Phenetic analysis of anemone coronaria (ranunculaceae) and related species

This study clarifies the taxonomic status of Anemone coronaria and segregates the species and A. coronaria infraspecific variants using morphological and morphometric analyses. Principal component analysis of the coronaria group was performed on 25 quantitative and qualitative characters, and morphometric analysis of the A. coronaria infraspecific variants was performed on 21 quantitative and qualitative characters. The results showed that the A. coronaria group clustered into four major groups: A. coronaria L., A. biflora DC, A. bucharica (Regel) Juz.ex Komarov, and a final group including A. eranthioides Regel and A. tschernjaewii Regel. The data on the A. coronaria infraspecific variants clustered into six groups: A. coronaria L. var. coronaria L., var. cyanea Ard., var. albiflora Rouy & Fouc., var. parviflora Regel, var. ventreana Ard., and var. rissoana Ard. © 2007 The Linnean Society of London

Morphology of scale lepidonts in the genusAphanius(Teleostei, Cyprinodontidae) using SEM

The microstructure of the anterior region of the scales in several species of the genus Aphanius was studied by SEM with the aim of determining whether scale morphology could be used to discriminate between the species of this genus. The characters examined concern the morphology of lepidonts, or “scale‐teeth”, their distribution and mode of implantation on the circuli. These characters were also subjected to UPGMA cluster analysis. Results from phenetic analysis of scale‐teeth characters agree overall with those of previously published morphological and biogeographical studies and in part with molecular analysis of the phylogenetic relationships between species of Aphanius. An affinity between A. danfordii and A. mento (found previously in studies based on osteological observations) was seen. The separation of A. apodus from the other species of the fasciatus group, which had also been noticed from molecular observations, was also observed, as well as the affinity of A. ginaonis with the group of A. dispar+A. sirhani. This study demonstrates that scale morphology can provide useful information on the relationships among species of the genus Aphanius encouraging the use of scale characters, combined with other traits, in phylogenetic analyses.

杉科植物的系统发育、 分类和地理分布

本文对杉科植物的分类系统作了回顾。以形态学为依据，参考其他学科的研究成果，用分支分析和表征分析两种方法探讨了杉科植物的系统演化关系．提出了新的分类系统。对杉科植物的系统分类作了修订．通过对各属现代分布和地史分布的研究，结合古地理和古气候资料，讨论了杉科植物的分布中心、起源时间、起源地、散布途径及现代分布格局的成因．主要结论如下： 1．属间关系：柳杉属是现存杉科植物中最原始的类群．水松属和落羽杉属关系密切，二者与柳杉属近缘．巨杉属和北美红杉属关系密切，是中级进化水平的类群．水杉属的系统位置比较孤立，与巨杉属和北美红杉属的关缘关系相对较近．杉木属、密叶杉属和台湾杉属关系密切，是杉科植物中的高级进化类群，其中台湾杉属最为进化． 2．系统排列：支持金松科的成立．将杉科分成5族，即柳杉族（仅含柳杉属）、落羽杉族（含水松属、落羽杉属）、北美红杉族（含巨杉属、北美红杉属）、水杉族（仅含水杉属）和杉木族（含杉木属、密叶杉属及台湾杉属）． 3．分类：经修订，杉科植物共9属12种4变种．将德昌杉木、米德杉木和厚皮杉木归并，作为杉木的变种，支持柳杉作为日本柳杉的变种、台湾杉木作为杉木的变种、秃杉和台湾杉归并的观点。 4．地理分布：我国长江、秦岭以南至华南一带是杉科的现代分布中心，我国华北北部及东北、朝鲜、日本和前苏联西伯利亚东南部等地可能为起源中心和早期分化中心，起源时间可追溯至早侏罗纪或晚三叠纪．杉科的现存各属均为古老的孑遗类群．

