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Cryptangieae has recently been revised based on morphology and molecular phylogeny, but cytogenetic data is still scarce. We conducted this study with the aim of investigating the occurrence of holocentric chromosomes and pseudomonads, as well as understanding the mode of chromosomal evolution in the tribe. We performed analyses of meiotic behavior, chromosome counts, and reconstruction of the ancestral state for the haploid number. We present novel cytogenetic data for eight potentially holocentric species: Cryptangium verticillatum, Krenakia junciforme, K. minarum, Lagenocarpus bracteosus, L. griseus, L. inversus, L. rigidus, and L. tenuifolius. Meiotic abnormalities were observed, with parallel spindles being particularly noteworthy. Intra-specific variations in chromosome number were not found, which may indicate an efficient genetic control for the elimination of abnormal nuclei. The inferred ancestral haploid number was n = 16, with dysploidy being the main evolutionary mechanism. At least five chromosomal fissions occurred in Krenakia (n = 21), followed by a further ascending dysploidy event in Lagenocarpus (n = 17). As proposed for Cyperaceae, it is possible that cladogenesis events in Cryptangieae were marked by numerical and structural chromosomal changes., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)

Changes in chromosome numbers, including polyploidy and dysploidy events, play a key role in eukaryote evolution as they could expediate reproductive isolation and have the potential to foster phenotypic diversification. Deciphering the pattern of chromosome-number change within a phylogeny currently relies on probabilistic evolutionary models. All currently available models assume time homogeneity, such that the transition rates are identical throughout the phylogeny. Here, we develop heterogeneous models of chromosome-number evolution that allow multiple transition regimes to operate in distinct parts of the phylogeny. The partition of the phylogeny to distinct transition regimes may be specified by the researcher or, alternatively, identified using a sequential testing approach. Once the number and locations of shifts in the transition pattern are determined, a second search phase identifies regimes with similar transition dynamics, which could indicate on convergent evolution. Using simulations, we study the performance of the developed model to detect shifts in patterns of chromosome-number evolution and demonstrate its applicability by analyzing the evolution of chromosome numbers within the Cyperaceae plant family. The developed model extends the capabilities of probabilistic models of chromosome-number evolution and should be particularly helpful for the analyses of large phylogenies that include multiple distinct subclades., (© 2023 The Authors. New Phytologist © 2023 New Phytologist Foundation.)

Large-scale changes in chromosome number have been associated with diversification rate shifts in many lineages of plants. For instance, several ancient rounds of polyploidization events have been inferred to promote genomic differentiation and/or isolation and, consequently, angiosperm diversification. Dysploidy, although less studied, has been suggested to also play an important role in angiosperm diversification. In this article, we aim to elucidate the role of chromosomal rearrangements on lineage diversification by analyzing a new comprehensive sedge (Cyperaceae) phylogenetic tree. Our null hypothesis is that the mode and tempo of chromosome evolution are to be homogeneous across the complete phylogeny. In order to discern patterns of diversification shifts and chromosome number changes within the family tree, we tested clade-specific chromosome evolution models for several subtrees according to previously reported increments of diversification rates. Results show that a complex, heterogeneous model composed of different clade-specific chromosome evolution transitions are significantly supported against the null hypothesis of a model with no chromosome number model transition events along the phylogeny. This could suggest a link between diversification and changes in chromosome number evolution although other possibilities are not discarded. Our methodological approach may allow identifying different patterns of chromosome evolution, as found for Cyperaceae, for other lineages at different evolutionary levels., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Meiotic drive, the class of meiotic mechanisms that drive unequal segregation of alleles among gametes, may be an important force in karyotype evolution. Its role in holocentric organisms, whose chromosomes lack localized centromeres, is poorly understood. We crossed two individuals of Carex scoparia (Cyperaceae) with different chromosome numbers (2n = 33 II  = 66 × 2n = 32 II  = 64) to obtain F1 individuals, which we then self-pollinated to obtain second-generation (F2) crosses. RAD-seq was performed for 191 individuals (including the parents, five F1 individuals and 184 F2 individuals). Our F2 linkage map based on stringent editing of the RAD-seq data set yielded 32 linkage groups. In the final map, 865 loci were located on a linkage map of 3966.99 cM (linkage groups ranged from 24.39 to 193.31 cM in length and contained 5-51 loci each). Three linkage groups exhibit more loci under segregation distortion than expected by chance; within linkage groups, loci exhibiting segregation distortion are clustered. This finding implicates meiotic drive in the segregation of chromosome variants, suggesting that selection of chromosome variants in meiosis may contribute to the establishment and fixation of chromosome variants in Carex, which is renowned for high chromosomal and species diversity. This is an important finding as previous studies demonstrate that chromosome divergence may play a key role in differentiation and speciation in Carex., (© 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.)

