DNA variation within Juncaceae: comparison of impact of organelle regions on phylogeny

A phylogenetic analysis of the Juncaceae was conducted to assess relationships among the genera Juncus, Luzula and five other small South American genera (Distichia, Marsippospermum, Oxychloë, Patosia and Rostkovia). We examined parallel datasets from organelles (mtDNA: atp1 gene, cpDNA: trnL intron, trnL-F intergenic spacer, rbcL gene) with respect to qualities relevant to the phylogenetic analysis of the Juncaceae. The main aim of our work was to produce a robust phylogeny of the Juncaceae validated by data from both organelles. Our data confirm the monophyly of the genus Luzula, but do not provide support for monophyly of the genus Juncus. The majority of taxa clustered within two subgenera, Agathryon and Juncus, morphologically supported by the presence or absence of bracteoles and cymose or racemose inflorescences, respectively. The subgenus Juncus is divided into two separate clades, the first closely related to the subgenus Agathryon and the second in the most basal part of the tree. Moreover, small South American genera clustered together with Juncus sect. Graminifolii and also with Juncus sect. Juncus. In fact, comparison of results from separate analyses of mitochondrial and plastome genes demonstrates that the general resolution of main topology of the atp1 tree is similar to the separate rbcL tree; the genus Juncus is better resolved, but the genus Luzula remains mainly polytomic.     

Phylogenetic relationships within Luzula DC. and Juncus L. (Juncaceae): A comparison of phylogenetic signals of trnL-trnF intergenic spacer, trnL intron and rbcL plastome sequence data

Juncus and Luzula are the largest, almost cosmopolitan, genera in the Juncaceae. Relationships within Juncus and Luzula and among other genera of Juncaceae (Distichia, Marsippospermum, Oxychloë, Patosia and Rostkovia) remain incompletely resolved. RbcL sequence data resolved a part of the supraspecific phylogeny, but many clades remain polytomic. For this reason, the non‐coding cpDNA regions, trnL intron and trnL‐trnF intergenic spacer, were sequenced. We intended to create hypotheses of relationships within Juncaceae and to test the classification of the sections, but a primary goal to this study was to assess the relationships within Juncus and Luzula and to test for monophyly of groups recognized from rbcL data (especially the monophyly of genus Luzula and the Southern Hemisphere Clade (SHC)). Furthermore, we tested the influence of different rooting and ingroup composition on the tree topology. The parsimony analyses revealed several well‐supported lineages. The traditionally distinguished genus Luzula is monophyletic and Juncus is non‐monophyletic. Two subgenera of Luzula (Pterodes and Luzula) are non‐monophyletic, while subg. Marlenia forms a sister group to the whole Luzula clade (trnL‐F data set). Within Juncus, both subgenus Juncus and subgenus Agathryon are non‐monophyletic. SHC is clustered not only with the South African J. lomatophylus and J. capensis, but also together with members of the section Juncus, Caespitosi and Graminifolii. These sections form a well‐separated sister group to the SHC. Within the genera Juncus and Luzula, monophyly is demonstrated for a number of groups (e.g., Juncus section Stygiopsis, Luzula section Luzula) but questioned for others (e.g., Juncus section Graminifolii). The unusual, separate positioning of Juncus trifidus and J. monanthos were clarified by trnL‐trnF sequence data, but vary within the tree topology depending on outgroup selection and also due to LBA phenomenon. © The Willi Hennig Society 2006.     

Pollen and ovule production in wind-pollinated species with special reference to Juncus

The reproductive biology of wind-pollinated species in terms of pollen and ovule production is rarely studied compared with zoophilous species, despite available hypotheses on the effect of growth form and life-history traits on reproductive investment. Here, we use published data and new data for species of Juncus and Luzula (Juncaceae) to test the hypotheses that, in wind-pollinated species, woody perennials should exhibit larger pollen–ovule (P/O) ratios than herbaceous species and that species with separate sexes have larger P/O ratios than homoecious species. In total, we report pollen and ovule production for 291 wind-pollinated species, including 19 Juncus and 5 Luzula species. Compared with other wind-pollinated species, Juncus exhibits unusually low P/O ratios (log P/O = 2.06 ± 0.46) because of high ovule production. We argue that the high ovule and seed production in Juncus, associated with frequent self-fertilization, may be beneficial in habitats preferred by the genus. In general, we found higher P/O ratios in woody perennials (log P/O = 4.37 ± 1.18) or in species with separate sexes (log P/O = 4.28 ± 1.12) than in herbaceous (log P/O = 3.51 ± 0.77) or homoecious (log P/O = 3.52 ± 0.80) species, respectively. However, when we analyzed woody perennials separately, we found no significant difference in P/O ratios between homoecious and nonhomoecious species. We argue that woody perennials, independent of dicliny, may be preferentially outcrossed and therefore exhibit decreased variation in mating systems compared with herbs. Because the degree of outcrossing correlates with P/O ratios, differences between homoecious and nonhomoecious woody perennials could be less pronounced.     

