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Evaluation of the monophyly of Fomitopsis using parsimony and MCMC methods

     Department of Biological Sciences, College of Natural Sciences, Seoul National University, San 56-1 Shillim-9-dong, Kwanak-gu, Seoul 151-747, Korea

	ABSTRACT

TOP ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION LITERATURE CITED

 

To evaluate the monophyly of Fomitopsis and elucidate phylogenetic relationships of its members, partial nuclear large subunit (partial 28S) ribosomal RNA genes were sequenced from 10 species of Fomitopsis and 15 related species. Phylogenetic analyses indicated that Fomitopsis was phylogenetically heterogeneous and its members were divided into three subgroups. The constrained tree excluding F. palustris (the type species of Pilatoporus) from Fomitopsis core group was rejected, thus rejecting the taxonomic concept to segregate Pilatoporus from Fomitopsis. The monophyly of taxa belonging to F. rosea complex was rejected, thus rejecting the complex definition based on morphological similarities. The exclusion of Piptoporus betulinus (the type species of Piptoporus) from Fomitopsis core group was rejected and Piptoporus proved to be heterogeneous in both best MP and MAP trees. The monophyly of F. officinalis with Fomitopsis core group also was rejected. Fomitopsis officinalis was closely related to Antrodia xantha and formed an independent lineage from Fomitopsis core group at the basal position of brown rotting fungi comprising Antrodia, Daedalea, Fomitopsis, Piptoporus and Postia. The MAP tree topology obtained from MCMC computation of Bayesian inference was similar to the one of the best MP tree based on the parsimony analysis but showed a higher likelihood score in the Kishino-Hasegawa test and reflected better evolutionary patterns for the phylogeny of Fomitopsis.

Key words: Bayesian inference, best MP tree, Kishino-Hasegawa test, MAP tree, 28S rDNA

	INTRODUCTION

TOP ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION LITERATURE CITED

 
Fomitopsis P. Karst. is a well-known genus in the modern classification system of polypores (Pouzar 1966) and includes brown rotting fungi with dimitic or trimitic hyphae. Fomitopsis is classified in the Polyporaceae, a large and artificial family composed of numerous genera with poroid hymenophores (Donk 1964) and placed in the polyporoid clade of Homobasidiomycetes (Hibbett and Thorn 2001). According to Donk’s (1974) and Gilbertson’s and Ryvarden’s (1986–1987) generic descriptions, members of Fomitopsis have characters as follows: the whitish to bright-colored, di- to trimitic context of the cap; the generative hyphae with clamps; mostly ellipsoid to cylindric, hyaline, smooth, IKI- spores; the tendency of the hymenophore to become layered; the presence of a laccate, glabrous crust covering the cap; and the brown rot type in contrast to the white rot activity of Trametes Fr. with same types of spores and hyphal systems as Fomitopsis.

Until recently, taxonomic delimitation of Fomitopsis has been controversial and remained insufficiently resolved (Kotlaba and Pouzar 1998). Bondartsev and Singer (1941) proposed that the species currently placed in Haploporus Bondartsev & Singer, Heterobasidion Bref. and Perenniporia Murrill with dextrinoid spores or hyphae, and Rigidoporus Murrill with generative hyphae without clamps also be included in the members of Fomitopsis. Corner (1989) neglected the type of rot as a generic character and treated Fomitopsis as a synonym of Trametes but did not formally transfer the species of Fomitopsis to Trametes (Ryvarden 1991). Fomitopsis rosea (Alb. & Schwein.) P. Karst. is closely related to F. pinicola (Sw.) P. Karst., the type species of Fomitopsis, while F. cajanderi (P. Karst.) Kotl. & Pouzar is closely related to the species of Daedalea Pers. sensu stricto sharing several important morphological characters, according to Nobles’ (1971) study. After Nobles’ view, Donk (1974) suggested the removal of F. cajanderi from Fomitopsis and the inclusion into Daedalea or any other related group, although F. cajanderi and F. rosea with pinkish to pinkish-vinaceous context were thought to be closely related to each other and hardly distinguishable at species level.