Premise of the Study: Understanding heterogeneity in species richness across the tree of life is a challenge in evolutionary biology. The sedge family, Cyperaceae, is classified into tribes that exhibit a roughly 200-fold range in species richness. The Cyperaceae present an excellent case study in the determinants of species richness within higher-level taxa., Methods: We used secondary calibration based on prior studies and fossils from a rush (Juncaceae) and five sedges to calibrate two previously published Cyperaceae phylogenies, then compared our results to previous molecular clock analyses. We used an information-theoretic approach to identify shifts in lineage diversification rates and phylogenetic generalized least squares to fit alternative models of clade species richness., Key Results: Our results suggest a late Cretaceous origin for Cyperaceae (76-89 mya). The inferred 0.06 speciation events Ma(-1) is comparable to overall diversification rates in the order Poales but faster than angiosperm background rates. A threefold increase in diversification rate at the base of the species-rich SDC+FAEC clade is correlated with climatic changes during the Paleocene-Eocene boundary (ca. 55 mya). The greater driver of among-clade variance in species richness, however, is clade age (simple R(2) = 0.334, P = 0.0006)., Conclusions: Although shifts in diversification rates play a role in the generation of heterogeneous patterns of species richness, our study demonstrates that variance in clade age alone explains ca. 33% of among-clade variation in species diversity, which stands in contrast to the general pattern for angiosperms.

Holocentric organisms, unlike typical monocentric organisms, have kinetochore activity distributed along almost the whole length of the chromosome. Because of this, chromosome rearrangements through fission and fusion are more likely to become fixed in holocentric species, which may account for the extraordinary rates of chromosome evolution that many holocentric lineages exhibit. Long blocks of genome synteny have been reported in animals with holocentric chromosomes despite high rates of chromosome rearrangements. Nothing is known from plants, however, despite the fact that holocentricity appears to have played a key role in the diversification of one of the largest angiosperm genera, Carex (Cyperaceae). In the current study, we compared genomes of Carex species and a distantly related Cyperaceae species to characterize conserved and rearranged genome regions. Our analyses span divergence times ranging between 2 and 50 million years. We also compared a C. scoparia chromosome‐level genome assembly with a linkage map of the same species to study rearrangements at a population level and suppression of recombination patterns. We found longer genome synteny blocks than expected under a null model of random rearrangement breakpoints, even between very distantly related species. We also found repetitive DNA to be non‐randomly associated with holocentromeres and rearranged regions of the genome. The evidence of conserved synteny in sedges despite high rates of chromosome fission and fusion suggests that conserved genomic hotspots of chromosome evolution related to repetitive DNA shape the evolution of recombination, gene order and crossability in sedges. This finding may help explain why sedges are able to maintain species cohesion even in the face of high interspecific chromosome rearrangements. [ABSTRACT FROM AUTHOR]

Geographic isolation and chromosome evolution are two of the major drivers of diversification in eukaryotes in general, and specifically, in plants. On one hand, range shifts induced by Pleistocene glacial oscillations deeply shaped the evolutionary trajectories of species in the Northern Hemisphere. On the other hand, karyotype variability within species or species complexes may have adaptive potential as different karyotypes may represent different recombination rates and linkage groups that may be associated with locally adapted genes or supergenes. Organisms with holocentric chromosomes are ideal to study the link between local adaptation and chromosome evolution, due to their high cytogenetic variability, especially when it seems to be related to environmental variation. Here, we integrate the study of the phylogeography, chromosomal evolution and ecological requirements of a plant species complex distributed in the Western Euro‐Mediterranean region (Carex gr. laevigata, Cyperaceae). We aim to clarify the relative influence of these factors on population differentiation and ultimately on speciation. We obtained a well‐resolved RADseq phylogeny that sheds light on the phylogeographic patterns of molecular and chromosome number variation, which are compatible with south‐to‐north postglacial migration. In addition, landscape genomics analyses identified candidate loci for local adaptation, and also strong significant associations between the karyotype and the environment. We conclude that karyotype distribution in C. gr. laevigata has been constrained by both range shift dynamics and local adaptation. Our study demonstrates that chromosome evolution may be responsible, at least partially, for microevolutionary patterns of population differentiation and adaptation in Carex. [ABSTRACT FROM AUTHOR]

