Table of Contents

01 July 2021, Volume 59 Issue 4
Cover illustration: Landscape: Carex reuteriana Boiss. ssp. reuteriana. Urbión river, Viniegra de Arriba, La Rioja, Spain. Photo by P. Jiménez-Mejías. Spike: Carex reuteriana ssp. mauritanica (Boiss. & Reuter) Jim.-Mejías & Luceño. La Cimbarra, Jaén, Spain. Photo by S. Martín-Bravo. Designed by P. Jiménez-Mejías.
    Issue Information
  • Editorial
  • Pedro Jiménez-Mejías and Isabel-Larridon
    J Syst Evol. 2021, 59(4): 623-626.

    Cyperaceae are among the 10 most diverse angiosperm families and the third largest among monocots (Christenhusz & Byng, 2016), with a critical ecological role in wetlands and in high-latitude and high-elevation ecosystems. Sedges represent an ideal model plant 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 (Larridon et al., 2021a).

    In the last two decades, molecular phylogenetics has revolutionized our understanding of the sedge family. The first phylogenetic approaches beyond morphology used chromosomes (e.g., Heilbron, 1924), relationships with parasitic fungi (e.g., Savile & Calder, 1954), and flavonoids (e.g., Kukkonen, 1971). However, the current systematic framework of Cyperaceae started to take root with the advent of the first suprageneric phylogeny of Cyperaceae (based on a single chloroplast marker -rbcL- and a limited sampling; Muasya et al., 1998) and the first molecular phylogeny of Carex s.l. (based on nuclear -ITS- sequence data; Starr et al., 1999). Through collaboration and technical advances such as high-throughput sequencing, we have now achieved much more in-depth sampling of taxa and DNA regions. Thanks to these efforts, the latest evolutionary relationships retrieved for the sedge family have obtained stronger support than in previous works. On the one hand, new phylogenomic approaches have generated a wealth of sequence data, allowing re-investigation of fast-evolving Cyperaceae lineages in which relationships could not be resolved using Sanger sequencing data (Larridon et al., 2020). On the other hand, the increasing availability of bioclimatic data, digitized herbarium material, communication channels, plant material interchange opportunities, and new bioinformatic tools has allowed the gathering, analysis, and processing of information in a way that was not possible just a decade ago. This has enabled continuous and successful collaborations among researchers across the globe, and it has opened new research horizons for the international Cyperaceae research community to investigate the systematics, taxonomy, biogeography, ecology, morphology, and evolution of key characters in sedges such as chromosomes and C4 photosynthesis. The achievements of the Global Carex Group (GCG) serve as a best-practice example. In 2013, this consortium of researchers initiated a collaborative sampling effort that led to an on-hand sampling of about 80% of the approximately 2000 species of the giant genus Carex. Among other milestones, the GCG has conducted a massive sequencing effort (Jiménez-Mejías et al., 2016a), performed a thorough revision of the fossil record of Carex (Jiménez-Mejías et al., 2016b), and provided Carex with a robust backbone phylogeny of its major lineages using phylogenomics (Villaverde et al., 2020). Together, this allowed for the first time the possibility of addressing the biogeographic history of Carex from a global perspective using a sampling of >60% of the c. 2000 spp. of the genus (Martín-Bravo et al., 2019). Moreover, with the recent creation of the International Sedge Society, wider and even more ambitious research projects involving the entire international Cyperaceae research community will soon be possible. This Special Issue brings together a series of the most modern studies on the systematics and evolution of Cyperaceae that are the result of the new opportunities offered by our data-rich era and international collaboration.

    The increased availability of DNA sequence data has led to higher-level taxonomic changes in Cyperaceae. Previously organized into four subfamilies, 14 tribes, and 104 genera (Goetghebeur, 1998), the earliest DNA sequence studies (e.g., Muasya et al., 2009a2009b) demonstrated that many of these traditional groups were defined by plesiomorphies and homoplasies, which meant that numerous tribes and genera were unnatural. 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., 2018a2018b; Léveillé-Bourret & Starr, 2019). In this Special Issue, Starr et al. (2021) and Larridon et al. (2021a) use targeted sequencing data in concert with traditional data sources to propose new tribal rearrangements and re-circumscriptions. 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. Grade that involves four tribes, one of which is new. Larridon et al. (2021a) use a representative sampling of almost all the recognized sedge genera to provide a new classification of the family supported by phylogenomic data. This paper also provides a complete overview of the classification history of Cyperaceae.

