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Botanisches Institut, Universität Essen, 45117 Essen, Germany
Ulrik Søchting
Department of Mycology, Botanical Institute, University of Copenhagen, Ø. Farimagsgade 2D, DK-1353 Copenhagen K, Denmark
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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The phylogenetic relationships of the lichen genus Placopsis and related genera in the Agyriales were analyzed using molecular data. We obtained a total of 66 new sequences from the nuclear ITS, LSU and the mitochondrial SSU rDNA. Phylogenetic analyses were conducted in a Bayesian and a maximum-parsimony framework. Our analyses show that Placopsis is paraphyletic with members of Orceolina nesting within the genus. A morphological character supporting the Placopsis-Orceolina clade is the non-amyloid ascus. The section Aspiciliopsis as defined by sunken fruiting bodies is not supported, but the type species of Aspiciliopsis is more closely related to Orceolina. This clade shares apothecia with reduced amphithecia as apomorphic character. We suggest resurrecting the generic name Aspiciliopsis. Trapelia is the sister genus to Placopsis and Aspiciliopsis/Orceolina.
Key words: Agyriaceae, Agyriales, ITS rDNA, molecular phylogeny, mt SSU rDNA, nu LSU rDNA, Orceolina, Trapelia
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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, Follmann et al 1991, Lumbsch et al 1993, Brodo 1995, Moberg and Carlin 1996, 1999, Lumbsch 1997, Galloway 2001a, b). They preferably grow in oceanic habitats on rocks or soil. The crustose thalli spread into rosette forms and are pale whitish to greenish in color. Most species in the genus are characterized by disciform apothecia and the symbiotic association with two different photobionts: green algae and cyanobacteria. The vernacular name, "bull's eye lichens" refers to the large, pink to brown cephalodia containing the cyanobionts, which often are located at the center of the thallus (Brodo et al 2001). The genus has a mainly southern-hemisphere distribution, with the greatest species diversity in South America and Australia/New Zealand (Lamb 1947, Galloway 1985, 2001a). Several taxa are known from Antarctica, the sub-Antarctic islands of the Indian Ocean (Lamb 1947, Øvstedal and Lewis Smith 2001), and New Guinea (Aptroot and Sipman 1991, Lumbsch et al 1993). Four species occur in North America (P. cribellans, P. gelida, P. lambii, P. roseonigra) (Brodo 1995, Brodo et al 2001), and two in Europe (P. gelida and P. lambii) (Lamb 1947, Moberg and Carlin 1996).
The genus has a rather uniform secondary chemistry. Most species are characterized by the gyrophoric acid chemosyndrome (Hertel and Leuckert 1969, Lamb 1947, Lumbsch et al 1993, Brodo 1995), and some taxa possess the depsidones fumarprotocetraric acid, salacinic acid (Lamb 1947) and stictic acid (Follmann et al 1991, Lumbsch 1997, Henssen 2003). Placopsis formerly was included in the family Trapeliaceae (Hertel 1969, Eriksson and Hawksworth 1998) or in the Pertusariaceae (Henssen and Jahns 1973). It currently is placed in the Agyriaceae (Lumbsch 1997, Eriksson 1999), which is an older name for Trapeliaceae and Saccomorphaceae (Rambold and Triebel 1990). This placement recently was confirmed in molecular studies using nuclear LSU and ITS sequence data (Lumbsch et al 2001a, Poulsen et al 2001).
A close relationship between the genera Placopsis and Trapelia, due to similar structures of the ascus apices and paraphyses, has been suggested by several authors (Magnusson 1932, Lamb 1947, Hertel 1969, 1970, Lumbsch et al 1993, Brodo 1995). Trapelia typically differs from Placopsis in that it lacks cephalodia. However, the generic delimitation of the two genera is problematic because some taxa, such as P. roseonigra, lack differentiated cephalodia but still are associated with cyanobacteria (Brodo 1995). Such structures also occur in other groups of lichens and are called paracephalodia (Poelt and Mayrhofer 1988). Wirth (1995) mentions another species of Placopsis that lacks cephalodia (P. lambii), an observation challenged by Moberg and Carlin (1996), who claim that P. lambii possesses cephalodia.
