Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences
The high sequence divergence within the small subunit ribosomal RNA gene (SSU rDNA) of foraminifera makes it difficult to establish the homology of individual nucleotides across taxa. Alignment-based approaches so far relied on time-consuming manual alignments and discarded up to 50% of the sequence...
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ftpubmed:oai:pubmedcentral.nih.gov:2808177 2023-05-15T18:00:35+02:00 Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences Aurahs, Ralf Göker, Markus Grimm, Guido W. Hemleben, Vera Hemleben, Christoph Schiebel, Ralf Kučera, Michal 2009-11-11 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808177 http://www.ncbi.nlm.nih.gov/pubmed/20140067 en eng Libertas Academica http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808177 http://www.ncbi.nlm.nih.gov/pubmed/20140067 Copyright © 2009 The authors. http://creativecommons.org/licenses/by/2.0 This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/2.0/). CC-BY Methodology Text 2009 ftpubmed 2013-09-02T20:41:48Z The high sequence divergence within the small subunit ribosomal RNA gene (SSU rDNA) of foraminifera makes it difficult to establish the homology of individual nucleotides across taxa. Alignment-based approaches so far relied on time-consuming manual alignments and discarded up to 50% of the sequenced nucleotides prior to phylogenetic inference. Here, we investigate the potential of the multiple analysis approach to infer a molecular phylogeny of all modern planktonic foraminiferal taxa by using a matrix of 146 new and 153 previously published SSU rDNA sequences. Our multiple analysis approach is based on eleven different automated alignments, analysed separately under the maximum likelihood criterion. The high degree of congruence between the phylogenies derived from our novel approach, traditional manually homologized culled alignments and the fossil record indicates that poorly resolved nucleotide homology does not represent the most significant obstacle when exploring the phylogenetic structure of the SSU rDNA in planktonic foraminifera. We show that approaches designed to extract phylogenetically valuable signals from complete sequences show more promise to resolve the backbone of the planktonic foraminifer tree than attempts to establish strictly homologous base calls in a manual alignment. Text Planktonic foraminifera PubMed Central (PMC) |
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English |
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Methodology |
spellingShingle |
Methodology Aurahs, Ralf Göker, Markus Grimm, Guido W. Hemleben, Vera Hemleben, Christoph Schiebel, Ralf Kučera, Michal Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences |
topic_facet |
Methodology |
description |
The high sequence divergence within the small subunit ribosomal RNA gene (SSU rDNA) of foraminifera makes it difficult to establish the homology of individual nucleotides across taxa. Alignment-based approaches so far relied on time-consuming manual alignments and discarded up to 50% of the sequenced nucleotides prior to phylogenetic inference. Here, we investigate the potential of the multiple analysis approach to infer a molecular phylogeny of all modern planktonic foraminiferal taxa by using a matrix of 146 new and 153 previously published SSU rDNA sequences. Our multiple analysis approach is based on eleven different automated alignments, analysed separately under the maximum likelihood criterion. The high degree of congruence between the phylogenies derived from our novel approach, traditional manually homologized culled alignments and the fossil record indicates that poorly resolved nucleotide homology does not represent the most significant obstacle when exploring the phylogenetic structure of the SSU rDNA in planktonic foraminifera. We show that approaches designed to extract phylogenetically valuable signals from complete sequences show more promise to resolve the backbone of the planktonic foraminifer tree than attempts to establish strictly homologous base calls in a manual alignment. |
format |
Text |
author |
Aurahs, Ralf Göker, Markus Grimm, Guido W. Hemleben, Vera Hemleben, Christoph Schiebel, Ralf Kučera, Michal |
author_facet |
Aurahs, Ralf Göker, Markus Grimm, Guido W. Hemleben, Vera Hemleben, Christoph Schiebel, Ralf Kučera, Michal |
author_sort |
Aurahs, Ralf |
title |
Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences |
title_short |
Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences |
title_full |
Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences |
title_fullStr |
Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences |
title_full_unstemmed |
Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences |
title_sort |
using the multiple analysis approach to reconstruct phylogenetic relationships among planktonic foraminifera from highly divergent and length-polymorphic ssu rdna sequences |
publisher |
Libertas Academica |
publishDate |
2009 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808177 http://www.ncbi.nlm.nih.gov/pubmed/20140067 |
genre |
Planktonic foraminifera |
genre_facet |
Planktonic foraminifera |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808177 http://www.ncbi.nlm.nih.gov/pubmed/20140067 |
op_rights |
Copyright © 2009 The authors. http://creativecommons.org/licenses/by/2.0 This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/2.0/). |
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CC-BY |
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1766169729700986880 |