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Phylogenetic analysis of mitochondrial mutation rate variation in the angiosperm tribe Sileneae
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
2009 (English)In: BMC Evolutionary Biology, ISSN 1471-2148, Vol. 9, 260- p.Article in journal (Refereed) Published
Abstract [en]

Background: Recent phylogenetic studies have revealed that the   mitochondrial genome of the angiosperm Silene noctiflora   (Caryophyllaceae) has experienced a massive mutation-driven   acceleration in substitution rate, placing it among the fastest   evolving eukaryotic genomes ever identified. To date, it appears that   other species within Silene have maintained more typical substitution   rates, suggesting that the acceleration in S. noctiflora is a recent   and isolated evolutionary event. This assessment, however, is based on   a very limited sampling of taxa within this diverse genus.   Results: We analyzed the substitution rates in 4 mitochondrial genes   (atp1, atp9, cox3 and nad9) across a broad sample of 74 species within   Silene and related genera in the tribe Sileneae. We found that S.   noctiflora shares its history of elevated mitochondrial substitution   rate with the closely related species S. turkestanica. Another section   of the genus (Conoimorpha) has experienced an acceleration of   comparable magnitude. The phylogenetic data remain ambiguous as to   whether the accelerations in these two clades represent independent   evolutionary events or a single ancestral change. Rate variation among   genes was equally dramatic. Most of the genus exhibited elevated rates   for atp9 such that the average tree-wide substitution rate for this   gene approached the values for the fastest evolving branches in the   other three genes. In addition, some species exhibited major   accelerations in atp1 and/or cox3 with no correlated change in other   genes. Rates of nonsynonymous substitution did not increase   proportionally with synonymous rates but instead remained low and   relatively invariant.   Conclusion: The patterns of phylogenetic divergence within Sileneae   suggest enormous variability in plant mitochondrial mutation rates and   reveal a complex interaction of gene and species effects. The variation   in rates across genomic and phylogenetic scales raises questions about   the mechanisms responsible for the evolution of mutation rates in plant   mitochondrial genomes.

Place, publisher, year, edition, pages
2009. Vol. 9, 260- p.
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-100792DOI: 10.1186/1471-2148-9-260ISI: 000271889800001OAI: oai:DiVA.org:uu-100792DiVA: diva2:211019
Correction in: BMC Evolutionary Biology, vol. 10, article nr. 12, doi: 10.1186/1471-2148-10-12Available from: 2009-04-07 Created: 2009-04-07 Last updated: 2010-12-08Bibliographically approved
In thesis
1. Phylogenetic Relationships of Silene sect. Melandrium and Allied Taxa (Caryophyllaceae), as Deduced from Multiple Gene Trees
Open this publication in new window or tab >>Phylogenetic Relationships of Silene sect. Melandrium and Allied Taxa (Caryophyllaceae), as Deduced from Multiple Gene Trees
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis focuses on phylogenetic relationships among some of the major lineages in Silene subgenus Behenantha (Caryophyllaceae) using DNA sequences from multiple, potentially unlinked gene regions from a large taxonomic and geographic sample. Both traditional phylogenetic analyses and a strategy to infer species trees and gene trees in a joint approach are used. A new strategy to optimize species classifications, based on the likelihoods of the observed gene trees, is presented.

Silene latifolia, S. dioica and the other dioecious species previously classified in section Elisanthe are not closely related to the type of the section (S. noctiflora). The correct name for the group of dioecious species is section Melandrium. The chloroplast DNA data presented indicate a geographic, rather than a taxonomic, structure in section Melandrium. The nuclear genes investigated correlate more to the current taxonomy, although hybridization has likely been influencing the relationships within section Melandrium.

Incongruence between different parts of the gene SlXY1 in two Silene lineages is investigated, using phylogenetic methods and a novel probabilistic, multiple primer-pair PCR approach. The incongruence is best explained by ancient hybridization and recombination events.

A survey of mitochondrial substitution rate variation in Sileneae is presented. Silene section Conoimorpha, S. noctiflora and the closely related S. turkestanica have elevated synonymous substitution rates in the mitochondrial genes investigated.

Morphological and phylogenetic data reject that the Californian S. multinervia should be treated as a synonym to the Asian S. coniflora, as has previously been suggested. Furthermore, none of the genes investigated, or a chromosome count, support the inclusion of S. multinervia in section Conoimorpha. Data from multiple genes suggest that S. noctiflora and S. turkestanica form a sister group to section Conoimorpha. The calyx nervature, which is a potential synapomorphy for S. multinervia and section Conoimorpha, may be explained either by parallelism or by sorting effects.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2009. 40 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 639
Silene, Elisanthe, Melandrium, Conoimorpha, Caryophyllaceae, Silene multinervia, relative dating, extreme substitution rates, phylogeny, BEST, BEAST, cpDNA, mtDNA, RNA polymerase, RPA2, RPB2, RPD2, SlX1, SlY1, ITS, introgression, incongruent phylogenies, chromosome count, coalescent, Bayes Factors
National Category
Biological Systematics
Research subject
Systematic Botany
urn:nbn:se:uu:diva-100806 (URN)978-91-554-7511-6 (ISBN)
Public defence
2009-05-20, Lindahlsalen, EBC, Norbyvägen 18A, Uppsala, 09:30 (English)
Available from: 2009-04-29 Created: 2009-04-07 Last updated: 2009-05-11Bibliographically approved

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