Family Juncaceae: promising source of biologically active natural phenanthrenes

Phenanthrenes represent a relatively small group of aromatic secondary metabolites, which can be divided into three main subgroups (mono-, di-, and triphenanthrenes). Phenanthrenes are reported as an intensively researched field in phytochemistry according to their structural diversity and promising biological activities. Because of their limited occurrence phenanthrenes are considered to be as important taxonomic markers. Juncaceae is a relatively large plant family divided into seven genera of which Juncus and Luzula are the most important ones from phytochemical and pharmacological points of view. To date, almost one hundred natural phenanthrenes have been isolated but only from eight (Juncus acutus, J. effusus, J. inflexus, J. maritimus, J. roemerianus, J. setchuensis, J. subulatus, and Luzula luzuloides) Juncaceae species, including mono-, and diphenanthrenes, and phenanthrene glucosides. Great deal of the isolated compounds are substituted with a vinyl group. This substitution is characteristic exclusively to Juncaceae species. Juncusol (2) was isolated from every investigated species. The richest source of phenanthrenes, as well as the most extensively investigated species is J. effusus. Several isolated compounds possessed different biological activities, e.g. antiproliferative, antimicrobial, anti-inflammatory, antioxidant, spasmolytic, anxiolytic, and antialgal effects. Among them, dehydroeffusol (60) is the most promising one, as it showed antimicrobial, anxiolytic, sedative, spasmolytic, cellular protective and antiproliferative activities. The aim of this review is to summarize the occurrence of phenanthrenes in the family Juncaceae, and give a comprehensive overview of their isolation, structural characteristics and biological activities.     

TrnL–trnF Intergenic Spacer and trnL Intron Define Major Clades Within Luzula and Juncus (Juncaceae): Importance of Structural Mutations

Seven hundred fifty-two to one thousand ninety-seven base pairs of the trnL intron and trnL–trnF intergenic spacer of the chloroplast DNA of 55 Juncaceae taxa (Juncus, Luzula, Rostkovia, and Oxychloë) was sequenced. Seventeen structural mutations (13 indels marked A to M, 3 parts of the trnF pseudogene, and insertion o within a pseudogene) within the chloroplast trnL–trnF region were examined as possible indicators for phylogenetic relationships in Juncaceae. Juncus trifidus (section Steirochloa) was clearly separated from the other taxa by two large (>80 bp) indels. The Southern Hemisphere clade was strongly supported by a unique insertion (334 bp) in the trnL intron. The monophyly of Luzula was supported by three small (<10 bp) indels in the trnL-F spacer. They were found in all 22 examined members that represent the taxonomic and geographical diversity of the genus Luzula. A tandemly duplicated tRNA pseudogene was found in the Juncus subgenus Juncus species and is supported by four small unique indels too. The acceptor stem and D-domain-encoding regions are separated by a unique 8-bp insertion. The T-domain and acceptor stem-encoding regions were not found in the pseudogene repeats. Only the Juncus sections Ozophyllum and Iridifolii contain the 5 acceptor stem, D-domain, and anticodon domain of the tRNAF encoding DNA. The structural mutations in the trnL intron and the trnL–trnF intergenic spacer are useful for phylogenetic reconstruction in the Juncaceae.     

Chromosome and genome size variation in Luzula (Juncaceae), a genus with holocentric chromosomes

The present study examines chromosome and genome size evolution in Luzula (woodrush; Juncaceae), a monocot genus with holocentric chromosomes. Detailed karyotypes and genome size estimates were obtained for seven Luzula spp., and these were combined with additional data from the literature to enable a comprehensive cytological analysis of the genus. So that the direction of karyotype and genome size changes could be determined, the cytological data were superimposed onto a phylogenetic tree based on the trnL‐F and internal transcribed spacer (ITS) DNA regions. Overall, Luzula shows considerable cytological variation both in terms of chromosome number (2n = 6–66) and genome size (15‐fold variation; 2C = 0.56–8.51 pg; 547.7–8322.8 Mb). In addition, there is considerable diversity in the genomic mechanisms responsible, with the range of karyotypes arising via agmatoploidy (chromosome fission), symploidy (chromosome fusion) and/or polyploidy accompanied, in some cases, by the amplification or elimination of DNA. Viewed in an evolutionary framework, no broad trend in karyotype or genome evolution was apparent across the genus; instead, different mechanisms of karyotype evolution appear to be operating in different clades. It is clear that Luzula exhibits considerable genomic flexibility and tolerance to large, genome‐scale changes. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 529–541.     

