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1. High species richness in the lichen genus Peltigera (Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science

Author

Magain, N., Miadlikowska, J., Goffinet, B., Goward, T., Pardo-De La Hoz, C.J., Jüriado, I., Simon, A., Mercado-Díaz, J.A., Barlow, T., Moncada, B., Lücking, R., Spielmann, A., Canez, L., Wang, L.S., Nelson, P., Wheeler, T., Lutzoni, F., Sérusiaux, E., Magain, N., Miadlikowska, J., Goffinet, B., Goward, T., Pardo-De La Hoz, C.J., Jüriado, I., Simon, A., Mercado-Díaz, J.A., Barlow, T., Moncada, B., Lücking, R., Spielmann, A., Canez, L., Wang, L.S., Nelson, P., Wheeler, T., Lutzoni, F., and Sérusiaux, E.

Abstract

Applying molecular methods to fungi establishing lichenized associations with green algae or cyanobacteria has repeatedly revealed the existence of numerous phylogenetic taxa overlooked by classical taxonomic approaches. Here, we report taxonomical conclusions based on multiple species delimitation and validation analyses performed on an eight-locus dataset that includes world-wide representatives of the dolichorhizoid and scabrosoid clades in section Polydactylon of the genus Peltigera. Following the recommendations resulting from a consensus species delimitation approach and additional species validation analysis (BPP) performed in this study, we present a total of 25 species in the dolichorhizoid clade and nine in the scabrosoid clade, including respectively 18 and six species that are new to science and formally described. Additionally, one combination and three varieties (including two new to science) are proposed in the dolichorhizoid clade. The following 24 new species are described: P. appalachiensis, P. asiatica, P. borealis, P. borinquensis, P. chabanenkoae, P. clathrata, P. elixii, P. esslingeri, P. flabellae, P. gallowayi, P. hawaiiensis, P. holtanhartwigii, P. itatiaiae, P. hokkaidoensis, P. kukwae, P. massonii, P. mikado, P. nigriventris, P. orientalis, P. rangiferina, P. sipmanii, P. stanleyensis, P. vitikainenii and P. willdenowii; the following new varieties are introduced: P. kukwae var. phyllidiata and P. truculenta var. austroscabrosa ; and the following new combination is introduced: P. hymenina var. dissecta. Each species from the dolichorhizoid and scabrosoid clades is morphologically and chemically described, illustrated, and characterised with ITS sequences. Identification keys are provided for the main biogeographic regions where species from the two clades occur. Morphological and chemical characters that are commonly used for species identification in the genus Peltigera cannot be applied to unambiguously recognise most molecularly circum

Published
2023
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2. Refined families of dothideomycetes: Dothideomycetidae and pleosporomycetidae

Author

Hongsanan, S., Hyde, K. D., Phookamsak, R., Wanasinghe, D.N., McKenzie, E.H.C., Sarma, V.V., Boonmee, S., Lücking, R., Bhat, D.J., Liu, N.G., Tennakoon, D.S., Pem, D., Karunarathna, A., Jiang, S.H., Jones, E. B. Gareth, Phillips, Alan J. L., Manawasinghe, I.S., Tibpromma, S., Jayasiri, S.C., Sandamali, D.S., Jayawardena, R. S., Wijayawardene, Nalin N., Ekanayaka, A.H., Jeewon, R., Lu, Y.Z., Dissanayake, Asha J., Zeng, X.Y., Luo, Z.L., Tian, Q., Phukhamsakda, C., Thambugala, K.M., Dai, Dong Qin, Chethana, K. W. Thilini, Samarakoon, M.C., Ertz, D., Bao, D.F., Doilom, M., Liu, J.K., Pérez-Ortega, Sergio, Suija, A., Senwanna, C., Wijesinghe, S.N., Konta, S., Niranjan, M., Zhang, S. N., Ariyawansa, H. A., Jiang, Hong-Bo, Zhang, J. F., Norphanphoun, C., Hongsanan, S., Hyde, K. D., Phookamsak, R., Wanasinghe, D.N., McKenzie, E.H.C., Sarma, V.V., Boonmee, S., Lücking, R., Bhat, D.J., Liu, N.G., Tennakoon, D.S., Pem, D., Karunarathna, A., Jiang, S.H., Jones, E. B. Gareth, Phillips, Alan J. L., Manawasinghe, I.S., Tibpromma, S., Jayasiri, S.C., Sandamali, D.S., Jayawardena, R. S., Wijayawardene, Nalin N., Ekanayaka, A.H., Jeewon, R., Lu, Y.Z., Dissanayake, Asha J., Zeng, X.Y., Luo, Z.L., Tian, Q., Phukhamsakda, C., Thambugala, K.M., Dai, Dong Qin, Chethana, K. W. Thilini, Samarakoon, M.C., Ertz, D., Bao, D.F., Doilom, M., Liu, J.K., Pérez-Ortega, Sergio, Suija, A., Senwanna, C., Wijesinghe, S.N., Konta, S., Niranjan, M., Zhang, S. N., Ariyawansa, H. A., Jiang, Hong-Bo, Zhang, J. F., and Norphanphoun, C.

