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Embryographs of the genera of Fuireneae s.l. Bolboschoenus: A, B. fluviatilis (Torr.) Soják; B, B. maritimus (L.) Palla; C, B. grandispicus (Steud.) Lewej. & Lobin; Fuirena: D, F. abnormalis C.B.Clarke; E, F. ciliaris (L.) Roxb.; F, F. incompleta Nees; G, F. pachyrrhiza Ridl.; H, F. scirpoidea Michx.; I, F. stricta Steud.; J, F. trilobites C.B.Clarke; K, F. umbellata Rottb.; Actinoscirpus and Schoenoplectus: L, A. grossus (L.f.) Goetgh. & D.A.Simpson; M, S. californicus (C.A.Mey.) Soják; N, S. lacustris (L.) Palla; O, S. litoralis (Schrad.) Palla; Pseudoschoenus and Schoenoplectiella: P, P. inanis (Thunb.) Oteng-Yeb; Q, S. dissachantha (S.T.Blake) Lye; R, S. juncea (Willd.) (S); S, S. juncoides (Roxb.) Lye; T, S. laevis (S.T.Blake) Lye; U, S. lateriflora (J.F.Gmel.) Lye; V, S. lineolata (Franch. & Sav.) J.Jung & H.K.Choi; W, S. mucronata (L.) J.Jung & H.K.Choi; X, S. praelongata (Poir.) Lye; Y, S. roylei (Nees) Lye; Z, S. smithii (A.Gray) Hayas.; a, S. vohemarensis (Cherm.) Lye; b, S. paludicola (Kunth) Palla; c, S. rhodesicus (Podlech) Lye). Scale bars 100 μm. See Data S3 for the voucher information of the studied embryographs.
Source publication
Molecular phylogenetic studies based on Sanger sequences have shown that Cyperaceae tribe Fuireneae s.l. is paraphyletic. However, taxonomic sampling in these studies has been poor, topologies have been inconsistent, and support for the backbone of trees has been weak. Moreover, uncertainty still surrounds the morphological limits of Schoenoplectie...
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... members of Fuireneae s.l. possess embryos with a more or less mushroom-shaped or top-shaped outline, with leaf primordia in a basal position and a lateral displacement of the root cap (Fig. 5). While rare in the family, fungiform embryos are also typical for tribe Eleocharideae and are sometimes found in some of the largest Abildgaardieae embryos, suggesting that this special morphology is a plesiomorphy for Fuireneae s.l. ( Semmouri et al., 2019). Nonetheless, subtle differences can be found among the different clades, and ...
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... has the largest embryos in Fuireneae s.l. (Table 1), with at least two species possessing embryos over a millimeter in length and more than half a millimeter in width. The embryo of Bolboschoenus is fungiform, with a broadened, rhomboid scutellum (Figs. 5, 6). The root cap is well differentiated, in a lateral position, and separated from the scutellum by a notch. The first leaf is well developed, Fig. 3. Phylogenetic reconstruction of relationships in tribe Fuireneae s.l. and related tribes based on analysis of the supercontigs data set. Species tree inferred in ASTRAL from RAxML gene ...
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... Actinoscirpus, Pseudoschoenus, Schoenoplectus, and Schoenoplectiella possess very similar embryos (Figs. 5, 6), two groups can be distinguished, which we designate here as Schoenoplectus-type I and Schoenoplectus-type II given their similarity. Whereas the scutellum in Actinoscirpus and Schoenoplectus s.s. is turbinate to rhomboid in shape, with straight to convex lower margins, the scutellum of Pseudoschoenus and Schoenoplectiella is often umbonate, with a distinct knob at the apex, or strongly pileate, with the margins clearly incurved (Schoenoplectus-type II). ...
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... the nine species of African Schoenoplectus nested within our Schoenoplectiella Clade, Van der Veken (1965) includes embryographs for three of these: Schoenoplectus rhodesicus, S. paludicola, and S. muricinux. All three possess strongly pileate, Schoenoplectus-type II embryos (Figs. 5, 6), and are more consistent in size with species of Schoenoplectiella than Schoenoplectus (Table 1). In summary, four groups of embryos are distinguished within Fuireneae s.l. and each corresponds to one of the four major clades retrieved in molecular studies, here recognized as tribes. ...