    Molecular phylogenetic studies have equally contributed to rearrangements at the generic level. Main changes to generic circumscriptions occurred in tribes Schoeneae (e.g., Elliott & Muasya, 2017; Larridon et al., 2018a2018b; Barrett et al., 20202021a2021b), 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., 20112014). 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.

    At the infrageneric level, the GCG re-examines the classification of the giant genus Carex. Being one of the three largest non-apomictic genera of the world, the revision and recircumscription of Carex started by merging it with its segregate genera to become monophyletic (GCG, 2015) and has continued through a series of later publications (e.g., Jiménez-Mejías et al., 2016; Villaverde et al., 2020). In this Special Issue, Roalson et al. (2021) re-evaluate the infrageneric classification of Carex using a systematic perspective and organizing principles that will serve as a roadmap to future research on Carex.

    At lower taxonomic levels, much work remains to resolve relationships between species, uncover previously undescribed diversity, and unravel species complexes. Here, using an integrated taxonomy approach, Reznicek et al. (2021) monograph Carex sect. Schiedeanae, a highly diverse group in Mexico, where they describe 10 new species. In the same line, Lu et al. (2021) revise the phylogenetic relationships and morphological limits of two Carex sections whose delimitation has been unclear—sects. Confertiflorae and Molliculae—and provide the first insights into Carex phylogeography in Eastern Asia. These examples show the strength of combining multiple data sources to investigate the evolution and diversity of Cyperaceae lineages and it demonstrates that considerable work is still needed on understudied lineages and geographic regions, as also found by recent studies in other sedge groups (e.g., Jiménez-Mejías et al., 2021; Luceño et al., 2021). Using population genomics based on RADseq data and ecological niche modeling, Nygaard et al. (2021) found that Carex jemtlandica and C. lepidocarpa in Carex sect. Ceratocystis represent separately evolving entities that remain distinct in sympatry despite ongoing hybridization and introgression. As such, we are moving toward solving the long-standing questions about taxon limits within this species complex, a problem evaluated multiple times using Sanger sequencing (Jiménez-Mejías et al., 20122017) and allozyme variation (Hedrén & Prentice, 1996; Hedrén, 20022004; Blackstock, 2007) without clear resolution. Population genomics using GBS, RADseq, or targeted sequencing methods offer hope to tackle many more species complexes in future, as has already been shown in previous research efforts on sedges (Escudero et al., 2014; Maguilla et al., 2017; Léveillé-Bourret et al., 2020; Luceño et al., 2021).

    Recently, deeply sampled phylogenetic data sets of several species-rich Cyperaceae lineages have been the subject of both biogeographical and diversification analyses (e.g., Spalink et al., 2016a2016b; Martín-Bravo et al., 2019; Larridon et al., 2021c2021d). Here, two new studies help further understand biogeographical and diversification patterns in Cyperaceae. Benítez-Benítez et al. (2021) uncover the geographical vs. ecological diversification patterns in Carex sect. Phacocystis by integrating a phylogeny of 82% of extant species of this large group with GBIF occurrence data. Elliott et al. (2021) show that the genus Schoenus (Cyperaceae) is now monophyletic after recent taxonomic work in the last few years (Elliott & Muasya, 2017; Barrett et al., 2019; Barrett et al., 2020; Barrett et al., 2021b). Their study also indicates that Schoenus originated in the Western Australian biodiversity hotspot, from where it diversified into a lineage of >150 extant species dispersed around the globe.

