@ARTICLE{TreeBASE2Ref18194,
author = {Gert Worheide and Scott A. Nichols and Julia Goldberg},
title = {Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies},
year = {2004},
keywords = {},
doi = {},
url = {},
pmid = {},
journal = {Molecular Phylogenetics and Evolution},
volume = {},
number = {},
pages = {},
abstract = {The internal transcribed spacer regions (ITS1 and ITS2) of the tandemly repeated nuclear ribosomal DNA clusters are frequently used as markers for fine scale analyses in diverse animals. In certain taxa, ITS is nearly exclusively used for population level or inter-specific studies, despite the frequent presence of divergent paralogs within individual genomes that can be phylogenetically confounding. For the first time, we survey diverse marine sponges to determine the extent and phylogenetic implications of intragenomic polymorphisms (IGPs) exhibited at their ITS loci. We discover that the extent of IGP varies greatly between taxa (with most taxa exhibiting very few) and cannot be predicted by taxonomy. Furthermore, we demonstrate that ITS can be phylogenetically informative between species when moderate levels of IGPs are detected, but that ITS paralogy can interfere with population level studies. We caution against the routine use of ITS in phylogenetic studies of sponges without 1) screening for IGPs in every specimen sampled; 2) including all divergent paralogs in phylogenetic analyses; 3) testing ITS data using other single-copy, unlinked loci (such as nuclear introns).}
}
Citation for Study 1214
Citation title:
"Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies".
This study was previously identified under the legacy study ID S1127
(Status: Published).
Citation
Worheide G., Nichols S., & Goldberg J. 2004. Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies. Molecular Phylogenetics and Evolution, null.
Authors
-
Worheide G.
-
Nichols S.
-
Goldberg J.
Abstract
The internal transcribed spacer regions (ITS1 and ITS2) of the tandemly repeated nuclear ribosomal DNA clusters are frequently used as markers for fine scale analyses in diverse animals. In certain taxa, ITS is nearly exclusively used for population level or inter-specific studies, despite the frequent presence of divergent paralogs within individual genomes that can be phylogenetically confounding. For the first time, we survey diverse marine sponges to determine the extent and phylogenetic implications of intragenomic polymorphisms (IGPs) exhibited at their ITS loci. We discover that the extent of IGP varies greatly between taxa (with most taxa exhibiting very few) and cannot be predicted by taxonomy. Furthermore, we demonstrate that ITS can be phylogenetically informative between species when moderate levels of IGPs are detected, but that ITS paralogy can interfere with population level studies. We caution against the routine use of ITS in phylogenetic studies of sponges without 1) screening for IGPs in every specimen sampled; 2) including all divergent paralogs in phylogenetic analyses; 3) testing ITS data using other single-copy, unlinked loci (such as nuclear introns).
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S1214
- Other versions:
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- Show BibTeX reference
@ARTICLE{TreeBASE2Ref18194,
author = {Gert Worheide and Scott A. Nichols and Julia Goldberg},
title = {Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies},
year = {2004},
keywords = {},
doi = {},
url = {},
pmid = {},
journal = {Molecular Phylogenetics and Evolution},
volume = {},
number = {},
pages = {},
abstract = {The internal transcribed spacer regions (ITS1 and ITS2) of the tandemly repeated nuclear ribosomal DNA clusters are frequently used as markers for fine scale analyses in diverse animals. In certain taxa, ITS is nearly exclusively used for population level or inter-specific studies, despite the frequent presence of divergent paralogs within individual genomes that can be phylogenetically confounding. For the first time, we survey diverse marine sponges to determine the extent and phylogenetic implications of intragenomic polymorphisms (IGPs) exhibited at their ITS loci. We discover that the extent of IGP varies greatly between taxa (with most taxa exhibiting very few) and cannot be predicted by taxonomy. Furthermore, we demonstrate that ITS can be phylogenetically informative between species when moderate levels of IGPs are detected, but that ITS paralogy can interfere with population level studies. We caution against the routine use of ITS in phylogenetic studies of sponges without 1) screening for IGPs in every specimen sampled; 2) including all divergent paralogs in phylogenetic analyses; 3) testing ITS data using other single-copy, unlinked loci (such as nuclear introns).}
}
- Show RIS reference
TY - JOUR
ID - 18194
AU - Worheide,Gert
AU - Nichols,Scott A.
AU - Goldberg,Julia
T1 - Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies
PY - 2004
KW -
UR -
N2 - The internal transcribed spacer regions (ITS1 and ITS2) of the tandemly repeated nuclear ribosomal DNA clusters are frequently used as markers for fine scale analyses in diverse animals. In certain taxa, ITS is nearly exclusively used for population level or inter-specific studies, despite the frequent presence of divergent paralogs within individual genomes that can be phylogenetically confounding. For the first time, we survey diverse marine sponges to determine the extent and phylogenetic implications of intragenomic polymorphisms (IGPs) exhibited at their ITS loci. We discover that the extent of IGP varies greatly between taxa (with most taxa exhibiting very few) and cannot be predicted by taxonomy. Furthermore, we demonstrate that ITS can be phylogenetically informative between species when moderate levels of IGPs are detected, but that ITS paralogy can interfere with population level studies. We caution against the routine use of ITS in phylogenetic studies of sponges without 1) screening for IGPs in every specimen sampled; 2) including all divergent paralogs in phylogenetic analyses; 3) testing ITS data using other single-copy, unlinked loci (such as nuclear introns).
L3 -
JF - Molecular Phylogenetics and Evolution
VL -
IS -
ER -
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