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... sensu Goetghebeur, 1986;Semmouri et al., 2019). Interestingly, the close relationships between the genera Actinoscirpus and Schoenoplectus s.s. (Schoenoplectus Clade), and between Pseudoschoenus and Schoenoplectiella s.l. (including tropical, largely African Schoenoplectus; the Schoenoplectiella Clade), are also supported by embryo morphology (Fig. 5). Whereas the scutellum in Actinoscirpus and Schoenoplectus s.s. is turbinate to rhomboid in shape (variant 2 sensu Van der Veken, 1965), species in the Schoenoplectiella Clade possess an umbonate or strongly pileate scutellum in the form of a mushroom cap with incurved margins (variant 3 sensu Van der Veken, ...
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... quartet support with blue for agreeing genes, red for disagreeing genes, and gray for uninformative genes. Fig. S4. Phylogenetic reconstruction of the relationships in tribe Fuireneae s.l. and related tribes based on analysis of the exons data set. Concatenated IQ-TREE analysis from RAxML gene trees. Numbers by nodes represent bootstrap support. Fig. S5. Phylogenetic reconstruction of the relationships in tribe Fuireneae s.l. and related tribes based on analysis of the supercontigs data set. Concatenated IQ-TREE analysis from RAxML gene trees. Numbers by nodes represent bootstrap support. Fig. S6. Phylogenetic reconstruction of the relationships in tribe Fuireneae s.l. and related ...
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... members of Fuireneae s.l. possess embryos with a more or less mushroom-shaped or top-shaped outline, with leaf primordia in a basal position and a lateral displacement of the root cap (Fig. 5). While rare in the family, fungiform embryos are also typical for tribe Eleocharideae and are sometimes found in some of the largest Abildgaardieae embryos, suggesting that this special morphology is a plesiomorphy for Fuireneae s.l. ( Semmouri et al., 2019). Nonetheless, subtle differences can be found among the different clades, and ...
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... has the largest embryos in Fuireneae s.l. (Table 1), with at least two species possessing embryos over a millimeter in length and more than half a millimeter in width. The embryo of Bolboschoenus is fungiform, with a broadened, rhomboid scutellum (Figs. 5, 6). The root cap is well differentiated, in a lateral position, and separated from the scutellum by a notch. The first leaf is well developed, J. Syst. Evol. 59(4): 809-832, 2021 www.jse.ac.cn and pie charts at nodes correspond to quartet support with blue for agreeing genes, red for disagreeing genes, and gray for uninformative ...
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... Actinoscirpus, Pseudoschoenus, Schoenoplectus, and Schoenoplectiella possess very similar embryos (Figs. 5, 6), two groups can be distinguished, which we designate here as Schoenoplectus-type I and Schoenoplectus-type II given their similarity. Whereas the scutellum in Actinoscirpus and Schoenoplectus s.s. is turbinate to rhomboid in shape, with straight to convex lower margins, the scutellum of Pseudoschoenus and Schoenoplectiella is often umbonate, with a distinct knob at the apex, or strongly pileate, with the margins clearly incurved (Schoenoplectus-type II). ...
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... of Pseudoschoenus and Schoenoplectiella is often umbonate, with a distinct knob at the apex, or strongly pileate, with the margins clearly incurved (Schoenoplectus-type II). These two groups correspond to the taxonomically significant embryo variants 2 and 3 of the Scirpus-type embryo sensu Van der Veken (1965) highlighted by Pignotti (2003) (Figs. 5, 6), and are more consistent in size with species of Schoenoplectiella than Schoenoplectus (Table 1). In summary, four groups of embryos are distinguished within Fuireneae s.l. and each corresponds to one of the four major clades retrieved in molecular studies, here recognized as tribes. While no embryo of Schoenoplectus section ...
