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rbcL
Kinds of rbcL Terms modified by rbcL Selected AbstractsPHYLOGENETIC RELATIONSHIP OF COLEOCHAETE AND CHAETO-SPHAERIDIUM (COLEOCHAETALES) BASED ON THE CHLOROPLAST GENES RBCL AND ATPBJOURNAL OF PHYCOLOGY, Issue 2000Cimino M. T. The freshwater green algal genera Coleochaete and Chaetosphaeridium form the order Coleochaetales sensu Mattox and Stewart (Charophyceae). To test the monophyly of this order, a data set was compiled consisting of the chloroplast genes rbcL and atpB from nine species of Coleochaete, six strains of Chaetosphaeridium, and other representative green algae and embryophytes. Phylogenetic analyses of these data indicate that Coleochaete and Chaetosphaeridium form a monophyletic group that diverged late in basal streptophyte evolution. By contrast, published analyses of nuclear encoded small subunit ribosomal DNA (rDNA) data for similar taxa do not support a monophyletic Coleochaetales. These analyses suggest Chaetosphaeridium is an early branching lineage within Streptophyta and/or that Chaetosphaeridium forms a lineage with the unicellular flagellate Mesostigma (Mesostigmatophyceae). A close relationship of Chaetosphaeridium and Mesostigma is not supported by the rbcL and atpB data. Reexamination of morphological characters suggests a monophyletic Coleochaetales is supported by several characters that include branching filamentous habit, unicellular apical growth, sheathed hairs, and rotating plastids. [source] Interaction between a dislocation and monovalent anion in various alkali halide crystalsCRYSTAL RESEARCH AND TECHNOLOGY, Issue 10 2010Y. KohzukiArticle first published online: 30 AUG 2010 Abstract It was investigated from (L0/L)2 versus ,0 curve that the Friedel relation between the effective stress and the average length of dislocation segments, L, is appropriate for the interaction between a dislocation and the monovalent anion in various alkali halides single crystals (NaCl: Br - , NaBr: Cl - or I - , KCl: Br - or I - , and RbCl: Br - or I - ). Here, L0 represents the average spacing of monovalent anions on a slip plane and ,0 is the bending angle at which the dislocation breaks away from the anion at the temperature of 0 K. This is because the anions are the weak obstacles such as impede the dislocation at ,0 above about 150 degrees, where the Friedel relation agrees with the Fleischer one (L02 = L2(,,,0)/2). Furthermore, the values of (L /L0) were found to be within 4.05 to 5.87 for the crystals. (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Capillary electrophoretic and computational study of the complexation of valinomycin with rubidium cationELECTROPHORESIS, Issue 5 2009Sille Ehala Abstract This study is focused on the characterization of interactions of valinomycin (Val), a macrocyclic dodecadepsipeptide antibiotic ionophore, with rubidium cation, Rb+. Capillary affinity electrophoresis was employed for the experimental evaluation of the strength of the Val,Rb+ complex. The study involved the measurement of the change of effective electrophoretic mobility of Val at increasing concentration of Rb+ cation in the BGE. From the dependence of Val effective electrophoretic mobility on the Rb+ cation concentration in the BGE (methanolic solution of 100,mM Tris, 50,mM acetic acid, 0,1,mM RbCl), the apparent binding (stability) constant (Kb) of the Val,Rb+ complex in methanol was evaluated as log,Kb=4.63±0.27. According to the quantum mechanical density functional theory calculations employed to predict the most probable structure of Val,Rb+ complex, Val is stabilized by strong non-covalent bond interactions of Rb+ with six ester carbonyl oxygen atoms so that the position of the "central" Rb+ cation in the Val cage is symmetric. [source] Prediction of Activity Coefficients for Uni-univalent Electrolytes in Pure Aqueous SolutionCHEMICAL ENGINEERING & TECHNOLOGY (CET), Issue 5 2010J. I. Partanen Abstract Parameter-free activity coefficient equations were tested in addition to those containing one, two, three or four electrolyte-dependent parameters with the experimental activity coefficients obtained from the literature data for aqueous solutions of the following electrolytes at 298.15 K: KCl, NaCl, RbCl, KBr, RbBr, CsBr, KI, RbI, KNO3, and KH2PO4. The experimental activity coefficients of each electrolyte considered can be reproduced within the uncertainty of the measurements up to the molality of the saturated solution by using a three-parameter equation of the extended Hückel type. The best Hückel equations are given for all electrolytes in question. The results from the present studies reveal that the parameter-free equations can be reliably used in thermodynamic studies only for very dilute electrolyte solutions. On the other hand, in most cases, a good agreement with the experimental data is obtained with the one-parameter equations of Bromley [14] and Kusik and Meissner [13], with the two-parameter equation of Bretti et al. [15], and with the three- or four-parameter equation of Hamer and Wu [19] in addition to the three-parameter Pitzer equation [23], with almost all parameter values suggested in the literature. In several cases, these equations seem to apply to much higher molalities than those used in the parameter estimations. Therefore, the best of these equations may have important applications in calculations associated with the dissolution and crystallization processes of these salts. [source] Changes in Rubisco and Rubisco activase gene expression and polypeptide content in Pinus halepensis M. subjected to ozone and droughtPLANT CELL & ENVIRONMENT, Issue 1 2001J. Pelloux ABSTRACT The regulation of ribulose-1,5-biphosphate carboxlase/oxygenase (Rubisco) and Rubisco activase was followed for 3 months in an experiment studying the effects of ozone and water stress on Aleppo pine. Rubisco activity was shown to be reduced by 30% in the presence of ozone, whereas no significant effect of water stress was noticed. The effect of combined stresses on Rubisco activity was similar to the effect of ozone. The changes in protein quantity of Rubisco large subunit (LSU) and Rubisco activase (RCA), compared with control plants, were similar to that of the Rubisco activity. Using homologous probes obtained by reverse transcription (RT)-polymerase chain reaction (PCR), rbcL and rca transcript quantities were quantified during the course of the experiment. RbcL and rca mRNA quantities decreased in ozone and after drought. Changes in rbcL transcript quantity in needles subjected to the combination of ozone and drought were similar to the ones detected when drought was applied alone. On the contrary, the pattern of rca changes under the combination of the two stresses was similar to that of ozone applied alone. A positive correlation existed between the effects of ozone on Rubisco activase and Rubisco LSU protein quantities, which was not so obvious by comparing transcript quantities. This could suggest a potential post-transcriptional coordinated regulation of the two proteins under stress-imposed conditions. [source] Phylogenetic relatedness and plant invader success across two spatial scalesDIVERSITY AND DISTRIBUTIONS, Issue 3 2009Marc W. Cadotte ABSTRACT Aim, Successful invaders often possess similar ecological traits that contribute to success in new regions, and thus under niche conservatism, invader success should be phylogenetically clustered. We asked if the degree to which non-native plant species are phylogenetically related is a predictor of invasion success at two spatial scales. Location, Australia , the whole continent and Royal National Park (south-eastern Australia). Methods, We used non-native plant species occupancy in Royal National Park, as well as estimated continental occupancy of these species from herbarium records. We then estimated phylogenetic relationships using molecular data from three gene sequences available on GenBank (matK, rbcL and ITS1). We tested for phylogenetic signals in occupancy using Blomberg's K. Results, Whereas most non-native plants were relatively scarce, there was a strong phylogenetic signal for continental occupancy, driven by the clustering of successful species in Asteraceae, Caryophyllaceae, Poaceae and Solanaceae. However, we failed to detect a phylogenetic signal at the park scale. Main Conclusions, Our results reveal that at a large spatial scale, invader success is phylogenetically clustered where ecological traits promoting success appear to be shared among close relatives, indicating that phylogenetic relationships can be useful predictors of invasion success at large spatial scales. At a smaller, landscape scale, there was no evidence of phylogenetic clustering of invasion success, and thus, relatedness plays a much reduced role in determining the relative success of invaders. [source] Evolution and biogeography of the austral genus Phyllocladus (Podocarpaceae)JOURNAL OF BIOGEOGRAPHY, Issue 10 2004Steven J. Wagstaff Abstract Aim, To infer evolutionary relationships within the genus Phyllocladus and among its close relatives by phylogenetic analysis of DNA sequences. Interpret the inferred relationships in association with the fossil record to examine the origin and diversification of the genus. Location, Australasia. Methods, Phylogenetic analyses of rbcL, matK and internal transcribed spacer (ITS) sequences representing all of the extant species of Phyllocladus and a selection of outgroups from Podocarpaceae and Araucariaceae. Results, The rbcL and matK sequences exhibit little variation within Phyllocladus, but ally its members to Podocarpaceae although its immediate sister remains unclear. The ITS sequences resolve all five species of Phyllocladus and two intraspecific ecotypes of P. alpinus. Main conclusions,Phyllocladus forms a distinct lineage that diverged early in the evolutionary history of Podocarpaceae. The fossil record indicates that the genus was more widely distributed and morphologically diverse during the early Tertiary than at present. Although of Mesozoic origin, the level of sequence variation within Phyllocladus suggests that the extant species radiated during the late Tertiary c. 6.3 ± 0.9 Ma. New Zealand is the present centre of species diversity. [source] The biogeography of Gunnera L.: vicariance and dispersalJOURNAL OF BIOGEOGRAPHY, Issue 7 2003Livia Wanntorp Abstract Aim The genus Gunnera is distributed in South America, Africa and the Australasian region, a few species reaching Hawaii and southern Mexico in the North. A cladogram was used to (1) discuss the biogeography of Gunnera and (2) subsequently compare this biogeographical pattern with the geological history of continents and the patterns reported for other Southern Hemisphere organisms. Location Africa, northern South America, southern South America, Tasmania, New Zealand, New Guinea/Malaya, Hawaii, North America, Antarctica. Methods A phylogenetic analysis of twenty-six species of Gunnera combining morphological characters and new as well as published sequences of the ITS region, rbcL and the rps16 intron, was used to interpret the biogeographical patterns in Gunnera. Vicariance was applied in the first place and dispersal was only assumed as a second best explanation. Results The Uruguayan/Brazilian Gunnera herteri Osten (subgenus Ostenigunnera Mattfeld) is sister to the rest of the genus, followed sequentially upwards by the African G. perpensa L. (subgenus Gunnera), in turn sister to all other, American and Australasian, species. These are divided into two clades, one containing American/Hawaiian species, the other containing all Australasian species. Within the Australasian clade, G. macrophylla Blume (subgenus Pseudogunnera Schindler), occurring in New Guinea and Malaya, is sister to a clade including the species from New Zealand and Tasmania (subgenus Milligania Schindler). The southern South American subgenus Misandra Schindler is sister to a clade containing the remaining American, as well as the Hawaiian species (subgenus Panke Schindler). Within subgenus Panke, G. mexicana Brandegee, the only North American species in the genus, is sister to a clade wherein the Hawaiian species are basal to all south and central American taxa. Main conclusions According to the cladogram, South America appears in two places, suggesting