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Evolution of a RNA polymerase gene family in Silene (Caryophyllaceae) - incomplete concerted evolution and topological congruence among paralogues
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Systematic Botany.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Systematic Botany.
2004 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 53, no 6, 914-932 p.Article in journal (Refereed) Published
Abstract [sv]

Four low-copy nuclear DNA intron regions from the second largest subunits of the RNA polymerase gene family (RPA2, RPB2, RPD2a, and RPD2b), the internal transcribed spacers (ITSs) from the nuclear ribosomal regions, and the rps16 intron from the chloroplast were sequenced and used in a phylogenetic analysis of 29 species from the tribe Sileneae (Caryophyllaceae). We used a low stringency nested polymerase chain reaction (PCR) approach to overcome the difficulties of constructing specific primers for amplification of the low copy nuclear DNA regions. Maximum parsimony analyses resulted in largely congruent phylogenetic trees for all regions. We tested overall model congruence in a likelihood context using the software PLATO and found that ITSs, RPA2, and RPB2 deviated from the maximum likelihood model for the combined data. The topology parameter was then isolated and topological congruence assessed by nonparametric bootstrapping. No strong topological incongruence was found. The analysis of the combined data sets resolves previously poorly known major relationships within Sileneae. Two paralogues of RPD2 were found, and several independent losses and incomplete concerted evolution were inferred. The among-site rate variation was significantly lower in the RNA polymerase introns than in the rps16 intron and ITSs, a property that is attractive in phylogenetic analyses.

Place, publisher, year, edition, pages
2004. Vol. 53, no 6, 914-932 p.
Keyword [en]
DNA-Directed RNA Polymerases/*genetics, Evolution; Molecular, Introns, Phylogeny, Polymerase Chain Reaction, Research Support; Non-U.S. Gov't, Silene/*genetics
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-91242DOI: 10.1080/10635150490888840PubMedID: 15764560OAI: oai:DiVA.org:uu-91242DiVA: diva2:163905
Available from: 2004-01-13 Created: 2004-01-13 Last updated: 2014-01-27Bibliographically approved
In thesis
1. Disentangling the Reticulate History of Polyploids in Silene (Caryophyllaceae)
Open this publication in new window or tab >>Disentangling the Reticulate History of Polyploids in Silene (Caryophyllaceae)
2004 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

DNA sequences from the rps16 intron and the psbE-petL spacer from the chloroplast genome, the ribosomal nuclear ITS region, and introns from the low copy nuclear genes RPA2, RPB2, RPD2a and RPD2b, are in different combinations used to infer phylogenetic relationships in Sileneae (Caryophyllaceae). Used in concert, the biparentally inherited nuclear regions are useful to distinguish between paralogy due to allopolyploidy and single gene duplications, respectively, because the latter are not expected to give rise to repeated phylogenetic patterns in potentially unlinked sequence regions. In addition, the sequences resolve previously poorly known relationships in the tribe Sileneae. Several independent losses and incomplete concerted evolution are inferred between the two RPD2 paralogues in a subgroup of Silene.

An allopolyploid origin is suggested for the tetraploid S. aegaea, with the maternal ancestor from the diploid S. pentelica lineage, and the paternal contributor from the diploid S. sedoides lineage.

Silene involucrata originated as an allotetraploid with the diploid lineage of Arctic S. uralensis as cytoplasmic donor and the diploid Siberian/Northeast Asian S. ajanensis lineage as pollen donor. A subsequent allopolyploidization with the S. ajanensis lineage as pollen donor and the tetraploid S. involucrata lineage as cytoplasmic donor resulted in the hexaploid lineage of S. sorensenis sensu lato.

A monophyletic origin of the North American polyploids is rejected. One lineage consists of tetraploid S. menziesii and its diploid allies. A separate lineage leads to a clade consisting of both diploid and polyploid Arctic, European and Asian taxa in addition to the majority of the North American polyploids. The tetraploid S. californica and the hexaploid S. hookeri are derived from separate allopolyploidization events between these two lineages.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2004. 20 p.
Series
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1104-232X ; 924
Keyword
Biology, Silene, Sileneae, polyploidy, low copy nuclear DNA, RNA polymerase, RPA2, RPB2, RPD2, internal transcribed spacer, rps16, psbE-petL, concerted evolution, reticulate evolution, lineage sorting, Biologi
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-3918 (URN)91-554-5845-9 (ISBN)
Public defence
2004-02-06, Lindahlsalen, EBC, Norbyvägen 18 A, Uppsala, 10:00
Opponent
Supervisors
Available from: 2004-01-13 Created: 2004-01-13 Last updated: 2011-03-07Bibliographically approved

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