花楸属的系统学初步研究

花楸属隶属于蔷薇科苹果亚科，全世界约有100种左右，主要分布在北半球的亚洲、欧洲和北美洲。广义的花楸属包括下述六个亚属，即Subg. Aria, Subg. Chamaemespilus, Subg. Micromeles, Subg. Torminalis, Subg. Cormus, Subg. Sorbus。由于缺乏野外工作和标本不够丰富等原因，部分亚属的分类处理尚不能令人满意。同时，该属的范围及其属下部分类群的系统位置存在一定的争议。本文对广义花楸属的属下类群进行了研究，通过分支分析和表征分析以及分子系统学两方面的研究，对该属的属下类群的系统位置进行了探讨。 1、分支分析和表征分析 选取了广义花楸属（Sorbus L.）属下6个亚属的34种植物作为研究对象，并以Pyrus, Crataegus, Photinia, Malus和Cotoneaster作为外类群来研究花楸属属下类群的分类关系，对该属典型的30个形态性状数据进行编码，进行了分支分析和表征分析。结果表明，广义花楸属是一个非单系类群，外类群完全镶嵌于其中。广义花楸属属下的6个亚属各自也不能形成单系，只有花楸亚属（Subg. Sorbus）形成不严格的单系。因此，我们初步认为，花楸属应该仅包含复叶类群（Subg. Sorbus），或者还会有Subg. Cormus。由于其余的4个亚属尚不能形成规则的单系或聚类，因此进一步的研究宜采用分类群的更多性状或运用分子系统学的途径。 2、分子系统学 通过对花楸属23个种类的两个DNA片段：核nrDNA的ITS和叶绿体cpDNA的trnL-F进行简约分析，构建了广义花楸属5个亚属及其与近缘属的系统发育树。结果显示，由于外类群大多镶嵌于广义花楸属中，故花楸属不能形成一个单系。其中单叶类群Subg. Aria聚类较明显，并且得到了很高的支持率，而且该亚属与外类群Crataegus和Cotoneaster的关系要比它与其它亚属的关系更近，至于其是否是独立的属还有待进一步的研究。该属中的复叶类群Subg. Sorbus在图中并不能形成严格的单系，其分类位置值得重新考虑。

Testing the boundaries of closely related daisy taxa using metabolomic profiling

Advances in high-throughput, comprehensive small molecule analytical techniques have seen the development of the field of metabolomics. The coupling of mass spectrometry with high-resolution chromatography provides extensive chemical profiles from complex biological extracts. These profiles include thousands of compounds linked to gene expression, and can be used as taxonomic characters. Studies have shown metabolite profiles to be taxon specific in a range of organisms, but few have investigated taxonomically problematic plant taxa. This study used a phenetic analysis of metabolite profiles to test taxonomic boundaries in the Olearia phlogopappa (Asteraceae) complex as delimited by morphological data. Metabolite profiles were generated from both field- and shade house-grown material, using liquid chromatography-mass spectrometry (LC-MS). Aligned profiles of 51 samples from 12 taxa gave a final dataset of over 10,000 features. Multivariate analyses of field and shade house material gave congruent results, both confirming the distinctiveness of the morphologically defined species and subspecies in this complex. Metabolomics has great potential in alpha taxonomy, especially for testing the boundaries of closely related taxa where DNA sequence data has been uninformative.

Molecular and Pathogenic Diversity Among Brazilian Isolates of Xanthomonas albilineans Assessed with SSR Marker Loci

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Functional characterization of sugarcane mustang domesticated transposases and comparative diversity in sugarcane, rice, maize and sorghum

Transposable elements (TEs) account for a large portion of plant genomes, particularly in grasses, in which they correspond to 50%-80% of the genomic content. TEs have recently been shown to be a source of new genes and new regulatory networks. The most striking contribution of TEs is referred as "molecular domestication", by which the element coding sequence loses its movement capacity and acquires cellular function. Recently, domesticated transposases known as mustang and derived from the Mutator element have been described in sugarcane. In order to improve our understanding of the function of these proteins, we identified mustang genes from Sorghum bicolor and Zea mays and performed a phenetic analysis to assess the diversity and evolutionary history of this gene family. This analysis identified orthologous groups and showed that mustang genes are highly conserved in grass genomes. We also explored the transcriptional activity of sugarcane mustang genes in heterologous and homologous systems. These genes were found to be ubiquitously transcribed, with shoot apical meristem having the highest expression levels, and were downregulated by phytohormones. Together, these findings suggest the possible involvement of mustang proteins in the maintenance of hormonal homeostasis.

