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The genus Molossus of the free-tailed bat family Molossidae is morphologically conservative and the level of genetic divergence is also low among many species, which has masked the actual species diversity in the genus. We analyzed the evolutionary relationships among species within Molossus using three mitochondrial (COI, Cytb, and 16S RNA), and two nuclear genes (RAG2 and β-fib) from more than 400 specimens across the Neotropics. We also investigated the genetic integrity of currently recognized species, especially those with broad geographic distributions and controversial taxonomic arrangements. Maximum likelihood and Bayesian phylogenetic reconstructions show that some recognized species are not monophyletic. The use of combined mitochondrial and nuclear genes as well as the use of only mitochondrial markers revealed more robust phylogenies than those for individual data sets and those restricted to the two nuclear genes. We recovered the recently described M. fentoni and M. alvarezi, validated M. milleri and M. verrilli as distinct species relative to M. molossus, and confirmed that the name M. barnesi should be considered as a junior synonym of M. coibensis. Additionally, M. rufus appears to be a complex of cryptic species, showing that the broadly distributed genus Molossus is more diverse than previously reported. [ABSTRACT FROM AUTHOR]

Abstract Distribution of rhizobial species is affected by geographical isolation and selected by leguminous hosts, however, little is known about the molecular evolution of rhizobia nodulating the same legume in different eco-environments. In present study, the microevolution of Bradyrhizobium associated with the leguminous grass Kummerowia grown in exurban areas and cultivated in urban areas in China was investigated. Total 14 genospecies, including seven new groups, were identified based on a concatenated sequence analysis of taxonomic markers (SMc00019, truA and thrA) for 94 representative strains. Results demonstrated that lower levels of nucleotide diversity were found in the strains isolated from urban areas compared with those isolated from exurban areas, based on the evolutional analyses of three housekeeping genes (atpD, glnII and recA), two symbiosis-related genes (nodC and nifH), and the taxonomic markers. Moreover, compared with urban areas, gene exchange and recombination occurred more frequently among the genospecies isolated from exurban areas, regardless of the geographical distribution. Finally, the evolutionary lineage of Bradyrhizobium strains isolated from urban areas was independent of that of the strains isolated from exurban areas. In summary, the evolutionary history of Kummerowia bradyrhizobia may have been gradually segregated to different evolutionary lineages, irrespective of distinct biogeography. [ABSTRACT FROM AUTHOR]

Barleria is a genus of ~300 species of herbs and shrubs in Africa and Asia, with highest diversity in tropical East Africa and southern Africa. The genus is part of Barlerieae (Acanthaceae), a lineage that is distinguished from other Acanthaceae by quincuncial corolla aestivation. Unequivocal synapomorphies have yet to be identified for Barleria. However, among Barlerieae, species of Barleria can be recognized by the combination of 4‐partite calyces with the anterior and posterior lobes usually larger than the two lateral lobes, pollen with a coarsely reticulate (honeycomb) exine and the corolla limb variously subactinomorphic to strongly zygomorphic but never markedly bilabiate with a hooded upper lip. All Barleria that we have observed also have filaments that twist through 180° and cross just distal to the synstapetal zone. Barleria species have previously been classified into two subgenera and seven sections based on differences in leaf axil spine systems; configuration of the corolla, androecium and stigma; and morphology of the capsule and seed. We tested the subgeneric classification of Barleria by sampling 53 Barleria species and 9 outgroup species for three plastid intergenic spacers (trnS‐G, ndhF‐rpl32‐trnL(UAG)) and the nuclear region nrITS. We found a monophyletic Barleria and support for the two currently recognized subgenera; four of seven currently recognized sections are monophyletic but one of these four, sect. Fissimura, is nested within other sections. Species of sect. Fissimura unexpectedly resolved in subg. Barleria with strong support, although previous classifications placed the section in subg. Prionitis. We propose recognizing two subgenera (i.e., Barleria, Prionitis), the latter comprising three sections (i.e., Prionitis, Somalia, Stellatohirta). Barleria encompasses remarkable morphological diversity; we used an ultrametric tree to examine the evolution of nine morphological traits used to define infrageneric taxa in previous classifications. All characters evolved homoplasiously, but a few states (e.g., woody capsule septa) are supported as synapomorphies, and combinations of characters can be used to delimit subgenera. Members of subg. Barleria have 4‐seeded capsules that lack a prominent beak, with a transition to 2‐seeded capsules in the clade that corresponds to sect. Fissimura. In contrast, members of subg. Prionitis have 2‐seeded capsules (reversed to 4‐seeded in most members of one clade of sect. Somalia) that generally have a prominent beak. Additionally, we surveyed pollen morphology for 15 species sampled from across the classification. Pollen is consistently tricolporate with a coarse honeycomb exine. We provide an infrageneric classification and key to infrageneric taxa of Barleria. [ABSTRACT FROM AUTHOR]

Jurinea (Asteraceae: Cardueae) is a large Eurasian genus of about 180 species with centres of diversity in Central and Southwest Asia and the eastern Mediterranean. The genus includes many species with adaptations to xero‐ and chasmophytic habitats and comprises numerous endemics, especially in the Caucasus. Generic delimitations between Jurinea and closely related genera have been difficult to assess, as have the phylogenetic relationships with the genera Himalaiella, Jurinella and Lipschitziella, each of which has been suggested as congeneric with Jurinea. A molecular phylogenetic investigation at both the specific and the generic level to establish the generic delimitation of Jurinea and to evaluate the intergeneric relationships of the genus with other members of the Cardueae was hitherto lacking. In this study, we reconstruct the phylogenetic relationships between Jurinea and several closely related genera based on a representative taxon sampling using DNA sequence data of nuclear (ITS, ETS) and plastid DNA regions (trnK/matK, trnL‐F). We also evaluate the infrageneric classification of Jurinea. Our results indicate that Jurinea is polyphyletic in its current circumscription, as the species J. gedrosiaca and J. cartilaginea are placed within the subtribe Centaureineae of the Cardueae. The rest of Jurinea is monophyletic and split into two major clades corresponding to the western and eastern range of the distribution area of the genus. The sister clade of Jurinea is composed of Himalaiella and Lipschitziella. Jurinella, which was segregated from Jurinea based on achene morphology, is congeneric with Jurinea. Like in other speciose Eurasian genera, the currently recognised sections do not reflect natural groups, whereas most clades found through molecular phylogenetic inference correlate with geographic patterns. A clade that exclusively comprises Caucasian endemics, including the narrow endemics of J. sect. Neobellae, was found. This clade represents an interesting study group for possible radiation events of Jurinea in the Caucasus. [ABSTRACT FROM AUTHOR]

Chamaecrista is a monophyletic genus, but most of its infrageneric categories have been shown to be paraphyletic, including series Rigidulae which currently comprises 30 species, all endemic to Brazil and most occurring in the cerrado vegetation of the central highlands of the country. This molecular phylogenetic study tests the monophyly of C. ser. Rigidulae based on a broad sampling, considers its relationship with members of C. sect. Absus subsect. Absus, and estimates its divergence time in relation to the age of the genus. For that, individual and combined analyses were performed by the parsimony and Bayesian methods using chloroplast (trnL‐F) and nuclear (ITS1‐5.8S‐ITS2) markers and a matrix containing 75 taxa of Chamaecrista (29 belonging to series Rigidulae), 6 of Senna and 1 of Cassia. The analyses showed that series Rigidulae, as traditionally circumscribed, is polyphyletic. When C. brachyblepharis and C. ciliolata are excluded and C. botryoides and C. sincorana included, the series is resolved as monophyletic, comprising 30 species here designated as the Rigidulae clade. This clade is further subdivided into two geographically and genetically structured subclades, the first containing 23 species, mostly from the highlands of Goiás State, and the second with 6 species from the Espinhaço Range, running north to south through central Bahia and Minas Gerais States. Divergence time analyses suggest that the Rigidulae clade originated about 5 million years ago. The recent radiation of the series repeats that seen in other species‐rich genera in the Cerrado Biome, thus corroborating previous hypotheses about the recent age of the biome. The Rigidulae clade, as here circumscribed, has the following morphological synapomorphies: asymmetric flowers with their posterior petals similar to a typical papilionoid standard petal, and leaflets divaricate along the leaf rachis. [ABSTRACT FROM AUTHOR]

