Phylogenetic support values are not necessarily informative : the case of the Serialia hypothesis (a mollusk phylogeny)

Background: Molecular phylogenies are being published increasingly and many biologists rely on the most recent topologies. However, different phylogenetic trees often contain conflicting results and contradict significan
Background: Molecular phylogenies are being published increasingly and many biologists rely on the most recent topologies. However, different phylogenetic trees often contain conflicting results and contradict significant background data. Not knowing how reliable traditional knowledge is, a crucial question concerns the quality of newly produced molecular data. The information content of DNA alignments is rarely discussed, as quality statements are mostly restricted to the statistical support of clades. Here we present a case study of a recently published mollusk phylogeny that contains surprising groupings, based on five genes and 108 species, and we apply new or rarely used tools for the analysis of the information content of alignments and for the filtering of noise (masking of random-like alignment regions, split decomposition, phylogenetic networks, quartet mapping). Results: The data are very fragmentary and contain contaminations. We show that that signal-like patterns in the data set are conflicting and partly not distinct and that the reported strong support for a "rather surprising result" (monoplacophorans and chitons form a monophylum Serialia) does not exist at the level of primary homologies. Split-decomposition, quartet mapping and neighbornet analyses reveal conflicting nucleotide patterns and lack of distinct phylogenetic signal for the deeper phylogeny of mollusks. Conclusion: Even though currently a majority of molecular phylogenies are being justified with reference to the 'statistical' support of clades in tree topologies, this confidence seems to be unfounded. Contradictions between phylogenies based on different analyses are already a strong indication of unnoticed pitfalls. The use of tree-independent tools for exploratory analyses of data quality are highly recommended. Concerning the new mollusk phylogeny more convincing evidence is needed.
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Metadaten
Author:Johann Wolfgang Wägele, Harald Letsch, Annette Klussmann-Kolb, Christoph Mayer, Bernhard Misof, Heike Wägele
URN:urn:nbn:de:hebis:30-64344
URL:http://www.frontiersinzoology.com/content/6/1/12
DOI:http://dx.doi.org/doi:10.1186/1742-9994-6-12
ISSN:1742-9994
Parent Title (English):Frontiers in zoology
Publisher:BioMed Central
Place of publication:London
Document Type:Article
Language:English
Date of Publication (online):2009/07/17
Date of first Publication:2009/06/26
Publishing Institution:Univ.-Bibliothek Frankfurt am Main
Release Date:2009/07/17
Volume:6
Issue:12
Pagenumber:15
First Page:1
Last Page:15
Note:
© 2009 Wägele et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
HeBIS PPN:214032817
Institutes:Biowissenschaften
Dewey Decimal Classification:570 Biowissenschaften; Biologie
Sammlungen:Universitätspublikationen
Sondersammelgebiets-Volltexte
Licence (German):License LogoCreative Commons - Namensnennung 2.0

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