@ARTICLE{TreeBASE2Ref18889,
author = {Michael David Pirie and Aelys M. Humphreys and Chlo? Galley and Nigel P. Barker and G. Anthony Verboom and David Allan Orlovich and Suzy J Draffin and Kelvin Lloyd and Carlos M. Baeza and Maria Negritto and Eduardo Ruiz and J. Hugo Cota Sanchez and Elizabeth Reimer and Hans Peter Linder},
title = {A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses. },
year = {2008},
keywords = {Coding and non-coding DNA sequence data; Conflict; Danthonioideae; Missing data; Phylogeny reconstruction; Poaceae; Sampling strategy; Supermatrix },
doi = {10.1016/j.ympev.2008.05.030},
url = {http://www.sciencedirect.com/science/article/B6WNH-4SMWFF1-2/1/be9983df338663c9f67b6f4dcf0debf1},
pmid = {18599319},
journal = {Molecular Phylogenetics and Evolution},
volume = {48},
number = {3},
pages = {1106--1119},
abstract = {Phylogeny reconstruction is challenging when branch lengths vary and when different genetic loci show conflicting signals. The number of DNA sequence characters required to obtain robust support for all the nodes in a phylogeny becomes greater with denser taxon sampling. We test the usefulness of an approach mixing densely sampled, variable non-coding sequences (trnL-F; rpl16; atpB-rbcL; ITS) with sparsely sampled, more conservative protein coding and ribosomal sequences (matK; ndhF; rbcL; 26S), for the grass subfamily Danthonioideae. Previous phylogenetic studies of Danthonioideae revealed extensive generic paraphyly, but were often impeded by insufficient character and taxon sampling and apparent inter-gene conflict. Our variably-sampled supermatrix approach allowed us to represent 79% of the species with up to c. 9900 base pairs for taxa representing the major clades. A ?taxon duplication? approach for taxa with conflicting phylogenetic signals allowed us to combine the data whilst representing the differences between chloroplast and nuclear encoded gene trees. This approach efficiently improves resolution and support whilst maximising representation of taxa and their sometimes composite evolutionary histories, resulting in a phylogeny of the Danthonioideae that will be useful both for a wide range of evolutionary studies and to inform forthcoming realignment of generic delimitations in the subfamily.}
}
Citation for Study 10427
Citation title:
"A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses. ".
Study name:
"A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses. ".
This study is part of submission 10417
(Status: Published).
Citation
Pirie M.D., Humphreys A., Galley C., Barker N., Verboom G., Orlovich D.A., Draffin S.J., Lloyd K., Baeza C., Negritto M., Ruiz E., Cota sanchez J., Reimer E., & Linder H. 2008. A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses. Molecular Phylogenetics and Evolution, 48(3): 1106-1119.
Authors
-
Pirie M.D.
(submitter)
+4961313922928
-
Humphreys A.
-
Galley C.
-
Barker N.
-
Verboom G.
-
Orlovich D.A.
6434799060
-
Draffin S.J.
-
Lloyd K.
-
Baeza C.
-
Negritto M.
-
Ruiz E.
-
Cota sanchez J.
-
Reimer E.
-
Linder H.
Abstract
Phylogeny reconstruction is challenging when branch lengths vary and when different genetic loci show conflicting signals. The number of DNA sequence characters required to obtain robust support for all the nodes in a phylogeny becomes greater with denser taxon sampling. We test the usefulness of an approach mixing densely sampled, variable non-coding sequences (trnL-F; rpl16; atpB-rbcL; ITS) with sparsely sampled, more conservative protein coding and ribosomal sequences (matK; ndhF; rbcL; 26S), for the grass subfamily Danthonioideae. Previous phylogenetic studies of Danthonioideae revealed extensive generic paraphyly, but were often impeded by insufficient character and taxon sampling and apparent inter-gene conflict. Our variably-sampled supermatrix approach allowed us to represent 79% of the species with up to c. 9900 base pairs for taxa representing the major clades. A ?taxon duplication? approach for taxa with conflicting phylogenetic signals allowed us to combine the data whilst representing the differences between chloroplast and nuclear encoded gene trees. This approach efficiently improves resolution and support whilst maximising representation of taxa and their sometimes composite evolutionary histories, resulting in a phylogeny of the Danthonioideae that will be useful both for a wide range of evolutionary studies and to inform forthcoming realignment of generic delimitations in the subfamily.
