Phenotypic study by numerical taxonomy of strains belonging to the genus Aeromonas

AIMS: This study was undertaken to cluster and identify a large collection of Aeromonas strains. METHODS AND RESULTS: Numerical taxonomy was used to analyse phenotypic data obtained on 54 new isolates taken from water, fish, snails, sputum and 99 type and reference strains. Each strain was tested for 121 characters but only the data for 71 were analysed using the 'SSM' and 'SJ' coefficients, and the UPGMA clustering algorithm. At SJ values of > or = 81.6% the strains clustered into 22 phenons which were identified as Aer. jandaei, Aer. hydrophila, Aer. encheleia, Aer. veronii biogroup veronii, Aer. trota, Aer. caviae, Aer. eucrenophila, Aer. ichthiosmia, Aer. sobria, Aer. allosaccharophila, Aer. media, Aer. schubertii and Aer. salmonicida. The species Aer. veronii biogroup sobria was represented by several clusters which formed two phenotypic cores, the first related to reference strain CECT 4246 and the second related to CECT 4835. A good correlation was generally observed among this phenotypic clustering and previous genomic and phylogenetic data. In addition, three new phenotypic groups were found, which may represent new Aeromonas species. CONCLUSIONS: The phenetic approach was found to be a necessary tool to delimitate and identify the Aeromonas species. SIGNIFICANCE AND IMPACT OF THE STUDY: Valuable traits for identifying Aeromonas as well as the possible existence of new Aeromonas species or biotypes are indicated.     

中国沙拐枣属植物的数值分类研究

选择了中国19种沙拐枣属（CalligonumL.)植物,共测定及引用了35个形态分类指标,应用单因素方差分析（MANOVA）和主成分分析（PCA）,分别对形态因子进行了单元和多元分析。结果表明,所有的种间形态指标均差异显著,冠幅（BC）,木质枝枝节长度（LKWB）,果实直径（DF）,雄蕊长度（SL）,同化枝枝节长度（LKAS）和同化枝化枝角度（ARAS）指标在沙拐枣属植物的数值分类上,具有很强的差异性分析意义。依据平方欧氏距离,应用类平均法（UPGMA）将19种沙拐枣植物聚为5类,系统聚类结论与主成分分析的三维排序结果基本一致,与传统的形态分类结果有一定的差异。     

甘肃省白刺属植物的数量分类研究

根据白刺属植物的46个形态学、解剖学和细胞学性状指标,对甘肃省分布的5种白刺进行了数值分类研究。根据种问欧氏距离,应用类平均法(UPGMA)进行聚类,结果表明：泡果白刺(Nitraria sphaerocarpa)和小果白刺(N.sibirico)间具有较强的亲缘关系,与其它3种的亲缘关系较远;毛瓣白刺(N.praevisa)、唐古特白刺(N.tangutorum)和大果白刺(N.roborowskii)可以归为一类。其中的毛瓣白刺和唐古特白刺之间的亲缘关系最为相近。     

A specification of numerical taxonomy: Thermodynamical taxonomy

Thermodynamic taxonomy (ThT) is established from both a theoretical and pragmatical point of view. An application of thermodynamic taxonomy is given.     

Emergence of the genus Homo: From concept to taxonomy

The main goal of this paper is to present an overview of hypotheses concerning early Homo specimens and to discuss the definition of the genus Homo in the light of recent discoveries. For some authors, all the specimens attributed to early Homo belong to one unique species. For others, this group (Homo habilis sensu lato) is heterogeneous and could be splitted into two groups: H. habilis and Homo rudolfensis. Some researchers have also proposed to put the species habilis and rudolfensis into the genera Australopithecus or Kenyanthropus. Therefore, two scenarios concerning first humans seem to emerge. An emergence of the genus Homo, as early as 2.8 Ma, with Homo sp. specimens and the species H. habilis and H. rudolfensis, another at 1.9 Ma with Homo ergaster. According to the recent archaeological and paleoanthropological discoveries, these criteria often considered to be crucial for the definition of the genus Homo, as the cranial capacity, the humanlike manipulative abilities, the habitual erect posture and bipedal gait, the language ability and the capacity to make tools are now obsolete.     

Anthropometry and numerical taxonomy in clinical genetics: An example of applied biological anthropology

Biological anthropologists can contribute a unique perspective as well as technical expertise to the diagnosis and classification of genetic disorders. Anthropometry has been used with increasing frequency to characterize syndromes and to establish ranges of variation within syndromes. The specific anthropometric-radiologic technique of metacarpophalangeal pattern profile analysis has proven useful in discriminating individuals with the Prader-Labhart-Willi (PLW) syndrome from unaffected persons. Analysis of these data also indicate a negative correlation between age and Z-score transformations of individual hand bone lengths. These findings sound a cautionary note to clinical investigators who would use the Z-score transformation to standardize for age and sex. Problems encountered in the classification of genetic syndromes afford many parallels with those faced by anthropologists in the classification of living and fossil populations. The reliance on “key” traits and the necessity of focusing on pedigree analysis results in a deemphasis of the total range of variation and typological thinking. Application of numerical taxonomic techniques to the classification of the heterogeneous connective tissue disease osteogenesis imperfecta (OI) illustrates the heuristic value of this technique and points out the need to consider phenotypic overlap when defining typologies. Clinical genetics affords just one example of an area in medicine where the unique training and generalist perspective of the biological anthropologist is in demand. The decline in the availability of positions in the traditional academic habitat for biological anthropologists makes it imperative that graduate students be aware of alternatives and that they obtain training in the practical skills which such alternatives will demand.     

