Recognition of two major clades and early diverged groups within the subfamily Cyperoideae (Cyperaceae) including Korean sedges

Jung, Jong-Yun; Choi, Hong‐Keun

doi:10.1007/s10265-012-0534-2

Cited by 33 publications

(87 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Continued work towards inclusion of more informative molecular regions or increasing 550 taxonomic sampling has resulted in good support for seven major lineages within a clade consisting of tribes Cariceae, Dulichieae and Scirpeae (CDS), but relationships between these major lineages and the identity of Cariceae's sister group has remained elusive (Léveillé-Bourret et al 2014). Previous studies have placed Cariceae sister to a monophyletic Scirpeae (Muasya et al 2009) or nested within a paraphyletic Scirpeae and sister to either a Trichophorum Clade 555 (Léveillé-Bourret et al 2014), the genus Calliscirpus (Gilmour et al 2013) or a clade consisting 29/52 of the Scirpus Clade + Zameioscirpus Clade (Jung and Choi 2012). The only consistency has been the poor support for all backbone relationships, a consequence of a rapid radiation (ca.…”

Section: Phylogenetic and Taxonomic Implicationsmentioning

confidence: 99%

Resolving Rapid Radiations Within Angiosperm Families Using Anchored Phylogenomics

Léveillé‐Bourret

Starr

Ford

et al. 2017

Preprint

View full text Add to dashboard Cite

Abstract. -Despite the promise that molecular data would provide a seemingly unlimited source of independent characters, many plant phylogenetic studies are based on only two regions, the plastid genome and nuclear ribosomal DNA (nrDNA). Their popularity can be explained by high copy numbers and universal PCR primers that make their sequences easily amplified and converted into parallel datasets. Unfortunately, their utility is limited by linked loci and limited 20 characters resulting in low confidence in the accuracy of phylogenetic estimates, especially when rapid radiations occur. In another contribution on anchored phylogenomics in angiosperms, we presented flowering plant-specific anchored enrichment probes for hundreds of conserved nuclear genes and demonstrated their use at the level of all angiosperms. In this contribution, we focus on a common problem in phylogenetic reconstructions below the family level: weak or unresolved 25 backbone due to rapid radiations (≤ 10 million years) followed by long divergence, using the Cariceae-Dulichieae-Scirpeae clade (CDS, Cyperaceae) as a test case. By comparing our nuclear matrix of 461 genes to a typical Sanger-sequence dataset consisting of a few plastid genes (matK, ndhF) and an nrDNA marker (ETS), we demonstrate that our nuclear data is fully compatible with the Sanger dataset and resolves short backbone internodes with high support in both 30 concatenated and coalescence-based analyses. In addition, we show that nuclear gene tree incongruence is inversely proportional to phylogenetic information content, indicating that incongruence is mostly due to gene tree estimation error. This suggests that large numbers of conserved nuclear loci could produce more accurate trees than sampling rapidly evolving regions prone to saturation and long-branch attraction. The robust phylogenetic estimates obtained here, 35and high congruence with previous morphological and molecular analyses, are strong evidence for a complete tribal revision of CDS. The anchored hybrid enrichment probes used in this study should be similarly effective in other flowering plant groups. [Carex, coalescent based species peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/110296 doi: bioRxiv preprint first posted online Léveillé- Bourret et al. 2016 Anchored phylogenomics resolves plant radiation 3/52 tree, flowering plants, low-copy nuclear genes, low-level phylogenetics, universal hybrid enrichment probes] 40peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/110296 doi: bioRxiv preprint first posted online Léveillé- Bourret et al. 2016 Anchored phylogenomics resolves plant radiation 4/52One of the strongest arguments for the use of molecular data in phylogenetic reconstruction was that it provided a seemingly unlimited source of independe...

show abstract

Section: Phylogenetic and Taxonomic Implicationsmentioning

confidence: 99%

Resolving Rapid Radiations Within Angiosperm Families Using Anchored Phylogenomics

Léveillé‐Bourret

Starr

Ford

et al. 2017

Preprint

View full text Add to dashboard Cite

show abstract

“…However, selected Scleria species have been included in the sampling of larger Cyperaceae phylogenies. Most of these studies show Scleria to be the sister taxon of tribe Bisboeckelereae (Muasya & al., 1998;Hirahara & al., 2007;Hinchliff & al., 2010;Jung & Choi, 2013;Viljoen & al., 2013), while other studies point towards Sclerieae nested in a paraphyletic Bisboeckelereae (Muasya & al., 2009;Hinchliff & Roalson, 2013). In Hinchliff & Roalson (2013), 12 species of Scleria were included, but no morphologically recognisable groupings were retrieved.…”

Section: Nees 1842mentioning

confidence: 99%

Phylogenetics, ancestral state reconstruction, and a new infrageneric classification of Scleria (Cyperaceae) based on three DNA markers

