Time to update the sectional classification of Ilex (Aquifoliaceae): New insights from Ilex phylogeny,morphology, and distribution

Resolving the infrageneric classification of species-rich genera has been challenging in plant taxonomy. Ilex L. is a subcosmopolitan genus with over 600 species of dioecious trees and shrubs. Many classification systems based on morphological data have been proposed during the past 250 years. However, these systems (such as Loesener's and Galle's systems) may not truly reflect Ilex's evolutionary trajectories because most of those system's infrageneric hierarchies are not monophyletic. In this study, we reconstructed a phylogeny of Ilex L. comprising 15 moderately to highly supported clades using rigorously identified samples (202 species) and closely authenticated gene sequences of three nuclear genes [internal transcribed spacer (ITS), external transcribed spacer (ETS), and nepGS]. The newly generated phylogenetic tree resembles essentially that of the nuclear tree of Manen et al., but shows conspicuous topological differences with the phylogeny of Yao et al. Closely scrutinizing morphological variation and distributional patterns of 202 species, this study found that most lineages of Ilex identified herein are well defined by a particular trait or a combination of morphological and distributional traits, displaying phylogeny–morphology–distribution conformity that has seldom been uncovered in previous studies. Given the general phylogeny–morphology–distribution conformity revealed in this genus, we put forward an updated sectional classification system for Ilex that temporarily contains 14 sections. The new classification will provide a robust framework for studying the evolution and diversification of this ecologically and economically important genus.     

Physiological properties,conjugation and taxonomy ofCephaloascus fragrans Hanawa 1920 (syn:Ascocybe grovesii Wells 1954)

Summary It has been established that the type cultures ofCephaloascus fragrans Hanawa 1920,Ascocybe grovesii Wells 1954 and a culture isolated from oakwood from Japan are identical. Conjugation in this organism has been observed. The taxonomic position of this organism in theAscomycetes was discussed. If this organism is incorporated in the classification ofLodder andKreger-van Rij, it seems justified by taxonomical reasons to create a new subfamily: theCephaloascoideae.     

Are classification and phytopathological diversity compatible in Xanthomonas?

The genus Xanthomonas is characterized by its phytopathogenic diversity and the host specificity of its members. In the past, the classification of the members of this genus has been based primarily on the criterion of host specificity. This has led to a classification system which focused only on naming phytopathogenic variants on different hosts. Extensive taxonomic examination of Xanthomonas has shown that the phytopathogenic specialization of the bacteria is not correlated with the actual relationships within the genus. Based upon total genomic DNA homology, the genus has been reclassified into 20 species. At present, non-pathogenic xanthomonads are frequently isolated from plant material. As these strains often cannot be classified to existing species, it becomes clear that the diversity of the genus is much greater than expected from the phytopathogenic subpopulation, which has been the primary subject in the past. The example of Xanthomonas also illustrates that attempts to divide bacterial populations into discrete taxa conflict with the actual continuous nature of biodiversity. Received 16 April 1996/ Accepted in revised form 27 September 1996     

Intelligent Bayes Classifier (IBC) for ENT infection classification in hospital environment

Electronic Nose based ENT bacteria identification in hospital environment is a classical and challenging problem of classification. In this paper an electronic nose (e-nose), comprising a hybrid array of 12 tin oxide sensors (SnO₂) and 6 conducting polymer sensors has been used to identify three species of bacteria, Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), and Pseudomonas aeruginosa (P. aeruginosa) responsible for ear nose and throat (ENT) infections when collected as swab sample from infected patients and kept in ISO agar solution in the hospital environment. In the next stage a sub-classification technique has been developed for the classification of two different species of S. aureus, namely Methicillin-Resistant S. aureus (MRSA) and Methicillin Susceptible S. aureus (MSSA). An innovative Intelligent Bayes Classifier (IBC) based on "Baye's theorem" and "maximum probability rule" was developed and investigated for these three main groups of ENT bacteria. Along with the IBC three other supervised classifiers (namely, Multilayer Perceptron (MLP), Probabilistic neural network (PNN), and Radial Basis Function Network (RBFN)) were used to classify the three main bacteria classes. A comparative evaluation of the classifiers was conducted for this application. IBC outperformed MLP, PNN and RBFN. The best results suggest that we are able to identify and classify three bacteria main classes with up to 100% accuracy rate using IBC. We have also achieved 100% classification accuracy for the classification of MRSA and MSSA samples with IBC. We can conclude that this study proves that IBC based e-nose can provide very strong and rapid solution for the identification of ENT infections in hospital environment.     

