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Molecular evolution of rDNA in early diverging Metazoa: first comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera.

Voigt O, Erpenbeck D, Wörheide G - BMC Evol. Biol. (2008)

Bottom Line: We found base compositional and structural differences in SSU rRNA among Demospongiae, Hexactinellida (glass sponges) and Calcarea (calcareous sponges).Therefore, these features can provide alternative support for sequence-based topologies and give insights into the evolution of the molecule itself.To encourage and facilitate the application of rRNA models in phylogenetics of early metazoans, we present 52 SSU rRNA secondary structures over the taxonomic range of Porifera in a database, along with some basic tools for relevant format-conversion.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dept. of Geobiology, Geoscience Centre Göttingen, University of Göttingen, D-37077 Göttingen, Germany. ovoigt@gwdg.de

ABSTRACT

Background: The cytoplasmic ribosomal small subunit (SSU, 18S) ribosomal RNA (rRNA) is the most frequently-used gene for molecular phylogenetic studies. However, information regarding its secondary structure is neglected in most phylogenetic analyses. Incorporation of this information is essential in order to apply specific rRNA evolutionary models to overcome the problem of co-evolution of paired sites, which violates the basic assumption of the independent evolution of sites made by most phylogenetic methods. Information about secondary structure also supports the process of aligning rRNA sequences across taxa. Both aspects have been shown to increase the accuracy of phylogenetic reconstructions within various taxa.Here, we explore SSU rRNA secondary structures from the three extant classes of Phylum Porifera (Grant, 1836), a pivotal, but largely unresolved taxon of early branching Metazoa. This is the first phylogenetic study of poriferan SSU rRNA data to date that includes detailed comparative secondary structure information for all three sponge classes.

Results: We found base compositional and structural differences in SSU rRNA among Demospongiae, Hexactinellida (glass sponges) and Calcarea (calcareous sponges). We showed that analyses of primary rRNA sequences, including secondary structure-specific evolutionary models, in combination with reconstruction of the evolution of unusual structural features, reveal a substantial amount of additional information. Of special note was the finding that the gene tree topologies of marine haplosclerid demosponges, which are inconsistent with the current morphology-based classification, are supported by our reconstructed evolution of secondary structure features. Therefore, these features can provide alternative support for sequence-based topologies and give insights into the evolution of the molecule itself. To encourage and facilitate the application of rRNA models in phylogenetics of early metazoans, we present 52 SSU rRNA secondary structures over the taxonomic range of Porifera in a database, along with some basic tools for relevant format-conversion.

Conclusion: We demonstrated that sophisticated secondary structure analyses can increase the potential phylogenetic information of already available rDNA sequences currently accessible in databases and conclude that the importance of SSU rRNA secondary structure information for phylogenetic reconstruction is still generally underestimated, at least among certain early branching metazoans.

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Related in: MedlinePlus

Phylogeny inferred with PHASE. Nodes that differ from the topology published by Redmond et al. [41] are encircled. The boxed clades correspond to the excerpt displayed in Fig. 6. Support values are given at, or close to the corresponding node (values from analyses with PHASE/MrBayes; where the same support values were found in both analyses, only one number is shown; '<' = support values below 50; '-' = node not recovered in MrBayes analysis.). Monophyletic higher taxa are assigned.
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Figure 5: Phylogeny inferred with PHASE. Nodes that differ from the topology published by Redmond et al. [41] are encircled. The boxed clades correspond to the excerpt displayed in Fig. 6. Support values are given at, or close to the corresponding node (values from analyses with PHASE/MrBayes; where the same support values were found in both analyses, only one number is shown; '<' = support values below 50; '-' = node not recovered in MrBayes analysis.). Monophyletic higher taxa are assigned.

Mentions: Most demosponges possess a SSU rRNA molecule with the common metazoan secondary structure. Remarkable exceptions are only found within the marine Haplosclerida (Figs. 4, 5, 6), which possess insertions that are long enough to be predicted to form additional helices. Those helices are found within known variable regions for eukaryotes and appear in the 5' strand of Helix E23_1/2, the 5'strand within Helix E23_14 and the 3' strand of helix 43.