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... sensu Goetghebeur, 1986;Semmouri et al., 2019). Interestingly, the close relationships between the genera Actinoscirpus and Schoenoplectus s.s. (Schoenoplectus Clade), and between Pseudoschoenus and Schoenoplectiella s.l. (including tropical, largely African Schoenoplectus; the Schoenoplectiella Clade), are also supported by embryo morphology (Fig. 5). Whereas the scutellum in Actinoscirpus and Schoenoplectus s.s. is turbinate to rhomboid in shape (variant 2 sensu Van der Veken, 1965), species in the Schoenoplectiella Clade possess an umbonate or strongly pileate scutellum in the form of a mushroom cap with incurved margins (variant 3 sensu Van der Veken, ...
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... quartet support with blue for agreeing genes, red for disagreeing genes, and gray for uninformative genes. Fig. S4. Phylogenetic reconstruction of the relationships in tribe Fuireneae s.l. and related tribes based on analysis of the exons data set. Concatenated IQ-TREE analysis from RAxML gene trees. Numbers by nodes represent bootstrap support. Fig. S5. Phylogenetic reconstruction of the relationships in tribe Fuireneae s.l. and related tribes based on analysis of the supercontigs data set. Concatenated IQ-TREE analysis from RAxML gene trees. Numbers by nodes represent bootstrap support. Fig. S6. Phylogenetic reconstruction of the relationships in tribe Fuireneae s.l. and related ...
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This paper provides a linear classification of two subfamilies, 24 tribes, 10 subtribes and 95 genera of the monocot family Cyperaceae (Poales), based on a stable phylogenetic framework resulting from years of morphological, molecular phylogenetic and phylogenomic studies. The family includes c. 5687 species. The most species-rich tribes are the mo...
Citations
... This has caused confusion in regard to species identification and sparked controversy in the taxonomy of Cyperaceae [7][8][9]. Therefore, more comprehensive explorations should be conducted such as HybSeq bait and targeted sequencing combined with traditional classification, to establish more accurate and reliable classification systems [10,11]. ...
Background
Cyperus stoloniferus is an important species in coastal ecosystems and possesses economic and ecological value. To elucidate the structural characteristics, variation, and evolution of the organelle genome of C. stoloniferus, we sequenced, assembled, and compared its mitochondrial and chloroplast genomes.
Results
We assembled the mitochondrial and chloroplast genomes of C. stoloniferus. The total length of the mitochondrial genome (mtDNA) was 927,413 bp, with a GC content of 40.59%. It consists of two circular DNAs, including 37 protein-coding genes (PCGs), 22 tRNAs, and five rRNAs. The length of the chloroplast genome (cpDNA) was 186,204 bp, containing 93 PCGs, 40 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 81 and 129 tandem repeats, respectively, and 346 and 1,170 dispersed repeats, respectively, both of which have 270 simple sequence repeats. The third high-frequency codon (RSCU > 1) in the organellar genome tended to end at A or U, whereas the low-frequency codon (RSCU < 1) tended to end at G or C. The RNA editing sites of the PCGs were relatively few, with only 9 and 23 sites in the mtDNA and cpDNA, respectively. A total of 28 mitochondrial plastid DNAs (MTPTs) in the mtDNA were derived from cpDNA, including three complete trnT-GGU, trnH-GUG, and trnS-GCU. Phylogeny and collinearity indicated that the relationship between C. stoloniferus and C. rotundus are closest. The mitochondrial rns gene exhibited the greatest nucleotide variability, whereas the chloroplast gene with the greatest nucleotide variability was infA. Most PCGs in the organellar genome are negatively selected and highly evolutionarily conserved. Only six mitochondrial genes and two chloroplast genes exhibited Ka/Ks > 1; in particular, atp9, atp6, and rps7 may have undergone potential positive selection.
Conclusion
We assembled and validated the mtDNA of C. stoloniferus, which contains a 15,034 bp reverse complementary sequence. The organelle genome sequence of C. stoloniferus provides valuable genomic resources for species identification, evolution, and comparative genomic research in Cyperaceae.
