The phylogeny of halichondrid demosponges: past and present re-visited with DNA-barcoding data

Halichondrid sponges play a pivotal role in the classification of demosponges as changes in their classification has had direct consequences for the classification of Demospongiae. Historically, the systematics of halichondrids has been unstable. During the 1950s, the order was divided into two subclasses, which were based on empirical and assumed reproductive data. Subsequent morphological and biochemical analyses postulated the re-merging of halichondrid families, but recent molecular data indicate their polyphyly. Here we review the classification history of halichondrid taxa, compare it with the current and predominantly ribosomal molecular data, and support the new phylogenetic hypotheses with mitochondrial data from DNA barcoding.     

An evaluation of support for order-level monophyly and interrelationships within the class Demospongiae using partial data from the large subunit rDNA and cytochrome oxidase subunit I

Large subunit ribosomal DNA (LSU rDNA) sequence data from 120 taxa and cytochrome oxidase subunit 1(COI) sequence data from 27 taxa are analyzed separately and together to estimate the internal phylogeny of the class Demospongiae and to evaluate how consistent these data are with pre-existing hypotheses of relationship concerning order-level monophyly and relationships. The monophyly of Porifera is only slightly inconsistent with LSU data, which do not support the monophyly of the class Demospongiae regardless of the inclusion or exclusion of Homoscleromopha (this result is likely due to the placement of a single hexactinellid taxon within the Demospongiae), however, no LSU support is found for the monophyly of Silicea (Demospongiae+Hexactinellida) unless homoscleromorphs are excluded. Neither the subclasses Ceractinomorpha and Tetractinomorpha, nor the orders Halichondrida, Hadromerida, and Haplosclerida are supported as monophyletic under any data partition. The haplosclerid suborders Haplosclerina and Petrosina are supported as monophyletic to the exclusion of the suborder Spongillina, and the orders Dictyoceratida, Verongida, Poecilosclerida, Astrophorida, Spirophorida, Homosclerophorida, and Agelasida are largely reconstructed as monophyletic, with the exception of few anomalously placed taxa. Few inter-order relationships are strongly supported by any data partition, but there is moderate support for a verongid+chondrosid clade and a tetractinellid+halichondrid clade. Furthermore, LSU data strongly support the existence of two novel clades that do not correspond to the existing classification and that show no morphological uniformity. Finally, every data partition supports the monophyly of a clade that includes the order Agelasida, some members of the genus Axinella, and two taxa tentatively identified as belonging to the orders Hadromerida and Halichondrida.     

Indigenous demosponge spicules in a Late Devonian stromatoporoid basal skeleton from the Frasnian of Belgium

This paper records the first example of a demosponge spicule framework in a single specimen of a Devonian stromatoporoid from the Frasnian of southern Belgium. The small sample (2.5 × 2 cm) is a component in a brecciated carbonate from a carbonate mound in La Boverie Quarry 30 km east of Dinant. Because of the small size of the sample, generic identification is not confirmed, but the stromatoporoid basal skeleton is similar to the genus Stromatopora. The spicules are arranged in the calcified skeleton, but not in the gallery space, and are recrystallized as multi‐crystalline calcite. The spicules fall into two size ranges: 10–20 μm diameter and 500–2000 μm long for the large ones and between 5–15 μm diameter and 50–100 μm length for the small ones. In tangential section, the spicules are circular, they have a simple structure, and no axial canal has been preserved. The large spicules are always monaxons, straight or slightly curved styles or strongyles. The spicules most closely resemble halichondrid/axinellid demosponge spicules and are important rare evidence of the existence of spicules in Palaeozoic stromatoporoids, reinforcing the interpretation that stromatoporoids were sponges. The basal skeleton may have had an aragonitic spherulitic mineralogy. Furthermore, the spicules indicate that this stromatoporoid sample is a demosponge.     

梧桐科分类学研究评述

梧桐科(Sterculiaceae)是锦葵目中的一个多型科,主要分布于热带和亚热带地区,只有少数种可分布到温带地区。由于该科植物的形态特征较为多样化,至今对于它的范围和所包含的属种数目在各国学者间仍没有达成共识。该文从梧桐科的分类地位和系统关系、属的分类地位和亲缘关系以及分类学新特征在梧桐科分类中的应用3个方面入手,分析了梧桐科分类学研究的历史、现状和存在的问题,特别是把来自分子资料的研究结果与传统分类进行了比较分析,试图为梧桐科的分类学研究提供更多的帮助。     

Essai d'analyse biométrique du caryotype de l'Amphibien UrodèleSalamandra salamandra L.

