Molecular systematics

Molecular systematics of hysteriaceous
bitunicate ascomycetes 

By Eric W.A. Boehm

Recently, Boehm et al. (2009a, b) have presented a four (2009a) and five (2009b) gene phylogeny, using data sets obtained from the nuSSU, nuLSU, TEF1, RPB1 & RPB2 nuclear loci, to address evolutionary questions among “hysteriaceous” bitunicate ascomycetes belonging to or previously affilitated with the HysteriaceaeGloniaceaeMytilinidiaceae and Patellariaceae. The webpage “Cultures & GenBank”  on this site provides the list of cultures and the GenBank Accession Numbers for all taxa surveyed to date. The full DNA matrix and trees for both studies are available on TREEBASE at: http://www.treebase.org/treebase/console.html. (Enter “Boehm” under authors and go to study #1 & 2). Full DNA matirx alignment files and final trees can also be accessed directly below. A total of 165 taxa were surveyed for both papers, with 514 GenBank Accessions (257 of them newly sequenced entries) as follows: 136 for the nuSSU, 156 for nuLSU, 101 for TEF1, 90 for RPB2 and 28 for RPB1Erratum (corrigendum): In Boehm et al. 2009b, the publication specifies four genes sequenced, when actually five were in the analysis. This has been updated on TREEBASE (see above) and is reflected on this website (see Cultures & GenBank).

(1) Boehm et al. 2009a: Analysis #1: 3442bp DNA for 66 taxa using RAxML analysis.

(2) Boehm et al. 2009a: Analysis #2: 3596bp DNA for 80 taxa using Bayesian analysis.

(3) Boehm et al. 2009b: Analysis #1: 6582bp DNA for 121 taxa using RAxML Analysis.

(4) Boehm et al. 2009b:Analysis #2: 6582 bp DNA for 121 taxa using Bayesian Analysis.

(5) TREE Fig. 2 Boehm et al. 2009a

(6) TREE Fig. 3 Boehm et al. 2009a

(7) TREE Fig. 1 Boehm et al. 2009b

We are broadly interested in the evolution of character states traditionally used to define higher taxa within each family. Essentially, we wish to address whether morphological features historically used in the classification of these fungi are phylogenetically informative in the context of sequence-based phylogenies. This would have bearing on which morphological features are phylogenetically significant, and therefore useful for a natural delineation of higher taxa. Morphological character states traditionally used to classify these fungi have related primarily to features associated with (1) the pseudothecium, (2) the peridium, (3) the hamathecium, and (4) differences in ascospore symmetry (Barr 1987, 1990a). Character states within each family relate primarily to ascospore septation and pigmentation (Zogg 1962). Questions addressed included the following: Will DNA & protein sequence data confirm or negate previous classifications based on morphological character states related to: (1) peridial wall thickness; (2) centrum development; (3) pseudoparaphyses type; and (4) ascospore symmetry? Will genera, previously defined by ascospore septation and pigmentation patterns form monophyletic groups or will the molelcular data show them to be heterogenous entities? Are morphological character states in these two families synapomorphies, as previously assumed, or will they constitute plesiomorphies that emerge in unrelated groups? If change does occur, how will this affect the classification of hysteriaceous fungi? If the latter, what kinds of selective pressures may be operative to drive convergent evolution in these families? Some summary highlights follow:

Boehm E.W.A, Schoch, CL & Spatafora JW. 2009a. On the evolution of the Hysteriaceae and Mytilinidiaceae (Pleosporomycetidae, Dothideomycetes, Ascomycota) using four nuclear genes. Mycological Research 113(4): 461-479.

Abstract: We present a molecular phylogenetic analysis for two families within the Pleosporomycetidae (Dothideomycetes), the Hysteriaceae, and the Mytilinidiaceae, using four nuclear genes, the ribosomal LSU and SSU, transcription elongation factor 1 a and the second largest RNA polymerase II subunit. Multigene phylogenies provide strong support for the monophyly of the Hysteriaceae and of the Mytilinidiaceae, both within the Pleosporomycetidae. However, sequence data also indicate that both families are not closely related within the subclass. Although core groups for many of the genera in the Hysteriaceae have been defined, HysteriumGloniopsis, and Hysterographium are polyphyletic, with affinities not premised on spore septation and pigmentation. Glonium is also polyphyletic, but along two highly divergent lines. The genus lies outside of the Hysteriaceae, and finds close affinities instead with the family Mytilinidiaceae, for which we propose Gloniaceae fam. nov. to accommodate the type, G. stellatum and related forms. The genus Psiloglonium is reinstated within the Hysteriaceae, with P. lineare, as type, to accommodate non-subiculate species, with apically obtuse didymospores. Farlowiella is removed from the Hysteriaceae, but remains within the Pleosporomycetidae. In contrast, despite divergent spore morphologies, the genera Mytilinidion and Lophium form a strongly supported clade, thus defining a highly monophyleticMytilinidiaceae, adjacent to the Gloniaceae, for which we propose the Mytilinidiales ord. nov. The genus Ostreichnion, previously in the Mytilinidiaceae, is here transferred to the Hysteriaceae. It is concluded that the evolution of the hysterothecium occurred multiple times within the Pleosporomycetidae, and alone it is not a synapomorphic character state for the Hysteriaceae.

Final_Fig_2_jpg_web

Combined ribosomal (nuSSU & nuLSU) and protein (TEF1 & RPB2) phylogeny for the Dothideomycetes, with representative species from outlying groups including the ArthoniomycetesLecanoromycetesEurotiomycetesSordariomycetes, and Leotiomycetes, taken from http://www.aftol.org/. Taxa belonging to the HysteriaceaeMytilinidiaceaeGloniaceae and Patellariaceae are highlighted in grey, as are the genera Farlowiella and Glyphium, listed as incertae sedis. The tree represents Dataset 1 and carries all four fully sequenced genes for a total alignment consisting of 3,442 characters with 12% missing, for the 66 fungal taxa presented. The tree is the most likely tree obtained by maximum likelihood. Nodal values are as follows: Bayesian posterior probability / maximum likelihood bootstrap (Fig. 2 from Boehm et al. 2009a).

