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

Abstract

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.

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

“…Consistent with previous studies ( Oxelman and Lidén 1995 , Oxelman 1996 , Eggens et al 2007 , Jafari et al 2020 ), our results reveal that S. sect. Rigidulae s.l.…”

“… Rigidulae sensu Chowdhuri (1957) , circumscribed as S. sect. Muscipula (Tzvelev) Oxelman, F.Jafari & Gholipour ( Jafari et al 2020 ), is sister to S. sect. Arenosae in the species tree (PP = 0.88, Fig.…”

“… Silene L. is a large genus of the family Caryophyllaceae , with around 870 currently ( Jafari et al 2020 ) recognized species that are mainly distributed in the northern hemisphere, South Africa and South America, in temperate to arctic regions and a wide range of habitats ( Manning and Goldblatt 2012 , Frajman et al 2018 , Jafari et al 2020 ). Chowdhuri (1957) delimited 44 sections and his taxonomy has been applied by authors of local floras in the Mediterranean region and SW Asia, including Palestine ( Zohary 1966 ), Turkey ( Coode and Cullen 1967 ), the Iranian Highlands ( Melzheimer 1988 ), the Flora Europaea ( Chater et al 1993 ), and Iraq ( Townsend et al 2016 ).…”

“…There have been several regionally focused studies (e.g., Greuter 1995 , Oxelman and Greuter 1997 ) that amended the taxonomy of Chowdhuri (1957) , and a number of molecular studies (e.g., Oxelman and Lidén 1995 , Desfeux and Lejeune 1996 , Oxelman et al 1997 , Popp and Oxelman 2004 , Eggens 2006 , Eggens et al 2007 , Popp and Oxelman 2007 , Petri and Oxelman 2011 , Rautenberg et al 2012 , Aydin et al 2014a , Naciri et al 2017 ) that revealed the artificial nature of many sections as defined by Chowdhuri (1957) . Jafari et al (2020) outlined a new, revised system taking the phylogenetic information into account.…”

Long-read transcriptome and other genomic resources for the angiospermSilene noctiflora

“…Based on a phylogenetic analysis (Figure 3), these two duplications are shared with S. undulata but none of the other sampled Silene species. Thus, these duplications likely occurred after the Silene section Elisanthe (including S. noctiflora, S. undulata, and S. turkestanica) diverged from the other members of the genus (Jafari et al 2020).…”