@ARTICLE{TreeBASE2Ref18554,
author = {Diego San Mauro and David J. Gower and Tim Massingham and Mark Wilkinson and Rafael Zardoya and James A. Cotton},
title = {Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1},
year = {2009},
keywords = {},
doi = {10.1093/sysbio/syp043},
url = {},
pmid = {},
journal = {Systematic Biology},
volume = {58},
number = {},
pages = {425--438},
abstract = {In molecular phylogenetic studies, a major aspect of experimental design concerns the choice of markers and taxa. While previous studies have investigated the phylogenetic performance of different genes and the effectiveness of increasing taxon sampling, their conclusions are partly contradictory, probably because they are highly context specific and dependent on the group of organisms used in each study. Goldman (1998) introduced a method for experimental design in phylogenetics based on the expected information to be gained that has barely been used in practice. Here we use this method to explore the phylogenetic utility of mitochondrial (mt) genes, mt genomes, and nuclear rag1 for studies of the systematics of caecilian amphibians, as well as the effect of taxon addition on the stabilization of a controversial branch of the tree. Overall phylogenetic information estimates per gene, specific estimates per branch of the tree, estimates for combined (mitogenomic) data sets, and estimates as a hypothetical new taxon is added to different parts of the caecilian tree are calculated and compared. In general, the most informative data sets are those for mt transfer and ribosomal RNA genes. Our results also show at which positions in the caecilian tree the addition of taxa have the greatest potential to increase phylogenetic information with respect to the controversial relationships of Scolecomorphus, Boulengerula, and all other teresomatan caecilians. These positions are, as intuitively expected, mostly (but not all) adjacent to the controversial branch. Generating whole mitogenomic and rag1 data for additional taxa joining the Scolecomorphus branch may be a more efficient strategy than sequencing a similar amount of additional nucleotides spread across the current caecilian taxon sampling. The methodology employed in this study allows an a priori evaluation and testable predictions of the appropriateness of particular experimental designs to solve specific questions at different levels of the caecilian phylogeny.}
}
Citation for Study 10063
Citation title:
"Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1".
This study was previously identified under the legacy study ID S2403
(Status: Published).
Citation
San mauro D., Gower D., Massingham T., Wilkinson M., Zardoya R., & Cotton J. 2009. Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1. Systematic Biology, 58: 425-438.
Authors
-
San mauro D.
-
Gower D.
-
Massingham T.
-
Wilkinson M.
-
Zardoya R.
-
Cotton J.
Abstract
In molecular phylogenetic studies, a major aspect of experimental design concerns the choice of markers and taxa. While previous studies have investigated the phylogenetic performance of different genes and the effectiveness of increasing taxon sampling, their conclusions are partly contradictory, probably because they are highly context specific and dependent on the group of organisms used in each study. Goldman (1998) introduced a method for experimental design in phylogenetics based on the expected information to be gained that has barely been used in practice. Here we use this method to explore the phylogenetic utility of mitochondrial (mt) genes, mt genomes, and nuclear rag1 for studies of the systematics of caecilian amphibians, as well as the effect of taxon addition on the stabilization of a controversial branch of the tree. Overall phylogenetic information estimates per gene, specific estimates per branch of the tree, estimates for combined (mitogenomic) data sets, and estimates as a hypothetical new taxon is added to different parts of the caecilian tree are calculated and compared. In general, the most informative data sets are those for mt transfer and ribosomal RNA genes. Our results also show at which positions in the caecilian tree the addition of taxa have the greatest potential to increase phylogenetic information with respect to the controversial relationships of Scolecomorphus, Boulengerula, and all other teresomatan caecilians. These positions are, as intuitively expected, mostly (but not all) adjacent to the controversial branch. Generating whole mitogenomic and rag1 data for additional taxa joining the Scolecomorphus branch may be a more efficient strategy than sequencing a similar amount of additional nucleotides spread across the current caecilian taxon sampling. The methodology employed in this study allows an a priori evaluation and testable predictions of the appropriateness of particular experimental designs to solve specific questions at different levels of the caecilian phylogeny.
