Lepidocollema, are mostly tropical with some extensions through the subtropical region into warm temperate regions. The highest number of genera is found in the Southern Hemisphere, particularly in South America, possibly reflecting a long and complex biogeographical history in that part of the world. Three genera are confined to the Northern Hemisphere, two in the Atlantic-Mediterranean part of Europe (Nevesia and Pectenia) and one in North America (Fuscopannaria). Fuscopannaria is the largest genus of the family in the temperate zone and is particularly species-rich in the North Pacific region, although a few species extend into the Southern Hemisphere. Psoroma s. str. is genuinely bipolar, with far more species in the Southern Hemisphere than elsewhere.

Synopsis of Genera in the Pannariaceae

In this section, we briefly treat all genera currently accepted by us, the delimitation of which mostly emerge from the phylogenetic estimate (Fig. 1), but also on grounds of previous phylogenetic estimates as well as morphological and chemical data. We also include genera that were not part of the phylogeny, which we refer to the family based on other than phylogenetic evidence. Finally, we present an identification key to the accepted genera.

Genera in bold font (whether italicized or not) are accepted genera. A star in front of the name indicates that no member of the genus was included in our phylogeny. Genera in regular font are names for genera that are considered here as synonyms and should be abandoned. We provide full descriptions of newly established genera.

Austrella P. M. Jørg. (Fig. 5D) was described by Jørgensen (2004) for the type species A. arachnoidea and A. brunnea, which are characterized by the formation of apothecia from non-lichenized fungal hyphae, a thick subhymenium of densely packed tissue, and the lack of an apical apparatus in the asci. We provisionally retain the genus as originally conceived, although we note that Austrella has an uncertain position within Clade 2c.

Austroparmeliella (P. M. Jørg.) P. M. Jørg. comb. nov.

MycoBank No.: MB807983

Parmeliella sect. Austroparmeliella P. M. Jørg., Bibl. Lich. 88: 244 (2004).

Generitype: A. lacerata (P. M. Jørg.) P. M. Jørg. (Fig. 5C)

Thallus bluish grey, composed of squamules that form a lace-like crust. Squamules usually deeply incised, 2–3 mm wide, up to 75 µm thick; upper cortex 10–15 µm thick, cellular; medulla up to 50 µm thick, of loosely arranged, intricate hyphae enclosing clusters of Nostoc; lower cortex of a single cell-layer or lacking in parts of the thallus.

Apothecia frequent, often grouped, c. 1 mm diam., becoming convex at maturity, with red-brown disc surrounded by pale rim; proper exciple paraplectenchymatous, 30–50 µm wide. Subhymenium colourless, flat, 100–150 µm thick, of intricately interwoven hyphae. Hymenium 100–150 µm µm high, I+ deep blue. Asci cylindrical, with apical amyloid ring structure, 8-spored; ascospores colourless with smooth wall, broadly ellipsoid, non-septate.

Pycnidia not observed.

Chemistry

No lichen substances found (Jørgensen 2004).

Notes

This is a genus of small, Southern Hemispheric Parmeliella-like species with finely divided squamules, often with cortex on all sides. A further difference from Parmeliella s. str. is the narrow, flat, colourless subhymenium, as opposed to the often lentil-shaped, brownish subhymenium in Parmeliella. Our phylogeny suggests a sister-group relationship with Psorophorus, the members of which differ in the hemiamyloid hymenia and in forming thalline apothecial margins. Five species of Austroparmeliella are recognized here, the four species treated by Jørgensen (2004) and ‘Santessoniellaelongata (Henssen 1997). The latter, although not known to produce apothecia, is transferred here to Austroparmeliella on account of the presence of a lower cortex.

Degelia Arv. & D. J. Galloway (Fig. 2A) was originally described to accommodate Coccocarpia-like, Southern Hemisphere species with apothecia similar to Parmeliella (Arvidsson & Galloway 1981), but with different asci (without an apical amyloid tube). Jørgensen & James (1990) added the three species of the Northern Hemispheric ‘Parmeliellaplumbea group known at the time (D. plumbea, D. atlantica, and D. ligulata), and later Blom & Lindblom (2009) added one more species, Degelia cyanoloma. A separate section, Amphiloma P. M. Jørg. & P. James, with D. plumbea as its type species, was established for this group of species (Jørgensen & James 1990). Members of sect. Amphiloma possess a Nostoc photobiont, whereas other species are lichenized with Scytonema. A third section, Frigidae P. M. Jørg., was described by Jørgensen (2004) for three subantarctic species with a thick paraplectenchymatous upper cortex and a poorly developed secondary thalline corona. The type species of this section is D. subcincinnata (Nyl.) P. M. Jørg.

Fig. 2. Representatives of Clade 1. A, Degelia gayana; B, Pectenia plumbea; C, Degeliella rosulata; D, Parmeliella triptophylla; E, Joergensenia cephalodina; F, Siphulastrum squamosum; G, Leioderma pycnophorum; H, Erioderma leylandii. Photographs: Jan Berge. In colour online.

Our phylogeny (Fig. 1) indicates that Degelia as currently understood is non-monophyletic and that the monophyletic section Amphiloma should be recognized as a separate genus. Therefore, we introduce the new name Pectenia for this section (see below).

Degelia sect. Frigidae was not represented in our phylogeny. However, a member of this section, D. symptychia (Tuck.) P. M. Jørg., was represented in the phylogeny of Spribille & Muggia (2013) and was shown to belong in Steinera in the Koerberiaceae. Unfortunately, sequence data is currently lacking for the type species, D. subcincinnata, which is why we refrain from further taxonomic and nomenclatural changes at the moment.

In Degelia s. str., there may be a problem with heterogeneity in what has been treated as D. gayana, the type species, unless this species-level non-monophyly is caused by incomplete lineage sorting or another (undetected) case of non-orthology (Fig. 1).

Degeliella P. M. Jørg. (Fig. 2C) was described by Jørgensen (2004) to accommodate D. rosulata (P. M. Jørg. & D. J. Galloway) P. M. Jørg., the type species, and D. versicolor (Müll. Arg.) P. M. Jørg. (Jørgensen 2004). Morphologically, it was separated from Degelia on account of the non-amyloid hymenium and ascus, a feature shared by the closely related genera Siphulastrum and Leioderma (Galloway & Jørgensen 1987; Jørgensen 1998). Degeliella rosulata possesses a cyanobacterial photobiont and smooth ascospores, whereas D. versicolor has a green-algal primary photobiont and warted ascospores. In our phylogeny, the type species D. rosulata forms a monophyletic group with fair support (0·94 posterior probability), together with Siphulastrum and Leioderma. Degeliella versicolor (Fig. 7E) is unlikely to be monophyletic together with the type species and may deserve generic recognition (see Psoromaria).

Erioderma Fée (Fig. 2H) includes more than 30 species. The genus has a complex chemistry (Jørgensen & Arvidsson 2002) and is recognized by an ascomatal ontogeny unique to the family (Keuck 1977).

Fuscoderma (D. J. Galloway & P. M. Jørg.) P. M. Jørg. & D. J. Galloway (Fig. 5B) is a genus of five known species, two of which are represented in our phylogeny. They form a monophyletic group and are obviously distantly related to Leioderma, under which they were originally placed as a subgenus (Galloway & Jørgensen 1987). Fuscoderma belongs in Clade 2c, where it is the sister of the Andean genus Nebularia (see below). Fuscoderma is recognized by squamulose to subfoliose, heteromerous thalli with a Nostoc photobiont and brownish tomentum on the lower side, a non-amyloid hymenium (except the gel surrounding asci), a lack of amyloid apical structures in the asci, and the production of vicanicin and/or norvicanicin (Jørgensen & Galloway 1989).

Fuscopannaria P. M. Jørg. (Fig. 3D) is a genus of c. 50 species that was separated from Pannaria on account of the hemiamyloid hymenium, asci with an amyloid apical ring structure, and the production of fatty acids and terpenoids but not pannarin (Jørgensen 1978, 1994). In addition, most species are small-squamulose and form apothecia with a variably developed thalline margin, which can sometimes even be missing.

Fig. 3. Representatives of Clade 2a. A, Nevesia sampaiana; B, Protopannaria pezizoides; C, Leciophysma finmarkicum; D, Fuscopannaria leucosticta. Photographs: Jan Berge. In colour online.

The majority of the species, including the type F. leucosticta (Tuck.) P. M. Jørg., form a monophyletic group if F. sampaiana and F. laceratula are excluded. However, whereas F. sampaiana is included here in the newly described genus Nevesia (see below), we refrain from a formal placement of F. laceratula, awaiting improved taxon sampling. ‘Fuscopannarialaceratula is set apart by its combination of secondary chemistry (atranorin) and a Scytonema-like photobiont (Jørgensen 2005a ).

Moelleropsis nebulosa (Hoffm.) Gyeln. (Fig. 6A) is nested within Fuscopannaria, as suggested already by Ekman & Jørgensen (2002), although scarce taxon sampling prevented them from definitively placing Moelleropsis in synonymy. This situation has unfortunate nomenclatural consequences, since Moelleropsis is an older name than Fuscopannaria. We retain the use of Fuscopannaria, including Moelleropsis, pending a final decision based on a proposal to conserve Fuscopannaria against Moelleropsis (Jørgensen et al. 2013).

Subgenus Micropannaria P. M. Jørg. was established to comprise F. leucophaea and related species (Jørgensen 1994) but was later described as a separate genus, Vahliella P. M. Jørg. (Jørgensen 2008); it is now placed in the currently monogeneric Vahliellaceae (Wedin et al. 2011; Spribille & Muggia 2013).

