@ARTICLE{TreeBASE2Ref15540,
author = {Koen Geuten and Tim Massingham and P. Darius and Erik Smets and Nick Goldman},
title = {Experimental Design Criteria in Phylogenetics: Where to add Taxa.},
year = {2007},
keywords = {},
doi = {10.1080/10635150701499563},
url = {},
pmid = {},
journal = {Systematic Biology},
volume = {56},
number = {4},
pages = {609--622},
abstract = {Accurate phylogenetic inference is a topic of intensive research and debate, and has been studied in response to many different factors: for example, differences in the method of reconstruction, the shape of the underlying tree, the substitution model and varying quantities and types of data. Investigating whether the conditions used might lead to inaccurate inference has been attempted through elaborate data exploration but less attention has been given to creating a unified methodology to enable experimental designs in phylogenetic analysis to be improved and so avoid suboptimal conditions. Experimental design has been part of the field of statistics since the seminal work of Fisher in the early twentieth century and a large body of literature exists on how to design optimum experiments. Here we investigate the use of the Fisher information matrix to decide between candidate positions for adding a taxon to a fixed topology, and introduce a parameter transformation that permits comparison of these different designs. This extension to Goldman (1998) thus allows investigation of `where to add taxa' in a phylogeny. We compare three different measures of the total information for selecting the position to add a taxon to a tree. Our methods are illustrated by investigating the behaviour of the three criteria when adding a branch to model trees, and by applying the different criteria to two biological examples: a simplified taxon-sampling problem in the balsaminoid Ericales and the phylogeny of seed plants.}
}
Citation for Study 1811
Citation title:
"Experimental Design Criteria in Phylogenetics: Where to add Taxa.".
This study was previously identified under the legacy study ID S1785
(Status: Published).
Citation
Geuten K., Massingham T., Darius P., Smets E., & Goldman N. 2007. Experimental Design Criteria in Phylogenetics: Where to add Taxa. Systematic Biology, 56(4): 609-622.
Authors
-
Geuten K.
-
Massingham T.
-
Darius P.
-
Smets E.
-
Goldman N.
Abstract
Accurate phylogenetic inference is a topic of intensive research and debate, and has been studied in response to many different factors: for example, differences in the method of reconstruction, the shape of the underlying tree, the substitution model and varying quantities and types of data. Investigating whether the conditions used might lead to inaccurate inference has been attempted through elaborate data exploration but less attention has been given to creating a unified methodology to enable experimental designs in phylogenetic analysis to be improved and so avoid suboptimal conditions. Experimental design has been part of the field of statistics since the seminal work of Fisher in the early twentieth century and a large body of literature exists on how to design optimum experiments. Here we investigate the use of the Fisher information matrix to decide between candidate positions for adding a taxon to a fixed topology, and introduce a parameter transformation that permits comparison of these different designs. This extension to Goldman (1998) thus allows investigation of `where to add taxa' in a phylogeny. We compare three different measures of the total information for selecting the position to add a taxon to a tree. Our methods are illustrated by investigating the behaviour of the three criteria when adding a branch to model trees, and by applying the different criteria to two biological examples: a simplified taxon-sampling problem in the balsaminoid Ericales and the phylogeny of seed plants.
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S1811
- Other versions:
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NeXML
- Show BibTeX reference
@ARTICLE{TreeBASE2Ref15540,
author = {Koen Geuten and Tim Massingham and P. Darius and Erik Smets and Nick Goldman},
title = {Experimental Design Criteria in Phylogenetics: Where to add Taxa.},
year = {2007},
keywords = {},
doi = {10.1080/10635150701499563},
url = {},
pmid = {},
journal = {Systematic Biology},
volume = {56},
number = {4},
pages = {609--622},
abstract = {Accurate phylogenetic inference is a topic of intensive research and debate, and has been studied in response to many different factors: for example, differences in the method of reconstruction, the shape of the underlying tree, the substitution model and varying quantities and types of data. Investigating whether the conditions used might lead to inaccurate inference has been attempted through elaborate data exploration but less attention has been given to creating a unified methodology to enable experimental designs in phylogenetic analysis to be improved and so avoid suboptimal conditions. Experimental design has been part of the field of statistics since the seminal work of Fisher in the early twentieth century and a large body of literature exists on how to design optimum experiments. Here we investigate the use of the Fisher information matrix to decide between candidate positions for adding a taxon to a fixed topology, and introduce a parameter transformation that permits comparison of these different designs. This extension to Goldman (1998) thus allows investigation of `where to add taxa' in a phylogeny. We compare three different measures of the total information for selecting the position to add a taxon to a tree. Our methods are illustrated by investigating the behaviour of the three criteria when adding a branch to model trees, and by applying the different criteria to two biological examples: a simplified taxon-sampling problem in the balsaminoid Ericales and the phylogeny of seed plants.}
}
- Show RIS reference
TY - JOUR
ID - 15540
AU - Geuten,Koen
AU - Massingham,Tim
AU - Darius,P.
AU - Smets,Erik
AU - Goldman,Nick
T1 - Experimental Design Criteria in Phylogenetics: Where to add Taxa.
PY - 2007
KW -
UR - http://dx.doi.org/10.1080/10635150701499563
N2 - Accurate phylogenetic inference is a topic of intensive research and debate, and has been studied in response to many different factors: for example, differences in the method of reconstruction, the shape of the underlying tree, the substitution model and varying quantities and types of data. Investigating whether the conditions used might lead to inaccurate inference has been attempted through elaborate data exploration but less attention has been given to creating a unified methodology to enable experimental designs in phylogenetic analysis to be improved and so avoid suboptimal conditions. Experimental design has been part of the field of statistics since the seminal work of Fisher in the early twentieth century and a large body of literature exists on how to design optimum experiments. Here we investigate the use of the Fisher information matrix to decide between candidate positions for adding a taxon to a fixed topology, and introduce a parameter transformation that permits comparison of these different designs. This extension to Goldman (1998) thus allows investigation of `where to add taxa' in a phylogeny. We compare three different measures of the total information for selecting the position to add a taxon to a tree. Our methods are illustrated by investigating the behaviour of the three criteria when adding a branch to model trees, and by applying the different criteria to two biological examples: a simplified taxon-sampling problem in the balsaminoid Ericales and the phylogeny of seed plants.
L3 - 10.1080/10635150701499563
JF - Systematic Biology
VL - 56
IS - 4
SP - 609
EP - 622
ER -
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