Circumscriptions of the Australasian tribes Ophiorrhizeae and Pomazoteae (Rubiaceae) as well as their generic relationships and limits have long remained unsettled. These tribes were originally delimited by Bremekamp based on the lack of raphides and testa cell patterns (thick‐ versus thin‐walled testa cells, respectively). Some authors have synonymized the two or treated Pomazoteae as a synonym of other tribes despite the fact that the matter has never been sufficiently addressed. We performed molecular phylogenetic analyses of Ophiorrhizeae sensu Bremer & Manen (i.e., comprising Coptophyllum, Lerchea, Neurocalyx, Ophiorrhiza, Spiradiclis and Xanthophytum) based on sequence data from four plastid and two nuclear markers. Coptophyllum (= Pomazota, type of Pomazoteae), Lerchea and Xanthophytum together with seven other genera, were traditionally classified in Pomazoteae. We also investigated for the first time the two Pomazoteae genera Keenania and Leptomischus. Our analyses resolved Leptomischus as sister to the Rubioideae tribe Argostemmateae and we here formally classify this genus in that tribe. Ophiorrhizeae sensu Bremer and Manen is paraphyletic with respect to Keenania. Pomazoteae is polyphyletic, with most of its genera (including Coptophyllum) belonging in Ophiorrhizeae. Its tribal status cannot be held. Testa cell patterns are evolutionarily labile, and seem to have no phylogenetic value at tribal level. Our study strongly supports a broadly delimited Ophiorrhizeae that contains mostly suffrutescent herbs. Within Ophiorrhizeae as here defined, Neurocalyx is sister to the rest of the tribe, followed by Xanthophytum. The Coptophyllum‐Lerchea clade is sister to a large clade formed by Keenania, Ophiorrhiza and Spiradiclis. Ophiorrhiza is paraphyletic with respect to Keenania and Spiradiclis, and was resolved in two well‐supported lineages, the Ophiorrhiza‐Keenania and Ophiorrhiza‐Spiradiclis lineages. Accordingly, we formally transferred all validly published names from Keenania and Spiradiclis to Ophiorrhiza, resulting in 40 new combinations and 15 new names. [ABSTRACT FROM AUTHOR]

Pyrularia is a small parasitic genus of the Santalales with two to five species exhibiting a well‐known classical intercontinental disjunct distribution between eastern Asia (EA) and eastern North America (ENA). Pyrularia and another santalaceous genus Buckleya represent the only two parasitic plant lineages with the EA–ENA disjunction. The present study was carried out to assess the species number and molecular and morphological differentiation in Pyrularia, and to reconstruct the biogeography of the Pyrularia clade (Pyrularia and its close allies) using dating and biogeographic inferences. A phylogenetic analysis based on two nuclear and seven plastid markers strongly supported the monophyly of Pyrularia and revealed two highly distinct subclades corresponding to EA and ENA within the genus. Incongruent topologies within the eastern Asian lineage were found between the nuclear and the plastid datasets, which may be attributed to incomplete lineage sorting. Morphometric and phylogenetic analyses suggest that Pyrularia in eastern Asia may best be treated as a single species, P. edulis. Molecular dating based on four markers suggested that the divergence time between the intercontinental species was in the late Miocene at 5.58 Ma (95% HPD: 2.08–11.72 Ma), which was close to the split of the trans‐Pacific clades within the other parasitic EA–ENA disjunct genus Buckleya. The EA–ENA disjunction in the only two parasitic genera may have resulted from the fragmentation of the mesophytic temperate forests in the late Miocene. The Pyrularia clade (including the close allies of Pyrularia) was inferred to have originated in Africa, then dispersed to Asia, and subsequently to North America via the Bering land bridge, resulting in the current intercontinental EA–ENA distribution of Pyrularia. [ABSTRACT FROM AUTHOR]

Phytochelatin synthase isolated from microorganisms, yeasts, algae and plant, serve a fundamental role in reducing heavy metals. In this research the in silico PCS gene structure ( SoPCS ) of sugarcane, its secondary and 3D protein structure, physicochemical properties, cell localization and phylogenetic tree were predicted utilizing bioinformatics tools. SoPCS expression in the leaves and roots of sugarcane in tissue culture treated with cadmium was also studied utilizing real time PCR. The predicted SoPCS gene contains 1524 nucleotides, a protein encoded with 508 amino acids of which the molecular weight is 55953.3 Da, 6 exons and 5 introns. The subcellular position of the enzyme is mitochondrion or cytoplasmic. Two domains belonging to the phytochelatin synthase family with similar features was found in Pfam having more than 97% similarity with the predicted SoPCS protein. Phylogeny analyses of plant species were well isolated from other organisms. Ten disulfide-bonded cysteines were excluded from the structure of SoPCS . The predicted 3D structure of SoPCS showed that it is able to bind to L-gamma-glutamylcysteine as substrate. The binding site sequence of PCS included amino acids 52(Q),55(P),56(A),57(F), 58(C),103(G),104(I),151(S),163(G),165(F),206(D), 213(R). The common amino acid with conserved sequence in the binding site of the plant was 103Gly. Gene expression indicated that SoPCS has an important role in the response of sugarcane to cadmium with potential use in genetic engineering to remove metal contaminants in the environment. This is the first characterization of a PCS from sugarcane. [ABSTRACT FROM AUTHOR]

Abstract Four novel Gram-stain-positive, non spore forming and fructose-6-phosphate phosphoketolase-positive strains were isolated from the faeces of a cotton top tamarin (Saguinus oedipus) and an emperor tamarin (Saguinus imperator). Phylogenetic analyses based on 16S rRNA revealed that bifidobacterial strains TRE 1T exhibit close phylogenetic relatedness to Bifidobacterium catulorum DSM 103154 (96.0%) and Bifidobacterium tissieri DSM 100201 (96.0%); TRE DT and TRE HT were closely related to Bifidobacterium longum subsp. longum ATCC 15708T with similarity values of 97.4% and 97.5%, respectively; TRI 7T was closely related to Bifidobacterium tissieri DSM 100201 (96.0%). The Average Nucleotide Identity (ANI) and in silico DDH (isDDH) analysis with closest neighbour supported an independent phylogenetic position of all strains with values ranged from 74 to 85% for ANI and from 24 to 28% for isDDH. DNA base composition of the four strains was in the range of 58.3–63.5 mol% G + C. Based on the phylogenetic, genotypic and phenotypic data, the strains TRE 1T, TRE DT, TRE HT and TRI 7T clearly represent four novel taxa within the genus Bifidobacterium for which the names Bifidobacterium primatium sp. nov. (type strain TRE 1T = DSM 100687T = JCM 30945T), Bifidobacterium scaligerum sp. nov. (type strain TRE DT = DSM 103140T = JCM 31792T), Bifidobacterium felsineum sp. nov. (type strain TRE HT = DSM 103139T = JCM 31789T) and Bifidobacterium simiarum sp. nov. (type strain TRI 7T = DSM 103153T = JCM 31793) are proposed. [ABSTRACT FROM AUTHOR]

Abstract Many marine Alphaproteobacteria of the Roseobacter group show a characteristic swim-or-stick lifestyle, for which motility is a crucial trait. Three phylogenetically distinct flagellar gene clusters (FGCs) have been identified in Rhodobacteraceae that have been named fla1 , fla2 and fla3 according to their relative abundance. In addition to the flagellar-dependent swimming and swarming motility, pilus-dependent twitching mediates bacterial locomotion. Furthermore, filament independent modes of motility, namely gliding and sliding, have been described for various microorganisms. However, no mode of motility other than swimming has so far been described for roseobacters. In the present study, we investigated motility, distribution of flagellar systems and the phylogeny of 120 genome-sequenced Rhodobacteraceae. The phylogenetically broad taxon sampling that included 114 type strains revealed the presence of at least ten distinct clades that were statistically well supported. The investigation of the actual physiological capacity for swimming motility on soft agar plates showed that only about half of the 120 tested strains were motile under the tested conditions. Seven strains developed a conspicuous dendritic motility phenotype that was reminiscent of the swarming motility in Pseudomonas aeruginosa. The observed dendritic motility in two strains (i.e. Sulfitobacter pseudonitzschiae DSM 26842 and Roseovarius pacificus DSM 29589) was particularly surprising because they did not harbor any genes of the FGC. Accordingly, it was concluded that this form of dendritic motility was independent of a flagellum. A comparative genomics approach allowed a remarkable number of pilus-related candidate genes to be identified for this novel type of motility in Rhodobacteraceae. [ABSTRACT FROM AUTHOR]

Abstract Four bacterial strains designated 410T, 441, 695T and 736 were isolated from maize root in Beijing, P. R. China. Based on 16S rRNA gene phylogeny, the four strains formed two clusters in the genus Caulobacter. Since strain 441 was a clonal variety of strain 410T, only three strains were selected for further taxonomic studies. The whole genome average nucleotide identity (ANI) value between strains 410T and 695T was 94.65%, and both strains shared less than 92.10% ANI values with their close phylogenetic neighbors Caulobacter vibrioides DSM 9893T, Caulobacter segnis ATCC 21756T and Caulobacter flavus CGMCC 1.15093T. Strains 410T and 695T contained Q-10 as the sole ubiquinone and their major fatty acids were C 16:0, 11-methyl C18:1ω 0 , 11-methyl C 18: 1 ω 7c, summed feature 3 (C 16:1ω7c and/or C16:1ω 1 ω 7c and/or C 16: 1 ω 6c) and summed feature 8 (C 18:1ω7c and/or C18:1ω 1 ω 7c and/or C 18: 1 ω 6c). Their major polar lipids consisted of glycolipids and phosphatidylglycerol, and phenotypic tests differentiated them from their closest phylogenetic neighbors. Based on the results obtained, it is proposed that the three strains represent two novel species, for which the names Caulobacter zeae sp. nov. (type strain 410T = CGMCC 1.15991 = DSM 104304) and Caulobacter radicis sp. nov. (type strain 695T = CGMCC 1.16556 = DSM 106792) are proposed. [ABSTRACT FROM AUTHOR]