Background and Aims Despite chromosomal evolution being one of the major drivers of diversification in plants, we do not yet have a clear view of how new chromosome rearrangements become fixed within populations, which is a crucial step forward for understanding chromosomal speciation. Methods In this study, we test the role of genetic drift in the establishment of new chromosomal variants in the context of hybrid dysfunction models of chromosomal speciation. We genotyped 178 individuals from seven populations (plus 25 seeds from one population) across the geographical range of Carex helodes (Cyperaceae). We also characterized karyotype geographical patterns of the species across its distribution range. For one of the populations, we performed a detailed study of the fine-scale, local spatial distribution of its individuals and their genotypes and karyotypes. Key Results Synergistically, phylogeographical and karyotypic evidence revealed two main genetic groups: southwestern Iberian Peninsula vs. northwestern African populations; and within Europe our results suggest a west-to-east expansion with signals of genetic bottlenecks. Additionally, we inferred a pattern of descending dysploidy, plausibly as a result of a west-to-east process of post-glacial colonization in Europe. Conclusions Our results give experimental support to the role of geographical isolation, drift and inbreeding in the establishment of new karyotypes, which is key in the speciation models of hybrid dysfunction. [ABSTRACT FROM AUTHOR]

Background and Aims While variation in genome size and chromosome numbers and their consequences are often investigated in plants, the biological relevance of variation in chromosome size remains poorly known. Here, we examine genome and mean chromosome size in the cyperid clade (families Cyperaceae, Juncaceae and Thurniaceae), which is the largest vascular plant lineage with predominantly holocentric chromosomes. Methods We measured genome size in 436 species of cyperids using flow cytometry, and augment these data with previously published datasets. We then separately compared genome and mean chromosome sizes (2C/2 n) amongst the major lineages of cyperids and analysed how these two genomic traits are associated with various environmental factors using phylogenetically informed methods. Key Results We show that cyperids have the smallest mean chromosome sizes recorded in seed plants, with a large divergence between the smallest and largest values. We found that cyperid species with smaller chromosomes have larger geographical distributions and that there is a strong inverse association between mean chromosome size and number across this lineage. Conclusions The distinct patterns in genome size and mean chromosome size across the cyperids might be explained by holokinetic drive. The numerous small chromosomes might function to increase genetic diversity in this lineage where crossovers are limited during meiosis. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Carex section Schoenoxiphium (Cariceae, Cyperaceae) is endemic to the Afrotropical biogeographic region and is mainly distributed in southern and eastern Africa, with its center of diversity in eastern South Africa. The taxon was formerly recognized as a distinct genus and has a long history of taxonomic controversy. It has also an important morphological and molecular background in particular dealing with the complexity of its inflorescence and the phylogenetic relationships of its species. We here present a fully updated and integrative monograph of Carex section Schoenoxiphium based on morphological, molecular and cytogenetic data. A total of 1,017 herbarium specimens were examined and the majority of the species were studied in the field. Previous molecular phylogenies based on Sanger-sequencing of four nuclear and plastid DNA regions and RAD-seq were expanded. For the first time, chromosome numbers were obtained, with cytogenetic counts on 44 populations from 15 species and one hybrid. Our taxonomic treatment recognizes 21 species, one of them herein newly described (C. gordon-grayae). Our results agree with previous molecular works that have found five main lineages in Schoenoxiphium. We provide detailed morphological descriptions, distribution maps and analytical drawings of all accepted species in section Schoenoxiphium, an identification key, and a thorough nomenclatural survey including 19 new typifications and one nomen novum. [ABSTRACT FROM AUTHOR]

Aim: Madagascar is renowned for its unparalleled biodiversity and endemism. With many ecosystems under threat, research is urgently needed on its unique plant diversity. This applies both to Madagascar's forests and treeless vegetation types. Sedges (Cyperaceae) are among the top 10 species‐richest angiosperm families in Madagascar (310 native species, 38% endemic), of which two‐thirds occur in open habitats. We aimed to infer the evolutionary history of sedges in Madagascar, by estimating the number, age and origins of endemic lineages, and how they diversified on the island. We tested contrasting hypotheses of (a) few colonizations but important in situ radiations against (b) a high number of anagenetic colonizations. Location: Madagascar and the surrounding Indian Ocean islands, integrated within a global dataset. Taxon: Sedge family Cyperaceae. Methods: We estimated time‐calibrated molecular phylogenies encompassing a large proportion of Madagascar's known sedge flora (incl. 55% of native species), integrating sequence data for 1,382 accessions representing almost 25% of the c. 5,600 sedge species worldwide, combined with ancestral area reconstruction, diversification analyses and Bayesian stochastic mapping. Results: Cyperaceae lineages arrived in Madagascar from c. 40 Mya with many arriving more recently. About 20 endemic lineages of Cyperaceae occur on the island, of which only six encompass more than five species. All except one of the endemic lineages that diversified in Madagascar use the C3 photosynthetic pathway. The main biogeographical links of Madagascar's sedge flora are to Southern and Tropical Africa. Main conclusions: The biogeographical history of Cyperaceae in Madagascar is a chronicle of relatively recent multiple in and out processes of long‐distance dispersal colonizations constrained by distance. Also, the Madagascar region is not only a 'sink' for immigrant taxa, in situ diversification and dispersal to other regions also occurred. Some of the most diverse endemic lineages show clear adaptation to local environments. [ABSTRACT FROM AUTHOR]