Kotlaba and Pouzar (1990, 1998) suggested a narrow concept of Fomitopsis and combined F. rosea into a new genus, Rhodofomes Kotl. & Pouzar (type species: Rhodofomes roseus [Alb. & Schwein.] Kotl. & Pouzar), and F. palustris (Berk. & M.A. Curtis) Gilb. & Ryvarden into another new genus, Pilatoporus Kotl. & Pouzar (type species: Pilatoporus palustris (Berk. & M.A. Curtis) Kotl. & Pouzar). Rhodofomes is characterized by thin-walled spores, the presence of clamps on thin-walled generative hyphae, the rosy context and the absence of a resinous crust on the pileal surface. Pilatoporus shares a trimitic hyphal system and hyaline hyphae with Fomitopsis and Rhodofomes but has pseudoskeletal hyphae provided with conspicuous clamp connections (Kotlaba and Pouzar 1990). Carranza-Morse and Gilbertson (1986) defined F. rosea complex, with F. cajanderi, F. carnea (Blume & Nees) Imazeki, F. cupreorosea (Berk.) J. Carranza & Gilb., F. dochmia (Berk. & Broome) Ryvarden, F. feei (Fr.) Kreisel, F. lilacinogilva (Berk.) J.E. Wright & J.R. Deschamps and F. rosea, with these characters: the rosy context, at least when young; dimitic or trimitic hyphal systems; hyaline, smooth, cylindric to allantoid spores; and no special structures in hymenium with an exception of cystidioles present in F. cajanderi and F. dochmia. However, it has not been confirmed that F. rosea complex based upon morphological similarities is still maintained in molecular phylogenetic analyses.

To elucidate phylogenetic relationships of Fomitopsis and related members, Bayesian inference and maximum parsimony were used in this study. The Bayesian inference is useful in estimating phylogenetic trees from DNA sequence data (Yang and Rannala 1997, Larget and Simon 1999) and employs stochastic simulation of the Markov chain Monte Carlo (MCMC) method to obtain trees with highest posterior probabilities (Gelman et al 1995) calculated according to Bayes’ theorem (Huelsenbeck et al 2001). Among trees generated from MCMC computation for a given sequence dataset (Huelsenbeck and Ronquist 2001), the final tree can be determined with one of criteria for mean approach and maximum a priori (MAP) (Durbin et al 1998). Mean approach produces one consensus tree out of all generated trees. Thus, it reduces the probability of occurrence of local maxima (Durbin et al 1998) happening in maximum likelihood computation but increases the probability of occurrence of polytomies in tree topology. On the other hand, MAP criterion (Durbin et al 1998) has relatively high probability of occurrence of local maxima but confers higher resolution upon the tree than mean approach. For the resolved topology of ingroups of the phylogenetic tree, MAP approach seemed to be appropriate in phylogenetic studies at intra- and intergeneric levels and was applied here to reconstruct the Bayesian phylogenetic tree of Fomitopsis.

The purpose of this study was to evaluate the monophyly of Fomitopsis and clarify relevant taxonomic questions in Fomitopsis and related polyporoid taxa. To evaluate whether Fomitopsis is monophyletic, members of genera Antrodia P. Karst., Daedalea, Piptoporus P. Karst. and Postia Fr. were incorporated along with F. pinicola (the type species of Fomitopsis), F. officinalis (Vill.) Bondartsev & Singer, F. palustris and F. spraguei (Berk. & M.A. Curtis) Gilb. & Ryvarden, and six species of F. rosea complex TABLE I). Those non-Fomitopsis members are all brown rotting fungi that share many morphological characters with the members of Fomitopsis (Gilbertson and Ryvarden 1986). Two brown rot species, Laetiporus sulphureus (Bull.) Murrill & Phaeolus schweinitzii (Fr.) Pat., were used as outgroups to root phylogenetic trees.