an historical explanation for northern South America to be separate from southern South America. Following a well-known biogeographical pattern of vicariance, Africa is the sister area to the combined southern South America/Australasian clade. Within the Australasian clade, New Zealand is more closely related to New Guinea/Malaya than to southern South America, a pattern found in other plant cladograms, contradictory to some of the patterns supported by animal clades and by the geological hypothesis, respectively. The position of the Tasmanian G. cordifolia, nested within the New Zealand clade indicates dispersal of this species to Tasmania. The position of G. mexicana, the only North American species, as sister to the remaining species of subgenus Panke together with the subsequent sister relation between Hawaii and southern South America, may reflect a North American origin of Panke and a recolonization of South America from the north. This is in agreement with the early North American fossil record of Gunnera and the apparent young age of the South American clade. [source] PHYLOGENETIC RELATIONSHIPS WITHIN THE GENUS HYPNEA (GIGARTINALES, RHODOPHYTA), WITH A DESCRIPTION OF H. CAESPITOSA SP.JOURNAL OF PHYCOLOGY, Issue 2 2010Species discrimination within the gigartinalean red algal genus Hypnea has been controversial. To help resolve the controversy and explore phylogeny within the genus, we determined rbcL sequences from 30 specimens of 23 species within the genus, cox1 from 22 specimens of 10 species, and psaA from 16 species. We describe H. caespitosa as a new species characterized by a relatively slender main axis; a pulvinate growth habit with entangled, anastomosing, and subulate uppermost branches; and unilaterally borne tetrasporangial sori. The new species occurs in the warm waters of Malaysia, the Philippines, and Singapore. The phylogenetic trees of rbcL, psaA, and cox1 sequences showed a distant relationship of H. caespitosa to H. pannosa J. Agardh from Baja California and the marked differentiation from other similar species. The rbcL + psaA tree supported monophyly of the genus with high bootstrap values and posterior probabilities. The analysis revealed three clades within the genus, corresponding to three sections, namely, Virgatae, Spinuligerae, and Pulvinatae first recognized by J. G. Agardh. Exceptions were H. japonica T. Tanaka in Pulvinatae and H. spinella (C. Agardh) Kütz. in Spinuligerae. [source] PRIMARY CARBON AND NITROGEN METABOLIC GENE EXPRESSION IN THE DIATOM THALASSIOSIRA PSEUDONANA (BACILLARIOPHYCEAE): DIEL PERIODICITY AND EFFECTS OF INORGANIC CARBON AND NITROGEN,JOURNAL OF PHYCOLOGY, Issue 5 2009Espen Granum Diel periodicity and effects of inorganic carbon (Ci) and NO3, on the expression of 11 key genes for primary carbon and nitrogen metabolism, including potential C4 photosynthesis, in the marine diatom Thalassiosira pseudonana Hasle et Heimdal were investigated. Target gene transcripts were measured by quantitative reverse transcriptase,PCR, and some of the gene-encoded proteins were analyzed by Western blotting. The diatom was grown with a 12 h photoperiod at two different Ci concentrations maintained by air-equilibration with either 380 ,L · L,1 (near-ambient) or 100 ,L · L,1 (low) CO2. Transcripts of the principal Ci and NO3, assimilatory genes RUBISCO LSU (rbcL) and nitrate reductase displayed very strong diel oscillations with peaks at the end of the scotophase. Considerable diel periodicities were also exhibited by the ,-carboxylase genes phosphoenolpyruvate carboxylase (PEPC1 and PEPC2) and phosphoenolpyruvate carboxykinase (PEPCK), and the Benson,Calvin cycle gene sedoheptulose,bisphosphatase (SBPase), with peaks during mid- to late scotophase. In accordance with the transcripts, there were substantial diel periodicities in PEPC1, PEPC2, PEPCK, and especially rbcL proteins, although they peaked during early to mid-photophase. Inorganic carbon had some transient effects on the ,-carboxylase transcripts, and glycine decarboxylase P subunit was highly up-regulated by low Ci concentration, indicating increased capacity for photorespiration. Nitrogen-starved cells had reduced amounts of carbon metabolic gene transcripts, but the PEPC1, PEPC2, PEPCK, and rbcL transcripts increased rapidly when NO3, was replenished. The results suggest that the ,-carboxylases in T. pseudonana play key anaplerotic roles but show no clear support for C4 photosynthesis. [source] TAXONOMIC STUDY OF TWO NEW GENERA OF FUSIFORM GREEN FLAGELLATES, TABRIS GEN.JOURNAL OF PHYCOLOGY, Issue 2 2009On the basis of LM, we isolated strains of two species of fusiform green flagellates that could be assigned to former Chlorogonium (Cg.) Ehrenb. One species, "Cg."heimii Bourr., lacked a pyrenoid in its vegetative cells and required organic compounds for growth. The other was similar to Cg. elongatum (P. A. Dang.) Francé and "Cg."acus Nayal, but with slightly smaller vegetative cells. Their molecular phylogeny was also studied based on combined 18S rRNA, RUBISCO LSU (rbcL), and P700 chl a -apoprotein A2 (psaB) gene sequences. Both species were separated from Chlorogonium emend., Gungnir Nakada and Rusalka Nakada, which were formerly assigned to Chlorogonium. They were accordingly assigned to new genera, Tabris Nakada gen. nov. and Hamakko (Hk.) Nakada gen. nov. as T. heimii (Bourr.) Nakada comb. nov. and Hk. caudatus Nakada sp. nov., respectively. Tabris is differentiated from other genera of fusiform green flagellates by its vegetative cells, which only have two apical contractile vacuoles and lack a pyrenoid in the chloroplast. Hamakko, on the other hand, is distinguishable by the fact that its pyrenoids in vegetative cells are penetrated by flattened thylakoid lamellae. [source] GENETIC DIVERSITY AND INTROGRESSION IN TWO CULTIVATED SPECIES (PORPHYRA YEZOENSIS AND PORPHYRA TENERA) AND CLOSELY RELATED WILD SPECIES OF PORPHYRA (BANGIALES, RHODOPHYTA),JOURNAL OF PHYCOLOGY, Issue 2 2009Kyosuke Niwa We investigated the genetic variations of the samples that were tentatively identified as two cultivated Porphyra species (Porphyra yezoensis Ueda and Porphyra tenera Kjellm.) from various