This study provides new insights on the phylogenetic position of the lichenicolous fungal genus Abrothallus based on six molecular markers(nuSSU,nuLSU,mtSSU,RPB1,RPB2 and TEF-α).In a broad-scale analysis,we detected ...This study provides new insights on the phylogenetic position of the lichenicolous fungal genus Abrothallus based on six molecular markers(nuSSU,nuLSU,mtSSU,RPB1,RPB2 and TEF-α).In a broad-scale analysis,we detected high support for inclusion of the genus within Dothideomycetes.A further analysis provided support for Abrothallus as a member of the subclass Pleosporomycetidae as a sister group of Jahnulales,an order of aquatic Dothideomycetes.Given the exclusive characters of this group of apotheciate fungi within the Dothidiomycetes,a new monotypic order Abrothallales is here introduced together with the new family Abrothallaceae.In a multi-locus analysis(based on the six loci indicated above plus ITS)restricted to 12 putative Abrothallus species,two clearly separated clades were observed:one comprising species growing on lichens of the families Parmeliaceae and Ramalinaceae,and the second including species that live on lichens of the order Peltigerales and the family Cladoniaceae.展开更多
A phylogenetic analysis of nuLSU and ITS sequences representing genera previously included in Dacampiaceae indicates that the family is strongly polyphyletic and that the type species of Dacampia is placed in Pleospor...A phylogenetic analysis of nuLSU and ITS sequences representing genera previously included in Dacampiaceae indicates that the family is strongly polyphyletic and that the type species of Dacampia is placed in Pleosporales.The genus Munkovalsaria s.str.is placed in Didymosphaeriaceae(Pleosporales).Polycoccum s.str.and two species of Clypeococcum are shown to form a new lineage sister to the Trypetheliaceae in Trypetheliales and described here as Polycoccaceae.Other members of Polycoccum s.lat.are included in the Pleosporales and are closely related to lichenicolous Phoma-like species of the family Phaeosphaeriaceae.The genus Didymocyrtis is resurrected for these species and for lichenicolous species previously assigned to Diederichia,Diederichomyces,Leptosphaeria and Phoma.The genera Diederichia and Diederichomyces are synonymized with Didymocyrtis.The new combinations Didymocyrtis bryonthae,D.cladoniicola,D.foliaceiphila,D.infestans,D.kaernefeltii,D.melanelixiae,D.pseudeverniae,D.ramalinae,D.slaptoniensis and D.xanthomendozae are made,and the new name D.epiphyscia is introduced for Phoma physciicola.Some anamorph-teleomorph relationships are resolved,such as Didymocyrtis ramalinae–Phoma ficuzzae and Didymocyrtis consimilis–Phoma caloplacae,the phylogenetic results being supported by single ascospore cultures that lead to the asexual stage producing pycnidia and conidia in culture.Speciation by host switching is assumed to be important in the genus Didymocyrtis.An identification key to Didymocyrtis species is provided.展开更多
This study focuses on the genus Encoelia and the subfamily Encoelioideae in the morphologically and ecologically diverse Helotiales.The 28S and 18S rDNA as well as tef1,rpb1 and rpb2 were sequenced for 70 species.Phyl...This study focuses on the genus Encoelia and the subfamily Encoelioideae in the morphologically and ecologically diverse Helotiales.The 28S and 18S rDNA as well as tef1,rpb1 and rpb2 were sequenced for 70 species.Phylogenetic analyses revealed Encoelia and Encoelioideae to be highly polyphyletic,with species distributed among eight major lineages.Encoelia fascicularis and E.pruinosa belonged to Sclerotiniaceae and were combined in a new genus,Sclerencoelia.Rutstroemiaceae comprised E.tiliacea and Dencoeliopsis johnstonii,both accepted in Rutstroemia.The type of Encoelia,E.furfuracea,was closely related to species of Velutarina,Cenangiopsis and Crumenulopsis.These species together with members of Hemiphacidiaceae formed a clade conforming to the emended concept of Cenangiaceae,introduced here.Another resurrected family,Cordieritidaceae,comprised E.fimbriata,E.heteromera and species of Ameghiniella,Cordierites,Diplocarpa and Ionomidotis,characterised by inamyloid asci and a positive ionomidotic reaction.Encoelia glauca showed closest affinities with Chlorociboria species in Chlorociboriaceae.A new genus,Xeropilidium,with sporodochial and pycnidial synanamorphs,was described for the distinct encoelioid member of the Chaetomellaceae,previously known as E.fuckelii.Morphological and ecological synapomorphies were distinguished from convergent characters to delimit monophyletic taxa including encoelioid fungi.Incorporation of public sequences from various biological samples in ITS rDNA analyses allowed identification of sequenced organisms at species,genus,or family level and added information on the ecology of seversal taxa.Members of Cenangiaceae appeared to be widespread as endophytes.Inclusion of encoelioid genera in Chaetomellaceae and Sclerotiniaceae added xylicolous saprotrophs to these families.展开更多