Abstract Two closely related, thermophilic bacteria, designated strains YIM 76954T and YIM 76947, were isolated from the Rehai Geothermal Field, Tengchong, Yunnan province, south-west China. Polyphasic approach and whole genome sequencing were used to determine the taxonomy status and genomic profiles of the novel strains. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates were closely related to Thermus scotoductus SE-1T (97.1% sequence similarity), and T. amyloliquefaciens YIM 77409T (96.6%). The strains could be differentiated from most recognized Thermus species by their whitish to slight reddish colony color, distinct DNA fingerprinting profiles and low ANI values. Cells stained Gram-negative, rod-shaped of diameter 0.2–0.5 μm and length 1.5–5.0 μm. Growth occurred at 50–75 °C, pH 6.0–9.0 and in the presence of up to 1.0% (w/v) NaCl concentration. Thiosulfate was found to enhance cell growth, besides improving the intensity of its colony color. Oxygen, nitrate, sulfur, and Fe(III) could be used as terminal electron acceptors for growth. MK-8 was the major respiratory menaquinone. Major fatty acids were iso-C 17:0 , iso-C 15:0 , anteiso-C 17:0 , and anteiso-C 15:0. The genome size was 2.26 Mbp with 65.5% average GC content. A total of 2374 genes was predicted, comprising 2322 protein-coding and 52 RNA genes. On the basis of the polyphasic evidence presented, it is proposed that strain YIM 76954T represents a novel species of the genus Thermus , for which the name Thermus tenuipuniceus sp. nov. is proposed. The type strain is YIM 76954T (=JCM 30350T = KCTC 4677T). [ABSTRACT FROM AUTHOR]

Abstract In this study, the genetic diversity and identification of Bradyrhizobium symbionts of Crotalaria zanzibarica , the most widely-distributed invasive legume in Taiwan, and other sympatric legume species growing along riverbanks of Taiwan were evaluated for the first time. In total, 59 and 54 Bradyrhizobium isolates were obtained from C. zanzibarica and its coexisting legume species, respectively. Based on the multilocus sequence analysis (MLSA) of concatenated four housekeeping genes (dnaK - glnII - recA - rpoB gene sequences, 1901 bp), the 113 isolates displayed 53 unique haplotypes and grouped into 21 clades. Of these clades, 11 were found to be congruent to already defined Bradyrhizobium species, while the other 10 clades were found to not be congruent to any defined species. In particular, the C. zanzibarica isolates belong to 14 MLSA clades, six of which overlapped with the isolates of coexisting legumes. According to the nodA gene sequences (555 bp) obtained from the 105 isolates, these isolates were classified into three known nodA clades, III.2, III.3 and VII and were further clustered into 10 groups. Furthermore, the C. zanzibarica isolates were clustered into 8 nodA groups, five of which overlapped with the isolates from coexisting legumes. Additionally, the nodA genes of the isolates from native species were dominated by Asian origin, while those from C. zanzibarica were dominated by American origin. In conclusion, C. zanzibarica is a promiscuous host capable of recruiting diverse Bradyrhizobium symbionts, some of which are phylogenetically similar to the symbionts of coexisting legumes in Taiwan. [ABSTRACT FROM AUTHOR]

Arthrostylidium, a Neotropical genus of 31 mostly clambering woody bamboo species, is a member of subtribe Arthrostylidiinae, which is closely allied to subtribe Guaduinae. Arthrostylidium has long been a catchall for species within its subtribe that display unusual morphology. While attempting to clarify the circumscription of Arthrostylidium, we discovered three West Indian species (A. angustifolium, A. farctum, A. pinifolium) that possess putative Guaduinae features. We test the hypothesis that these three species should be classified within subtribe Guaduinae and revise their taxonomy. Phylogenetic inference based on sequences of four plastid markers (ndhF, trnC-rpoB, trnD-trnT, rps16-trnQ) recovered Arthrostylidium as polyphyletic, with A. angustifolium, A. farctum, and A. pinifolium forming a well-supported clade sister to the Guaduinae. Parametric bootstrap tests uphold this topology as significant. Detailed morphological and anatomical analyses revealed A. angustifolium, A. farctum, and A. pinifolium lack characteristics diagnostic for Arthrostylidiinae but conform to Guaduinae. Based on the morphological and molecular results, we erect the new genus Tibisia within subtribe Guaduinae, transfer Arthrostylidium angustifolium, A. farctum, and A. pinifolium to Tibisia as T. angustifolia, T. farcta, and T. pinifolia, and provide keys to the genera of Guaduinae and the species of Tibisia. These findings demonstrate convergent evolution in a number of macromorphological characters that have been important for generic identification, and reinforce the diagnostic value of leaf anatomy for subtribal determination among the Neotropical woody bamboos. [ABSTRACT FROM AUTHOR]

Abstract The aim of the present study was to characterize rhizobia isolated from the root nodules of Trigonella foenum-graecum (fenugreek) cultivated in the sub-himalayan region of Uttarakhand by means of morphological, physiological, biochemical and molecular characteristics to know their phylogenetic relationships. The genetic relatedness amongst twenty root nodule isolates of fenugreek was analyzed employing PCR-RFLP (ARDRA) analysis of 16S rDNA amplicons, ERIC-PCR and sequencing technique. Restriction analysis of the amplified 16S rRNA gene and ERIC-PCR of fenugreek rhizobia led to the identification of three ribotypes that appear to represent three distinct species: Ensifer (Sinorhizobium) meliloti, Rhizobium leguminosarum and Burkholderia sp. Based on plant growth promoting activities four isolates RHT2, RHT8, RHT12 and RHT19 were selected from three distinct groups and identified as Ensifer (Sinorhizobium) meliloti , Burkholderia sp., Burkholderia sp., Rhizobium leguminosarum by 16S rDNA sequences. The majority of isolates is closely related to Ensifer (Sinorhizobium) meliloti. This study clearly shows that the characterization of symbionts of fenugreek will reveal additional diversity. Highlights • Genetic diversity among microorganisms has been widely studied by PCR-based techniques, which involve the use of primers based on conserved regions of the rRNA genes and digested with a combination of resriction enzymes and/or on short repetitive elements present in the bacterial genome, ERIC (enterobacterial repetitive intergenic consensus), which yields genomic fingerprints specific to pathovars and strains of Gram-negative bacteria. The ERIC profiles are specific for bacterial strains within a species. 16S rDNA genes are ubiquitous in living organism and, therefore, 16S rDNA operon are present in multiple copies and amplimers generated by PCR ribotyping indicate inter and intra-species genetic diversity in the number and structure of ribosomal operon. Following methods were commonly used to study the genetic diversity among bacterial isolates. Amplified Ribosomal DNA Restriction Analysis (ARDRA) and Enterobacterial repetitive consensus sequences (ERIC). • Restriction analysis of the amplified 16S rRNA gene and ERIC-PCR of fenugreek rhizobia led to the identification of three ribotypes that appear to represent three distinct species: Ensifer meliloti, Rhizobium leguminosarum and Burkholderia sp. and same was confirmed by 16S rDNA sequences. The majority of isolates is closely related to Ensifer meliloti. • High diversity of nodulating rhizobia was found which provides sufficient effective strains of indigenous rhizobia that may play both direct and indirect roles in promoting plant growth and disease suppression in Trigonella foenum-graecum. [ABSTRACT FROM AUTHOR]

Factors that control individual survival dynamics are pivotal determinants of forest diversity. Numerous studies have examined the relative importance of habitat variables and neighborhood effects on individual survival, while few studies have examined this importance in different forest types that largely vary topography. We examined the role of conspecific negative density dependence (CNDD), phylogenetic negative density dependence (PNDD) and habitat variables across life stages in two temperate old-growth forests in Northeast China. Using generalized linear mixed models (GLMMs), we tested whether individual survival is related to neighborhood effects and habitat variables. Our results showed that the relative importance of neighborhood effects and habitat variables to focal individual survival varied among life stages and sites. However, the best-fit models for three life stages (with the exception of seedling stage in the BKPF) at both sites all included habitat variables, indicating that these variables contribute to the patterns of focal individual survival. We found evidence of a CNDD effect, and the strength of this effect decreased as the life stages progressed and varied from a negative effect at the seedling stage to a positive one at the adult stage. This result confirms that the importance of CNDD-based survival at the seedling stage plays a particularly significant role in promoting the coexistence of tree species and maintaining forest diversity. We found evidence of PNDD in our forest, and the impact of heterospecific phylogenetic relatedness on focal individual survival was significantly negative; the strength of PNDD increased as the life stages progressed. The CNDD and PNDD widely varied among species, indicating the importance of including the relative abundance, life history strategies and functional traits of species when determining the factors that affect species sensitivity to neighborhood effects. The results of our study demonstrated that CNDD, PNDD and habitat variables all influence the individual survival of these temperate old-growth forests, but the relative importance of these factors vary among life stages and species. Our results highlight the importance of combining multiple species, life stages, functional traits and large-scale studies for investigating elements that affect species coexistence in tree communities. [ABSTRACT FROM AUTHOR]