natural populations in Japan using molecular analyses of plastid and nuclear DNA. From PCR-RFLP analyses using nuclear internal transcribed spacer (ITS) rDNA and plastid RUBISCO spacer regions and phylogenetic analyses using plastid rbcL and nuclear ITS-1 rDNA sequences, our samples from natural populations of P. yezoensis and P. tenera showed remarkably higher genetic variations than found in strains that are currently used for cultivation. In addition, it is inferred that our samples contain four wild Porphyra species, and that three of the four species, containing Porphyra kinositae, are closely related to cultivated Porphyra species. Furthermore, our PCR-RFLP and molecular phylogenetic analyses using both the nuclear and plastid DNA demonstrated the occurrence of plastid introgression from P. yezoensis to P. tenera and suggested the possibility of plastid introgression from cultivated P. yezoensis to wild P. yezoensis. These results imply the importance of collecting and establishing more strains of cultivated Porphyra species and related wild species from natural populations as genetic resources for further improvement of cultivated Porphyra strains. [source] MOLECULAR PHYLOGENY OF DISCOSPORANGIUM MESARTHROCARPUM (PHAEOPHYCEAE) WITH A REINSTATEMENT OF THE ORDER DISCOSPORANGIALES,JOURNAL OF PHYCOLOGY, Issue 1 2007Hiroshi Kawai A molecular phylogenetic analysis of the little-studied filamentous brown alga Discosporangium mesarthrocarpum (Meneghini) Hauck using rbcL and partial 18S rDNA sequences revealed that the species forms a monophyletic clade with Choristocarpus tenellus (Kütz.) Zanardini that is sister to all other brown algae. Although D. mesarthrocarpum has unique disk-shaped plurilocular reproductive organs, D. mesarthrocarpum and C. tenellus share the following basic morphological features, which are considered to be plesiomorphic characters in the brown algae: (1) apical (and diffuse) growth; (2) uniseriate, subdichotomously branched filaments; (3) multiple chloroplasts per cell without pyrenoids; and (4) lack of heterotrichy and of phaeophycean hairs. The rbcL DNA sequence of an Australian D. mesarthrocarpum specimen showed considerable deviation from Mediterranean and Macaronesian specimens. Therefore, the presence of a second species in the genus is suggested; however, the taxonomic treatment of this putative species is not pursued in the present report. Regarding the higher-ranking systematic position of D. mesarthrocarpum, reinstatement of Discosporangiaceae and Discosporangiales is proposed, and the inclusion of Choristocarpaceae in the order is also suggested. Under short-day and long-day culture conditions at 15°C,25°C, Mediterranean D. mesarthrocarpum exhibited a direct type of life history, with a succession of uniseriate filamentous thalli bearing characteristic disk-shaped plurilocular zoidangia, but thalli did not survive at 10°C and below. [source] TAXONOMIC REEXAMINATION OF 17 SPECIES OF NITELLA SUBGENUS TIEFFALLENIA (CHARALES, CHAROPHYCEAE) BASED ON INTERNAL MORPHOLOGY OF THE OOSPORE WALL AND MULTIPLE DNA MARKER SEQUENCES,JOURNAL OF PHYCOLOGY, Issue 1 2005Hidetoshi Sakayama In an attempt to reconstruct the natural taxonomic system for Nitella, 17 species of Nitella subgenus Tieffallenia were reexamined using SEM observations of the internal morphology of the oospore wall (IMOW) and phylogenetic analyses of 4553 base pairs from multiple DNA markers (atpB, rbcL, psaB, and ITS-5.8S rRNA genes). Our SEM observations identified three types of IMOW: homogeneous (HG), weakly spongy (W-SG), and strongly spongy (S-SG) types. Based on differences in the IMOW, species with reticulate or tuberculate oospore wall ornamentation in the external morphology of the oospore wall (EMOW) were subdivided into two distinct groups (characterized by the HG or S-SG types of IMOW, respectively), which were robustly separated from each other in our molecular phylogenetic analyses. In our molecular phylogeny, the subgenus Tieffallenia consisted of four robust monophyletic groups,three clades of the HG type and a spongy (S-SG and W-SG) type clade,that were characterized by differences in the IMOW and EMOW. In addition, our SEM observations and sequence data verified the distinct status of five species (N. japonica Allen, N. oligospira A. Braun, N. vieillardii stat. nov., N. imperialis stat. nov., and N. morongii Allen) that R. D. Wood had assigned as infraspecific taxa. Moreover, our SEM observations of the IMOW also suggested that N. megaspora (J. Groves) Sakayama originally identified by LM includes at least two distinct species, characterized by W-SG and S-SG types of IMOW, respectively. [source] MORPHOLOGY, LIFE HISTORY, AND MOLECULAR PHYLOGENY OF STSCHAPOVIA FLAGELLARIS (TILOPTERIDALES, PHAEOPHYCEAE) AND THE ERECTION OF THE STSCHAPOVIACEAE FAM.JOURNAL OF PHYCOLOGY, Issue 6 2004The phenology, life history, ultrastructure of reproductive structures, and molecular phylogeny using rbcL and rDNA (5.8S, internal transcribed spacer 2, and partial 26S) gene sequences of Stschapovia flagellaris, endemic to the northwestern Pacific Ocean, were studied. This species was first classified in the order Delamareales together with Delamarea, Coelocladia, and Cladothele. Those three genera, however, were later transferred to Dictyosiphonales, whereas the systematic position of Stschapovia remained unclear. At Abashiri, Hokkaido, Japan, the species regenerated by forming a new erect thallus from a perennial crustose holdfast or by presumably parthenogenetic development of eggs released from the erect thallus. There was no alternation of generations. In winter, the monoecious erect thallus formed reproductive structures (i.e. plurilocular antheridia and oogonia) in the thickened part of the thallus. Sperm had a chloroplast with an eyespot and a long anterior and short posterior flagellum. Eggs contained numerous disc-shaped chloroplasts, physodes, and vacuoles. Neither sexual attraction of the presumptive sperm by eggs nor their sexual fusion was observed. Molecular phylogenetic analyses revealed the closest phylogenetic relationship between Stschapovia and Halosiphonaceae, and they grouped with