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Conflicting phylogenetic signals in the SlX1/Y1 gene in Silene
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
Department of Plant Sciences, University of Oxford, UK.
Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Mathematical Statistics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
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2008 (English)In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 8, no 1, 299- p.Article in journal (Refereed) Published
Abstract [en]

Background: Increasing evidence from DNA sequence data has revealed that phylogenies based on different genes may drastically differ from each other. This may be due to either inter- or intralineage processes, or to methodological or stochastic errors. Here we investigate a spectacular case where two parts of the same gene (SlX1/Y1) show conflicting phylogenies within Silene (Caryophyllaceae). SlX1 and SlY1 are sex-linked genes on the sex chromosomes of dioecious members of Silene sect. Elisanthe.

Results: We sequenced the homologues of the SlX1/Y1 genes in several Sileneae species. We demonstrate that different parts of the SlX1/Y1 region give different phylogenetic signals. The major discrepancy is that Silene vulgaris and S. sect. Conoimorpha (S. conica and relatives) exchange positions. To determine whether gene duplication followed by recombination (an intralineage process) may explain the phylogenetic conflict in the Silene SlX1/Y1 gene, we use a novel probabilistic, multiple primer-pair PCR approach. We did not find any evidence supporting gene duplication/loss as explanation to the phylogenetic conflict.

Conclusion: The phylogenetic conflict in the Silene SlX1/Y1 gene cannot be explained by paralogy or artefacts, such as in vitro recombination during PCR. The support for the conflict is strong enough to exclude methodological or stochastic errors as likely sources. Instead, the phylogenetic incongruence may have been caused by recombination of two divergent alleles following ancient interspecific hybridization or incomplete lineage sorting. These events probably took place several million years ago. This example clearly demonstrates that different parts of the genome may have different evolutionary histories and stresses the importance of using multiple genes in reconstruction of taxonomic relationships.

Place, publisher, year, edition, pages
2008. Vol. 8, no 1, 299- p.
National Category
Biological Systematics
Research subject
Systematic Botany
Identifiers
URN: urn:nbn:se:uu:diva-100783DOI: 10.1186/1471-2148-8-299ISI: 000264070900001OAI: oai:DiVA.org:uu-100783DiVA: diva2:211014
Available from: 2009-04-07 Created: 2009-04-07 Last updated: 2017-12-13Bibliographically 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.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 639
Keyword
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
Identifiers
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)
Opponent
Supervisors
Available from: 2009-04-29 Created: 2009-04-07 Last updated: 2009-05-11Bibliographically approved

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