Two Cantharellus species collected from different forest types in northern Iran are reported as new to the country. Phylogenetic analyses of DNA sequences from the internal transcribed spacer 2 (ITS2), nuclear ribosomal large subunit (nLSU), RNA polymerase II (RPB2) and translation elongation factor 1-a gene (TEF1) are presented. Cantharellus alborufescens was collected in slightly acidic soils and C. ferruginascens in moderate acidic soils. Illustrations from fresh material are provided for both species. [ABSTRACT FROM AUTHOR]

Two remarkable crepidotoid agarics were collected many times from Kerala State, India. Detailed morphological and molecular analysis indicated that one is an undescribed species of Crepidotus while the other represents Simocybe amara which represents a new Asian record. Complete morphological descriptions, photographs and comparisons with phenetically similar species are provided. [ABSTRACT FROM AUTHOR]

We investigated the timing of origin and past connections between Andean and Atlantic Seasonally Dry Tropical Forests in South America based on the biogeographical history of Amorimia, a genus of Malpighiaceae restricted to South America. We used a time-calibrated phylogenetic tree based on three cpDNA (ndhF, rpl16, trnQ-rps16) and two nrDNA (ETS, ITS) regions including all currently accepted species in Amorimia for ancestral area reconstructions. Our results show that: (1) the ancestor of Amorimia originated in Atlantic dry forests around 22 Ma,(2) ancestors of both Amorimia subgenera arose in southern Brazilian dry forests from 18 to 14 Ma,(3) the remaining lineages in the genera diversified from mid-Miocene to the late-Pliocene,and (4) a history of two expansion events during early and middle Miocene, besides several colonization events in different nuclei of dry forests in South America is suggested. [ABSTRACT FROM AUTHOR]

Tribe Marrubieae (Lamiaceae: Lamioideae) comprises about 91 species classified in four genera distributed from Europe to West and Central Asia and North Africa. Here, we present a phylogenetic analysis of cpDNA (rpl32-trnL, rps16, trnL intron, trnL-trnF spacer) and nuclear ribosomal (ITS) sequence data of 68 accessions representing all genera and most sections of Marrubieae. Our taxon sampling covers is dense for the genera Ballota and Marrubium, including a total of 60 of 85 currently recognized taxa (species and subspecies). Parsimony and Bayesian analyses of individual nrITS and cpDNA markers, as well as the combined plastid dataset, produced largely congruent trees. Our results confirm the monophyly of tribe Marrubieae. All analyses retrieved four well supported clades in the tribe. The phylogenetic position of the genera Acanthoprasium and Moluccella is consistent with previous studies and both are recovered as monophyletic. The most important result of the present study is the splitting of the genus Ballota, in its traditional concept, into two well-supported clades matching well with the genera Ballota and Pseudodictamnus. Moreover, Marrubium, in its current circumscription, is paraphyletic, but will become monophyletic by transferring Ballota deserti to this genus. In conclusion, we propose the recognition of five genera in tribe Marrubieae: Acanthoprasium, Ballota, Moluccella, Marrubium and the resurrected segregate Pseudodictamnus. The required new combinations are proposed. [ABSTRACT FROM AUTHOR]

Eugenia, comprising ca. 1100 species, is the largest genus of Neotropical Myrtaceae. Eugenia sect. Umbellatae (formerly referred to as "clade 9") is the most speciose lineage of Eugenia. This study aims to better delimit E. sect. Umbellatae, to identify and understand relationships between manageable subgroups of this large clade for future discrete systematic studies and to explain biogeographical patterns in the genus. In total, 103 samples were used in this study. These include representatives of the nine clades of the "Eugenia group" with a particular focus on Eugenia clade 9, representing the morphological and geographical diversity found in the genus. Phylogenetic reconstructions were performed using maximum likelihood (ML) and Bayesian inference (BI) for the combined dataset, using the markers ITS, rpl16, psbA-trnH, rpl32-trnL, trnQ-rps16. The resultant tree was fossil calibrated and used for historical biogeographical analysis using DEC implemented in RASP. The mid Oligocene is the most likely period in which the crown node of Eugenia s.l. diversified. The earliest Eugenia appear to be associated with dry biomes and to have arisen from non-tropical southern South America, as did ancestors of the earliest American Myrteae. Eugenia subg. Pseudeugenia also most likely diversified in dry biomes, while E. subg. Hexachlamys and E. subg. Eugenia are likely to have diverged in the Atlantic Forests biome. Eugenia sect. Umbellatae is morphologically very variable,some clades can be circumscribed based on morphology while some remain morphologically undiagnosable. The study presented here provides discussion of the earliest origins of Eugenia and its response to climate-driven changes in the Neotropics as humid, forest biomes became more widespread in the Miocene. In addition, important practical conclusions are drawn regarding relationships within Eugenia. Three clades are newly classified as subgenera: E. subg. Pseudeugenia (including species of E. sect. Pseudeugenia),E. subg. Hexachlamys (including E. sect. Hexachlamys) and E. subg. Eugenia (including E. sect. Umbellatae, E. sect. Jossinia, E. sect. Phyllocalyx, E. sect. Pilothecium, E. sect. Racemosae, E. sect. Schizocalomyrtus, E. sect. Speciosae and Eugenia sect. Excelsae). Two previously unidentified clades are published as E. sect. Excelsae and recognized as E. sect. Jossinia, the latter consisting entirely of Old World species. [ABSTRACT FROM AUTHOR]

Dihydrosphingosine C4 hydroxylase (DSH), a diiron-binding membrane enzyme, catalyzes the hydration of dihydrosphingosine and acyl-sphinganine to produce phytosphingosine and phytoceramide, respectively. Rice has two types of DSH homologs: general DSHs, namely DSH1, DSH2 and DSH4, and others that show spatial expression profiles, namely DSH3 and DSH5. The general DSHs exist in many plant species. These DSHs showed similarity in their functions and complemented the yeast sur2D mutation. In contrast, homologs of DSH3 and DSH5 were found only in monocot plants. Phylogenetic analysis placed these DSHs in different clades that are evolutionarily divergent from those of the general DSHs. DSH3 and DSH5 showed low-level expression. DSH5 expression was specifically in vascular bundle tissues. Ectopic expression of DSH5 induced a dwarf phenotype characterized by severe growth inhibition and an increase in the thickness of the leaf body caused by enlargement of bulliform cells in the leaves. However, no significant difference was observed in the amount of sphingolipid species. DSH5 did not complement the yeast sur2D mutation, implying that DSH5 has little effect on sphingolipid metabolism. These findings suggested that DSH3 and DSH5 originated and diverged in monocot plants. [ABSTRACT FROM AUTHOR]

Two non-pathogenic strains R89-1 and R90 T isolated from poppy seed ( Papaver somniferum L.) wastes were phenotypically and genotypically characterized. Multilocus sequence analysis (MLSA) was conducted with six genes ( atpD , glnA , gyrB , recA , rpoB , 16S rRNA). The strains represented a new species which clustered with Agrobacterium rubi NBRC 13261 T and Agrobacterium skierniewicense Ch11 T type strains. MLSA was further accompanied by whole-genome phylogeny, in silico DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses for both strains. ANI and dDDH values were deep below the species delineation threshold. Phenotypic features of the novel strains unequivocally allowed their differentiation from all other Agrobacterium species. Unlike other agrobacteria, the strains were salt sensitive and were able to biotransform morphine alkaloids. The dominant cellular fatty acids are 18:1 w7c, 16:0 and 12:0 aldehyde/16:1 iso I/14:0 3OH summed in feature 2 and the major respiratory quinine is Q-10 (87%). The DNA G + C content is 56 mol%. Microbial community analysis indicated probable association with P. somniferum plant material. Altogether, these characteristics showed that strains R90 T and R89-1 represent a new species of the genus Agrobacterium which we propose to name Agrobacterium bohemicum . The type strain of A. bohemicum is R90 T (=CCM 8736 T = DSM 104667 T ). [ABSTRACT FROM AUTHOR]

Zehneria is a genus of small creepers and climbers from the Old-World Tropics and Subtropics. In its broadest circumscription, it comprises up to 94 species and its centre of diversity is Southeast Asia. Zehneria has been split into several smaller genera but this remained controversial mainly due to morphological plasticity of the species groups and lack of comprehensive molecular data. Here, we use one nuclear DNA (ITS1-5.8S-ITS2) and three plastid DNA regions (trnL-trnF, rpl20-rps12, matK) sequenced for about half of the species in Zehneria and its segregate genera Anangia, Neoachmandra, and Pilogyne to test the monophyly of the genus and analyse the evolutionary history of the group. We find that Zehneria s.l. is monophyletic and splitting is not supported by molecular, morphological or biogeographical evidence. Within Zehneria, we recover two strongly supported clades, one consisting mainly of species placed in Pilogyne, the other including Anangia, Neoachmandra and the type of Zehneria. Both clades comprise African, Asian, and Australian/Pacific Island species, which is evidence for high dispersal capacity in this young bird-dispersed group. For India, we accept the five species Z. bodinieri, Z. hookeriana, Z. maysorensis, Z. odorata, and Z. thwaitesii. For Myanmar, we increase the number of known species from four to eight, including three still unnamed species. The diversity hotspots for the genus, however, remain Indonesia and Thailand with together 25 species. [ABSTRACT FROM AUTHOR]

