Size, frequency, and phylogenetic signal of multiple-residue indels in sequence alignment of introns.
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| Title: | Size, frequency, and phylogenetic signal of multiple-residue indels in sequence alignment of introns. |
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| Authors: | Pons, Joan1 joan.pons@upf.edu, Vogler, Alfried P.1 |
| Source: | Cladistics. Apr2006, Vol. 22 Issue 2, p144-156. 13p. 2 Diagrams, 2 Charts, 2 Graphs. |
| Subjects: | Nucleotide sequence, Character sets (Data processing), Homology (Biology), Taxonomy, Biological classification |
| Abstract: | Indels in DNA sequences frequently affect more than a single nucleotide, creating problems for alignment, character coding and phylogenetic analysis. However, the size and frequency of multiple-residue indels is not usually tested, and with popular alignment packages their reconstruction is indirectly acheived by reducing the affine (gap extension) cost. We explored the length distribution of indels in intron sequences of the gene Mp20 by modifying the gap opening and gap extension costs. Given a “known” tree for the study group, global homology levels were greatest under low gap cost, with gap extension costs of roughly 0.4-fold the opening cost. Different approaches to gap coding and weighting suggested that taxonomic congruence was correlated with high frequencies of multiple-position indels, with a maximum indel length of 2–5 bp and few indels above 15 bp, but also including a proportion of indels > 100 bp. Only a small minority of indels could be reconstructed as single-position indels. Consequently, tree topologies improved when homologous multinucleotide indels were recoded as binary characters which are otherwise highly homoplastic and weighted characters in single-position coding. In tree-generating alignment procedures as implemented in POY, where gap penalty determines the character weight during tree search, the problem of assigning inappropriately high weight to multiple-residue indels could partly be overcome by setting the extension costs to about 0.4-fold lower than gap opening costs. We conclude that multiple consecutive gap positions are not independent characters and hence methods for parsimony reconstruction of long indels are required. Finally, we also observed a general lack of correlation between taxonomic and character congruence, demonstrating the difficulties of applying congruence criteria to decide among competing alignments. This highlights the value of recent model-based alignment procedures which can implement the statistical distributions of indel size classes, and do not rely on potentially circular strategies for optimizing overall congruence. © The Willi Hennig Society 2006. [ABSTRACT FROM AUTHOR] |
| Copyright of Cladistics is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Links: – Type: pdflink Text: Availability: 0 |
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| Header | DbId: egs DbLabel: Engineering Source An: 22419554 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Size, frequency, and phylogenetic signal of multiple-residue indels in sequence alignment of introns. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Pons%2C+Joan%22">Pons, Joan</searchLink><relatesTo>1</relatesTo><i> joan.pons@upf.edu</i><br /><searchLink fieldCode="AR" term="%22Vogler%2C+Alfried+P%2E%22">Vogler, Alfried P.</searchLink><relatesTo>1</relatesTo> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Cladistics%22">Cladistics</searchLink>. Apr2006, Vol. 22 Issue 2, p144-156. 13p. 2 Diagrams, 2 Charts, 2 Graphs. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Nucleotide+sequence%22">Nucleotide sequence</searchLink><br /><searchLink fieldCode="DE" term="%22Character+sets+%28Data+processing%29%22">Character sets (Data processing)</searchLink><br /><searchLink fieldCode="DE" term="%22Homology+%28Biology%29%22">Homology (Biology)</searchLink><br /><searchLink fieldCode="DE" term="%22Taxonomy%22">Taxonomy</searchLink><br /><searchLink fieldCode="DE" term="%22Biological+classification%22">Biological classification</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Indels in DNA sequences frequently affect more than a single nucleotide, creating problems for alignment, character coding and phylogenetic analysis. However, the size and frequency of multiple-residue indels is not usually tested, and with popular alignment packages their reconstruction is indirectly acheived by reducing the affine (gap extension) cost. We explored the length distribution of indels in intron sequences of the gene Mp20 by modifying the gap opening and gap extension costs. Given a “known” tree for the study group, global homology levels were greatest under low gap cost, with gap extension costs of roughly 0.4-fold the opening cost. Different approaches to gap coding and weighting suggested that taxonomic congruence was correlated with high frequencies of multiple-position indels, with a maximum indel length of 2–5 bp and few indels above 15 bp, but also including a proportion of indels > 100 bp. Only a small minority of indels could be reconstructed as single-position indels. Consequently, tree topologies improved when homologous multinucleotide indels were recoded as binary characters which are otherwise highly homoplastic and weighted characters in single-position coding. In tree-generating alignment procedures as implemented in POY, where gap penalty determines the character weight during tree search, the problem of assigning inappropriately high weight to multiple-residue indels could partly be overcome by setting the extension costs to about 0.4-fold lower than gap opening costs. We conclude that multiple consecutive gap positions are not independent characters and hence methods for parsimony reconstruction of long indels are required. Finally, we also observed a general lack of correlation between taxonomic and character congruence, demonstrating the difficulties of applying congruence criteria to decide among competing alignments. This highlights the value of recent model-based alignment procedures which can implement the statistical distributions of indel size classes, and do not rely on potentially circular strategies for optimizing overall congruence. © The Willi Hennig Society 2006. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Cladistics is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1111/j.1096-0031.2006.00088.x Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 13 StartPage: 144 Subjects: – SubjectFull: Nucleotide sequence Type: general – SubjectFull: Character sets (Data processing) Type: general – SubjectFull: Homology (Biology) Type: general – SubjectFull: Taxonomy Type: general – SubjectFull: Biological classification Type: general Titles: – TitleFull: Size, frequency, and phylogenetic signal of multiple-residue indels in sequence alignment of introns. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Pons, Joan – PersonEntity: Name: NameFull: Vogler, Alfried P. IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 04 Text: Apr2006 Type: published Y: 2006 Identifiers: – Type: issn-print Value: 07483007 Numbering: – Type: volume Value: 22 – Type: issue Value: 2 Titles: – TitleFull: Cladistics Type: main |
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