Pinus uncinata Ramond taxonomy based on needle characters

 11 needle characters of Pinus uncinata Ramond from the Spanish Pyrenees, P. mugo Turra from the Tatra Mountains, and P. sylvestris L. from N.E. Poland were analysed. It was shown that P. uncinata is much more closely related to P. mugo than to P. sylvestris. Nevertheless P. uncinata remains distinct from both in a number of the characters examined. The species differs from P. mugo especially in the length of the needles and in the distance between the vascular bundles. It differs from P. sylvestris in such characters as the number of resin canals, thickness of epidermis cells and the distance between the vascular bundles. Width of epidermis cells was similar in all taxa studied. Received May 31, 2000 Accepted February 13, 2001     

Polyphasic taxonomy of Aspergillus fumigatus and related species

The variability within Aspergillus fumigatus Fresenius and related species was examined using macro-, micro-morphology, growth temperature regimes and extrolite patterns. In addition, DNA analyses including partial beta-tubulin, calmodulin and actin gene sequences were used. Detailed examination of strains, considered as A. fumigatus earlier, showed that they could be divided into four groups including A. fumigatus sensu stricto, A. lentulus and two new species. The intraspecific genetic variability within A. fumigatus sensu stricto was low, the sequence differences among 23 strains of the species was at most two bases in each partial beta-tubulin and calmodulin gene. However, intraspecific morphological diversity within the species was high and delineation of the species was equivocal. Therefore, beta-tubulin and calmodulin gene sequences could be critical determinants for the delineation of the A. fumigatus sensu stricto species. A. lentulus including isolates from clinical origin, Korean soil and from a dolphin clustered into an isolated group based on beta-tubulin, calmodulin and actin gene sequences, differing from A. fumigatus by morphological characters, growth temperature and extrolite profile. A. lentulus produces the extrolites auranthine, cyclopiazonic acid, a dimeric indole of unknown structure, neosartorin, some pyripyropens, terrein and some tryptoquivalins and tryptoquivalons. Two pair of isolates (CBS 117194, 117186 and 117520, 117519) clustered into separate groups from A. fumigatus and the other Aspergillus section Fumigati species, including the teleomorph Neosartorya, are proposed as two new species. A. fumigatiaffinis spec. nov. produces the extrolites auranthine, cycloechinulin, helvolic acid, neosartorin, palitantin, pyripyropens, tryptoquivalins and tryptoquivalons, and A. novofumigatus spec. nov. produces the extrolites cycloechinuline, helvolic acid, neosartorin, palitantin and terrein.     

Phylogenetic significance of morphological characters in the taxonomy of Pestalotiopsis species

There has been considerable disagreement regarding the relationships among Pestalotiopsis species and their delimitations. A molecular phylogenetic analysis was conducted on 32 species of Pestalotiopsis in order to evaluate the utility of morphological characters currently used in their taxonomy. Phylogenetic relationships were inferred from nucleotide sequences in the ITS regions and 5.8S gene of the rDNA under four optimality criteria: maximum parsimony, weighted parsimony, maximum likelihood, and neighbor joining. Phylogenies estimated from all analyses yielded trees of essentially similar topology and revealed 3 major groups that correspond with morphology-based classification systems. Molecular data indicated that the genus contains two distinct lineages based on pigmentation of median cells and four distinct groupings based on morphology of apical appendages. The analyses did not support reliability of other phenotypic characters of this genus, such as spore dimensions. Characters with particular phylogenetic significance are discussed in relation to the taxonomy of Pestalotiopsis.     

Foliar anatomy of neotropical Salicaceae: potentially useful characters for taxonomy

The taxonomy of neotropical Salicaceae, a family that now includes the majority of the former Flacourtiaceae, has been problematic, especially because they display very diverse morphology and have several characteristics in common with many other families. Recent phylogenetic studies have proposed substantial changes at both family and generic levels. Considering the importance of anatomy as an aid for taxonomy, the gathering of anatomical data for the family is fundamental to help clarify the taxonomic problems. Leaves belonging to Abatia americana (four samples), Banara brasiliensis (2), Casearia arborea (4), C. decandra (5), C. gossypiosperma (2), C. obliqua (1), C. sylvestris (3), C. ulmifolia (3), Prockia crucis (3), and Xylosma prockia (4) and the closely related Carpotroche brasiliensis (3) from Achariaceae, were studied by standard microscopy techniques. The leaves were anatomically described, emphasizing their differences and similarities. Similar characters for the neotropical Salicaceae (former Flacourtiaceae) and Salicaceae strictu sensu were recognized, such as the presence of salicoid leaf teeth, brachyparacytic stomata, secondary growth of the petiole, abundance of crystals, collateral and arch-shaped vascular system at the midrib, and sclerenchyma accompanying the bundles. These data demonstrate that leaf anatomy can provide evidence to assist with the taxonomy of Salicaceae, at family, generic, and specific levels.     