Melomastia is a genus of saprobic fungal species found on wood, with 29 species epithets listed in Index Fungorum. The classification of species in the genus has been a challenge due to a high degree of morphological overlap and a lack of DNA based phylogenies. The present study clarifies the phylogenetic placement of the genus and with an additional new species based on a fresh collection from Italy. The new species, Melomastia italica, is described based on morphological and relationships inferred from phylogenetic analyses of SSU and LSU sequence data. Melomastia is accommodated within the family Pleurotremaceae in the class Dothideomycetes. The phylogenetic relationships and intergeneric taxonomy within the family Pleurotremaceae are revisited, while Dyfrolomyces maolanensis is transferred to the genus Melomastia. [ABSTRACT FROM AUTHOR]

A revision of Resinicium collections (Basidiomycota, Hymenochaetales) from French Guiana and French West Indies is provided, and a new species, Resinicium grandisporum sp. nov., supported by morphological as well as phylogenetic analyses based on ITS rDNA sequences, is described and illustrated. An updated key of the genus Resinicium is also provided, which includes species previously described from outside of the studied area. [ABSTRACT FROM AUTHOR]

The "Relhania clade" is a relatively species-poor lineage that is sister to the remaining members of the paper daisy tribe Gnaphalieae. Although the monophyly of the Relhania clade is well established, previous molecular studies are based on fairly sparse sampling. Here, we explore clade membership and generic circumscription using plastid and nuclear DNA sequence data, and near-complete species-level sampling of all putative member genera. Two subclades are recovered within the Relhania clade: (i) clade I housing the genera Alatoseta, Athrixia, Pentatrichia and Phagnalon, all monophyletic as currently circumscribed; and (ii) clade II, containing the genera Antithirixia, Comborhiza, Oedera, Oreoleyesera, Relhania and Rosenia; the annual or otherwise "short-lived" genera Leysera, Nestlera and Rhynchopsidium; as well as a subclade in which the monospecific Arrowsmithia is embedded within Macowania. A new taxonomic treatment involving 12 new combinations is proposed for the two latter genera. Only demonstrably monophyletic and diagnosable genera are recognised, involving the erection of a novel monospecific genus, Fluminaria, to house Macowania pinifolia, and the transfer of the remaining members of Macowania to Arrowsmithia. Updated descriptions and keys are provided. [ABSTRACT FROM AUTHOR]

Subtribe Amsinckiinae, currently containing 13 genera and approximately 287 species, is a speciesrich group of the family Boraginaceae. Past studies assessing relationships had a limited sample size and generally weak support. Here we study phylogenetic relationships of Amsinckiinae using a large sample size and considerably more sequence data in order to evaluate the interrelationships of genera and clades within this group. Using highthroughput, genome skimming sequencing of 139 samples of Amsinckiinae and four outgroup taxa, maximum likelihood and Bayesian analyses of separate plastome, cistron, and mitochondrial datasets are presented. In almost all analyses the common ancestor of the Amsinckiinae gives rise to an Andersonglossum or to an Andersonglossum + Adelinia clade. Most genera, including Amsinckia, Eremocarya, Greeneocharis, Harpagonella, Oreocarya, and Pectocarya, are consistently monophyletic with strong support. Plagiobothrys is confirmed to be nonmonophyletic, composed of three clades conforming to generic sections. Cryptantha is also nonmonophyletic, with most species within a strongly supported Cryptantha s.str. clade, but some nesting within Johnstonella or our Maritimae clade, all with strong support. Although genome skimming verifies the monophyly of many genera and clades of Amsinckiinae, relationships among those clades and along the backbone of the trees remain uncertain, their elucidation possibly a factor of short branch lengths and likely requiring different types of molecular data. Our study may serve as a baseline for future work on the morphology, reproductive biology, and biogeography of the Amsinckiinae. [ABSTRACT FROM AUTHOR]

Whether Mahonia should be recognized as a distinct genus or subsumed under Berberis has long been debated since its publication in 1818. Although recent molecular phylogenetic studies showed the paraphyly of Mahonia and some advocated a broadly defined Berberis to include Mahonia, the acceptance of Berberis s.l. is far from universal. Due to insufficient sampling and analytical issues of outgroup rooting, taxon misidentification, and the inclusion of a problematic GenBank DNA sequence, we argue that the phylogenetic status of Mahonia and consequently the circumscription of Berberis s.l. remains problematic. In particular, Berberis claireae and Mahonia sect. Horridae, taxa both inhabiting xeric habitats and characterized by a transitional morphology between Berberis s.str. and typical Mahonia (core Mahonia), have not been adequately sampled and well-positioned phylogenetically. With the inclusion of these key species and an expanded sampling of core Mahonia, we re-examine the phylogenetic relationships of Berberis s.l. using the internal transcribed spacer (ITS) of nrDNA, and three coding regions (accD, ndhF, rbcL) and one non-coding region (psbA-trnH) of the chloroplast genome. Our analyses reveal four clades within Berberis s.l., corresponding to Berberis s.str., B. claireae, core Mahonia, and Mahonia sect. Horridae, with the latter three (all compoundleaved) forming a paraphyletic grade sister to simple-leaved Berberis. Because of morphological and ecological distinctness of these four clades and their deep stem divergences equivalent to other genera of Berberidaceae, we propose a new classification of Berberis s.l. by applying a strict definition of Berberis (≡ Berberis s.str.), reinstating Mahonia (≡ core Mahonia), and proposing the two new genera Alloberberis nom. & stat. nov. (≡ Mahonia sect. Horridae) and Moranothamnus gen. nov. (≡ B. claireae). This revised classification is consistent with the traditional perception of Berberis and results in a monophyletic Mahonia, maintaining the stable usage of these two household names in both academic and non-academic commun [ABSTRACT FROM AUTHOR]

Sesleria (Poaceae) is a species-rich, taxonomically difficult genus due to high morpho-anatomical variability and weak differentiation of many species. It is distributed throughout western Eurasia and North Africa with highest taxonomic diversity on the Balkan Peninsula. Of the more than 40 species only two are diploid, all others are tetra- to dodecaploid, and many species comprise several ploidy cytotypes. We sequenced the plastid trnL-ndhF region and produced amplified fragment length polymorphisms (AFLPs) from a comprehensive, ploidy-cytotyped sampling including 292 populations, and produced nuclear ribosomal internal transcribed spacer (ITS) sequences for a subsample. Our first aim was to determine the relationships among Sesleria and putatively closely related genera. Further, we explored whether diploid S. sphaerocephala and S. ovata should be treated as separate genera Sesleriella and Psilathera as proposed previously, or rather included in Sesleria, following most recent Floras. Finally, we tested previous hypotheses of infrageneric classifications. In the ITS phylogeny tetra- to dodecaploid Sesleria s.str. grouped with diploid S. ovata whereas diploid S. sphaerocephala was more distantly related. In contrast, in the plastid phylogeny Sesleria s.str. grouped with S. sphaerocephala, whereas S. ovata was sister to Echinaria. This suggests an allopolyploid origin of Sesleria s.str. with S. sphaerocephala acting as maternal and S. ovata as paternal species. The lack of monophyly of Sesleria s.l. thus supports the recognition of S. ovata and S. sphaerocephala as separate genera Psilathera and Sesleriella. Their segregation, which is also supported by morphology, increases the number of angiosperm genera endemic to the European Alps from three to five. In congruence with the plastid sequences, AFLPs resolved the traditionally recognized sections (sect. Argenteae, sect. Sesleria) as non-overlapping clusters and identified S. vaginalis as a probably recently evolved intersectional hybrid. Within the two sections, several informal species groups could be recognized, which show limited congruence with those proposed in the most comprehensive taxonomic treatment of the genus. From an evolutionary point of view it is obvious that ancient as well as recent hybridization coupled with polyploidisation have played a crucial role in diversification within Sesleria. [ABSTRACT FROM AUTHOR]

Taxon delimitation and classification remains one of the fundamental bases of evolutionary studies and is especially challenging because processes by which new biological entities arise are complex and non-linear over time, although continuous. Sisyrinchium (ca. 140 to 216 taxa) is one of the most species-rich genera of Iridaceae, largely widespread in the Americas. Recent molecular phylogenetic studies have shown that the systematics of the genus is in need of substantial revision. Different data sources were investigated to establish an updated infrageneric classification based on phylogenetic principles. Monophyletic sections of Sisyrinchium were circumscribed using a new phylogenetic framework established from an increased sampling of taxa (107 species), and complementary approaches were combined to provide the most comprehensive infrageneric treatment of the genus proposed so far. Additionally, numerous molecular synapomorphies were identified to reinforce previous taxonomic treatments of tribe Sisyrinchieae (six genera) at the generic level. Major lineages of Sisyrinchium were concordantly resolved with mostly strong to full support by the DNA regions used in the study and ten sections characterized by unique combinations of molecular, morphological and geographical diagnostic characters were recognized. The phylogenetic trees respectively based on plastid + mitochondrial and nuclear ITS DNA regions were generally congruent except for two unplaced species (S. chilense, S. elegantulum) for which ancestral reticulation events were detected. New circumscriptions were provided for seven sections (sect. Cephalanthum, sect. Echthronema, sect. Hydastylus, sect. Segetia , sect. Sisyrinchium, sect. Spathirhachis, sect. Viperella) while three sections (sect. Morphanthus, sect. Rhizilineum, sect. Trichoparcus) were newly described. This work constitutes a robust contribution to elucidate the systematics of Sisyrinchium and emphasizes the need of integrative taxonomic approaches using multiple data sources, not only to improve the delimitation of taxa but also to investigate their evolutionary history. [ABSTRACT FROM AUTHOR]

