A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.

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A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families. / Miadlikowska, Jolanta; Kauff, Frank; Högnabba, Filip; Oliver, Jeffrey C; Molnár, Katalin; Fraker, Emily; Gaya, Ester; Hafellner, Josef; Hofstetter, Valérie; Gueidan, Cécile; Kukwa, Martin; Lücking, Robert; Björk, Curtis; Sipman, Harrie J M; Burgaz, Ana Rosa; Thell, Arne; Passo, Alfredo; Myllys, Leena; Goward, Trevor; Fernández-Brime, Samantha; Hestmark, Geir; Lendemer, James; Thorsten Lumbsch, H; Schmull, Michaela; Schoch, Conrad; Sérusiaux, Emmanuël; Maddison, David R; Elizabeth Arnold, A; Lutzoni, François; Stenroos, Soili.

I: Molecular Phylogenetics and Evolution, Vol. 79, Nr. Online 18 April 2014, 2014, s. 132-168.

Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

Harvard

Miadlikowska, J, Kauff, F, Högnabba, F, Oliver, JC, Molnár, K, Fraker, E, Gaya, E, Hafellner, J, Hofstetter, V, Gueidan, C, Kukwa, M, Lücking, R, Björk, C, Sipman, HJM, Burgaz, AR, Thell, A, Passo, A, Myllys, L, Goward, T, Fernández-Brime, S, Hestmark, G, Lendemer, J, Thorsten Lumbsch, H, Schmull, M, Schoch, C, Sérusiaux, E, Maddison, DR, Elizabeth Arnold, A, Lutzoni, F & Stenroos, S 2014, 'A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.', Molecular Phylogenetics and Evolution, vol. 79, nr. Online 18 April 2014, s. 132-168. https://doi.org/10.1016/j.ympev.2014.04.003

APA

CBE

Miadlikowska J, Kauff F, Högnabba F, Oliver JC, Molnár K, Fraker E, Gaya E, Hafellner J, Hofstetter V, Gueidan C, Kukwa M, Lücking R, Björk C, Sipman HJM, Burgaz AR, Thell A, Passo A, Myllys L, Goward T, Fernández-Brime S, Hestmark G, Lendemer J, Thorsten Lumbsch H, Schmull M, Schoch C, Sérusiaux E, Maddison DR, Elizabeth Arnold A, Lutzoni F, Stenroos S. 2014. A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families. Molecular Phylogenetics and Evolution. 79(Online 18 April 2014):132-168. https://doi.org/10.1016/j.ympev.2014.04.003

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Author

Miadlikowska, Jolanta ; Kauff, Frank ; Högnabba, Filip ; Oliver, Jeffrey C ; Molnár, Katalin ; Fraker, Emily ; Gaya, Ester ; Hafellner, Josef ; Hofstetter, Valérie ; Gueidan, Cécile ; Kukwa, Martin ; Lücking, Robert ; Björk, Curtis ; Sipman, Harrie J M ; Burgaz, Ana Rosa ; Thell, Arne ; Passo, Alfredo ; Myllys, Leena ; Goward, Trevor ; Fernández-Brime, Samantha ; Hestmark, Geir ; Lendemer, James ; Thorsten Lumbsch, H ; Schmull, Michaela ; Schoch, Conrad ; Sérusiaux, Emmanuël ; Maddison, David R ; Elizabeth Arnold, A ; Lutzoni, François ; Stenroos, Soili. / A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families. I: Molecular Phylogenetics and Evolution. 2014 ; Vol. 79, Nr. Online 18 April 2014. s. 132-168.

RIS

TY - JOUR

T1 - A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.

AU - Miadlikowska, Jolanta

AU - Kauff, Frank

AU - Högnabba, Filip

AU - Oliver, Jeffrey C

AU - Molnár, Katalin

AU - Fraker, Emily

AU - Gaya, Ester

AU - Hafellner, Josef

AU - Hofstetter, Valérie

AU - Gueidan, Cécile

AU - Kukwa, Martin

AU - Lücking, Robert

AU - Björk, Curtis

AU - Sipman, Harrie J M

AU - Burgaz, Ana Rosa

AU - Thell, Arne

AU - Passo, Alfredo

AU - Myllys, Leena

AU - Goward, Trevor

AU - Fernández-Brime, Samantha

AU - Hestmark, Geir

AU - Lendemer, James

AU - Thorsten Lumbsch, H

AU - Schmull, Michaela

AU - Schoch, Conrad

AU - Sérusiaux, Emmanuël

AU - Maddison, David R

AU - Elizabeth Arnold, A

AU - Lutzoni, François

AU - Stenroos, Soili

PY - 2014

Y1 - 2014

N2 - The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 635 newly generated and 3307 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module ("Hypha") of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.

AB - The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 635 newly generated and 3307 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module ("Hypha") of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.

KW - classification

KW - cumulative supermatrix

KW - Lecanoromycetes

KW - lichenized fungi

KW - systematics

U2 - 10.1016/j.ympev.2014.04.003

DO - 10.1016/j.ympev.2014.04.003

M3 - Article

VL - 79

SP - 132

EP - 168

JO - Molecular Phylogenetics and Evolution

T2 - Molecular Phylogenetics and Evolution

JF - Molecular Phylogenetics and Evolution

SN - 1095-9513

IS - Online 18 April 2014

ER -