Defining hotspots of characteristic species for multiple taxonomic groups in the Netherlands

Biogeographical zonation based on single taxa poses major limitations on planning for nature conservation. This paper identifies biogeographical patterns of multiple taxa in the Netherlands, where no endemics are present at species level, on the basis of characteristic species. We used occurrence data on five species groups in order to identify spatially coherent, ecologically important regions. TWINSPAN was used to cluster grid squares according to similarity in species composition for each taxonomic group. Species that are characteristic of each of the clusters were identified using a preference index, and corresponding clusters among the taxonomic groups were identified with Kappa statistics. Regions containing characteristic species for several taxonomic groups were defined as ‘hotspots’. Stepwise discriminant analysis was then used to characterize these hotspots according to differences in environmental conditions. The analysis yielded five regions that are clearly distinct in terms of species composition for individual taxonomic groups. Each region is characterized by a set of unique species that occur in the zonation of at least two of the taxonomic groups. Stepwise discriminant analysis revealed significant environmental differences among these regions. The concept of hotspots as operationalized in this study can make nature conservation planning more efficient. In combination, the hotspots defined here comprise the majority of the species occurring in the Netherlands for the studied groups. Therefore, this regionalization should be taken into account when prioritizing nature conservation efforts.     

The development of adipocytes in primary stromal-vascular culture of fetal pig adipose tissue

Primary cultures of stromal-vascular cells of adipose tissue from fetuses at 70 and 110 days of gestation were evaluated as potential model systems for studies of fetal adipocyte differentiation and proliferation. In the cultures, fat cells developed as very discrete clusters. Fat cell cluster development was dependent on initial cell density and time. Histochemical analysis for NADP-dependent dehydrogenases revealed an age of donor effect. Similar levels of enzymes (malate and glucose-6-phosphate dehydrogenase) were apparent in fat cell clusters and stromal cells in cultures of cells from fetuses at 70 days of gestation. These enzymes were only present in fat cell clusters in cultures of cells from fetuses at 110 days of gestation. The distribution of histochemically detectable esterase activity was dependent on the cell density at time of analysis. In areas of high cell density, esterase was restricted to fat cell clusters whereas, both stromal cells and fat cells were esterase reactive in areas of low cell density. Omitting PMS from the dehydrogenase media revealed differences in enzyme reactions of cells grown on collagen-coated and uncoated glass surfaces. These studies demonstrate that primary cultures of stromal-vascular cells from 110-day-old fetuses would be a useful system to identify factors involved in adipocyte proliferation and differentiation.     

Clustering of hemodynamic and metabolic abnormalities and of anthropometric characteristics in men and women, aged 21-60 years.

The associations between fat pattern and metabolic profile were evaluated, using cluster analysis, in 214 males and 244 females (aged 21-60 years). The subjects were randomly selected from the patients of one general practice in Castel D'Azzano (Italy). The metabolic status was indexed by blood pressure, blood glucose, uric acid, serum triglycerides, total cholesterol, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol (both total and percentage). Fat pattern was evaluated using six skinfolds and three circumferences. The analyses were performed separately on anthropometric and metabolic variables for each sex. The analyses were repeated five times to evaluate the stability of the cluster solution. Anthropometric rather than metabolic variables provided a more stable solution for cluster analysis. Anthropometric clusters showed significantly different metabolic patterns. Most of the differences disappeared when a body mass index (BMI) effect was taken into account but not when an adjustment for waist to hip ratio (WHR) was made. On the other hand, neither BMI nor WHR was able to fully account for the differences in metabolic profiles of metabolic clusters. Cross-classification results of anthropometric and metabolic cluster membership showed a significant, although moderate, degree of association between the two classification sets. These results indicate that in both sexes anthropometric characteristics contribute to a limited degree to the metabolic profile and that the associations probably reflect a complex mechanism.     