Combined ribosomal (nuSSU & nuLSU) and protein (TEF1 & RPB2) phylogeny for the Dothideomycetes, with extensive representation from the two currently recognised subclasses, namely the Pleosporomycetidae (HysterialesPleosporalesMytilinidiales & Gloniaceae fam. incertae sedis) and the Dothideomycetidae (CapnodialesMyriangiales & Dothideales), with the JahnulalesBotryosphaeriales and the Tubeufiaceae listed as incertae sedis. Taxa belonging to the HysteriaceaeMytilinidiaceaeGloniaceae and Patellariaceae are highlighted in grey, as are the genera Farlowiella and Hysterographium fraxini and Hysterium hyalinum, as incertae sedis. The Arthoniomycetes were chosen as outgroup. This tree represents Dataset 2 and allows for additional missing data in the final matrix, and had 3,596 characters with 22% missing for a total of 80 fungal taxa. The tree is the most likely tree obtained by maximum likelihood. Values on nodes are as follows: Bayesian posterior probability / maximum likelihood bootstrap (Fig. 3 from Boehm et al. 2009a).

Boehm E.W.A., Mugambi G., Miller AN, Huhndorf S, Maricowitz S, Spatafora J.W., & Schoch CL. 2009b. A phylogenetic reappraisal of the HysteriaceaeMytilinidiaceae & Gloniaceae, with keys to world species. Studies in Mycology 64: 49-83.

Abstract: A reappraisal of the phylogenetic integrity of bitunicate ascomycete fungi belonging to or previously affiliated with the HysteriaceaeMytilinidiaceaeGloniaceae and Patellariaceae is presented, based on an analysis of 121 isolates and four nuclear genes, the ribosomal large and small subunits, transcription elongation factor 1 andthe second largest RNA polymerase II subunit. A geographically diverse and high density taxon sampling strategy was employed, including multiple isolates/species from thefollowing genera: Anteaglonium (6/4), Encephalographa (1/1), Farlowiella (3/1), Gloniopsis (8/4), Glonium (4/2), Hysterium (12/5), Hysterobrevium (14/3), Hysterographium (2/1), Hysteropatella (2/2), Lophium (4/2), Mytilinidion (13/10), Oedohysterium (5/3), Ostreichnion (2/2), Patellaria (1/1), Psiloglonium (11/3), Quasiconcha (1/1), Rhytidhysteron (8/3), and 24 outgroup taxa. Sequence data indicate that although the Hysteriales are closely related to the Pleosporales, sufficient branch support exists for their separationinto separate orders within the Pleosporomycetidae. The Mytilinidiales are more distantly related within the subclass and show a close association with the Gloniaceae. Although there are examples of concordance between morphological and molecular data, these are few. Molecular data instead support the premise of a large number of convergent evolutionary lineages, which do not correspond to previously held assumptions of synapomorphy relating to spore morphology. Thus, within the Hysteriaceae, the genera GloniopsisGloniumHysterium and Hysterographium are highly polyphyletic. This necessitated the transfer of two species of Hysterium to Oedohysterium gen.nov. (Od. insidens comb. nov. and Od. sinense comb. nov.), the description of a new species, Hysterium barrianum sp. nov., and the transfer of two species of Gloniopsis to Hysterobrevium gen. nov. (Hb. smilacis comb. nov. and Hb. constrictum comb. nov.). While Hysterographium, with the type Hg. fraxini, is removed from the Hysteriaceae, some of its species remain within the family, transferred here to Oedohysterium (Od. pulchrum comb. nov.), Hysterobrevium (Hb. mori comb. nov.) and Gloniopsis (Gp. subrugosa comb. nov.); the latter genus, in addition to the type, Gp. praelonga, with two new species, Gp. arciformis sp. nov. and Gp. kenyensis sp. nov. The genus Glonium is now divided into Anteaglonium (Pleosporales), Glonium (Gloniaceae), and Psiloglonium (Hysteriaceae). The hysterothecium has evolved convergently no less than five times within the Pleosporomycetidae (e.g., AnteagloniumFarlowiellaGloniumHysterographium and the Hysteriaceae). Similarly, thin-walled mytilinidioid (e.g., Ostreichnion) and patellarioid (e.g., Rhytidhysteron) genera, previously in the Mytilinidiaceae and Patellariaceae, respectively, transferred here to the Hysteriaceae, have also evolved at least twice within the subclass. As such, character states traditionally considered to represent synapomorphies among these fungi, whether they relate to spore septation or the ascomata, in fact, represent symplesiomorphies, and most likely have arisen multiple times through convergent evolutionary processes in response to common selective pressures.

Combined ribosomal (nuSSU & nuLSU) and protein (TEF1 & RPB2) phylogeny for bitunicate ascomycetes belonging to or previously affiliated with the HysteriaceaeMytilinidiaceaeGloniaceae and Patellariaceae. Also included are representatives from allied groups such as the PleosporlaesJahnulalesPatellariales, and Botryosphaeriales, as well as representatives from the DothidealesMyriangiales and Capnodiales in the Dothideomycetidae. The Arthoniomycetes, chosen as outgroup, are not presented here due to space limitations, but are available in the full tree on TreeBASE. The tree is the most likely tree obtained by maximum likelihood. Nodal values are as follows: Bayesian posterior probability / maximum likelihood bootstrap (Fig. 1 from Boehm et al. 2009b).