... Importantly, Brožová et al. (2022) fail to acknowledge that Larridon et al. (2021) presents a well supported, phylogeny-informed classification for the family with broad support from the Cyperaceae research community (as shown by the extensive authorship). Brožová et al. (2022) go on to state, "Recently, molecular phylogenetic studies on Cyperaceae have relied heavily on relatively few loci, such as a selection of plastid markers and the nuclear markers ITS and ETS (Semmouri et al., 2019;Léveillé-Bourret et al., 2018;Larridon et al., 2020;Starr et al., 2021;Villaverde et al., 2020aVillaverde et al., , 2020bVillaverde et al., , 2021." However, the last four studies listed (five in their list, as Villaverde et al., 2020a, 2020b refer to the same paper, Villaverde et al., 2020) are based on genome-scale high-throughput sequencing data, using either targeted sequencing (HybSeq) or restriction-site associated DNA sequencing (RAD-seq), with the latter study (Villaverde et al., 2021) Brožová et al. (2022) state: "The most recent study by Larridon et al. (2021) presented a comprehensive family-wide phylogenomic study of this family based on targeted sequencing using the Angiosperms353 probe kit sampling 311 accessions. ...
Broˇzov´a et al. (2022) present a study, “Toward finally unraveling the phylogenetic relationships of Juncaceae with respect to another cyperid family, Cyperaceae”, with the premise of revising the phylogenetic re-lationships in Juncaceae and Cyperaceae based on Sanger sequencing of one nuclear rDNA (ITS) and two plastid regions (the gene rbcL and the spacer trnL-F). While the paper highlights the need for ongoing taxo-nomic revision in Juncaceae, we are concerned that their analyses and conclusions could lead to nomenclatural instability and unnecessary confusion among researchers, particularly those working in cyperids (Cyperaceae, Juncaceae and Thurniaceae) and closely allied monocot lineages. Our concerns stem from the use of incomplete datasets and the failure to integrate recently published taxonomic literature. As a result, the systematic conclusions drawn by the authors are outdated and conflict with previous studies based on more complete phylogenomic datasets (e.g., Larridon et al., 2021), leading to unjustifiable (i.e., pro-posed recognition of non-monophyletic genera) and superfluous (i.e., already completed nomenclatural changes) recommendations.
While we acknowledge that Broˇzov´a et al. (2022) correctly show that Juncaceae is in need of further scientific attention, their conclusions about the larger clade containing both Cyperaceae and Juncaceae are based on a limited understanding of Cyperaceae taxonomy. As the au-thors accurately highlight in their Introduction, Cyperaceae and Jun-caceae are both well established as monophyletic families; the only studies that confused this issue were based on biased/incomplete sequence data, which was clarified nearly 20 years ago (e.g., Kristiansen et al., 2005; Dr´abkov´a & Vlˇcek, 2007). However, it is somewhat unclear from the outset whether Broˇzov´a et al. (2022) are more focused on Juncaceae (cf. Abstract, and the aims in the Introduction), or on cyperids (cf. Title, and the Introduction). By including Cyperaceae in their study, the authors risk taking the understanding of Cyperaceae taxonomy backwards since the paper presents outdated conclusions, potentially confounding readers.
... Recently, molecular phylogenetic studies on Cyperaceae have relied heavily on relatively few loci, such as a selection of plastid markers and the nuclear markers ITS and ETS (Semmouri et al., 2019;Léveillé-Bourret et al., 2018;Larridon et al., 2020;Starr et al., 2021;Villaverde et al., 2020aVillaverde et al., , 2020bVillaverde et al., , 2021. The most recent study by Larridon et al. (2021) presented a comprehensive family-wide phylogenomic study of this family based on targeted sequencing using the Angiosperms353 probe kit sampling 311 accessions. ...
... 22 tribes (depending on the author). Cyperaceae is generally studied more deeply than Juncaceae, and our datasets are not supposed to answer questions regarding fine-scale phylogeny at the level of species published recently (e.g., Barrett et al., 2019;Bauters et al., 2018;Global Carex Group, 2015;Elliott and Muasya, 2017, 2020bLarridon et al., 2018a,b;Léveillé-Bourret and Starr, 2019;Léveillé-Bourret et al., 2020;Roalson et al., 2019a,b;Villaverde et al., 2020;Starr et al. 2021;Larridon et al., 2021); therefore, we center our attention on the remaining problematic groups or taxa for which our combined data can shed light. Only two subfamilies were recognized in our data: Mapanioideae and Cyperoideae (e.g., Muasya et al., 2009). ...
