System Foundations of Natural Classification

2021 ◽  
Author(s):  
Boris F. Fomin ◽  
Oleg B. Fomin ◽  
Tamara L. Kachanova ◽  
Konstantin A. Turalchuk
Keyword(s):  
Natural Classification

A Perturbation Theory for the Population of Atomic Energy Levels in Non-Lte Plasmas

1988 ◽  
Vol 102 ◽  
pp. 343-347
Author(s):  
M. Klapisch
Keyword(s):  
Perturbation Theory ◽  
Small Parameter ◽  
Classification Scheme ◽  
Sum Rules ◽  
Energy Levels ◽  
Natural Classification ◽  
Quantum Numbers ◽  
Formal Expansion ◽  
Atomic Energy Levels ◽  
As Effects

AbstractA formal expansion of the CRM in powers of a small parameter is presented. The terms of the expansion are products of matrices. Inverses are interpreted as effects of cascades.It will be shown that this allows for the separation of the different contributions to the populations, thus providing a natural classification scheme for processes involving atoms in plasmas. Sum rules can be formulated, allowing the population of the levels, in some simple cases, to be related in a transparent way to the quantum numbers.

scholarly journals Towards a Natural Classification of Hyphodontia Sensu Lato and the Trait Evolution of Basidiocarps within Hymenochaetales (Basidiomycota)

2021 ◽  
Vol 7 (6) ◽  
pp. 478
Author(s):  
Xue-Wei Wang ◽  
Tom W. May ◽  
Shi-Liang Liu ◽  
Li-Wei Zhou
Keyword(s):  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Ancestral State ◽  
Trait Evolution ◽  
Natural Classification ◽  
Multiple Loci ◽  
The Family ◽  
Phylogenetic Perspective ◽  
Taxonomic Framework ◽  
First Time

Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.

Natural classification

1981 ◽  
Vol 20 (1) ◽  
pp. 37-91 ◽  
Author(s):  
Scott Atran
Keyword(s):  
Natural Classification

scholarly journals Towards a scientific status for micromolecular Systematics

1980 ◽  
Vol 10 (4) ◽  
pp. 845-862 ◽  
Author(s):  
Otto R. Gottlieb
Keyword(s):  
Information Retrieval ◽  
Secondary Metabolites ◽  
Shikimate Pathway ◽  
Oxidative Enzymes ◽  
Natural Classification ◽  
Plant Kingdom ◽  
Ecological Implications ◽  
Scientific Status ◽  
Entire Plant ◽  
Retrieval Device

Abstract While different biosynthetic groups of secondary metabolites (micromolecules) rarely accumulate in the same plant species, one such group may replace another in morphologically related taxa. The use of micromolecules as general systematic markers of the plant kingdom thus requires unifying postulates concerning their evolution patterns. Two such postulates — contraction of the shikimate pathway and blocking of oxidative enzymes — are illustrated with the aid of systematic considerations on the genera Aniba (Lauraceae) and Derris-Lonchocarpus (Leguminosae) which involve besides chemistry, morphology, ecology and geography. Extrapolation of the principles applied in these examples to the entire plant kingdom seems possible, an important fact, due to the ecological implications of micromolecules. In this sense, the paper opens the way, rather than simply to a more "natural" classification, to an information retrieval device of ecologically relevant facts about plants.

A natural classification of Lasiosphaeria based on nuclear LSU rDNA sequences

2004 ◽  
Vol 108 (1) ◽  
pp. 26-34 ◽  
Author(s):  
Andrew N. Miller ◽  
Sabine M. Huhndorf
Keyword(s):  
Lsu Rdna ◽  
Natural Classification ◽  
Rdna Sequences

scholarly journals Phyletic distribution and diversification of the Phage Shock Protein stress response system in bacteria and archaea

2021 ◽  
Author(s):  
Philipp F. Popp ◽  
Vadim M. Gumerov ◽  
Ekaterina P. Andrianova ◽  
Lisa Bewersdorf ◽  
Thorsten Mascher ◽  
...  
Keyword(s):  
Stress Response ◽  
Large Scale ◽  
Cell Envelope ◽  
Model Organisms ◽  
Microbial World ◽  
Natural Classification ◽  
Response System ◽  
Core Proteins ◽  
Envelope Stress

