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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.


Bayesian analysis of original alignment (Giribet et al. 2006) after masking of random-like alignment regions with ALISCORE. .Monophyly of Bivalvia is supported except for the inclusion of Laevipilina in this clade (compare also with Figs. 1, 2, 3)
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Figure 5: Bayesian analysis of original alignment (Giribet et al. 2006) after masking of random-like alignment regions with ALISCORE. .Monophyly of Bivalvia is supported except for the inclusion of Laevipilina in this clade (compare also with Figs. 1, 2, 3)

Mentions: Application of SAMS was performed in order to identify conserved clade-supporting positions (= putative homologies) for Serialia within the 28S fragment of the original alignment. Note that SAMS does not need a tree. This application represents all splits in an alignment and identifies putative primary homologies. Fig. 4 shows the first 50 splits with the highest support. There are only few splits with distinct underlying nucleotide patterns. The best split contains a clade composed of the two patellogastropods Cellana sp. and Eulepetopsis vitrea (17 asymmetrical positions and 14 noisy positions), which is also the longest branch in Fig. 5. The next column represents the split between the cephalopod group Coleoida vs. all other taxa, with 10 asymmetrical positions supporting the functional outgroup and 8 conserved positions supporting the functional ingroup (Coleoida). For the more basal nodes of the mollusk tree no conserved nucleotide patterns can be detected (see also Fig. 6). No split with conserved homologies supporting the group {Polyplacophora + Laevipilina antarctica} is present.


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)

Bayesian analysis of original alignment (Giribet et al. 2006) after masking of random-like alignment regions with ALISCORE. .Monophyly of Bivalvia is supported except for the inclusion of Laevipilina in this clade (compare also with Figs. 1, 2, 3)
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Bayesian analysis of original alignment (Giribet et al. 2006) after masking of random-like alignment regions with ALISCORE. .Monophyly of Bivalvia is supported except for the inclusion of Laevipilina in this clade (compare also with Figs. 1, 2, 3)
Mentions: Application of SAMS was performed in order to identify conserved clade-supporting positions (= putative homologies) for Serialia within the 28S fragment of the original alignment. Note that SAMS does not need a tree. This application represents all splits in an alignment and identifies putative primary homologies. Fig. 4 shows the first 50 splits with the highest support. There are only few splits with distinct underlying nucleotide patterns. The best split contains a clade composed of the two patellogastropods Cellana sp. and Eulepetopsis vitrea (17 asymmetrical positions and 14 noisy positions), which is also the longest branch in Fig. 5. The next column represents the split between the cephalopod group Coleoida vs. all other taxa, with 10 asymmetrical positions supporting the functional outgroup and 8 conserved positions supporting the functional ingroup (Coleoida). For the more basal nodes of the mollusk tree no conserved nucleotide patterns can be detected (see also Fig. 6). No split with conserved homologies supporting the group {Polyplacophora + Laevipilina antarctica} is present.

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.