... However, Caricoideae and Sclerioideae distinguished by Goetghebeur (1998) were not confirmed. The monophyly and main topology of the Cyperaceae tribes, as described by Semmouri et al. (2019), Starr et al. (2021) and Larridon et al. (2021), were confirmed. ...
Juncaceae is a cosmopolitan family belonging to the cyperid clade of Poales together with Cyperaceae and Thurniaceae. These families have global economic and ethnobotanical significance and are often keystone species in wetlands around the world, with a widespread cosmopolitan distribution in temperate and arctic regions in both hemispheres. Currently, Juncaceae comprises more than 474 species in eight genera: Distichia, Juncus, Luzula, Marsippospermum, Oreojuncus, Oxychloë, Patosia and Rostkovia. The phylogeny of cyperids has not been studied before in a complex view based on most sequenced species from all three families. In this study, most sequenced regions from chloroplast (rbcL, trnL, trnL-trnF) and nuclear (ITS1-5.8S-ITS2) genomes were employed from more than a thousand species of cyperids covering all infrageneric groups from their entire distributional range. We analyzed them by maximum parsimony, maximum likelihood, and Bayesian inference to revise the phylogenetic relationships in Juncaceae and Cyperaceae. Our major results include the delimitation of the most problematic paraphyletic genus Juncus, in which six new genera are recognized and proposed to recover monophyly in this group: Juncus, Verojuncus, gen. nov., Juncinella, gen. et stat. nov., Alpinojuncus, gen. nov., Australojuncus, gen. nov., Boreojuncus, gen. nov. and Agathryon, gen. et stat. nov. For these genera, a new category, Juncus supragen. et stat. nov., was established. This new classification places most groups recognized within the formal Juncus clade into natural genera that are supported by morphological characters.
... In tribe Scirpeae, the Linnean genus Scirpus L. was very heterogenous (Starr et al. 2021). Based on molecular phylogenetic and embryo morphology data, a series of new genera were described (e.g. ...
This paper provides a linear classification of two subfamilies, 24 tribes, 10 subtribes and 95 genera of the monocot family Cyperaceae (Poales), based on a stable phylogenetic framework resulting from years of morphological, molecular phylogenetic and phylogenomic studies. The family includes c. 5687 species. The most species-rich tribes are the monogeneric tribe Cariceae with c. 2003 species, and tribe Cypereae with c. 1131 species. The highest generic diversity is found in tribe Schoeneae (25 genera), which resulted in the recognition of eight subtribes to facilitate studying this group. The linear classification will help the organisation of Cyperaceae specimens in herbaria according to a systematic order and provides an easy-to-use summary of the current classification of the family.
... Most molecular phylogenetic studies so far have focused on Cyperoideae (e.g. Larridon et al., 2013Larridon et al., , 2018Larridon et al., , 2021bJiménez-Mejías et al., 2016;Starr et al., 2021), whereas the evolutionary relationships in Mapanioideae remain largely ununderstood. ...
Mapanoioideae are one of two subfamilies of Cyperaceae and consist of 186 species. Molecular phylogenetic relationships in subfamily Cyperoideae have recently been studied well, whereas evolutionary relationships in Mapanioideae remain little known. Subfamily Mapanioideae include two tribes. This study focuses on Hypolytreae, which is represented by three genera in Africa (Hypolytrum, Mapania and Principina). In this paper, we present the first molecular phylogenetic study of African Hypolytreae using a Sanger sequencing approach. We aim to (1) test whether Hypolytrum, Mapania and Principina are reciprocally monophyletic; (2) investigate whether the morphologically based sections in Hypolytrum and Mapania represent monophyletic taxa; (3) resolve species delimitation where multiple accessions could be sequenced and (4) explore the relationships of species occurring in West Tropical Africa vs. Central Africa. Our phylogenetic analyses strongly support Mapania and Hypolytrum as separate genera, but Principina is nested in Hypolytrum. This result is consistent with morphological differences. Mapania spp. are obligate rainforest species, but our results show that species from West Tropical Africa and species from Central Africa do not form separate clades. Dispersal between these regions may have happened during interglacial periods when the rainforest was continuous.
