A phylogenetic analysis of Doronicum (Asteraceae, Senecioneae) based on morphological, nuclear ribosomal (ITS), and chloroplast (trnL-F) evidence.

A phylogenetic analysis of the Old World genus Doronicum (26 species, 4 subspecies) based on sequence data of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA, the chloroplast spacer trnL-F, and morphology is presented. Congruence among the three data sets was explored by the computing of several indices, all of which suggest homogeneity between only the two molecular matrices. We argue that the morphological data set contains poor phylogenetic signal and advocate simultaneous analysis of the three data sets (total evidence approach) so that morphological characters are tested for homology by congruence with molecular data. The resulting phylogenetic hypothesis allows several well-supported conclusions including the placement of a Corsican endemic (D. corsicum), sister to the remainder of the genus, and the inference that an early southern European or Mediterranean diversification took place in the genus. Shifts in morphological characters (e.g., homocarpy to heterocarpy) are confirmed to have evolved several times. Results from comparative studies of sequence data of the chloroplast gene ndhF support inclusion of Doronicum in tribe Senecioneae.     

Segregation of histone fractions from purified rat pancreas nuclei by isoelectric focusing.

The present report describes the purification of nuclei from rat pancreas and the use of isoelectric focusing for the segregation of histone fractions, a heterogeneous mixture with respect to charge. This procedure employs gels of 5% polyacrylamide as support matrices, in 6.25 M urea, and spans a pH range of 7.5-10.8. It was, therefore, found adequate for study of the microheterogeneity of histones. The banding pattern of histone fractions in pancreas development using electrofocusing is presented.     

Systematics, molecular genetics and historical zoogeography of the viviparous freshwater gastropod Pseudopotamis (Cerithioidea, Pachychilidae): a relic on the Torres Strait Islands, Australia

Freshwater snails of the genus Pseudopotamis Martens, 1894 exemplify one of the most enigmatic distributional patterns among limnic organisms in Australasia. These viviparous cerithioidean gastropods are endemic to the Torres Strait Islands, located on the Sahul shelf corridor between Australia and New Guinea. The occurrence of the two constituent species is highly restricted: P. supralirata (Smith, 1887) on Prince of Wales Island, and P. semoni Martens, 1894 on Hammond Island. Long recognized erroneously as members of the heterogeneous, polyphyletic and widespread Thiaridae, morphological and molecular data presented here reveal that the taxon has to be placed within Pachychilidae, a family otherwise absent from Australia. Comparison with other South East Asian pachychilids, in particular Brotia H. Adams, 1866, Tylomelania Sarasin & Sarasin, 1897, and Jagora Köhler & Glaubrecht, 2003 suggests that Pseudopotamis is most closely related to taxa endemic to Sulawesi (Celebes), thus occurring disjunctly about 2000 km to the west of the Torres Strait. It is only with the Sulawesi pachychilids that Pseudopotamis shares its peculiar uterine brood pouch. Consequently, all pachychilid taxa east of the much-debated Wallace's line (east of Bali, Borneo and the Philippines) possess this uterine incubatory structure. In this paper the historical background of the discovery, the taxonomic history, and an evaluation of the systematic position of Pseudopotamis is provided, including molecular genetic data (genes of cytochrome c oxidase subunit I and 16S ribosomal DNA). Finally, based on the phylogenetic assignment and the recent distribution, implications for a historical biogeography are discussed utilizing a recently developed model for the palaeogeography in Australasia. According to these available data, we favour early vicariant event(s) over recent dispersal.     

On treatment of tuberculosis in heterogeneous populations

Global eradication of tuberculosis (TB) is an international agenda. Thus understanding effects of treatment of TB in different settings is crucial. In previous work, we introduced the framework for a mathematical model of epidemic TB in demographically distinct, heterogeneous populations. Simulations showed the importance of genetic susceptibility in determining endemic prevalence levels. In the work presented here, we include treatment and investigate different strategies for treatment of latent and active TB disease in heterogeneous populations. We illustrate how the presence of a genetically susceptible subpopulation dramatically alters effects of treatment in the same way a core population does in the setting of sexually transmitted diseases. In addition, we evaluate treatment strategies that focus specifically on this subpopulation, and our results indicate that genetically susceptible subpopulations should be accounted for when designing treatment strategies to achieve the greatest reduction in disease prevalence.     