Leaf cuticular alkanes of Solanum subg. Leptostemonum Dunal (Bitter) of some northeast Brazilian species: Composition and taxonomic significance

Solanum subgenus Leptostemonum (Dunal) Bitter comprises approximately 450 species, of which 110, including 58 endemics, occur in Brazil, which is recognized as one of the centers of diversity of the group. Due the great morphological plasticity and its large number of species, several taxonomic treatments have been proposed for the genus Solanum, but its infrageneric classification is problematic. The aim of this study was to analyze the alkane composition of the leaf epicuticular waxes of nine species of the subgenus Leptostemonum to evaluate the chemotaxonomic potential of the alkanes. As results, were identified in nine species thirty-one alkanes, including iso- and anteiso-alkanes. The major constituent of wax in most species was tritriacontane. Hentriacontane was the main constituent of Solanum paraibanum and Solanum torvum, and penta-triacontane was predominant in different populations of Solanum stramonifolium. The phenetic analysis of nine species based on the distribution profile of alkanes (Euclidean distance and UPGMA method) show three clusters with distinct main homolog. The profiles of alkanes showed some qualitative taxonomic value for species analyzed, although, a larger number of representative samples of this subgenus must be investigated. (C) 2012 Elsevier Ltd. All rights reserved.

Computerized key to the genus Bursaphelenchus Fuchs, analysis of species clusters based on morphology, using information of insect vectors and associated plants, with a revision of the genus.

The genus Bursaphelenchus includes B. xylophilus (Steiner et Buhrer, 1934) Nickle, 1981, which is of world economic and quarantine importance. Distinction among several species of the pinewood nematodes species complex (PWNSC) is often difficult. Besides standard morphology, morphometrics and molecular biology, new tools are welcome to better understand this group. The computerized (or e-) key of this genus, presented in this communication, includes 74 species (complete list of valid species of the world fauna) and 35 characters, that were used by the taxonomic experts of this group, in the original descriptions. Morphology of sex organs (male spicules and female vulval region) was digitized and classified to distinguish alternative types. Several qualitative characters with overlapping character states (expressions) were transformed into the morphometric indices with the discontinuous ranges (characters of ratios of the spicule dimensions). Characters and their states (expressions) were illustrated in detail and supplied by brief user-friendly comments. E-key was created in the BIKEY identification system (Dianov & Lobanov, 1996-2004). The system has built-algorithm ranging characters depending on their diagnostic values at each step of identification. Matrix of species and the character states (structural part of the e-key database) may be easily transformed using statistical packages into the dendrograms of general phenetic similarities (UPGMA, standard distance: mean character difference). It may be useful in the detailed analysis of taxonomy and evolution of the genus and in its splitting to the species groups based on morphology. The verification of the dendrogram using the information on the species links with insect vectors and their associated plants, provided an opportunity to recognize the five clusters (xylophilus, hunti, eremus sensu stricto, tusciae and piniperdae sensu stricto), which seem to be the natural species groups. The hypothesis about the origin and the first stages of the genus evolution is proposed. A general review of the genus Bursaphelenchus is presented.

Analysis of genetic diversity in Portuguese Ceratonia siliqua L. cultivars using RAPD and AFLP markers

Although carob (Ceratonia siliqua L.) is of great economic importance little is still known about the pattern of genetic variation within this species. Morphological characteristics based on 31 fruit and seeds of continuous characters determinant for agro-industrial uses, were compared with RAPD and AFLP markers for assessing genetic distances in 68 accessions of carob trees, from different cultivars, varieties and eco-geographic regions of Algarve. Eighteen selected RAPD primers applied to the 68 accessions produced a total of 235 fragments ranging from 200 to 2000 bp, of which 93 (40%) were polymorphic. Four AFLP selective primer combinations generated a total of 346 amplification fragments of which 110 were polymorphic. The average level of polymorphism based on four primer combinations was 31.8%. The phenetic trees based on RAPD and AFLP analyses gave high co-phenetic correlation values, and were found to be consistent in general with the analysis of morphological data, carried out on the same accessions. A number of RAPD and AFLP markers were found to be diagnostic for ‘Canela’ cultivar and 13 wild ungrafted trees.