    Large data sets also provide opportunities to address new questions. Here, Pender et al. (2021) show how trait evolution rates shape continental patterns of species richness in Carex, North America′s most diverse angiosperm genus, while Léveillé-Bourret et al. (2021) explore coevolution between parasitic rust fungi (Basidiomycota) and sedges and rushes. The data-rich era also allows for the Cyperaceae family to be used as a model family to investigate wider biological questions such as assessing the sensitivity of divergence time estimates to locus sampling, calibration points, and model priors (Villaverde et al., 2021), and assessing the effects of rapid chromosome number evolution on lineage diversification (Márquez-Corro et al., 2021).

    We hope that this set of papers will stimulate future integrative research in sedges and promote the use of this extraordinary family as a model for exploring the diversity and evolution of life on Earth.

  • Research Articles
  • Malene Nygaard, Petri Kemppainen, James D. M. Speed, Reidar Elven, Kjell Ivar Flatberg, Leif P. Galten, Narjes Yousefi, Heidi Solstad, and Mika Bendiksby
    J Syst Evol. 2021, 59(4): 627-641.
    Carex section Ceratocystis (Cyperaceae) is a group of recently evolved plant species, in which hybridization is frequent, introgression is documented, taxonomy is complex, and morphological boundaries are vague. Within this section, a unified taxonomic treatment of the Carex jemtlandicaCarex lepidocarpa species complex does not exist, and Norway may currently be the sole country accepting species rank for both. Carex jemtlandica is mainly confined to Fennoscandia and is thus a Fennoscandian conservation responsibility. This motivated us to test the principal hypothesis that both C. jemtlandica and C. lepidocarpa represent evolutionary significant units, and that both deserve their current recognition at species level. We investigated their evolutionary distinctiveness in Norway, using restriction site-associated DNA sequencing and ecological niche modeling. Our genomic results reveal two genetic clusters, largely corresponding to C. jemtlandica and C. lepidocarpa that also remain distinct in sympatry, despite clear indications of ongoing hybridization and introgression. The ecological niche modeling suggests that they occupy different environmental niches. Jointly, our results clearly show that C. jemtlandica and C. lepidocarpa represent separately evolving entities that should qualify recognition as evolutionary significant units. Given the high level of introgression compared to other hybridizing species pairs in Carex we recommend treating C. jemtlandica as a subspecies of C. lepidocarpa.
  • Carmen Benítez-Benítez, Santiago Martín-Bravo, Charlotte S. Bjorå, Sebastian Gebauer, Andrew L. Hipp, Matthias H. Hoffmann, Modesto Luceño, Tyril M. Pedersen, Anton Reznicek, Eric Roalson, Polina Volkova, Okihito Yano, Daniel Spalink, and Pedro Jiménez-Mejías
    J Syst Evol. 2021, 59(4): 642-667.
    Carex section Phacocystis (Cyperaceae) is one of the most diverse and taxonomically complex groups of sedges (between 116 and 147 species), with a worldwide distribution in a wide array of biomes. It has a very complicated taxonomic history, with numerous disagreements among different treatments. We studied the biogeography and niche evolution in a phylogenetic framework to unveil the relative contribution of geographical and ecological drivers to diversification of the group. We used a large species sampling of the section (82% of extant species) to build a phylogeny based on four DNA regions, constrained with a phylogenomic HybSeq tree and dated with six fossil calibrations. Our phylogenetic results recovered section Phacocystis s.s. (core Phacocystis) as sister to section Praelongae. Ancestral area reconstruction points toward the N Pacific as the cradle for the crown diversification of section Phacocystis during the Middle Miocene. Wide distributions were recurrently inferred across deep nodes. Large Northern Hemisphere lineages with geographical congruence were retrieved, pointing toward the importance of allopatric divergence at deep phylogenetic levels, whereas within-area speciation emerges as the predominant pattern at shallow phylogenetic level. The Southern Hemisphere (Neotropics, SW Pacific) was colonized several times from the Northern Hemisphere. The global expansion of Carex section Phacocystis did not entail major ecological changes along the inner branches of the phylogeny. Nevertheless, ecological differentiation seems to gain importance toward recent times.