... In addition, early evidence suggests that Angiosperms353 genes, if analyzed appropriately, can be phylogenetically informative across multiple taxonomic scales (including at the population level; Beck et al., 2021 [Preprint]; Slimp et al., 2021;Wenzell et al., 2021). Broad uptake of Angiosperms353 is now being reported at conferences (e.g., Lagomarsino and Jabaily, 2020), but to date, published empirical studies in which applications of Angiosperms353 have been fully explored remain relatively few in number (Brewer et al., 2019;Van Andel et al., 2019;Gaynor et al., 2020;Howard et al., 2020 [Preprint]; Larridon et al., 2020Larridon et al., , 2021aLarridon et al., , 2021bMurphy et al., 2020;Shee et al., 2020;Baker et al., 2021;Beck et al., 2021 [Preprint]; Starr et al., 2021). This special issue, and its companion in Applications in Plant Sciences, aims to address this gap, and to thoroughly explore the potential and pitfalls of this exciting new toolkit. ...
... Within each of the groups covered here, Angiosperms353 is resetting the phylogenetic baseline with far larger data quantities than have previously been utilized, including the sampling of many genera for which no DNA sequence data are currently available in public repositories (e.g., Buerki et al., 2021;Clarkson et al., 2021). In some families (e.g., Commelinaceae: Zuntini et al., 2021;Cunoniaceae: Pillon et al., 2021;Cyperaceae: Larridon et al., 2021b, Starr et al., 2021Sapindaceae: Buerki et al., 2021) classifications are being revised as a result. ...
... There is mounting evidence that the sequence data recovered by the Angiosperms353 probe set are sufficiently variable to reconstruct relationships at the species level, especially when noncoding sequences serendipitously captured from regions flanking the target genes (the so-called "splash zone") are also taken into account. A number of studies exploring the suitability of Angiosperms353 for species-level phylogenetic inference have already been published (e.g., Gaynor et al., 2020;Howard et al., 2020 [Preprint]; Larridon et al., 2020Larridon et al., , 2021aLarridon et al., , 2021bMurphy et al., 2020;Shee et al., 2020;Starr et al., 2021). In this issue, A. Thomas et al. (2021a) specifically investigated specieslevel relationships among recently radiated lineages in Veronica sect. ...
In this special issue of the American Journal of Botany, together with a companion issue of Applications in Plant Sciences, we gather a set of papers that focus on a new, common phylogenomic toolkit, the Angiosperms353 probe set, and illustrate its potential for evolutionary synthesis by promoting open collaboration across our community.
... At the tribal level, significant changes were made to the circumscription of tribe Schoeneae with the exclusion of lineages now placed in tribes Carpheae and Cladieae (Semmouri et al., 2019), and within the Scirpo-Caricoid Clade, where Scirpeae was narrowly defined and four new tribes were created (Léveillé-Bourret et al., 2018a. In this Special Issue, Starr et al. (2021) and use targeted sequencing data in concert with traditional data sources to propose new tribal rearrangements and recircumscriptions. Starr et al. (2021) focus on tribe Fuireneae s.l., a group long known to be paraphyletic (e.g., Semmouri et al., 2019), but whose circumscription had not changed due to a lack of support for trees. ...
... In this Special Issue, Starr et al. (2021) and use targeted sequencing data in concert with traditional data sources to propose new tribal rearrangements and recircumscriptions. Starr et al. (2021) focus on tribe Fuireneae s.l., a group long known to be paraphyletic (e.g., Semmouri et al., 2019), but whose circumscription had not changed due to a lack of support for trees. With the benefit of significant novel sequence data and a topology congruent with morphology and embryo features, they propose a new classification for the Fuireneae s.l. ...
... Main changes to generic circumscriptions occurred in tribes Schoeneae (e.g., Elliott & Muasya, 2017;Larridon et al., 2018aLarridon et al., , 2018bBarrett et al., 2020Barrett et al., , 2021aBarrett et al., , 2021b, Cariceae (Global Carex Group, 2015), Abildgaardieae (e.g., Roalson et al., 2019;Larridon et al., 2021b), Trichophoreae (Léveillé-Bourret et al, 2020), and Cypereae (e.g., Larridon et al., 2011Larridon et al., , 2014. In this Special Issue, using both a targeted sequencing and an nrDNA data set, Starr et al. (2021) also recircumscribe Schoenoplectus and Schoenoplectiella to be reciprocally monophyletic, two genera whose limits have never clearly been marked. ...
