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

Wägele JW, Letsch H, Klussmann-Kolb A, Mayer C, Misof B, Wägele H - Front. Zool. (2009)

Bottom Line: However, different phylogenetic trees often contain conflicting results and contradict significant background data.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53313 Bonn, Germany. w.waegele.zfmk@uni-bonn.de.

ABSTRACT

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 is highly recommended. Concerning the new mollusk phylogeny more convincing evidence is needed.

No MeSH data available.


Neighbornet graph for the 28S portion of the original alignment, the region for which data of Laevipilina is available. A set of short parallel edges supports a split that separates Laevipilina and most Polyplacophora (green), but a similar split unites Laevipilina with Bivalvia (red). The alignment does not contain a distinct nucleotide pattern supporting the Serialia.
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Figure 3: Neighbornet graph for the 28S portion of the original alignment, the region for which data of Laevipilina is available. A set of short parallel edges supports a split that separates Laevipilina and most Polyplacophora (green), but a similar split unites Laevipilina with Bivalvia (red). The alignment does not contain a distinct nucleotide pattern supporting the Serialia.

Mentions: In the network analysis of the original 28S rRNA fragment alignment we do find the Serialia group, at least at first sight, although the polyplacophoran Lepidopleurus cajetanus is not part of this clade (star in Fig. 3: placed at base of Brachiopod-Bivalvia 2 split). Exclusion of long-branch taxa (Cellana sp., Eulepetopsis vitrea, Creseis sp. and Cephalopoda) does not alter the network (Fig. 3), but the conflict in the data becomes more obvious. It is important to note that in this analysis, the support for a Serialia clade (excluding Lepidopleurus) is comparable to that of {Laevipilina and a subgroup of bivalves}, indicated by the length of the edges (green vs. red in Fig. 3). The weight (corresponding to branch length: [21]) for the first split is 0.0049, for the second split 0.0056.


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

Wägele JW, Letsch H, Klussmann-Kolb A, Mayer C, Misof B, Wägele H - Front. Zool. (2009)

Neighbornet graph for the 28S portion of the original alignment, the region for which data of Laevipilina is available. A set of short parallel edges supports a split that separates Laevipilina and most Polyplacophora (green), but a similar split unites Laevipilina with Bivalvia (red). The alignment does not contain a distinct nucleotide pattern supporting the Serialia.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2710323&req=5

Figure 3: Neighbornet graph for the 28S portion of the original alignment, the region for which data of Laevipilina is available. A set of short parallel edges supports a split that separates Laevipilina and most Polyplacophora (green), but a similar split unites Laevipilina with Bivalvia (red). The alignment does not contain a distinct nucleotide pattern supporting the Serialia.
Mentions: In the network analysis of the original 28S rRNA fragment alignment we do find the Serialia group, at least at first sight, although the polyplacophoran Lepidopleurus cajetanus is not part of this clade (star in Fig. 3: placed at base of Brachiopod-Bivalvia 2 split). Exclusion of long-branch taxa (Cellana sp., Eulepetopsis vitrea, Creseis sp. and Cephalopoda) does not alter the network (Fig. 3), but the conflict in the data becomes more obvious. It is important to note that in this analysis, the support for a Serialia clade (excluding Lepidopleurus) is comparable to that of {Laevipilina and a subgroup of bivalves}, indicated by the length of the edges (green vs. red in Fig. 3). The weight (corresponding to branch length: [21]) for the first split is 0.0049, for the second split 0.0056.

Bottom Line: However, different phylogenetic trees often contain conflicting results and contradict significant background data.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53313 Bonn, Germany. w.waegele.zfmk@uni-bonn.de.

ABSTRACT

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 is highly recommended. Concerning the new mollusk phylogeny more convincing evidence is needed.

No MeSH data available.