*Homothecium A. Massal. is a genus of five small-sized species with a gelatinous thallus from southern South America. The genus is morphologically and anatomically similar to Ramalodium, from which it differs mainly in the annular exciple (cupular in Ramalodium) and presence of an apical ring structure in the ascus (none in Ramalodium) (Henssen 1965, 1979). Although currently referred to the Collemataceae (Lumbsch & Huhndorf 2010) and not included in our phylogeny, we provisionally treat Homothecium as another genus in the Pannariaceae with non-septate ascospores and a gelatinous thallus.

Joergensenia Passo et al. (2008) (Fig 2E) and appears in our phylogeny as the sister group to the morphologically and chemically very different Erioderma. Joergensenia (Fig. 1) is aberrant in being the only genus in Clade 1 with a secondarily developed thalline margin in the apothecia (i.e. not an ontogenetically ‘true proper margin’). The thalline “corona” in the apothecia of a few species of Degelia and Degeliella is, according to Henssen & James (1980), not an ordinary thalline margin. Furthermore, Joergensenia is characterized by its strongly amyloid cap-shaped plug in the ascus apex.

*Kroswia P. M. Jørg. is a small genus (Jørgensen 2002) of three paleotropical species (Jørgensen & Gjerde 2012) that were formerly believed to be closely related to Physma (Swinscow & Krog 1988). However, the discovery of fertile material revealed characters in the hymenium, suggesting a close relationship with Fuscopannaria (Jørgensen 2007). The globose, brown-pigmented ascospores are unique in the family.

Leciophysma Th. Fr. (Fig. 3C) was treated in detail by Henssen (1965). The genus is monophyletic if Santessoniella saximontana P. M. Jørg. & T. Sprib. is included. Leciophysma is distantly related to the type species of Santessoniella, S. polychidioides, which is morphologically similar and sometimes difficult to distinguish from Leciophysma.

Leioderma Nyl. (Fig 2G) forms a monophyletic group in a clade together with Degeliella, Siphulastrum, Joergensenia, and Erioderma. Morphologically, Leioderma is similar to Erioderma, from which it differs by the lack of thallus chemistry. Leioderma as circumscribed here corresponds to Leioderma subgenus Leioderma of Galloway & Jørgensen (1987), whereas subgenus Fuscoderma corresponds to the genus Fuscoderma (see above).

*Leightoniella Henssen, with its only known species L. zeylanica (Cromb. ex Leight.) Henssen, is known only from the type material, which was described in detail by Henssen (1965). This genus has so far been classified in the Collemataceae (e.g., Lumbsch & Huhndorf 2010) and is characterized by the periclinally arranged hyphae in the exciple and the production of ‘supporting tissue’ along the thalline margin and thallus stalk (Henssen 1965). The thallus is gelatinous with cyanobacteria and ascospores are simple. Although not included in our phylogeny, we provisionally treat Leightoniella as another member of the Pannariaceae with a gelatinous thallus and simple ascospores.

Lepidocollema Vain. was described by Vainio (1890) to accommodate a single gelatinous, homoiomerous Parmeliella-like species with a Nostoc photobiont, L. carassense Vain., which has been collected only once, in Brazil. Vainio also noted the striking similarity with the apothecia of Parmeliella mariana (as Pannaria mariana), although he acknowledged the difference in thallus anatomy, P. mariana being heteromerous (albeit also contaning Nostoc). Although material of the type species was unavailable to us, we accept the genus here for a total of 24 tropical species, including ‘Parmeliellastylophora and ‘P.’ mariana (Figs 1 & 5E). Lepidocollema as understood here is characterized by the formation of large, flat rosettes on a thick layer of rhizohyphae, the presence of a cellular thalline cortex, apothecia with a thalline margin, asci with a wide apical ring structure, and thin-walled ascospores. The thallus is heteromerous in all species except the type species. The genus is sister to Physma (for differences see that genus). Most of the species have been treated in Parmeliella (e.g. Jørgensen & Galloway 1992), with which they are only distantly related.

* Leptogidium Nyl. was recently re-established for the type species L. dendriscum (Nyl.) Nyl., as well as L. contortum (Henssen) T. Sprib. & Muggia and L. stipitatum (Vězda & W. A. Weber) T. Sprib. & Muggia (Muggia et al. 2011). These species have traditionally been treated in Polychidium (Henssen 1963), from which they are easily distinguished by the photobiont being Scytonema instead of Nostoc.

Moelleropsis Gyeln. (Fig. 7A), with its single species M. nebulosa (Hoffm.) Gyeln., is nested within Fuscopannaria and should be reduced into synonymy with that genus.

Nebularia P. M. Jørg. gen. nov.

MycoBank No.: MB807981

Fuscodermi similis, sed thallo subtus sine tomento fusco et hymenio in iodo toto coerulescenti.

Generitype: Nebularia incrassata (P. M. Jørg.) P. M. Jørg.

(Fig. 5A)

Thallus brownish, composed of up to 3 mm wide squamules with up to 0·25 mm wide, thickened, digitate lobes; upper cortex prominent, cellular, up to 70 µm thick; medulla c. 150 µm thick, of intricately interwoven hyphae enclosing often densely packed clusters of Nostoc, individual cells 5–7 µm diam.

Apothecia up to 1·5 mm diam., reddish brown, flat, with paler, prominent rim; proper exciple paraplectenchymatous, up to 80 µm wide. Subhymenium poorly delimited, colourless with loosely interwoven hyphae, containing photobiont cells that penetrate marginally from below. Hymenium up to 150 µm thick, I+ deep blue. Asci cylindrical, with distinct apical amyloid tube, 8-spored; ascospores colourless with rugulose wall, globose to ellipsoid, non-septate.

Pycnidia not observed.

Chemistry

No lichen substances found (Jørgensen 2000; Jørgensen & Palice 2010).

Etymology

From Latin nebula (fog) and –aris (belonging to), as the species grows in ‘selvas nubladas’ (=foggy forests).

Notes

Nebularia is an Andean genus comprised of only two species, the type species N. incrassata and N. psoromoides. Both species were originally referred to Parmeliella, with which they are only distantly related according to our phylogeny. In our phylogeny, Nebularia belongs in Clade 2c, although support for relationships within that clade is poor. Nebularia is morphologically similar to Fuscoderma in the shiny apothecia with a prominent apothecial rim, and in photobiont cells penetrating into the subhymenium. The latter character is unique to the two genera within the family. However, the amyloid, I+ deep blue hymenium, as well as the absence of tomentum on the lower surface, sets Nebularia apart from Fuscoderma, which has a hemiamyloid hymenium and brown tomentum on the lower surface.

Nevesia P. M. Jørg., L. Lindblom, Wedin & S. Ekman gen. nov.

MycoBank No.: MB807982

Thallus crustaceo-squamulosus hypothallo distincto positus, castaneus cum sorediis granulatis eburneis, sine acidis lichenis. Apothecia matura et pycnidia ignota.

Generitype: Nevesia sampaiana (Tav.) P. M. Jørg., L. Lindblom, Wedin & S. Ekman.

(Fig. 3A)

Thallus consisting of 2–3 mm wide, chestnut brown, appressed, up to 200 µm thick squamules; hypothallus well developed, blue-black; upper cortex cellular, 50–60 µm thick; algal layer 50–70 µm thick, Nostoc cells 6–8 µm diam., in clusters; medulla 40–80 µm thick, of intricate, 3–4 µm wide hyphae, forming a lax plectenchyma, gradually merging into the hypothallus.

Apothecia with thalline margin, extremely rare, known only in an immature state without developed asci. Hymenium hemiamyloid.

Pycnidia not known.

Chemistry

No lichen substances found (Jørgensen 1978).

Etymology

Named in honour of the Portuguese lichenologist Carlos das Neves Tavares (1914–1972), who first recognized N. sampaiana (as Pannaria sampaiana) at species level (Tavares 1950). He had a keen interest in, and substantial knowledge of, the Pannariaceae, which he generously shared with PMJ when he started working on this group.

Notes

Nevesia is a monospecific genus. Originally included in Pannaria, its only species was later transferred to Fuscopannaria (Jørgensen 1994). It is not known with mature apothecia, and its former classification was essentially based on overall morphology, secondary chemistry, and the observation of a hemiamyloid reaction of the hymenium in immature apothecia (Jørgensen 1978, 1994). It differs from most species of Fuscopannaria in having a very well-developed hypothallus, and in the chestnut-coloured thallus lacking lichen substances. In our phylogeny, Nevesia is sister to a large group containing mainly Leciophysma, Protopannaria, and Fuscopannaria.

Pannaria Del. (Fig. 4C) is a genus of c. 80 species, with Pannaria rubiginosa being the type species. The genus is recognized by a squamulose or foliose thallus, apothecia with a thalline margin, an amyloid hymenium, asci without internal amyloid apical structures, and the presence of pannarin and related substances (Jørgensen 1994, 2001a ). Historically, Pannaria included squamulose species containing a Nostoc photobiont and apothecia with a thalline margin.

Fig. 4. Representatives of Clade 2b. A, Ramalodium succulentum; B, Staurolemma omphalarioides; C, Pannaria rubiginosa. Photographs: Jan Berge. In colour online.

Most members of Pannaria included here form a monophyletic group, although a few may belong elsewhere, such as P. isabellina, P. hispidula, P. orphnina, and P. dichroa. Pannaria isabellina (Fig. 6A) and P. hispidula (Fig. 6B) form a poorly supported group with Staurolemma and Ramalodium. Together with Pannaria s. str., they form the strongly supported group we refer to here as Clade 2b. It is currently impossible to confirm or rule out the possibility that P. isabellina and P. hispidula belong in Pannaria. Also, Pannaria dichroa and P. orphnina appear to be currently misclassified and belong to Clade 2c (see discussion under Psoroma).

Our results support the notion that Pannaria also includes taxa with a green-algal photobiont (in our phylogeny represented by P. sphinctrina and P. microphyllizans), previously treated in Psoroma (Jørgensen 2001a ). There is no support for the recognition of subgenus Lepidoleptogium (A. L. Sm.) P. M. Jørg., as the type species L. montagnei A. L. Sm. is a member of the Pannaria immixta complex, which is nested inside Pannaria s. str. in our phylogeny.

