@ARTICLE{TreeBASE2Ref17624,
author = {Julian R. Starr and Stephen A. Harris and David A. Simpson},
title = {Potential of the 5' and 3' ends of the intergenic spacer (IGS) of rDNA in the Cyperaceae: new sequences for lower-level phylogenies in sedges with an example from Uncinia Pers.},
year = {2003},
keywords = {ETS; IGS; rDNA; phylogenetic utility; Cyperaceae; Juncaceae},
doi = {10.1086/346168},
url = {},
pmid = {},
journal = {International Journal of Plant Sciences},
volume = {164},
number = {2},
pages = {213?227},
abstract = {In plants, the internal transcribed spacers (ITS; ca. 450 base pairs) of nuclear ribosomal DNA (rDNA) are the only well?characterized nuclear sequences that are both easily amplified and appropriately variable for addressing relationships at lower taxonomic levels. In this study, we assess the utility of rDNA noncoding fragments from the external transcribed spacer 1 (ETS 1f) and from the 5? end of the intergenic spacer (5' IGSf) for reconstructing lower?level relationships in the Cyperaceae. Phylogenetic analyses using the genus Uncinia (tribe Cariceae) as a model indicate that phylogenies inferred from ETS 1f and 5' IGSf sequences are congruent with those derived from ITS. Although ITS and ETS 1f sequences evolve at similar rates, 5' IGSf sequences evolve ca. 1.3 times faster. The combined analysis of all three regions (ca. 1414 bp) produced 3.6 times more informative characters than ITS and greater than 40 times more than trnT?L and trnL?F spacer data. Trees derived from combined analyses were the most robust and resolved. Infraspecific variation in the ETS 1f (0.0%?0.17%) and 5' IGSf (0.0%) was extremely low, indicating that variation within species will not be a problem for phylogenetic analysis. Amplification experiments indicate that ETS 1f primers are universal for the Cyperaceae (ca. 5000 spp.) and Juncaceae (ca. 300 spp.), while 5' IGSf primers are limited to tribe Cariceae (ca. 2300 spp.). Phylogenetic analyses suggest that sections Uncinia and Platyandrae are monophyletic but that series circumscriptions are largely artificial. A significant topological difference with key taxonomic and biogeographical implications between ITS and combined analyses stresses the importance of using all three noncoding regions to infer lower?level phylogenies.}
}
Citation for Study 926
Citation title:
"Potential of the 5' and 3' ends of the intergenic spacer (IGS) of rDNA in the Cyperaceae: new sequences for lower-level phylogenies in sedges with an example from Uncinia Pers.".
This study was previously identified under the legacy study ID S803
(Status: Published).
Citation
Starr J., Harris S., & Simpson D. 2003. Potential of the 5' and 3' ends of the intergenic spacer (IGS) of rDNA in the Cyperaceae: new sequences for lower-level phylogenies in sedges with an example from Uncinia Pers. International Journal of Plant Sciences, 164(2): 213?227.
Authors
-
Starr J.
-
Harris S.
-
Simpson D.
Abstract
In plants, the internal transcribed spacers (ITS; ca. 450 base pairs) of nuclear ribosomal DNA (rDNA) are the only well?characterized nuclear sequences that are both easily amplified and appropriately variable for addressing relationships at lower taxonomic levels. In this study, we assess the utility of rDNA noncoding fragments from the external transcribed spacer 1 (ETS 1f) and from the 5? end of the intergenic spacer (5' IGSf) for reconstructing lower?level relationships in the Cyperaceae. Phylogenetic analyses using the genus Uncinia (tribe Cariceae) as a model indicate that phylogenies inferred from ETS 1f and 5' IGSf sequences are congruent with those derived from ITS. Although ITS and ETS 1f sequences evolve at similar rates, 5' IGSf sequences evolve ca. 1.3 times faster. The combined analysis of all three regions (ca. 1414 bp) produced 3.6 times more informative characters than ITS and greater than 40 times more than trnT?L and trnL?F spacer data. Trees derived from combined analyses were the most robust and resolved. Infraspecific variation in the ETS 1f (0.0%?0.17%) and 5' IGSf (0.0%) was extremely low, indicating that variation within species will not be a problem for phylogenetic analysis. Amplification experiments indicate that ETS 1f primers are universal for the Cyperaceae (ca. 5000 spp.) and Juncaceae (ca. 300 spp.), while 5' IGSf primers are limited to tribe Cariceae (ca. 2300 spp.). Phylogenetic analyses suggest that sections Uncinia and Platyandrae are monophyletic but that series circumscriptions are largely artificial. A significant topological difference with key taxonomic and biogeographical implications between ITS and combined analyses stresses the importance of using all three noncoding regions to infer lower?level phylogenies.
