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Botanical Museum, Lund University, Östra Vallgatan 18, SE-223 61 Lund, Sweden
Stefan Ekman
Department of Biology, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
Martin Grube
Institute of Plant Science, Karl-Franzens University, Holteigasse 6, A-8010 Graz, Austria
Jan-Eric Mattsson
School of Life Sciences, Södertörn University College, SE-181 49 Huddinge, Sweden
Mats Wedin
Cryptogamic Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-10405 Stockholm, Sweden
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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The family Parmeliaceae (Lecanorales, Ascomycota) is possibly the largest, best known and most thoroughly studied lichen family within its order. Despite this fact the relationship between Parmeliaceae and other groups in Lecanorales is still poorly known. The aim of the present study is to contribute to finding the sister group of Parmeliaceae as an aid in future studies on the phylogeny and character evolution of the group. We do this by sampling all potential relatives to the Parmeliaceae that we have identified, i.e. Gypsoplaca, Japewia, Mycoblastus, Protoparmelia, and Tephromela, a good representation of the major groups within the Parmeliaceae s. lat. and a good representation of other taxa in the core Lecanorales. We use molecular data from two genes, the large subunit of the nuclear ribosomal RNA gene (nrLSU) and the small subunit of the mitochondrial ribosomal RNA gene (mrSSU), and a Bayesian analysis of the combined data. The results show that the closest relatives to Parmeliaceae are the two genera Protoparmelia and Gypsoplaca, which are crustose lichens. Parmeliaceae in our sense is a well supported group, including also the family segregates Alectoriaceae, Hypogymniaceae, Usneaceae and Anziaceae.
Key words: DNA, Gypsoplaca, Lecanorales, molecular, mrSSU, nrLSU, phylogeny, Protoparmelia
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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). Many of the groups included here belong to the earliest described lichen genera, e.g. Parmelia, Cetraria and Usnea, and many of the species are important components of diverse lichen communities in different vegetation types all around the world. Parmeliaceae currently is regarded as a uniform monophyletic group circumscribed by similarities in ascoma ontogeny and the anatomy of the characteristic cupular exciple (Henssen and Jahns 1973, Kärnefelt et al 1998). Although many family segregates have been suggested for groups obviously deviating in growth form (e.g. Alectoriaceae, Hypogymniaceae and Usneaceae; see Wedin et al 1999 for a list of suggested segregates and other family names considered synonyms to Parmeliaceae) a broad circumscription of Parmeliaceae is the most widely accepted. Several molecular phylogenies either have taken this concept as a starting assumption for analyses of the group (Mattsson and Wedin 1998; Thell et al 2002, 2004; Articus 2004) or support at least partly this view (Mattsson and Wedin 1999, Persoh and Rambold 2002). However to our surprise no one seems to have tested this concept by including representatives of all commonly accepted family segregates in a phylogenetic analysis. In the most recent Outline of the Ascomycota (Eriksson 2006) only the family segregate Anziaceae is accepted.
Numerous recent studies have focussed on the delimitation and reclassification of groups related to Parmelia s. lat. within the Parmeliaceae (e.g. Blanco et al 2004a, 2004b, 2005; Thell et al 2004). However, despite being such a widespread, well known and well studied lichen group, the relationships among Parmeliaceae and other groups in Lecanorales are poorly known. Although several molecular studies show that Lecanorales (sensu Wiklund and Wedin 2003, Wedin et al 2005) forms a monophyletic group, excluding among others the families Umbilicariaceae, Candelariaceae and Acarosporaceae (Lücking et al 2004, Lumbsch et al 2004, Reeb et al 2004, Persoh et al 2004, Wedin et al 2005), the detailed sister group relation of Parmeliaceae is not yet known. This is hampering the investigations of the phylogenetic relationships within Parmeliaceae s. lat. and investigations of morphological evolution within the group because proper outgroup rooting with a known close relative currently is not possible.