The fungal genus Collemopsidium comprises species that develop so-called borderline lichen symbioses with algae or cyanobacteria.Together with morphologically similar pyrenocarpous fungi it has been assigned to the fa...The fungal genus Collemopsidium comprises species that develop so-called borderline lichen symbioses with algae or cyanobacteria.Together with morphologically similar pyrenocarpous fungi it has been assigned to the family Xanthopyreniaceae.The adscription of this family to higher taxonomic ranks remain uncertain.Using sequence data of five nuclear genomic regions(nuLSU,nuSSU,tef1-α,rpb1 and rpb2)and onemitochondrial locus(mtSSU)we found that the studied representatives of this family are placed in the Dothideomyceta,yet relationships with the classes Dothideomycetes and Arthoniomycetes remain uncertain.We describe the new order Collemopsidiales to accommodate the genus Collemopsidium(paraphyletic as currently understood)and the lichenicolous genus Zwackhiomyces.Using five fungal fossils as calibrations points,we infer an age of c.230 Mya for the crown of Collemopsidiales.Based on two molecular markers,we also provide insight into the global diversity of marine species of the genus Collemopsidium.According to the species delimitation algorithm GMYC,c.26 putative species exist,far more than the six species recognized hitherto.We have confirmed this result by comparing the two alternative species models by means of Bayes factors,using path sampling and stepping-stone sampling algorithms to estimate the marginal likelihood of each model.Finally,our observations suggest rock-boring ability evolved in parallel in the different lineages within this group of fungi.展开更多
Fungi other than the lichen mycobiont frequently co-occur within lichen thalli and on the same rock in harsh environments.In these situations dark-pigmented mycelial structures are commonly observed on lichen thalli,w...Fungi other than the lichen mycobiont frequently co-occur within lichen thalli and on the same rock in harsh environments.In these situations dark-pigmented mycelial structures are commonly observed on lichen thalli,where they persist under the same stressful conditions as their hosts.Here we used a comprehensive sampling of lichen-associated fungi from an alpine habitat to assess their phylogenetic relationships with fungi previously known from other niches.The multilocus phylogenetic analyses suggest that most of the 248 isolates belong to the Chaetothyriomycetes and Dothideomycetes,while a minor fraction represents Sordariomycetes and Leotiomycetes.As many lichens also were infected by phenotypically distinct lichenicolous fungi of diverse lineages,it remains difficult to assess whether the culture isolates represent these fungi or are from additional cryptic,extremotolerant fungi within the thalli.Some of these strains represent yet undescribed lineages within Chaethothyriomycetes and Dothideomycetes,whereas other strains belong to genera of fungi,that are known as lichen colonizers,plant and human pathogens,rock-inhabiting fungi,parasites and saprotrophs.The symbiotic structures of the lichen thalli appear to be a shared habitat of phylogenetically diverse stress-tolerant fungi,which potentially benefit from the lichen niche in otherwise hostile habitats.展开更多
Melaspileaceae is a heterogeneous group of Ascomycota including lichenized,lichenicolous and saprobic fungi.A first phylogenetic study of Melaspileaceae is presented and is based on mtSSU and nuLSU sequence data.We ob...Melaspileaceae is a heterogeneous group of Ascomycota including lichenized,lichenicolous and saprobic fungi.A first phylogenetic study of Melaspileaceae is presented and is based on mtSSU and nuLSU sequence data.We obtained 49 new sequences for 28 specimens representing 15 species.The genera Buelliella,Hemigrapha,Karschia,Labrocarpon and Melaspilea s.str.are included in a molecular phylogeny for the first time.Melaspileaceae is recovered as polyphyletic,with members placed in two main lineages of Dothideomycetes.Melaspilea s.str.is included in Eremithallales.Eremithallaceae is placed in synonymy with Melaspileaceae.The genus Encephalographa is placed in Melaspileaceae.The genera Buelliella,Karschia,Labrocarpon and several members of Melaspilea are demonstrated to belong to Asterinales,while Hemigrapha is confirmed in this order.The genera Melaspileella,Melaspileopsis,Stictographa are reinstated for former Melaspilea species now placed in Asterinales.Karschia cezannei is described as new,and the new combinations Melaspilea costaricensis,M.enteroleuca,M.urceolata,Melaspileella proximella and Melaspileopsis diplasiospora are made.Melaspileaceae as newly defined includes lichenized and saprobic species.The lichenicolous and saprobic life styles form different intermixed lineages in Asterinales that do not include lichenized taxa.The phylogenetic data provide a first framework for dismantling further the genus Melaspilea for which most of the species are expected to belong to Asterinales.展开更多