Within the genus Placopsis, the sections Placopsis (as Euplacopsis) and Aspiciliopsis are distinguished (e.g., Lamb 1947). This distinction is based mainly on the structure of the ascomata, which are raised slightly above the thallus surface (= lecanoroid) in Euplacopsis and sunken (= aspicilioid) in Aspiciliopsis. Furthermore, the cephalodia are more depressed in the section Aspiciliopsis. Originally the section Aspiciliopsis Müll. Arg. was described by Müller (1884:135) in the genus Placodium for a single species, viz P. macrophthalmum. Later the section was raised to generic level by Choisy (1929:526) to accommodate A. macrophthalma. Some authors followed this position (Dodge 1948:174, Hafellner 1984), whereas others preferred not to accept Aspiciliopsis at generic rank because they could not find fundamental differences between the two groups (Lamb 1947, Hertel 1970, Lumbsch 1997). Moreover, aspicilioid ascomata can be found in many unrelated groups of lichenized ascomycetes and thus are likely to have evolved several times (Hafellner 1991). Recently an additional Placopsis species with sunken ascomata has been found (P. stellata) and was placed in the section Aspiciliopsis with P. macrophthalma (Henssen 2003). Galloway (2001a:58) reports the occurrence of further, still undescribed, Placopsis, sect. Aspiciliopsis species in New Zealand.
The genus Orceolina is an endemic taxon to the sub-Antarctic islands, which currently includes two species, O. antarctica and O. kerguelensis (Poulsen et al 2001). It was placed near Placopsis and Trapelia due to similar hymenial characters (Choisy 1929, Hertel 1969, 1970). However, it has a unique anatomical thallus structure, including very thick (up to 250 µm) cortical layers (Hertel 1969, Lumbsch 1997, Poulsen et al 2001). Its apothecia are immersed deeply in the thallus, whereas in Placopsis sect. Aspiciliopsis they are only slightly sunken. In addition, the ascus type in Orceolina differs from that in Placopsis and Trapelia in that it lacks an apical thickening (Hertel 1969, Lumbsch 1997). In contrast to most Placopsis spp. no lichen substances could be detected in this genus (Hertel and Leuckert 1969).
All of the above mentioned genera belong to the family Agyriaceae, which is part of the order Agyriales (Lumbsch 1997, Lumbsch et al 2001a, b). This order includes mostly lichenized ascomycetes characterized by crustose, placodioid to squamulose thalli, apothecia as fruiting bodies, unitunicate, weakly amyloid asci, hyaline ascospores and a hamathecium with true paraphyses. The Agyriaceae shows ascohymenial, hemiangiocarpous ascoma development and a cupular or, when reduced, annular exciple. It is characterized chemically by the presence of orcinol depsides and ß-orcinol depsidones (Lumbsch 1997).
In this study we evaluated the proposed subgeneric division within Placopsis, the phylogenetic position of the genus and, with the help of molecular characters, its relationship to the closely related genera Trapelia and Orceolina. We used ITS sequences to illuminate the relationships within Placopsis. To confirm the branching order within the genus, we also sequenced a part of the nuclear LSU rRNA gene and, as an independent locus, part of the mitochondrial SSU rDNA. We analyzed all three datasets in combination. Subsequently we added further taxa of the Agyriaceae to determine the position of Placopsis within the family. For this analysis, we used nu LSU and mt SSU sequences, because this combination of data has proved to produce highly resolved and strongly supported phylogenetic estimates in various studies of the Ascomycota (Lindemuth et al 2001, Schmitt et al 2001, 2002).
The phylogenetic analyses were performed in a maximum-parsimony and a Bayesian framework (Larget and Simon 1999, Huelsenbeck et al 2001). Bayesian analysis consists essentially of maximum-likelihood (ML) comparisons of trees in which the tree topology and ML parameters are permuted using a Markov chain Monte Carlo (MCMC) method. The trees are sampled periodically and are considered to be drawn from a posterior probability distribution. Thus the frequency with which they are sampled indicates their probability. The posterior probabilities of individual branches also are calculated easily because they are equal to the proportion of their occurrence in trees that are visited during the MCMC analysis.
An advantage of the Bayesian approach is its robustness over traditional tree building methods. It considers all potential trees, weighted according to the probability that each is correct, while other common phylogenetic methods, such as ML or MP, select only a single or several equally optimal trees. It is likely that such an approach takes a better account of the phylogenetic status quo (Huelsenbeck et al 2000). Furthermore, the posterior probability values, used to indicate the confidence of individual branches, are natural measures of nodal support and are easier to interpret than measures based on parsimony or likelihood (e.g., bootstrap values) (Lewis 2001). A practical gain of the MrBayes program (Huelsenbeck and Ronquist 2001) is that it enables the calculation of complicated, and thus more realistic, models of nucleotide substitution in a reasonable amount of time because the phylogenetic trees and the confidence values for individual branches are obtained simultaneously.