A possible candidate for the sister group of Parmeliaceae is Protoparmelia. This genus has been classified usually in Lecanoraceae because it includes crustose lichens with single, one-celled hyaline ascospores and an ascus of the Lecanora-type (Hafellner 1984; Eriksson and Hawksworth 1989, 1995). Studies of the ascoma ontogeny (Miyawaki 1991, Henssen 1995) however showed that Protoparmelia possesses the cupular exciple (cup-shaped structure below the hymenium) so typical for Parmeliaceae, and in the latest version of the Outline of Ascomycota (Eriksson 2005) Protoparmelia is listed as a member of Parmeliaceae. Several recent studies of Parmeliaceae phylogeny consequently use Protoparmelia as out-group, even though this is an untested assumption and Protoparmelia might just as well be a member of the ingroup.
There are further possible sister group candidates however. A number of crustose groups, based on anatomical characteristics, could be related to Parmeliaceae. These include Mycoblastaceae and Tephromelataceae, Japewia (currently in Ramalinaceae), and our previous, preliminary, analyses of lecanoralean lichens also placed the enigmatic genus Gypsoplaca close to Parmeliaceae. Gypsoplaca (Gypsoplacaceae) includes just one species, G. macrophylla.
The aim of the present study is to contribute to the circumscription of a natural, monophyletic group corresponding to the family Parmeliaceae. We also wish to suggest possible sister groups of Parmeliaceae, whereby further and more detailed studies of the phylogeny and character evolution within this group may be aided. We do this by sampling DNA sequence data from the type species of the family (Parmelia saxatilis), representatives of all recently accepted family segregates (Alectoriaceae, Anziaceae, Hypogymniaceae, Usneaceae) plus the deviant Menegazzia and all potential close relatives of the Parmeliaceae that we have been able to identify (Gypsoplaca, Japewia, Mycoblastus, Protoparmelia, Tephromela and Calvitimela). It should be pointed out that, although Parmeliaceae at present contains almost 90 genera, our selection represents a fair selection of the morphological and taxonomical diversity in this group. Finally we have included a good representation of other taxa in the Lecanorales. Lecanoraceae, a family of crustose lichens showing similarities with the Parmeliaceae in ascoma characteristics, was particularly well sampled.
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MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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). The outgroup species Caloplaca flavorubescens and Xanthoria parietina were chosen because they belong to Lecanorales sensu Wiklund and Wedin (2003) but are not closely related to any of the main target families Lecanoraceae or Parmeliaceae (Andersen and Ekman 2004).
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, Döring et al 2000 and Wiklund and Wedin (2003) or the PCR cycling parameters included an initial hold at 94 C for 5 min, then denaturation at 94 C for 1 min, annealing at 56 C for 1 min, decreasing 1 C per cycle for the first six of the 39 cycles (touchdown), and extension at 72 C for 3 min. We amplified the first part of the large subunit of the nuclear ribosomal RNA gene (nrLSU) and the first part of the small subunit of the mitochondrial ribosomal RNA gene (mrSSU).
Sequence alignment and phylogenetic analyses.— –
A total of 54 ingroup taxa and two outgroup taxa were aligned by hand. The alignment, which included 838 sites of nrLSU and 763 sites of mrSSU, was submitted to TreeBASE (study accession number S1769, matrix accession number M3227). For Calvitimela armeniaca and C. aglaea only the LSU gene was successfully sequenced. Ambiguously aligned parts were excluded. Gaps were treated as missing data. Phylogenetic analyses were carried out with Bayesian inference. Congruence between data partitions was tested by inspecting posterior probability scores 
0.95 resulting from separate Bayesian analyses including all taxa, also C. armeniaca and C. aglaea for which mrSSU sequence data is lacking (de Queiroz 1993, Miadlikowska and Lutzoni 2000). Conflicts between the two datasets were considered significant if two relationships (one monophyletic and the other nonmonophyletic) for the same set of taxa were supported by pp 0.95.
Bayesian tree inference was carried out with MrBayes version 3.1.2 (Ronquist and Huelsenbeck 2003). A suitable likelihood model was selected with decision theory as implemented in the software DT-ModSel (Minin et al 2003). The TrN+I+G model was found to be optimal for the nrLSU dataset while the TVM+I+G model was optimal for the mrSSU dataset. These models include respectively three and five reversible substitution types. However MrBayes does not allow the implementation of models having between three and five substitution types. Therefore, following the recommendation by Huelsenbeck and Rannala (2004), we chose the next more complicated model allowed in MrBayes (viz. GTR). We consequently implemented separate GTR+I+G models for each of the two partitions. All likelihood parameters, except branch lengths (assumed to be proportional across partitions) and tree topology, were unlinked. The number of discrete categories to be used in the gamma model was estimated according to the method used by Andersen and Ekman (2004). This procedure resulted in a discrete gamma model with eight categories for the nrLSU dataset and seven for the mrSSU data.