Phyllariaceae and Tilopteridaceae (Tilopteridales s. s.). Stschapovia and Tilopteridaceae have several important morphological similarities: chloroplasts lacking pyrenoids, lack of sexual reproduction despite the release of obvious sperm, occurrence of monoecious gametophytes, and similarity in the early developmental pattern of the erect thallus. In conclusion, we propose the establishment of the new family Stschapoviaceae to accommodate Stschapovia and the placement of the family in the order Tilopteridales together with Tilopteridaceae, Halosiphonaceae, and Phyllariaceae. [source] PHYLOGENY OF AULACOSEIRA (BACILLARIOPHYTA) BASED ON MOLECULES AND MORPHOLOGY,JOURNAL OF PHYCOLOGY, Issue 4 2004Stacy M. Edgar The phylogeny of 67 populations representing 45 species of Aulacoseira Thwaites was estimated by maximum parsimony methods using a combination of nucleotide sequence data and qualitative and quantitative morphological characteristics of the silica cell wall gathered primarily from original observation by LM and SEM. A new type of character using continuous quantitative variables that describe the ontogenetic-allometric trajectories of cell wall characteristics over the life cycle (size range) of diatoms is introduced. In addition to the 45 Aulacoseira species, the phylogeny also incorporated one Miosira Krammer, Lange-Bertalot, and Schiller species and two outgroup species (Melosira varians Agardh and Stephanopyxis nipponica Gran & Yendo). Fifteen species, represented by 24 populations, also contained molecular data from the nuclear genome (18S rDNA), and 11 of these species (18 populations) contained data from the chloroplast genome (rbcL) as well, which were sequenced or downloaded from GenBank. The phylogeny of Aulacoseira is composed of five major clades: 1) an A. crenulata (Ehrenburg) Thwaites and A. italica (Ehrenburg) Simonsen clade, which is the most basal; 2) an A. granulata (Ehrenburg) Simonsen complex clade; 3) an A. ambigua (Grunow) Simonsen clade; 4) an A. subarctica (O. Müller) Haworth and A. distans (Ehrenburg) Simonsen clade; and 5) an A. islandica (O. Müller) Simonsen clade that also contained endemic species from Lake Baikal, Siberia and many extinct Aulacoseira taxa. Monophyly of Aulacoseira can only be achieved if Miosira is no longer given separate generic status. [source] PHYLOGENY OF THE DASYCLADALES (CHLOROPHYTA, ULVOPHYCEAE) BASED ON ANALYSES OF RUBISCO LARGE SUBUNIT (rbcL) GENE SEQUENCES,JOURNAL OF PHYCOLOGY, Issue 4 2003Frederick W. Zechman The phylogeny of the green algal Order Dasycladales was inferred by maximum parsimony and Bayesian analyses of chloroplast-encoded rbcL sequence data. Bayesian analysis suggested that the tribe Acetabularieae is monophyletic but that some genera within the tribe, such as Acetabularia Lamouroux and Polyphysa Lamouroux, are not. Bayesian analysis placed Halicoryne Harvey as the sister group of the Acetabularieae, a result consistent with limited fossil evidence and monophyly of the family Acetabulariaceae but was not supported by significant posterior probability. Bayesian analysis further suggested that the family Dasycladaceae is a paraphyletic assemblage at the base of the Dasycladales radiation, casting doubt on the current family-level classification. The genus Cymopolia Lamouroux was inferred to be the basal-most dasycladalean genus, which is also consistent with limited fossil evidence. Unweighted parsimony analyses provided similar results but primarily differed by the sister relationship between Halicoryne Lamouroux and Bornetella Munier-Chalmas, thus supporting the monophyly of neither the families Acetabulariaceae nor Dasycladaceae. This result, however, was supported by low bootstrap values. Low transition-to-transversion ratios, potential loss of phylogenetic signal in third codon positions, and the 550 million year old Dasycladalean lineage suggest that dasyclad rbcL sequences may be saturated due to deep time divergences. Such factors may have contributed to inaccurate reconstruction of phylogeny, particularly with respect to potential inconsistency of parsimony analyses. Regardless, strongly negative g1 values were obtained in analyses including all codon positions, indicating the presence of considerable phylogenetic signal in dasyclad rbcL sequence data. Morphological features relevant to the separation of taxa within the Dasycladales and the possible effects of extinction on phylogeny reconstruction are discussed relative to the inferred phylogenies. [source] EFFECT OF TAXON SAMPLING, CHARACTER WEIGHTING, AND COMBINED DATA ON THE INTERPRETATION OF RELATIONSHIPS AMONG THE HETEROKONT ALGAE,JOURNAL OF PHYCOLOGY, Issue 2 2003Leslie R. Goertzen Nuclear ribosomal small subunit and chloroplast rbcL sequence data for heterokont algae and potential outgroup taxa were analyzed separately and together using maximum parsimony. A series of taxon sampling and character weighting experiments was performed. Traditional classes (e.g. diatoms, Phaeophyceae, etc.) were monophyletic in most analyses of either data set and in analyses of combined data. Relationships among classes and of heterokont algae to outgroup taxa were sensitive to taxon sampling. Bootstrap (BS) values were not always predictive of stability of nodes in taxon sampling experiments or between analyses of different data sets. Reweighting sites by the rescaled consistency index artificially inflates BS values in the analysis of rbcL data. Inclusion of the third codon position from rbcL enhanced signal despite the superficial appearance of mutational saturation. Incongruence between data sets was largely due to placement of a few problematic taxa, and so data were combined. BS values for the combined analysis were much higher than for analyses of each data set alone, although combining data did not improve support for heterokont monophyly. [source] MOLECULAR AND MORPHOLOGICAL DATA IDENTIFY A CRYPTIC SPECIES COMPLEX IN ENDOPHYTIC MEMBERS OF THE GENUS COLEOCHAETE BRÉB. (CHAROPHYTA: COLEOCHAETACEAE),JOURNAL OF PHYCOLOGY, Issue 6 2002Matthew T. Cimino The genus Coleochaete Bréb. is a relatively small group of freshwater microscopic green algae with about 