	MATERIALS AND METHODS

TOP ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION LITERATURE CITED

Phylogenetic analyses.— – Using Clustal X version 1.83 (Thompson et al 1997) (gap opening penalty = 10.0; gap extension penalty = 0.05), 32 sequences were aligned with 12 sequences retrieved from GenBank database (http://www.ncbi.nlm.nih.gov/). Using BioEdit version 5.0.9 (Hall 1999), ambiguous and uninformative variable sites were excluded and an optimized sequence dataset of length 376 nucleotides was submitted to subsequent phylogenetic analyses. To determine the model of nucleotide substitution that best fits the sequence dataset, Modeltest version 3.06 (Posada and Crandall 1998) was used. This practice has two methods: hierarchical likelihood ratio test (hLRT) that examines models if they are accepted or rejected at each level of a hierarchical hypothesis-testing framework and Akaike information criterion (AIC) that rewards models for good fit but penalizes them for unnecessary parameters (Posada and Crandall 1998). The nucleotide substitution models selected by hLRT and AIC were compared and the one with a higher likelihood score was chosen in the subsequent phylogenetic analyses. Phylogenetic analyses were performed based on maximum parsimony and Bayesian inference (Huelsenbeck et al 2001). Parsimony analysis was conducted with PAUP 4.0b10 (Swofford 2002) with tree bisection reconnection (TBR) branch swapping and maxtrees unrestricted. All gaps were treated as missing data. Among most parsimonious (MP) trees generated by parsimony method, the tree with maximum likelihood score based on the selected DNA substitution model (Posada and Crandall 1998) was chosen for display and was indicated as best MP.

To evaluate confidence in internal nodes for the best MP tree, 1000 nonparametric bootstrap replications (resampling size = 1 000; TBR; maxtrees, unrestricted) were used (Felsenstein 1985). MrBayes version 3.0b4 software (Huelsenbeck and Ronquist 2001) was used to reconstruct the Bayesian tree of Fomitopsis and related taxa. MrBayes offers the best fitting tree for a given sequence dataset using MCMC that modifies the tree topology according to posterior probabilities through branch swapping for nearest neighbor interchange (NNI) (Huelsenbeck and Ronquist 2001). The Bayesian phylogenetic tree was reconstructed according to these conditions: (i) the model of nucleotide substitution resulted from Modeltest was used to reconstruct Bayesian trees; (ii) four Markov chains (number of generations = 2 000 000; frequency of sampling trees = one per 1000 generations) were set according to specific conditions for running Markov chains (Hall 2001); (iii) burn-in was set at 10 000 to discard trees obtained before 10 000th generation when Markov chains reached convergent and stationary likelihood values (Hall 2001); (iv) PAUP 4.0b10 was used to reconstruct a MAP tree with maximum posterior probability among 2000 sampled trees; (v) the posterior probability of each node was estimated based on the frequency at which the node was resolved among 2000 sampled trees with the consensus option of 50% majority-rule. The posterior probability of the node is referred to as Bayesian support value (Simmons et al 2004). All trees were rooted by two outgroups, L. sulphureus and P. schweinitzii, and the aligned sequences were deposited at TreeBase (SN1721). Constrained trees based on several hypotheses for the phylogenetic relationships of Fomitopsis were constructed with MacClade 4 (Maddison and Maddison 2000) and PAUP 4.0b10, and the Kishino-Hasegawa test (Kishino and Hasegawa 1989) was performed to evaluate the significance of those hypotheses. The congruence between best MP and MAP tree topologies also was examined by the Kishino-Hasegawa test.

	RESULTS

TOP ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION LITERATURE CITED

 
Selection of the model of nucleotide substitution.— – We amplified partial 28S ribosomal DNA from 13 strains of 10 Fomitopsis species and 20 strains of 15 related white and brown rotting fungi and determined their nucleotide sequences. The nucleotide length determined from partial 28S ribosomal DNA was about 600 bp long. From the results of hLRT and AIC examinations in Modeltest, TrN+I+G and TVM+I+G models respectively were selected for the sequence dataset (TABLE II). The two models were not significantly different in prior information of base frequency, gamma distribution shape parameter, proportion of invariable sites and rate matrix (TABLE II). However, the TVM+I+G model selected by AIC method showed a higher likelihood score than that of the TrN+I+G model selected by hLRT, so the former was chosen to be the best fitting evolutionary model for the sequence dataset in this study.

View larger version (41K): [in this window] [in a new window]   FIG. 2. Best MP tree of partial nuclear large subunit rDNA sequences. Sequences of Laetiporus sulphureus and Phaeolus schweinitzii were used as outgroups to root tree. Fomitopsis taxa within clades are indicated in boldface and marked as black vertical bars and non-Fomitopsis as blank vertical bars. Bootstrap values are shown at nodes supported by more than 50% from 1000 replications, and bold lines are used where branches are supported by more than 90%.

View larger version (11K): [in this window] [in a new window]   FIG. 3. Plot of likelihood scores that MCMC generated using the priors determined from the values of TVM+I+G. Range of "a" is the consensus region where the log likelihood scores reached a plateau and "b" the MAP point at the 1 089 000th generation. Number of generations = 2 000 000; frequency of sampling trees = 1000; burn-in = 10 000.