The karyotype ofSalamandra salamandra (Urodela, Salamandridae) was analysed from squash preparations of adult testes. The 24 chromosomes, ranged in decreasing order, can be classified into three principal groups of 8 chromosomes each. Only the elements composing the 2nd group can be identified individually by means of their length or arm-ratio. In the 1st and the 3rd groups, possibilities of classification are still doubtful. In order not to introduce an artificial classification which might result from technical imperfections, a statistical test has been performed to ascertain the hypothesis that neighbouring pairs have equal mean lengths or equal mean arm-ratios. The statistical method proposed herein is related to analysis of variance, but differs from usual methods owing to the fact that the doubtfulness of the classification in each of the 35 studied figures is taken into account.      

芦苇生态型研究进展

芦苇生态幅极广,适生于多种生境类型。不同的环境选择压力如水深、盐度、养分、气候等交互影响致使芦苇个体及种群间发生不同程度的分化和变异,形成了形态、生理或遗传上互有差异、异地性的不同生态型。尽管基于芦苇表型变异以及遗传变异进行生态型划分的研究已开展很多,但针对芦苇生态型变异规律及其可能的形成机制的认知仍存在较多分歧。在总结近年来有关芦苇生态型研究文献的基础上,通过对影响芦苇生态型变异的主要因素——环境因素和遗传因素的分析,以期为芦苇生态型的划分及其可能的形成机制提供新的研究思路。(1)空间尺度的选择应成为研究者分析、划分芦苇生态型的首要定位。在较大的地理空间尺度上,高度异质性的生境导致某些性状的变异式样具有相对的不连续性,可作为不同芦苇生态型鉴别与描述的主要依据;(2)在合理的尺度定位、取样设计和统计分析的基础上开展的表型变异研究,及进一步基于种群水平的分子标记研究(分子指纹特征或特有等位基因),可为芦苇生态型的鉴定、划分提供更为可靠的参考数据,并且可以甄别生境差异(环境响应)和遗传变异对芦苇不同生态型分化的贡献;(3)应同时进行不同生态型的特定性状与功能(株高、茎粗、生物量、生理抗逆性、水体污染物净化能力等)的定位,推动优良基因型的选育与扩繁。     

PolyACO+: a multi-level polygon-based ant colony optimisation classifier

Ant colony optimisation (ACO) for classification has mostly been limited to rule-based approaches where artificial ants walk on datasets in order to extract rules from the trends in the data, and hybrid approaches which attempt to boost the performance of existing classifiers through guided feature reductions or parameter optimisations. A recent notable example that is distinct from the mainstream approaches is PolyACO, which is a proof-of-concept polygon-based classifier that resorts to ACO as a technique to create multi-edged polygons as class separators. Despite possessing some promise, PolyACO has some significant limitations, most notably, the fact of supporting classification of only two classes, including two features per class. This paper introduces PolyACO+, which is an extension of PolyACO in three significant ways: (1) PolyACO+ supports classifying multiple classes, (2) PolyACO+ supports polygons in multiple dimensions enabling classification with more than two features, and (3) PolyACO+ substantially reduces the training time compared to PolyACO by using the concept of multi-levelling. This paper empirically demonstrates that these updates improve the algorithm to such a degree that it becomes comparable to state-of-the-art techniques such as SVM, neural networks, and AntMiner+.     

A rapid classification protocol for the CATH Domain Database to support structural genomics

In order to support the structural genomic initiatives, both by rapidly classifying newly determined structures and by suggesting suitable targets for structure determination, we have recently developed several new protocols for classifying structures in the CATH domain database (http://www.biochem.ucl.ac.uk/bsm/cath). These aim to increase the speed of classification of new structures using fast algorithms for structure comparison (GRATH) and to improve the sensitivity in recognising distant structural relatives by incorporating sequence information from relatives in the genomes (DomainFinder). In order to ensure the integrity of the database given the expected increase in data, the CATH Protein Family Database (CATH-PFDB), which currently includes 25,320 structural domains and a further 160,000 sequence relatives has now been installed in a relational ORACLE database. This was essential for developing more rigorous validation procedures and for allowing efficient querying of the database, particularly for genome analysis. The associated Dictionary of Homologous Superfamilies [Bray,J.E., Todd,A.E., Pearl,F.M.G., Thornton,J.M. and Orengo,C.A. (2000) Protein Eng., 13, 153-165], which provides multiple structural alignments and functional information to assist in assigning new relatives, has also been expanded recently and now includes information for 903 homologous superfamilies. In order to improve coverage of known structures, preliminary classification levels are now provided for new structures at interim stages in the classification protocol. Since a large proportion of new structures can be rapidly classified using profile-based sequence analysis [e.g. PSI-BLAST: Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Nucleic Acids Res., 25, 3389-3402], this provides preliminary classification for easily recognisable homologues, which in the latest release of CATH (version 1.7) represented nearly three-quarters of the non-identical structures.     