Parmeliella Müll. Arg. (Fig. 2D) was originally established for squamulose members of the Pannariaceae with apothecia lacking a thalline margin. In later treatments (e.g., Jørgensen 1978), it was restricted to include species with an amyloid apical ring structure and a lack of lichen substances in the thallus. Even after the separation of Degelia (see above), Parmeliella remained heterogeneous. Most species of Parmeliella form a monophyletic group, although P. incrassata, P. lacerata, P. mariana, and P. stylophora are obviously misclassified. However, Parmeliella can be retained as a monophyletic entity, including the type species P. triptophylla and the majority of species in the genus, if the tropical Parmeliella mariana group is moved to Lepidocollema, and P. lacerata and P. incrassata are referred to the new genera Austroparmeliella and Nebularia, respectively. In its revised circumscription, Parmeliella is a mostly temperate genus including small-squamulose species, generally without chemical substances and apothecia without a thalline margin, but with an amyloid hymenium producing asci with an internal apical tube structure.

It is noteworthy that the likewise tropical Parmeliella pannosa (Sw.) Nyl., which is often confused with P. mariana, belongs in Parmeliella s. str. Parmeliella pannosa has a narrow and tube-like amyloid apical structure typical of the genus, whereas species of Lepidocollema have a broader ring-like apical structure.

Pectenia P. M. Jørg., L. Lindblom, Wedin & S. Ekman nom. et stat. nov.

MycoBank No.: MB807984

Degelia sect. Amphiloma (Fr.) P. M. Jørg. & P. James, Bibl. Lich. 38: 261 (1990).

Generitype: Pectenia plumbea (Lightf.) P. M. Jørg., L. Lindblom, Wedin & S. Ekman.

(Fig. 2B)

Thallus blue-grey, placodioid, appearing thick and rigid, in orbicular patches up to 10 cm diam., up to 250 µm thick. Upper cortex cellular, up to 40 µm thick. Photobiont layer 60–100 µm thick, with Nostoc cells 6–8 µm diam., in clusters. Medulla up to 150 µm thick, composed of parallel, branched, short-celled, horizontally aligned hyphae forming a compact plectenchyma, gradually merging into the hypothallus. Hypothallus thick, felt-like, blue-black, often extending beyond the ascending marginal lobes.

Apothecia laminal, usually abundant, biatorine with brown disc and a paler rim. Proper exciple up to 100 µm wide, consisting of isodiametric cells. Subhymenial layers pale yellowish brown, up to 150 µm thick, composed of intricately interwoven hyphae. Hymenium 100–150 µm high, colourless except for brown pigment in uppermost part, I+ persistently blue. Paraphyses unbranched. Asci clavate to cylindrical, with an apical dark-amyloid plug. Ascospores 8 per ascus, colourless, ellipsoid with smooth wall and without perispore, non-septate.

Pycnidia infrequent, mostly marginal, protruding, black, up to 0·2 mm wide. Conidiophores short-celled, producing conidia terminally and laterally. Conidia bacilliform, 1–3×1 µm.

Chemistry

No lichen substances found (Jørgensen & James 1990).

Etymology

From the Latin generic name of scallop, Pecten, due to the grooved scallop-like pattern often found on the upper surface of the species in this genus.

Notes

The name Amphiloma cannot be used at generic level, since it is occupied by two older homonyms (Jørgensen 1978). Consequently, we establish the new name Pectenia based on sect. Amphiloma and with the same type species, P. plumbea. Pectenia is mainly confined to Europe and adjacent Africa, mostly along the Atlantic coast. However, P. plumbea also occurs in a restricted region in North-East America (Blom & Lindblom 2009; Richardson et al. 2010).

Physma A. Massal. (Fig. 5F), previously treated in the Collemataceae, belongs in the Pannariaceae, as also shown by Wedin et al. (2009) and Otálora et al. (2010). In our phylogeny, Physma is the sister group to the Parmeliella mariana group, referred here to Lepidocollema. Physma is characterized by a leathery thallus with a dense upper pseudocortex (unlike the cellular cortex in Lepidocollema), and thick-walled ascospores with a markedly swollen epispore.

Fig. 5. Representatives of Clade 2c and Xanthopsoroma. A, Nebularia incrassata; B, Fuscoderma applanatum; C, Austroparmeliella lacerata; D, Austrella arachnoidea; E, Lepidocollema marianum; F, Physma byrsaeum; G, Psorophorus pholidotus; H, Psoroma hypnorum; I, Xanthopsoroma contextum. Photographs: Jan Berge. In colour online.

Protopannaria (Gyeln.) P. M. Jørg. & S. Ekman (Fig. 3B) is comprised of seven known crustose-squamulose species without secondary chemistry, apothecia with a thalline margin, and amyloid hymenia with asci lacking internal amyloid structures (Jørgensen 2001a , b , 2004, 2007; Øvstedal & Fryday 2011). In our phylogeny, P. pezizoides is sister to Santessoniella grisea (Hue) Henssen (Fig. 6D). An undescribed species closely related to Santessoniella crossophylla (Tuck.) P. M. Jørg. (Fig. 6C) is sister to P. pezizoides and S. grisea. Unlike P. pezizoides, the two species of ‘Santessoniella’ have a hemiamyloid hymenium and an internal apical ring structure in the asci. These differences make it unlikely that they can be included in Protopannaria, despite strong branch support in our phylogeny. At the moment, we retain Protopannaria in its current circumscription and refrain from suggesting alternative classifications for the two species of ‘Santessoniella’. We note, however, that relationships and generic boundaries in this group are in need of further study.

Fig. 6. Five members of the Pannariaceae with uncertain generic affiliation. A, Pannaria isabellina; B, Pannaria hispidula; C, Santessoniella crossophylla; D, Santessoniella grisea; E, Degeliella versicolor. Photographs: Jan Berge. In colour online.

Psoroma Ach. ex Michx (Fig. 5H) traditionally accommodated Pannaria-like species with a green-algal photobiont and a thalline margin surrounding the apothecia. Jørgensen (2001a ) restricted the circumscription of the genus to include close relatives of the type species Psoroma hypnorum (Vahl) Gray, that is, small-squamulose, bryophilous species without lichen substances, and with an amyloid tube- or ring-like structure in the ascus apex. Branch support within Clade 2c in our phylogeny is poor and provides little guidance for revised generic delimitations. We provisionally retain Psoroma more or less as currently understood, with few amendments: ‘Pannariadichroa and ‘P.’ orphnina (along with the two similar species ‘P.’ obscurior and ‘P.’ xanthorioides) are referred here to Psoroma despite their cyanobacterial photobiont, because our phylogeny provides support for their exclusion from Pannaria. Indeed, in accordance with their phylogenetic placement, the asci of these species have a wide amyloid ring structure, which can, however, be difficult to observe. ‘Pannariaorphnina is the type species of the genus Siphulina (Hue) C. W. Dodge (Jørgensen 2005b ), which accordingly becomes a taxonomic synonym of Psoroma. Furthermore, although Psoroma tenue does not form a monophyletic group with the rest of Psoroma in our phylogeny, there is no support for its exclusion. Chemically, however, P. tenue and its relatives deviate from the rest of Psoroma by producing porphyrilic acid and related substances. We refrain from transferring ‘Santessoniellaarctophila, sister to P. tenue with high support, to Psoroma or any other genus in the absence of a well-resolved phylogeny. We have, however, chosen to include Santessoniella polychidioides (and its close relative S. macrospora) in Psoroma, because there is reasonable support (0·92 posterior probability) for a close relationship with P. aphthosum and because branch attachment frequencies calculated by Phyutility show that the remaining posterior probability (0·08) is divided between two other positions nested inside our understanding of Psoroma. This choice makes Santessoniella a taxonomic synonym of Psoroma. With these amendments, Psoroma includes species with small-squamulose or rarely small-fruticose thalli with a green-algal or cyanobacterial primary photobiont, and mostly a lack of secondary chemistry (the presence of porphyrilic acid and related substances in Psoroma tenue and relatives being an exception, if included).

Our phylogenetic tree indicates that the widespread P. hypnorum, type species of the genus, is paraphyletic. Further investigations need to determine whether this observation is caused by incomplete lineage sorting or the occurrence of multiple species within P. hypnorum as currently delimited. Psoroma hypnorum specimen III deviates conspicuously from other specimens in having a cyanobacterial (Nostoc) photobiont instead of the standard primary green-algal one (Holien & Jørgensen 2000). The cyanobacterial photobiont confers dramatic modifications to overall lichen morphology towards a growth form similar to taxa currently classified in Santessoniella. Our phylogeny indicates, however, that the fungal component of the cyanobacterial morph is closely related to at least some green-algal representatives (here P. hypnorum specimen V; see Fig. 1). It should also be pointed out that the determination of the P. fruticulosum specimen used to generate the sequences was questioned by Passo et al. (2008).

Psoromaria Nyl. ex Hue may deserve recognition as a genus (see Degeliella). It originally contained two species, P. subdescendens Nyl. (=Degeliella versicolor) and P. descendens Nyl. (=Psoromidium aleuroides). The former was later selected as lectotype (Clements & Shear 1931: 319). Galloway & James (1985) treated both species in Psoromidium Stirt. (as P. aleuroides and P. versicolor), whereas Jørgensen (2004) referred P. versicolor to Degeliella, regarding it as the green counterpart of D. rosulata. In doing so, the older name Psoromaria was unfortunately overlooked. Although we note that Psoromaria may be available for Degeliella versicolor if treated as a separate genus, we refrain from nomenclatural changes at the moment, in anticipation of taxonomical and nomenclatural clarifications in the group.