Blechnaceae is a worldwide family of leptosporangiate ferns composed of about 250 species. Most of the species in the family were recognised under a single large genus Blechnum until recently, when a new classification proposed the recognition of 24 genera. Given this new systematics of Blechnaceae, which largely resolves the genus-level relationships in the family, there is a need for phylogenetic research to investigate relationships within the majority of the newly proposed genera. In this paper, we unravel the phylogenetic relationships and the historical biogeography of the species of Lomaridium, a genus including most of the hemiepiphytic species in the Blechnaceae. Our sampling includes 11 species, which represents 85% of the diversity in the genus and which covers the entire geographic distribution of the group. We constructed two datasets with three plastid markers: one for phylogenetic analyses (maximum likelihood, Bayesian inference) with four outgroups from phylogenetically close genera (Brainea, Lomaria, Sadleria, Woodwardi); and a second for molecular dating and historical biogeographic analyses that included a larger set of outgroups so that we could accurately reconstruct ancestral events at the base of Lomaridium, under different models. We are able to recognize four highly supported lineages: L. contiguum and the L. schottii, L. attenuatum, and L. fragile clades. Our results date the origin of Lomaridium at some point during the Paleocene epoch, and the most likely geographic area for its origin is Australia plus tropical Central and South America. Several dispersal events are inferred, all of which are most likely long-distance dispersal events. From Australia, we infer a first dispersal event that brought the ancestor of the extant species L. contiguum to New Caledonia. In Central and South America, Lomaridium continued to diversify and colonized additional areas, including the Caribbean (L. binervatum), some Pacific islands (L. schottii), and Africa and Madagascar. While our goal in the current study was not to estimate the biogeographic or diversification history of all Blechnaceae, our analyses do suggest that the early history of the family was complex biogeographically, with extensive long-distance dispersal events. Lomaridium exemplifies this high dispersal capacity, as a genus with only a modest number of species that have reached far-flung regions of the globe via numerous long-distance dispersal events. [ABSTRACT FROM AUTHOR]

Leaf forms are diverse in angiosperms, and different types of cells are differentiated depending on the species. Rice leaves are composed of a leaf blade, a leaf sheath and the junction region between them. Cells with characteristic features, such as bulliform cells and sclerenchyma cells, are differentiated in the leaf blade, together with standard epidermal and mesophyll cells. To understand the genetic mechanism underlying leaf morphogenesis in rice, we focused on a mutant, halfpipe- like leaf1 (hal1), whose leaves are adaxially curled. Histological observation revealed that the bulliform cells, which are responsible for leaf rolling under dry conditions, were small in size and abnormal in shape in a semidominant hal1- d mutant. Bulliform cell files were often ambiguous in semi-transparent hal1-d leaves cleared by the TOMEI method, suggesting that the bulliform cells were undeveloped. Therefore, a reduction in the growth of the bulliform cells seemed to be a major cause of leaf curling in the hal1-d mutant. The hal1-d mutation also affected the size of the leaf blade and the spikelet. [ABSTRACT FROM AUTHOR]

The Gnaphalieae (Asteraceae) are a cosmopolitan tribe with around 185 genera and 2000 species. The New World is one of the centers of diversity of the tribe with 24 genera and over 100 species, most of which form a clade called the Luciliagroup with 21 genera. However, the generic classification of the Luciliagroup has been controversial with no agreement on delimitation or circumscription of genera. Especially controversial has been the taxonomic value of achenial trichomes and molecular studies have shown equivocal results so far. The major aims of this paper are to provide a nearly complete phylogeny of the Luciliagroup at generic level and to discuss the evolutionary trends and taxonomic significance of achenial trichome morphology. We conducted a phylogenetic analysis of the New World Gnaphalieae with nrDNA (ETS, ITS) sequence data from a sampling of 18 genera of the Luciliagroup and utilized these results to examine morphological evolution of achenial trichome types and presence of apical myxogenic cells. Seven wellsupported subclades can be recognized within the Luciliagroup (L1-L7). These results support Brazilian and Andean Berroa, Facelis, Lucilia, and Micropsis forming a clade (L1), the inclusion of Chilean Lucilia under Belloa (L2), the monophyly of Stuckertiella + Gamochaeta + Gamochaetopsis (L3), Chevreulia + Cuatrecasasiella (L4) and Antennaria (L5) excluding Antennaria linearifolia, which is resolved in a monophyletic group together with Jalcophila, Loricaria and Mniodes (L6), and the recognition of Gnaphaliothamnus (L7) removed from Brazilian taxa of Chionolaena (L2). Ancestral character state reconstruction of achenial trichome morphology suggests that clades are homogeneous in terms of trichome type, but with exceptions that make it highly homoplastic. Conversely, our results suggest that the presence of myxogenic apical cells is less homoplastic and that closely related species tend to resemble each other more than expected under random variation. Keywords achenial trichome; Luciliagroup; morphology; nrDNA; phylogeny; South America [ABSTRACT FROM AUTHOR]

Recent phylogenetic reconstruction of the Aizooideae (Aizoaceae) revealed that it and several of its genera are polyphyletic. Whereas the previous phylogeny was only based on chloroplast markers, we utilize here both nuclear and chloroplast markers. The four chloroplast markers together produce a well-resolved and well-supported phylogenetic hypothesis, while many branches in the tree derived from the nuclear internal transcribed spacer (ITS) are unsupported. The position of Acrosanthes as sister to Mesembryanthemoideae + Ruschioideae and the close relationship of Tetragonia schenckii to Tribulocarpus (Sesuvioideae) is highly supported by both nuclear and chloroplast markers. We revise the classification of the Aizoaceae, redefining subfamilial and generic boundaries to maintain monophyly. A new fifth subfamily, the Acrosanthoideae subfam. nov., is created for Acrosanthes, an isolated sister-lineage to the Mesembryanthemoideae + Ruschioideae. It is the only subfamily endemic to mesic fynbos and all other subfamilies are mainly associated with the more arid karroid vegetation. Basal, shortly stipitate ovules and a xerochastic, parchment-like capsule are synapomorphies for the Acrosanthoideae. The Eurasian endemic annual, Aizoanthemum hispanicum, is not related to the southern African species of Aizoanthemum and is placed in a new genus, Aizoanthemopsis gen. nov. The southern African genera Galenia and Plinthus are embedded within Aizoon. These genera were separated by differences in the size of their flowers. Since these features are highly homoplasious, we place all three under an enlarged Aizoon, which can be recognized by capsules with reduced expanding tissue as well as leaves and/or stems that are covered with silvery hairs or hair-like or rounded papillae. The Aizooideae now consist of the genera Aizoanthemopsis, Aizoanthemum, Aizoon, Gunniopsis and Tetragonia, with a total of 116 species. Our results also have consequences in the Sesuvioideae, where the generic name Anisostigma is resurrected for Tetragonia schenckii. The two species of Tribulocarpus and the monotypic Anisostigma are sister to the other Sesuvioideae and are characterized by tubular flowers. Since we have synapomorphies for the clade consisting of Anisostigma + Tribulocarpus and for the remainder of the Sesuvioideae (i.e., circumscissile capsules and seeds completely enveloped by an aril), we recognize two tribes, Sesuvieae and Anisostigmateae tr. nov., within the Sesuvioideae. For the expanded concept of Aizoon and for Tetragonia, we propose a new subgeneric classification to reflect the major clades retrieved. In Aizoon, four of the six subgenera are new and for Tetragonia, two of the four subgenera are new. We provide keys to the subfamilies of the Aizoaceae, to the genera and subgenera of the Aizooideae and also to the tribes of the Sesuvioideae. Distribution maps are provided for the Aizooideae, Acrosanthoideae and for the little-known Anisostigma schenckii. [ABSTRACT FROM AUTHOR]