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MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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) and ITS4 (White et al 1990), nuclear LSU rDNA with the primers pairs AL1R (Döring et al 2000) and LR6 (Vilgalys homepage: http://www.biology.duke.edu/fungi/mycolab/primers.htm), and the mitochondrial SSU rDNA with mrSSU 1 (Zoller et al 1999) and MSU7 (Zhou and Stanosz 2001). Primers were selected to ensure that at least one primer of each pair was fungal specific to avoid amplification of photobiontic DNA. The 50 µL PCR reactions contained 5 µL buffer, 20 µL dNTP mix, 5 µL of each primer (10 µM), 0.2 µL AmpliTaq (Amersham), 1 µL genomic extract and 14 µL water. Thermal cycling parameters were: initial denaturation for 3 min at 95 C, followed by 30 cycles of 1 min at 95 C, 1 min at 50 C (ITS1F/ITS4, mrSSU1/MSU7) or 53 C (AL1R/LR6), 1 min at 73 C, and a final elongation for 7 min at 73 C. Amplification products were viewed on 1.8% agarose gels stained with ethidium bromide and subsequently purified with a DNA purification kit (Qiagen). DNA quantities were estimated photometrically (Eppendorf BioPhotometer). Fragments were sequenced with the Big Dye Terminator reaction kit (ABI PRISM, Applied Biosystems). Sequencing was performed with the same primers used for amplification. Cycle sequencing was executed with this program: 25 cycles of 95 C for 30 s, 48 C for 15 s, 60 C for 4 min. Sequenced products were precipitated with 10 µL of deionized sterile water, 2 µL of 3 M NaOAc, and 50 µL of 95% EtOH before they were loaded on an ABI 300 or ABI 377 (Applied Biosystems) automatic sequencer.
Sequence alignment and analysis –
Nuclear ITS, LSU and mitochondrial SSU sequences were aligned separately using the program SAM (Sequence Alignment and Modelling System) (Karplus et al 1998). ITS data subsequently were analyzed singly and in combination with nu LSU and mt SSU alignments. In the triple dataset, the missing nu LSU fragment of P. stellata was coded as "?". Another dataset containing additional taxa of the Agyriaceae subsequently was produced. In this combined analysis of nu LSU and mt SSU sequences, missing nu LSU fragments of Placopsis stellata, Placynthiella oligotropha, Ptychographa xylographoides and Trapeliopsis viridescens, and missing mt SSU fragments of Placopsis argillacea and Trapeliopsis pseudogranulosa were coded as "?". The alignments are available in TreeBASE (http://herbaria.harvard.edu/treebase/SN1306).
Maximum-parsimony analyses were conducted using PAUP* (Swofford 1998). We ran 1000 replicates with random-sequence additions. Gaps were treated as missing characters. Bootstrapping was performed based on 2000 replicates with simple sequence additions.
The Bayesian analyses were performed using the MrBayes 2.01 program (Huelsenbeck and Ronquist 2001). Being a maximum likelihood-related approach, Bayesian analysis requires probabilistic models for the process of nucleotide substitution. These models were obtained for each dataset with a likelihood ratio test (Huelsenbeck and Crandall 1997) as implemented in the program ModelTest 3.06 (Posada and Crandall 1998). The Markov chain Monte Carlo process was set so that eight chains ran simultaneously for 500 000 generations. Trees were sampled every 10th generation for a total of 50 000 trees. The chains (i.e., the log likelihood sum) reached apparent stationarity around the 10 000th generation. Because trees produced before the ln likelihood sum converges on a stable value are less likely (Huelsenbeck and Ronquist 2001), the first 10 000 generations (i.e., the first 1000 trees) were deleted as the "burn in" of the chain. Of the remaining 49 000 trees, a majority-rule consensus tree was calculated using PAUP* (Swofford 1998). Values above the branches indicate posterior probabilities. Posterior probabilities equal to and above 95 are considered significant. Branch lengths were obtained using the "sumt" option of MrBayes.
We selected species of Trapelia and Trapeliopsis as outgroup for the analyses concerning the proposed subgeneric division within Placopsis and its relationship to Orceolina (ITS and the combined ITS+ nu LSU+ mtSSU datasets) because a close relationship of these taxa has been suggested before (e.g., Hertel 1969). In the second analysis, to determine the phylogenetic position of Placopsis within the Agyriales, we chose three members of the Pertusariales as outgroup because this order was shown to be a sister order to Agyriales in recent molecular studies (Lumbsch and Schmitt 2001, Lumbsch et al 2002).
