A new taxonomic backbone for the infrageneric classification of the species‐rich genus Silene (Caryophyllaceae)

The systematization of species in plant taxonomy based on the phylogenetic relationships among them are of utmost importance and also very challenging in large genera. In those, phylogenetic results often may suggest substantially different relationships than previous classifications, and call for large‐scale taxonomic revisions. Delimitation of the genus Silene has been and is still somewhat controversial, and recent molecular phylogenetic studies have settled several monophyletic groups that differ substantially from previous taxonomies. The infrageneric taxonomy of Silene s.str. has not been updated as a whole taking the phylogenetic information into account. In this study, we review previous phylogenetic results based on multiple loci, and conducted comprehensive gene tree analyses based on the nrDNA ITS and cpDNA rps16 regions for 1586 and 944 samples representing 415 and 397 species, respectively, including Silene and its allies, as well as a species tree analysis including 262 samples representing 243 species. We sampled representatives from all 44 sections recognized in the most recent global revision of the genus. The results support the recognition of three subgenera, i.e., S. subg. Behenantha, S. subg. Lychnis and S. subg. Silene, which is partly in agreement with previous molecular phylogenetic findings and contradicts all previous traditional classifications. Silene sect. Atocion, with a few annual species showing a narrow distribution range in the eastern Mediterranean, is treated as incertae sedis because of its uncertain phylogenetic position, possibly due to exceptionally high substitution rates. Silene subg. Lychnis, weakly supported as sister to the other subgenera, splits into three main clades and includes four sections. Silene subg. Behenantha, which forms a possible sister group in relation to S. subg. Silene, is poorly resolved basally and includes a large number of mostly small clades recognized as 18 sections. In S. subg. Silene, 11 sections are recognized, among which four are broadly circumscribed: S. sect. Auriculatae, S. sect. Sclerocalycinae, S. sect. Silene and S. sect. Siphonomorpha. Silene sect. Acutifoliae and S. sect. Portenses are described here as new taxa, whereas new status or new combinations are proposed for S. sect. Anotites, S. sect. Muscipula, S. sect. Petrocoma, S. sect. Pulvinatae, S. sect. Sclerophyllae and S. sect. Uebelinia. Five new combinations and two new names are proposed for taxa in Silene formerly assigned to Lychnis and Uebelinia. The correct infrageneric nomenclature compatible with the new infrageneric system is provided along with synonymy and type citations. Shortcomings of this study, such as the lack of a morphological diagnostic key and sparse sampling of some large sections, are listed and discussed.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156144/5/tax12230.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156144/4/tax12230-sup-0006-Supinfo06.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156144/3/tax12230-sup-0001-Supinfo01.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156144/2/tax12230-sup-0007-FigureS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156144/1/tax12230_am.pd

Systematics in Sileneae (Caryophyllaceae) – Taxonomy and Phylogenetic patterns

The focus for the first part of the thesis is on the systematics of species belonging to Silene subgenus Silene. Phylogenetic relationships are inferred from DNA sequences from both the plastid (the rps16 intron) and the nuclear (ITS, intron of the RPB2 gene) genomes. Silene section Rigidulae is shown to be non-monophyletic in its previous circumscription, but instead consisting of six separate clades, each correlated to the geographical distribution of the included species. The taxonomic consequences for each clade are discussed. One of the clades is recognized as a new section and described as Silene sect. Arenosae sect. nov. The morphological descriptions of the species are formalized using a novel implementation of the Prometheus Description Model. Two proposals are included in the thesis, one to reject the name Silene polyphylla L., which is a senior synonym to S. portensis L. Silene linearis Decne. is proposed for conservation against the rarely used S. linearis Sweet. Silene antirrhina, a weedy American annual, is strongly supported as sister to the Hawaiian endemic species of Silene, suggesting an American origin for these. Two of the endemics have evolved woodiness after introduction to Hawaii. In the second part of the thesis we use four nuclear DNA regions, (introns from RPA2, RPB2, RPD2a, RPD2b), and the chloroplast psbE-petG spacer. A framework is developed to evaluate different phylogenetic explanations for conflicting gene trees, where divergence times are used to discriminate among inter- and intralineage processes. The incongruences observed regarding the relationships among the three major lineages of Heliosperma are best explained by homoploid hybridization. The pattern regarding the origin of Heliosperma itself is more complicated and is likely to include several reticulate events. Two lineages have probably been involved in the origin of Heliosperma, one leading to Viscaria and Atocion and the other to Eudianthe and/or Petrocoptis

Phylogeny and species delimitation in Silene sect. Arenosae (Caryophyllaceae): a new section

A putatively monophyletic group of annual Silene species is revised taxonomically and described as the new section S. sect. Arenosae. The species of this section were previously treated as a part of a widely circumscribed and polyphyletic S. sect. Rigidulae. Silene sect. Arenosae as circumscribed here consists of nine species. Members of the section show a predominantly E Mediterranean to SW Asian distribution pattern from Turkey southward to Egypt and eastward to Iran and Pakistan, although most of the species have a limited distribution range. The species of S. sect. Arenosae are characterized by narrowly lanceolate calyx teeth, which are often highly polymorphic, and lanceolate to oblanceolate (non-spathulate) basal leaves. The provided taxonomic revision is based on morphological characters and supported by phylogenetic analyses of two nuclear loci (nrITS and an intron of the RPB2 gene) and one chloroplast locus (the intron of the rps16 gene). The species descriptions are formalized using a novel implementation of the Prometheus Description Model

Phylogeny and species delimitation in Silene sect. Arenosae (Caryophyllaceae) : a new section

A putatively monophyletic group of annual Silene species is revised taxonomically and described as the new section S. sect. Arenosae. The species of this section were previously treated as a part of a widely circumscribed and polyphyletic S. sect. Rigidulae. Silene sect. Arenosae as circumscribed here consists of nine species. Members of the section show a predominantly E Mediterranean to SW Asian distribution pattern from Turkey southward to Egypt and eastward to Iran and Pakistan, although most of the species have a limited distribution range. The species of S. sect. Arenosae are characterized by narrowly lanceolate calyx teeth, which are often highly polymorphic, and lanceolate to oblanceolate (non-spathulate) basal leaves. The provided taxonomic revision is based on morphological characters and supported by phylogenetic analyses of two nuclear loci (nrITS and an intron of the RPB2 gene) and one chloroplast locus (the intron of the rps16 gene). The species descriptions are formalized using a novel implementation of the Prometheus Description Model