Aim: Colonization of new areas may entail shifts in diversification rates linked to biogeographical movement (dispersification), which may involve niche evolution if species were not exapted to new environments. Scleria (Cyperaceae) includes c. 250 species and has a pantropical distribution suggesting an extraordinary capacity for long‐distance dispersal and colonization. We investigate patterns of diversification in Scleria, and whether they are coupled with colonization events, climate niche shifts or both. Location: Tropics and subtropics. Taxon: Nutrushes Scleria (Cyperaceae). Methods: We used molecular data from three DNA regions sequenced for 278 accessions representing 140 Scleria taxa (53% of species) to develop a chronogram, model ancestral ranges and measure rates of diversification. Integrating data from 12,978 digitized and georeferenced herbarium records, we investigated niche evolution. Results: High dispersal rates in Scleria, a genus with multiple dispersal syndromes, make reconstruction of ancestral ranges at deep nodes in the phylogeny highly equivocal. Main dispersal and colonization events involve movements from South to Central America (c. 19), from Africa to Madagascar (c. 12), from Asia to Oceania (c. 7), from Africa to South America (c. 7) and Central America to South America (c. 6). The two main shifts in diversification rates happened during the warm period of the Miocene. Main conclusions: Dispersification from South America to Africa without climate niche shift seems to explain the diversification shift in section Hypoporum implying that species were exapted. Shifts in climate niche evolution predate the second shift in diversification rates suggesting lineages were exapted prior to biogeographical movements. Within subgenus Scleria, colonizations of Asia and Madagascar by sections Elatae and Abortivae, respectively, are coupled with niche shifts suggesting that these colonizations involved climate niche adaptation. [ABSTRACT FROM AUTHOR]

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The megadiverse genus Carex (c. 2000 species, Cyperaceae) has a nearly cosmopolitan distribution, displaying an inverted latitudinal richness gradient with higher species diversity in cold‐temperate areas of the Northern Hemisphere. Despite great expansion in our knowledge of the phylogenetic history of the genus and many molecular studies focusing on the biogeography of particular groups during the last few decades, a global analysis of Carex biogeography and diversification is still lacking. For this purpose, we built the hitherto most comprehensive Carex‐dated phylogeny based on three markers (ETS–ITS–matK), using a previous phylogenomic Hyb‐Seq framework, and a sampling of two‐thirds of its species and all recognized sections. Ancestral area reconstruction, biogeographic stochastic mapping, and diversification rate analyses were conducted to elucidate macroevolutionary biogeographic and diversification patterns. Our results reveal that Carex originated in the late Eocene in E Asia, where it probably remained until the synchronous diversification of its main subgeneric lineages during the late Oligocene. E Asia is supported as the cradle of Carex diversification, as well as a "museum" of extant species diversity. Subsequent "out‐of‐Asia" colonization patterns feature multiple asymmetric dispersals clustered toward present times among the Northern Hemisphere regions, with major regions acting both as source and sink (especially Asia and North America), as well as several independent colonization events of the Southern Hemisphere. We detected 13 notable diversification rate shifts during the last 10 My, including remarkable radiations in North America and New Zealand, which occurred concurrently with the late Neogene global cooling, which suggests that diversification involved the colonization of new areas and expansion into novel areas of niche space. [ABSTRACT FROM AUTHOR]

Abstract: Systematically quantifying diversity across landscapes is necessary to understand how clade history and ecological heterogeneity contribute to the origin, distribution, and maintenance of biodiversity. Here, we chart the spatial structure of diversity among all species in the sedge family (Cyperaceae) throughout the USA and Canada. We first identify areas of remarkable species richness, phylogenetic diversity, and functional trait diversity, and highlight regions of conservation priority. We then test predictions about the spatial structure of this diversity based on the historical biogeography of the family. Incorporating a phylogeny, over 400 000 herbarium records, and a database of functional traits mined from online floras, we find that species richness and functional trait diversity peak in the Northeastern USA, while phylogenetic diversity peaks along the Gulf of Mexico. Floristic turnover among assemblages increases significantly with distance, but phylogenetic turnover is twice as rapid along latitudinal gradients as along longitudinal gradients. These patterns reflect the expected distribution of Cyperaceae, which originated in the tropics but radiated in temperate regions. We identify assemblages with an abundance of rare, range‐restricted lineages, and assemblages composed of species generally lacking from diverse regions. We argue that both of these metrics are useful for developing targeted conservation strategies. We use the data generated here to establish future research priorities, including the testing of a series of hypotheses regarding the distribution of chromosome numbers, photosynthetic pathways, and resource partitioning in sedges. [ABSTRACT FROM AUTHOR]