Certain Investigations on Melanoma Detection Using Non-Subsampled Bendlet Transform with Different Classifiers

Skin is the largest organ and outer enclosure of the integumentary system that protects the human body from pathogens. Among various cancers in the world, skin cancer is one of the most commonly diagnosed cancer which can be either melanoma or non-melanoma. Melanoma cancers are very fatal compared with non-melanoma cancers but the chances of survival rate are high when diagnosed and treated earlier. The main aim of this work is to analyze and investigate the performance of Non-Subsampled Bendlet Transform (NSBT) on various classifiers for detecting melanoma from dermoscopic images. NSBT is a multiscale and multidirectional transform based on second order shearlet system which precisely classifies the curvature over other directional representation systems. Here two-phase classification is employed using k-Nearest Neighbour (kNN), Naive Bayes (NB), Decision Trees (DT) and Support Vector Machines (SVM). The first phase classification is used to classify the images of PH2 database into normal and abnormal images and the second phase classification classifies the abnormal images into benign and malignant. Experimental result shows the improvement in classification accuracy, sensitivity and specificity compared with the state of art methods.     

Reorganising the order Bacillales through phylogenomics

Bacterial classification at higher taxonomic ranks such as the order and family levels is currently reliant on phylogenetic analysis of 16S rRNA and the presence of shared phenotypic characteristics. However, these may not be reflective of the true genotypic and phenotypic relationships of taxa. This is evident in the order Bacillales, members of which are defined as aerobic, spore-forming and rod-shaped bacteria. However, some taxa are anaerobic, asporogenic and coccoid. 16S rRNA gene phylogeny is also unable to elucidate the taxonomic positions of several families incertae sedis within this order. Whole genome-based phylogenetic approaches may provide a more accurate means to resolve higher taxonomic levels. A suite of phylogenomic approaches were applied to re-evaluate the taxonomy of 80 representative taxa of eight families (and six family incertae sedis taxa) within the order Bacillales. This showed several anomalies in the current family and order level classifications including the existence of four Bacillaceae and two Paenibacillaceae “family” clades. Furthermore, the families Staphylococcaceae and Listeriaceae belong to the sister order Lactobacillales. Finally, we propose a consensus phylogenomic approach which may diminish algorithmic biases associated with single approaches and facilitate more accurate classification of a broad range of taxa at the higher taxonomic levels.     

Computer-assisted analysis of epiluminescence microscopy images of pigmented skin lesions.

BACKGROUND: Epiluminescence microscopy (ELM) is a noninvasive clinical tool recently developed for the diagnosis of pigmented skin lesions (PSLs), with the aim of improving melanoma screening strategies. However, the complexity of the ELM grading protocol means that considerable expertise is required for differential diagnosis. In this paper we propose a computer-based tool able to screen ELM images of PSLs in order to aid clinicians in the detection of lesion patterns useful for differential diagnosis. METHODS: The method proposed is based on the supervised classification of pixels of digitized ELM images, and leads to the construction of classes of pixels used for image segmentation. This process has two major phases, i.e., a learning phase, where several hundred pixels are used in order to train and validate a classification model, and an application step, which consists of a massive classification of billions of pixels (i.e., the full image) by means of the rules obtained in the first phase. RESULTS: Our results show that the proposed method is suitable for lesion-from-background extraction, for complete image segmentation into several typical diagnostic patterns, and for artifact rejection. Hence, our prototype has the potential to assist in distinguishing lesion patterns which are associated with diagnostic information such as diffuse pigmentation, dark globules (black dots and brown globules), and the gray-blue veil. CONCLUSIONS: The system proposed in this paper can be considered as a tool to assist in PSL diagnosis.     