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RESULTS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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), including estimation of invariant sites and assuming a discrete gamma distribution for all three alignments. The Bayesian ITS analysis revealed a paraphyletic genus Placopsis with Orceolina kerguelensis nested within (Fig. 1A). The clade including all Placopsis spp. and Orceolina is well supported (posterior probability 100). Within this clade Placopsis macrophthalma and Orceolina kerguelensis form a supported sister relationship (pp 97). Placopsis is not significantly supported (pp 87). The two Placopsis spp. with sunken ascomata included in the study, P. macrophthalma and P. stellata, do not form a monophyletic group. Most branches within the genus Placopsis are not supported. The monophyletic genus Trapelia is a sister group to the Placopsis-Orceolina clade supported by 100% posterior probability. The ITS-single-gene analysis using maximum parsimony included 129 parsimony-informative sites and yielded six most-parsimonious trees (327 steps, CI = 0.65, RI = 0.74). In the consensus tree Orceolina is again nested within Placopsis (Fig. 1B). The Orceolina-Placopsis clade has 100% bootstrap support, however, most relationships within this clade are neither supported nor resolved. The relationships and the branching order within the genus Placopsis are more lucid in the phylogenetic trees inferred from the triple dataset, including ITS, nu LSU and mt SSU sequences (Fig. 2). The topology of this tree inferred by Bayesian analysis is basically the same as the one obtained from the Bayesian ITS-single-gene tree, but the posterior probabilities are higher. All branches, except the clade including P. stellata, P. rhodophthalma and P. parellina, are supported by 100% pp. The clades including Orceolina kerguelensis and Placopsis macrophthalma, as well as the rest of the Placopsis spp., each form a supported monophyletic group (pp 100). Placopsis macrophthalma and P. stellata are in independent, significantly supported clades: P. macrophthalma forms a sister-group relationship to Orceolina, while P. stellata is nested within Placopsis s.str. The maximum-parsimony three-gene analysis yielded the same topology (tree not shown).
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). In the Bayesian analysis of nu LSU and mt SSU sequences, the basic topology within the Placopsis-Orceolina clade agrees with the three-gene analysis (Fig. 3). The monophyletic Trapelia is the closest relative to the Placopsis-Orceolina clade (pp 100). Placynthiella is basal to the above-mentioned group and the monophyletic Trapeliopsis is basal to that. Two genera with lirelliform apothecia, Ptychographa and Xylographa, form a supported monophyletic group, which is basal to Trapeliopsis. Ainoa mooreana and Anzina carneonivea are both on independent branches at the base of the monophyletic Agyriaceae. All of these relationships are significantly supported (pp 100). The maximum-parsimony analysis of the Agyriaceae inferred from nu LSU and mt SSU data yielded six most-parsimonious trees (1244 steps, CI = 0.52, RI = 0.77). The consensus resulted in basically the same tree topology concerning the relationships of genera as the Bayesian analysis (tree not shown).
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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), does not cluster with P. macrophthalma. It is included in a well-supported monophyletic group (pp 99) with species of Placopsis sect. Placopsis. Therefore a distinction of the section Aspiciliopsis, defined by sunken fruiting bodies, is not supported in this molecular study. Our results suggest that aspicilioid fruiting bodies are an apomorphic character in the Orceolina-P. marcrophthalma clade but also have evolved independently in P. stellata. It is interesting to note that the thalline margin in Orceolina spp. and P. macrophthalma has a strongly reduced amphithecium (thalline margin), while showing a distinct exciple and amphithecium in P. stellata (Henssen 2003). This structure is typical for Placopsis s.str. (Lamb 1947). Further morphological and chemical differences between P. macrophthalma and P. stellata include the different shape of the ascomata (roundish versus star-shaped/hysteroid), the size of the cephalodia and chemistry (gyrophoric acid chemosyndrome versus stictic acid chemosyndrome) (Henssen 2003). Hysteroid (lirelliform) apothecia also can be found in other genera of the Agyriaceae, such as Ptychographa and Xylographa. An anatomical character, which is shared by all members of the Orceolina-Placopsis clade, is the non-amyloid ascus (Lumbsch 1997). All other members of the Agyriaceae included in this study show a weak amyloid-ascus reaction. The unique thallus structure in Orceolina and its deviating ascus type seem to have limited taxonomical value. This is in agreement with Lumbsch et al (2001a), who showed that taxa with different ascus types occur in the monophyletic Agyriaceae. Our results support the distinction of P. macrophthalma from Placopsis s.str. as was suggested by Choisy (1929), Dodge (1948) and Hafellner (1984). It is proposed here to resurrect the generic name Aspiciliopsis with the single species A. macrophthalma. Placopsis stellata, recently placed in sect. Aspiciliopsis belongs to Placopsis s.str. An alternative solution would be to merge P. macrophthalma and Orceolina in a single genus. However, due to strongly deviating anatomical, morphological and chemical characters we prefer to keep Orceolina separate. Cephalodia can be found in all but one Placopsis spp. but not in Orceolina. Thus, they either might have arisen independently in A. macrophthalma and in Placopsis s.str. or they have been lost in the Orceolina clade.