Programs for evaluating and characterising bacterial taxonomic data

Three programs are described for evaluating and characterisingdata collected during numerical taxonomic studies of bacteria.The program VARIANCE compares replicate cultures and evaluatesthe reproducibility of each character. Also it identifies thosecharacters that should be excluded from subsequent taxonomicanalysis because of their poor reproducibility. GPROPS summarisesthe properties of clusters of strains that have been definedfrom a cluster analysis, it can produce a probabilistic identificationmatrix and compares each strain within a cluster with the HypotheticalMean Organism (HMO) of that cluster. OVCLUST is an implementationof the program described by Sneath (1979) which calculates overlapstatistics between major clusters. These programs are designedto complement the CLUSTAN package (Wishart, 1982) which is oftenused for cluster analysis of bacterial taxonomic data. The programswere written in FORTRAN 77 and implemented on an IBM PC usingMS–DOS. Received on November 13, 1986; accepted on January 8, 1987     

Taxonomic studies on Senecio aquaticus (Asteraceae). A recommendation for the taxonomic status of Aquaticus and Barbareifolius

Aquaticus and Barbareifolius are two subgroups of Senecio aquaticus s. l. (Asteraceae) that have been recognized at various taxonomic levels in European taxonomic literature. In this paper we present the results of morphological studies on S. aquaticus s. l. in order to establish the taxonomic status of these two subgroups. Using multivariate morphometric techniques (discriminant analysis and principal component analysis), we examined the diagnostic potential of 60 macro-morphological characters and studied the delimitation of Aquaticus and Barbareifolius. Seven of the characters studied were included in the discriminant function of the stepwise discriminant analysis and are therefore considered to be the most reliable diagnostic characters of Aquaticus and Barbareifolius. Barbareifolius has, amongst other distinguishing traits, a more divaricate inflorescence than Aquaticus. Because both subgroups are distinct but overlapping clusters in multivariate morphometric space, and because clear differences in their geographical distribution are absent, we recommend the taxonomic status of variety to both groups. Following the rules of nomenclature, Aquaticus and Barbareifolius should therefore be named S. aquaticus Hill var. aquaticus and S. aquaticus Hill var. barbareifolius (Krock.) Wimm. & Grab.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 145 , 489–498.     

Analysis of differences in the structure of ribosomal DNA from two sibling species: Drosophila melanogaster and Drosophila simulans

Southern-blot hybridization studies have revealed structural differences within the ribosomal DNA clusters of two sibling species, Drosophila melanogaster and Drosophila simulans. The approach used was shown to be suitable for taxonomic identification of the species examined.     

Heterogeneity of ribosomal proteins among Streptomyces species and its application to identification

The ribosomal proteins from 11 Streptomyces strains representing various numerical taxonomic clusters were compared by two-dimensional PAGE. The protein patterns were specific for each species and were unaffected by acridine dye treatment, suggesting genetic stability of ribosomal proteins. An attempt was made to identify one strain of Streptomyces by both traditional taxonomic methods and analysis of the ribosomal protein patterns. Both methods identified the strain as Streptomyces lavendulae, and protein pattern analysis also showed that Streptomyces avidinii was closely related to this species. The practical application of ribosomal protein patterns in Streptomyces taxonomy was therefore demonstrated.     

Numerical taxonomic analysis of imperfect yeast species in Candida and Torulopsis shows no basis for generic separation

A numerical taxonomic analysis was performed on 79 phenotypic characters of 147 imperfect yeast species currently assigned to the genus Candida. The characters used were drawn from two monographs on yeast taxonomy. The analysis revealed 10 clusters of three or more species that were similar at the level of 75% or more, and seven clusters containing only one or two species. None of the 10 major clusters contained exclusively species that were traditionally assigned to the genus Torulopsis, while the 12 Candida species of basidiomycetous affinity fell into three clusters with only one species of ascomycetous affinity included. Statistical determination of the five most important differential characters for each cluster failed to show the property of pseudomycelium/mycelium formation as significant for any cluster. The study provides no evidence to support a distinction between taxa that were formerly divided between the genera Candida and Torulopsis and supports previous proposals that these genera should be fused.     

Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes

The diversity of freshwater bacterioplankton communities has not been extensively studied despite their key role in foodwebs and the cycling of carbon and associated major elements. In order to explore and characterize the composition of bacterioplankton associated with cyanobacterial blooms, large 16S rRNA clone libraries from four lakes experiencing such blooms were analysed. The four libraries contained 1461 clones, of which 559 were prokaryotic sequences of non-cyanobacterial origin. These clones were classified into 158 operational taxonomic units affiliated mainly with bacterial divisions commonly found in freshwater systems, e.g. Proteobacteria, Bacteriodetes, Actinobacteria, Verrucomicrobia and Planctomycetes. Richness and evenness of non-cyanobacterial clones were similar to other clone libraries obtained for freshwater bacterioplankton, suggesting that bacterial communities accompanying cyanobacterial blooms are as diverse as non-bloom communities. Many of the identified operational taxonomic units grouped with known freshwater clusters but the libraries also contained novel clusters of bacterial sequences that may be characteristic for cyanobacterial blooms. About 25% of the operational taxonomic units were detected in more than one lake. Even so, 16S rRNA heterogeneity analysis demonstrated large differences in community composition between lakes regardless of their similar characteristics and close proximity. Hence even the similar environmental conditions created by different cyanobacterial blooms may foster very dissimilar bacterial communities, which could indicate that the genetic diversity in lake bacteria have been underestimated in the past.     