对金缕梅科现代分类系统的评述

为了进一步研究金缕梅科的系统与进化,作者详细介绍了该科的分类历史及各个分类系统;根据现代植物系统学研究的原理和方法,着重对金缕梅科的５个现代主要分类系统,Ｈａｒｍｓ（１９３０）,张宏达（１９７３,１９７９）,Ｂｏｇｌｅｅｔａｌ．（１９８０）,Ｅｎｄｒｅｓｓ（１９８９）和李建华（Ｌｉ,１９９７）进行了详细的分析、比较和评述,在此基础上提出自己的观点,认为李建华的分类系统有一定合理性,但他对个别属的处理和族的划分仍有不妥之处     

Classification of cryo-electron sub-tomograms using constrained correlation

Cryo-electron tomography (CET) is currently the only three-dimensional imaging technique capable of visualizing macromolecules in their cellular context at close-to-native conditions with a resolution in the nanometer range. An important component for the analysis of the data is their classification, which should discriminate among various macromolecules, conformational changes and interaction partners. Missing structure factors, typically in a wedge-shaped region in Fourier space if single-axis tilting is performed, hamper classification of cryo-electron tomographic data. Here, we describe a classification method for three-dimensional (3D) sub-tomograms extracted from cryo-electron tomograms, which takes the missing wedge into account and provides reliable results. The similarity of the individually aligned sub-tomograms is scored by constrained correlation. Subsequently, they are clustered based on their pairwise correlation values. In order to demonstrate the feasibility of this approach, we apply the proposed method to simulated tomographic data of the chaperone thermosome in different conformations. By comparison of the principal components of the resulting matrix we show that the proposed metric is significantly less prone to the orientation of the missing wedge compared to the unconstrained correlation. Moreover, we apply our classification method to an experimental dataset of GroEL with and without GroES, where we achieve a distinct discrimination between the putative GroEL and GroEL/GroES complexes.     

基于脑电四阶累积量的运动意识分类研究

提出了基于四阶累积量为脑电特征的意识任务分类思想.对被测试者想象左右手运动时的脑电归一化四阶累积量（峭度）及其动态变化情况进行了研究.结果表明,归一化四阶累积量能较好地反映左右手运动想象的脑电特征变化.在此基础上,进行了基于脑电四阶累积量的左右手运动意识识别和分类研究,实验结果表明,正确识别率能达到87.5%.由于四阶累积量的计算比较简单,而且可在线计算,因此可以认为,基于脑电四阶累积量为特征的运动意识分类及其在脑机接口技术中的应用,具有较高的实际应用价值.     

Traditional knowledge among Zapotecs of Sierra Madre Del Sur, Oaxaca. Does it represent a base for plant resources management and conservation?

ABSTRACT: Traditional classification systems represent cognitive processes of human cultures in the world. It synthesizes specific conceptions of nature, as well as cumulative learning, beliefs and customs that are part of a particular human community or society. Traditional knowledge has been analyzed from different viewpoints, one of which corresponds to the analysis of ethnoclassifications. In this work, a brief analysis of the botanical traditional knowledge among Zapotecs of the municipality of San Agustin Loxicha, Oaxaca was conducted. The purposes of this study were: a) to analyze the traditional ecological knowledge of local plant resources through the folk classification of both landscapes and plants and b) to determine the role that this knowledge has played in plant resource management and conservation. The study was developed in five communities of San Agustin Loxicha. From field trips, plant specimens were collected and showed to local people in order to get the Spanish or Zapotec names; through interviews with local people, we obtained names and identified classification categories of plants, vegetation units, and soil types. We found a logic structure in Zapotec plant names, based on linguistic terms, as well as morphological and ecological caracteristics. We followed the classification principles proposed by Berlin [6] in order to build a hierarchical structure of life forms, names and other characteristics mentioned by people. We recorded 757 plant names. Most of them (67%) have an equivalent Zapotec name and the remaining 33% had mixed names with Zapotec and Spanish terms. Plants were categorized as native plants, plants introduced in pre-Hispanic times, or plants introduced later. All of them are grouped in a hierarchical classification, which include life form, generic, specific, and varietal categories. Monotypic and polytypic names are used to further classify plants. This holistic classification system plays an important role for local people in many aspects: it helps to organize and make sense of the diversity, to understand the interrelation among plants-soil-vegetation and to classify their physical space since they relate plants with a particular vegetation unit and a kind of soil. The locals also make a rational use of these elements, because they know which crops can grow in any vegetation unit, or which places are indicated to recollect plants. These aspects are interconnected and could be fundamental for a rational use and management of plant resources.     