... The combination of molecular data and morphological evidence is now supporting new taxonomic rearrangements in sedges (e.g. Míguez et al., 2018;Oda et al., 2019;Benítez-Benítez et al., 2021;Jiménez-Mejías et al., 2021;Larridon et al., 2021;. In addition, while relatively little with other sources of data, morphological and micromorphological characters of nutlets have successfully been employed in Carex taxonomy. ...
Carex sect. Confertiflorae s.l. is a medium sized species group (ca. 40 species) with its center of diversity in E Asia (China and Japan). According to morphological traits, the section has been proposed to split into two sections (sects. Confertiflorae sensu Ohwi and Molliculae Ohwi) up to five different ones (sects. Confertiflorae s.s., Molliculae, Dispalatae Ohwi, Ischnostachyae Ohwi and Alliiformes Akiyama). Recent phylogenetic reconstructions showed Confertiflorae s.l. not to be monophyletic, since species traditionally considered part of it were found to belong to other clades, while species traditionally ascribed to other sections were nested within it. In this study, we investigated the phylogenetic structure, morphological affinities, and biogeographic history of sect. Confertiflorae s.l. We performed a taxon-based approach to explore the morphological affinities of the species considered in sect. Confertiflorae and compared the micromorphology of the nutlets of almost all the taxa using SEM. We included 40 samples representing 31 species/subspecies of sect. Confertiflorae s.l., and used two nuclear (ETS and ITS) and three plastid (trnL-F, matK and rpl32-trnLUAG) molecular markers to reconstruct the phylogeny of the group. The phylogenetic analyses confirmed the polyphyly of sect. Confertiflorae s.l., whose representatives were found within five distinct clades. From these, two clades, sect. Confertiflorae and sect. Molliculae were found to be closely related and contained the majority of the species. The composition of the two clades agreed with the morphological structure of the group, and we confirmed an exclusive combination of features (viz. color of basal sheaths, presence of bract sheath, peduncle of lowest spike, inflorescence sex distribution, shape of pistillate glume apex, and color and veins of utricle, among others) characterizing each of the two clades. The origin of the two clades was found to be in the early Pliocene while the majority of the diversification events within each clade took place during the Pleistocene. This illustrate that despite Asia has been regarded as having little potential ecological space for Carex to diversify because its climate stability, groups of sedges sub-endemic from that area may have a fairly recent origin related to glaciations. We proposed the rearrangement of sect. Confertiflorae as previously conceived as three independent sections: the monotypic Alliiformes, sect. Molliculae, and sect. Paludosae.
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... Hence, reducedrepresentation sequencing methods have been developed to sample hundreds of nuclear, orthologous single-copy genes for plant phylogenetic studies (Kadlec et al., 2017;Couvreur et al., 2019;Johnson et al., 2019;Villaverde et al., 2018Villaverde et al., , 2020, allowing users to yield data sets of a larger scale for phylogenetics without the bioinformatic challenges and costs associated with whole-genome sequencing. Larridon et al. (2020) provided an overview of earlier high-throughput sequencing studies on Cyperaceae, whereas more recent studies relying on genomic data already show alternative phylogenetic structure in certain sedge groups not previously recovered using Sanger sequencing (Léveillé-Bourret et al., 2018c;Larridon et al., 2020;Starr et al., 2021;Villaverde et al., 2020Villaverde et al., , 2021. ...
... In addition, 36 accessions enriched with the Angiosperms I kit for Anchored Phylogenomics (Léveillé-Bourret et al., 2018c), including Khaosokia caricoides D.A.Simpson, were mined for reads overlapping with the data generated using the Angiosperms353 probes, as were 6 accessions enriched with Cyperaceae-specific probes , and 20 transcriptomes available on GenBank (Table S1). Angiosperms353 data for most accessions were newly generated for this study, following the protocol established by Baker et al. (2021). In addition, some data were obtained from recent studies (Larridon et al., , 2021cStarr et al., 2021; Table S1). ...