Molecular evolution of rDNA in early diverging Metazoa: first comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera.

Voigt O, Erpenbeck D, Wörheide G - BMC Evol. Biol. (2008)

Phylogeny inferred with PHASE. Nodes that differ from the topology published by Redmond et al. [41] are encircled. The boxed clades correspond to the excerpt displayed in Fig. 6. Support values are given at, or close to the corresponding node (values from analyses with PHASE/MrBayes; where the same support values were found in both analyses, only one number is shown; '<' = support values below 50; '-' = node not recovered in MrBayes analysis.). Monophyletic higher taxa are assigned.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2289807&req=5

Figure 5: Phylogeny inferred with PHASE. Nodes that differ from the topology published by Redmond et al. [41] are encircled. The boxed clades correspond to the excerpt displayed in Fig. 6. Support values are given at, or close to the corresponding node (values from analyses with PHASE/MrBayes; where the same support values were found in both analyses, only one number is shown; '<' = support values below 50; '-' = node not recovered in MrBayes analysis.). Monophyletic higher taxa are assigned.
Mentions: Most demosponges possess a SSU rRNA molecule with the common metazoan secondary structure. Remarkable exceptions are only found within the marine Haplosclerida (Figs. 4, 5, 6), which possess insertions that are long enough to be predicted to form additional helices. Those helices are found within known variable regions for eukaryotes and appear in the 5' strand of Helix E23_1/2, the 5'strand within Helix E23_14 and the 3' strand of helix 43.

Bottom Line: We found base compositional and structural differences in SSU rRNA among Demospongiae, Hexactinellida (glass sponges) and Calcarea (calcareous sponges).Therefore, these features can provide alternative support for sequence-based topologies and give insights into the evolution of the molecule itself.To encourage and facilitate the application of rRNA models in phylogenetics of early metazoans, we present 52 SSU rRNA secondary structures over the taxonomic range of Porifera in a database, along with some basic tools for relevant format-conversion.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dept. of Geobiology, Geoscience Centre Göttingen, University of Göttingen, D-37077 Göttingen, Germany. ovoigt@gwdg.de

ABSTRACT

Background: The cytoplasmic ribosomal small subunit (SSU, 18S) ribosomal RNA (rRNA) is the most frequently-used gene for molecular phylogenetic studies. However, information regarding its secondary structure is neglected in most phylogenetic analyses. Incorporation of this information is essential in order to apply specific rRNA evolutionary models to overcome the problem of co-evolution of paired sites, which violates the basic assumption of the independent evolution of sites made by most phylogenetic methods. Information about secondary structure also supports the process of aligning rRNA sequences across taxa. Both aspects have been shown to increase the accuracy of phylogenetic reconstructions within various taxa.Here, we explore SSU rRNA secondary structures from the three extant classes of Phylum Porifera (Grant, 1836), a pivotal, but largely unresolved taxon of early branching Metazoa. This is the first phylogenetic study of poriferan SSU rRNA data to date that includes detailed comparative secondary structure information for all three sponge classes.

Results: We found base compositional and structural differences in SSU rRNA among Demospongiae, Hexactinellida (glass sponges) and Calcarea (calcareous sponges). We showed that analyses of primary rRNA sequences, including secondary structure-specific evolutionary models, in combination with reconstruction of the evolution of unusual structural features, reveal a substantial amount of additional information. Of special note was the finding that the gene tree topologies of marine haplosclerid demosponges, which are inconsistent with the current morphology-based classification, are supported by our reconstructed evolution of secondary structure features. Therefore, these features can provide alternative support for sequence-based topologies and give insights into the evolution of the molecule itself. To encourage and facilitate the application of rRNA models in phylogenetics of early metazoans, we present 52 SSU rRNA secondary structures over the taxonomic range of Porifera in a database, along with some basic tools for relevant format-conversion.

Conclusion: We demonstrated that sophisticated secondary structure analyses can increase the potential phylogenetic information of already available rDNA sequences currently accessible in databases and conclude that the importance of SSU rRNA secondary structure information for phylogenetic reconstruction is still generally underestimated, at least among certain early branching metazoans.

Show MeSH
Related in: MedlinePlus