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About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S10063
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@ARTICLE{TreeBASE2Ref18554,
author = {Diego San Mauro and David J. Gower and Tim Massingham and Mark Wilkinson and Rafael Zardoya and James A. Cotton},
title = {Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1},
year = {2009},
keywords = {},
doi = {10.1093/sysbio/syp043},
url = {},
pmid = {},
journal = {Systematic Biology},
volume = {58},
number = {},
pages = {425--438},
abstract = {In molecular phylogenetic studies, a major aspect of experimental design concerns the choice of markers and taxa. While previous studies have investigated the phylogenetic performance of different genes and the effectiveness of increasing taxon sampling, their conclusions are partly contradictory, probably because they are highly context specific and dependent on the group of organisms used in each study. Goldman (1998) introduced a method for experimental design in phylogenetics based on the expected information to be gained that has barely been used in practice. Here we use this method to explore the phylogenetic utility of mitochondrial (mt) genes, mt genomes, and nuclear rag1 for studies of the systematics of caecilian amphibians, as well as the effect of taxon addition on the stabilization of a controversial branch of the tree. Overall phylogenetic information estimates per gene, specific estimates per branch of the tree, estimates for combined (mitogenomic) data sets, and estimates as a hypothetical new taxon is added to different parts of the caecilian tree are calculated and compared. In general, the most informative data sets are those for mt transfer and ribosomal RNA genes. Our results also show at which positions in the caecilian tree the addition of taxa have the greatest potential to increase phylogenetic information with respect to the controversial relationships of Scolecomorphus, Boulengerula, and all other teresomatan caecilians. These positions are, as intuitively expected, mostly (but not all) adjacent to the controversial branch. Generating whole mitogenomic and rag1 data for additional taxa joining the Scolecomorphus branch may be a more efficient strategy than sequencing a similar amount of additional nucleotides spread across the current caecilian taxon sampling. The methodology employed in this study allows an a priori evaluation and testable predictions of the appropriateness of particular experimental designs to solve specific questions at different levels of the caecilian phylogeny.}
}
- Show RIS reference
TY - JOUR
ID - 18554
AU - San Mauro,Diego
AU - Gower,David J.
AU - Massingham,Tim
AU - Wilkinson,Mark
AU - Zardoya,Rafael
AU - Cotton,James A.
T1 - Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1
PY - 2009
UR - http://dx.doi.org/10.1093/sysbio/syp043
N2 - In molecular phylogenetic studies, a major aspect of experimental design concerns the choice of markers and taxa. While previous studies have investigated the phylogenetic performance of different genes and the effectiveness of increasing taxon sampling, their conclusions are partly contradictory, probably because they are highly context specific and dependent on the group of organisms used in each study. Goldman (1998) introduced a method for experimental design in phylogenetics based on the expected information to be gained that has barely been used in practice. Here we use this method to explore the phylogenetic utility of mitochondrial (mt) genes, mt genomes, and nuclear rag1 for studies of the systematics of caecilian amphibians, as well as the effect of taxon addition on the stabilization of a controversial branch of the tree. Overall phylogenetic information estimates per gene, specific estimates per branch of the tree, estimates for combined (mitogenomic) data sets, and estimates as a hypothetical new taxon is added to different parts of the caecilian tree are calculated and compared. In general, the most informative data sets are those for mt transfer and ribosomal RNA genes. Our results also show at which positions in the caecilian tree the addition of taxa have the greatest potential to increase phylogenetic information with respect to the controversial relationships of Scolecomorphus, Boulengerula, and all other teresomatan caecilians. These positions are, as intuitively expected, mostly (but not all) adjacent to the controversial branch. Generating whole mitogenomic and rag1 data for additional taxa joining the Scolecomorphus branch may be a more efficient strategy than sequencing a similar amount of additional nucleotides spread across the current caecilian taxon sampling. The methodology employed in this study allows an a priori evaluation and testable predictions of the appropriateness of particular experimental designs to solve specific questions at different levels of the caecilian phylogeny.
L3 - 10.1093/sysbio/syp043
JF - Systematic Biology
VL - 58
IS -
SP - 425
EP - 438
ER -
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