*Psoromidium Stirt. was reinstated by Galloway (1983) and Galloway & James (1985) for two species, the type species P. wellingtonii Stirt. [=P. aleuroides (Stirt.) D. J. Galloway] and P. versicolor (Müll. Arg.) D. J. Galloway. The latter was later transferred to the new genus Degeliella (see that genus and Psoromaria). Psoromidium aleuroides is characterized by a thallus of adpressed squamules resting on a distinct hypothallus, a green-algal primary photobiont and distinct cephalodia with Nostoc, an amyloid hymenium, an ascus with an apical ring structure, and a lack of secondary chemistry (Galloway & James 1985). Apart from the evanescent apothecial thalline margin in species of Psorophorus (Elvebakk et al. 2010), morphology suggests a close relationship between the two genera. If proven synonymous, Psoromidium is the older name. We provisionally retain Psoromidium, although we note that further studies are needed.

Psorophorus Elvebakk & Hong (Fig. 5G) was recently described by Elvebakk et al. (2010) for the type species P. pholidotus (Mont.) Elvebakk and P. fuegiensis (Zahlbr.) Elvebakk & Hong. Both species were included in our phylogeny and together form a well-supported monophyletic group sister to Austroparmeliella lacerata. The relationship with Psoromidium needs further study (see that genus).

Ramalodium Nyl. (Fig. 4A) currently comprises six species, R. succulentum Nyl. being the type (Henssen 1965, 1979, 1999). We included only the type species in our phylogeny (as did Wedin et al. 2009). Ramalodium succulentum is recovered as sister to Staurolemma. Ramalodium and Staurolemma have been considered closely related on morphological grounds, the main difference between the genera being the lecideine apothecia in Ramalodium and zeorine apothecia in Staurolemma (Henssen 1999).

Santessoniella Henssen, the type species of which is S. polychidioides (Zahlbr.) Henssen (Fig. 7B), was originally established by Henssen (1997) for a set of six small, often subfruticose and sometimes gelatinous species with Parmeliella-like apothecia (Henssen 1997). The genus continued to be used in this sense, and another seven species have later been described or transferred to that genus (Jørgensen 1998, 1999, 2005a ; Henssen 2000; Henssen & Kantvilas 2000; Spribille et al. 2007; Jørgensen & Palice 2010).

Fig. 7. Type species of two abandoned genera. A, Moelleropsis nebulosa, referred here to Fuscopannaria; B, Santessoniella polychidioides, referred here to Psoroma. Photographs: Jan Berge. In colour online.

Our phylogeny includes five species of Santessoniella, the type species S. polychidioides, S. arctophila, S. saximontana, an undescribed species close to S. crossophylla, and S. grisea. These species are dispersed across much of the tree and constitute the most extreme example of genus-level non-monophyly in our investigation. The type species Santessoniella polychidioides is nested inside Psoroma with moderate support. Morphologically, it may be considered a cyanobacterial expression of a Psoroma, not unlike the cyanobacterial morph of P. hypnorum (Holien & Jørgensen 2000; P. hypnorum III in our tree). It is noteworthy, however, that the asci of S. polychidioides and relatives are more narrowly cylindrical than in Psoroma s. str., with a tube-like amyloid internal structure as opposed to the wider ring-like structure in Psoroma s. str. In addition, the hymenial reaction is more pronouncedly hemiamyloid in S. polychidioides and relatives, rapidly changing from blue-green to red-brown, whereas in Psoroma s. str. the reaction is blackish blue, turning slowly to sordid blue. Santessoniella saximontana is nested inside Leciophysma with high support and seems to share morphological characteristics of that genus (Henssen 1965). Santessoniella grisea and the undescribed relative of S. crossophylla are closely related to Protopannaria, from which they differ markedly with respect to morphology. Finally, S. arctophila seems to be closely related to Psoroma tenue. Their relationships remain unclear and we refrain here from assigning them to a genus.

Siphulastrum Müll. Arg. (Fig. 2F) is a genus of four species, one of which is the type species S. triste Müll. Arg. (Jørgensen 2003). The genus is characterized by a heteromerous thallus with a Scytonema photobiont, a hemiamyloid hymenial reaction, lack of apical structures in the asci, presence of argopsin in the thallus, and a dense upper cortex of incrassate cells with small cell lumina. Unfortunately, material of the type species itself was not available for our study, although the included species, S. squamosum, conforms to the generic characteristics and is likely to be closely related to the type species. In our phylogenetic tree, Siphulastrum is the sister group to Leioderma and Degeliella rosulata.

Staurolemma Körb. (Fig. 4B) includes eight known species (Jørgensen 2010) and is typified by S. dalmaticum Körb., a synonym of S. omphalarioides (Anzi) P. M. Jørg. & Henssen. We included two species in our phylogeny, which form a monophyletic group with high support. Furthermore, Staurolemma is the sister group to Ramalodium in our phylogeny as well as that of Wedin et al. (2009). This corroborates the view that the two genera are closely related on morphological grounds, differing mainly in apothecial anatomy (Henssen 1999).

Note that ‘Staurolemma sp. nov.’ included in the phylogeny of Wedin et al. (2009) has been described as S. oculatum P. M. Jørg. & Aptroot (Jørgensen 2010).

*Steineropsis T. Sprib. & Muggia was described for the single species S. alaskana T. Sprib. & Muggia by Spribille et al. (2010). This species superficially resembles a Placopsis and the thallus is characterized by a paraplectenchymatous upper cortex, which extends into the medulla. Apothecia and pycnidia have not been described. Steineropsis alaskana was sister to Protopannaria in the phylogeny of Spribille & Muggia (2013).

Xanthopsoroma Elvebakk & Hong (Fig. 5I) was established to accommodate the type species X. contextum (Stirt.) Elvebakk and X. soccatum (R. Br. ex Crombie) Elvebakk, two Southern Hemispheric species previously treated in Psoroma and containing usnic acid and a series of terpenoids (Elvebakk et al. 2010). Support for its monophyly in our phylogeny is poor. Surrounding branches have high support, but we cannot exclude the possibility that Xanthopsoroma is paraphyletic. However, at least one, possibly both members of the genus are likely to be sister to Clade 2a–c (Fig. 1).

Provisional key to the genera

  1. 1 Thallus gelatinous, mostly without lichen substances (PD−) ... 2

    Thallus not gelatinous, often with lichen substances (PD+) ... 11

  2. 2(1) Thallus subfruticose to fruticulose, sometimes nearly granular ... 3

    Thallus squamulose to foliose ... 5

  3. 3(2) Thallus applanate, finely and dichotomously dissected; photobiont Scytonema; medullary hyphae parallel to cortex; tropical ... Leptogidium

    Thallus erect, consisting of coarser and often irregular branches; photobiont Nostoc; medullary hyphae at an angle to the cortex, usually in a reticulate pattern temperate ... 4

  4. 4(3) Lobes up to 0·3 mm wide, sometimes nearly granular; hyphal walls distinctly gelatinized ... Leciophysma

    Lobes up to 1 mm wide, more or less squamulose; hyphal walls not or weakly gelatinized ... Psoroma pro parte (‘Santessoniella’ s. str.)

  5. 5(2) Apothecia without thalline margin; thallus mostly squamulose or nearly subfruticose; Southern Hemisphere ... 6

    Apothecia with thalline margin; thallus with wider, flattened lobes, subfoliose to foliose; tropical ... 7

  6. 6(5) Thallus membranaceous; excipulum annular; asci with internal apical amyloid ring or tube ... Homothecium

    Thallus squamulose (to subfruticose); excipulum cupular; asci without internal apical amyloid structures ... Ramalodium

  7. 7(5) Thallus with fan-shaped lobes, tawny, with pannarin (PD+); asci without internal apical amyloid structures ... Pannaria lurida group

    Thallus with narrow, elongated lobes, bluish grey, without pannarin (PD−); asci with internal apical amyloid ring structures ... 8

  8. 8(7) Thallus homoiomerous, containing terpenoids; ascospores globose, faintly brownish ... Kroswia

    Thallus heteromerous, without secondary substances; ascospores ellipsoid, colourless ... 9

  9. 9(8) Thallus resting on a distinct mat of protruding blackish rhizohyphae; cortex cellular, one-layered; Brazil ... Lepidocollema carassense

    Thallus without protruding rhizohyphae; cortex multi-layered; paleotropical ... 10

  10. 10(9) Thallus with narrow, elongated lobes; cortex of 1–3 cell layers; apothecia stipitate without supportive tissue; Sri Lanka ... Leightoniella zeylanica

    Thallus with wider lobes; cortex of densely agglutinated hyphae; apothecia sessile with supportive tissue; widespread in the tropics ... Physma

  11. 11(1) Thallus with green-algal photobiont ... 12

    Thallus with cyanobacterial photobiont ... 19

  12. 12(11) Asci without internal amyloid apical structures ... 13

    Asci with internal amyloid apical structures ... 14

  13. 13(12) Thallus squamulose-foliose, with pannarin and related substances (PD+); apothecia with thalline margin ... Pannaria

    Thallus of closely adpressed squamules, without secondary substances; apothecia biatorine, without thalline margin ... Degeliella versicolor

  14. 14(12) Squamules with a yellow tinge, with usnic acid ... Xanthopsoroma

    Squamules without a yellow tinge, without usnic acid ... 15

  15. 15(14) Apothecia often proliferating, without thalline margin; thallus with cottony prothallus ... Psoromidium

    Apothecia single, with distinct thalline margin; thallus without cottony prothallus ... 16

  16. 16(15) Thallus with pannarin (PD+); asci with distinct apical amyloid cap-shaped plug ... Joergensenia cephalodina

    Thallus without pannarin (PD−); asci with amyloid apical ring structures ... 17

  17. 17(16) Apothecia flat, often with convex, dark brown disc ... Fuscopannaria viridescens

    Apothecia urceolate with concave, light or orange-brown disc ... 18

  18. 18(17) Squamules appressed, resting on a distinct blackish prothallus; corticolous ... Psorophorus