The phylogeny of the Acarosporaceae(Lecanoromycetes,Acarosporomycetidae,Acarosporales)is investigated using data from three molecular markers;nuclear ITS-LSU rDNA,mitochondrial SSU andβ-tubulin.Acarosporaceae is show...The phylogeny of the Acarosporaceae(Lecanoromycetes,Acarosporomycetidae,Acarosporales)is investigated using data from three molecular markers;nuclear ITS-LSU rDNA,mitochondrial SSU andβ-tubulin.Acarosporaceae is shown to be constituted by six main clades;Myriospora,Timdalia,Pleopsidium,a clade composed by BAcarospora^rhizobola and BA.^terricola,the poorly supported Sarcogyne clade(including several Polysporina and Acarospora species)and the Acarospora clade(including the type of Polysporina,P.simplex,and several other Polysporina species).The common ancestor of the Acarosporaceae did not produce strongly black pigmented(carbonized or melanized)ascomata,but this trait has arisen secondarily and independently numerous times in the evolution of the group.The number of changes in character states of both carbonized epihymenium and carbonized exciple are considerably more than the minimum number.The genera Sarcogyne and Polysporina—largely circumscribed based on the presence of black pigmented ascomata—are shown to be distinctly non-monophyletic.The presence of green algae in the ascoma margin(lecanorine or lecideine ascomata)may vary even within single species.展开更多
基金The work by AS was supported by a grant awarded by the Estonian Science Foundation no.GP1LM7321,target-financing project SF0180012s09 and the European Regional Development Fund(Centre of Excellence FIBIR)。
文摘This study provides new insights on the phylogenetic position of the lichenicolous fungal genus Abrothallus based on six molecular markers(nuSSU,nuLSU,mtSSU,RPB1,RPB2 and TEF-α).In a broad-scale analysis,we detected high support for inclusion of the genus within Dothideomycetes.A further analysis provided support for Abrothallus as a member of the subclass Pleosporomycetidae as a sister group of Jahnulales,an order of aquatic Dothideomycetes.Given the exclusive characters of this group of apotheciate fungi within the Dothidiomycetes,a new monotypic order Abrothallales is here introduced together with the new family Abrothallaceae.In a multi-locus analysis(based on the six loci indicated above plus ITS)restricted to 12 putative Abrothallus species,two clearly separated clades were observed:one comprising species growing on lichens of the families Parmeliaceae and Ramalinaceae,and the second including species that live on lichens of the order Peltigerales and the family Cladoniaceae.
文摘A phylogenetic analysis of nuLSU and ITS sequences representing genera previously included in Dacampiaceae indicates that the family is strongly polyphyletic and that the type species of Dacampia is placed in Pleosporales.The genus Munkovalsaria s.str.is placed in Didymosphaeriaceae(Pleosporales).Polycoccum s.str.and two species of Clypeococcum are shown to form a new lineage sister to the Trypetheliaceae in Trypetheliales and described here as Polycoccaceae.Other members of Polycoccum s.lat.are included in the Pleosporales and are closely related to lichenicolous Phoma-like species of the family Phaeosphaeriaceae.The genus Didymocyrtis is resurrected for these species and for lichenicolous species previously assigned to Diederichia,Diederichomyces,Leptosphaeria and Phoma.The genera Diederichia and Diederichomyces are synonymized with Didymocyrtis.The new combinations Didymocyrtis bryonthae,D.cladoniicola,D.foliaceiphila,D.infestans,D.kaernefeltii,D.melanelixiae,D.pseudeverniae,D.ramalinae,D.slaptoniensis and D.xanthomendozae are made,and the new name D.epiphyscia is introduced for Phoma physciicola.Some anamorph-teleomorph relationships are resolved,such as Didymocyrtis ramalinae–Phoma ficuzzae and Didymocyrtis consimilis–Phoma caloplacae,the phylogenetic results being supported by single ascospore cultures that lead to the asexual stage producing pycnidia and conidia in culture.Speciation by host switching is assumed to be important in the genus Didymocyrtis.An identification key to Didymocyrtis species is provided.
基金supported by the Estonian Science Agency(project IUT20-30)the European Regional Development Fund(Centre of Excellence EcolChange).