  • Yi-Fei Lu, Xiao-Feng Jin, Hiroshi Ikeda, Okihito Yano, Carmen Benítez-Benítez, Wei-Jie Chen, Yong-Di Liu, Pedro Jiménez-Mejías, and Ming-Jian Yu
    J Syst Evol. 2021, 59(4): 668-686.
    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, as species traditionally considered part of it were found to belong to other clades, whereas 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 employed 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-trnL UAG) 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 (namely 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; however, the majority of the diversification events within each clade took place during the Pleistocene. This illustrates that although Asia has been regarded as having little potential ecological space for Carex to diversify due to 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.
  • Tamara Villaverde, Enrique Maguilla, Modesto Luceño, and Andrew L. Hipp
    J Syst Evol. 2021, 59(4): 687-697.
    Restriction site-associated DNA sequencing (RAD-seq) and related methods have become relatively common approaches to resolve species-level phylogeny. It is not clear, however, whether RAD-seq data matrices are well suited to relaxed clock inference of divergence times, given the size of the matrices and the abundance of missing data. We investigated the sensitivity of Bayesian relaxed clock estimates of divergence times to alternative analytical decisions on an empirical RAD-seq phylogenetic matrix. We explored the relative contribution of secondary calibration strategies, amount of missing data, and the data partition analyzed to overall variance in divergence times inferred using BEAST MCMC analyses of Carex section Schoenoxiphium (Cyperaceae)—a recent radiation for which we have nearly complete species sampling of RAD-seq data. The crown node for Schoenoxiphium was estimated to be 15.22 (9.56–21.18) Ma using a single calibration point and low missing data, 11.93 (8.07–16.03) Ma using multiple calibration points and low missing data, and 8.34 (5.41–11.22) using multiple calibrations but high missing data. We found that using matrices with more than half of the individuals with missing data inferred younger mean ages for all nodes. Moreover, we have found that our molecular clock estimates are sensitive to the positions of the calibration(s) in our phylogenetic tree (using matrices with low missing data), especially when only a single calibration was applied to estimate divergence times. These results argue for sensitivity analyses and caution in interpreting divergence time estimates from RAD-seq data.
  • Anton A. Reznicek, María del Socorro González-Elizondo, Marlene Hahn, Mira Garner, and Andrew L. Hipp
    J Syst Evol. 2021, 59(4): 698-725.
    Carex section Schiedeanae (subg. Euthyceras) has long been thought to comprise at most five species of Mexican sedges. Our morphological studies in the field and herbarium, however, supported by more recent DNA sequencing work, demonstrate that the section is, in fact, three times as species-rich, making it one of the largest sections in Mexico. Its 15 species range from Chihuahua to Tamaulipas south to Veracruz and Oaxaca; a single species, Carex muriculata, extends into the United States. The section has unusual inflorescences with simple (except in Carex complexa), uniformly androgynous, sessile spikes, utriculiform cladoprophylls, and perigynia with a unique combination of pubescence types composed of papillae; unicellular, simple hairs; and (in many species) multicellular tubercles. We recognize five previously described species (C. muriculataCarex perstrictaCarex schiedeana, Carex stellata, and Carex vizarronensis) and describe 10 additional species (Carex angustilepis, Carex cabralii, Carex complexa, Carex dentata, Carex gypsophila, Carex mesophila, Carex paneroi, Carex planilamina, Carex revoluta, and Carex tehuacana). We have expanded the morphological features used in the section to include particularly anther, staminate scale, and style features, and more detailed micromorphology of the perigynia, especially indumentum. In total, 13 of the 15 species recognized herein, with a total of 32 individuals, were examined for ETS and ITS for phylogenetic reconstruction. Phylogenetically, the xeric species (plus C. paneroi) form a grade leading to a clade of the more mesophytic species adapted to forest understories, plus the unique cliff dwelling C. complexa.
    Carex section Schiedeanae (subg. Euthyceras) is revised to consist of 15 species, including 10 species described here. They range from one species reaching into the southeastern United States to southern Mexico. All species essentially occur in calcareous soils (including one gypsum endemic) and many occur in very dry habitats and display local endemism.
