Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences
The high sequence divergence within the small subunit ribosomal RNA gene (SSU rDNA) of foraminifera makes it difficult to establish the homology of individual nucleotides across taxa. Alignment-based approaches so far relied on time-consuming manual alignments and discarded up to 50% of the sequence...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
SAGE Publishing
2009-11-01
|
| Series: | Bioinformatics and Biology Insights |
| Online Access: | http://la-press.com/using-the-multiple-analysis-approach-to-reconstruct-phylogenetic-relat-a1734 |
| _version_ | 1811258517149974528 |
|---|---|
| author | Ralf Aurahs Markus Göker Guido W. Grimm Vera Hemleben Christoph Hemleben Ralf Schiebel Michal Kučera |
| author_facet | Ralf Aurahs Markus Göker Guido W. Grimm Vera Hemleben Christoph Hemleben Ralf Schiebel Michal Kučera |
| author_sort | Ralf Aurahs |
| collection | DOAJ |
| description | The high sequence divergence within the small subunit ribosomal RNA gene (SSU rDNA) of foraminifera makes it difficult to establish the homology of individual nucleotides across taxa. Alignment-based approaches so far relied on time-consuming manual alignments and discarded up to 50% of the sequenced nucleotides prior to phylogenetic inference. Here, we investigate the potential of the multiple analysis approach to infer a molecular phylogeny of all modern planktonic foraminiferal taxa by using a matrix of 146 new and 153 previously published SSU rDNA sequences. Our multiple analysis approach is based on eleven different automated alignments, analysed separately under the maximum likelihood criterion. The high degree of congruence between the phylogenies derived from our novel approach, traditional manually homologized culled alignments and the fossil record indicates that poorly resolved nucleotide homology does not represent the most significant obstacle when exploring the phylogenetic structure of the SSU rDNA in planktonic foraminifera. We show that approaches designed to extract phylogenetically valuable signals from complete sequences show more promise to resolve the backbone of the planktonic foraminifer tree than attempts to establish strictly homologous base calls in a manual alignment. |
| first_indexed | 2024-04-12T18:14:55Z |
| format | Article |
| id | doaj.art-6d758312562e42a6afd17d370b8fccf6 |
| institution | Directory Open Access Journal |
| issn | 1177-9322 |
| language | English |
| last_indexed | 2024-04-12T18:14:55Z |
| publishDate | 2009-11-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Bioinformatics and Biology Insights |
| spelling | doaj.art-6d758312562e42a6afd17d370b8fccf62022-12-22T03:21:40ZengSAGE PublishingBioinformatics and Biology Insights1177-93222009-11-0120093155177Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA SequencesRalf AurahsMarkus GökerGuido W. GrimmVera HemlebenChristoph HemlebenRalf SchiebelMichal KučeraThe high sequence divergence within the small subunit ribosomal RNA gene (SSU rDNA) of foraminifera makes it difficult to establish the homology of individual nucleotides across taxa. Alignment-based approaches so far relied on time-consuming manual alignments and discarded up to 50% of the sequenced nucleotides prior to phylogenetic inference. Here, we investigate the potential of the multiple analysis approach to infer a molecular phylogeny of all modern planktonic foraminiferal taxa by using a matrix of 146 new and 153 previously published SSU rDNA sequences. Our multiple analysis approach is based on eleven different automated alignments, analysed separately under the maximum likelihood criterion. The high degree of congruence between the phylogenies derived from our novel approach, traditional manually homologized culled alignments and the fossil record indicates that poorly resolved nucleotide homology does not represent the most significant obstacle when exploring the phylogenetic structure of the SSU rDNA in planktonic foraminifera. We show that approaches designed to extract phylogenetically valuable signals from complete sequences show more promise to resolve the backbone of the planktonic foraminifer tree than attempts to establish strictly homologous base calls in a manual alignment.http://la-press.com/using-the-multiple-analysis-approach-to-reconstruct-phylogenetic-relat-a1734 |
| spellingShingle | Ralf Aurahs Markus Göker Guido W. Grimm Vera Hemleben Christoph Hemleben Ralf Schiebel Michal Kučera Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences Bioinformatics and Biology Insights |
| title | Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences |
| title_full | Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences |
| title_fullStr | Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences |
| title_full_unstemmed | Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences |
| title_short | Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences |
| title_sort | using the multiple analysis approach to reconstruct phylogenetic relationships among planktonic foraminifera from highly divergent and length polymorphic ssu rdna sequences |
| url | http://la-press.com/using-the-multiple-analysis-approach-to-reconstruct-phylogenetic-relat-a1734 |
| work_keys_str_mv | AT ralfaurahs usingthemultipleanalysisapproachtoreconstructphylogeneticrelationshipsamongplanktonicforaminiferafromhighlydivergentandlengthpolymorphicssurdnasequences AT markusgoumlker usingthemultipleanalysisapproachtoreconstructphylogeneticrelationshipsamongplanktonicforaminiferafromhighlydivergentandlengthpolymorphicssurdnasequences AT guidowgrimm usingthemultipleanalysisapproachtoreconstructphylogeneticrelationshipsamongplanktonicforaminiferafromhighlydivergentandlengthpolymorphicssurdnasequences AT verahemleben usingthemultipleanalysisapproachtoreconstructphylogeneticrelationshipsamongplanktonicforaminiferafromhighlydivergentandlengthpolymorphicssurdnasequences AT christophhemleben usingthemultipleanalysisapproachtoreconstructphylogeneticrelationshipsamongplanktonicforaminiferafromhighlydivergentandlengthpolymorphicssurdnasequences AT ralfschiebel usingthemultipleanalysisapproachtoreconstructphylogeneticrelationshipsamongplanktonicforaminiferafromhighlydivergentandlengthpolymorphicssurdnasequences AT michalkucera usingthemultipleanalysisapproachtoreconstructphylogeneticrelationshipsamongplanktonicforaminiferafromhighlydivergentandlengthpolymorphicssurdnasequences |