15 recognized species. Although Coleochaete has long been considered to be a close relative of embryophytes, a comprehensive study of the genus has not been published since Pringsheim's 1860 monograph. As part of a systematic study of Coleochaete, we investigated four accessions of the genus that are morphologically similar to the endophytic species C. nitellarum Jost. Each of the four cultures was determined to be capable of endophytic growth in Nitella C. A. Agardh, a member of the closely related order Charales. Maximum likelihood and maximum parsimony analyses were performed on nucleotide data from the chloroplast genes atpB and rbcL that were sequenced from 16 members of the Coleochaetales and from other members of the Charophyceae, embryophytes, and outgroup taxa. These analyses indicate that the Coleochaetales are monophyletic and that the endophytic accessions are members of the scutata group of species. In addition, cell size and nucleotide data suggest that at least three different endophytic species may be represented. Herbivory, nutritional benefits, and substrate competition are three hypotheses that could explain the evolution and maintenance of the endophytic habit in Coleochaete. These data also imply that diversity in the genus may be markedly underestimated. [source] SYNTHESIS OF MOLECULAR RESEARCH ON BATRACHOSPERMUM HELMINTHOSUM (RHODOPHYTA) FROM STREAM REACHES IN EASTERN NORTH AMERICAJOURNAL OF PHYCOLOGY, Issue 2001Article first published online: 24 SEP 200 Vis, M. L., Hall, M. M., Machesky, N. J. & Miller, E. J. Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701 USA The freshwater red alga Batrachospermum helminthosum was collected from eleven streams throughout the species range in eastern North America as follows: three stream reaches from Ohio, and one each from Michigan, Indiana, Tennessee, Louisiana, North Carolina, Connecticut, Rhode Island and Massachusetts. The molecular marker technique of inter-simple sequence repeats (ISSR) and sequence data from the plastid encoded rubisco large subunit gene (rbcL), the mitochondrial COX2-COX3 gene spacer region, and the nuclear region of ITS1-5.8S rDNA-ITS2 were employed to examine biogeographic trends in this alga. Analysis of the rbcL sequence revealed 5 genotypes with one genotype representing individuals from seven stream reaches. Data from the ISSR molecular markers gave a distinct banding pattern for each of 165 individuals examined. ISSR results showed all individuals within a reach clustered together but did not provide well-defined groupings based on stream reach. The sequence data for the COX2-COX3 gene spacer was invariant among individuals from a stream reach. The individuals from Connecticut, Rhode Island and 2 Ohio stream reaches were identical and similarly the individuals from the North Carolina and another Ohio location did not vary in sequence so that seven genotypes were recorded among the individuals from the eleven stream reaches. Analysis of the ITS1-5.8S rDNA-ITS2 region showed sequence variation not only among individuals from different streams but also among individuals from the same reach. The utility and congruency of these data sets to answer biogeographic questions will be discussed. [source] PHYLOGENETIC RELATIONSHIP OF COLEOCHAETE AND CHAETO-SPHAERIDIUM (COLEOCHAETALES) BASED ON THE CHLOROPLAST GENES RBCL AND ATPBJOURNAL OF PHYCOLOGY, Issue 2000Cimino M. T. The freshwater green algal genera Coleochaete and Chaetosphaeridium form the order Coleochaetales sensu Mattox and Stewart (Charophyceae). To test the monophyly of this order, a data set was compiled consisting of the chloroplast genes rbcL and atpB from nine species of Coleochaete, six strains of Chaetosphaeridium, and other representative green algae and embryophytes. Phylogenetic analyses of these data indicate that Coleochaete and Chaetosphaeridium form a monophyletic group that diverged late in basal streptophyte evolution. By contrast, published analyses of nuclear encoded small subunit ribosomal DNA (rDNA) data for similar taxa do not support a monophyletic Coleochaetales. These analyses suggest Chaetosphaeridium is an early branching lineage within Streptophyta and/or that Chaetosphaeridium forms a lineage with the unicellular flagellate Mesostigma (Mesostigmatophyceae). A close relationship of Chaetosphaeridium and Mesostigma is not supported by the rbcL and atpB data. Reexamination of morphological characters suggests a monophyletic Coleochaetales is supported by several characters that include branching filamentous habit, unicellular apical growth, sheathed hairs, and rotating plastids. [source] PHYLOGENETIC AND BIOGEOGRAPHIC AFFINITIES OF THE HALYMENIALES AND RHODYMENIALES (RHODOPHYTA) FROM THE GULF OF MEXICOJOURNAL OF PHYCOLOGY, Issue 2000B. Gavio Generic and species concepts within the red algal assemblages Halymeniales and Rhodymeniales are discussed for taxa inhabiting the western Gulf of Mexico. Two principal biogeographic assemblages occur: an off-shore deep-water group (including Coelarthrum cliftonii, Halymenia spp., Botryocladia spp., Gloiocladia) representing remnants of a Tethyan distribution, and a near-shore intertidal flora (comprising Rhodymenia, Grateloupia and Prionitis) which instead reveals biogeographic affinities with the Carolinian Province. These two distinct marine floras will be contrasted phylogenetically based on DNA sequence analysis inferred from chloroplast-encoded rbcL. The generic descriptions of Grateloupia and Prionitis are in need of taxonomic revision based on a survey of species from Caribbean and Pacific Mexico. [source] A SYSTEMATIC STUDY OF GIGAR-TINACEAE FROM PACIFIC NORTH AMERICA BASED ON MOLECULAR AND MORPHOLOGICAL EVIDENCEJOURNAL OF PHYCOLOGY, Issue 2000J.R. Hughey Greater than 50 species of Gigartinaceae have been described from Pacific North America, about half of which are currently recognized. Although the family is treated extensively in the taxonomic literature, many of the species are still confused and a comprehensive revision is required. We sequenced the rbcL (RuBisCO) gene and ITS (Internal Transcribed Spacer) 1, 2, and 5.8S regions from a large number of recent