文摘This study focuses on the genus Encoelia and the subfamily Encoelioideae in the morphologically and ecologically diverse Helotiales.The 28S and 18S rDNA as well as tef1,rpb1 and rpb2 were sequenced for 70 species.Phylogenetic analyses revealed Encoelia and Encoelioideae to be highly polyphyletic,with species distributed among eight major lineages.Encoelia fascicularis and E.pruinosa belonged to Sclerotiniaceae and were combined in a new genus,Sclerencoelia.Rutstroemiaceae comprised E.tiliacea and Dencoeliopsis johnstonii,both accepted in Rutstroemia.The type of Encoelia,E.furfuracea,was closely related to species of Velutarina,Cenangiopsis and Crumenulopsis.These species together with members of Hemiphacidiaceae formed a clade conforming to the emended concept of Cenangiaceae,introduced here.Another resurrected family,Cordieritidaceae,comprised E.fimbriata,E.heteromera and species of Ameghiniella,Cordierites,Diplocarpa and Ionomidotis,characterised by inamyloid asci and a positive ionomidotic reaction.Encoelia glauca showed closest affinities with Chlorociboria species in Chlorociboriaceae.A new genus,Xeropilidium,with sporodochial and pycnidial synanamorphs,was described for the distinct encoelioid member of the Chaetomellaceae,previously known as E.fuckelii.Morphological and ecological synapomorphies were distinguished from convergent characters to delimit monophyletic taxa including encoelioid fungi.Incorporation of public sequences from various biological samples in ITS rDNA analyses allowed identification of sequenced organisms at species,genus,or family level and added information on the ecology of seversal taxa.Members of Cenangiaceae appeared to be widespread as endophytes.Inclusion of encoelioid genera in Chaetomellaceae and Sclerotiniaceae added xylicolous saprotrophs to these families.
基金SPO,IGB and AdR were supported by grant CTM2012-38222-C02-02IGB was supported by grant FPU AP2012-3556SPO is currently supported by the grant RYC-2014-16784,all from the Spanish Ministry of Economy and Competitiveness.
文摘The fungal genus Collemopsidium comprises species that develop so-called borderline lichen symbioses with algae or cyanobacteria.Together with morphologically similar pyrenocarpous fungi it has been assigned to the family Xanthopyreniaceae.The adscription of this family to higher taxonomic ranks remain uncertain.Using sequence data of five nuclear genomic regions(nuLSU,nuSSU,tef1-α,rpb1 and rpb2)and onemitochondrial locus(mtSSU)we found that the studied representatives of this family are placed in the Dothideomyceta,yet relationships with the classes Dothideomycetes and Arthoniomycetes remain uncertain.We describe the new order Collemopsidiales to accommodate the genus Collemopsidium(paraphyletic as currently understood)and the lichenicolous genus Zwackhiomyces.Using five fungal fossils as calibrations points,we infer an age of c.230 Mya for the crown of Collemopsidiales.Based on two molecular markers,we also provide insight into the global diversity of marine species of the genus Collemopsidium.According to the species delimitation algorithm GMYC,c.26 putative species exist,far more than the six species recognized hitherto.We have confirmed this result by comparing the two alternative species models by means of Bayes factors,using path sampling and stepping-stone sampling algorithms to estimate the marginal likelihood of each model.Finally,our observations suggest rock-boring ability evolved in parallel in the different lineages within this group of fungi.
基金supported by the Austrian project FWF P24114-B16.
文摘Fungi other than the lichen mycobiont frequently co-occur within lichen thalli and on the same rock in harsh environments.In these situations dark-pigmented mycelial structures are commonly observed on lichen thalli,where they persist under the same stressful conditions as their hosts.Here we used a comprehensive sampling of lichen-associated fungi from an alpine habitat to assess their phylogenetic relationships with fungi previously known from other niches.The multilocus phylogenetic analyses suggest that most of the 248 isolates belong to the Chaetothyriomycetes and Dothideomycetes,while a minor fraction represents Sordariomycetes and Leotiomycetes.As many lichens also were infected by phenotypically distinct lichenicolous fungi of diverse lineages,it remains difficult to assess whether the culture isolates represent these fungi or are from additional cryptic,extremotolerant fungi within the thalli.Some of these strains represent yet undescribed lineages within Chaethothyriomycetes and Dothideomycetes,whereas other strains belong to genera of fungi,that are known as lichen colonizers,plant and human pathogens,rock-inhabiting fungi,parasites and saprotrophs.The symbiotic structures of the lichen thalli appear to be a shared habitat of phylogenetically diverse stress-tolerant fungi,which potentially benefit from the lichen niche in otherwise hostile habitats.