... Angiosperms353 data for most accessions were newly generated for this study, following the protocol established by Baker et al. (2021). In addition, some data were obtained from recent studies (Larridon et al., , 2021cStarr et al., 2021; Table S1). ...
Cyperaceae (sedges) are the third largest monocot family and are of considerable economic and ecological importance. Sedges represent an ideal model family to study evolutionary biology because of their species richness, global distribution, large discrepancies in lineage diversity, broad range of ecological preferences, and adaptations including multiple origins of C4 photosynthesis and holocentric chromosomes. Goetghebeur’s seminal work on Cyperaceae published in 1998 provided the most recent complete classification at tribal and generic level, based on a morphological study of Cyperaceae inflorescence, spikelet, flower and embryo characters plus anatomical and other information. Since then, several family‐level molecular phylogenetic studies using Sanger sequence data have been published. Here, more than 20 years after the last comprehensive classification of the family, we present the first family‐wide phylogenomic study of Cyperaceae based on targeted sequencing using the Angiosperms353 probe kit sampling 311 accessions. Additionally, 62 accessions available from GenBank were mined for overlapping reads and included in the phylogenomic analyses. Informed by this backbone phylogeny, a new classification for the family at the tribal, subtribal and generic levels is proposed. The majority of previously recognized suprageneric groups are supported, and for the first time we establish support for tribe Cryptangieae as a clade including the genus Koyamaea. We provide a taxonomic treatment including identification keys and diagnoses for the 2 subfamilies, 24 tribes and 10 subtribes and basic information on the 95 genera. The classification includes five new subtribes in tribe Schoeneae: Anthelepidinae, Caustiinae, Gymnoschoeninae, Lepidospermatinae and Oreobolinae.
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In the present investigation, nutlet morphological and micro‐morphological characters were analyzed using Light Microscope (LM) and Scanning Electron Microscope (SEM) in 38 taxa under 13 genera from the sub‐family Cyperoideae of Cyperaceae to find out whether these characters are taxonomically important or not. Nutlet morphology and surface characters of the representative taxa from all the possible tribes under the sub‐family Cyperoideae namely, Fuireneae, Cypereae, Cariceae, Abildgaardieae, Eleocharideae, Pseudoschoeneae, Schoenoplecteae, and Sclerieae were evaluated for their taxonomic significance. Cluster analysis was employed considering nutlet morphological characters to determine the overall similarity among the taxa based on 153 character states. Except in few specified cases, grouping of the taxa in the clusters is in accordance to the taxonomic treatments made by recent Cyperologists. Nutlets in the tribe Abildgaardieae showed maximum level of variability in size, shape, and surface ornamentation at the level of higher taxon, but showed specificity at the species level. Tuberculate, striate‐reticulate, and transversely wavy ridged surface ornamentations were found in different species of Fimbristylis . Previously described cryptic variation, and effect of different ploidy level were not reflected in nutlet surface morphology and micromorphology in Fimbristylis dichotoma and F. ovata complexes which was previously made the taxa taxonomically very difficult. Serrulate anticlinal wall in F. bisumbellata was the most unique in Fimbristylis . Species under the megadiverse genus Carex representing the tribe Cariceae showed very unique type of surface ornamentation. Surface walls of all the studied species of Carex were characterized by polygonal epidermal cells with single conical silica body (2–3 per cell in C. speciosa ) of variable length and sizes. Most interestingly, in C. nubigena , presence of the central silica body and peripheral satellites was not consistent. Based on the presence and absence, two different variants under the species were identified. In C. nubigena , when silica body was present, epidermal cells were characterized by central conical silica body surrounded by variable number of satellites. The present investigation first time reports this novel nutlet surface character in C. nubigena . Among the studied characters, length and height of conical, height of apex, and width of apex are variable among Carex species. On the other hand, exclusion of the genera Schoenoplectiella and Schoenoplectus from tribe Scirpeae s.l. and placement under the tribes Pseudoschoeneae and Schoenoplecteae (respectively) was also supported by the present investigation. The present study also confirms that nutlet morphological and micro‐morphological characters are useful in identification and arrangement of different taxa under the subfamily Cyperoideae of Cyperaceae. Result of the present investigation was correlated and discussed in comparative manner with the treatments of the recent past.