Chromosome numbers of Panamanian Lecythidaceae and their use in subfamilial classification

Nine species of Lecythidaceae subfamily Lecythidoideae in four genera whose chromosome numbers were previously unknown, have 17 as their basic chromosome number:Eschweilera pittieri, three other unidentified species ofEschweilera, Grias cauliflora, Gustavia dubia, G. superba, Lecythis minor, andL. tuyrana. All are diploid exceptGustavia superba, which is tetraploid.Couroupita guianensis, which was previously—and probably incorrectly—reported to have a gametic chromosome number of 18, also hasn = 17. The known chromosome numbers support recognizing at least three of Niedenzu’s subfamilies: Planchonioideae withx = 13, Napoleonaeoideae withx = 16, and Lecythidoideae withx = 17. His fourth subfamily, Foetidioideae, with one genus of five species, has not been counted. Cytological data have been and probably will be useful in indicating to what subfamily problematic genera belong and in showing interesting phytogeographic patterns within the family. On the other hand, cytological data provide no recognizable clues relating the Lecythidaceae to other families.     

Chromosome numbers in the genus Mimosa L.: cytotaxonomic and evolutionary implications

Chromosome numbers were determined for 125 accessions of 92 taxa of Mimosa from all five of Barneby??s (Mem New York Bot Gard 65:1?C835, 1991) taxonomic sections. For 69 species, 1 subspecies and 8 varieties, chromosome numbers are presented for the first time, for 6 species and 1 variety previously published data have been confirmed and for 3 species and 2 varieties different numbers were found. Results show that 74% of the accessions were diploid (2n?=?2x?=?26) and 26% polyploid, these mostly tetraploid (2n?=?4x?=?52) but with two triploid (2n?=?3x?=?39). These results double the number of Mimosa species for which the chromosome count is known from less than 10% previously reported to more than 20%, representing an important advance in the cytotaxonomy of this legume genus. These results together with literature data show that ca. 78% of Mimosa species are diploid. Polyploids are present in most of the taxonomic sections and in different lineages across the genus. No particular chromosome number is restricted to a given section or lineage. A possible relation between geography, species distribution, polyploidy and invasiveness was detected, however, further studies based on more accessions, especially from higher latitudes, are required before firm conclusions can be drawn.     

Luteolin and daphnetin derivatives in the juncaceae and their systematic significance

During a chemosystematic survey of 38 representative species of the Juncaceae for leaf and stem flavonoids, the 5-methyl ether of luteolin was discovered for the first time in plants. It occurs both free and as the 7-glucoside; its identity was confirmed by synthesis. Flavone sulphates were also found in the family and the 7-glucosidesulphates of luteolin and chrysoeriol were characterised for the first time. 7,3′,4′-Trihydroxyflavone and its 7-glucoside, not previously reported in the monocotyledons, were found in three species. The presence of luteolin 5-methyl ether or its glucoside in 70% of the species surveyed serves to distinguish the Juncaceae from the morphologically related Centrolepidaceae, Restionaceae and Thurniaceae. Flavone C-glycosides, common in grasses and sedges, were found only in Prionium, a genus which on anatomical grounds is anomalous in the Juncaceae. Among other phenolics detected during the survey, the uncommon 7,8-dihydroxycoumarin, daphnetin, was identified in Juncus effusus and its 8-methyl ether in four Luzula species. Taken together, these chemical findings show that the Juncaceae are very distinctive in their phenolic pattern and confirm the correctness of assigning them an isolated position in a separate order, the Juncales. The results indicate that the Juncaceae are chemically specialized, in spite of the facts that the family has been regarded as ancestral to the Cyperaceae and Gramineae and that they have been assigned a low advancement index by Sporne.     

Comparison of seven DNA extraction and amplification protocols in historical herbarium specimens of juncaceae

Seven DNA extraction protocols were used to obtain DNA from herbarium specimens ofJuncus andLuzula (Juncaceae) of various ages. DNA of historical samples is difficult to extract, and the extracts are seldom of good quality. The quality of DNA obtained was estimated by using a spectrophotometer to measure the A260/280 absorbance ratio. The total DNA yield was measured by a fluorometer. The results indicate the success of using both mixer mill grinding and a DNeasy Plant Kit. Another extraction protocol (grinding with mortar and pestle, using liquid nitrogen) yielded DNA from many samples. Modified CTAB extraction, with a lengthy precipitation, usually provided good amounts of DNA. Other protocols did not give satisfactory results.     