View larger version (44K): [in this window] [in a new window]   FIG. 4. MAP tree of partial nuclear large subunit rDNA sequences constructed by MrBayes. Laetiporus sulphureus and Phaeolus schweinitzii were used as outgroups to root tree. Fomitopsis taxa within clades are indicated in boldface and marked as black vertical bars and non-Fomitopsis ones as blank vertical bars. Bayesian support values of the 50% majority-rule consensus tree for 2000 sampled Bayesian trees are marked at nodes supported by more than 50%. Bold lines show where branches are supported by more than 90%.

	DISCUSSION

TOP ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION LITERATURE CITED

Fomitopsis core group of clade B.— – In this study, the major group of Fomitopsis consisted of F. pinicola, F. feei, F. palustris, F. cupreorosea, F. lilacinogilva, F. spraguei and F. dochmia, along with P. betulinus in best MP tree and P. betulinus, D. quercina, and P. portentosus in MAP tree. The clade B, Fomitopsis core group, was supported weakly in best MP and MAP trees with less than 50% bootstrap and 50% Bayesian support values (FIGS. 2, 4). To test whether clade B is homogeneous for Fomitopsis, it needs to be examined whether F. lilacinogilva and P. betulinus belongs to Fomitopsis. Fomitopsis lilacinogilva used to be called T. lilacinogilva (Berk.) Lloyd, and the taxonomic position of F. lilacinogilva has been controversial. However, F. lilacinogilva has annual, biennial or perennial basidiocarps of brown rotting activity in comparison with most Trametes species that usually have annual basidiocarps of white rotting activity. In both best MP and MAP trees, the clade of F. cupreorosea and F. lilacinogilva was well supported by 99% bootstrap and 100% Bayesian values. These morphological and molecular data support the nomenclature of Wright and Deschamps (1975), who renamed T. lilacinogilva as F. lilacinogilva, and suggest that F. lilacinogilva is a natural member of Fomitopsis. In both trees F. lilacinogilva CBS 421.84 and F. cupreorosea CBS 236.87 had no phylogenetic variation from each other, while F. lilacinogilva CBS 422.84 was differentiated phylogenetically from F. lilacinogilva CBS 421.84 and F. cupreorosea CBS 236.87, indicating a possibility that F. lilacinogilva CBS 421.84 could be a misidentified strain of F. cupreorosea.

In Fomitopsis core group, Fomitopsis is not monophyletic without the inclusion of P. betulinus, the type species of Piptoporus, which lends support to the transfer of this species to Fomitopsis. Piptoporus betulinus shares these characters with Fomitopsis: dimitic to trimitic hyphal systems with clamped generative hyphae; mostly ellipsoid to cylindric, hyaline, smooth, and IKI- basidiospores (Donk 1974, Gilbertson and Ryvarden 1986). However, the basidiocarp of P. betulinus is annual and its substrate is restricted to Betula L., which is quite different from Fomitopsis members with perennial basidiocarps living on substrates of both conifers and hardwoods. Although P. betulinus was clustered weakly with other members of Fomitopsis core group, the Kishino-Hasegawa test showed that the exclusion of P. betulinus from Fomitopsis core group was not acceptable statistically (TABLE III). The transfer of P. betulinus seemed to be plausible, but there was another Piptoporus, P. portentosus in this Fomitopsis core group and a third Piptoporus, P. soloniensis in clade A, proving that Piptoporus was also heterogeneous. The inclusion of P. betulinus into Fomitopsis certainly requires additional studies with more strains of the species and the genus to draw inclusive conclusions for Piptoporus. Daedalea quercina and P. portentosus were clustered with F. feei and F. palustris in the MAP tree, while these species were grouped with P. rennyi, A. variiformis and P. placenta in the best MP tree. The best MP tree constrained in the same way as the MAP tree was statistically accepted by the Kishino-Hasegawa test (P = 0.924, TABLE III), suggesting that two different phylogenetic positions of D. quercina and P. portentosus in both trees are dependable topologically.