Prior distributions were set to uniform for tree topology, gamma shape parameter and the proportion of invariable sites, to a flat dirichlet for the rate matrix and state frequencies and to exponential for the branch lengths (with inverse scale parameter 10). The two partitions were allowed to evolve at different rates by setting the rate prior to variable. Three parallel runs of Markov chain Monte Carlo were performed, each with 12 chains, 11 of which were incrementally heated with a temperature of 0.15. The appropriate degree of heating was determined by observing swap rates between chains in preliminary runs. Analyses were diagnosed every 100 000 generations in the last 50% of the tree sample and automatically halted when convergence was reached. Convergence was defined as a standard deviation of splits (of frequency 0.1) between runs below 0.01. Every 100th tree was sampled.
A maximum likelihood (ML) analysis was carried out to obtain a second measure of branch support. We used the software RAxML-VI-HPC v2.0 (Stamatakis, Ludwig, Meier 2005; Stamatakis Website at http://www.ics.forth.gr/~stamatak/). RAxML implements only the GTR model, which is hard-coded into the software. Partitioning data with independent models is allowed (but interpartition rate heterogeneity is not allowed). We divided our data into the same two partitions as in the Bayesian analysis. Rate heterogeneity among sites was assumed to be gamma distributed with four rate categories (the only number of rate categories allowed by RAxML). We could not assume a proportion of sites to be invariable because this is not allowed by RAxML. Branch support was assessed with 1000 bootstrap replicates. Random addition sequence parsimony trees were used as starting trees for likelihood optimization. In the initial rearrangement pruned subtrees were allowed to be reinserted up to 10 nodes away from their original position. Model parameters were optimized up to a difference of 0.1 ln likelihood units. For classification purposes branch support was considered strong if its posterior probability was 0.95 or higher and its bootstrap proportion was 75% or higher.
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RESULTS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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). No significant incongruence between the two datasets was detected and they consequently were combined. A total of 1601 sites were included in the final combined analysis. The majority rule consensus tree of the Bayesian analysis, based on the final 50% of three parallell runs of length 6 600 000 generations, is presented (FIG. 1) together with posterior probabilities and likelihood bootstrap proportions of branches.
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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, Persoh and Rambold 2002) but also provides evidence for the inclusion of Anziaceae and Menegazzia in Parmeliaceae. This family, together with Gypsoplacaceae and Protoparmelia, forms a group that received strong support (pp = 1.00, bootstrap = 76). In the majority rule consensus tree Protoparmelia forms the sister group of Parmeliaceae, but this has low support (pp = 0.48, FIG. 2). A closer look at the possible topologies of the three branches Parmeliaceae s. str., Protoparmelia and Gypsoplaca shows that another topology is almost as probable (FIG. 2). With a posterior probability of 0.45 Protoparmelia and Gypsoplaca together form a sister group of Parmeliaceae, while a topology where Gypsoplaca alone is sister of Parmeliaceae has low support (pp = 0.07). We at present cannot decide whether Protoparmelia, or a group consisting of Gypsoplaca and Protoparmelia, is the sister group of Parmeliaceae. We thus cannot support including Protoparmelia in Parmeliaceae, as suggested by some authors, without including also Gypsoplacaceae in the family. To accept Protoparmelia as a crustose Parmeliaceae is admittedly not difficult because it shares the cupular exciple widely accepted as a characteristic feature for Parmeliaceae. However this feature occurs, with some variations, also in Caloplaca, Collema, Rinodina and Lecanora, which are not closely related to Parmeliaceae. Gypsoplaca however lacks a cupular exciple and has a strongly aberrant apothecium ontogeny and anatomy. The matter of classification of these groups is obviously difficult and we refrain from suggesting any changes at this moment.