Multivariate adaptive embedding (MAE) for the identification of bacterial pathogens in the field

In this work, we demonstrate a new classification machine based on multivariate adaptive embedding (MAE) that is capable of a robust identification of potential bacterial biological warfare agents (BWA). By employing Raman spectroscopy, this method proves to be reliable in application, easy to use and while retaining spectral quality, it is much faster than the often used support vector machines (SVM) and other supervised multivariate statistical classification machines. The multivariate adaptive embedding multi‐species classification ability was developed in order to serve as a real‐time detection method for biological threat detection and pathogen identification. A mean classification accuracy of 99.25±0.45% could be achieved with a representative set of biological warfare agents and simulant bacteria as a first approach for a user‐friendly and fieldable classification application for first responders and researchers.     

A framework infrageneric classification of Carex (Cyperaceae) and its organizing principles

Phylogenetic studies of Carex L. (Cyperaceae) have consistently demonstrated that most subgenera and sections are para- or polyphyletic. Yet, taxonomists continue to use subgenera and sections in Carex classification. Why? The Global Carex Group (GCG) here takes the position that the historical and continued use of subgenera and sections serves to (i) organize our understanding of lineages in Carex, (ii) create an identification mechanism to break the ~2000 species of Carex into manageable groups and stimulate its study, and (iii) provide a framework to recognize morphologically diagnosable lineages within Carex. Unfortunately, the current understanding of phylogenetic relationships in Carex is not yet sufficient for a global reclassification of the genus within a Linnean infrageneric (sectional) framework. Rather than leaving Carex classification in its current state, which is misleading and confusing, we here take the intermediate steps of implementing the recently revised subgeneric classification and using a combination of informally named clades and formally named sections to reflect the current state of our knowledge. This hybrid classification framework is presented in an order corresponding to a linear arrangement of the clades on a ladderized phylogeny, largely based on the recent phylogenies published by the GCG. It organizes Carex into six subgenera, which are, in turn, subdivided into 62 formally named Linnean sections plus 49 informal groups. This framework will serve as a roadmap for research on Carex phylogeny, enabling further development of a complete reclassification by presenting relevant morphological and geographical information on clades where possible and standardizing the use of formal sectional names.     

基于无人机多源遥感数据的亚热带森林树种分类

树种多样性是生态学研究的重要内容,树木的种类和空间分布信息可有效服务于可持续森林管理。但在复杂林分条件下,获取高精度分类结果的难度大。而无人机遥感可获取局域超精细数据,为树种分类精度的提高提供了可能。基于可见光、高光谱、激光雷达等多源无人机遥感数据,探究其在亚热带林分条件下的树种分类潜力。研究发现:(1)随机森林分类器总体精度和各树种的F1分数最高,适合亚热带多树种的分类制图,其区分13种类别(8乔木,4草本)的总体精度为95.63%,Kappa系数为0.948;(2)多源数据的使用可以显著提高分类精度,全特征模型精度最高,且高光谱和激光雷达数据显著影响全特征模型分类精度,可见光纹理数据作用较小;(3)分类特征重要性从大到小排序为结构信息,植被指数,纹理信息,最小噪声变换分量。     

A revised classification of the Apocynaceae s.l.

The Asclepiadaceae, as traditionally defined, have repeatedly been shown to be an apomorphic derivative of the Apocynaceae. It has often been recommended that the Asclepiadaceae be subsumed within the Apocynaceae in order to make the latter monophyletic. To date, however, no comprehensive, unified classification has been established. Here we provide a unified classification for the Apocynaceae, which consists of 424 genera distributed among five subfamilies: Rauvolfioideae, Apocynoideae, Periplocoideae, Secamonoideae, and Asclepiadoideae. Keys to the subfamilies and tribes are provided, with lists of genera that (as far as we have been able to ascertain) are recognized in each tribe.     

Hyperspectral imaging of mucosal surfaces in patients

The aim of this study was to proof applicability of hyperspectral imaging for the analysis and classification of human mucosal surfaces in vivo. The larynx as a prototypical anatomically well‐defined surgical test area was analyzed by microlaryngoscopy with a polychromatic lightsource and a synchronous triggered monochromatic CCD‐camera. Image stacks (5 benign, 7 malignant tumors) were analyzed by established software (principal component analysis PCA, hyperspectral classification, spectral profiles). Hyperspectral image datacubes were analyzed and classified by conventional software. In PCA, images at 590–680 nm loaded most onto the first PC which typically contained 95% of the total information. Hyperspectral classification clustered the data highlighting altered mucosa. The spectral profiles clearly differed between the different groups. Hyperspectral imaging can be applied to mucosal surfaces. This approach opens the way to analyze spectral characteristics of histologically different lesions in order to build up a spectral library and to allow non‐touch optical biopsy. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)