Abstract

The class Dothideomycetes is the largest and most ecologically diverse class of fungi, comprising endophytes, epiphytes, saprobes, human and plant pathogens, lichens, and lichenicolous, nematode trapping and rock-inhabiting taxa. Members of this class are mainly characterized by bitunicate asci with fissitunicate dehiscence, and occur on broad range of hosts in aquatic and terrestrial habitats. Since the last monograph of families of Dothideomycetes in 2013, numerous novel species, genera, families and orders have been discovered. This has expanded information which has led to the modern classification in Dothideomycetes. In this paper, we provide a refined updated document on families of Dothideomycetes with emphasis on Dothideomycetidae and Pleosporomycetidae. We accept three orders with 25 families and four orders with 94 families in Dothideomycetidae and Pleosporomycetidae, respectively. The new family Paralophiostomataceae is introduced in Pleosporales. Each family is provided with an updated description, notes, including figures to represent the morphology, list of accepted genera, and economic and ecological significances. We also provide an overall phylogenetic tree of families in Dothideomycetes based on combined analysis of LSU, SSU, rpb-2 and tef1 sequence data, and phylogenetic trees for each order in Dothideomycetidae and Pleosporomycetidae. Family-level trees are provided for the families which include several genera such as Mycosphaerellaceae and Teratosphaeriaceae. Two new genera (Ligninsphaeriopsis and Paralophiostoma) are introduced. Five new species (Biatrisopora borsei, Comoclathris galatellae, Ligninsphaeriopsis thailandica, Paralophiostoma hysterioides and Torula thailandica) are introduced based on morphology and phylogeny, together with nine new reports and seven new collections from different families.

Published
2020

3. Notes for genera: Ascomycota

Author

Wijayawardene, Nalin N., Hyde, K.D., Rajeshkumar, Kunhiraman C., Hawksworth, D.L., Madrid, H., Kirk, P.M., Braun, U., Singh, R.V., Crous, P. W., Kukwa, M., Lücking, R., Kurtzman, Cletus P., Yurkov, A., Haelewaters, D., Aptroot, A., Thorsten Lumbsch, H., Timdal, E., Ertz, D., Etayo, Javier, Phillips, Alan J. L., Groenewald, J. Z., Papizadeh, M., Selbmann, Laura, Dayarathne, Monika C., Weerakoon, G., Gareth Jones, E.B., Suetrong, S., Tian, Q., Castañeda-Ruiz, R.F., Bahkali, A.H., Pang, K.L., Tanaka, K., Dai, Dong Qin, Sakayaroj, J., Hujslová, M., Lombard, L., Shenoy, B.D., Suija, A., Maharachchikumbura, Sajeewa S. N., Thambugala, K.M., Wanasinghe, D.N., Sharma, B.O., Gaikwad, S., Pandit, G., Zucconi, L., Onofri, Silvano, Egidi, E., Raja, H.A., Kodsueb, R., Pérez-Ortega, Sergio, Prieto, M., Quijada, L., Wijayawardene, Nalin N., Hyde, K.D., Rajeshkumar, Kunhiraman C., Hawksworth, D.L., Madrid, H., Kirk, P.M., Braun, U., Singh, R.V., Crous, P. W., Kukwa, M., Lücking, R., Kurtzman, Cletus P., Yurkov, A., Haelewaters, D., Aptroot, A., Thorsten Lumbsch, H., Timdal, E., Ertz, D., Etayo, Javier, Phillips, Alan J. L., Groenewald, J. Z., Papizadeh, M., Selbmann, Laura, Dayarathne, Monika C., Weerakoon, G., Gareth Jones, E.B., Suetrong, S., Tian, Q., Castañeda-Ruiz, R.F., Bahkali, A.H., Pang, K.L., Tanaka, K., Dai, Dong Qin, Sakayaroj, J., Hujslová, M., Lombard, L., Shenoy, B.D., Suija, A., Maharachchikumbura, Sajeewa S. N., Thambugala, K.M., Wanasinghe, D.N., Sharma, B.O., Gaikwad, S., Pandit, G., Zucconi, L., Onofri, Silvano, Egidi, E., Raja, H.A., Kodsueb, R., Pérez-Ortega, Sergio, Prieto, M., and Quijada, L.