collections and identified a discrete of number data sets. These were analysed in comparison with the morphological evidence for each of the taxa. Uncertain of the possibility that our operational taxonomic units may not correspond to the types, we developed a protocol for isolating PCR-friendly DNA from herbarium specimens, some reaching back as far as 1670. The DNA profiles of types and historically important specimens were compared to those for recently collected silica gel-dried and formalin-fixed material and assigned correct names. Species studied ranged from Alaska to Mexico and the Gulf of California and were compared to outgroup taxa from Pacific South America and the Southern Ocean. Particular attention was paid to variations in morphology as they relate to habitat with emphasis on the presence or absence of different morphological forms among sympatric and allopatric populations. We recognize 10 species in Chondracanthus (including one new combination and one new species) and 16 species in Mazzaella (including two new combinations and two new species). Finally, we tested a phylogenetic hypothesis inferred for the Gigartinaceae from rbcL sequences for congruence with one generated from ITS sequences. [source] SPECIES PHYLOGENY OF COSMARIUM AND STAURASTRUM (DESMIDIACEAE) BASED ON RBC L SEQUENCESJOURNAL OF PHYCOLOGY, Issue 2000O.-M. Lee Cosmarium and Staurastrum are the two most diverse genera of placoderm desmids (Family Desmidiaceae), with approximately 1100 and 800 species, respectively. Phylogenetic analysis of relationships of species has been extremely difficult. In a monograph of North American placoderm desmids, Prescott et al. described early phylogenetic work that concluded Staurastrum to be polyphyletic and certainly polymorphic. Likewise, Cosmarium has also been viewed as polyphyletic, and a number of workers have proposed splitting these genera. The classical view of West and West grouped species within each genus into two divisions and 6,8 sections based on wall features and semicell shape. We sequenced rbcL from 18 species of Cosmarium (2 divisions, 7 sections) and 12 species of Staurastrum (2 divisions and 7 sections) and performed a phylogenetic analysis (parsimony, maximum likelihood, bootstrap) using other placoderm desmids and Zygnematales as outgroups. The results exhibit little support for the monophyly of sections or divisions of the two genera. Furthermore, although there is support for the monophyly of clades within each genus, there is also support for a separate clade containing species from both genera. [source] GLOBAL SYSTEMATIC AND PHYLOGENETIC ANALYSIS OF SARGASSUM IN THE GULF OF MEXICO, CARIBBEAN AND PACIFIC BASINJOURNAL OF PHYCOLOGY, Issue 2000N. Phillips Sargassum is one of the most species-rich genera in the brown algae with over 400 described species worldwide. The bulk of these species occurs in Pacific-Indian ocean waters with only a small portion found on the Atlantic side of the Isthmus of Panama. Sargassum also has one of the most subdivided and complex taxonomic systems used within the algae. Systematic distinctions within the genus are further complicated by high rates of phenotypic variability in several key morphological characters. Molecular analyses in such systems should allow testing of systematic concepts while providing insights into speciation and evolutionary patterns. Global molecular phylogenetic analyses using both conserved and variable regions of the Rubisco operon (rbcL and rbcL-IGS-rbcS) were performed with species from the Gulf of Mexico, Caribbean, and Pacific basin. Results confirm earlier analyses based on rbcL-IGS- rbcS from Pacific species at the subgeneric and sectional level while providing additional insights into the systematics and phylogenetics on a global scale. For example, species east of the Isthmus of Panama form a distinct well-resolved clade within the tropical subgenus. This result in sharp contrast to traditional systematic treatments but provides a window into the evolutionary history of this genus in the Pacific and Atlantic Ocean basins and a possible means to time speciation events. [source] Evaluation of 10 plant barcodes in Bryophyta (Mosses)JOURNAL OF SYSTEMATICS EVOLUTION, Issue 1 2010Yan LIU Abstract DNA barcoding is a molecular tool that uses a standardized DNA region to identify species. Our preliminary study reported here is the first attempt to specifically focus on universality and attributes of candidate barcodes across a wide systematic range of mosses. We tested eight previously proposed plant barcoding regions (atpF-atpH, ITS2, matK, psbK-psbI, rbcL, rpoB, rpoC1, and trnH-psbA) and two popular phylogenetic markers (rps4 and trnL-trnF of cpDNA) in 49 moss species and 9 liverwort species, representing half of the orders in moss lineages. The ITS2, rbcL, rpoC1, rps4, trnH-psbA and trnL-trnF regions showed good universality, and therefore the efficacy of these loci as DNA barcodes was further evaluated in 36 mosses and 2 liverworts, each of which included two to three individuals per taxa. The five loci, viz. rbcL, rpoC1, rps4, trnH-psbA and trnL-trnF, were easy to amplify and sequence and showed significant inter-specific genetic variability, making them potentially useful DNA barcodes for mosses. The best performing single loci were the rbcL and rpoC1 coding regions. Several loci showed equivalent performance and combinations of them did not greatly increase their discrimination capacity. In addition, phylogenies generated from each of the separate regions and multi-locus combinations by using best-fit and Kimura 2-parameter models were compared, but no significant difference was found. [source] Phylogeographic analysis of the red seaweed Palmaria palmata reveals a Pleistocene marine glacial refugium in the English ChannelMOLECULAR ECOLOGY, Issue 3 2005JIM PROVAN Abstract Phylogeography has provided a new approach to the analysis of the postglacial history of a wide range of taxa but, to date, little is known about the effect of glacial periods on the marine biota of Europe. We have utilized a combination of nuclear, plastid and mitochondrial genetic markers to study the