  • Global Carex Group, Eric H. Roalson, Pedro Jiménez-Mejías, Andrew L. Hipp, Carmen Benítez-Benítez, Leo P. Bruederle, Kyong-Sook Chung, Marcial Escudero, Bruce A. Ford, Kerry Ford, Sebastian Gebauer, Berit Gehrke, Marlene Hahn, Muhammad Qasim Hayat, Mathias H. Hoffmann, Xiao-Feng Jin, Sangtae Kim, Isabel Larridon, Étienne Léveillé-Bourret, Yi- Fei Lu, Modesto Luceño, Enrique Maguilla, Jose Ignacio Márquez-Corro, Santiago Martín-Bravo, Tomomi Masaki, Mónica Míguez, Robert F. C. Naczi, Anton A. Reznicek, Daniel Spalink, Julian R. Starr, Uzma, Tamara Villaverde, Marcia J. Waterway, Karen L. Wilson, and Shu-Ren Zhang
    J Syst Evol. 2021, 59(4): 726-762.
    Phylogenetic studies of Carex L. (Cyperaceae) have consistently demonstrated that most subgenera and sections are para- or polyphyletic. Yet, taxonomists continue to use subgenera and sections in Carex classification. Why? The Global Carex Group (GCG) here takes the position that the historical and continued use of subgenera and sections serves to (i) organize our understanding of lineages in Carex, (ii) create an identification mechanism to break the ~2000 species of Carex into manageable groups and stimulate its study, and (iii) provide a framework to recognize morphologically diagnosable lineages within Carex. Unfortunately, the current understanding of phylogenetic relationships in Carex is not yet sufficient for a global reclassification of the genus within a Linnean infrageneric (sectional) framework. Rather than leaving Carex classification in its current state, which is misleading and confusing, we here take the intermediate steps of implementing the recently revised subgeneric classification and using a combination of informally named clades and formally named sections to reflect the current state of our knowledge. This hybrid classification framework is presented in an order corresponding to a linear arrangement of the clades on a ladderized phylogeny, largely based on the recent phylogenies published by the GCG. It organizes Carex into six subgenera, which are, in turn, subdivided into 62 formally named Linnean sections plus 49 informal groups. This framework will serve as a roadmap for research on Carex phylogeny, enabling further development of a complete reclassification by presenting relevant morphological and geographical information on clades where possible and standardizing the use of formal sectional names.
    Major clades and classification units of Carex (Cyperaceae) as recognized in the revised classification presented. Formal classification units including subgenera and sections and informal classification units (clades) are recognized to reorganize the infrageneric classification of the genus.
  • Jocelyn E. Pender, Andrew L. Hipp, Marlene Hahn, and Julian R. Starr
    J Syst Evol. 2021, 59(4): 763-775.
    Ecological opportunity has been associated with increases in diversification rates across the tree of life. Under an ecological diversification model, the emergence of novel environments is hypothesized to promote morpho- and ecospace evolution. Whether this model holds at the clade level within the most species-rich angiosperm genus found in North America (Carex, Cyperaceae) is yet to be tested. Recent works demonstrate a temporal coupling of climate cooling and widespread colonization of Carex in North America, implicating ecological diversification. In addition, research has consistently found asymmetric patterns of lineage-level diversification in the genus. Why does variation in clade sizes exist in the genus? Is ecological diversification involved? In this study, we tested whether rates of morphological and ecological trait evolution are correlated with clade-level species richness in Carex of North America north of Mexico. We constructed a phylogeny of 477 species—an almost complete regional sample. We estimated rates of evolution of morphological traits, habitat, and climatic niche and assessed whether differences in rates of evolution correlate with species richness differences in replicate non-nested sister clades. Our work demonstrates significant positive correlations between climatic niche rates, habitat and reproductive morphological evolution, and species richness. This coupling of trait and niche evolution and species richness in a diverse, continental clade sample strongly suggests that the ability of clades to explore niche and functional space has shaped disparities in richness and functional diversity across the North American flora region. Our findings highlight the importance of the evolutionary history of trait and niche evolution in shaping continental and regional floras.