Abstract: Aim: To disentangle the importance of the Beringian land bridges during the Pliocene and Quaternary periods in order to explain the current distribution of circumpolar plants with potential for long‐distance dispersal. Location: Circumpolar (Arctic and Antarctic). Methods: We sampled all extant species in Carex section Glareosae (26 species and 2 subspecies) and analysed 14 DNA regions, including the nrDNA regions ETS and ITS, three nuclear single‐copy genes (CATP, G3PDH and GZF), and nine cpDNA regions: 5′trnK intron, atpIH, matK, ndhJ‐trnF, psbA‐trnH, rpl32‐trnL, rps16, trnC‐ycf6 and ycf6‐psbM. After testing for outlier proportions, we used Bayesian inference, maximum likelihood and a species‐tree approach to infer phylogenetic relationships between species; divergence times were estimated using Beast2. We then performed biogeographical analyses using “BioGeoBEARS” to estimate ancestral areas by means of reticulate models. Finally, lineage through time (LTT) and diversification pattern analyses were performed using Bamm. Results: Carex section Glareosae is a monophyletic group that diverged c. 6.56 Ma (4.54–8.51 Ma at 95% highest posterior density interval). We show that within‐area cladogenetic speciation events and anagenetic dispersal (including some vicariance events) play an important role in shaping distribution in species with potential for long‐distance dispersal. Diversification patterns show constant diversification rates over time. Main conclusions: The Bering Strait may have played an important role in shaping the current distribution of the species in the section, facilitating dispersal between Asia and North America during glacial periods when the Beringian land bridges were open. Nevertheless, we cannot discount long‐distance dispersal as an alternative major force shaping the species distribution in the section. [ABSTRACT FROM AUTHOR]

PREMISE OF THE STUDY: Bipolar species represent the greatest biogeographical disjunction on Earth, raising many questions about the colonization and adaptive processes behind such striking distribution. We investigated climatic niche differences of five Carex bipolar species in North and South America to assess niche shifts between these two regions. Moreover, we assessed potential distribution changes with future climate change. M ETHODS: We used 1202 presence data points from herbarium specimens and 19 bioclimatic variables to assess climatic niche differences and potential distributions among the five species using ordination methods and Maxent. KEY RESULTS: The niche overlap analyses showed low levels of niche filling and high climatic niche expansion between North and South America. Carex macloviana and C. maritima showed the greatest niche expansion (60% and 96%, respectively), followed by C. magellanica (45%) and C. microglochin (39%). Only C. canescens did not colonize new environments (niche expansion = 0.2%). In contrast, all species but C. magellanica had niche filling that was <40%; hence, they are absent in the south from many environments they inhabit in North America. Climate change will push all species toward higher latitudes and elevation, reducing the availability of suitable environments. C ONCLUSIONS: The colonization of South America seems to have involved frequent climatic niche shifts. Most species have colonized new environments from those occupied in the North. Observed niche shifts appear congruent with time since colonization and with current genetic structure within species. In these cold-dwelling species, climate change will most likely decrease their suitable environments in the future. [ABSTRACT FROM AUTHOR]

About 30 plant species occur at high latitudes in both hemispheres, thus achieving a so-called bipolar distribution. Six of these species belong to Carex, of which just one, Carex canescens, occurs on two different landmasses in the Southern Hemisphere (South America and Oceania). The goals of this study are (1) to test the various hypotheses accounting for the bipolar disjunction of C. canescens and (2) to elucidate if C. canescens migrated twice from the Northern Hemisphere to the Southern Hemisphere or if it dispersed from South America to Oceania (or vice versa). We obtained and analysed DNA sequences from the nuclear internal and external transcribed spacers (ITS and ETS) and from the plastid 5′ trnK and rps16 introns from 57 populations of C. canescens spanning its bipolar range. We characterized the species distribution climatically by adding 1995 presence data points from the Global Biodiversity Information Facility. Our results suggest a Northern Hemisphere origin of C. canescens during the Pleistocene and two independent long distance-dispersal events to South America and Australia, by either direct dispersal or mountain-hopping. Long-distance dispersal appears to be the most widespread process resulting in the bipolar distribution of Carex spp. [ABSTRACT FROM AUTHOR]

