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New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias.

Nesnidal MP, Helmkampf M, Meyer A, Witek A, Bruchhaus I, Ebersberger I, Hankeln T, Lieb B, Struck TH, Hausdorf B - BMC Evol. Biol. (2013)

Bottom Line: Our results contrast previous findings based on rDNA sequences and phylogenomic datasets which supported monophyletic Polyzoa (= Bryozoa sensu lato) including Ectoprocta, Entoprocta and Cycliophora, Brachiozoa including Brachiopoda and Phoronida as well as Kryptrochozoa including Brachiopoda, Phoronida and Nemertea, thus rendering Lophophorata polyphyletic.Our attempts to identify the causes for the conflicting results revealed that Polyzoa, Brachiozoa and Kryptrochozoa are supported by character subsets with deviating amino acid compositions, whereas there is no indication for compositional heterogeneity in the character subsets supporting the monophyly of Lophophorata.This suggests that the cleavage pattern is highly plastic and has changed several times within lophophorates.

View Article: PubMed Central - HTML - PubMed

Affiliation: Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany. hausdorf@zoologie.uni-hamburg.de.

ABSTRACT

Background: Within the complex metazoan phylogeny, the relationships of the three lophophorate lineages, ectoprocts, brachiopods and phoronids, are particularly elusive. To shed further light on this issue, we present phylogenomic analyses of 196 genes from 58 bilaterian taxa, paying particular attention to the influence of compositional heterogeneity.

Results: The phylogenetic analyses strongly support the monophyly of Lophophorata and a sister-group relationship between Ectoprocta and Phoronida. Our results contrast previous findings based on rDNA sequences and phylogenomic datasets which supported monophyletic Polyzoa (= Bryozoa sensu lato) including Ectoprocta, Entoprocta and Cycliophora, Brachiozoa including Brachiopoda and Phoronida as well as Kryptrochozoa including Brachiopoda, Phoronida and Nemertea, thus rendering Lophophorata polyphyletic. Our attempts to identify the causes for the conflicting results revealed that Polyzoa, Brachiozoa and Kryptrochozoa are supported by character subsets with deviating amino acid compositions, whereas there is no indication for compositional heterogeneity in the character subsets supporting the monophyly of Lophophorata.

Conclusion: Our results indicate that the support for Polyzoa, Brachiozoa and Kryptrochozoa gathered so far is likely an artifact caused by compositional bias. The monophyly of Lophophorata implies that the horseshoe-shaped mesosomal lophophore, the tentacular feeding apparatus of ectoprocts, phoronids and brachiopods is, indeed, a synapomorphy of the lophophorate lineages. The same may apply to radial cleavage. However, among phoronids also spiral cleavage is known. This suggests that the cleavage pattern is highly plastic and has changed several times within lophophorates. The sister group relationship of ectoprocts and phoronids is in accordance with the interpretation of the eversion of a ventral invagination at the beginning of metamorphosis as a common derived feature of these taxa.

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Bayesian inference reconstruction with the CAT model based on 41,292 amino acid positions derived from 196 proteins of 58 taxa. Bayesian posterior probabilities are shown to the right of the nodes; posterior probabilities equal to 1.0 are indicated by black circles. The colour of the branches visualizes the percentage of missing data.
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Figure 1: Bayesian inference reconstruction with the CAT model based on 41,292 amino acid positions derived from 196 proteins of 58 taxa. Bayesian posterior probabilities are shown to the right of the nodes; posterior probabilities equal to 1.0 are indicated by black circles. The colour of the branches visualizes the percentage of missing data.

Mentions: The complete dataset that we compiled for the phylogenomic analysis of the relationships of the lophophorate lineages comprised 196 genes from 58 metazoan taxa. The corresponding super-alignment spans 41,292 amino acid positions and has 50.4% data coverage. A PhyloBayes analysis of this dataset with the CAT model (Figure 1) revealed strong support for the monophyly of Lophophorata (Bayesian posterior probability (BPP): 0.99) and the monophyly of Ectoprocta + Phoronida (BPP: 0.99). A maximum likelihood analysis with the LG model (Figure 2) confirmed these relationships, albeit without statistical support or only weak support (bootstrap support (BS) for Lophophorata: 37%; for Ectoprocta + Phoronida: 55%). A selection of those positions from the complete dataset where data are available from at least 50% of all included taxa increased data coverage to 72.4%. The percentage of known character states increased especially in the less well-covered smaller phyla that are the focus of our study (compare the colour coding of the branches in Figures 1 and 2 versus Figures 3 and 4). This can also been seen in density distributions of shared missing data, which is strongly shifted to lower values in the reduced dataset (compare Additional file 1: Figure S1 and Additional file 2: Figure S2). Phylogenomic analyses of this dataset encompassing 15,849 sites (Figures 3 and 4) confirmed the monophyly of Lophophorata (BPPred: 1.00; BSred: 37%) and the monophyly of Ectoprocta + Phoronida (BPPred: 1.00; BSred: 57%) and, thus, show that these groupings are not artifacts resulting from the amount of missing data. However, rather than based solely on the amount of missing data artificial signal for a grouping of taxa might also stem from a strong degree of overlap in missing data shared between taxa, if the missing data are not randomly distributed across the taxa, but are systematically biased [54-56]. Hierarchical clustering analyses based on the degree of overlap in missing data shared between taxa (Additional file 1: Figure S1 and Additional file 2: Figure S2) corroborate that neither Lophophorata nor Ectoprocta + Phoronida are artifacts caused by shared missing data. The taxa belonging to these groups do not cluster in these analyses, but are scattered among other lophotrochozoan taxa.


New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias.

