A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA
Identifying species is challenging in the case of organisms for which primarily molecular data are available. Even if morphological features are available, molecular taxonomy is often necessary to revise taxonomic concepts and to analyze environmental DNA sequences. However, clustering approaches to...
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ftdoajarticles:oai:doaj.org/article:1f3a62d7fbe94fd99fe32b1e72b3c8da 2023-05-15T18:00:30+02:00 A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA Markus Göker Guido W. Grimm Alexander F. Auch Ralf Aurahs Michal Kučera 2010-01-01T00:00:00Z https://doi.org/10.4137/EBO.S5504 https://doaj.org/article/1f3a62d7fbe94fd99fe32b1e72b3c8da EN eng SAGE Publishing https://doi.org/10.4137/EBO.S5504 https://doaj.org/toc/1176-9343 1176-9343 doi:10.4137/EBO.S5504 https://doaj.org/article/1f3a62d7fbe94fd99fe32b1e72b3c8da Evolutionary Bioinformatics, Vol 6 (2010) Evolution QH359-425 article 2010 ftdoajarticles https://doi.org/10.4137/EBO.S5504 2022-12-31T00:21:55Z Identifying species is challenging in the case of organisms for which primarily molecular data are available. Even if morphological features are available, molecular taxonomy is often necessary to revise taxonomic concepts and to analyze environmental DNA sequences. However, clustering approaches to delineate molecular operational taxonomic units often rely on arbitrary parameter choices. Also, distance calculation is difficult for highly alignment-ambiguous sequences. Here, we applied a recently described clustering optimization method to highly divergent planktonic foraminifera SSU rDNA sequences. We determined the distance function and the clustering setting that result in the highest agreement with morphological reference data. Alignment-free distance calculation, when adapted to the use with partly non-homologous sequences caused by distinct primer pairs, outperformed multiple sequence alignment. Clustering optimization offers new perspectives for the barcoding of species diversity and for environmental sequencing. It bridges the gap between traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both genetic divergence and given species concepts. Article in Journal/Newspaper Planktonic foraminifera Directory of Open Access Journals: DOAJ Articles Evolutionary Bioinformatics 6 EBO.S5504 |
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Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
topic |
Evolution QH359-425 |
spellingShingle |
Evolution QH359-425 Markus Göker Guido W. Grimm Alexander F. Auch Ralf Aurahs Michal Kučera A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA |
topic_facet |
Evolution QH359-425 |
description |
Identifying species is challenging in the case of organisms for which primarily molecular data are available. Even if morphological features are available, molecular taxonomy is often necessary to revise taxonomic concepts and to analyze environmental DNA sequences. However, clustering approaches to delineate molecular operational taxonomic units often rely on arbitrary parameter choices. Also, distance calculation is difficult for highly alignment-ambiguous sequences. Here, we applied a recently described clustering optimization method to highly divergent planktonic foraminifera SSU rDNA sequences. We determined the distance function and the clustering setting that result in the highest agreement with morphological reference data. Alignment-free distance calculation, when adapted to the use with partly non-homologous sequences caused by distinct primer pairs, outperformed multiple sequence alignment. Clustering optimization offers new perspectives for the barcoding of species diversity and for environmental sequencing. It bridges the gap between traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both genetic divergence and given species concepts. |
format |
Article in Journal/Newspaper |
author |
Markus Göker Guido W. Grimm Alexander F. Auch Ralf Aurahs Michal Kučera |
author_facet |
Markus Göker Guido W. Grimm Alexander F. Auch Ralf Aurahs Michal Kučera |
author_sort |
Markus Göker |
title |
A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA |
title_short |
A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA |
title_full |
A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA |
title_fullStr |
A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA |
title_full_unstemmed |
A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA |
title_sort |
clustering optimization strategy for molecular taxonomy applied to planktonic foraminifera ssu rdna |
publisher |
SAGE Publishing |
publishDate |
2010 |
url |
https://doi.org/10.4137/EBO.S5504 https://doaj.org/article/1f3a62d7fbe94fd99fe32b1e72b3c8da |
genre |
Planktonic foraminifera |
genre_facet |
Planktonic foraminifera |
op_source |
Evolutionary Bioinformatics, Vol 6 (2010) |
op_relation |
https://doi.org/10.4137/EBO.S5504 https://doaj.org/toc/1176-9343 1176-9343 doi:10.4137/EBO.S5504 https://doaj.org/article/1f3a62d7fbe94fd99fe32b1e72b3c8da |
op_doi |
https://doi.org/10.4137/EBO.S5504 |
container_title |
Evolutionary Bioinformatics |
container_volume |
6 |
container_start_page |
EBO.S5504 |
_version_ |
1766169618468044800 |