Abstract

Knowledge of the relationships and thus the classification of fungi, has developed rapidly with increasingly widespread use of molecular techniques, over the past 10-15 years, and continues to accelerate. Several genera have been found to be polyphyletic, and their generic concepts have subsequently been emended. New names have thus been introduced for species which are phylogenetically distinct from the type species of particular genera. The ending of the separate naming of morphs of the same species in 2011, has also caused changes in fungal generic names. In order to facilitate access to all important changes, it was desirable to compile these in a single document. The present article provides a list of generic names of Ascomycota (approximately 6500 accepted names published to the end of 2016), including those which are lichen-forming. Notes and summaries of the changes since the last edition of ‘Ainsworth & Bisby’s Dictionary of the Fungi’ in 2008 are provided. The notes include the number of accepted species, classification, type species (with location of the type material), culture availability, life-styles, distribution, and selected publications that have appeared since 2008. This work is intended to provide the foundation for updating the ascomycete component of the “Without prejudice list of generic names of Fungi” published in 2013, which will be developed into a list of protected generic names. This will be subjected to the XIXth International Botanical Congress in Shenzhen in July 2017 agreeing to a modification in the rules relating to protected lists, and scrutiny by procedures determined by the Nomenclature Committee for Fungi (NCF). The previously invalidly published generic names Barriopsis, Collophora (as Collophorina), Cryomyces, Dematiopleospora, Heterospora (as Heterosporicola), Lithophila, Palmomyces (as Palmaria) and Saxomyces are validated, as are two previously invalid family names, Bartaliniaceae and Wiesneriomycetaceae. Four species of L

Published
2017

4. A without-prejudice list of generic names of fungi for protection under the International Code of Nomenclature for algae, fungi, and plants

Author

Kirk, P.M., Stalpers, J.A., Braun, U., Crous, P.W., Hansen, K., Hawksworth, D.L., Hyde, K.D., Lücking, R., Lumbsch, T.H., Rossman, A.Y., Seifert, K.A., Stadler, M., Kirk, P.M., Stalpers, J.A., Braun, U., Crous, P.W., Hansen, K., Hawksworth, D.L., Hyde, K.D., Lücking, R., Lumbsch, T.H., Rossman, A.Y., Seifert, K.A., and Stadler, M.

Abstract

As a first step towards the production of a List of Protected Generic Names for Fungi, a without-prejudice list is presented here as a basis for future discussion and the production of a List for formal adoption. We include 6995 generic names out of the 17072 validly published names proposed for fungi and invite comments from all interested mycologists by 31 March 2014. The selection of names for inclusion takes note of recent major publications on different groups of fungi, and further the decisions reached so far by international working groups concerned with particular families or genera. Changes will be sought in the Code to provide for this and lists at other ranks to be protected against any competing unlisted names, and to permit the inclusion of names of lichen-forming fungi. A revised draft will be made available for further discussion at the 10th International Mycological Congress in Bangkok in August 2014. A schedule is suggested for the steps needed to produce a list for adoption by the International Botanical Congress in August 2017. This initiative provides mycologists with an opportunity to place nomenclature at the generic level on a more secure and stable base.