Chromosome numbers and generic relationships in subtribe Stephanomeriinae (Compositae: Ichorieae)

Chromosome numbers are reported from over 230 populations representing species in eight genera. First counts are reported for three species ofStephanomeria, five species ofLygodesmia, and one species ofPinaropappus. Base chromosome numbers,x = 6, 7, 8, and 9 are known in the subtribe;x = 9 is found in six of the 12 genera and presumably is the ancestral base number for the subtribe. Two phyletic lines, aMalacothrix line and aStephanomeria line are recognized on morphological grounds. A key to the 12 genera is provided.     

Maximum likelihood inference implies a high, not a low, ancestral haploid chromosome number in Araceae, with a critique of the bias introduced by 'x'

Background and Aims

For 84 years, botanists have relied on calculating the highest common factor for series of haploid chromosome numbers to arrive at a so-called basic number, x. This was done without consistent (reproducible) reference to species relationships and frequencies of different numbers in a clade. Likelihood models that treat polyploidy, chromosome fusion and fission as events with particular probabilities now allow reconstruction of ancestral chromosome numbers in an explicit framework. We have used a modelling approach to reconstruct chromosome number change in the large monocot family Araceae and to test earlier hypotheses about basic numbers in the family.

Methods

Using a maximum likelihood approach and chromosome counts for 26 % of the 3300 species of Araceae and representative numbers for each of the other 13 families of Alismatales, polyploidization events and single chromosome changes were inferred on a genus-level phylogenetic tree for 113 of the 117 genera of Araceae.

Key Results

The previously inferred basic numbers x = 14 and x = 7 are rejected. Instead, maximum likelihood optimization revealed an ancestral haploid chromosome number of n = 16, Bayesian inference of n = 18. Chromosome fusion (loss) is the predominant inferred event, whereas polyploidization events occurred less frequently and mainly towards the tips of the tree.

Conclusions

The bias towards low basic numbers (x) introduced by the algebraic approach to inferring chromosome number changes, prevalent among botanists, may have contributed to an unrealistic picture of ancestral chromosome numbers in many plant clades. The availability of robust quantitative methods for reconstructing ancestral chromosome numbers on molecular phylogenetic trees (with or without branch length information), with confidence statistics, makes the calculation of x an obsolete approach, at least when applied to large clades.     

Karyology of some Convolvulaceae species occurring in NE Brazil inselbergs

Eighteen species belonging to family Convolvulaceae occurring in northeastern Brazil were analyzed to identify the karyotypic variability among rupicolous and non-rupicolous species. The count of 2n = 56 for Evolvulus sp., is the first report of polyploidy for the genus. The similarities among the karyotypes of species of Ipomoea, Merremia, and Operculina suggest that x = 15 is the basic secondary number for these genera, while x = 13 has been observed in Evolvulus. The genus Jacquemontia, with 2n = 18 is karyologically distinct from the other genera of the family. Intraspecific numerical chromosomal variations were not detected, nor were any karyological variations related to the rocky habitat characteristic of inselbergs. The occurrence of other plant groups with polyploid forms linked to this type of habitat suggests that the family Convolvulaceae is karyologically stable. We discuss variations in chromosome numbers, base numbers, and their implications in the evolution of the principal groups within the Convolvulaceae.     

Cytology of SW Asian Chenopodiaceae: new data from Iran and a review of previous records and correlations with life forms and C<Subscript>4</Subscript> photosynthesis

The mitotic chromosome numbers of 35 species belonging to 25 genera from East Azerbaijan Province of Iran and meiotic numbers of five species of Salicornia from different parts of Iran of family Chenopodiaceae are reported. Some of them are first reports and some are first counts from Iran. Based on a review of previously published reports, 145 species and 46 genera occurring in SW Asia have been cytologically studied either based on populations within or surrounding regions. The nomenclature and generic position of all these species are updated based on recent phylogenetic and taxonomic studies. The polyploidy percentage of 26.2 % is beyond the average known in flowering plants, which is surprising for dominant plants of saline and desert ecosystems. The polyploidy of annual plants is only 16 % and that of perennials 19 %, respectively. It was found that C₄ plants represent lower polyploidy levels than C₃ plants. This is correlated by the fact that large number of annuals in the area is C₄ and secondly, polyploidy may constrain niche advantageous in C₄ plants. However, presence of different cytotypes in the widespread species is advantageous as they can occupy different niches. The basic chromosome numbers in chenopods is x = 9 with few derived exceptions in Spinacia (x = 6), Camphorosma (x = 6) and some species of Petrosimonia (x = 8).     