Aim We set out to explain the bipolar distribution of Carex maritima, clarifying the direction and timing of dispersal. We also tested mountain-hopping and direct long-distance dispersal hypotheses, as well as the relationship of C. maritima with biotic and abiotic factors that could explain the bipolar distribution. Location Arctic/boreal latitudes of both hemispheres. Methods Molecular and bioclimatic data were obtained for C. maritima and related species from section Foetidae. We sequenced two ( rps16 and 5′ trnK intron) plastid DNA regions (cp DNA) and the external and internal transcribed spacers ( ETS and ITS) of the nuclear ribosomal gene region (nr DNA) and inferred phylogenetic relationships, divergence time estimates and biogeographical patterns using maximum likelihood, statistical parsimony, Bayesian inference and ecological niche modelling. Results Carex maritima populations from the Southern Hemisphere were genetically and ecologically differentiated from their northern counterparts and formed a monophyletic group nested within a paraphyletic C. maritima. Divergence time analysis estimated a middle-late Pleistocene divergence of the southern lineage (0.23 Ma; 95% highest posterior density: 0.03-0.51 Ma). Southern Hemisphere populations are more stenotopic than the Northern Hemisphere ones, which tolerate harsher conditions. Main conclusions Our results point to a middle-late Pleistocene migration of C. maritima by long-distance dispersal, either directly or via mountain-hopping, from the Northern Hemisphere to the Southern Hemisphere. [ABSTRACT FROM AUTHOR]

Aim The bipolar disjunction, a biogeographical pattern defined by taxa with a distribution at very high latitudes in both hemispheres (> 55° N; > 52° S), is only known to occur in about 30 vascular plant species. Our aim was to use the bipolar species Carex arctogena to test the four classic hypotheses proposed to explain this exceptional disjunction: convergent evolution, vicariance, mountain-hopping and direct long-distance dispersal. Location Arctic/boreal and temperate latitudes of both hemispheres. Methods A combination of molecular and bioclimatic data was used to test phylogeographical hypotheses in C. arctogena. Three chloroplast markers ( atpF -atpH , matK and rps16) and the nuclear ITS region were sequenced for all species in Carex sections Capituligerae and Longespicatae; Carex rupestris, C. obtusata and Uncinia triquetra were used as outrgroups. Phylogenetic relationships, divergence-time estimates and biogeographical patterns were inferred using maximum likelihood, statistical parsimony and Bayesian inference. Results Carex sections Capituligerae and Longespicatae formed a monophyletic group that diverged during the late Miocene. Two main lineages of C. arctogena were inferred. Southern Hemisphere populations of C. arctogena shared the same haplotype as a widespread circumboreal lineage. Bioclimatic data show that Southern and Northern Hemisphere populations currently differ in their ecological regimes. Main conclusions Two of the four hypotheses accounting for bipolar disjunctions may be rejected. Our results suggest that direct long-distance dispersal, probably southwards and mediated by birds, best explains the bipolar distribution of C. arctogena. [ABSTRACT FROM AUTHOR]

PREMISE OF THE STUDY: Fahrenholz's rule states that common ancestors of extant parasites were parasites of the common ancestors of extant hosts. Consequently, parasite phylogeny should mirror host phylogeny. The smut fungi genus Anthracoidea (Anthracoideaceae) is mainly hosted by species of the genus Carex (Cyperaceae). Whether smut fungi phylogeny mirrors sedge phylogeny is still under debate. METHODS: The nuclear large subunit DNA region (LSU; 57 accessions) from 31 Anthracoidea species and the ITS, ETS, and trnl-F-spacer-trnl. intron complex from 41 Carex species were used to infer the phylogenetic history of parasites and their hosts using a maximum likelihood approach. Event-based and distance-based cophylogenetic methods were used to test the hypothesis of whether the phylogeny of smut fungi from the genus Anthracoidea matches the phylogeny of the sedge Carex species they host. RESULTS: Cophylogenetic reconstructions taking into account phylogenetic uncertainties based on event-based analyses demonstrated that the Anthracoidea phylogeny has significant topological congruence with the phylogeny of their Carex hosts. A distance-based test was also significant; therefore, the phylogenies of Anthracoide and Carex are partially congruent. COMCLUSIONS: The phylogenetic congruence of Anthracoidea and Carex is partially based on smut fungi species being preferentially hosted by closely related sedges (host conservatism). In addition, many different events rather than only codivergence events are inferred. All of this evidence suggests that host-shift speciation rather than cospeciation seems to explain the cophylogenetic patterns of Anthracoidea and Carex. [ABSTRACT FROM AUTHOR]