Keywords
ETS; IGS; rDNA; phylogenetic utility; Cyperaceae; Juncaceae
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S926
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- Show BibTeX reference
@ARTICLE{TreeBASE2Ref17624,
author = {Julian R. Starr and Stephen A. Harris and David A. Simpson},
title = {Potential of the 5' and 3' ends of the intergenic spacer (IGS) of rDNA in the Cyperaceae: new sequences for lower-level phylogenies in sedges with an example from Uncinia Pers.},
year = {2003},
keywords = {ETS; IGS; rDNA; phylogenetic utility; Cyperaceae; Juncaceae},
doi = {10.1086/346168},
url = {},
pmid = {},
journal = {International Journal of Plant Sciences},
volume = {164},
number = {2},
pages = {213?227},
abstract = {In plants, the internal transcribed spacers (ITS; ca. 450 base pairs) of nuclear ribosomal DNA (rDNA) are the only well?characterized nuclear sequences that are both easily amplified and appropriately variable for addressing relationships at lower taxonomic levels. In this study, we assess the utility of rDNA noncoding fragments from the external transcribed spacer 1 (ETS 1f) and from the 5? end of the intergenic spacer (5' IGSf) for reconstructing lower?level relationships in the Cyperaceae. Phylogenetic analyses using the genus Uncinia (tribe Cariceae) as a model indicate that phylogenies inferred from ETS 1f and 5' IGSf sequences are congruent with those derived from ITS. Although ITS and ETS 1f sequences evolve at similar rates, 5' IGSf sequences evolve ca. 1.3 times faster. The combined analysis of all three regions (ca. 1414 bp) produced 3.6 times more informative characters than ITS and greater than 40 times more than trnT?L and trnL?F spacer data. Trees derived from combined analyses were the most robust and resolved. Infraspecific variation in the ETS 1f (0.0%?0.17%) and 5' IGSf (0.0%) was extremely low, indicating that variation within species will not be a problem for phylogenetic analysis. Amplification experiments indicate that ETS 1f primers are universal for the Cyperaceae (ca. 5000 spp.) and Juncaceae (ca. 300 spp.), while 5' IGSf primers are limited to tribe Cariceae (ca. 2300 spp.). Phylogenetic analyses suggest that sections Uncinia and Platyandrae are monophyletic but that series circumscriptions are largely artificial. A significant topological difference with key taxonomic and biogeographical implications between ITS and combined analyses stresses the importance of using all three noncoding regions to infer lower?level phylogenies.}
}
- Show RIS reference
TY - JOUR
ID - 17624
AU - Starr,Julian R.
AU - Harris,Stephen A.
AU - Simpson,David A.
T1 - Potential of the 5' and 3' ends of the intergenic spacer (IGS) of rDNA in the Cyperaceae: new sequences for lower-level phylogenies in sedges with an example from Uncinia Pers.
PY - 2003
KW - ETS; IGS; rDNA; phylogenetic utility; Cyperaceae; Juncaceae
UR - http://dx.doi.org/10.1086/346168
N2 - In plants, the internal transcribed spacers (ITS; ca. 450 base pairs) of nuclear ribosomal DNA (rDNA) are the only well?characterized nuclear sequences that are both easily amplified and appropriately variable for addressing relationships at lower taxonomic levels. In this study, we assess the utility of rDNA noncoding fragments from the external transcribed spacer 1 (ETS 1f) and from the 5? end of the intergenic spacer (5' IGSf) for reconstructing lower?level relationships in the Cyperaceae. Phylogenetic analyses using the genus Uncinia (tribe Cariceae) as a model indicate that phylogenies inferred from ETS 1f and 5' IGSf sequences are congruent with those derived from ITS. Although ITS and ETS 1f sequences evolve at similar rates, 5' IGSf sequences evolve ca. 1.3 times faster. The combined analysis of all three regions (ca. 1414 bp) produced 3.6 times more informative characters than ITS and greater than 40 times more than trnT?L and trnL?F spacer data. Trees derived from combined analyses were the most robust and resolved. Infraspecific variation in the ETS 1f (0.0%?0.17%) and 5' IGSf (0.0%) was extremely low, indicating that variation within species will not be a problem for phylogenetic analysis. Amplification experiments indicate that ETS 1f primers are universal for the Cyperaceae (ca. 5000 spp.) and Juncaceae (ca. 300 spp.), while 5' IGSf primers are limited to tribe Cariceae (ca. 2300 spp.). Phylogenetic analyses suggest that sections Uncinia and Platyandrae are monophyletic but that series circumscriptions are largely artificial. A significant topological difference with key taxonomic and biogeographical implications between ITS and combined analyses stresses the importance of using all three noncoding regions to infer lower?level phylogenies.
L3 - 10.1086/346168
JF - International Journal of Plant Sciences
VL - 164
IS - 2
ER -