Contribution to the Karyological Knowledge of Mediterranean Romulea Species (Iridaceae)

Eighteen chromosome counts are reported in nine Mediterranean Romulea species. Among them, four species have a wide distribution range (R. bulbocodium, R. columnae, R. ramiflora and R. rollii) and five are narrow central Mediterranean endemics (R. bocchierii, R. ligustica, R. linaresii, R. requienii and R. revelieri). Chromosome numbers range from 2n?=?3x?=?27 in one R. columnae accession to 2n?=?6x?=?54 in R. linaresii. Our results only partially agree with previous reports, and the chromosome number records of R. bocchierii, R. ligustica, R. linaresii subsp. linaresii and R. revelieri presented here are completely new. According to our data and contrary to previous statements, x?=?9 seems to be the basic chromosome number in this group of Mediterranean Romulea. Moreover, a highly significant negative correlation between the chromosome size and ploidy level was found.     

First report of chromosome numbers of the Carlemanniaceae (Lamiales)

The Carlemanniaceae comprises two small genera that are restricted to East Asia: the Carlemannia and Silvianthus. These genera were previously placed in the Rubiaceae or Caprifoliaceae, but are now considered a distinct family that is probably related to the Oleaceae in the Lamiales. The family is still poorly understood with respect to its morphological characteristics. Here, we present the first report of the chromosome numbers of the family using species from both genera, i.e., Carlemannia tetragona, Silvianthus bracteatus ssp. bracteatus, and S. bracteatus ssp. clerodendroides. The species were compared with the chromosome numbers of Oleaceae and associated families using a Bayesian tree that was generated from rbcL and ndhF sequence data from Genbank. C. tetragona had 2n = 30 (x = 15), whereas the two subspecies of Silvianthus had 2n = 38 (x = 19). Comparisons of chromosome numbers support the distinctness of the Carlemanniaceae, not only from the Oleaceae (x = 11, 13, 23), but also from the Tetrachondraceae (x = 10, 11), a family that is possibly related to the Carlemanniaceae and/or Oleaceae in the Lamiales. The notable difference in chromosome number between Carlemannia and Silvianthus, as well as the differences in other characteristics (pollen, seed, and fruit morphology), suggests that the family split early in its evolution.     

CHROMOSOME NUMBERS OF CAMPANULACEAE. III. REVIEW AND INTEGRATION OF DATA FOR SUBFAMILY LOBELIOIDEAE

Chromosome numbers are now known for 153 species in 21 genera of Lobelioideae (Campanulaceae); this represents almost 13% of the species and 70% of the genera in the subfamily. Numbers reported are n = 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 21, 35, 70. The subfamily as a whole has x = 7; the best documented exception is Downingia and its allies with x = 11. Only four genera show interspecific variation in chromosome number: Downingia (n = 6, 8, 9, 10, 11, 12); Lobelia (n = 6, 7, 9, 12, 13, 14, 19, 21); Pralia (n = 6, 7, 13, 14, 21, 35, 70); and Solenopsis (n = 11, 14). Intraspecific variation occurs in 13 species, with as many as four different cytotypes in one species. The herbaceous members of the subfamily as a group are quite variable, showing the entire range of chromosome numbers, including numerous dysploids, but are predominantly diploid. The woody species, by contrast, are much less variable; nearly all of the species are tetraploid, with only a few diploids and hexaploids and no dysploid numbers known. These data support the hypothesis that woodiness is apomorphic within the subfamily. A general trend of higher chromosome numbers at higher latitudes and higher elevations is evident within the subfamily. The chromosome number of Apetahia raiateensis (n = 14) is reported here for the first time, on the basis of a count made about 30 years ago by Peter Raven.     

Juncus x stuckeyi (Juncaceae), a natural hybrid from northern Ohio

Hybrids betweenJuncus alpinus andJ. torreyi (Juncaceae) have been discovered in abandoned limestone quarries and on sandy beaches of Lake Erie in Erie and Ottawa counties, Ohio. The plants are morphologically intermediate in height, inflorescence length, number of glomerules per inflorescence, and number of flowers per glomerule. Both parents are diploid, 2n= 40; the hybrid is also diploid, 2n= 40, but at metaphase I both univalents and unequal bivalents are present. Using starch gel electrophoresis, ten enzymes were studied. The parents show differences in the allozymes of malic dehydrogenase, esterase, and malic enzyme. At each of these loci, the hybrids exhibit both the parental allozymes. Morphological and chromosomal data, augmented by the flavonoid and electrophoretic studies, confirm the hybrid nature of the newly discovered plants. The new taxon is described and namedJuncus xstuckeyi.