Prediction of biogas potentials using quick laboratory analyses: Upgrading previous models for application to heterogeneous organic matrices

This study presents an upgrading of the mathematical models to predict anaerobic biogasification potential (ABP) through quick laboratory analyses that have been presented in an earlier study. The aim is to widen the applicability of the models to heterogeneous organic substrates and to improve their reliability through a deeper statistical approach.Three multiple-step linear regressions were obtained using biomass oxygen demand in 20 h (OD₂₀) plus the volatile solids content (VS) of 23 new samples of heterogeneous organic matrices, of 46 samples presented in the earlier work and of the data set comprising all the 69 samples. The two variables chosen were found to be suitable for very heterogeneous materials. To judge the prediction quality, a validation procedure was performed with 12 new samples using model efficiency indexes. The proposed model had good prediction ability for a large variety of organic substrates, and allows the calculation of the ABP value within only 2-day’s laboratory work instead of the 60–90 days required to obtain ABP by anaerobic test.     

Phytogeographic analysis of taxa endemic to the Yucatán Peninsula using geographic information systems, the domain heuristic method and parsimony analysis of endemicity

Abstract. The distribution of plant taxa endemic to the Yucatán Peninsula was studied using Parsimony Analysis of Endemicity (PAE). The known distribution of 162 endemic plant taxa was plotted and the DOMAIN method together with environmental data were used to model the potential distribution for each taxon. The Peninsula was divided into a grid of quarter‐degree cells for the purpose of identifying distribution patterns. A total of 294 cells were analysed using known collection records and potential distribution of endemic taxa data. Two data matrices were constructed, a matrix of known distribution and a matrix of both the known and potential distribution. The two matrices were included in the PAE to identify areas of endemism. The areas determined with the known distribution were restricted and almost half of them remained unresolved, whereas with the potential distribution, approximately 90% of the cells were assigned to any one of the endemicity areas. Four endemism areas were identified: the Yucatán dry zone, Yucatán, El Petén and Belize. The areas of Yucatán and El Petén could be explained by current and Pleistocene climatic conditions and their congruence with other biological groups. Analysis of the potential distribution identified areas with patterns that share current environmental characteristics and a palaeoclimate history. Potential distribution modelling can eliminate uncertainties in biogeographical analysis caused by lack of data distribution and sample variation and produce information about the relationships between areas and taxa as well as the environmental affinities of taxa.     

Discrete molecular weight components of the organic matrices of mollusc shells

Discrete molecular weight components form part of the soluble fraction of the organic matrices of mollusc shells. The number of these components, their relative migration distances and concentrations vary greatly in the specimens analysed. The discrete molecular weight constituents from the organic matrices of species of the same genus are most similar. The presence of these components shows that organic matrices are heterogeneous and presumably capable of performing diverse functions.     

Estrogenic, anti-estrogenic and cytotoxic effects elicited by water from the type localities of the endangered goodeid fish Girardinichthys viviparus

Girardinichthys viviparus is a Mexican endangered endemic fish species living only in Lake Texcoco (LTX), one of two extant type localities for this species. The other type locality is Lake Zumpango (LZ). LTX and LZ are fed by wastewater treated at secondary level that contains several endocrine disrupting chemicals. Our goal was to assess the estrogenic and anti-estrogenic effects elicited in G. viviparus by water from the two type localities and by these same matrices enriched with PCBs in order to understand potential damage due to increased xenobiotic levels. Estrogenic and anti-estrogenic effects were evaluated in vitro by E-screen assay in MCF-7 cells and cytotoxicity by MTT assay. PCBs were quantified in type localities. In vivo vitellogenin (VTG) induction was determined by a hybrid ELISA in adult laboratory-born fish exposed during 1, 2, 4, 8 and 16 days to LTX or LZ water in static exposure systems, and by the same matrices enriched with PCBs. We found PCBs only in LTX, but the water from both type localities elicit estrogenic and anti-estrogenic effects in vitro. Cytotoxicity was not observed in MCF-7 cells exposed to LTX or LZ water. VTG induction was higher with LTX water than with LZ water; also the response of males was greater than in females. In the PCB-enriched matrices, VTG induction in both sexes exposed to LTX water was reduced compared to un-enriched matrices. Thus, the sublethal increases in PCB levels may be hazardous to both sexes since they are linked probably to hepatotoxicity.     