Published
2013

5. A class-wide phylogenetic assessment of Dothideomycetes

Author

Schoch, C. L., Crous, P. W., Groenewald, J. Z., Boehm, E. W. A., Burgess, T. I., de Gruyter, J., de Hoog, G. S., Dixon, L. J., Grube, M., Gueidan, C., Harada, Y., Hatakeyama, S., Hirayama, K., Hosoya, T., Huhndorf, S. M., Hyde, K. D., Jones, E. B. G., Kohlmeyer, J., Kruys, Åsa, Li, Y. M., Lücking, R., Lumbsch, H. T., Marvanová, L., Mbatchou, J. S., McVay, A. H.., Miller, A. N., Mugambi, G. K., Muggia, L., Nelsen, M. P., Nelson, P., Owensby, C. A., Phillips, A. J. L., Phongpaichit, S., Pointing, S. B., Pujade-Renaud, V., Raja, H. A., Plata, E. Rivas, Robbertse, B., Ruibal, C., Sakayaroj, J., Sano, T., Selbmann, L., Shearer, C. A., Shirouzu, T., Slippers, B., Suetrong, S., Tanaka, K., Volkmann-Kohlmeyer, B., Wingfield, M. J., Wood, A. R., Woudenberg, J. H. C., Yonezawa, H., Zhang, Y., Spatafora, J. W., Schoch, C. L., Crous, P. W., Groenewald, J. Z., Boehm, E. W. A., Burgess, T. I., de Gruyter, J., de Hoog, G. S., Dixon, L. J., Grube, M., Gueidan, C., Harada, Y., Hatakeyama, S., Hirayama, K., Hosoya, T., Huhndorf, S. M., Hyde, K. D., Jones, E. B. G., Kohlmeyer, J., Kruys, Åsa, Li, Y. M., Lücking, R., Lumbsch, H. T., Marvanová, L., Mbatchou, J. S., McVay, A. H.., Miller, A. N., Mugambi, G. K., Muggia, L., Nelsen, M. P., Nelson, P., Owensby, C. A., Phillips, A. J. L., Phongpaichit, S., Pointing, S. B., Pujade-Renaud, V., Raja, H. A., Plata, E. Rivas, Robbertse, B., Ruibal, C., Sakayaroj, J., Sano, T., Selbmann, L., Shearer, C. A., Shirouzu, T., Slippers, B., Suetrong, S., Tanaka, K., Volkmann-Kohlmeyer, B., Wingfield, M. J., Wood, A. R., Woudenberg, J. H. C., Yonezawa, H., Zhang, Y., and Spatafora, J. W.

Abstract

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.

Published
2009
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6. A class-wide phylogenetic assessment of Dothideomycetes

Author

Schoch, C.L, Crous, P.W., Groenewald, Johannes Z., Boehm, E.W.A., Burgess, T.I., De Gruyter, J., De Hoog, G.S., Dixon, L.J., Grube, M., Gueidan, C., Harada, Y., Hatakeyama, S., Hirayama, K., Hosoya, T., Huhndorf, S.M., Hyde, Kevin D., Jones, E.B.G., Kohlmeyer, J., Kruys, Å., Li, Y.M., Lücking, R., Lumbsch, H.T., Marvanová, L., Mbatchou, J.S., McVay, A.H., Miller, A.N., Mugambi, G.K., Muggia, L., Nelsen, M.P., Nelson, P., Owensby, C.A., Phillips, A.J.L., Phongpaichit, S., Pointing, S.B., Pujade-Renaud, Valérie, Raja, H.A., Rivas Plata, E., Robbertse, B., Ruibal, C., Sakayaroj, J., Sano, T., Selbmann, L., Shearer, C.A., Shirouzu, T., Slippers, Bernard, Suetrong, S., Tanaka, K., Volkmann-Kohlmeyer, B., Wingfield, M.J., Wood, A.R., Woudenberg, J.H.C., Yonezawa, H., Zhang, Y., Schoch, C.L, Crous, P.W., Groenewald, Johannes Z., Boehm, E.W.A., Burgess, T.I., De Gruyter, J., De Hoog, G.S., Dixon, L.J., Grube, M., Gueidan, C., Harada, Y., Hatakeyama, S., Hirayama, K., Hosoya, T., Huhndorf, S.M., Hyde, Kevin D., Jones, E.B.G., Kohlmeyer, J., Kruys, Å., Li, Y.M., Lücking, R., Lumbsch, H.T., Marvanová, L., Mbatchou, J.S., McVay, A.H., Miller, A.N., Mugambi, G.K., Muggia, L., Nelsen, M.P., Nelson, P., Owensby, C.A., Phillips, A.J.L., Phongpaichit, S., Pointing, S.B., Pujade-Renaud, Valérie, Raja, H.A., Rivas Plata, E., Robbertse, B., Ruibal, C., Sakayaroj, J., Sano, T., Selbmann, L., Shearer, C.A., Shirouzu, T., Slippers, Bernard, Suetrong, S., Tanaka, K., Volkmann-Kohlmeyer, B., Wingfield, M.J., Wood, A.R., Woudenberg, J.H.C., Yonezawa, H., and Zhang, Y.