    Squamules loosely scattered over the substratum, without prothallus; usually bryophilous or terricolous ... Psoroma

  19. 19(11) Thallus of closely appressed, chestnut brown squamules with cream-coloured soralia; hypothallus blue-black; photobiont Nostoc; nearly always sterile; Atlantic-Mediterranean ... Nevesia sampaiana

    Thallus with different combination of characters ... 20

  20. 20(19) Thallus a small, placodioid, Placopsis-like rosette with opuntioid lobules and a thick, paraplectenchymatous upper cortex; sterile ... Steineropsis alaskana

    Thallus with different combination of characters ... 21

  21. 21(20) Apothecia with secondary thalline margin ... 22

    Apothecia without secondary thalline margin, or rarely with thalline corona ... 25

  22. 22(21) Thallus on distinct blackish hypothallus, without lichen substances or pigments; tropical ... Lepidocollema

    Thallus not on distinct hypothallus, often with lichen substances or pigments ... 23

  23. 23(22) Thallus squamulose-foliose, usually with pannarin (PD+); asci without internal, apical amyloid structures ... Pannaria

    Thallus small-squamulose, usually without pannarin (PD−), rarely with pannarin (but then also with argopsin); asci with internal amyloid ring structures ... 24

  24. 24(23) Apothecia with distinct thalline margin, disc orange-brown, hymenium amyloid ... Protopannaria

    Apothecia with variably developed thalline margin, disc brown to blackish; hymenium hemiamyloid ... Fuscopannaria

  25. 25(21) Thallus foliose, not closely appressed to substratum, upper surface usually with hairs ... 26

    Thallus squamulose or placodioid, often closely appressed to substratum, upper surface without hairs ... 27

  26. 26(25) Thallus always hairy, often with stiff prominent hairs; apothecia usually marginal and stalked, if otherwise always PD+ orange (eriodermin) ... Erioderma

    Thallus arachnoid-tomentose or glabrous, with laminal, sessile apothecia, PD− ... Leioderma

  27. 27(25) Thallus placodioid, often forming large circular blue-grey thalli with well-developed bluish black rhizohyphae ... 28

    Thallus not placodioid, without or with brownish rhizohyphae ... 31

  28. 28(27) Hymenium non-amyloid; asci without internal apical amyloid structures; photobiont Scytonema ... Degeliella rosulata

    Hymenium amyloid; asci with internal apical amyloid structures; photobiont Scytonema or Nostoc ... 29

  29. 29(28) Thallus thin and Coccocarpia-like, with a Scytonema photobiont; upper cortex prosoplectenchymatous, consisting of a few cell layers of periclinally arranged hyphae; Southern Hemisphere ... Degelia sect. Degelia

    Thallus thick and rigid; upper cortex paraplectenchymatous, consisting of several layers of anticlinally arranged hyphae ... 30

  30. 30(29) Photobiont Nostoc; thallus losely attached to substratum, with upper surface having prominent longitudinal ridges; Northern Hemisphere ... Pectenia

    Photobiont Scytonema, thallus appressed to substratum, with smooth upper surface; Subantarctic ... Degelia sect. Frigidae

  31. 31(27) Apothecia surrounded by a thin weft of hyphae; asci narrowly elongate, thin-walled, without internal apical structures ... Austrella

    Apothecia not surrounded by a weft of hyphae; asci wider, clavate to cylindrical, thick-walled, with internal apical amyloid structures ... 32

  32. 32(31) Apothecia with thick proper exciple, containing elements of the formative supporting tissue and photobiont cells penetrating into the subhymenium ... 33

    Apothecia with thin proper exciple, without supporting tissue or photobiont cells in the subhymenium ... 34

  33. 33(32) Lower surface with small, curled brownish hairs; hymenium hemiamyloid; Southern Hemisphere ... Fuscoderma

    Lower surface without brownish hairs; hymenium amyloid; Andean Mountains ... Nebularia

  34. 34(32) Thallus thick and often shiny, containing argopsin (PD+); cortical cells thick-walled; hymenium hemiamyloid; mostly terricolous ... Siphulastrum

    Thallus thin and usually dull, without argopsin (PD−); cortical cells thin-walled; hymenium amyloid; mostly corticolous ... 35

  35. 35(34) Thallus often forming both upper and lower cortex; subhymenium flat, colourless ... Austroparmeliella

    Thallus only with upper cortex; subhymenium often lentil-shaped, brownish ... Parmeliella

New Species-level Combinations

In this section, we list species-level combinations necessitated by the generic classification proposed above.

Austroparmeliella chilensis (Hue) P. M. Jørg. comb. nov.

MycoBank No.: MB807985

Placynthium chilense Hue, Bull. Soc. Linn. Normandie ser. 5, 9: 158–159 (1906); type: Chile, Cordillera de Ranco, Lechler 3016 (PC—lectotype! fide Henssen 1997: 83).

Austroparmeliella elongata (Henssen) P. M. Jørg. comb. nov.

MycoBank No.: MB807986

Santessoniella elongata Henssen, Symb. Bot. Ups. 32: 83–84 (1997); type: Argentina, Rio Negro, Parque Nacional Nahuel Huapi, Puerto Blest, 1973, Vobis & Henssen 24606a (H—holotype!).

Austroparmeliella lacerata (P. M. Jørg.) P. M. Jørg. comb. nov.

MycoBank No.: MB807987

Parmeliella lacerata P. M. Jørg., Lichenologist 30: 537 (1998); type: Republic of South Africa, Western Cape, Riviersonderend, Oubos Forest, 1996, Nordin 4542 (UPS—holotype!).

Austroparmeliella rakiurae (P. M. Jørg. & D. J. Galloway) P. M. Jørg. comb. nov.

MycoBank No.: MB807988

Parmeliella rakiurae P. M. Jørg. & D. J. Galloway, Bibl. Lich. 88: 244 (2004); type: New Zealand, Stewart Island, Port Pegasus, track from Disappointment Cove to Broad Bay, coastal forest on Olearia bark, 29 July 2001, Galloway 0845 (BG—holotype!).

Austroparmeliella rosettiformis (Henssen) P. M. Jørg. comb. nov.

MycoBank No.: MB807989

Santessoniella rosettiformis Henssen, Lichenologist 32: 18 (2000); type: Chile, Prov. Arauco, Parque Nacional Contulma, 1973, Vobis & Henssen 24281 (H—holotype!).

Leciophysma saximontana (T. Sprib. et al.) P. M. Jørg., Wedin & S. Ekman comb. nov.

MycoBank No.: MB807990

Santessoniella saximontana T. Sprib., P. M. Jørg. & M. Schulz, Bibl. Lich. 98: 288 (2007); type: Canada, British Columbia, Rocky Mts., Albert River drainage, 2006, Spribille 21173 & Houde (CANL—holotype!).

Lepidocollema adpressum (P. M. Jørg.) P. M. Jørg. comb. nov.

MycoBank No.: MB807991

Parmeliella adpressa P. M. Jørg., Journ. Japanese Bot. 76: 289 (2001); type: Japan, Shinano Prov., Mt. Kinpu, alt. 2100–2450 m, Jinzenji 176 (TNS—holotype!).

Lepidocollema allochroum (Makhija & Adaw.) P. M. Jørg. comb. nov.

MycoBank No.: MB807992

Parmeliella allochroa Makhija & Adawad, Mycotaxon 71: 327 (1999); type: India, Nicobar Islands, Car Nicobar, Kimus, on coconut palm, 29 December 1986, Patwardhan & Sethy 86.787 (AMH—holotype!).

Lepidocollema borbonicum (P. M. Jørg. & Schumm) P. M. Jørg. comb. nov.

MycoBank No.: MB807993

Parmeliella borbonica P. M. Jørg. & Schumm, Lichenologist 42: 697 (2010); type: La Réunion, Takamaka, low mountain forest near the electrostation, alt. 790 m, 10 September 2009, Frahm & Schumm (BG—holotype!).

Lepidocollema brisbanense (C. Knight) P. M. Jørg. comb. nov.

MycoBank No.: MB807994

Pannaria brisbanensis C. Knight in J. Shirley, Proc. Royal Soc. Queensland 6: 194 (1890); type: Australia, Queensland, Brisbane River, Shirley 113 (WELT—lectotype! fide Jørgensen & Galloway 1992).

Lepidocollema cineratum (Zahlbr.) P. M. Jørg. comb. nov.

MycoBank No.: MB807995

Pannaria cinerata Zahlbr. in H. Magn. & Zahlbr., Ark. Bot. 31A(1): 72 (1943); type: USA, Hawaii, Kauai, Kauhao, 1000 m, 8 February 1910, Faurie 274 (W—holotype!).

Lepidocollema endoluteum (P. M. Jørg.) P. M. Jørg. comb. nov.

MycoBank No.: MB807996

Parmeliella endolutea P. M. Jørg., Lichenologist 39: 239 (2007); type: Philippines, Prov. Rizal, Mt. Irid, Herre (LAM—holotype!).

Lepidocollema endomiltum (Vain.) P. M. Jørg. comb. nov.

MycoBank No.: MB807997

Pannaria endomilta Vain., Ann. Acad. Sci. Fenn. ser. A 15, 6: 15 (1921); type: Philippines, Mindanao, Davao, Mt. Apo, 6000 ft., 21 April 1904, Copeland 1090 p.p. (TUR-V 12168—holotype!).

Lepiodocollema exornatum (Zahlbr.) P. M. Jørg. comb. nov.

MycoBank No.: MB807998

Pannaria cinerata var. exornata Zahlbr. in H. Magn. & Zahlbr., Ark. Bot. 31A(1): 72 (1943); type: USA, Hawaii, Maui, Hana, September 1909, Faurie 559 (W—lectotype! fide Jørgensen 2003).

Lepidocollema fuscatum (P. M. Jørg.) P. M. Jørg. comb. nov.