* Premise of the study: In organisms with holocentric chromosomes like Carex species, chromosome number evolution has been hypothesized to be a result of fission, fusion, and/or translocation events. Negative, positive, or the absence of correlations have been found between chromosome number and genome size in Carex. * Methods: Using the inferred diploid chromosome number and 80 genome size measurements from 26 individuals and 20 populations of Carex gr. laevigata, we tested the null hypothesis of chromosome number evolution by duplication and deletion of whole chromosomes. * Key results: Our results show a significant positive correlation between genome size and chromosome number, but the slope of such correlation supports the hypothesis of proliferation and removal of repetitive DNA fragments to explain genome size variation rather than duplication and deletion of whole chromosomes. * Conclusions: Our results refine the theory of the holokinetic drive: this mechanism is proposed to facilitate repetitive DNA removal (or any segmental deletion) when smaller homologous chromosomes are preferentially inherited, or repetitive DNA proliferation (or any segmental duplication) when larger homologs are preferred. This study sheds light on how karyotype evolution plays an important role in the diversification of the species of the genus Carex. [ABSTRACT FROM AUTHOR]

Determining phylogenetic relationships among very closely related species has remained a challenge for evolutionary biologists due to interlocus phylogenetic discordance and the difficulty of obtaining variable markers. Here, we used a Genotyping-by-Sequencing (GBS) approach to sample a reduced representation genomic data set and infer the phylogeny of seven closely related species in the genus Carex (Cyperaceae). Past attempts to reconstruct phylogenetic relationships among these species produced conflicting and poorly-supported results. We inferred a robust phylogeny based on >3000 GBS loci and >1300 SNPs (with a minimum sequence depth within individuals of 10) using maximum likelihood and Bayesian inference. We also tested for historical introgression using the D -statistic test. We compared these analyses with partitioned RAD analysis, which is designed to identify suboptimal trees reflecting secondary phylogenetic signal that may be obscured by the dominant signal in the data. Phylogenetic analyses yielded fully resolved trees with high support. We found two main clades, one grouping Carex scoparia populations and C. waponahkikensis , and a second clade grouping C. longii , C. vexans , C. suberecta and C. albolutescens . We detected marginally significant signals of introgression between C. scoparia and C. suberecta or C. albolutescens, and we rejected a hybrid origin hypothesis for C. waponahkikensis. Our results demonstrate the power of NGS data sets for resolving some of the most difficult phylogenetic challenges where traditional phylogenetic markers have failed. [ABSTRACT FROM AUTHOR]

Background and Aims The sedge genus Carex, the most diversified angiosperm genus of the northern temperate zone, is renowned for its holocentric chromosomes and karyotype variability. The genus exhibits high variation in chromosome numbers both among and within species. Despite the possibility that this chromosome evolution may play a role in the high species diversity of Carex, population-level patterns of molecular and cytogenetic differentiation in the genus have not been extensively studied. Methods Microsatellite variation (11 loci, 461 individuals) and chromosomal diversity (82 individuals) were investigated in 22 Midwestern populations of the North American sedge Carex scoparia and two Northeastern populations. Key Results Among Midwestern populations, geographic distance is the most important predictor of genetic differentiation. Within populations, inbreeding is high and chromosome variation explains a significant component of genetic differentiation. Infrequent dispersal among populations separated by >100 km explains an important component of molecular genetic and cytogenetic diversity within populations. However, karyotype variation and correlation between genetic and chromosomal variation persist within populations even when putative migrants based on genetic data are excluded. Conclusions These findings demonstrate dispersal and genetic connectivity among widespread populations that differ in chromosome numbers, explaining the phenomenon of genetic coherence in this karyotypically diverse sedge species. More generally, the study suggests that traditional sedge taxonomic boundaries demarcate good species even when those species encompass a high range of chromosomal diversity. This finding is important evidence as we work to document the limits and drivers of biodiversity in one of the world's largest angiosperm genera. [ABSTRACT FROM PUBLISHER]

Abstract: The holocentric structure promotes chromosome rearrangements by fission, fusion, translocation, and inversion, which have been thought to promote differentiation and speciation. The Carex laevigata group (Cyperaceae) comprises four species: two restricted endemics from the western Mediterranean (Carex camposii, 2n =72, and Carex paulo-vargasii, 2n =74–75), and two more widespread species, found mostly in Western Europe (C. laevigata, 2n =69–84, and Carex binervis, 2n =72–74). We tested the selection for chromosome number by climatic variables by controlling for the non-independence of the data using generalized linear mixed model (GLMM). We obtained chromosome counts as well as DNA sequences for the 5′trnK intron and the trnV-ndhC intergenic spacer in the chloroplast genome from 181 individuals from 53 populations representing these four species. We also climatically characterized the sites where the 53 populations were found using the WorldClim database. Our results show that the best predictor of chromosome number variation is the climatic environment rather than neutral evolutionary processes like founder events and migration patterns. These results support the adaptive value of the holocentric chromosomes and their role in promoting differentiation and eventually speciation. [Copyright &y& Elsevier]