Limonium (Plumbaginaceae) is a nearly cosmopolitan halophytic genus with ca. 350 species, a large number of which occurs in the Mediterranean region. We have generated a sequence dataset of several plastid (trnK intron including the matK gene, petD intron with the petB-petD spacer, trnL intron with the trnL-trnF spacer) and one nuclear region (nrITS), spanning the major lineages within the genus (102 accessions representing 76 species of Limonium) and related genera. Bayesian inference, maximum likelihood and maximum parsimony analyses converge on a Limonium clade that includes the genera Afrolimon, Eremolimon and Linczevskia. Plastid and nuclear trees congruently depict a number of major clades, most of them with a characteristic vegetative morphology and growing in specific habitats. Although the position of Afrolimon is incongruently resolved as the sister of a subclade comprising Limonium vulgare and relatives in the plastid trees versus being the sister to a Limonium sogdianum--L. bellidifolium--L. aureum clade in the nrITS tree, both genomic compartments show that Afrolimon is deeply nested in Limonium. Eremolimon is resolved as a close relative of L. sogdianum and L. ferganense based on plastid and nuclear genomic compartments. Our phylogenetic analysis resulted in an improved picture of internal relationships. Apart from the monophyletic subgenera Limonium subg. Limonium and L. subg. Pteroclados, nine wellsupported clades of L. subg. Limonium are evident, several of which are predominantly constituted by species of a certain geographic range. A subclade of IranoTuranian species (L. iranicum, L. suffruticosum and relatives) is shown to be unrelated to a L. axillare subclade, indicating an independent origin of the woody habit in these two lineages. Limonium sect. Iranolimon sect. nov. is described for the IranoTuranian woody lineage. The new combination L. sect. Circinaria comb. nov., is established for taxa sometimes included in Afrolimon. [ABSTRACT FROM AUTHOR]

Ludwigia (Onagraceae) is a worldwide wetland genus with 83 species currently classified as members of 23 sections. Past studies have documented the morphological diversity and complex evolutionary history. Here we provide the first comprehensive molecular phylogeny of Ludwigia, using our new data to examine the existing evolutionary hypotheses. We employed both nuclear (ITS, waxy) and chloroplast (rps16, rpl16, trnL-trnF, trnL-CD, trnG) DNA regions for this study. Our results suggest that the North Temperate haplostemonous (NTH) group and a second group that includes all other species of Ludwigia (clade B) form strongly supported sister clades. In the NTH group, a monophyletic sect. Ludwigia is sister to the Microcarpium complex, but sect. Microcarpium and sect. Isnardia are not monophyletic. In clade B, the multi-species sections Jussiaea and Macrocarpon are well-supported monophyletic clades, but others, including the largest sect. Myrtocarpus, are not monophyletic. In sum, this first molecular phylogeny of Ludwigia clarifies and supports several major relationships in the genus but also highlights parts of the classification that should be changed. Our results imply that allopolyploidy played an important role in the evolutionary history of the genus, giving rise to complex patterns of relationships that are not yet adequately reflected in the classification. [ABSTRACT FROM AUTHOR]

The Old World fern genus Pyrrosia is one of the largest genera in Polypodiaceae. It is estimated to contain up to 100 species distributed in tropical and subtropical South and East Asia, from New Zealand to Siberia and from Africa to Polynesia. The monophyly of Pyrrosia has frequently been questioned, previous molecular analyses have produced conflicting results, and earlier infrageneric classifications have been controversial. We tested the monophyly of the genus and resolved the relationships within the genus using nuclear DNA data and combined plastid and nuclear DNA data. Our study shows that the recently established genus Hovenkampia is confirmed to be sister to Platycerium. Nuclear data do not recover the monophyly of the Niphopsis clade identified by plastid data pointing to the possibility of ancient hybridization between the Niphopsis and the Niphobolus clades. The combined plastid and nuclear data resolve Pyrrosia into four major clades confirming earlier findings. Three of the four major clades are further resolved into four, four, and six subclades, respectively, and the relationships among the major clades and subclades are well resolved. Based on molecular and non-molecular evidence Pyrrosia is classified into four subgenera: P. subg. Pyrrosia, P. subg. Neoniphopsis, P. subg. Niphobolus, and P. subg. Niphopsis, and the latter three are further classified into four, six, and four sections, respectively. A key to the infrageneric taxa is given. A nomenclatural account of each infrageneric taxon is provided. [ABSTRACT FROM AUTHOR]

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Artemisia subg. Seriphidium is one of the largest groups within Artemisia, encompassing more than one hundred species, some of them having considerable ecological and economical importance. However, the evolution of subg. Seriphidium has received less attention in comparison to other subgenera of Artemisia, probably, apart from the difficulty of sampling throughout its very large distribution area, because of the low molecular and morphological variability observed in previous studies. Here, we use thorough taxonomic sampling within both Artemisia and subg. Seriphidium to reconstruct the evolutionary history of the subgenus, employing nuclear and plastid DNA sequences as well as various phylogenetic, biogeographic and diversification dynamics tools to analyse the data. Our results show that subg. Seriphidium is not monophyletic, but segregated into two main clades: one large monophyletic group corresponding to the formerly recognised sect. Seriphidium and a second, small clade, phylogenetically distant from the first. Biogeographic and diversification analyses indicate that a rapid radiation of species within sect. Seriphidium occurred in Central Asia during the Miocene-Pliocene transition. The results of our biogeographic analysis suggest that this diversification process started around the Tian-Shan, Pamir and Hindu Kush mountain ranges, subsequently expanding into the Eurasian continent. Finally, we uncovered numerous incongruences between taxonomic and genetic information in several sect. Seriphidium species, which could be explained by morphological uniformity, hybridisation and/or incomplete lineage sorting processes. [ABSTRACT FROM AUTHOR]

Despite the recent publication of several phylogenies focused on Rhinantheae, which has been expanded to include three Asian endemic genera, few studies so far have dealt with particular genera within the tribe. Here, we focus on Odontites and related genera because of the high morphological variability of the group and its unclear generic boundaries. Phylogenetic analyses were performed for nrDNA (ITS) and cpDNA (trnK region and rps16 intron) datasets, using Bayesian and Parsimony analyses. Our results cast doubt on the inclusion of Pterygiella and related genera within the Rhinantheae and support the paraphyly of Phtheirospermum, making it necessary to propose three new combinations to avoid it. Odontites is recircumscribed to include Bartsiella, Bornmuellerantha, and Macrosyringion, but not Odontitella. Within Odontites, five distinct lineages are identified. These are distinguishable either by morphological synapomorphies or by a combination of several character states. Most of the Odontites species are regarded as monophyletic. In the O. vernus and O. luteus complexes, some taxonomic changes are made to avoid paraphyly, which results in three new combinations. [ABSTRACT FROM AUTHOR]

Helianthemum is the largest, most widely distributed and most taxonomically complex genus of the Cistaceae. To examine the intrageneric phylogenetic relationships in Helianthemum, we used sequence data from plastid DNA (ndhF, psbA-trnH, trnLtrnF) and the nuclear ITS region. The ingroup consisted of 95 species and subspecies (2 subgenera, 10 sections) from throughout the range of Helianthemum, while the outgroup was composed of 30 species representing all the genera in the Cistaceae (Cistus Crocanthemum, Fumana, Halimium, Hudsonia, Lechea, Tuberaria) plus Anisoptera thurifera subsp. polyandra (Dipterocarpaceae). To infer phylogenetic relationships, we analysed three different matrices (cpDNA, nrDNA, cpDNA + nrDNA concatenated) using maximum likelihood and Bayesian inference, and performed molecular dating to estimate the ages of origin of the main clades using a Bayesian approach. The cpDNA + nrDNA concatenated dataset provided the highest Bayesian posterior probabilities and bootstrap support values, and the results supported the monophyly of the genus Helianthemum and its sister relationship to a clade consisting of all species of Cistus, Crocanthemum, Halimium, Hudsonia and Tuberaria. This result means that we did not retrieve the sister relationship between Helianthemum and Crocanthemum (plus Hudsonia) that could be expected according to previous published studies. Despite their different statistical support, the topology of the inner branches of all the consensus trees showed that Helianthemum is characterized by the emergence of three major clades in agreement with above-species taxonomy, although unresolved polytomies still remain towards the tips of the trees (species and subspecies). Clade I (mainly distributed in Mediterranean and alpine environments in European and western Asiatic mountain chains) fully coincided with subg. Plectolobum, whereas subg. Helianthemum was retrieved in clade II (arid and semi-arid environments from Macaronesia, the Mediterranean, subtropical northern Africa, Anatolia and central Asia) and clade III (Mediterranean ecosystems around the Mediterranean Basin). The burst of diversification during the Plio-Pleistocene detected in the three main clades of Helianthemum is concomitant with the Messinian salinity crisis, the onset of Mediterranean climatic conditions, and Quaternary glaciations, as found in many other groups of Mediterranean plants. Thus, the general lack of resolution in the trees can be attributed to rapid species diversification and events of reticulate evolution. A series of further taxonomic and evolutionary inferences can be drawn from our analyses: (i) no species occupied an early-diverging position with regard the rest of the species; (ii) a close relationship between H. caput-felis and subg. Plectolobum; (iii) an unexpected close relationship between H. squamatum/ H. syriacum (and H. motae), H. lunulatum/ H. pomeridianum and among H. songaricum/ H. antitauricum/ H. germanicopolitanum; (iv) a close relationship between incertae sedis species and sect. Eriocarpum; and (v) the existence of a monophyletic lineage consisting of Canary Islands species formerly ascribed to sect. Argyrolepis or sect. Lavandulaceum within sect. Helianthemum. [ABSTRACT FROM AUTHOR]

