Nuclear ribosomal pseudogenes resolve a corroborated monophyly of the eucalypt genus Corymbia despite misleading hypotheses at functional ITS paralogs

Ochieng, Joel W., Henry, Robert J., Baverstock, Peter R., Steane, Dorothy A. and Shepherd, Mervyn (2007) Nuclear ribosomal pseudogenes resolve a corroborated monophyly of the eucalypt genus Corymbia despite misleading hypotheses at functional ITS paralogs. Molecular Phylogenetics and Evolution, 44 2: 752-764. doi:10.1016/j.ympev.2007.04.017


Author Ochieng, Joel W.
Henry, Robert J.
Baverstock, Peter R.
Steane, Dorothy A.
Shepherd, Mervyn
Title Nuclear ribosomal pseudogenes resolve a corroborated monophyly of the eucalypt genus Corymbia despite misleading hypotheses at functional ITS paralogs
Formatted title
Nuclear ribosomal pseudogenes resolve a corroborated monophyly of the eucalypt genus Corymbia despite misleading hypotheses at functional ITS paralogs
Journal name Molecular Phylogenetics and Evolution   Check publisher's open access policy
ISSN 1055-7903
1095-9513
Publication date 2007-08-01
Sub-type Article (original research)
DOI 10.1016/j.ympev.2007.04.017
Volume 44
Issue 2
Start page 752
End page 764
Total pages 13
Place of publication Maryland Heights, MO, United States
Publisher Academic Press
Language eng
Formatted abstract
Divergent paralogs can create both obstacles and opportunities for phylogenetic reconstruction. Phylogenetic relationships among eucalypt genera have been incongruent among datasets in previous studies, where morphological characters supported monophyly of the genus Corymbia, while intergenic spacers of the nuclear ribosomes (ITS) and chloroplast loci (trnL, trnH, psbA) showed Corymbia as either equivocal or paraphyletic. Ribosomal DNA occurs in multiple copies in a genome. We cloned and sequenced the nrITS to investigate if gene duplication was the cause of incongruence among trees in the eucalypts. Three ITS riboforms, two of them widespread, were recovered within some genomes. One of the ITS riboforms recovered a robust phylogeny showing Corymbia as a monophyletic genus, corroborating the evidence from morphology, fossil data, a recent ITS/ETS dataset and microsatellites (SSRs). Compelling evidence suggested that this divergent riboform is a pseudogene, i.e., non-functional paralog: comparatively lower GC content suggesting lower structural stability, deamination-like mutations at potential methylation sites, lack of conserved helices and hairpins and conspicuously lower thermodynamic stability in secondary structures. Phylogenies from the apparently functional riboform retained Corymbia as paraphyletic. We show here that pseudogenes can recover a well-corroborated phylogeny whereas their functional paralogs show misleading hypotheses. We explain that phylogenetic signals may be obscured when functional constraints in ITS necessitate compensatory mutations in the secondary structure helices involved in RNA transcription, whereas pseudogenes mutate under neutrality.
Keyword Pseudogene
Paralog
Paraphyletic
Ribosomal Its
Riboform
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
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Created: Tue, 08 Mar 2011, 02:12:37 EST