Bauters

Asselman

Simpson

et al. 2016

TAXON

View full text Add to dashboard Cite

The genus Scleria (Cyperaceae), with ca. 250 species, is placed in the monotypic tribe Sclerieae. It has a primarily pantropical distribution. Previously, infrageneric classifications have been proposed but none has been based on molecular phylogenetic evidence and most studies have treated the genus from only one geographical region. In this study, DNA portions from 101 species of Scleria from across its distributional range and all infrageneric groups were extracted and amplified for three molecular markers: the coding chloroplast marker ndhF, the chloroplast intron rps16 and the nuclear ribosomal region ITS. Phylogenetic hypotheses were constructed using Bayesian inference and maximum likelihood approaches. Additionally, ancestral states of four morphological characters were reconstructed at important nodes using the program BayesTraits. A new infrageneric classification based on molecular evidence and supported by morphology is presented. Scleria is confirmed as monophyletic and sister to tribe Bisboeckelereae. A subdivision of Scleria into four subgenera (S. subg. Browniae, S. subg. Hypoporum, S. subg. Scleria, S. subg. Trachylomia) is supported by our results. In this paper, twelve major clades are recovered within Scleria subg. Scleria. Clear morphological diagnostic features match these clades. Ancestral state reconstruction indicates that androgynous spikelets, a zoniform hypogynium, a paniculate inflorescence with staminate and subandrogynous spikelets, and normal linear leaves are ancestral in Scleria. Androgynous spikelets are found in the three first‐branching subgenera, while in S. subg. Scleria an evolutionary shift towards subandrogynous and strictly unisexual spikelets is noted. Hypogynia are generally well developed with the exception of S. subg. Hypoporum, where the hypogynium is reduced or even lost. Inflorescences in Scleria vary from short, densely paniculate and pyramidal to subcapitate, only in S. subg. Hypoporum a glomerate‐spicate inflorescence is found. The pseudopremorse leaf habit arose only once within S. subg. Scleria. Scleria sect. Scleria shows a reversal to normal leaf tips.

show abstract

“…remains unsatisfactory because it is defined by the same plesiomorphic characters that have been used since the earliest of classifications, and its status as a natural tribe has been questioned for decades (Goetghebeur, , ; Bruhl, ). Molecular phylogenetic analyses have since shown that Scirpeae forms a strongly supported clade with Cariceae, Dulichieae, the recently discovered Sumatroscirpeae, and the enigmatic monospecific genus Khaosokia D.A.Simpson & al., a lineage comprising ~2250 species, or approximately 41% of all Cyperaceae (Simpson & al., ; Muasya & al., ; Jung & Choi, ; Léveillé‐Bourret & al., ) (Figs. ).…”

Section: Introductionmentioning

confidence: 99%

Molecular and morphological data reveal three new tribes within the Scirpo‐Caricoid Clade (Cyperoideae, Cyperaceae)

Léveillé‐Bourret

Starr

2019

TAXON

View full text Add to dashboard Cite

The circumscription of the circumboreal tribe Scirpeae has been contentious since the earliest infrafamilial classifications of the Cyperaceae (>100 genera,~5500 species). Molecular phylogenetic studies place Scirpeae in a strongly supported clade with the enigmatic genus Khaosokia and tribes Cariceae, Dulichieae, and Sumatroscirpeae, a lineage comprising more than 40% of all Cyperaceae species. This lineage was previously known as the Cariceae-Dulichieae-Scirpeae (CDS) clade. Here we informally characterize it as the "Scirpo-Caricoid Clade". Previous phylogenetic and phylogenomic studies of the Scirpo-Caricoid Clade have shown Scirpeae to be paraphyletic, forming four distinct lineages that are successive sisters to a Cariceae+Sumatroscirpeae clade, thus confirming decade-old suspicions that the modern circumscription of Scirpeae is unnatural. Using a total-evidence phylogenetic analysis incorporating three plastid markers (matK, ndhF, rps16), two nuclear ribosomal markers (ETS-1f, ITS), and 64 morphological characters, this study confirms the paraphyly of Scirpeae, the isolated phylogenetic position of Khaosokia, and identifies morphological synapomorphies for seven monophyletic lineages that are here recognized as tribes. Our new classification places for the first time all genera of the Scirpo-Caricoid Clade into natural tribes that are identifiable using morphological and embryological characters. Three new tribes are proposed: Calliscirpeae tr. nov., Khaosokieae tr. nov. and Trichophoreae tr. nov. Diagnoses for all tribes of the Scirpo-Caricoid Clade, an identification key to all currently recognized Cyperaceae tribes, and identification keys for all genera of the Scirpo-Caricoid Clade are provided.

show abstract

Recognition of two major clades and early diverged groups within the subfamily Cyperoideae (Cyperaceae) including Korean sedges

Cited by 33 publications

References 39 publications

Resolving Rapid Radiations Within Angiosperm Families Using Anchored Phylogenomics

Resolving Rapid Radiations Within Angiosperm Families Using Anchored Phylogenomics

Phylogenetics, ancestral state reconstruction, and a new infrageneric classification of Scleria (Cyperaceae) based on three DNA markers

Molecular and morphological data reveal three new tribes within the Scirpo‐Caricoid Clade (Cyperoideae, Cyperaceae)

Contact Info

Product

Resources

About