Placopsis gelida and P. lambii are quite similar in morphological and ecological habit and originally were distinguished by the presence/absence of cephalodia (Wirth 1995). Later, chemistry proved to be the most reliable character for their unambiguous separation (Moberg and Carlin 1996). This deviating feature is supported in the present study because the two taxa do not form a sister relationship but appear on independent statistically supported branches.
Trapelia is a monophyletic group, including the African species T. chiodectonoides and three European taxa. The genus is a close relative to the Placopsis-Orceolina complex in all analyses, which is in agreement with earlier molecular studies (Lumbsch et al 2001a). Distinctive features between Trapelia and Placopsis include mainly anatomical features of the ascomata (Brodo 1995, Lumbsch 1997). The apothecia in Placopsis have a well-developed zeorine margin, whereas in Trapelia the outer apothecial margin (amphithecium) is strongly reduced so that the fruiting body appears biatorine. Ascus apices of Trapelia show a ring-like amyloid structure, which is not present in Placopsis. These distinctive features typically correlate with the presence (Placopsis) or absence (Trapelia) of cephalodia. We unfortunately could not include the enigmatic P. roseonigra, which forms paracephalodia and therefore might hold an intermediate position between Placopsis and Trapelia, because no fresh material of this rare lichen was available at the time of the study.
The genus Placopsis with its sister group (Aspiciliopsis + Orceolina) and the genera Trapelia and Placynthiella appear to be derived within the Agyriaceae. These taxa are characterized by sparsely branched paraphyses, while Trapeliopsis, which is basal to these genera, has richly branched paraphyses.
Two taxa with lirelliform fruiting bodies, Ptychographa xylographoides and Xylographa vitiligo, form a supported monophyletic group basal to the above-mentioned genera. Ainoa mooreana formerly was included in the genus Trapelia. Due to deviating anatomical characters and ITS sequences, Ainoa was segregated at the genus level (Lumbsch et al 2001a). The isolated position of Ainoa is confirmed in the present study. Anzina is a basal member of the Agyriaceae and differs from the remaining Agyriaceae in that it has an annular exciple and a deviating ascus type that lacks a well-defined tholus.
A major improvement of this study, in comparison with a previous study of the phylogeny of the Agyriaceae based on ITS data only (Lumbsch et al 2001a), is the confidence of individual branches. In the former study, the relationships within the family Agyriaceae could not be resolved or had only weak support. In the current analysis, however, the topology is resolved and all major clades are significantly supported. This finding emphasizes the utility of combined nuclear LSU and mitochondrial SSU sequences to resolve the phylogeny in this group of lichens.
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ACKNOWLEDGMENTS |
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k Palice (Prague), Harrie Sipman (Berlin) and Einar Timdal (Oslo) for sending fresh material for DNA extraction. Charlotte Hansen (Copenhagen) excellently supported our laboratory work and Nora Wirtz (Essen) kindly provided four new sequences. We are very grateful to Steffen Pauls (Biebergemünd) who improved the manuscript linguistically. This study was supported by an IHP grant at Copenhagen Biosystematics Centre (COBICE) to IS and by a grant from the Deutsche Forschungsgesellschaft to HTL. |
FOOTNOTES |
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2 Current address: Field Museum of Natural History, Department of Botany, 1400 S. Lake Shore Drive, Chicago, IL 60605, U.S.A.
Accepted for publication March 11, 2003.
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LITERATURE CITED |
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  F. Lutzoni, F. Kauff, C. J. Cox, D. McLaughlin, G. Celio, B. Dentinger, M. Padamsee, D. Hibbett, T. Y. James, E. Baloch, et al. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits Am. J. Botany, October 1, 2004; 91(10): 1446 - 1480. [Abstract] [Full Text] [PDF]
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