Using a multigene phylogenetic analysis to assess generic delineation and character evolution in Verrucariaceae (Verrucariales, Ascomycota)

Verrucariaceae are a family of mostly crustose lichenized ascomycetes colonizing various habitats ranging from marine and fresh water to arid environments. Phylogenetic relationships among members of the Verrucariaceae are mostly unknown and the current morphology-based classification has never been confronted to molecular data. A multilocus phylogeny (nuLSU, nuSSU and RPB1) was reconstructed for 83 taxa representing all main genera of this family to provide a molecular phylogenetic framework necessary to assess the current morphology-based classification. Four main well-supported monophyletic groups were recovered, one of which contains seven robust monophyletic subgroups. Most genera, as traditionally delimited, were not monophyletic. A few taxonomic changes are proposed here to reconcile the morphology-based classification with the molecular phylogeny (Endocarpon diffractellum comb. nov., Heteroplacidium fusculum comb. nov., and Bagliettoa marmorea comb. nov.). Ancestral state reconstructions show that the most recent common ancestor of the Verrucariaceae was most likely crustose with a weakly differentiated upper cortex, simple ascospores, and hymenium free of algae. As shown in this study, the use of symplesiomorphic traits to define Verrucaria, the largest and type genus for the Verrucariaceae, as well as the non monophyly of the genera Polyblastia, Staurothele and Thelidium, explain most of the discrepancies between the current classification based on morphological similarity and a classification using monophyly as a grouping criterion.     

Streptomyces thermonitrificans sp.n., a thermophilic streptomycete

A new species of thermophilicStreptomyces has been isolated from a soil sample collected in Bombay. Its morphological characteristics and physiological behaviour have been studied in detail. It has thus been found to belong to Series XVI-Thermophilus of Waksman's scheme of classification (1961). Its similarity to and differences from a few known species are described. It has been designated asStreptomyces thermonitrificans.     

New classification of <Emphasis Type="Italic">HLA-DRB1</Emphasis>alleles in rheumatoid arthritis susceptibility: a combined analysis of worldwide samples

Introduction  

Rheumatoid arthritis (RA) is a complex polygenic disease of unknown etiology. HLA-DRB1 alleles encoding the shared epitope (SE) (RAA amino acid pattern in positions 72 to 74 of the third hypervariable region of the DRβ1 chain) are associated with RA susceptibility. A new classification of HLA-DRB1 SE alleles has been developed by Tezenas du Montcel and colleagues to refine the association between HLA-DRB1 and RA. In the present study, we used RA samples collected worldwide to investigate the relevance of this new HLA-DRB1 classification in terms of RA susceptibility across various Caucasoid and non-Caucasoid patients.     

Spermatogenesis in Triatoma williami Galvão,Souza and Lima (1965) (Hemiptera,Triatominae)

Cytogenetics has proven to be an important tool in the study of triatomine taxonomy. Triatoma williami is a triatomine that has been classified within the Matogrossensis subcomplex. In this study, the cytogenetic technique of lacto-aceto-orcein was used to confirm the karyotype of this species, which was found to be 2n = 22 (20A + XY). In this study, metaphases I and II were analyzed and the heteropyknotic pattern during the spermatogenesis and spermiogenesis was described, with results that corroborated the classification of T. williami in the Matogrossensis subcomplex.     

Unravelling the systematics of Nodularia (Bivalvia,Unionidae) species from eastern Russia

Conservation efforts have been hindered by data deficient conservation status assessments, especially due to taxonomic problems. This is especially true for many eastern Russian species of freshwater mussels, where distinct classification systems have complicated their delimitation and identification. Nodularia is a widespread eastern Asian freshwater mussel genus, present from Vietnam in the south to the Magadan region in eastern Russia in the north. The number of recognized species in the genus Nodularia in eastern Russia has been inflated over the last several decades due to the use of a typological species concept, the so-called 'Comparatory Method'. This method uses a single diagnostic character for species delimitation, i.e., the arc of maximal convexity of the shell's outline. Using this classification system, 10 species were recognized for far eastern Russia under the genus Nodularia Conrad, 1853, divided into three subgenera: Nodularia s. str., Amurunio and Magadaninaia. Since it is not supported by any other classification methods, the current comparatory classification is rejected by many Russian and international scientists, who only recognize a single species for that region, i.e., Nodularia douglasiae. Therefore, the aim of the present study is to clarify the taxonomy and systematics of the Nodularia genus in far eastern Russia and adjacent territories, using a multiple dataset approach that combines distribution with detailed conchological and anatomical analyses with morphometry and COI barcoding molecular techniques. All analyses performed in this study support the existence of a single Nodularia species in eastern Russia, i.e., N. douglasiae.     

