Indel evolution of mammalian introns and the utility of non-coding nuclear markers in eutherian phylogenetics

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dc.contributor.authorMatthee C.A.
dc.contributor.authorEick G.
dc.contributor.authorWillows-Munro S.
dc.contributor.authorMontgelard C.
dc.contributor.authorPardini A.T.
dc.contributor.authorRobinson T.J.
dc.date.accessioned2011-05-15T15:57:21Z
dc.date.available2011-05-15T15:57:21Z
dc.date.issued2007
dc.description.abstractNuclear DNA intron sequences are increasingly used to investigate evolutionary relationships among closely related organisms. The phylogenetic usefulness of intron sequences at higher taxonomic levels has, however, not been firmly established and very few studies have used these markers to address evolutionary questions above the family level. In addition, the mechanisms driving intron evolution are not well understood. We compared DNA sequence data derived from three presumably independently segregating introns (THY, PRKC I and MGF) across 158 mammalian species. All currently recognized extant eutherian mammalian orders were included with the exception of Cingulata, Dermoptera and Scandentia. The total aligned length of the data was 6366 base pairs (bp); after the exclusion of autapomorphic insertions, 1511 bp were analyzed. In many instances the Bayesian and parsimony analyses were complementary and gave significant posterior probability and bootstrap support (>80) for the monophyly of Afrotheria, Euarchontoglires, Laurasiatheria and Boreoeutheria. Apart from finding congruent support when using these methods, the intron data also provided several indels longer than 3 bp that support, among others, the monophyly of Afrotheria, Paenungulata, Ferae and Boreoeutheria. A quantitative analysis of insertions and deletions suggested that there was a 75% bias towards deletions. The average insertion size in the mammalian data set was 16.49 bp ± 57.70 while the average deletion was much smaller (4.47 bp ± 14.17). The tendency towards large insertions and small deletions is highlighted by the observation that out of a total of 17 indels larger than 100 bp, 15 were insertions. The majority of indels (>60% of all events) were 1 or 2 bp changes. Although the average overall indel substitution rate of 0.00559 per site is comparable to that previously reported for rodents and primates, individual analyses among different evolutionary lineages provide evidence for differences in the formation rate of indels among the different mammalian groups. © 2006 Elsevier Inc. All rights reserved.
dc.description.versionArticle
dc.identifier.citationMolecular Phylogenetics and Evolution
dc.identifier.citation42
dc.identifier.citation3
dc.identifier.issn10557903
dc.identifier.other10.1016/j.ympev.2006.10.002
dc.identifier.urihttp://hdl.handle.net/10019.1/10354
dc.subjectspacer DNA
dc.subjectanimal
dc.subjectarticle
dc.subjectevaluation
dc.subjectgene deletion
dc.subjectgene expression regulation
dc.subjectgenetic marker
dc.subjectgenetic procedures
dc.subjecthuman
dc.subjectintron
dc.subjectmolecular evolution
dc.subjectphylogeny
dc.subjectAnimals
dc.subjectDNA, Intergenic
dc.subjectEvolution, Molecular
dc.subjectGenetic Markers
dc.subjectGenetic Techniques
dc.subjectHumans
dc.subjectIntrons
dc.subjectMutagenesis, Insertional
dc.subjectPhylogeny
dc.subjectSequence Deletion
dc.subjectAfrotheria
dc.subjectCingulata
dc.subjectDermoptera
dc.subjectEuarchontoglires
dc.subjectEutheria
dc.subjectFerae
dc.subjectLaurasiatheria
dc.subjectMammalia
dc.subjectPaenungulata
dc.subjectPrimates
dc.subjectRodentia
dc.subjectScandentia
dc.titleIndel evolution of mammalian introns and the utility of non-coding nuclear markers in eutherian phylogenetics
dc.typeArticle
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