MycoBank No.: MB807999

Parmeliella fuscata P. M. Jørg., Bryologist 106: 123 (2003); type: India, Maharasta, Ambenali, on road to Pratapgad, felled tree at bridge, 2 November 1973, Hale 40045 (US—holotype!).

Lepidocollema granuliferum (P. M. Jørg.) P. M. Jørg. comb. nov.

MycoBank No.: MB808000

Parmeliella granulifera P. M. Jørg., Bibl. Lich. 78: 129 (2001); type: Australia, Northern Territory, Channel Island, prawn farm, landward edge of mangroves, 1991, Benfield (BRI—holotype!).

Lepidocollema imbricatulum (Müll. Arg.) P. M. Jørg. comb. nov.

MycoBank No.: MB808001

Pannaria imbricatula Müll. Arg., Flora 64: 507 (1881); type: Brazil, São Paolo, prope Apiahy, Puiggari 148 p.p. (G—holotype!).

Lepidocollema leiostroma (Nyl.) P. M. Jørg. comb. nov.

MycoBank No.: MB808002

Pannaria leiostroma Nyl. in Leight., Trans. Linn. Soc. London 27: 165 (1869); type: Sri Lanka, Thwaites (BM—holotype!).

Lepidocollema macrosporum (Makhija & Adawad.) P. M. Jørg. comb. nov.

MycoBank No.: MB808003

Parmeliella macrospora Makhija & Adawad., Mycotaxon 71: 332 (1999); type: India, Nicobar Island, Car Nicobar, Kimus, 1986, Sethy & Nagarkar 86.778 (AMH—holotype!).

Lepidocollema marianum (Fr.) P. M. Jørg. comb. nov.

MycoBank No.: MB808004

Parmelia mariana Fr., Syst. Orb. Veg. I: 284 (1825); type: Mariana Islands, Gaudichaud (UPS—holotype!).

Lepidocollema montanum (P. M. Jørg. & Sipman) P. M. Jørg. comb. nov.

MycoBank No.: MB808005

Parmeliella montana P. M. Jørg. & Sipman, J. Hattori Bot. Lab. 100: 711 (2006); type: Papua New Guinea, Morobe Distr., Mt. Kaindi, Wau, 1973, Kashiwadani 10541 (TNS—holotype!).

Lepidocollema nitidum (P. M. Jørg. & Sipman) P. M. Jørg. comb. nov.

MycoBank No.: MB808006

Parmeliella nitida P. M. Jørg. & Sipman, J. Hattori Bot. Lab. 100: 712 (2006); type: Papua New Guinea, Simbu Prov., Mt. Wilhelm, Pindaunde valley, near hut on S-shore of Lake Piunde, W slope of valley, c. 3700 m, 6 August 1992, Sipman 35688 (B—holotype!).

Lepidocollema pannarioides (P. M. Jørg. & Sipman) P. M. Jørg. comb. nov.

MycoBank No.: MB808007

Parmeliella pannaroides P. M. Jørg. & Sipman, J. Hattori Bot. Lab. 100: 713 (2006); type: Papua New Guinea, Western Highland Distr., Mt. Wilhelm, en route from Kombugomanubo to the Pindaunde Lakes, 1974, Kashiwadani 11064 (TNS—holotype!).

Lepidocollema papillatum (P. M. Jørg.) P. M. Jørg. comb. nov.

MycoBank No.: MB808008

Parmeliella papillata P. M. Jørg., Bibl. Lich. 78: 133 (2001); type: Australia, Queensland, Cardwell Range, 45 km NW of Cardwell, 1986, Elix 20169 & Streimann (CANB—holotype!).

Lepidocollema polyphyllinum (P. M. Jørg.) P. M. Jørg. comb. nov.

MycoBank No.: MB808009

Parmeliella polyphyllina P. M. Jørg., Bibl. Lich. 78: 134 (2001); type: Australia, Queensland, Hugh Nelson Range, along Plath Road, 15 km S of Atherton, alt. 1080 m, 25 June 1984, Elix 16363 & Streimann (CANB—holotype!).

Lepidocollema stylophorum (Vain.) P. M. Jørg. comb. nov.

MycoBank No.: MB808010

Pannaria stylophora Vain., Add. Lichenogr. Antill.: 102 (1915); type: Guadeloupe, Sofaga, ad corticem Sapii aucupari, Duss 1387 (TUR-V 12107—holotype!).

Lepidocollema wainioi (Zahlbr.) P. M. Jørg. comb. nov.

MycoBank No.: MB808011

Pannaria wainioi Zahlbr., Cat. Lich. Univ. 3: 261 (1924); type: Philippines, Mindanao, Butuan, alt. 15 m, 1911, Weber 1387 (TUR-V 12178—lectotype! fide Jørgensen 2003).

Lepidocollema zeylanicum (P. M. Jørg.) P. M. Jørg. comb. nov.

MycoBank No.: MB808012

Parmeliella zeylanica P. M. Jørg., Lichenologist 41: 257 (2009); type: Sri Lanka, Nuwara Elyia, near the Golf Club, 1964, Degelius As-438 (UPS—holotype!).

Nebularia incrassata (P. M. Jørg.) P. M. Jørg. comb. nov.

MycoBank No.: MB808013

Parmeliella incrassata P. M. Jørg., Lichenologist 32: 141 (2000); type: Ecuador, Pichincha, eastern slopes of Cerro Iliniza, alt. 4200 m, epiphyte on Polylepis, 7 March 1972, Arvidsson & Nilsson (GB—holotype!).

Nebularia psoromoides (P. M. Jørg. & Palice) P. M. Jørg. comb. nov.

MycoBank No.: MB808014

Parmeliella psoromoides P. M. Jørg. & Palice, Nordic J. Bot. 28: 625 (2010); type: Ecuador, Carchi, Volcan Chiles, páramo c. 1·5 km south-west of the top, 4050 m a.s.l., 13 July 1999, Palice 11977 (PRA—holotype!).

Nevesia sampaiana (Tav.) P. M. Jørg., L. Lindblom, Wedin & S. Ekman comb. nov.

MycoBank No.: MB808015

Pannaria sampaiana Tav., Port. Acta Biol. ser. B 3: 76–77 (1950); type: Portugal, Minho, Serra do Gerês, between S. Bento da Porta Alberta and Freitas, 1948, Tavares 2829 (LISU—holotype!).

Pectenia atlantica (Degel.) P. M. Jørg., L. Lindblom, Wedin & S. Ekman comb. nov.

MycoBank No.: MB808016

Parmeliella atlantica Degel., Acta Phytogeogr. Suec. 7: 131 (1935); type: Ireland, Killarney, near Muckross lake, 1933, Degelius (UPS—holotype!).

Pectenia cyanoloma (Schaer.) P. M. Jørg., L. Lindblom, Wedin & S. Ekman comb. nov.

MycoBank No.: MB808017

Parmelia plumbea var cyanoloma Schaer., Enum. Criticae Lich. Eur.: 36 (1850); type: France, Normandie, in sylva Briquebec, Delise (G—lectotype! fide Jørgensen 1978).

Pectenia ligulata (P. M. Jørg. & P. James) P. M. Jørg., L. Lindblom, Wedin & S. Ekman comb. nov.

MycoBank No.: MB808018

Degelia ligulata P. M. Jørg. & P. James, Bibl. Lich. 38: 266 (1990); type: Portugal, Azores, Faial, Santa Maria, Anjos, on mossy earth bank, 1976, James (BM—holotype!).

Pectenia plumbea (Lightf.) P. M. Jørg., L. Lindblom, Wedin & S. Ekman comb. nov.

MycoBank No.: MB808019

Lichen plumbeus Lightf., Fl. Scot. 2: 826 (1777); type: Great Britain (OXF-DILL 179: 73a—lectotype! fide Jørgensen 1978).

Psoroma dichroum (Hook. f. & Taylor) P. M. Jørg. comb. nov.

MycoBank No.: MB808020

Lecanora dichroa Hook.f. & Taylor, J. Bot. London 3: 643 (1844); type: Kerguelen, Christmas harbour, Hooker 1844 (FH—lectotype! fide Dodge 1948).

Psoroma macrosporum (P. M. Jørg. & Palice) P. M. Jørg. comb. nov.

MycoBank No.: MB808021

Santessoniella macrospora P. M. Jørg. & Palice, Nord. J. Bot. 28: 626 (2010); type: Ecuador, Carchi: surroundings of Laguna Verde, 1·5–1·8 km SSE of Volcan Chiles, 4000 m a.s.l., 12 July 1999, Palice 2750 (PRA—holotype!).

Psoroma obscurius (Nyl.) P. M. Jørg. comb. nov.

MycoBank No.: MB808022

Pannaria obscurior Nyl. in Cromb., J. Bot. London 13: 334 (1875); type: Kerguelen, Observatory Bay, December 1874, Eaton (BM—holotype!).

Psoroma orphninum (Hue) P. M. Jørg. comb. nov.

MycoBank No.: MB808023

Siphula orphnina Hue, 2me Exped. Antarct. FranV., Lich.: 19 (1915); type: South Shetland, Livingston Island, South Bay, Johnson's Peak, 300–350 m, 8 February 1998, Søchting 7833 (BG—neotype! fide Jørgensen 2005b ).

Psoroma polychidioides (Zahlbr.) P. M. Jørg. comb. nov.

MycoBank No.: MB808024

Lemmopsis polychidioides Zahlbr. in Skottsb.: Nat. Hist. of Juan Fernandez Easter Isl. 2: 333 (1924); type: Chile, Juan Fernandez, Mastierra, Cordon Chifladores, 17 April 1917, Skottsberg & Skottsberg 408 (UPS—holotype!).

Psoroma xanthorioides (P. M. Jørg.) P. M. Jørg. comb. nov.

MycoBank No.: MB808025

Pannaria xanthorioides P. M. Jørg., Bibl. Lich. 88: 238 (2004); type: Heard Island, near the summit of Scarlet Hill, 6 January 2001, Gremmen H-0663 (CANB—holotype!).