A Consideration of the Species Relationships in Subtribe Brassicinae (Cruciferae) in View of Cluster Analysis of Morphological Characters

Abstract The taxonomic relationships of 53 species (122 strains) in subtribe Brassicinae were studied by using Euclidian distances calculated from 53 metric characters. Through cluster analysis applied to the species and subspecies in the genus Brassica , six large clusters could be defined. By the same method, Diplotaxis was grouped into four clusters, Erucastrum into two, and Sinapis into two. These clusters coincided in general with the taxonomic sections of Schulz (1936), but some exceptions were noted. Most of the exceptional species were those placed in critical positions by cytogenetical observations. It was found that cluster grouping reflected the cytogenetical relations of species fairly well.
Relationships among clusters and genera are represented by a Euclidian distance matrix, and the evolutionary trends of those taxa are discussed. Clusters B-3 (in Brassica) , D-1 ( in Diplotaxis ) and E-1 (in Erucastrum ) are closely related to each other, forming a complex. This complex is closely related to Sinapidendron. It is postulated that this complex and Sinapidendron might have retained some characters in common with their putative ancestor. Species in the other clusters are considered to be derived from that hypothetical ancestor in the course of evolutionary divergence.     

Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling

Phylogenetic profiling, a network inference method based on gene inheritance profiles, has been widely used to construct functional gene networks in microbes. However, its utility for network inference in higher eukaryotes has been limited. An improved algorithm with an in-depth understanding of pathway evolution may overcome this limitation. In this study, we investigated the effects of taxonomic structures on co-inheritance analysis using 2,144 reference species in four query species: Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens. We observed three clusters of reference species based on a principal component analysis of the phylogenetic profiles, which correspond to the three domains of life—Archaea, Bacteria, and Eukaryota—suggesting that pathways inherit primarily within specific domains or lower-ranked taxonomic groups during speciation. Hence, the co-inheritance pattern within a taxonomic group may be eroded by confounding inheritance patterns from irrelevant taxonomic groups. We demonstrated that co-inheritance analysis within domains substantially improved network inference not only in microbe species but also in the higher eukaryotes, including humans. Although we observed two sub-domain clusters of reference species within Eukaryota, co-inheritance analysis within these sub-domain taxonomic groups only marginally improved network inference. Therefore, we conclude that co-inheritance analysis within domains is the optimal approach to network inference with the given reference species. The construction of a series of human gene networks with increasing sample sizes of the reference species for each domain revealed that the size of the high-accuracy networks increased as additional reference species genomes were included, suggesting that within-domain co-inheritance analysis will continue to expand human gene networks as genomes of additional species are sequenced. Taken together, we propose that co-inheritance analysis within the domains of life will greatly potentiate the use of the expected onslaught of sequenced genomes in the study of molecular pathways in higher eukaryotes.     

Plasma FFA responses to prolonged walking in untrained men and women

Gender differences in plasma FFA responses to 90 min of treadmill walking at 35% VO2max were investigated in six men and six women following an overnight fast. The subjects represented average values for maximal oxygen uptake and body fat percentage for age and gender. Mean plasma FFA concentration at 45 and 90 min of exercise were significantly (P less than 0.05) higher for women (0.82 mmol X 1(-1), 0.88 mmol X 1(-1)) than men (0.42 mmol X 1(-1), 0.59 mmol X 1(-1)). Lower R values for women throughout the exercise period indicated a greater percentage fat in total metabolism than for men while the FFA/glycerol results supported greater lipolytic activity for women. The uniformity of percent fat in metabolism for women from rest to exercise showed that FFA release from adipose tissue increased rapidly with the onset of exercise which was not the case for men. Comparison of metabolic data as well as a statistical analysis (ANCOVA) controlling for the influence of VO2max and percentage body fat on FFA plasma concentration suggested that gender differences in FFA responses to prolonged submaximal exercise can be expected to occur in untrained subjects.     