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questioned the placement in Lecanoraceae, mainly because of the tholus shape, which differed slightly from that of Lecanora. Hertel (1984) added the presence of lobaric acid in Protoparmelia to the list of characters not in concordance with a placement in Lecanoraceae. Later Miyawaki (1991) studied apothecial structures in P. badia and found a cupular exciple that is surrounded by a "saucer-shaped layer" of algal cells, which characterizes Parmeliaceae according to Henssen and Jahns (1973). Therefore they proposed a classification of Protoparmelia within Parmeliaceae. According to Henssen (1995) most members of Parmeliaceae have a distinctly heteromerous thallus and subcrustaceous and foliose species have both an upper and a lower cortex. Typically this thallus is attached to the substrate either by rhizines, an umbilicus or by rhizoidal hyphae. In this respect Protoparmelia differs from the general pattern, but this did not prevent Henssen from accepting the genus as a member of Parmeliaceae s. lat.
The lichen genus Gypsoplaca includes just one species, G. macrophylla, which is brown, crustose or squamiform (Timdal 1990). Timdal erected this genus and the new family Gypsoplacaceae due to a remarkable ascoma ontogeny, which is characterized by an undelimited ascoma formed by paraphyses and ascogenous hyphae growing into the upper cortex and transforming it into a hymenium. The cortex is of "Kegelrinden" type (Poelt 1958, Timdal 1990). The asci are clavate, surrounded by an amyloid, gelatinous sheet and have a well developed, amyloid tholus with a deeper amyloid tube and usually an ocular chamber (Timdal 1990). This type of ascus is not rare and occurs for example among some of the Cetraria-like genera of Parmeliaceae (Thell et al 1995, Wedin et al 2000).
A few comments are needed concerning interesting phylogenetic relationships outside the focus of this study, the Parmeliaceae. Cladoniaceae, Stereocaulaceae and Miriquidica garovaglii together form a supported sister clade (pp = 0.97) of the group with Parmeliaceae, Gypsoplacaceae and Protoparmelia. The relationship as sister clades however is not supported. The genus Miriquidica currently is classified in Lecanoraceae, but it should be noted that the species used in the analysis is not the type species. Another clade (without support) includes Lecanoraceae including Japewia. Although this has no support in the present analysis, a similar pattern where Lecanoraceae, Parmeliaceae, Cladoniaceae and Stereocaulaceae together form a monophyletic group has been found in other phylogenetic analyses (Wedin et al 2000, Persoh et al 2004). The support for Ramalinaceae is high (pp = 1.0, bootstrap value 99) if Tephromela and Japewia, both classified in the Ramalinaceae (Eriksson 2006), are excluded from that family. Japewia instead might belong in the Lecanoraceae, although branch support for this is low. Tephromela, Calvitimela and Mycoblastus together form a monophyletic group with high support (pp = 1.0, bootstrap value 93) but the two latter genera might not be monophyletic. Because of low branch support inside this group we cannot tell whether two families, Tephromelataceae and Mycoblastaceae, or just one family, Mycoblastaceae (including Tephromelataceae), should be recognized. However the results confirm that Tephromela does not belong to Ramalinaceae (Ekman and Wedin 2000) and that Calvitimela, contrary to the suggestion by Eriksson (2006), does not belong to Lecanoraceae. The close relationship among Mycoblastus, Tephromela and Calvitimela is perhaps somewhat surprising. Although they are morphologically similar there are considerable anatomic differences (e.g. in ascus anatomy, number and size of spores, and paraphyses) (Hafellner 1984). A more detailed molecular study is needed to investigate both the generic circumscription in the group and the taxonomy at family level.
We have found that Parmeliaceae appears to be a well supported group that includes also the sometimes recognized family segregates Alectoriaceae, Hypogymniaceae, Usneaceae and Anziaceae. Further studies are needed to identify well supported natural groups within this family and to identify morphological synapomorphies that can be used to characterize them. The closest relatives to the large macrolichens within Parmeliaceae are likely to be crustose or squamiform microlichens. This has potentially substantial implications for future investigations of phylogeny and character evolution in this group.
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ACKNOWLEDGMENTS |
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FOOTNOTES |
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1 Corresponding author. E-mail: ulf.arup{at}botmus.lu.se
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