@ARTICLE{TreeBASE2Ref20079,
author = {Adrian Schneider and Gina M. Cannarozzi},
title = {Support Patterns from Different Outgroups Provide a Strong Phylogenetic Signal},
year = {2009},
keywords = {outgroups, phylogeny, Mammalia, reconstruction artifacts},
doi = {10.1093/molbev/msp034},
url = {http://mbe.oxfordjournals.org/content/26/6/1259.full},
pmid = {192401},
journal = {Molecular Biology and Evolution},
volume = {26},
number = {6},
pages = {1259--1272},
abstract = {It is known that the accuracy of phylogenetic reconstruction decreases when more distant outgroups are used. We quantify this phenomenon with a novel scoring method, the outgroup score pOG. This score expresses if the support for a particular branch of a tree decreases with increasingly distant outgroups. Large-scale simulations confirmed that the outgroup support follows this expectation and that the pOG score captures this pattern. The score often identifies the correct topology even when the primary reconstruction methods fail, particularly in the presence of model violations. In simulations of problematic phylogenetic scenarios such as rate variation among lineages (which can lead to long-branch attraction artifacts) and quartet-based reconstruction, the pOG analysis outperformed the primary reconstruction methods. Because the pOG method does not make any assumptions about the evolutionary model (besides the decreasing support from increasingly distant outgroups), it can detect cases of violations not treated by a specific model or too strong to be fully corrected. When used as an optimization criterion in the construction of a tree of 23 mammals, the outgroup signal confirmed many well-accepted mammalian orders and superorders. It supports Atlantogenata, a clade of Afrotheria and Xenarthra, and suggests an Artiodactyla?Chiroptera clade.}
}
Citation for Study 11961
Citation title:
"Support Patterns from Different Outgroups Provide a Strong Phylogenetic Signal".
Study name:
"Support Patterns from Different Outgroups Provide a Strong Phylogenetic Signal".
This study is part of submission 11961
(Status: Published).
Citation
Schneider A., & Cannarozzi G.M. 2009. Support Patterns from Different Outgroups Provide a Strong Phylogenetic Signal. Molecular Biology and Evolution, 26(6): 1259-1272.
Authors
-
Schneider A.
(submitter)
-
Cannarozzi G.M.
Abstract
It is known that the accuracy of phylogenetic reconstruction decreases when more distant outgroups are used. We quantify this phenomenon with a novel scoring method, the outgroup score pOG. This score expresses if the support for a particular branch of a tree decreases with increasingly distant outgroups. Large-scale simulations confirmed that the outgroup support follows this expectation and that the pOG score captures this pattern. The score often identifies the correct topology even when the primary reconstruction methods fail, particularly in the presence of model violations. In simulations of problematic phylogenetic scenarios such as rate variation among lineages (which can lead to long-branch attraction artifacts) and quartet-based reconstruction, the pOG analysis outperformed the primary reconstruction methods. Because the pOG method does not make any assumptions about the evolutionary model (besides the decreasing support from increasingly distant outgroups), it can detect cases of violations not treated by a specific model or too strong to be fully corrected. When used as an optimization criterion in the construction of a tree of 23 mammals, the outgroup signal confirmed many well-accepted mammalian orders and superorders. It supports Atlantogenata, a clade of Afrotheria and Xenarthra, and suggests an Artiodactyla?Chiroptera clade.
Keywords
outgroups, phylogeny, Mammalia, reconstruction artifacts
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S11961
- Other versions:
Nexus
NeXML
- Show BibTeX reference
@ARTICLE{TreeBASE2Ref20079,
author = {Adrian Schneider and Gina M. Cannarozzi},
title = {Support Patterns from Different Outgroups Provide a Strong Phylogenetic Signal},
year = {2009},
keywords = {outgroups, phylogeny, Mammalia, reconstruction artifacts},
doi = {10.1093/molbev/msp034},
url = {http://mbe.oxfordjournals.org/content/26/6/1259.full},
pmid = {192401},
journal = {Molecular Biology and Evolution},
volume = {26},
number = {6},
pages = {1259--1272},
abstract = {It is known that the accuracy of phylogenetic reconstruction decreases when more distant outgroups are used. We quantify this phenomenon with a novel scoring method, the outgroup score pOG. This score expresses if the support for a particular branch of a tree decreases with increasingly distant outgroups. Large-scale simulations confirmed that the outgroup support follows this expectation and that the pOG score captures this pattern. The score often identifies the correct topology even when the primary reconstruction methods fail, particularly in the presence of model violations. In simulations of problematic phylogenetic scenarios such as rate variation among lineages (which can lead to long-branch attraction artifacts) and quartet-based reconstruction, the pOG analysis outperformed the primary reconstruction methods. Because the pOG method does not make any assumptions about the evolutionary model (besides the decreasing support from increasingly distant outgroups), it can detect cases of violations not treated by a specific model or too strong to be fully corrected. When used as an optimization criterion in the construction of a tree of 23 mammals, the outgroup signal confirmed many well-accepted mammalian orders and superorders. It supports Atlantogenata, a clade of Afrotheria and Xenarthra, and suggests an Artiodactyla?Chiroptera clade.}
}
- Show RIS reference
TY - JOUR
ID - 20079
AU - Schneider,Adrian
AU - Cannarozzi,Gina M.
T1 - Support Patterns from Different Outgroups Provide a Strong Phylogenetic Signal
PY - 2009
KW - outgroups
KW - phylogeny
KW - Mammalia
KW - reconstruction artifacts
UR - http://mbe.oxfordjournals.org/content/26/6/1259.full
N2 - It is known that the accuracy of phylogenetic reconstruction decreases when more distant outgroups are used. We quantify this phenomenon with a novel scoring method, the outgroup score pOG. This score expresses if the support for a particular branch of a tree decreases with increasingly distant outgroups. Large-scale simulations confirmed that the outgroup support follows this expectation and that the pOG score captures this pattern. The score often identifies the correct topology even when the primary reconstruction methods fail, particularly in the presence of model violations. In simulations of problematic phylogenetic scenarios such as rate variation among lineages (which can lead to long-branch attraction artifacts) and quartet-based reconstruction, the pOG analysis outperformed the primary reconstruction methods. Because the pOG method does not make any assumptions about the evolutionary model (besides the decreasing support from increasingly distant outgroups), it can detect cases of violations not treated by a specific model or too strong to be fully corrected. When used as an optimization criterion in the construction of a tree of 23 mammals, the outgroup signal confirmed many well-accepted mammalian orders and superorders. It supports Atlantogenata, a clade of Afrotheria and Xenarthra, and suggests an Artiodactyla?Chiroptera clade.
L3 - 10.1093/molbev/msp034
JF - Molecular Biology and Evolution
VL - 26
IS - 6
SP - 1259
EP - 1272
ER -