Analysis of differences in amino acid substitution patterns, using multilevel G-tests

In this paper, a new algorithm is presented, which makes possible multilevel comparison of BLOSUM protein substitution matrices based on data from different groups of organisms. As an example, a comparison between substitution matrices based on data from two groups of bacterial genomes with different GC content is presented. Our approach includes evaluating the number of amino acid pairs in BLOCKS databases created separately for the two groups of bacteria using protein sequences deposited in the COG database. Differences of distributions of amino acid pair counts are tested using the chi-squared based G-test. Different analysis levels make it possible to distinguish different patterns of amino acid substitution. Application of the algorithm reveals statistically significant differences in amino acid substitution patterns between AT-rich and GC-rich groups of bacterial organisms. The differences are particularly visible in the overall substitution pattern, amino acid conservation pattern and in comparison of substitution patterns for single amino acids. The algorithm presented in this paper can be considered a novel method for multi-level comparison of amino acid substitution patterns. The presented approach is not limited to bacterial organisms and BLOSUM substitution matrices. Statistically significant differences between substitution patterns in the two groups of bacterial organisms with respect to amino acid conservation pattern can be the evidence of different rate of evolutionary change between AT-rich and GC-rich bacterial organisms.     

Correspondence Analysis of species by environmental variable matrices

Abstract. Correspondence Analysis of species by environmental variables matrices is a relatively simple method for handling matrices which include many species and variables. If columns represent species and rows represent the states in which the environmental variables have been divided, each element of the matrix shows the number of releves in which the simultaneous occurrence of that species and that environmental variable state have been recorded. In this paper the use of the method for presence-absence data is considered. The method is appropriate for studies whose main purpose is to look for broad correlations between groups of environmental variables and groups of species. It is particularly useful for handling heterogeneous data sets including rare species and species-poor releves, a situation in which Correspondence Analysis and Canonical Correspondence Analysis are frequently complicated by the production of axes explaining the relationship between rare species and species-poor releves. Examples are presented with artificial data as well as with real data collected in the Mexican portion of the Chihuahuan Desert (Bolsón de Mapimi). It is shown for the Mapimi data that the method is robust to the partition of variables into different numbers of states.     

Analysis and simulation of a stochastic, discrete-individual model of STD transmission with partnership concurrency

Deterministic differential equation models indicate that partnership concurrency and non-homogeneous mixing patterns play an important role in the spread of sexually transmitted infections. Stochastic discrete-individual simulation studies arrive at similar conclusions, but from a very different modeling perspective. This paper presents a stochastic discrete-individual infection model that helps to unify these two approaches to infection modeling. The model allows for both partnership concurrency, as well as the infection, recovery, and reinfection of an individual from repeated contact with a partner, as occurs with many mucosal infections. The simplest form of the model is a network-valued Markov chain, where the network's nodes are individuals and arcs represent partnerships. Connections between the differential equation and discrete-individual approaches are constructed with large-population limits that approximate endemic levels and equilibrium probability distributions that describe partnership concurrency. A more general form of the discrete-individual model that allows for semi-Markovian dynamics and heterogeneous contact patterns is implemented in simulation software. Analytical and simulation results indicate that the basic reproduction number R(0) increases when reinfection is possible, and the epidemic rate of rise and endemic levels are not related by 1-1/R(0), when partnerships are not point-time processes.     

Subsampling Herbarium Collections to Assess Geographic Diversity Gradients: A Case Study with Endemic Orchidaceae and Rubiaceae in Cameroon