New scanning electron microscopic method for determination of adipocyte size in humans and mice

Objective: To evaluate a new scanning electronic microscopic (EM) method for assessing fat cell sizes and compare fat cell size distribution in human adipose tissue from different fat depots before and after weight loss. Research Methods and Procedures: Identical human fat tissue biopsies were separated into two fractions: one used to prepare a fat cell suspension by collagenase digestion followed by photomicrography (collagenase method) and the other fixed in formalin for EM analysis. The EM method was evaluated further by determining fat cell sizes from lean and ob/ob mice. Finally, the EM method was used to assess fat cell sizes in biopsies of different human depots from before and after weight loss. Results: Fat cell size distributions measured by the two methods were not identical, but differences were generally small. The EM method reproduced the well‐documented fat cell size difference between lean and ob/ob mice. Large variation was detected in fat cell distributions among three depots in humans. Weight loss reduced fat cell sizes in subjects with large baseline fat cells but had no effect in subjects with small baseline fat cell sizes. Discussion: Our results suggest that the EM method may be a useful alternative for fat cell size analysis of clinical samples.     

Congruence of individual responsiveness to dietary cholesterol and to saturated fat in humans

Previous experiments have shown that differences between humans in the response of serum cholesterol to dietary cholesterol are at least partly reproducible and stable over a prolonged period. In this study it was investigated whether enhanced sensitivity to dietary cholesterol and saturated fat go together. The subjects had also participated in three or four experiments dealing with the reproducibility of the effect on blood cholesterol of either adding cholesterol to the diet in normal subjects (NORM-EGG group; n = 23) or of cessation of egg consumption in subjects with a high habitual egg intake (HAB-EGG group; n = 24). In the present experiment the NORM-EGG subjects were fed a mixed natural diet providing 21% of energy as polyunsaturated and 11% as saturated fat (P/S2 ratio, 1.9) for 3 weeks, and one providing 5% of energy as polyunsaturated fat and 23% as saturated fat (P/S ratio, 0.2) for the next 3 weeks. The HAB-EGG group was fed the same diets in reverse order. The serum cholesterol concentrations were higher on the low P/S diet than on the high P/S diet (on average 23% in normal subjects and 16% in habitual egg eaters). The correlation coefficient between each subject's serum cholesterol response to fatty acids and his or her average response to dietary cholesterol in the dietary cholesterol experiments was 0.62 for the normal subjects (P less than 0.01) and 0.15 for the HAB-EGG group. We conclude that modest differences in responsiveness of serum cholesterol to dietary saturated fat do exist in humans, and that, in people of normal cholesterol intake, responsiveness to dietary cholesterol and to saturated fat tend to go together.     

Exploring diversity in cryptorhynchine weevils (Coleoptera) using distance-, character- and tree-based species delineation

Species boundaries are studied in a group of beetles, the western Palaearctic Cryptorhynchinae. We test for congruence of 'traditionally' identified morphospecies with species inferred through parsimony networks, distance-based clustering and the ultrametric tree-based generalized mixed yule-coalescent (GMYC) approach. For that purpose, we sequenced two variable fragments of mitochondrial DNA (CO1 and 16S) for a total of 791 specimens in 217 species of Cryptorhynchinae. Parsimony networks, morphology-calibrated distance clusters and the different tree-based species inferences all achieved low congruence with morphospecies, at best 60%. Although the degree of match with morphospecies was often similar for the different approaches, the composition of clusters partially varied. A barcoding gap was absent in morphospecies-oriented distances as well as for GMYC species clusters. This demonstrates that not only erroneous taxonomic assignments, incomplete lineage sorting, hybridization, or insufficient sampling can compromise distance-based identification, but also differences in speciation rates and uneven tree structure. The initially low match between morphospecies and the different molecular species delineation methods in this case study shows the necessity of combining the output of various methods in an integrative approach. Thereby we obtain an idea about the reliability of the different results and signals, which enables us to fine-tune sampling, delineation technique and data collection, and to identify species that require taxonomic revision.     