Abstract

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.

Published
2009

7. A class-wide phylogenetic assessment of Dothideomycetes

Author

Schoch, C.L, Crous, P.W., Groenewald, Johannes Z., Boehm, E.W.A., Burgess, T.I., De Gruyter, J., De Hoog, G.S., Dixon, L.J., Grube, M., Gueidan, C., Harada, Y., Hatakeyama, S., Hirayama, K., Hosoya, T., Huhndorf, S.M., Hyde, Kevin D., Jones, E.B.G., Kohlmeyer, J., Kruys, Å., Li, Y.M., Lücking, R., Lumbsch, H.T., Marvanová, L., Mbatchou, J.S., McVay, A.H., Miller, A.N., Mugambi, G.K., Muggia, L., Nelsen, M.P., Nelson, P., Owensby, C.A., Phillips, A.J.L., Phongpaichit, S., Pointing, S.B., Pujade-Renaud, Valérie, Raja, H.A., Rivas Plata, E., Robbertse, B., Ruibal, C., Sakayaroj, J., Sano, T., Selbmann, L., Shearer, C.A., Shirouzu, T., Slippers, Bernard, Suetrong, S., Tanaka, K., Volkmann-Kohlmeyer, B., Wingfield, M.J., Wood, A.R., Woudenberg, J.H.C., Yonezawa, H., Zhang, Y., Schoch, C.L, Crous, P.W., Groenewald, Johannes Z., Boehm, E.W.A., Burgess, T.I., De Gruyter, J., De Hoog, G.S., Dixon, L.J., Grube, M., Gueidan, C., Harada, Y., Hatakeyama, S., Hirayama, K., Hosoya, T., Huhndorf, S.M., Hyde, Kevin D., Jones, E.B.G., Kohlmeyer, J., Kruys, Å., Li, Y.M., Lücking, R., Lumbsch, H.T., Marvanová, L., Mbatchou, J.S., McVay, A.H., Miller, A.N., Mugambi, G.K., Muggia, L., Nelsen, M.P., Nelson, P., Owensby, C.A., Phillips, A.J.L., Phongpaichit, S., Pointing, S.B., Pujade-Renaud, Valérie, Raja, H.A., Rivas Plata, E., Robbertse, B., Ruibal, C., Sakayaroj, J., Sano, T., Selbmann, L., Shearer, C.A., Shirouzu, T., Slippers, Bernard, Suetrong, S., Tanaka, K., Volkmann-Kohlmeyer, B., Wingfield, M.J., Wood, A.R., Woudenberg, J.H.C., Yonezawa, H., and Zhang, Y.

Abstract

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.