Taxonomy of mayapple rust: the genus Allodus resurrected

Mayapple rust is a common, disfiguring disease that is widespread in temperate eastern North America wherever the host, Podophyllum peltatum, occurs. Puccinia podophylli, the etiological agent of this rust, has been shown to be distantly related to both Puccinia and Uromyces as exemplified by their types. A systematic study was made to determine the generic classification of P. podophylli. Phylogenetic analyses of two rDNA loci from multiple specimens support the recognition of this taxon as a separate genus of Pucciniaceae. Based on historical literature and type material, P. podophylli was found to represent the type of the forgotten genus Allodus and it is correctly named Allodus podophylli. A neotype is designated for Puccinia podophylli Schwein. (≡ Allodus podophylli) and a lectotype is designated for Aecidium podophylli.     

CLASSIFY: A group teaching exercise in microbial identification and numerical taxonomy using a Commodore 64 microcomputer

An exercise designed to teach the basic principles of numerical taxonomy is described. The exercise utilizes a computer program, CLASSIFY, written in BASIC for the Commodore 64 microcomputer, which will accept student data obtained from the identification of bacteria, calculate the similarity coefficients, and perform Single Linkage Cluster Analysis. Bacterial identification can be achieved using live cultures and rapid identification kits, or, alternatively, via the bacterial culture simulation program, BUG SIMULATOR, which would be useful for data generation by students inexperienced in handling microbes (e.g. secondary school students).     

A genome sequence-based approach to taxonomy of the genus Nocardia

The genus Nocardia includes both pathogens and producers of useful secondary metabolites. Although 16S rRNA analysis is required to accurately discriminate among phylogenetic relationships of the Nocardia species, most branches of 16S rRNA-based phylogenetic trees are not reliable. In this study, we performed in silico analyses of the genome sequences of Nocardia species in order to understand their diversity and classification for their identification and applications. Draft genome sequences of 26 Nocardia strains were determined. Phylogenetic trees were prepared on the basis of multilocus sequence analysis of the concatenated sequences of 12 genes (atpD-dnaJ-groL1-groL2-gyrB-recA-rpoA-secA-secY-sodA-trpB-ychF) and a bidirectional best hit. To elucidate the evolutionary relationships of these genes, the genome-to-genome distance was investigated on the basis of the average nucleotide identity, DNA maximal unique matches index, and genome-to-genome distance calculator. The topologies of all phylogenetic trees were found to be essentially similar to each other. Furthermore, whole genome-derived and multiple gene-derived relationships were found to be suitable for extensive intra-genus assessment of the genus Nocardia.     

Physiological and biochemical contributions to the taxonomy of the genus Prototheca

16 strains of the genus Prototheca do not produce extracellular amylolytic enzymes. The base composition of their DNA shows rather continuous values from 62% to 78% GC (guanine + cytosine). Their assignment to four species and their possible relationship with Chlorella protothecoides are discussed.Abbreviations Used GC guanine + cytosine - SSC saline sodium citrate     

Physiological and biochemical contributions to the taxonomy of the genus Prototheca

Prototheca zopfii (12 strains) is able to use glucose, fructose, propanol, glycerol, and acetate as sources of carbon for growth. One of the strains is biochemically (utilization also of galactose and mannose), and two strains are morphologically slightly different.Two strains can be identified as P. wikerhamii. They exhibit good growth with glucose, fructose, galactose, trehalose, propanol, glycerol, acetate, and glutamate as sources of carbon. P. spec. 263-2 grows only with glucose and acatate. P. zopfii and P. wickerhamii are able to use urea, glycine, and glutamate as sources of nitrogen. P. spec. 263-2, on the other hand, cannot utilize these organic nitrogen compounds for growth.Four strains of Chlorella protothecoides are able to use glucose, fructose, galactose, and acetate as sources of carbon for growth in the dark. Three of them utilize also mannose, trehalose, and glutamate. Two strains can grow with glycerol, and one is able to use lactose. — Urea and glycine can serve as sources of nitrogen for the four strains of C. protothecoides. Glutamate supports growth of three strains, and one strain is able to use nicotinamide.     

Physiological and biochemical contributions to the taxonomy of the genus Chlorella

Starch hydrolysis, i.e., the production of extracellular amylolytic enzymes, was found to be a specific character for most species of the genus Chlorella. C. fusca var. vacuolata, C. spec. 211-30, and C. spec. 211-11r hydrolyse starch, whereas C. vulgaris, C. fusca var. rubescens, C. zofingiensis, C. fusca var. fusca, C. minutissima, C. homosphaera, C. kessleri, C. luteoviridis, and C. protothecoides are unable to hydrolyse starch. Only C. sorokiniana and C. saccharophila appear heterogenous; within C. sorokiniana, 7 strains hydrolyse starch and 9 do not; and within C. saccharophila, 6 strains exhibit amylolytic activity and 2 do not. — A key for the identification, according to 9 easily determined physiological and biochemical characters, of the Chlorella species is presented.