AbstractThe bacterial cell envelope is an essential structure that protects the cell from environmental threats, while simultaneously serving as communication interface and diffusion barrier. Therefore, maintaining cell envelope integrity is of vital importance for all microorganisms. Not surprisingly, evolution has shaped conserved protection networks that connect stress perception, transmembrane signal transduction and mediation of cellular responses upon cell envelope stress. The phage shock protein (PSP) stress response is one of such conserved protection networks. Most of the knowledge about the Psp response comes from studies in the Gram-negative model bacterium, Escherichia coli where the Psp system consists of several well-defined protein components. Homologous systems were identified in representatives of Proteobacteria, Actinobacteria, and Firmicutes; however, the Psp system distribution in the microbial world remains largely unknown. By carrying out a large-scale, unbiased comparative genomics analysis, we found components of the Psp system in many bacterial and archaeal phyla and demonstrated that the PSP system deviates dramatically from the proteobacterial prototype. Two of its core proteins, PspA and PspC, have been integrated in various (often phylum-specifically) conserved protein networks during evolution. Based on protein sequence and gene neighborhood analyses of pspA and pspC homologs, we built a natural classification system of PSP networks in bacteria and archaea. We performed a comprehensive in vivo protein interaction screen for the PSP network newly identified in the Gram-positive model organism Bacillus subtilis and found a strong interconnected PSP response system, illustrating the validity of our approach. Our study highlights the diversity of PSP organization and function across many bacterial and archaeal phyla and will serve as foundation for future studies of this envelope stress response beyond model organisms.

scholarly journals The role of catchment classification in rainfall-runoff modeling

2011 ◽  
Vol 8 (3) ◽  
pp. 6113-6153 ◽  
Author(s):  
Y. He ◽  
A. Bárdossy ◽  
E. Zehe
Keyword(s):  
Classification Scheme ◽  
Intrinsic Value ◽  
Climatic Conditions ◽  
Ungauged Basins ◽  
Classification Methods ◽  
Rainfall Runoff ◽  
Catchment Hydrology ◽  
Natural Classification ◽  
Runoff Modeling

Abstract. A sound catchment classification scheme is a fundamental step towards improved catchment hydrology science and prediction in ungauged basins. Two categories of catchment classification methods are presented in the paper. The first one is based directly on physiographic properties and climatic conditions over a catchment and regarded as a Linnaean type or natural classification scheme. The second one is based on numerical clustering and regionalization methods and considered as a statistical or arbitrary classification scheme. This paper reviews each category including what has been done since recognition of the intrinsic value of catchment classification, what is being done in the current research, as well as what is to be done in the future.

scholarly journals Splitting the Pisonia birdcatcher trees: re-establishment of Ceodes and Rockia (Nyctaginaceae, Pisonieae)

PhytoKeys ◽  
2020 ◽  
Vol 152 ◽  
pp. 121-136
Author(s):  
Elson Felipe Sandoli Rossetto ◽  
Marcos A. Caraballo-Ortiz
Keyword(s):  
Original Description ◽  
General Distribution ◽  
Phylogenetic Study ◽  
Natural Classification ◽  
Line Drawings ◽  
Dichotomous Key ◽  
Representative Species ◽  
Molecular Phylogenetic Study ◽  
Molecular Phylogenetic ◽  
Reproductive Characters