Published
2009

8. The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

Author

Schoch, C.L., Sung, G.H., López-Giráldez, F., Townsend, J.P., Miadlikowska, J., Hofstetter, V., Robbertse, B., Brandon Matheny, P., Kauff, F., Wang, Z., Gueidan, C., Andrie, R.M., Trippe, K., Ciufetti, L.M., Wynns, A., Fraker, E., Hodkinson, B.P., Bonito, G., Groenewald, J.Z., Arzanlou, M., de Hoog, G.S., Crous, P.W., Hewitt, D., Pfister, D.H., Peterson, K., Gryzenhout, M., Wingfield, M.J., Aptroot, A., Suh, S.O., Blackwell, M., Hillis, D.M., Griffith, G.W., Castlebury, L.A., Rossman, A.Y., Lumbsch, H.T., Lücking, R., Büdel, B., Rauhut, A., Diederich, P., Ertz, D., Geiser, D.M., Hosaka, K., Inderbitzin, P., Kohlmeyer, J., Volkmann-Kohlmeyer, B., Mostert, L., O'Donnell, K., Sipman, H., Rogers, J.D., Shoemaker, R.A., Sugiyama, J., Summerbell, R.C., Untereiner, W., Johnston, P.R., Stenroos, S., Zuccaro, A., Dyer, P.S., Crittenden, P.D., Cole, M.S., Hansen, K., Trappe, J.M., Yahr, R., Lutzoni, F., Spatafora, J.W., Schoch, C.L., Sung, G.H., López-Giráldez, F., Townsend, J.P., Miadlikowska, J., Hofstetter, V., Robbertse, B., Brandon Matheny, P., Kauff, F., Wang, Z., Gueidan, C., Andrie, R.M., Trippe, K., Ciufetti, L.M., Wynns, A., Fraker, E., Hodkinson, B.P., Bonito, G., Groenewald, J.Z., Arzanlou, M., de Hoog, G.S., Crous, P.W., Hewitt, D., Pfister, D.H., Peterson, K., Gryzenhout, M., Wingfield, M.J., Aptroot, A., Suh, S.O., Blackwell, M., Hillis, D.M., Griffith, G.W., Castlebury, L.A., Rossman, A.Y., Lumbsch, H.T., Lücking, R., Büdel, B., Rauhut, A., Diederich, P., Ertz, D., Geiser, D.M., Hosaka, K., Inderbitzin, P., Kohlmeyer, J., Volkmann-Kohlmeyer, B., Mostert, L., O'Donnell, K., Sipman, H., Rogers, J.D., Shoemaker, R.A., Sugiyama, J., Summerbell, R.C., Untereiner, W., Johnston, P.R., Stenroos, S., Zuccaro, A., Dyer, P.S., Crittenden, P.D., Cole, M.S., Hansen, K., Trappe, J.M., Yahr, R., Lutzoni, F., and Spatafora, J.W.

Abstract

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

Published
2009

9. A class-wide phylogenetic assessment of Dothideomycetes

Author

Schoch, C.L., Crous, P.W., Groenewald, J.Z., Boehm, E.W.A., Burgess, T.I., de Gruyter, J., de Hoog, G.S., Dixon, L.J., Grube, M., Gueidan, C., Harada, Y., Hatakeyama, S., Hirayama, K., Hosoya, T., Huhndorf, S.M., Hyde, K.D., Jones, E.B.G., Kohlmeyer, J., Kruys, Å., Li, Y.M., Lücking, R., Lumbsch, H.T., Marvanová, L., Mbatchou, J.S., McVay, A.H., Miller, A.N., Mugambi, G.K., Muggia, L., Nelsen, M.P., Nelson, P., Owensby, C.A., Phillips, A.J.L., Phongpaichit, S., Pointing, S.B., Pujade-Renaud, V., Raja, H.A., Rivas Plata, E., Robbertse, B., Ruibal, C., Sakayaroj, J., Sano, T., Selbmann, L., Shearer, C.A., Shirouzu, T., Slippers, B., Suetrong, S., Tanaka, K., Volkmann-Kohlmeyer, B., Wingfield, M.J., Wood, A.R., Woudenberg, J.H.C., Yonezawa, H., Zhang, Y., Spatafora, J.W., Schoch, C.L., Crous, P.W., Groenewald, J.Z., Boehm, E.W.A., Burgess, T.I., de Gruyter, J., de Hoog, G.S., Dixon, L.J., Grube, M., Gueidan, C., Harada, Y., Hatakeyama, S., Hirayama, K., Hosoya, T., Huhndorf, S.M., Hyde, K.D., Jones, E.B.G., Kohlmeyer, J., Kruys, Å., Li, Y.M., Lücking, R., Lumbsch, H.T., Marvanová, L., Mbatchou, J.S., McVay, A.H., Miller, A.N., Mugambi, G.K., Muggia, L., Nelsen, M.P., Nelson, P., Owensby, C.A., Phillips, A.J.L., Phongpaichit, S., Pointing, S.B., Pujade-Renaud, V., Raja, H.A., Rivas Plata, E., Robbertse, B., Ruibal, C., Sakayaroj, J., Sano, T., Selbmann, L., Shearer, C.A., Shirouzu, T., Slippers, B., Suetrong, S., Tanaka, K., Volkmann-Kohlmeyer, B., Wingfield, M.J., Wood, A.R., Woudenberg, J.H.C., Yonezawa, H., Zhang, Y., and Spatafora, J.W.

Abstract

We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon

Published
2009

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