    We tested whether rates of morphological and ecological trait evolution are correlated with clade-level species richness in Carex of North America north of Mexico using a non-nested sister clade comparison method. Our work demonstrates significant positive correlations between climatic niche rates, habitat and reproductive morphological evolution, and species richness. Our findings highlight the importance of the evolutionary history of trait and niche evolution in shaping continental and regional floras.
  • José I. Márquez-Corro, Santiago Martín-Bravo, Pedro Jiménez-Mejías, Andrew L. Hipp, Daniel Spalink, Robert F. C. Naczi, Eric H. Roalson, Modesto Luceño, and Marcial Escudero
    J Syst Evol. 2021, 59(4): 776-790.
    Changes in holocentric chromosome number due to fission and fusion have direct and immediate effects on genome structure and recombination rates. These, in turn, may influence ecology and evolutionary trajectories profoundly. Sedges of the genus Carex (Cyperaceae) comprise ca. 2000 species with holocentric chromosomes. The genus exhibits a phenomenal range in the chromosome number (2n = 10 − 132) with almost not polyploidy. In this study, we integrated the most comprehensive cytogenetic and phylogenetic data for sedges with associated climatic and morphological data to investigate the hypothesis that high recombination rates are selected when evolutionary innovation is required, using chromosome number evolution as a proxy for recombination rate. We evaluated Ornstein–Uhlenbeck models to infer shifts in chromosome number equilibrium and selective regime. We also tested the relationship between chromosome number and diversification rates. Our analyses demonstrate significant correlations between morphology and climatic niche and chromosome number in Carex. Nevertheless, the amount of chromosomal variation that we are able to explain is very small. We recognized a large number of shifts in mean chromosome number, but a significantly lower number in climatic niche and morphology. We also detected a peak in diversification rates near intermediate recombination rates. In combination, these analyses point toward the importance of chromosome evolution to the evolutionary history of Carex. Our work suggests that the effect of chromosome evolution on recombination rates, not just on reproductive isolation, may be central to the evolutionary history of sedges.
  • Tammy L. Elliott, Ruan van Mazijk, Russell L. Barrett, Jeremy J. Bruhl, Simon Joly, Ngalirendwe Muthaphuli, Karen L. Wilson, and A. Muthama Muasya
    J Syst Evol. 2021, 59(4): 791-808.
    The predominantly austral genus Schoenus L. is the largest genus in tribe Schoeneae and one of the ten most species-rich Cyperaceae genera, with over 150 accepted species found mostly in Australia, New Zealand, southeast Asia, and southern Africa. Here, we use data based on two nuclear and three plastid DNA regions to present one of the most comprehensive phylogenetic reconstructions of a genus in Cyperaceae to date, covering over 70% of described species of Schoenus. After recent taxonomic realignments in the last 4 years have both added and removed species from the genus, we show that Schoenus is now monophyletic. In addition, our results indicate that Schoenus originated in Western Australia in the Paleocene and eventually dispersed to surrounding continents, but rarely back. The diversification rate of the genus appears to have slightly decreased over time, and there has not been an increase associated with the establishment of the Cape clade endemic to the sclerophyllous fynbos vegetation type, such as has been reported in other plant lineages endemic to the Cape region. These results will serve as a template to understanding the complex patterns of genome size evolution and to untangle drivers of diversification in this genus.
  • Julian R. Starr, Pedro Jiménez-Mejías, Alexandre R. Zuntini, Étienne Léveillé-Bourret, Ilias Semmouri, Muthama Muasya, William J. Baker, Grace E. Brewer, Niroshini Epitawalage, Isabel Fairlie, Félix Forest, Izai A. B. Sabino Kikuchi, Lisa Pokorny, and Isabel Larridon
    J Syst Evol. 2021, 59(4): 809-832.