We gratefully acknowledge the following herbaria for assistance: AMH, B, BG, BM, BRI, CANB, CANL, FH, G, GB, H, LAM, LISU, OXF, PC, PRA, TNS, TUR, UPS, US, W, and WELT. We are indebted to Frances Anderson, André Aptroot, Franz Berger, Pieter van den Boom, William R. Buck, Arve Elvebakk, Javier Etayo, David J. Galloway, Dag Olav Øvstedal, Zdenek Palice, Mac Pitcher, Felix Schumm, Harrie Sipman, Ulrik Søchting, Tor Tønsberg, Dalip K. Upreti, as well as the curators of BG, NBM, NMW, PRA, S, and UPS for providing us with material that was used to obtain sequence data. We thank Birgit Kanz, Heidi Lie Andersen, and the staff at the Molecular Systematics Laboratory at the Swedish Museum of Natural History for assisting with laboratory work. Special thanks are due to Astri Botnen for help in handling herbarium material, Jan Berge for taking the colour photographs, and Beate Helle for arranging the photographs into complete illustrations. This work was supported by the Research Council of Norway (grant no. 128388/420 to SE), the Swedish Research Council (grants VR 621-2006-3760, VR 621-2009-5372, and VR 621-2012-3990 to MW), and the University Museum of Bergen (Olaf Grolle Olsens legat to PMJ).

Supplementary Material

For supplementary material accompanying this paper visit http://dx.doi.org/10.1017/S002428291400019X

