@ARTICLE{TreeBASE2Ref23078,
author = {Jolanta Maria Miadlikowska and Frank Kauff and Filip H?gnabba and Jeffrey C Oliver and Katalin Moln?r and Emily Fraker and Ester Gaya and Josef Hafellner and Valerie Hofstetter and Cecile Gueidan and Martin Kukwa and Robert L?cking and Curtis Bj?rk and Harrie Sipman and Ana Rosa Burgaz and Arne Thell and Alfredo Passo and Leena Myllys and Trevor Goward and Samantha Fern?ndez-Brime and Geir Hestmark and James Lendemer and H. Thorsten Lumbsch and Michaela Schmull and Conrad L Schoch and Emmanu?l S?rusiaux and David Robert Maddison and A Elizabeth Arnold and Francois Lutzoni and Soili Stenroos},
title = {A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families},
year = {2014},
keywords = {Classification; Cumulative supermatrix, Lecanoromycetes; Lichenized fungi; Maximum likelihood; Multi-gene phylogeny; Systematics},
doi = {10.1016/j.ympev.2014.04.003},
url = {http://},
pmid = {},
journal = {Molecular Phylogenetics and Evolution},
volume = {79},
number = {},
pages = {132--168},
abstract = {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. }
}
Citation for Study 15652
Citation title:
"A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families".
Study name:
"A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families".
This study is part of submission 15652
(Status: Published).
Citation
Miadlikowska J.M., Kauff F., H?gnabba F., Oliver J.C., Moln?r K., Fraker E., Gaya E., Hafellner J., Hofstetter V., Gueidan C., Kukwa M., L?cking R., Bj?rk C., Sipman H., Burgaz A.R., Thell A., Passo A., Myllys L., Goward T., Fern?ndez-brime S., Hestmark G., Lendemer J., Lumbsch H.T., Schmull M., Schoch C.L., S?rusiaux E., Maddison D.R., Arnold A.E., 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: 132-168.
Authors
-
Miadlikowska J.M.
(submitter)
9196607287
-
Kauff F.
-
H?gnabba F.
-
Oliver J.C.
-
Moln?r K.
-
Fraker E.
-
Gaya E.
-
Hafellner J.
-
Hofstetter V.
-
Gueidan C.
-
Kukwa M.
-
L?cking R.
-
Bj?rk C.
-
Sipman H.
-
Burgaz A.R.
-
Thell A.
-
Passo A.
-
Myllys L.
-
Goward T.
-
Fern?ndez-brime S.
-
Hestmark G.
-
Lendemer J.
-
Lumbsch H.T.
-
Schmull M.
-
Schoch C.L.
-
S?rusiaux E.
-
Maddison D.R.
541 737 2834
-
Arnold A.E.
-
Lutzoni F.
-
Stenroos S.
Abstract
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.
Keywords
Classification; Cumulative supermatrix, Lecanoromycetes; Lichenized fungi; Maximum likelihood; Multi-gene phylogeny; Systematics
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S15652
- Other versions:
Nexus
NeXML
- Show BibTeX reference
@ARTICLE{TreeBASE2Ref23078,
author = {Jolanta Maria Miadlikowska and Frank Kauff and Filip H?gnabba and Jeffrey C Oliver and Katalin Moln?r and Emily Fraker and Ester Gaya and Josef Hafellner and Valerie Hofstetter and Cecile Gueidan and Martin Kukwa and Robert L?cking and Curtis Bj?rk and Harrie Sipman and Ana Rosa Burgaz and Arne Thell and Alfredo Passo and Leena Myllys and Trevor Goward and Samantha Fern?ndez-Brime and Geir Hestmark and James Lendemer and H. Thorsten Lumbsch and Michaela Schmull and Conrad L Schoch and Emmanu?l S?rusiaux and David Robert Maddison and A Elizabeth Arnold and Francois Lutzoni and Soili Stenroos},
title = {A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families},
year = {2014},
keywords = {Classification; Cumulative supermatrix, Lecanoromycetes; Lichenized fungi; Maximum likelihood; Multi-gene phylogeny; Systematics},
doi = {10.1016/j.ympev.2014.04.003},
url = {http://},
pmid = {},
journal = {Molecular Phylogenetics and Evolution},
volume = {79},
number = {},
pages = {132--168},
abstract = {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. }
}
- Show RIS reference
TY - JOUR
ID - 23078
AU - Miadlikowska,Jolanta Maria
AU - Kauff,Frank
AU - H?gnabba,Filip
AU - Oliver,Jeffrey C
AU - Moln?r,Katalin
AU - Fraker,Emily
AU - Gaya,Ester
AU - Hafellner,Josef
AU - Hofstetter,Valerie
AU - Gueidan,Cecile
AU - Kukwa,Martin
AU - L?cking,Robert
AU - Bj?rk,Curtis
AU - Sipman,Harrie
AU - Burgaz,Ana Rosa
AU - Thell,Arne
AU - Passo,Alfredo
AU - Myllys,Leena
AU - Goward,Trevor
AU - Fern?ndez-Brime,Samantha
AU - Hestmark,Geir
AU - Lendemer,James
AU - Lumbsch,H. Thorsten
AU - Schmull,Michaela
AU - Schoch,Conrad L
AU - S?rusiaux,Emmanu?l
AU - Maddison,David Robert
AU - Arnold,A Elizabeth
AU - Lutzoni,Francois
AU - Stenroos,Soili
T1 - A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families
PY - 2014
KW - Classification; Cumulative supermatrix
KW - Lecanoromycetes; Lichenized fungi; Maximum likelihood; Multi-gene phylogeny; Systematics
UR - http://dx.doi.org/10.1016/j.ympev.2014.04.003
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.
L3 - 10.1016/j.ympev.2014.04.003
JF - Molecular Phylogenetics and Evolution
VL - 79
IS -
SP - 132
EP - 168
ER -