We compiled herbarium specimen data to provide an improved characterization of geographic patterns of diversity using indices of species diversity and floristic similarity based on rarefaction principles. A dataset of 3650 georeferenced plant specimens belonging to Orchidaceae and Rubiaceae endemic to Atlantic Central Africa was assembled to assess species composition per half‐degree or one‐degree grid cells. Local diversity was measured by the expected number of species (S_k) per grid cell found in subsamples of increasing size and compared with raw species richness (S_R). A nearly unbiased estimator of the effective number of species per grid cell was also used, allowing quantification of ratios of ‘true diversity’ between grid cells. Species turnover was measured using a presence/absence‐based similarity index (Sørensen) and an abundance‐based index that corrects for sampling bias (NNESS). Our results confirm that the coastal region of Cameroon is more diverse in endemic species than those more inland. The southern part of this coastal forest is, however, as diverse as the more intensively inventoried northern part, and should also be recognized as an important center of endemism. A strong congruence between Sørensen and NNESS similarity matrices lead to similar delimitations of floristic units. Hence, heterogeneous sampling seems to confer more bias when measuring patterns of local diversity using raw species richness than species turnover using Sørensen index. Overall, we argue that subsampling methods represent a useful way to assess diversity gradients using herbarium specimens while correcting for heterogeneous sampling effort. Abstract in French is available in the online version of this article.     

OMERO: flexible, model-driven data management for experimental biology

Data-intensive research depends on tools that manage multidimensional, heterogeneous datasets. We built OME Remote Objects (OMERO), a software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices and tables. OMERO's design and flexibility have enabled its use for light-microscopy, high-content-screening, electron-microscopy and even non-image-genotype data. OMERO is open-source software, available at http://openmicroscopy.org/.     

History of Katayama disease: schistosomiasis japonica in Katayama district, Hiroshima, Japan

Historical account of Katayama disease is presented as a centenary record since the discovery of Schistosoma japonicum in Japan in 1904. The ever unknown endemic disease was called Katayama disease. Katayama district, Hiroshima Prefecture is one of endemic areas of schistosomiasis japonica in Japan. The causative parasite was first discovered in a human case in Katayama district. After the discovery of the parasite, life history, diagnosis, treatment, control measures and even eradication have been worked out, attempted and succeeded in Katayama district together with other endemic areas in Japan. Hiroshima Prefecture declared safety from the disease in 1980.     

Disentangling environmental correlates of vascular plant biodiversity in a Mediterranean hotspot

We determined the environmental correlates of vascular plant biodiversity in the Baetic‐Rifan region, a plant biodiversity hotspot in the western Mediterranean. A catalog of the whole flora of Andalusia and northern Morocco, the region that includes most of the Baetic‐Rifan complex, was compiled using recent comprehensive floristic catalogs. Hierarchical cluster analysis (HCA) and detrended correspondence analysis (DCA) of the different ecoregions of Andalusia and northern Morocco were conducted to determine their floristic affinities. Diversity patterns were studied further by focusing on regional endemic taxa. Endemic and nonendemic alpha diversities were regressed to several environmental variables. Finally, semi‐partial regressions on distance matrices were conducted to extract the respective contributions of climatic, altitudinal, lithological, and geographical distance matrices to beta diversity in endemic and nonendemic taxa. We found that West Rifan plant assemblages had more similarities with Andalusian ecoregions than with other nearby northern Morocco ecoregions. The endemic alpha diversity was explained relatively well by the environmental variables related to summer drought and extreme temperature values. Of all the variables, geographical distance contributed by far the most to spatial turnover in species diversity in the Baetic‐Rifan hotspot. In the Baetic range, climate was the most significant driver of nonendemic species beta diversity, while lithology and climate were the main drivers of endemic beta diversity. Despite the fact that Andalusia and northern Morocco are presently separated by the Atlantic Ocean and the Mediterranean Sea, the Baetic and Rifan mountain ranges have many floristic similarities – especially in their western ranges – due to past migration of species across the Strait of Gibraltar. Climatic variables could be shaping the spatial distribution of endemic species richness throughout the Baetic‐Rifan hotspot. Determinants of spatial turnover in biodiversity in the Baetic‐Rifan hotspot vary in importance between endemic and nonendemic species.     

Linear Discrimination,Ordination, and the Visualization of Selection Gradients in Modern Morphometrics