    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 Schoenoplectiella, a genus of mainly small, amphicarpic annuals that was recently segregated from Schoenoplectus. Consequently, despite ample evidence from molecular analyses that Fuireneae s.l. might consist of two to four tribal lineages, no taxonomic changes have yet been made. Here, we use the Angiosperms353 enrichment panel for targeted sequencing to (i) clarify the relationships of Fuireneae s.l. with the related tribes Abildgaardieae, Eleocharideae, and Cypereae; (ii) define the limits of Fuireneae s.s., and (iii) test the monophyly of Fuireneae s.l. genera with emphasis on Schoenoplectus and Schoenoplectiella. Using more than a third of Fuireneae s.l. diversity, our phylogenomic analyses strongly support six genera and four major Fuireneae s.l. clades that we recognize as tribes: Bolboschoeneae stat.nov., Fuireneae s.s., Schoenoplecteae, and Pseudoschoeneae tr. nov. These results are consistent with morphological, micromorphological (nutlet epidermal cell shape), and embryo differences detected for each tribe. At the generic level, most sub-Saharan African perennials currently treated in Schoenoplectus are transferred to Schoenoplectiella. Our targeted sequencing results show that these species are nested in Schoenoplectiella, and their treatment here is consistent with micromorphological and embryo characters shared by all Schoenoplectiella species. Keys to recognized tribes and genera are provided.
  • Étienne Léveillé-Bourret, Quinn Eggertson, Sarah Hambleton, and Julian R. Starr
    J Syst Evol. 2021, 59(4): 833-851.
    Plants play important roles as habitat and food for a tremendous diversity of specialist animals and fungi. The disappearance of any plant species can lead to extinction cascades of its associated biota. In consequence, documenting the diversity and specificity of plant-associated organisms is of high practical relevance in biodiversity conservation. Here, we present the first large-scale molecular investigation into the diversity, host specificity, and cophylogenetic congruence of an especially rich plant–fungal association, the rust fungi (Pucciniaceae) of Cyperaceae and Juncaceae. Using the largest rust fungi DNA barcoding dataset published to date (252 sequences, 82 taxa), we reject the presence of a global ITS2-28S barcode gap, but find a local gap in Cyperaceae–Juncaceae rusts, and suggest the existence of many cryptic species in North America, with some broadly circumscribed species possibly corresponding to >10 cryptic species. We test previous hypotheses of correlations between the phylogenies of rust fungi and their Cyperaceae–Juncaceae hosts using a combination of global-fit and event-based cophylogenetic methods. A significant cophylogenetic signal is detected between rusts and their hosts, but the small number of cospeciations argues for preferential host jumps as the driving process behind these correlations. In addition, temporal congruence between the origin of major Carex clades and their rusts suggests that host diversification may have promoted parasite diversification. Finally, we discuss the relevance of rust infection patterns to the systematics of Cyperaceae, highlight some taxonomic problems uncovered by the analyses, and call attention to the promise of DNA barcoding for bridging knowledge gaps in poorly studied plant-associated microorganisms.
    Phylogenies of Cyperaceae, Juncaceae, and their rusts (Pucciniaceae) are congruent, despite few cospeciation events, suggesting that preferential host jumps generated the cophylogenetic signal. Host diversification may have promoted parasite diversification, given the temporal congruence between the origin of major Carex clades and their rusts. This large DNA barcoding effort (252 sequences, 82 taxa) also uncovered many potential cryptic species.
  • Isabel Larridon, Alexandre R. Zuntini, Étienne Léveillé-Bourret, Russell L. Barrett, Julian R. Starr, A. Muthama Muasya, Tamara Villaverde, Kenneth Bauters, Grace E. Brewer, Jeremy J. Bruhl, Suzana M. Costa, Tammy L. Elliott, Niroshini Epitawalage, Marcial Escudero, Isabel Fairlie, Paul Goetghebeur, Andrew L. Hipp, Pedro Jiménez-Mejías, Izai A.B. Sabino Kikuchi, Modesto Luceño, José Ignacio Márquez-Corro, Santiago Martín-Bravo, Olivier Maurin, Lisa Pokorny, Eric H. Roalson, Ilias Semmouri, David A. Simpson, Daniel Spalink, W. Wayt Thomas, Karen L. Wilson, Martin Xanthos, Félix Forest, and William J. Baker
    J Syst Evol. 2021, 59(4): 852-895.
    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 due to 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. In addition, 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.