New Insights into the Systematics of the Schoenoxiphium Clade (Carex, Cyperaceae)

Abstract

Editor: Erika EdwardsPremise of research. The Schoenoxiphium clade (Carex, Cyperaceae) exhibits a high species diversity in South Africa and a complex taxonomy. Previous phylogenetic studies did not resolve the species relationships within the Schoenoxiphium clade due to the lack of informative characters in DNA markers used. Our aim is to resolve the species relationships within the Schoenoxiphium clade by adding information from more markers and more samples to information from previous studies.Methodology. We sampled 19 out of 20 recognized species in the former genus Schoenoxiphium. Four DNA regions (two nuclear ribosomal: internal transcribed spacer, external transcribed spacer; two plastid: matK and rps16) were sequenced for 134 samples. Phylogenetic reconstruction was performed using Bayesian inference and maximum likelihood analyses.Pivotal results. The monophyly of the Schoenoxiphium clade was confirmed. Five main clades with strong support were retrieved in congruence with a previous phylogeny. Although species relationships within these clades are still partially unresolved, our phylogeny highlights the need for the description of at least two new species in this group.Conclusions. The monophyly of the former genus Schoenoxiphium, taken together with its morphological synapomorphies and the recent phylogenetic studies and subsequent recircumscription of the genus Carex to include all nested genera, advises the consideration of this clade as a section (Carex sect. Schoenoxiphium Baillon). Additional investigations based on genomic sequencing are needed to fully resolve the species relationships within each of the five main clades.

An integrative monograph of Carex section Schoenoxiphium (Cyperaceae)

“…Previous molecular phylogenies focused on section Schoenoxiphium were based on a relatively small number of DNA regions (nuclear ITS and ETS; plastid trnL-F, matK and rps16). They found a well-supported internal phylogenetic backbone composed of five strongly supported main clades (Clades A-E; Gehrke et al, 2010;Villaverde et al, 2017;, although species relationships remained partially unresolved, sometimes suggesting the existence of cryptic species, which have been recently described (Márquez-Corro et al, 2017;this study). Furthermore, the available phylogenetic evidence suggests a complex evolutionary history, as illustrated by a documented case of intersectional hybridization followed by recombination involving section Schoenoxiphium (Clade E) and another member of subgenus Psyllophorae (C. camptoglochin V.I.Krecz., section Junciformes) (Gehrke et al, 2010).…”

“…clade, C. distachya Desf. clade; Gehrke et al, 2010;Villaverde et al, 2017;Roalson et al, 2020). The subgeneric classification of Carex has recently been rearranged following a genomic Hyb-Seq Carex phylogeny (Villaverde et al, 2020).…”

“…Taxonomy in section Schoenoxiphium is complex and characterized by long-standing problems regarding species circumscription and nomenclature (Villaverde et al, 2017). Thus, previous taxonomic treatments have considerably varied in the number of accepted species (6 in Kükenthal, 1909;15 in Kukkonen, 1978, 1983, and in Gordon-Gray, 1995c.…”

Multi‐locus phylogeny of Ludwigia (Onagraceae): Insights on infra‐ generic relationships and the current classification of the genus

“…Cloning to test for multiple copies is often recommended, although this approach adds significant cost to a research project, particularly as the number of included taxa increases, and often with no improvement in phylogenetic signal. Irrespective of these recommendations, numerous recent phylogenetic studies continue to be published based on ITS and/or low-copy nuclear markers for which clon ing was not carried out (see, for example, Tank & Olmstead, 2009;Wahlert & al., 2014;Aubriot & al., 2016;Plunkett & Nicolas, 2016;Franzke & al., 2017;Glon & al., 2017;Villaverde & al., 2017).…”

A new classification ofCarex(Cyperaceae) subgenera supported by a HybSeq backbone phylogenetic tree

“…Subsequent phylogenetic works, adding new species to the sampling, further clarified which species and sections comprised each of the clades (e.g. Siderostictae clade: Yano et al, 2014;Siderostictae and Carex clades: Starr, Janzen & Ford, 2015;Schoenoxiphium clade: Gerkhe et al, 2010, Villaverde et al, 2017; Carex as a whole: Waterway et al, 2015) but at the same time unmasked new conflicts: Starr et al (2015), for example, found that the Caricoid clade was only resolved when using likelihood and Bayesian inference and for certain sets of sampled genes. A substantial increase in taxon sampling was published soon thereafter by the Global Carex Group (2016a), who inferred a phylogenetic tree with 996 species (c. 50% of the genus) representing 110 of the 126 recognized sections (c. 92%) based on three loci (nuclear ITS and ETS and plastid matK).…”