<p>DNA sequences from the <i>rps16</i> intron and the <i>psbE-petL</i> spacer from the chloroplast genome, the ribosomal nuclear ITS region, and introns from the low copy nuclear genes <i>RPA2</i>, <i>RPB2</i>, <i>RPD2a</i> and <i>RPD2b</i>, are in different combinations used to infer phylogenetic relationships in <i>Sileneae</i> (<i>Caryophyllaceae</i>). 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 <i>Sileneae</i>. Several independent losses and incomplete concerted evolution are inferred between the two <i>RPD2</i> paralogues in a subgroup of <i>Silene</i>.</p><p>An allopolyploid origin is suggested for the tetraploid <i>S. aegaea</i>, with the maternal ancestor from the diploid <i>S. pentelica</i> lineage, and the paternal contributor from the diploid <i>S. sedoides</i> lineage.</p><p><i>Silene involucrata</i> originated as an allotetraploid with the diploid lineage of Arctic <i>S. uralensis</i> as cytoplasmic donor and the diploid Siberian/Northeast Asian <i>S. ajanensis</i> lineage as pollen donor. A subsequent allopolyploidization with the <i>S. ajanensis</i> lineage as pollen donor and the tetraploid <i>S. involucrata</i> lineage as cytoplasmic donor resulted in the hexaploid lineage of <i>S. sorensenis sensu lato</i>.</p><p>A monophyletic origin of the North American polyploids is rejected. One lineage consists of tetraploid <i>S. menziesii</i> 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 <i>S. californica</i> and the hexaploid <i>S. hookeri</i> are derived from separate allopolyploidization events between these two lineages.</p>

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.

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.