Fuzzy species distribution models: a way to represent plant communities spatially

Fuzzy set theory has generally been applied to smooth classification cut‐offs, with an unavoidable loss of information. In this commentary, I rely on both advantages and disadvantages of the methods proposed in Duff et al., in this issue of the Journal of Vegetation Science, to map the variability over space of vegetation classes based on fuzzy sets and species distribution models.     

A hierarchical ecological classification system along the NE Atlantic coast: focusing on the local scale (Cantabria,N Spain)

An ecological classification at the local scale may be a useful tool for conservation planning and for the implementation of specific management programmes in a region. For this purpose, a methodology previously applied on a small scale has been adapted to classify the coast of Cantabria (N Spain). This methodology includes a physical classification and biological validation. The shoreline was divided into 1 km stretches, and the abiotic variables (sea surface temperature, photosynthetically active radiation, significant wave height and coastal morphology) were recorded for each stretch. A hierarchical classification was proposed, with a first level that encompassed a grouping of quantitative variables based on SOM and k-mean analysis and a second level that subdivided the previous groups according to the categorical variable ‘coastal morphology’. To validate the classification using biological data, cover of intertidal macroalgal species was obtained at 14 sites along the study area, and several statistical analyses were applied to test the ecological significance of this classification. Three physical units were obtained (western (W), central (C) and eastern (E) coast), based on abiotic variables. Each group was then subdivided into subunits according to its coastal morphology (cliffs or wave-cut platforms). A general agreement between the macroalgal distribution and physical units was accomplished. In the lower intertidal, Bifurcaria bifurcata and Halopteris scoparia dominated the western and central areas, whereas Corallina spp./Ellisolandia elongata and Gelidium spp. were most abundant towards the east. In contrast, throughout the middle intertidal, Corallina. spp./E. elongata were the dominant taxa. The classification system developed in this study completes a hierarchical framework for classifying the NE Atlantic coast, a promising approach that permits the application of the most suitable resolution in each case study that could be applicable to a wide range of coastal areas.     

Concept and Classification of Coarse Woody Debris in Forest Ecosystems

Coarse woody debris (CWD) is generally considered as dead woody materials in various stages of decomposition, including sound and rotting logs, snags, and large branches. CWD is an important functional and structural component of forested ecosystems and plays an important role in nutrient cycling, long-term carbon storage, tree regeneration, and maintenance of heterogeneous environmental and biological diversity. However, the definition and classification of CWD have been the subject of a long debate in forest ecology. CWD has not been precisely defined. Recently, with the rapid development of landscape ecology in CWD, the USDA Forest Service and the Long Term Ecological Research (LTER) have provided a standardized definition and classification for CWD, which makes data comparison in landscape scale possible. Important characteristics of their definition include: (1) a minimum diameter (or an equivalent cross-section) of CWD ≥10 cm at the widest point (the woody debris with a diameter from 1 to 10 cm should be defined as fine woody debris, and the rest is litterfall); and (2) sound and rotting logs, snags, stumps, and large branches (located above the soil), and coarse root debris (larger than 1 cm in diameter). This classification has greatly facilitated CWD studies. Therefore, it has been widely applied in some countries (particularly in North America). However, this classification has long been a source of confusion for forest ecologists in China. Furthermore, different definitions and criteria are still adopted in individual studies, which makes the interpretation and generalization of their work difficult. This article reviewed recent progress in classifying CWD, with an emphasis on introducing the classification system of the USDA Forest Service and the LTER. It is expected that this review will help facilitate the development of standardized definition and classification suitable to forest ecosystems in China. Translated from Acta Ecologica Sinica, 2005, 25(1) (in Chinese)     

Relapse or reinfection: Classification of malaria infection using transition likelihoods

In patients with Plasmodium vivax malaria treated with effective blood-stage therapy, the recurrent illness may occur due to relapse from latent liver-stage infection or reinfection from a new mosquito bite. Classification of the recurrent infection as either relapse or reinfection is critical when evaluating the efficacy of an anti-relapse treatment. Although one can use whether a shared genetic variant exists between baseline and recurrence genotypes to classify the outcome, little has been suggested to use both sharing and nonsharing variants to improve the classification accuracy. In this paper, we develop a novel classification criterion that utilizes transition likelihoods to distinguish relapse from reinfection. When tested in extensive simulation experiments with known outcomes, our classifier has superior operating characteristics. A real data set from 78 Cambodian P. vivax malaria patients was analyzed to demonstrate the practical use of our proposed method.     