Abstract: The sedge family (Cyperaceae: Poales; ca. 5600 spp.) is a hyperdiverse cosmopolitan group with centres of species diversity in Africa, Australia, eastern Asia, North America, and the Neotropics. Carex, with ca. 40% of the species in the family, is one of the most species-rich angiosperm genera and the most diverse in temperate regions of the Northern Hemisphere, making it atypical among plants in that it inverts the latitudinal gradient of species richness. Moreover, Carex exhibits high rates of chromosome rearrangement via fission, fusion, and translocation, which distinguishes it from the rest of the Cyperaceae. Here, we use a phylogenetic framework to examine how the onset of contemporary temperate climates and the processes of chromosome evolution have influenced the diversification dynamics of Carex. We provide estimates of diversification rates and map chromosome transitions across the evolutionary history of the main four clades of Carex. We demonstrate that Carex underwent a shift in diversification rates sometime between the Late Eocene and the Oligocene, during a global cooling period, which fits with a transition in diploid chromosome number. We suggest that adaptive radiation to novel temperate climates, aided by a shift in the mode of chromosome evolution, may explain the large-scale radiation of Carex and its latitudinal pattern of species richness. [Copyright &y& Elsevier]

Abstract: Previous work on holocentric chromosomes in the angiosperm genus Carex demonstrates that many of the traditional sections are marked by different ranges of chromosome number, suggesting phylogenetic autocorrelation. It has been hypothesized that shifting constraints on chromosome rearrangements may limit the potential for hybridization among lineages, promoting speciation. In this study, we evaluated alternative evolutionary models to test for such transitions in Carex section Spirostachyae as well as the relative effects of several plausible drivers of intraspecific chromosome diversity. Chromosome number variation in section Spirostachyae shows significant phylogenetic signal, but no evidence of clade-specific shifts in chromosome number distribution. This gradual model of chromosome evolution contrasts with the shifting equilibrium model previously identified in a younger section of the same genus, suggesting that section Spirostachyae may have a more slowly evolving karyotype. Chromosome number variance, on the other hand, exhibits low phylogenetic signal. Average time of coalescence rather than geographic range or chromosome number itself predicts chromosome number variance, demonstrating a previously unreported relationship between population history and cytogenetic variation. [Copyright &y& Elsevier]

Carex sect. Spirostachyae comprises 25 species displaying the centre of diversity in Eurasia, while sect. Elatae comprises 22 species displaying the centre of diversity in tropical African mountainous regions. Phylogenetic analysis of the 136 ITS and 108 5′ trnK intron sequences of 23 species of sect. Spirostachyae and 20 species of sect. Elatae revealed that neither section is monophyletic. With the exclusion of C. montis-eeka (sect. Spirostachyae) and C. insularis, C. iynx and C. longibrachiata (sect. Elatae), the sects. Spirostachyae and Elatae constitute a monophyletic group of 38 species, 22 of which were previously included in sect. Spirostachyae and 16 of which were in sect. Elatae (considering C. thomasii as C. mannii ssp. thomasii). Two main groups with different edaphic preferences were identified in the core Spirostachyae, in congruence with some morphological features. One group comprises primarily acidophilus species including 11 species of sect. Spirostachyae and 16 species of sect. Elatae. The other group includes 11 basophilic species of sect. Spirostachyae. Incongruence between nuclear and plastid genomes was detected, suggesting hybridization or lineage sorting processes in the evolution of the core Spirostachyae. [ABSTRACT FROM AUTHOR]

The Strait of Gibraltar is the most important barrier disconnecting the landmasses of Europe and Africa on the western Mediterranean extreme. Carex helodes is a wind-pollinated species endemic to the western Mediterranean. Because molecular and cytogenetic data allow the inference of its evolutionary history, we analyzed variations in chromosome number, including meiotic chromosome behavior, amplified fragment length polymorphism (AFLP) fingerprints, and nucleotide substitutions in plastid and nuclear DNA sequences. Cytogeographic results showed that the African populations have stabilized at a single chromosome number of 2n = 74, whereas the most frequent cytotype in Iberia is 2n = 72. Phylogenetic reconstructions of 17 sequences from nine closely related species revealed that C. helodes is monophyletic and that the Moroccan populations are embedded in the Iberian lineages. The haplotype network is also consistent with a European origin of the northern African haplotype. AFLP analysis also revealed hierarchical levels of genetic variation compatible with a founder effect process responsible for the African populations. All sources of evidence support the hypothesis that the Strait of Gibraltar has been an effective gene-flow barrier, generating two isolated evolutionary lineages after their dispersal. Recent connections between the two lineages appear unlikely, whereas active gene flow occurs among populations within the two lineages. [ABSTRACT FROM AUTHOR]

A correction to the article "The East-West-North Colonization History of the Mediterranean and Europe by the Coastal Plant Carex Extensa (Cyperaceae)" that was published in the 2010 issue is presented.