biogeographic history of the red seaweed Palmaria palmata in the North Atlantic. Analysis of the nuclear rDNA operon (ITS1-5.8S-ITS2), the plastid 16S- trnI- trnA-23S-5S, rbcL- rbcS and rpl12- rps31- rpl9 regions and the mitochondrial cox2,3 spacer has revealed the existence of a previously unidentified marine refugium in the English Channel, along with possible secondary refugia off the southwest coast of Ireland and in northeast North America and/or Iceland. Coalescent and mismatch analyses date the expansion of European populations from approximately 128 000 bp and suggest a continued period of exponential growth since then. Consequently, we postulate that the penultimate (Saale) glacial maximum was the main event in shaping the biogeographic history of European P. palmata populations which persisted throughout the last (Weichselian) glacial maximum (c. 20 000 bp) in the Hurd Deep, an enigmatic trench in the English Channel. [source] Evidence for the adaptive evolution of the carbon fixation gene rbcL during diversification in temperature tolerance of a clade of hot spring cyanobacteriaMOLECULAR ECOLOGY, Issue 5 2003S. R. Miller Abstract Determining the molecular basis of enzyme adaptation is central to understanding the evolution of environmental tolerance but is complicated by the fact that not all amino acid differences between ecologically divergent taxa are adaptive. Analysing patterns of nucleotide sequence evolution can potentially guide the investigation of protein adaptation by identifying candidate codon sites on which diversifying selection has been operating. Here, I test whether there is evidence for molecular adaptation of the carbon fixation gene rbcL for a clade of hot spring cyanobacteria in the genus Synechococcus that has diverged in thermotolerance. Amino acid replacements during Synechococcus radiation have resulted in an increase in the number of hydrophobic residues in the RbcLs of more thermotolerant strains. A similar increase in hydrophobicity has been observed for many thermostable proteins. Maximum likelihood models which allow for heterogeneity among codon sites in the ratio of nonsynonymous to synonymous nucleotide substitutions estimated a class of amino acid sites as a target of positive selection. Depending on the model, a single amino acid site that interacts with a flexible element involved in the opening and closing of the active site was estimated with either low or moderate support to be a member of this class. Site-directed mutagenesis approaches are being explored in order to directly test its adaptive significance. [source] Species identification of Alnus (Betulaceae) using nrDNA and cpDNA genetic markersMOLECULAR ECOLOGY RESOURCES, Issue 4 2010BAO-QING REN Abstract One nuclear and three chloroplast DNA regions (ITS, rbcL, matK and trnH-psbA) were used to identify the species of Alnus (Betulaceae). The results showed that 23 out of all 26 Alnus species in the world, represented by 131 samples, had their own specific molecular character states, especially for three morphologically confused species (Alnus formosana, Alnus japonica and Alnus maritima). The discriminating power of the four markers at the species level was 10% (rbcL), 31.25% (matK), 63.6% (trnH-psbA) and 76.9% (ITS). For ITS, the mean value of genetic distance between species was more than 10 times the intraspecific distance (0.009%), and 13 species had unique character states that differentiated them from other species of Alnus. The trnH-psbA region had higher mean values of genetic distance between and within species (2.1% and 0.68% respectively) than any other region tested. Using the trnH-psbA region, 13 species are distinguished from 22 species, and seven species have a single diagnostic site. The combination of two regions, ITS and trnH-psbA, is the best choice for DNA identification of Alnus species, as an improvement and supplement for morphologically based taxonomy. This study illustrates the potential for certain DNA regions to be used as novel internet biological information carrier through combining DNA sequences with existing morphological character and suggests a relatively reliable and open taxonomic system based on the linked DNA and morphological data. [source] Testing candidate plant barcode regions in the MyristicaceaeMOLECULAR ECOLOGY RESOURCES, Issue 3 2008S. G. NEWMASTER Abstract The concept and practice of DNA barcoding have been designed as a system to facilitate species identification and recognition. The primary challenge for barcoding plants has been to identify a suitable region on which to focus the effort. The slow relative nucleotide substitution rates of plant mitochondria and the technical issues with the use of nuclear regions have focused attention on several proposed regions in the plastid genome. One of the challenges for barcoding is to discriminate closely related or recently evolved species. The Myristicaceae, or nutmeg family, is an older group within the angiosperms that contains some recently evolved species providing a challenging test for barcoding plants. The goal of this study is to determine the relative utility of six coding (Universal Plastid Amplicon , UPA, rpoB, rpoc1, accD, rbcL, matK) and one noncoding (trnH-psbA) chloroplast loci for barcoding in the genus Compsoneura using both single region and multiregion approaches. Five of the regions we tested were predominantly invariant across species (UPA, rpoB, rpoC1, accD, rbcL). Two of the regions (matK and trnH-psbA) had significant variation and show promise for barcoding in nutmegs. We demonstrate that a two-gene approach utilizing a moderately variable region (matK) and a more variable region (trnH-psbA) provides resolution among all the Compsonuera species we sampled including the recently evolved C. sprucei and C. mexicana. Our classification analyses based on nonmetric multidimensional scaling ordination, suggest that the use of two regions results in a decreased range of intraspecific variation relative to the distribution of interspecific divergence with 95% of the samples correctly identified in a sequence identification analysis. [source] | |||||||||||||||||||||||||||||||