苏铁属植物叶表皮特征及其分类学和古生态学意义

苏铁属(Cycas)作为一类古老的裸子植物,经历了漫长的演化历史,因此,深入研究其形态特征与环境的相互关系,有望为古环境重建提供重要参考依据。本文分析西双版纳和深圳两地植物园栽培环境下27种苏铁属植物的叶表皮特征及气孔参数的差异,并进一步探讨气孔参数与系统发育的关系。结果表明:(1)苏铁属内叶表皮特征保守稳定,具有一定的分类学意义:依据表皮细胞及气孔器特征划分了四种叶表皮类型,可为苏铁现生植物或化石的鉴定提供参考。(2)四种叶表皮类型指示了不同的原生生境特征,对古环境具有一定的指示意义。(3)同一环境下,气孔参数在属内的种间差异显著,其次,气孔指数在属内变化与系统发育有关,除气孔指数具显著的系统发育信号外,其余气孔参数均无显著系统发育信号。本研究结果表明气孔参数法重建古大气CO2浓度时,需尽可能利用亲缘关系相近、叶表皮和生境皆相似的代理种,并明确气孔参数与大气CO2分压的相关关系在种间的异同,从而提高该方法的有效性。     

The use of correlated ultrastructural and morphogenetic characters in evolutionary taxonomy of hypotrich ciliates

A new morphogenetic criterion, the "unit of turn-over" emerges from the dynamic analysis of hypotrich morphogenesis. The unit corresponds to the set of morphogenetically interdependent somatic structures whose turn-over is correlated to nuclear modifications. Hypotrichs are seen to conform to one of two very general modes of turn-over of their ciliary structures during a variety of morphogenetic processes, one in which all somatic cilia and their infraciliature are replaced, and the other in which only the cirral structures (not the dorsal dikinetids) undergo replacement. A strong correlation is observed between the type of turn-over occurring and ultrastructural features of the corresponding species. From an evolutionary point of view, these data lead to a new subdivision of hypotrichs, into the Euhypotrichina and the Pseudohypotrichina.     

Phylogenetic taxonomy of Hymenochaete and related genera (Hymenochaetales)

Species delimitation in Hymenochaete sensu lato was evaluated based on partial nucLSU rDNA sequences, isoenzyme analyses and morphological data. Analyses of LSU data revealed Hymenochaete sensu stricto and Pseudochaete as distinct monophyletic genera. Transfer of Hydnochaete olivacea into genus Pseudochaete and Dichochaete setosa into genus Hymenochaete (as H. resupinata) was supported by the results of molecular analyses. A new species Hymenochaete koeljalgii from Tanzania was described. The species of genus Hymenochaete sensu stricto were divided into four well-supported clades possessing no distinctive morphological characters.     

A numerical taxonomy of the pan species of Crinum based on morphological characters

Fourteen characters of 64 specimens from five taxa; Crinum rautanenianum Schinz, C. paludosum Verdoorn, C. carolo-schmidtii Dinter and C. lugardiae N. E. Brown, previously described within the complex and the more widespread C. macowanii Baker, were subjected to multivariate and univariate statistical analyses in order to circumscribe morphological species as objectively as possible. Results of the clustering and ordination analyses confirm the existence of five distinct phenetic species in the group. The most useful characters that provide taxonomic clarity are identified whilst previously used diagnostic features are discussed. A new key to the species based on examined specimens is provided. Distribution maps of members of this species complex are also presented.     

Numerical taxonomy of Skermania piniformis and related isolates from activated sludge

The microscopic morphology of nocardioforms causing foaming problems in activated sludge usually consists of filaments with branches at either right angles ( Nocardia amarae -Like Organisms, NALO) or acute angles (Pine Tree-Like Organisms, PTLO). Fifty-nine nocardioforms, mainly with PTLO morphology, isolated from mixed liquor and foam samples from Australian activated sludge plants, and 39 reference strains of nocardioforms, including type strains, were characterized using 109 morphological and physiological characters. Cluster Analysis and Principal Component Analysis showed that the activated sludge isolates clustered in six groups. All isolates that had typical PTLO morphology clustered unambiguously with the Skermania piniformis type strain (formerly called Nocardia pinensis ) showing that, unlike NALO, reliable unequivocal identification of S. piniformis , based on microscopic morphology in activated sludge, was possible. Other foam isolates whose morphology consisted of branches with both acute angles and right angles clustered as two separate groups, probably representing new species. These could not be confused microscopically with S. piniformis , despite some branches showing acute angles. The remaining three groups had typical NALO morphology. One of these groups did not cluster with any reference cultures and may be a new species or genus.     