References

Alfaro, M. E. & Holder, M. T. (2006) The posterior and the prior in Bayesian phylogenetics. Annual Review of Ecology, Evolution, and Systematics 37: 1942.
Altekar, G., Dwarkadas, S., Huelsenbeck, J. P. & Ronquist, F. (2004) Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20: 407415.
Arvidsson, L. & Galloway, D. J. (1981) Degelia, a new lichen genus in the Pannariaceae . Lichenologist 13: 2750.
Belnap, J. (2003) The world at your feet: desert biological soil crusts. Frontiers in Ecology and the Environment 1: 181189.
Blom, H. H. & Lindblom, L. (2009 [‘2010’]) Degelia cyanoloma (Schaerer) H. H. Blom & L. Lindblom comb. et stat. nov., a distinct species from western Europe. Lichenologist 42: 2327.
Bollback, J. P. (2002) Bayesian model adequacy and choice in phylogenetics. Molecular Biology and Evolution 19: 11711180.
Brown, J. M. & Lemmon, A. R. (2007) The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Systematic Biology 56: 643655.
Buckley, T. R. (2002) Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Systematic Biology 51: 509523.
Cannone, J., Subramanian, S., Schnare, M., Collett, J., D'Souza, L., Du, Y., Feng, B., Lin, N., Madabusi, L., Muller, K., et al. (2002) The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3: 2.
Clements, F. E. & Shear, C. L. (1931) The Genera of Fungi. New York: H. W. Wilson.
Cleveland, C. C., Townsend, A. R., Schimel, D. S., Fisher, H., Howarth, R. W., Hedin, L. O., Perakis, S. S., Latty, E. F., Von Fischer, J. C., Elseroad, A. et al. (1999) Global patterns of terrestrial biological nitrogen (N2) fixation in natural ecosystems. Global Biogeochemical Cycles 13: 623645.
Culberson, C. F. & Kristinsson, H. (1970) A standardized method for the identification of lichen products. Journal of Chromatography 46: 8593.
Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. (2012) jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772.
Dodge, C. W. (1948) Lichens and lichen parasites. British-Australian-New Zealand Antarctic Research Expedition 1929–1931, Report Series B, Zoology-Botany 7: 1276.
Edwards, S. V., Liu, L. & Pearl, D. K. (2007) High-resolution species trees without concatenation. Proceedings of the National Academy of Sciences of the United States of America 104: 59365941.
Ekman, S. & Blaalid, R. (2011) The devil in the details: interactions between the branch-length prior and likelihood model affect node support and branch lengths in the phylogeny of the Psoraceae . Systematic Biology 60: 541561.
Ekman, S. & Jørgensen, P. M. (2002) Towards a molecular phylogeny for the lichen family Pannariaceae . Canadian Journal of Botany 80: 625634.
Ekman, S., Andersen, H. L. & Wedin, M. (2008) The limitations of ancestral state reconstruction and the evolution of the ascus in the Lecanorales (lichenized Ascomycota). Systematic Biology 57: 141156.
Elvebakk, A., Robertsen, E. H., Park, C. H. & Hong, S. G. (2010) Psorophorus and Xanthopsoroma, two new genera for yellow-green, corticolous and squamulose lichen species, previously in Psoroma . Lichenologist 42: 563585.
Galloway, D. J. (1983) New taxa in the New Zealand lichen flora. New Zealand Journal of Botany 21: 191200.
Galloway, D. J. & James, P. W. (1985) The lichen genus Psoromidium Stirton. Lichenologist 17: 173188.
Galloway, D. J. & Jørgensen, P. M. (1987) Studies in the lichen family Pannariaceae II. The genus Leioderma Nyl. Lichenologist 19: 345400.
Gardner, P. P., Daub, J., Tate, J. G., Nawrocki, E. P., Kolbe, D. L., Lindgreen, S., Wilkinson, A. C., Finn, R. D., Griffiths-Jones, S., Eddy, S. R. et al. (2009) Rfam: updates to the RNA families database. Nucleic Acids Research 37: D136140.
Goldman, N. (1993) Statistical tests of models of DNA substitution. Journal of Molecular Evolution 36: 182198.
Guindon, S., Lethiec, F., Duroux, P. & Gascuel, O. (2005) PHYML online - a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Research 33: W557559.
Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W. & Gascuel, O. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology 59: 307321.
Hamada, M., Sato, K., Kiryu, H., Mituyama, T. & Asai, K. (2009) CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score. Bioinformatics 25: 32363243.
Henssen, A. (1963) Eine Revision der Flechtenfamilien Lichinaceae und Ephebaceae . Symbolae Botanicae Upsalienses 18: 1123.
Henssen, A. (1965) A review of the genera of the Collemataceae with simple spores (excluding Physma). Lichenologist 3: 2941.
Henssen, A. (1979) New species of Homothecium and Ramalodium from S America. Botaniska Notiser 132: 257282.
Henssen, A. (1997) Santessoniella, a new cyanophilic genus of lichenized ascomycetes. Symbolae Botanicae Upsalienses 32: 7593.
Henssen, A. (1999) New species of Ramalodium and Staurolemma from Australasia (Collemataceae, lichenized ascomycetes). Nova Hedwigia 68: 117130.
Henssen, A. (2000) Santessoniella rosettiformis, a new species from South America with notes on S. pulchella (Pannariaceae). Lichenologist 32: 5765.
Henssen, A. & Jahns, H. M. (1973 [‘1974’]) Lichenes. Eine Einführung in die Flechtenkunde. Stuttgart: Georg Thieme Verlag.
Henssen, A. & James, P. W. (1980) Parmeliella duplomarginata, a new lichen from New Zealand. Mycotaxon 11: 217229.
Henssen, A. & Kantvilas, G. (2000) Santessoniella rugosa (Pannariaceae), a new species from Tasmania. Lichenologist 32: 149153.
Holien, H. & Jørgensen, P. M. (2000) A blue-green Psoroma hypnorum found in Trøndelag, Central Norway. Graphis Scripta 11: 4952.
Huelsenbeck, J. P. & Rannala, B. (2004) Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Systematic Biology 53: 904913.
James, T. Y., Kauff, F., Schoch, C. L., Matheny, P. B., Hofstetter, V., Cox, C. J., Celio, G., Gueidan, C., Fraker, E., Miądlikowska, J. et al. (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443: 818822.
Jørgensen, P. M. (1978) The lichen family Pannariaceae in Europe. Opera Botanica 45: 1123.
Jørgensen, P. M. (1994) Studies in the lichen family Pannariaceae VI. The taxonomy and phytogeography of Pannaria Del. s. lat. Journal of the Hattori Botanical Laboratory 76: 197206.
Jørgensen, P. M. (1998) Studies in the lichen family Pannariaceae VII. On some poorly known Parmeliella-like species from the Southern Hemisphere. Lichenologist 30: 533541.
Jørgensen, P. M. (1999) Studies in the lichen family Pannariaceae VIII. Seven new parmelielloid lichens from New Zealand. New Zealand Journal of Botany 37: 257268.
Jørgensen, P. M. (2000) New or interesting Parmeliella species from the Andes and Central America. Lichenologist 32: 139147.
Jørgensen, P. M. (2001 a [‘2000’]) Survey of the lichen family Pannariaceae on the American continent, north of Mexico. Bryologist 103: 670704.
Jørgensen, P. M. (2001 b) Studies in the family Pannariaceae X. The lichen genus Protopannaria in the subantarctic islands. Cryptogamie, Mycologie 22: 6772.
Jørgensen, P. M. (2002) Kroswia, a new genus in the Pannariaceae . Lichenologist 34: 297303.
Jørgensen, P. M. (2003) Conspectus familiae Pannariaceae . Ilicifolia 4: 178.
Jørgensen, P. M. (2004) Further contributions to the Pannariaceae (lichenized Ascomycetes) of the Southern Hemisphere. Bibliotheca Lichenologica 88: 229253.
Jørgensen, P. M. (2005 a) Additions to the Pannariaceae of North America. Bryologist 108: 255258.
Jørgensen, P. M. (2005 b) Notes on two subantarctic pannariaceous lichens. Cryptogamie, Mycologie 26: 3743.
Jørgensen, P. M. (2007) New discoveries in Asian pannariaceous lichens. Lichenologist 39: 235243.
Jørgensen, P. M. (2008) Vahliella, a new lichen genus. Lichenologist 42: 221225.
Jørgensen, P. M. (2010) New discoveries in the lichen genus Staurolemma Körb. Nova Hedwigia 90: 153159.
Jørgensen, P. M. & Arvidsson, L. (2002) The genus Erioderma (Pannariaceae) in Ecuador and neighbouring countries. Nordic Journal of Botany 22: 87114.
Jørgensen, P. M. & Galloway, D. J. (1989) Studies in the lichen family Pannariaceae III. The genus Fuscoderma, with additional notes and a revised key to Leioderma . Lichenologist 21: 295301.
Jørgensen, P. M. & Galloway, D. J. (1992) Pannariaceae. Flora of Australia 54: 246293.
Jørgensen, P. M. & Gjerde, I. (2012) Notes on some pannariaceous lichens from New Caledonia. Cryptogamie, Mycologie 33: 39.
Jørgensen, P. M. & James, P. W. (1990) Studies in the lichen family Pannariaceae IV. The genus Degelia . Bibliotheca Lichenologica 38: 253276.
Jørgensen, P. M. & Palice, Z. (2010) Additions to the lichen family Pannariaceae in Ecuador. Nordic Journal of Botany 28: 623628.
Jørgensen, P. M., Ekman, S. & Wedin, M. (2013) (2143) Proposal to conserve the name Fuscopannaria against Moelleropsis (lichenized Ascomycota). Taxon 62: 629.
Katoh, K. & Toh, H. (2008) Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinformatics 9: 212.
Kauff, F. & Lutzoni, F. (2002) Phylogeny of the Gyalectales and Ostropales (Ascomycota, Fungi): among and within order relationships based on nuclear ribosomal RNA small and large subunits. Molecular Phylogenetics and Evolution 25: 138156.
Keuck, G. (1977) Ontogenetische-systematische Studie über Erioderma in Vergleich mit anderen cyanophilen Flechtengattungen. Bibliotheca Lichenologica 6: 1175.
Kirk, P. M., Cannon, P. F., Minter, D. W. & Stalpers, J. A. (eds) (2008) Ainsworth & Bisby's Dictionary of the Fungi. Wallingford, Oxon: CAB International.
Kiryu, H., Tabei, Y., Kin, T. & Asai, K. (2007) Murlet: a practical multiple alignment tool for structural RNA sequences. Bioinformatics 23: 15881598.
Kolaczkowski, B. & Thornton, J. W. (2007) Effects of branch length uncertainty on Bayesian posterior probabilities for phylogenetic hypotheses. Molecular Biology and Evolution 24: 21082118.
Kubatko, L. S. & Degnan, J. H. (2007) Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biology 56: 1724.
Lanfear, R., Calcott, B., Ho, S. Y. W. & Guindon, S. (2012) PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution 29: 16951701.
Lartillot, N. & Philippe, H. (2004) A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Molecular Biology and Evolution 21: 10951109.
Lartillot, N., Brinkmann, H. & Philippe, H. (2007) Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evolutionary Biology 7: S4.
Lartillot, N., Lepage, T. & Blanquart, S. (2009) PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25: 22862288.
Lemmon, A. R. & Moriarty, E. C. (2004) The importance of proper model assumption in Bayesian phylogenetics. Systematic Biology 53: 265277.
Lindblom, L. & Ekman, S. (2005) Molecular evidence supports the distinction between Xanthoria parietina and X. aureola (Teloschistaceae, lichenized Ascomycota). Mycological Research 109: 187199.
Lumbsch, H. T. & Huhndorf, S. M. (2010) Myconet Volume 14. Part One. Outline of Ascomycota – 2009. Part Two. Notes on Ascomycete Systematics. Nos. 4751–5113. Fieldiana, Life and Earth Sciences 1: 164.
Misof, B. & Misof, K. (2009) A Monte Carlo approach successfully identifies randomness in multiple sequence alignments: a more objective means of data exclusion. Systematic Biology 58: 2134.
Muggia, L., Nelson, P., Wheeler, T., Yakovchenko, L. S., Tønsberg, T. & Spribille, T. (2011) Convergent evolution of a symbiotic duet: the case of the lichen genus Polychidium (Peltigerales, Ascomycota). American Journal of Botany 98: 16471656.
Newton, M. A. & Raftery, A. E. (1994) Approximate Bayesian inference with the weighted likelihood bootstrap. Journal of the Royal Statistical Society Series B Methodological 56: 348.
Notredame, C. & Abergel, C. (2003) Using multiple alignment methods to assess the quality of genomic data analysis. In Bioinformatics and Genomes: Current Perspectives (Andrade, M. A., ed.): 3055. Wymondham: Horizon Scientific Press.
Notredame, C., Higgins, D. G. & Heringa, J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 302: 205217.
Nylander, J. A. A. (2004) MrAIC.pl. Version 1.4.4. Distributed by the author. URL: www.abc.se/~nylander/.
Otálora, M. A. G., Aragón, G., Molina, M. C., Martínez, I. & Lutzoni, F. (2010) Disentangling the Collema-Leptogium complex through a molecular phylogenetic study of the Collemataceae (Peltigerales, lichen-forming Ascomycota). Mycologia 102: 279290.
Otálora, M. A. G., Salvador, C., Martínez, I. & Aragón, G. (2013) Does the reproductive strategy affect the transmission and genetic diversity of bionts in cyanolichens? A case study using two closely related species. Microbial Ecology 65: 517530.
Øvstedal, D. O. & Fryday, A. M. (2011) A new species of Protopannaria (Pannariaceae, Ascomycota) from the southern New Zealand shelf islands, and additional records of Protopannaria from South America. Australasian Lichenology 68: 1215.
Passo, A., Stenroos, S. & Calvelo, S. (2008) Joergensenia, a new genus to accommodate Psoroma cephalodinum (lichenized Ascomycota). Mycological Research 112: 14651474.
Pupko, T., Huchon, D., Cao, Y., Okada, N. & Hasegawa, M. (2002) Combining multiple data sets in a likelihood analysis: which models are the best? Molecular Biology and Evolution 19: 22942307.
Rambaut, A. & Drummond, A. J. (2009) Tracer, Version 1.5. University of Edinburgh. URL: http://tree.bio.ed.ac.uk/software/tracer/.
Richardson, D. H. S., Anderson, F., Cameron, R. & Seaward, M. R. D. (2010) World distribution and ecology of Degelia plumbea s. l. British Lichen Society Bulletin 107: 5262.
Ronquist, F. & Huelsenbeck, J. P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 15721574.
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A. & Huelsenbeck, J. P. (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539542.
Schoch, C. L., Sung, G.-H., López-Giráldez, F., Townsend, J. P., Miądlikowska, J., Hofstetter, V., Robbertse, B., Matheny, P. B., Kauff, F., Wang, Z. et al. (2009) The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Systematic Biology 58: 224239.
Smith, S. A. & Dunn, C. W. (2008) Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 24: 715716.
Spribille, T. & Muggia, L. (2013) Expanded taxon sampling disentangles evolutionary relationships and reveals a new family in Peltigerales (Lecanoromycetidae, Ascomycota). Fungal Diversity 58: 171184.
Spribille, T., Jørgensen, P. M., Schulz, M. & Houde, I. (2007) Santessoniella saximontana, a new lichen species from British Columbia. Bibliotheca Lichenologica 96: 287297.
Spribille, T., Pérez-Ortega, S., Tønsberg, T. & Schirokauer, D. (2010) Lichens and lichenicolous fungi of the Klondike Gold Rush National Historic Park, Alaska, in a global biodiversity context. Bryologist 113: 439515.
Suchard, M. A., Kitchen, C. M. R., Sinsheimer, J. S. & Weiss, R. E. (2003) Hierarchical phylogenetic models for analyzing multipartite sequence data. Systematic Biology 52: 649664.
Swinscow, T. D. V. & Krog, H. (1988) Macrolichens of East Africa. London: British Museum (Natural History).
Tavares, C. N. (1950) Liquenes da Serra do Gerês. Portugalia Acta Biologica, Serie B 3: 1188.
Tuckerman, E. (1872) Genera Lichenum: An Arrangement of North American Lichens. Amherst: Edwin Nelson.
Vainio, E. (1890) Étude sur la classification naturelle et la morphologie des lichens du Brésil. Pars I. Acta Societatis pro Fauna et Flora Fennica 7: 1256.
Venditti, C., Meade, A. & Pagel, M. (2010) Phylogenies reveal new interpretation of speciation and the Red Queen. Nature 463: 349352.
Wedin, M. & Wiklund, E. (2004) The phylogenetic relationships of Lecanorales suborder Peltigerineae revisited. Symbolae Botanicae Upsalienses. 34: 469475.
Wedin, M., Jørgensen, P. M. & Wiklund, E. (2007) Massalongiaceae fam. nov., an overlooked monophyletic group among the cyanobacterial lichens (Peltigerales, Lecanoromycetes, Ascomycota). Lichenologist 39: 6167.
Wedin, M., Wiklund, E., Jørgensen, P. M. & Ekman, S. (2009) Slippery when wet: phylogeny and character evolution in the gelatinous cyanobacterial lichens (Peltigerales, Ascomycetes). Molecular Phylogenetics and Evolution 53: 862871.
Wedin, M., Jørgensen, P. M. & Ekman, S. (2011) Vahliellaceae, a new family of cyanobacterial lichens (Peltigerales, Ascomycetes). Lichenologist 43: 6772.
Yang, Z. (2006) Computational Molecular Evolution. Oxford: Oxford University Press.
Zahlbruckner, A. (1926) B. Spezieller Teil. In Die Natürlichen Pflanzenfamilien nebst ihren Gattungen und wichtigeren Arten insbesondere den Nutzpflanzen. Band 8. Flechten (Lichenes). 2nd ed. (Engler, A. & Prantl, K., eds): 61263. Leipzig: Wilhelm Engelmann.