Kotlaba and Pouzar (1990) proposed a new genus, Pilatoporus, and transferred F. palustris into it as a type species based on the presence of pseudoskeletal hyphae with conspicuous clamp connections. Although F. palustris was included in Fomitopsis core group by weak support values (FIGS. 2, 4), the Kishino-Hasegawa test (TABLE III) showed that the exclusion of F. palustris from Fomitopsis core group statistically was inappropriate, indicating that pseudoskeletal hyphae described by Kotlaba and Pouzar (1990) could not be a useful generic character for the segregation of F. palustris from Fomitopsis core group.

Fomitopsis cajanderi and F. rosea and Antrodia strains of clade A.— – Carranza-Morse and Gilbertson (1986) suggested F. rosea complex comprising F. cajanderi, F. cupreorosea, F. dochmia, F. feei, F. lilacinogilva and F. rosea. In best MP and MAP trees, F. feei, F. cupreorosea, F. lilacinogilva and F. dochmia of F. rosea complex were placed in clade B but F. cajanderi and F. rosea were positioned in clade A. In addition, the monophyly of F. rosea complex was rejected by the Kishino-Hasegawa test in the best MP tree (P = 0.001, TABLE III). These results indicate that F. rosea complex defined by Carranza-Morse and Gilbertson (1986) was not statistically and phylogenetically monophyletic. Fomitopsis rosea is closely related to F. pinicola, the type species of Fomitopsis, while F. cajanderi shares some morphological characters with Daedalea, according to Nobles’ (1971) study. However, phylogenetic positions for F. cajanderi and F. rosea in best MP and MAP trees (FIGS. 2, 4) indicate that these species are not closely related to the Fomitopsis core group including F. pinicola but distantly separated from D. quercina, the type species of Daedalea. In addition, the inclusion of F. cajanderi and F. rosea into Fomitopsis core group was rejected statistically by the Kishino-Hasegawa test (P = 0.004, TABLE III), suggesting that F. cajanderi and F. rosea should be separated from Fomitopsis. Kotlaba and Pouzar (1990) transferred F. rosea into their new genus Rhodofomes as a type species, but our findings showed that F. cajanderi and F. rosea were closely related to each other with little genetic variation, indicating that they should be placed in a same genus together. However, to determine whether F. cajanderi should be transferred into Rhodofomes, more taxonomic and phylogenetic studies with additional materials need to be achieved because other species are related to F. cajanderi and F. rosea in clade A.

In both trees (FIGS. 2, 4), two strains of Antrodia variiformis were clustered respectively with P. rennyi and the group of A. serialis and P. soloniensis. Gilbertson and Ryvarden (1986) suggested that the basidiocarp of A. variiformis is similar to that of A. serialis sharing a same type of substrate. Postia rennyi was characterized by the presence of chlamydospores along the margin of the basidiocarp. Although this fungus recently was reported in China (Ryvarden and Gilbertson 1994), it mostly is distributed in Europe (Gilbertson and Ryvarden 1987). In contrast, A. variiformis is a cosmopolitan fungus with no chlamydospores. Antrodia variiformis CBS 375.82 originally was isolated from gymnosperm wood from New York and deposited in CBS by Butin in 1982 (CBS Filamentous Fungi Database, http://www.cbs.knaw.nl/databases/index.htm). Such data indicate that A. variiformis CBS 375.82 of the USA origin clustered with P. rennyi could be a misidentified (or mishandled) strain. In addition, two strains of A. albida were placed separately as shown in best MP and MAP trees (FIGS. 2, 4). When our private ITS sequences from these two strains of A. albida (CBS 458.86, CBS 308.82) were compared with the one of A. albida AJ006680 [GenBank] from Yao et al (1999) and genetic distances were calculated among three sequences, sequence similarity between AJ006680 [GenBank] and CBS 458.86 was 98.6% while the one between AJ006680 [GenBank] and CBS 308.82 was 94%. The difference between two sequence similarities indicated that the CBS 308.82 strain could be another strain closely related to A. albida or a third that has been misidentified.