Linear discriminant analysis (LDA) is a multivariate classification technique frequently applied to morphometric data in various biomedical disciplines. Canonical variate analysis (CVA), the generalization of LDA for multiple groups, is often used in the exploratory style of an ordination technique (a low-dimensional representation of the data). In the rare case when all groups have the same covariance matrix, maximum likelihood classification can be based on these linear functions. Both LDA and CVA require full-rank covariance matrices, which is usually not the case in modern morphometrics. When the number of variables is close to the number of individuals, groups appear separated in a CVA plot even if they are samples from the same population. Hence, reliable classification and assessment of group separation require many more organisms than variables. A simple alternative to CVA is the projection of the data onto the principal components of the group averages (between-group PCA). In contrast to CVA, these axes are orthogonal and can be computed even when the data are not of full rank, such as for Procrustes shape coordinates arising in samples of any size, and when covariance matrices are heterogeneous. In evolutionary quantitative genetics, the selection gradient is identical to the coefficient vector of a linear discriminant function between the populations before vs. after selection. When the measured variables are Procrustes shape coordinates, discriminant functions and selection gradients are vectors in shape space and can be visualized as shape deformations. Except for applications in quantitative genetics and in classification, however, discriminant functions typically offer no interpretation as biological factors.     

POPULATION STRUCTURE OF MORPHOLOGICAL TRAITS IN CLARKIA DUDLEYANA. II. CONSTANCY OF WITHIN-POPULATION GENETIC VARIANCE

Recent quantitative genetic studies have attempted to infer long-term selection responsible for differences in observed phenotypes. These analyses are greatly simplified by the assumption that the within-population genetic variance remains constant through time and over space, or for the multivariate case, that the matrix of additive genetic variances and covariances (G matrix) is constant. We examined differences in G matrices and the association of these differences with differences in multivariate means (Mahalanobis D²) among 11 populations of the California endemic annual plant, Clarkia dudleyana. Based on nine continuous morphological traits, the relationship between Mahalanobis D² and a distance measure summarizing differences in G matrices reflected no concomitant change in (co)variances with changes in means. Based on both broad- and narrow-sense analyses, we found little evidence that G matrices differed between populations. These results suggest that both the additive and nonadditive (co)variances for traits have remained relatively constant despite changes in means.     

Weighted Diallel Analysis Across Environments: Combining Ability and Heterotic Pattern Models

The matrix algebra needed for analysing data from diallel experiments across several environments is provided. Practical considerations for subdividing large incidence matrices and appending constraint matrices are discussed to allow large experiments to be analysed on desk top computers. In particular, a combining ability model and heterotic pattern model have been used to show how heterogeneous variances can be accommodated by weighting. The models provide valuable information on the performance of lines in crosses, the heterotic patterns of the lines, and the heterotic groups to which they belong. The methodology is illustrated by application to a diallel cross conducted among 12 elite white modified opaque-2 maize inbred lines.     

The Roggeveldberge — Notes on a botanically hot area on a cold corner of the southern Great Escarpment, South Africa

Despite the Roggeveldberge comprising the montane heart of the celebrated Hantam-Roggeveld Centre of Plant Endemism (HRC), this section of the southern Great Escarpment in South Africa is botanically poorly known. A detailed physical, historical and phytogeographical overview of the Roggeveldberge is thus presented, and a checklist of 513 plant taxa is provided as a contribution towards a more complete flora for the Roggeveld-Komsberg Escarpment. The HRC is considered in detail, including various delimitations, and all species purported to be endemic to the HRC are reviewed and separated into actual endemics, near-endemics and species incorrectly considered as endemic.     

High resolution imaging of photosynthetic activities of tissues, cells and chloroplasts in leaves

Through imaging of chlorophyll fluorescence, it is possible to produce parameterized fluorescence images that estimate the operating quantum efficiency of photosystem II (PSII) photochemistry and which can be used to reveal heterogeneous patterns of photosynthetic performance within leaves. The operating quantum efficiency of PSII photochemistry is dependent upon the effective absorption cross-section of the light-harvesting system of PSII and the photochemical capacity of PSII. The effective absorption cross-section is decreased by the process of down-regulation, which is widely thought to operate within the pigment matrices of PSII and which results in non-photochemical quenching of chlorophyll fluorescence. The photochemical capacity is non-linearly related to the proportion of PSII centres in the 'open' state and results in photochemical quenching of chlorophyll fluorescence. Examples of heterogeneity of the operating quantum efficiency of PSII photochemistry during the induction of photosynthesis in maize leaves and in the chloroplast populations of stomatal guard cells of a leaf of Tradescantia albifora are presented, together with analyses of the factors determining this heterogeneity. A comparison of the operating quantum efficiency of PSII photochemistry within guard cells and adjacent mesophyll cells of Commelina communis is also made, before and after stomatal closure through a change in ambient humidity.