基金We would like to thank the curators of herbaria cited in Materials and Methods for the loan of specimens.Anders Nordin is warmly thanked for information provided about Gyalecta sprengeliana–Melaspilea urceolata material in UPS,Peter Poschlod for searching for the original material of Lichen cascarillae in REG,and AndréFraiture for help with the code of nomenclature.Andre Aptroot kindly shared with us useful information on the taxonomy of Melaspilea s.l.Marion Eichler,Rainer Cezanne,Harrie Sipman and Pieter van den Boom provided fresh specimens used in this study.Ann Bogaerts,Cyrille Gerstmans,Myriam Dehaan and Wim Baert are thanked for technical assistance.Collection and export permits,and support during field work were provided to DE by the Office National des Forêts(ONF)+DIREN(Reunion),the Institut Polaire Français Paul-Emile Victor(IPEV)in the frame of the program 136 SUBANTECO(Dr.David Renault&Dr.Maryvonne CharrierKerguelen)and the RAMK herbarium(Thailand).Finally,the first author acknowledges financial support from the Fonds National de la Recherche Scientifique(FNRS)from Belgium(F.R.F.C.2.4567.08).
文摘Melaspileaceae is a heterogeneous group of Ascomycota including lichenized,lichenicolous and saprobic fungi.A first phylogenetic study of Melaspileaceae is presented and is based on mtSSU and nuLSU sequence data.We obtained 49 new sequences for 28 specimens representing 15 species.The genera Buelliella,Hemigrapha,Karschia,Labrocarpon and Melaspilea s.str.are included in a molecular phylogeny for the first time.Melaspileaceae is recovered as polyphyletic,with members placed in two main lineages of Dothideomycetes.Melaspilea s.str.is included in Eremithallales.Eremithallaceae is placed in synonymy with Melaspileaceae.The genus Encephalographa is placed in Melaspileaceae.The genera Buelliella,Karschia,Labrocarpon and several members of Melaspilea are demonstrated to belong to Asterinales,while Hemigrapha is confirmed in this order.The genera Melaspileella,Melaspileopsis,Stictographa are reinstated for former Melaspilea species now placed in Asterinales.Karschia cezannei is described as new,and the new combinations Melaspilea costaricensis,M.enteroleuca,M.urceolata,Melaspileella proximella and Melaspileopsis diplasiospora are made.Melaspileaceae as newly defined includes lichenized and saprobic species.The lichenicolous and saprobic life styles form different intermixed lineages in Asterinales that do not include lichenized taxa.The phylogenetic data provide a first framework for dismantling further the genus Melaspilea for which most of the species are expected to belong to Asterinales.
基金This study was funded by grants to Martin Westberg by The Swedish Taxonomy Initiative(Svenska Artprojektet,administered by the Swedish Species Information Centre/ArtDatabanken)and was further supported by grants to Mats Wedin from the Swedish Research Council(VR 621-2009-5372,VR 621-2012-3990).The work of Kerry Knudsen was financially supported by the grant "Environmental aspects of sustainable development of society"42900/1312/3166 from the Faculty of Environmental Sciences,Czech University of Life Sciences Prague.We are grateful to the staff at the Molecular Systematics Laboratory at the Swedish Museum of Natural History for laboratory assistance,in particular Jan Ohlson and Bodil Cronholm.Valerie Reeb kindly shared unpublished details from on her work on Acarosporaceae.The first author would finally like to thank Ulf Arup(LD),Philippe Clerc(G),Leif Tibell(UPS),Toni Berglund(Karlskoga)and members of the Swedish Lichen Society for assistance during field work.
文摘The phylogeny of the Acarosporaceae(Lecanoromycetes,Acarosporomycetidae,Acarosporales)is investigated using data from three molecular markers;nuclear ITS-LSU rDNA,mitochondrial SSU andβ-tubulin.Acarosporaceae is shown to be constituted by six main clades;Myriospora,Timdalia,Pleopsidium,a clade composed by BAcarospora^rhizobola and BA.^terricola,the poorly supported Sarcogyne clade(including several Polysporina and Acarospora species)and the Acarospora clade(including the type of Polysporina,P.simplex,and several other Polysporina species).The common ancestor of the Acarosporaceae did not produce strongly black pigmented(carbonized or melanized)ascomata,but this trait has arisen secondarily and independently numerous times in the evolution of the group.The number of changes in character states of both carbonized epihymenium and carbonized exciple are considerably more than the minimum number.The genera Sarcogyne and Polysporina—largely circumscribed based on the presence of black pigmented ascomata—are shown to be distinctly non-monophyletic.The presence of green algae in the ascoma margin(lecanorine or lecideine ascomata)may vary even within single species.