Fomitopsis officinalis of clade C.— – The best MP and MAP trees show that the phylogenetic position of F. officinalis is close to the basal lineage of brown rotting fungi comprising Antrodia, Daedalea, Fomitopsis, Piptoporus and Postia. In the Kishino-Hasegawa test (TABLE III), monophyly of F. officinalis with Fomitopsis core group was rejected. In fact, F. officinalis is a synonym of Laricifomes officinalis (Vill.) Kotl. & Pouzar, the type species of Laricifomes Kotl. & Pouzar. The genus Laricifomes defined by Kotlaba and Pouzar (1957) was described on the basis of trimitic hyphal system with hyaline hyphae, presence of clamp connections solely on thin-walled generative hyphae, white chalky context, crumbly consistency, styptic properties and pileal surface without a resinous substance. Among characters describing Laricifomes, the presence of sclerids is an especially important key to separate Laricifomes from Fomitopsis (Kotlaba and Pouzar 1998). Sclerids are unique hyphal bodies present in context that are contorted and irregular, often lobed and thick-walled, but their taxonomic importance is not specified fully (Gilbertson and Ryvarden 1986). Although F. officinalis has sclerids, there has been confusion whether the hyphal system of F. officinalis is dimitic (Gilbertson and Ryvarden 1986, Ryvarden and Gilbertson 1993) or trimitic (Kotlaba and Pouzar 1957, 1998). On the other hand, the morphological characters of F. officinalis match well with the generic concepts of Antrodia, which are characterized mainly by the dimitic hyphal system with clamped generative hyphae and cylindric-ellipsoid, hyaline, thin-walled, smooth and nonamyloid basidiospores (Gilbertson and Ryvarden 1986). Ryvarden and Gilbertson (1993) described A. macrospora Bernicchia & De Domincis as having sclerid-like elements while the others of Antrodia lack such a structure (Gilbertson and Ryvarden 1986, 1993). Although F. officinalis was closely related to A. xantha in best MP and MAP trees where both species are topologically exchanged, F. officinalis was not clustered with any other taxa in this study. When Antrodia including A. macrospora and Laricifomes including L. concavus (Cooke) G. Cunn. and L. maire G. Cunn. are incorporated in a future study, it will be easier to evaluate the taxonomic implication of sclerids as a key character to species and determine the exact phylogenetic position and nomenclatural status of F. officinalis.

Phylogenetic reliability of the Bayesian method.— – The difference of criteria for tree reconstruction is subject to generate different branch patterns between best MP and MAP trees. MP generates the shortest tree with minimal number of total nucleotide substitutions (Felsenstein 1988), but MAP tree is obtained by selecting one with maximum posterior probability among generated trees. Maximum parsimony and Bayesian inference are accomplished by different tree search algorithms, heuristic search and MCMC process, respectively. Local maxima obtained by heuristic search of parsimony are different from those obtained by MCMC computation of Bayesian inference (Durbin et al 1998), indicating that the difference between criteria eventually generates topological conflicts between best MP and MAP trees. If topological uncertainties at weakly supported nodes are removed through tighter taxon sampling and multi-gene analysis with large character information, topological differences between both trees could be compared more exactly.

Bayesian support values (Bayesian posterior probabilities) and bootstrap values have statistical differences. The Bayesian support value represents an estimate of the probability that one clade is correct under a given substitution model and sequence data (Miller et al 2002). In contrast, the bootstrap value is the frequency that the topology of clade appears when repetitive processes are conducted with sequence data resampled from original data (Miller et al 2002). Wilcox et al (2002) suggested that Bayesian support values provided much closer estimates of phylogenetic accuracy than the estimates provided by corresponding bootstrap proportions. On the other hand, Simmons et al (2004) recently indicated that Bayesian support values generally were overestimated in comparison to common resampling-based support measures including the bootstrap and jackknife. Thus, they advised against considering posterior probabilities as universal probabilities, although it is appropriate to consider a posterior probability the probability of truth, and recommended the term posterior probability to refer to the probability conditional on data, models and priors. However, when the Kishino-Hasegawa test determined the topologies of two phylogenetic trees, the MAP tree based on Bayesian inference showed a higher likelihood score than the best MP tree, indicating that the relationships of Fomitopsis species in the MAP tree reflects better evolutionary patterns for the present sequence dataset than those in the best MP tree. In our study, Bayesian support values in the MAP tree were found to be comparatively higher than bootstrap values for the clades in the best MP tree, suggesting that the Bayesian algorithm could be properly applied to the phylogenetic analyses of Fomitopsis groups and also might be able to provide improved inference methods for brown rotting fungi.

View larger version (13K): [in this window] [in a new window]   FIG. 1. Rate matrices of nucleotide substitutions for hLRT and AIC generated by Modeltest.

	ACKNOWLEDGMENTS

	FOOTNOTES

 
Accepted for publication April 20, 2005.

¹ Corresponding author. E-mail: minervas{at}snu.ac.kr

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