ALARM CALLS OF THE EUROPEAN GROUND SQUIRREL SPERMOPHILUS CITELLUS AND THE TAURUS GROUND SQUIRREL S. TAURENSIS ENCODE INFORMATION ABOUT CALLER IDENTITY

ABSTRACT

Vocalizations of many mammalian species have been reported to encode information about caller identity. In this study, we analyzed 300 alarm calls from 10 free-living European Ground Squirrels Spermophilus citellus (30 per individual) and 300 alarm calls from 10 free-living Taurus Ground Squirrels S. taurensis (30 per individual), and tested the potential of these calls to encode information about the callers' identities. Discriminant analysis including all 10 European Ground Squirrel individuals correctly classified 98% of calls, and cross-validation reached a classification success of 97%. Correct classification of 98% and cross-validation of 98% was assigned when the analysis included only those individuals producing calls consisting of both elements (eight individuals). For the Taurus Ground Squirrel, correct classification was 95% and cross-validation 94% for all 10 animals. When only those individuals producing calls consisting of both elements were included (eight individuals), discriminant analysis led to 94% correct classification and cross-validation produced a classification success of 93%. These analyses demonstrate that the structure of alarm calls in these two closely related species is highly variable and that it has significant potential to encode information about caller identity.     

Serological classification of Bacillus sphaericus strains on the basis of toxicity to mosquito larvae

Summary A toxicity study of 54 Bacillus sphaericus strains isolated from vectors or breeding sites has led to a relatively homogeneous grouping of mosquito pathogenic strains into five H-serotypes among the nine serotypes determined. Each serotype seems to be characterized by a different level of toxicity and a classification of these five serotypes can be made on the basis of this toxicity. Within these serotypes, a scale of toxicity has been tentatively fixed and an arbitrary limit of toxicity suggested.     

EM Estimation of Diagnosis

The diagnosis/prognosis problem has already been introduced by the authors in previous papers as a classification problem for survival data. In this paper, the specific aspects of the estimation of the survival functions in diagnostic classes and the evaluation of the posterior probabilities of the diagnostic classes are addressed; a latent random variable Z is defined to denote the classification of censored and uncensored individuals, where early censored individuals cannot be immediately classified as Z is not observed. Parameter estimation of the mixture survival model thus derived is carried out using a proper version of the EM algorithm with given prior probabilities on Z and diagnostic/prognostic information provided by the observable covariates is also included into the model. Numerical examples using AIDS data and a simulation study are used to better outline the main features of the model and of the estimation methodology.     

Chemodiversity of the Essential Oil from Leaves of Abies nebrodensis (Lojac.) Mattei

Abies nebrodensis (Lojac .) Mattei (Pinaceae) is a species occurring in a very small population only in a restricted area of Sicily. Its taxonomic classification as different species has been object of discussion. In this work the chemical composition of the essential oil from the leaves is presented for the first time and compared to the essential oils from other euroasiatic species reported in literature. Peculiar characteristics of the essential oil of A. nebrodensis are highlighted.     

Evaluation of the Potential of five Housekeeping Genes for Identification of Quarantine Pseudomonas syringae

The Pseudomonas syringae species, containing approximately 60 pathovars, causes bacterial plant diseases on numerous crops and results in great economic losses. It is difficult to rapidly and accurately identify and detect P. syringae due to its complicated classification system. It has also been shown that housekeeping genes have great potential in phylogenetic analysis and classification of bacteria. In this study, phylogenetic analyses of five housekeeping genes, including 16S rRNA, rpoD, gapA, gltA and gyrB, were performed for 100 Pseudomonas strains. Our results showed that two housekeeping genes (rpoD and gapA) had the maximum ability in distinguishing the majority of Pseudomonas pathovars, whereas rpoD exhibited the best for precise and efficient detection of five P. syringae strains, which is of quarantine significance to China.