Keywords
Coding and non-coding DNA sequence data; Conflict; Danthonioideae; Missing data; Phylogeny reconstruction; Poaceae; Sampling strategy; Supermatrix
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S10427
- Other versions:
Nexus
NeXML
- Show BibTeX reference
@ARTICLE{TreeBASE2Ref18889,
author = {Michael David Pirie and Aelys M. Humphreys and Chlo? Galley and Nigel P. Barker and G. Anthony Verboom and David Allan Orlovich and Suzy J Draffin and Kelvin Lloyd and Carlos M. Baeza and Maria Negritto and Eduardo Ruiz and J. Hugo Cota Sanchez and Elizabeth Reimer and Hans Peter Linder},
title = {A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses. },
year = {2008},
keywords = {Coding and non-coding DNA sequence data; Conflict; Danthonioideae; Missing data; Phylogeny reconstruction; Poaceae; Sampling strategy; Supermatrix },
doi = {10.1016/j.ympev.2008.05.030},
url = {http://www.sciencedirect.com/science/article/B6WNH-4SMWFF1-2/1/be9983df338663c9f67b6f4dcf0debf1},
pmid = {18599319},
journal = {Molecular Phylogenetics and Evolution},
volume = {48},
number = {3},
pages = {1106--1119},
abstract = {Phylogeny reconstruction is challenging when branch lengths vary and when different genetic loci show conflicting signals. The number of DNA sequence characters required to obtain robust support for all the nodes in a phylogeny becomes greater with denser taxon sampling. We test the usefulness of an approach mixing densely sampled, variable non-coding sequences (trnL-F; rpl16; atpB-rbcL; ITS) with sparsely sampled, more conservative protein coding and ribosomal sequences (matK; ndhF; rbcL; 26S), for the grass subfamily Danthonioideae. Previous phylogenetic studies of Danthonioideae revealed extensive generic paraphyly, but were often impeded by insufficient character and taxon sampling and apparent inter-gene conflict. Our variably-sampled supermatrix approach allowed us to represent 79% of the species with up to c. 9900 base pairs for taxa representing the major clades. A ?taxon duplication? approach for taxa with conflicting phylogenetic signals allowed us to combine the data whilst representing the differences between chloroplast and nuclear encoded gene trees. This approach efficiently improves resolution and support whilst maximising representation of taxa and their sometimes composite evolutionary histories, resulting in a phylogeny of the Danthonioideae that will be useful both for a wide range of evolutionary studies and to inform forthcoming realignment of generic delimitations in the subfamily.}
}
- Show RIS reference
TY - JOUR
ID - 18889
AU - Pirie,Michael David
AU - Humphreys,Aelys M.
AU - Galley,Chlo?
AU - Barker,Nigel P.
AU - Verboom,G. Anthony
AU - Orlovich,David Allan
AU - Draffin,Suzy J
AU - Lloyd,Kelvin
AU - Baeza,Carlos M.
AU - Negritto,Maria
AU - Ruiz,Eduardo
AU - Cota Sanchez,J. Hugo
AU - Reimer,Elizabeth
AU - Linder,Hans Peter
T1 - A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses.
PY - 2008
KW - Coding and non-coding DNA sequence data; Conflict; Danthonioideae; Missing data; Phylogeny reconstruction; Poaceae; Sampling strategy; Supermatrix
UR - http://www.sciencedirect.com/science/article/B6WNH-4SMWFF1-2/1/be9983df338663c9f67b6f4dcf0debf1
N2 - Phylogeny reconstruction is challenging when branch lengths vary and when different genetic loci show conflicting signals. The number of DNA sequence characters required to obtain robust support for all the nodes in a phylogeny becomes greater with denser taxon sampling. We test the usefulness of an approach mixing densely sampled, variable non-coding sequences (trnL-F; rpl16; atpB-rbcL; ITS) with sparsely sampled, more conservative protein coding and ribosomal sequences (matK; ndhF; rbcL; 26S), for the grass subfamily Danthonioideae. Previous phylogenetic studies of Danthonioideae revealed extensive generic paraphyly, but were often impeded by insufficient character and taxon sampling and apparent inter-gene conflict. Our variably-sampled supermatrix approach allowed us to represent 79% of the species with up to c. 9900 base pairs for taxa representing the major clades. A ?taxon duplication? approach for taxa with conflicting phylogenetic signals allowed us to combine the data whilst representing the differences between chloroplast and nuclear encoded gene trees. This approach efficiently improves resolution and support whilst maximising representation of taxa and their sometimes composite evolutionary histories, resulting in a phylogeny of the Danthonioideae that will be useful both for a wide range of evolutionary studies and to inform forthcoming realignment of generic delimitations in the subfamily.
L3 - 10.1016/j.ympev.2008.05.030
JF - Molecular Phylogenetics and Evolution
VL - 48
IS - 3
SP - 1106
EP - 1119
ER -