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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 estimated from p-distances with SplitsTree and using the complete alignment from Giribeet et al. (2006) as in Figure 1, but without long-branch taxa (cephalopods, Cellana, Eulepetopsis, Peltodoris). Neither Bivalvia, nor Gastropoda are monophyletic. The Serialia are not supported.
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Figure 2: Neighbornet graph estimated from p-distances with SplitsTree and using the complete alignment from Giribeet et al. (2006) as in Figure 1, but without long-branch taxa (cephalopods, Cellana, Eulepetopsis, Peltodoris). Neither Bivalvia, nor Gastropoda are monophyletic. The Serialia are not supported.

Mentions: To reduce the noise in the original data set, we excluded the most conspicuous long branches identified visually in network analyses (cephalopods, and the three gastropods Cellana sp., Eulepetopsis vitrea and Peltodoris atromaculata, see Figs. 1 and Five). This selection (Fig. 2) does not improve the network, treeness is still missing, and there is a set of parallel edges separating a clade composed of the only monoplacophoran species and several Bivalvia species, the latter belonging to the highly derived Euheterodonta clade. Additional exclusion of gaps or application of substitution models altered the length of branches but not the general topology. Obviously, long branches are not the only cause for conflicts in this data set.


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 estimated from p-distances with SplitsTree and using the complete alignment from Giribeet et al. (2006) as in Figure 1, but without long-branch taxa (cephalopods, Cellana, Eulepetopsis, Peltodoris). Neither Bivalvia, nor Gastropoda are monophyletic. The Serialia are not supported.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Neighbornet graph estimated from p-distances with SplitsTree and using the complete alignment from Giribeet et al. (2006) as in Figure 1, but without long-branch taxa (cephalopods, Cellana, Eulepetopsis, Peltodoris). Neither Bivalvia, nor Gastropoda are monophyletic. The Serialia are not supported.
Mentions: To reduce the noise in the original data set, we excluded the most conspicuous long branches identified visually in network analyses (cephalopods, and the three gastropods Cellana sp., Eulepetopsis vitrea and Peltodoris atromaculata, see Figs. 1 and Five). This selection (Fig. 2) does not improve the network, treeness is still missing, and there is a set of parallel edges separating a clade composed of the only monoplacophoran species and several Bivalvia species, the latter belonging to the highly derived Euheterodonta clade. Additional exclusion of gaps or application of substitution models altered the length of branches but not the general topology. Obviously, long branches are not the only cause for conflicts in this data set.

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.