Nesnidal MP, Helmkampf M, Meyer A, Witek A, Bruchhaus I, Ebersberger I, Hankeln T, Lieb B, Struck TH, Hausdorf B - BMC Evol. Biol. (2013)

Bayesian inference reconstruction with the CAT model based on 41,292 amino acid positions derived from 196 proteins of 58 taxa. Bayesian posterior probabilities are shown to the right of the nodes; posterior probabilities equal to 1.0 are indicated by black circles. The colour of the branches visualizes the percentage of missing data.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4225663&req=5

Figure 1: Bayesian inference reconstruction with the CAT model based on 41,292 amino acid positions derived from 196 proteins of 58 taxa. Bayesian posterior probabilities are shown to the right of the nodes; posterior probabilities equal to 1.0 are indicated by black circles. The colour of the branches visualizes the percentage of missing data.
Mentions: The complete dataset that we compiled for the phylogenomic analysis of the relationships of the lophophorate lineages comprised 196 genes from 58 metazoan taxa. The corresponding super-alignment spans 41,292 amino acid positions and has 50.4% data coverage. A PhyloBayes analysis of this dataset with the CAT model (Figure 1) revealed strong support for the monophyly of Lophophorata (Bayesian posterior probability (BPP): 0.99) and the monophyly of Ectoprocta + Phoronida (BPP: 0.99). A maximum likelihood analysis with the LG model (Figure 2) confirmed these relationships, albeit without statistical support or only weak support (bootstrap support (BS) for Lophophorata: 37%; for Ectoprocta + Phoronida: 55%). A selection of those positions from the complete dataset where data are available from at least 50% of all included taxa increased data coverage to 72.4%. The percentage of known character states increased especially in the less well-covered smaller phyla that are the focus of our study (compare the colour coding of the branches in Figures 1 and 2 versus Figures 3 and 4). This can also been seen in density distributions of shared missing data, which is strongly shifted to lower values in the reduced dataset (compare Additional file 1: Figure S1 and Additional file 2: Figure S2). Phylogenomic analyses of this dataset encompassing 15,849 sites (Figures 3 and 4) confirmed the monophyly of Lophophorata (BPPred: 1.00; BSred: 37%) and the monophyly of Ectoprocta + Phoronida (BPPred: 1.00; BSred: 57%) and, thus, show that these groupings are not artifacts resulting from the amount of missing data. However, rather than based solely on the amount of missing data artificial signal for a grouping of taxa might also stem from a strong degree of overlap in missing data shared between taxa, if the missing data are not randomly distributed across the taxa, but are systematically biased [54-56]. Hierarchical clustering analyses based on the degree of overlap in missing data shared between taxa (Additional file 1: Figure S1 and Additional file 2: Figure S2) corroborate that neither Lophophorata nor Ectoprocta + Phoronida are artifacts caused by shared missing data. The taxa belonging to these groups do not cluster in these analyses, but are scattered among other lophotrochozoan taxa.

Bottom Line: Our results contrast previous findings based on rDNA sequences and phylogenomic datasets which supported monophyletic Polyzoa (= Bryozoa sensu lato) including Ectoprocta, Entoprocta and Cycliophora, Brachiozoa including Brachiopoda and Phoronida as well as Kryptrochozoa including Brachiopoda, Phoronida and Nemertea, thus rendering Lophophorata polyphyletic.Our attempts to identify the causes for the conflicting results revealed that Polyzoa, Brachiozoa and Kryptrochozoa are supported by character subsets with deviating amino acid compositions, whereas there is no indication for compositional heterogeneity in the character subsets supporting the monophyly of Lophophorata.This suggests that the cleavage pattern is highly plastic and has changed several times within lophophorates.

View Article: PubMed Central - HTML - PubMed

Affiliation: Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany. hausdorf@zoologie.uni-hamburg.de.

ABSTRACT

Background: Within the complex metazoan phylogeny, the relationships of the three lophophorate lineages, ectoprocts, brachiopods and phoronids, are particularly elusive. To shed further light on this issue, we present phylogenomic analyses of 196 genes from 58 bilaterian taxa, paying particular attention to the influence of compositional heterogeneity.

Results: The phylogenetic analyses strongly support the monophyly of Lophophorata and a sister-group relationship between Ectoprocta and Phoronida. Our results contrast previous findings based on rDNA sequences and phylogenomic datasets which supported monophyletic Polyzoa (= Bryozoa sensu lato) including Ectoprocta, Entoprocta and Cycliophora, Brachiozoa including Brachiopoda and Phoronida as well as Kryptrochozoa including Brachiopoda, Phoronida and Nemertea, thus rendering Lophophorata polyphyletic. Our attempts to identify the causes for the conflicting results revealed that Polyzoa, Brachiozoa and Kryptrochozoa are supported by character subsets with deviating amino acid compositions, whereas there is no indication for compositional heterogeneity in the character subsets supporting the monophyly of Lophophorata.

Conclusion: Our results indicate that the support for Polyzoa, Brachiozoa and Kryptrochozoa gathered so far is likely an artifact caused by compositional bias. The monophyly of Lophophorata implies that the horseshoe-shaped mesosomal lophophore, the tentacular feeding apparatus of ectoprocts, phoronids and brachiopods is, indeed, a synapomorphy of the lophophorate lineages. The same may apply to radial cleavage. However, among phoronids also spiral cleavage is known. This suggests that the cleavage pattern is highly plastic and has changed several times within lophophorates. The sister group relationship of ectoprocts and phoronids is in accordance with the interpretation of the eversion of a ventral invagination at the beginning of metamorphosis as a common derived feature of these taxa.

Show MeSH
Related in: MedlinePlus