Analysis of bacterial RM-systems through genome-scale analysis and related taxonomy issues

Recognition sites for type II restriction and modification enzymes in genomes of several bacteria are recognized as semi-palindromic motifs and are avoided at a significant degree. The key idea of contrast word analysis with respect to RMS recognition sites, is that under-represented words are likely to be selected against. Starting from over- or underrepresented words corresponding to RMS recognition sites in specific clades, the specificity of unknown R-M systems can be highlighted. Among the known restriction enzymes, that are described in the REBASE database of restriction and modification systems, many of their recognition sites are still uncharacterized. Eventually, this motivates studies aimed at assessing horizontal transferring events of RMS in micro-organisms through the analysis of word usage biases in well-determined genomic regions. A probabilistic model is built on a first-order Markovian chain. Statistics on the k-neighborhood of a word is carried out to assess the biological significance of a genomic motif. Efficient word counting procedures have been implemented and statistics are used for the assessment of the significance of individual words in large sequences. On the basis of the set of most avoided words, and in accordance to the IUPAC coding standards, suggestions are made regarding potential recognition sequences. In certain cases, a comparison of avoided palindromic words in taxonomically related bacteria shows a pattern of relatedness of their R-M systems. For strengthening this analysis, the primary protein structure of all type II R-M systems known in REBASE have been blasted against the nr-GENBANK database. The combination of these analyses has revealed some interesting examples of possible horizontal transfer events of R-M systems.     

The logical priority of the tree over characters and some of its consequences for taxonomy

The aim of the present paper is to explore the role of the character in phylogenetic systematics. I argue that too much emphasis is put on particular characters rather than congruence both in the choice of phylogenetic hypotheses and in taxonomic decisions. This means that the logical priority of the tree over the characters is neglected. To a large extent, this is a result of not paying enough attention to the individuality thesis which states that clades are historical individuals and hence contingent in nature.     

Ultrastructure and taxonomy of Paraphysomonas (Chrysophyceae) and related genera 2

This is the second of two accounts reporting on the occurrence and systematics of freshwater species of the colourless chrysophycean genus Paraphysomonas in the Cambridge area, using electron microscopy of whole mounts of both cells and scales and sections of scales. Twenty species are included here, eleven of which are new: P. cancellala, P. canistrum, P. homolepis, P. ignivoma, P. limbata, P. morchella, P. runcinifera, P. stelligera, P. stephanolepis, P. subquadrangularis and P. undulata. Five new subspecies are also established: P. circumvallata ssp. mediogranulata, P. poteriophora ssp. manubriata, P. punctata ssp. atrema , ssp. microlepis and ssp. simplicior. P. diademifera (Takahashi) comb. nov. [= Lepidochromonas diademifera (Takahashi) Kristiansen] has been included in Paraphysomonas since it has been found to be colourless and not pigmented as originally described and also to possess scales of a similar structure to those in other species of Paraphysomonas. One previously described species, P. inconspicua Takahashi, is here considered as a synonym of P. butcheri Pennick & Clarke. P. vacuolata Thomsen is removed from Paraphysomonas since it has been found to possess a chloroplast and will be included in a new genus in the third paper of this series. The 37 presently known species of Paraphysomonas have been arranged in 11 different groups according to similarities in scale structure. Consideration of the possible evolution of scale structure in Paraphysomonas and the possible interrelationships within the genus led to the conclusion that all species should be included in a single genus.     

Morphological and cytological investigations ofUlothrix zonata and taxonomy of the related species

The present communication deals with the observations made on the morphology, reproduction and cytology ofUlothrix zonata (Weber & Mohr)Kütz. in culture. The alga displays a remarkable phenotypic plasticity in nature as well as in culture. The present study provides additional evidence of karyology in support ofLokhorst andVroman's treatment ofU. zonata which merges a number of earlier described species in it. The cytological details and chromosome number (n = 10) determined for the Indian isolates ofU. zonata agree with those ofSarma for the British material.NBRI Research Publication No. 63 (N.S.)     

Ultrastructure and taxonomy of Paraphysomonas (Chrysophyceae) and related genera 3

New observations are presented on the internal ultrastructure of the scale–bearing chrysophycean genera Chromophysomonas, Chrysosphaerella , the new genus Polylepidomonas and 15 species of Paraphysomonas. These data show that the pigmented genera Chromophysomonas, Chrysosphaerella and Polylepidomonas have a generally similar internal structure and that their taxonomic separation is based only on differences in scale structure. The structure of Paraphysomonas resembles that of these genera but the cells always possess a leucoplast rather than a chloroplast. In cell structure, the pigmented genera resemble the naked genus Ochromonas while Paraphysomonas resembles Spumella , the colourless counterpart of Ochromonas. Evaluation of the differences between these genera and the scale–bearing genera Mallomonas and Synura has led to the conclusion that Chromophysomonas, Chrysosphaerella, Polylepidomonas and Paraphysomonas should no longer be classified within the family Mallomonadaceae. The new family Paraphysomonadaceae is established to include Chrysophyceae with an Ochromonas type of cell structure but which also produce silica scales.