Comprehensive DNA barcode coverage of North American birds

DNA barcoding seeks to assemble a standardized reference library for DNA-based identification of eukaryotic species. The utility and limitations of this approach need to be tested on well-characterized taxonomic assemblages. Here we provide a comprehensive DNA barcode analysis for North American birds including 643 species representing 93% of the breeding and pelagic avifauna of the USA and Canada. Most (94%) species possess distinct barcode clusters, with average neighbour-joining bootstrap support of 98%. In the remaining 6%, barcode clusters correspond to small sets of closely related species, most of which hybridize regularly. Fifteen (2%) currently recognized species are comprised of two distinct barcode clusters, many of which may represent cryptic species. Intraspecific variation is weakly related to census population size and species age. This study confirms that DNA barcoding can be effectively applied across the geographical and taxonomic expanse of North American birds. The consistent finding of constrained intraspecific mitochondrial variation in this large assemblage of species supports the emerging view that selective sweeps limit mitochondrial diversity.     

Enhanced dietary fat clearance in postobese women

The objective of this study was to examine the postprandial response to an exogenous fat source in eight weight-stable postobese subjects (2;-3 years after gastric bypass) and eight matched control women, using a stable isotope, [13C]oleate. After a high fat breakfast meal (1,062 cal, 67% fat), [13C]oleate in triglyceride (TG)-rich lipoproteins (Sf >400 and Sf 20;-400) and nonesterified fatty acids (NEFA), and 13C in breath CO2, were monitored over 8 h. There were no differences in resting energy expenditure, thermic effect of food, carbohydrate/fat oxidation ratio, breath 13CO2 enrichment, or fecal fat content between postobese and control subjects. Postprandially, there was no difference in S(f) 20;-400 TG or NEFA, but postobese subjects had lower Sf >400 incremental area under the curve (AUC) (- 33%, P < 0.0025) and glucose [P < 0.01 by repeated measures analysis of variance (RM ANOVA)]. Postprandial 13C in Sf >400 TG returned to fasting levels 4 h earlier in postobese subjects and was lower than in control subjects at 4 and 6 h (P < 0.05 by RM ANOVA). The greatest difference was in the [13C]NEFA profiles. In control subjects [13C]NEFA increased markedly over 8 h; postobese subject [13C]NEFA remained close to fasting nonenriched values, and was strikingly lower than in control subjects (72% lower by AUC, P < 0.0001 by RM ANOVA). Finally, postobese subjects tended to have lower postprandial insulin (P < 0.01, 4 h), lower postprandial acylation-stimulating protein, and lower fasting leptin (-46%, P < 0.02). This study demonstrates clear metabolic differences in exogenous dietary fat partitioning in postobese women. These findings are compatible with an increased efficiency of dietary fat storage and suggest one possible mechanism for promotion of weight regain in postobese individuals.     

Insect diversity of Acacia canopies in Mkomazi game reserve, north-east Tanzania

Here we analyse one of the largest insect samples taken so far from a tropical savannah habitat. We used insecticidal mist blowing to spray the canopy of 3i trees of six Acacia species, and obtained 41 099 insects of 492 recognisable taxonomic units (RTUs). In most cases, there were significant differences between individual trees between and within tree species with regard to their insect community. After we performed a standardisation procedure because of unequal sample size, cluster analysis showed that most tree species formed more or less distinct clusters, indicating a moderate level of insect host specificity. Considered by tree localities, clear clusters were visible only if one tree species was sampled. This finding suggests that there is no significant overlap in the insect communities between tree species at a local scale. We carried out a multivariate analysis of insect diversity using four different diversity measurements. Results differed depending on the measurement used and no significant association of simple tree characteristics, such as height, with insect diversity was detectable. Instead, time of the day and ant biomass seem to be of greater importance. These results emphasise the importance of using different diversity measurements to evaluate habitats with regard to their conservation value.     

Numerical classification of species of Vibrio and related genera

Data from 1091 strains of the family Vibrionaceae collected in five different studies have been merged into a single data matrix and analysed in a taxonomic study. A set of 142 characters was selected to compare these data. Seventy-nine characters were common to all studies, but data for the other 63 characters were incomplete. Cultures of 90 strains, examined in more than one of the original studies, were used to estimate test error and inter-study variability. The data from these replicate strains also allowed the problem of merging data from different studies to be assessed. Taxonomic resemblance was estimated on the basis of 111 characters using the S_SM coefficient and UPGMA clustering. A taxonomic analysis based on 999 strains, which included most of the major species of the family Vibrionaceae, gave 59 clusters and 44 unclustered strains. A table of properties of these phenons was produced. The results showed that data obtained from studies carried out at different times and in different locations, but using standard techniques, could be combined and used to provide useful taxonomic information.