Several genera of Nyctaginaceae, currently merged under Pisonia, have been described for the Indo-Pacific region. Results from a recent molecular phylogenetic study of tribe Pisonieae showed that Pisonia is non-monophyletic and comprises three well-supported lineages: one including typical Pisonia and allies (Pisonia s.str.), a clade of species which corresponds to the original description of Ceodes and a third lineage whose single representative was formerly treated under the monotypic genus Rockia. Thus, as part of an effort to achieve a natural classification for tribe Pisonieae, this work proposes to re-establish Ceodes and Rockia to accommodate taxa with inconspicuous glands on anthocarps, recognising 21 species (20 for the former and one for the latter), of which 16 are new combinations: Ceodes amplifoliacomb. nov., Ceodes artensiscomb. nov., Ceodes austro-orientaliscomb. nov., Ceodes browniicomb. nov., Ceodes caulifloracomb. nov., Ceodes coronatacomb. nov., Ceodes diandracomb. nov., Ceodes gigantocarpacomb. nov., Ceodes gracilescenscomb. nov., Ceodes lanceolatacomb. nov., Ceodes merytifoliacomb. nov., Ceodes muellerianacomb. nov., Ceodes rapaensiscomb. nov., Ceodes sechellarumcomb. nov., Ceodes taitensiscomb. nov. and Ceodes wagnerianacomb. nov. A general distribution of each species recognised in this work is also included, along with line drawings and colour pictures of representative species of Ceodes, Pisonia and Rockia and an updated dichotomous key based on reproductive characters for the nine genera (Ceodes, Cephalotomandra, Grajalesia, Guapira, Neea, Neeopsis, Pisonia, Pisoniella and Rockia) comprising the tribe Pisonieae. Résumé Plusieurs genres de Nyctaginaceae actuellement fusionnés sous Pisonia ont été décrits pour la région Indo-Pacifique. Les résultats d’une récente étude phylogénétique moléculaire de la tribu Pisonieae ont montré que Pisonia est non monophylétique et comprend trois lignées bien supportées: une comprenant Pisonia typique et ses alliés (Pisonia s.str.), un clade d’espèces qui correspond à la description originale de Ceodes et une troisième lignée dont l’unique représentant était auparavant traité sous le genre monotypique Rockia. Ainsi, dans le cadre d’un effort pour parvenir à une classification naturelle de la tribu Pisonieae, ce travail proposons de rétablir les Ceodes et Rockia pour accueillir des taxons avec des glandes discrètes sur les anthocarpes, reconnaissant 21 espèces (20 pour les premières et une pour les dernières), dont 16 sont de nouvelles combinaisons: Ceodes amplifoliacomb. nov., Ceodes artensiscomb. nov., Ceodes austro-orientaliscomb. nov., Ceodes browniicomb. nov., Ceodes caulifloracomb. nov., Ceodes coronatacomb. nov., Ceodes diandracomb. nov., Ceodes gigantocarpacomb. nov., Ceodes gracilescenscomb. nov., Ceodes lanceolatacomb. nov., Ceodes merytifoliacomb. nov., Ceodes muellerianacomb. nov., Ceodes rapaensiscomb. nov., Ceodes sechellarumcomb. nov., Ceodes taitensiscomb. nov. et Ceodes wagnerianacomb. nov. Une distribution générale de chaque espèce reconnue dans ce travail est également incluse, ainsi que des dessins au trait et des images en couleur des espèces représentatives de Ceodes, Pisonia et Rockia, et préparé une clé dichotomique mise à jour basée sur les caractères reproductifs des neuf genres (Ceodes, Cephalotomandra, Grajalesia, Guapira, Neea, Neeopsis, Pisonia, Pisoniella et Rockia) comprenant la tribu Pisonieae.

scholarly journals Names of phytopathogenic fungi: a practical guide

2021 ◽  
Author(s):  
Pedro W Crous ◽  
Amy Y Rossman ◽  
Catherine Aime ◽  
Cavan Allen ◽  
Treena Burgess ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Classification System ◽  
Driving Force ◽  
Pathogenic Fungi ◽  
Phytopathogenic Fungi ◽  
Plant Pathogenic Fungi ◽  
Natural Classification ◽  
Online Databases ◽  
As Species

Names of phytopathogenic fungi and oomycetes are essential to communicate knowledge about species and their biology, control, and quarantine as well as for trade and research purposes. Many plant pathogenic fungi are pleomorphic, meaning that they produce different asexual (anamorph) and sexual (teleomorph) morphs in their lifecycles. Because of this, more than one name has been applied to different morphs of the same species, which has confused users of names. The onset of DNA technologies makes it possible to connect different morphs of the same species, resulting in a move to a more natural classification system for fungi, in which a single name for a genus as well as species can now be used. The move to a single nomenclature, as well as the advent of molecular phylogeny and the introduction of polythetic taxonomic approaches has been the main driving force for the re-classification of fungi, including pathogens. Nonetheless, finding the correct name for species remains challenging, but there is a series of steps or considerations that could greatly simplify this process, as outlined here. In addition to various online databases and resources, a list of accurate names is herewith provided of the accepted names of the most common genera and species of phytopathogenic fungi.

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