Besides being one of the most popular ornamental bulbs in western horticulture, the Mediterranean genus Narcissus has been the subject of numerous studies focusing on a wide scope of topics, including cytogenetics, hybridization and the evolution of polymorphic sexual systems. Phylogenetic hypotheses based on chloroplast data have provided a backbone for the genus but a detailed phylogenetic framework is still lacking. To fill this gap, we present a phylogenetic study of the genus using five markers from three genomes: ndhF and matK (chloroplast DNA), cob and atpA (mitochondrial DNA), and ITS (nuclear ribosomal DNA). In addition, we use chromosome counts from 89 populations representing 69 taxa. All analyses confirm that Narcissus is monophyletic with two main lineages largely corresponding to subg. Hermione and subg. Narcissus, but with incongruences between organellar and nuclear ribosomal phylogenies. At the infrageneric levels, our phylogenetic results challenge well-established taxonomic groups, such as sect. Jonquillae, sect. Bulbocodii and sect. Pseudonarcissi, each of which contains at least two distinct lineages that do not constitute monophyletic groups, and highlight the influence of allopolyploid species in the monophyly of sections within subg. Hermione. The type of the genus and its section is also nested within sect. Pseudonarcissi supporting new nomenclatural changes. Our results also confirm the intersubgeneric hybrid nature of several hybrids including allopolyploids (e.g., N. dubius, N. tortifolius, N. miniatus). Morphological and cytogenetic evidence independently support the hypothesis that some of the incongruence can be attributed to hybridization, such as the splits of sect. Bulbocodii and sect. Pseudonarcissi or the disparate phylogenetic placements of sect. Aurelia and sect. Ganymedes. Together, this indicates a significant role for reticulate evolution in shaping the diversity of this genus. A Bayesian divergence time analysis suggests that the major diversification events took place during the Neogene and provides younger estimates for the main nodes than previous studies, which fit paleoclimatic and paleotectonic reconstructions of the western Mediterranean during this period. [ABSTRACT FROM AUTHOR]

Pinus tabuliformis forests are major components of temperature coniferous forests in North China. These forests harbor a remarkable richness of both animal and plant taxa while providing multiple goods and services. However, the species distribution patterns and the underlying mechanisms of community assembly for P. tabuliformis forests are still not very well understood. We analyzed the distribution patterns, construction, and main drivers of P. tabuliformis forests based on 113 forest plots (20 m × 30 m) in the mountain areas of Shanxi, in the eastern Loess Plateau, China. Our findings indicated the plant flora composition was rich, but significantly different among different mountain areas. A total of 357 species belonging to 227 genera, 71 families, 36 orders, 4 classes, and 3 phyla were recorded in the 113 plots. The species richness (SR) and phylogenetic diversity (PD) of the natural forests were higher than that of the artificial forests. The main influence factors of PD and the net relatedness index (NRI) were the natural environment, and then forest type and forest structure, and the relative roles were different for woody and herbaceous species in the different areas. Overall, the primary environmental drivers of PD were topographic conditions, including slope and slope position, followed by total phosphorus and water factors. The topographic and soil variables had primary impacts on the PD and NRI patterns on Mount Luliang, while climate and soil variables had strong independent effects on PD and NRI patterns on Mount Taihang. In addition, the differences in forest type and structure had strong effects in determining PD and NRI patterns in the plant community. The tendency of increasing phylogenetic clustering along the temperature gradient indicated that environmental filtering played an important role in community assembly at a broad scale. The differences of PD and NRI between artificial and natural forests indicated that forest origin, microhabitat, and interspecific competition played an important role in the PD and NRI patterns at a local scale. Our results indicated that conservation projects have been effective for conservation and restoration of the P. tabuliformis forests. However, some problems still need to be addressed in afforestation, management, and exploitation. [ABSTRACT FROM AUTHOR]

We studied date palm phytochelatin synthase type I (PdPCS1), which catalyzes the cytosolic synthesis of phytochelatins (PCs), a heavy metal binding protein, in plant cells. The gene encoding PdPCS1 ( Pdpcs ) consists of 8 exons and 7 introns and encodes a protein of 528 amino acids. PCs gene history was studied using Notung phylogeny. During evolution, gene loss from several lineages was predicted including Proteobacteria, Bilateria and Brassicaceae. In addition, eleven gene duplication events appeared toward interior nodes of the reconciled tree and four gene duplication events appeared toward the external nodes. These latter sequences belong to species with a second copy of PCs suggesting that this gene evolved through subfunctionalization. Pdpcs1 gene expression was measured in seedling hypocotyls exposed to Cd, Cu and Cr using quantitative real-time polymerase chain reaction (qPCR). A Pdpcs1 overexpression was evidenced in P. dactylifera seedlings exposed to metals suggesting that 1-the Pdpcs1 gene is functional, 2-there is an implication of the enzyme in metal detoxification mechanisms. Additionally, the structure of PdPCS1 was predicted using its homologue from Nostoc (cyanobacterium, NsPCS) as a template in Discovery studio and PyMol software. These analyses allowed us to identify the phytochelatin synthase type I enzyme in date palm (PdPCS1) via recognition of key consensus amino acids involved in the catalytic mechanism, and to propose a hypothetical binding and catalytic site for an additional substrate binding cavity. [ABSTRACT FROM AUTHOR]

In Tunisia, the increasing pharmacological demand for spontaneous capers is actually leading to progressive forest overexploitation and genetic erosion of the species that is actually represented by scattered populations. Therefore, inventories with emphasis on the characterization, management and conservation of this medicinal plant are becoming a great need. In this work, genetic and phylogenetic criteria based on isozyme markers were used for the prioritization of spontaneous Capparis spinosa L. populations for conservation according to Vane-Wright and collaborators taxic method. Enzymatic loci varied in their ability to detect variation and population analyses indicated that most of the variation is partitioned between rather than within populations. Fst , gene flow values, PCA and cluster analysis also revealed significant differentiation between all populations. When combing phylogenetic and genetic criteria we were able to prioritize some of the populations for conservation. Therefore, the standardization and the summatory of all indices indicated that the populations Nebeur, Nahli and Dyr rank as a priority for conservation. So far, results of the present study appear to justify the in situ conservation strategy, where core areas completely free from perturbation would be defined for the populations with the highest priority for conservation, with the populations presenting unique alleles. This would guarantee the maintenance of most of the species’ genetic variation. The ex situ conservation management strategy would imply the setting up of specialized nurseries and national collections that are still missing in the country to counteract population fragmentation, demographic loss and genetic erosion threatening such spontaneous populations. [ABSTRACT FROM AUTHOR]

Paleotropical woody bamboos (PWB) are phylogenetically and taxonomically intractable. Because previous studies included deficient samples or lacked informative characters for tree construction, phylogenetic relationships within the PWB remain incompletely resolved. This study presents the most extensively sampled phylogeny of the PWB with 18 plastid regions and a sample of 144 (35%) ingroup species representing 40 (85%) genera and 8 outgroup species. Results confirmed Melocanninae as the earliest diverging lineage from the rest of the group, and Hickeliinae (including Nastus s.str.) and Racemobambosinae are separately placed within the PWB. Bambusinae is phylogenetically heterogeneous and consists of the Dinochloa-Greslania-Mullerochloa-Neololeba-Sphaeroambos (DGMNS) assemblage, Temburongia simplex, and the core Bambusinae. The core Bambusinae may be redefined to include a basal grade, which contains Kinabaluchloa, Holttumochloa, Bonia, Neomicrocalamus, Temochloa, Soejatmia and an unidentified taxon, and the Bambusa-Dendrocalamus-Gigantochloa (BDG) complex. The BDG complex is extremely diverse in morphology and is subdivided into six subclades. Within the Melocanninae, Davidsea, Neohouzeaua and Ochlandra are closely related to Schizostachyum. Phylogenetic relationships are mostly supported by morphological and geographical evidence. In addition, novel interpretations are provided in the redelimitation of some taxa. [ABSTRACT FROM AUTHOR]

Out of ca. 700 species belonging to Silene, 15 to 35 were classified in S. sect. Saxifragoideae. This section has its highest diversity on the Balkan Peninsula, which was the most important European Pleistocene refugium. The most widespread of the species is S. saxifraga ranging from the Pyrenees to the Carpathians. Together with ten morphologically similar taxa it is often treated as the S. saxifraga group, but the relationships among the taxa are unclear and blurred due to the occurrence of transitional forms. In this study, we used sequences of the nuclear ribosomal internal transcribed spacer (ITS) and the plastid rps16 intron as well as amplified fragment length polymorphisms (AFLPs) to elucidate phylogenetic relationships among the taxa belonging to--or hypothesized to be closely related to--S. sect. Saxifragoideae, covering the section's entire geographical range. Phylogenetic analyses of 112 populations belonging to 33 taxa clarified previous classifications and showed that S. cephallenia, S. congesta, S. linoides, S. multicaulis, S. schwarzenbergeri and S. waldsteinii are clearly differentiated from all other taxa, which in turn form the newly circumscribed S. saxifraga group. Phylogenetic relationships within the latter are unresolved, and are governed by geographic proximity rather than by taxonomic identity. This is likely a result of recent rapid radiation and range expansion, as well as of convergent morphological evolution triggered by similar environmental selection pressures. The southern parts of the Balkan Peninsula are the centre of genetic diversity of the group, underlining the area's importance as a sanctuary of diversification of European biota. [ABSTRACT FROM AUTHOR]