Phylogenetic relationships of Malassezia species based on multilocus sequence analysis

Members of the genus Malassezia are lipophilic basidiomycetous yeasts, which are part of the normal cutaneous microbiota of humans and other warm-blooded animals. Currently, this genus consists of 14 species that have been characterized by phenetic and molecular methods. Although several molecular methods have been used to identify and/or differentiate Malassezia species, the sequencing of the rRNA genes and the chitin synthase-2 gene (CHS2) are the most widely employed. There is little information about the beta-tubulin gene in the genus Malassezia, a gene has been used for the analysis of complex species groups. The aim of the present study was to sequence a fragment of the beta-tubulin gene of Malassezia species and analyze their phylogenetic relationship using a multilocus sequence approach based on two rRNA genes (ITS including 5.8S rRNA and D1/D2 region of 26S rRNA) together with two protein encoding genes (CHS2 and beta-tubulin). The phylogenetic study of the partial beta-tubulin gene sequences indicated that this molecular marker can be used to assess diversity and identify new species. The multilocus sequence analysis of the four loci provides robust support to delineate species at the terminal nodes and could help to estimate divergence times for the origin and diversification of Malassezia species.

Seed image analysis and taxonomy of Diplotaxis DC. (Brassicaceae, Brassiceae)

The genus Diplotaxis, comprising 32 or 34 species, plus several additional infraspecific taxa, displays a considerable degree of heterogeneity in the morphology, molecular markers, chromosome numbers and geographical amplitude of the species. The taxonomic relationships within the genus Diplotaxis were investigated by phenetic characterisation of germplasm belonging to 27 taxa of the genus, because there is an increasing interest in Diplotaxis, since some of its species (D. tenuifolia, D. muralis) are gathered or cultivated for human consumption, whereas others are frequent arable weeds (D. erucoides) in many European vineyards. Using a computer-aided vision system, 33 morpho-colorimetric features of seeds were electronically measured. The data were used to implement a statistical classifier, which is able to discriminate the taxa within the genus Diplotaxis, in order to compare the resulting species grouping with the current infrageneric systematics of this genus. Despite the high heterogeneity of the samples, due to the great intra-population variability, the stepwise Linear Discriminant Analysis method, applied to distinguish the groups, was able to reach over 80% correct identification. The results obtained allowed us to confirm the current taxonomic position of most taxa and suggested the taxonomic position of others for reconsideration.

Raman microscopy of formamide-intercalated kaolinites treated by controlled-rate thermal analysis technology

Raman spectroscopy of formamide-intercalated kaolinites treated using controlled-rate thermal analysis technology (CRTA), allowing the separation of adsorbed formamide from intercalated formamide in formamide-intercalated kaolinites, is reported. The Raman spectra of the CRTA-treated formamide-intercalated kaolinites are significantly different from those of the intercalated kaolinites, which display a combination of both intercalated and adsorbed formamide. An intense band is observed at 3629 cm-1, attributed to the inner surface hydroxyls hydrogen bonded to the formamide. Broad bands are observed at 3600 and 3639 cm-1, assigned to the inner surface hydroxyls, which are hydrogen bonded to the adsorbed water molecules. The hydroxyl-stretching band of the inner hydroxyl is observed at 3621 cm-1 in the Raman spectra of the CRTA-treated formamide-intercalated kaolinites. The results of thermal analysis show that the amount of intercalated formamide between the kaolinite layers is independent of the presence of water. Significant differences are observed in the CO stretching region between the adsorbed and intercalated formamide.

Detailed analysis of a conservative difference approximation for the time fractional diffusion equation

Diffusion equations that use time fractional derivatives are attractive because they describe a wealth of problems involving non-Markovian Random walks. The time fractional diffusion equation (TFDE) is obtained from the standard diffusion equation by replacing the first-order time derivative with a fractional derivative of order α ∈ (0, 1). Developing numerical methods for solving fractional partial differential equations is a new research field and the theoretical analysis of the numerical methods associated with them is not fully developed. In this paper an explicit conservative difference approximation (ECDA) for TFDE is proposed. We give a detailed analysis for this ECDA and generate discrete models of random walk suitable for simulating random variables whose spatial probability density evolves in time according to this fractional diffusion equation. The stability and convergence of the ECDA for TFDE in a bounded domain are discussed. Finally, some numerical examples are presented to show the application of the present technique.