Close
Help




JOURNAL

Evolutionary Bioinformatics

A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA

Submit a Paper


Evolutionary Bioinformatics 2010:6 97-112

Original Research

Published on 09 Sep 2010

DOI: 10.4137/EBO.S5504


Further metadata provided in PDF



Sign up for email alerts to receive notifications of new articles published in Evolutionary Bioinformatics

Abstract

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.



Downloads

PDF  (791.93 KB PDF FORMAT)

RIS citation   (ENDNOTE, REFERENCE MANAGER, PROCITE, REFWORKS)

Supplementary Files 1  (1.62 MB ZIP FORMAT)

BibTex citation   (BIBDESK, LATEX)

XML




What Your Colleagues Say About Evolutionary Bioinformatics
Having just published in a Libertas Academica journal (Evolutionary Bioinformatics) for the first time, I can attest that I was impressed by the process. Every stage from submission to typesetting and correspondence on matters relating to publishing was simple and efficient. In addition to this, regular updates of the status of the manuscript (with clear explanation of the status) enabled the process to be transparent and informative. I would not hesitate to use Libertas Academica ...
Dr Kevin Arbuckle (University of Liverpool, Merseyside, UK)
More Testimonials

Quick Links


New article and journal news notification services