@ARTICLE{TreeBASE2Ref18651,
author = {Robert C. Thomson and H. Bradley Shaffer},
title = {Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles},
year = {2010},
keywords = {10.1093/sysbio/syp075},
doi = {10.1093/sysbio/syp075},
url = {},
pmid = {},
journal = {Systematic Biology},
volume = {59},
number = {1},
pages = {42--58},
abstract = {As phylogenetic datasets grow in size and number, objective methods to summarize this information are becoming increasingly important. Supermatrices can combine existing data directly, and in principle provide effective syntheses of phylogenetic information that may reveal new relationships. However, several serious difficulties exist in the construction of large supermatrices that must be overcome before these approaches will enjoy broad utility. We present analyses that examine the performance of sparse supermatrices constructed from large sequence databases for the reconstruction of species-level phylogenies. We develop a largely automated informatics pipeline that allows for the construction of sparse supermatrices from GenBank data. In doing so, we develop novel strategies for alleviating some of the outstanding impediments to accurate phylogenetic inference using these approaches. These include taxonomic standardization, automated alignment, and the identification of rogue taxa. We use turtles as an exemplar clade and present a well-supported species-level phylogeny for two thirds of all turtle species based on a ~50kb supermatrix consisting of 93% missing data. Finally, we discuss some of the remaining pitfalls and concerns associated with supermatrix analyses, provide comparisons to supertree approaches, and suggest areas for future research.}
}
Citation for Study 10160
Citation title:
"Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles".
This study was previously identified under the legacy study ID S2504
(Status: Published).
Citation
Thomson R.C., & Shaffer H. 2010. Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles. Systematic Biology, 59(1): 42-58.
Authors
Abstract
As phylogenetic datasets grow in size and number, objective methods to summarize this information are becoming increasingly important. Supermatrices can combine existing data directly, and in principle provide effective syntheses of phylogenetic information that may reveal new relationships. However, several serious difficulties exist in the construction of large supermatrices that must be overcome before these approaches will enjoy broad utility. We present analyses that examine the performance of sparse supermatrices constructed from large sequence databases for the reconstruction of species-level phylogenies. We develop a largely automated informatics pipeline that allows for the construction of sparse supermatrices from GenBank data. In doing so, we develop novel strategies for alleviating some of the outstanding impediments to accurate phylogenetic inference using these approaches. These include taxonomic standardization, automated alignment, and the identification of rogue taxa. We use turtles as an exemplar clade and present a well-supported species-level phylogeny for two thirds of all turtle species based on a ~50kb supermatrix consisting of 93% missing data. Finally, we discuss some of the remaining pitfalls and concerns associated with supermatrix analyses, provide comparisons to supertree approaches, and suggest areas for future research.
Keywords
10.1093/sysbio/syp075
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S10160
- Other versions:
Nexus
NeXML
- Show BibTeX reference
@ARTICLE{TreeBASE2Ref18651,
author = {Robert C. Thomson and H. Bradley Shaffer},
title = {Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles},
year = {2010},
keywords = {10.1093/sysbio/syp075},
doi = {10.1093/sysbio/syp075},
url = {},
pmid = {},
journal = {Systematic Biology},
volume = {59},
number = {1},
pages = {42--58},
abstract = {As phylogenetic datasets grow in size and number, objective methods to summarize this information are becoming increasingly important. Supermatrices can combine existing data directly, and in principle provide effective syntheses of phylogenetic information that may reveal new relationships. However, several serious difficulties exist in the construction of large supermatrices that must be overcome before these approaches will enjoy broad utility. We present analyses that examine the performance of sparse supermatrices constructed from large sequence databases for the reconstruction of species-level phylogenies. We develop a largely automated informatics pipeline that allows for the construction of sparse supermatrices from GenBank data. In doing so, we develop novel strategies for alleviating some of the outstanding impediments to accurate phylogenetic inference using these approaches. These include taxonomic standardization, automated alignment, and the identification of rogue taxa. We use turtles as an exemplar clade and present a well-supported species-level phylogeny for two thirds of all turtle species based on a ~50kb supermatrix consisting of 93% missing data. Finally, we discuss some of the remaining pitfalls and concerns associated with supermatrix analyses, provide comparisons to supertree approaches, and suggest areas for future research.}
}
- Show RIS reference
TY - JOUR
ID - 18651
AU - Thomson,Robert C.
AU - Shaffer,H. Bradley
T1 - Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles
PY - 2010
KW - 10.1093/sysbio/syp075
UR - http://dx.doi.org/10.1093/sysbio/syp075
N2 - As phylogenetic datasets grow in size and number, objective methods to summarize this information are becoming increasingly important. Supermatrices can combine existing data directly, and in principle provide effective syntheses of phylogenetic information that may reveal new relationships. However, several serious difficulties exist in the construction of large supermatrices that must be overcome before these approaches will enjoy broad utility. We present analyses that examine the performance of sparse supermatrices constructed from large sequence databases for the reconstruction of species-level phylogenies. We develop a largely automated informatics pipeline that allows for the construction of sparse supermatrices from GenBank data. In doing so, we develop novel strategies for alleviating some of the outstanding impediments to accurate phylogenetic inference using these approaches. These include taxonomic standardization, automated alignment, and the identification of rogue taxa. We use turtles as an exemplar clade and present a well-supported species-level phylogeny for two thirds of all turtle species based on a ~50kb supermatrix consisting of 93% missing data. Finally, we discuss some of the remaining pitfalls and concerns associated with supermatrix analyses, provide comparisons to supertree approaches, and suggest areas for future research.
L3 - 10.1093/sysbio/syp075
JF - Systematic Biology
VL - 59
IS - 1
SP - 42
EP - 58
ER -
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