Divergence Index Research Articles

Species convergence into life-forms in a hyperseasonal cerrado in central Brazil

Whether the functional structure of ecological communities is deterministic or historically contingent is still quite controversial. However, recent experimental tests did not find effects of species composition variation on trait convergence and therefore the environmental constraints should play the major role on community convergence into functional groups. Seasonal cerrados are characterized by a sharp seasonality, in which the water shortage defines the community functioning. Hyperseasonal cerrados experience additionally waterlogging in the rainy season. Here, we asked whether waterlogging modifies species convergences into life-forms in a hyperseasonal cerrado. We studied a hyperseasonal cerrado, comparing it with a nearby seasonal cerrado, never waterlogged, in Emas National Park, central Brazil. In each area, we sampled all vascular plants by placing 40 plots of 1 m(2) plots in four surveys. We analyzed the species convergences into life-forms in both cerrados using the Raunkiaer's life-form spectrum and the index of divergence from species to life-form diversity (IDD). The overall life-form spectra and IDDs were not different, indicating that waterlogging did not affect the composition of functional groups in the hyperseasonal cerrado. However, there was a seasonal variation in IDD values only in the hyperseasonal cerrado. As long as we did not find a seasonal variation in life-form diversity, the seasonal variation of convergence into life-forms in the hyperseasonal cerrado was a consequence of the seasonal variation of species diversity. Because of high functional redundancy of cerrado plants, waterlogging promoted a floristic replacement without major changes in functional groups. Thus, waterlogging in the hyperseasonal cerrado promoted seasonal changes in species convergence into life-forms by reducing species diversity.

The Effect of Dominance on the Use of the QST − FST Contrast to Detect Natural Selection on Quantitative Traits

THE comparison between Wright's among-population fixation index F ST (a descriptor of the effect of the breeding structure on population diversity for neutral genes) and Spitze's quantitative index of population divergence Q ST [defined as V b/( V b + 2 V w), where V b and V w are, respectively, the

Analysis of diurnal and vertical microbial diversity of a hypersaline microbial mat

Microbial mats are prokaryotic communities that provide model systems to analyze microbial diversity and ecophysiological interactions. Community diversity of microbial mat samples was assessed at 8:00 a.m. and 3:00 p.m. in a combined analysis consisting of 16S rRNA-denaturing gradient gel electrophoresis (DGGE) and phospholipid fatty acid (PLFA) profiles. The divergence index determined from PLFA and DGGE data showed that depth-related differences have a greater influence on diversity than temporal variations. Shannon and Simpson indices yielded similar values in all samples, which suggested the stable maintenance of a structurally diverse microbial community. The increased diversity observed at 3:00 p.m. between 2.5 and 4 mm can be explained mainly by diversification of anaerobic microorganisms, especially sulfate-reducing bacteria. In the afternoon sampling, the diversity index reflected a higher diversity between 4 and 5.5 mm depth, which suggested an increase in the diversity of strict anaerobes and fermenters. The results are consistent with the conclusion that hypersaline microbial mats are characterized by high degree of diversity that shifts in response to the photobiological adaptations and metabolic status of the microbial community.

Segment based image classification

Five aspatial and spatial classification methods were compared in this study: standard per‐pixel maximum likelihood classification; Kettig and Landgrebe's ECHO classification; maximum likelihood classification using the segment mean; classification using the segment divergence index; and maximum likelihood classification using the segment probability density function (PDF). The five classification methods were compared using test data from digital aerial imagery with a nominal 1‐m pixel size, and four multispectral bands, acquired over Morgantown, West Virginia, USA. Classification using the segment divergence index produced the lowest accuracy, followed by ECHO, standard maximum likelihood classification and classification with segment mean. The highest accuracy was obtained from classification using the segment PDF.

A Divergence Statistic for Industrial Localization

We propose a statistical index of industrial localization based on the Kullback-Leibler divergence. This index is particularly well suited to cases where industrial data are available only at the regional level. Unlike existing regional-level indices, our index can be employed to test the significance of industrial localization relative to a hypothesized reference distribution of probable locations across regions. In addition, one can test relative degrees of localization among industries. Finally, as with all Kullback-Leibler divergence indices, our index can be decomposed into components representing localization at various levels of spatial aggregation.

Distribution of indicator bacteria in Canyon Lake, California

The spatial and temporal distributions of indicator bacteria in a small, multiple-use source drinking water reservoir in Southern California, USA were quantified over the period August 2001–July 2002. High levels of total and fecal coliform bacteria were present in Canyon Lake (annual geometric mean concentrations±SEM of 3.93±0.02 and 3.02±0.03 log cfu/100 mL, respectively), while comparatively low levels of enterococci and E. coli were found (1.16±0.02 log cfu/100 mL and 0.30±0.03 log MPN/100 mL, respectively). As a result, these different indicator bacteria yielded quite divergent indices of water quality, with 72.1% of all surface samples ( n=294) exceeding the USEPA single-sample limit of 400 cfu/100 mL fecal coliform bacteria, while none (0%) of the samples exceeded the single-sample limit for E. coli ( n=194). Regression analyses found a positive correlation between total and fecal coliform bacteria ( R=0.50, significant at p<0.001) and between enterococci and E. coli ( R=0.51, significant at p<0.001), but no correlation or inverse correlations were found between coliform concentrations and enterococci and E. coli levels. External sources responsible for the high total and fecal coliform bacteria were not identified, although laboratory studies demonstrated growth of the coliform bacteria in lake water samples. Enterococci and E. coli were not observed to grow, however. Bacteria concentrations varied relatively little laterally across the lake, although strong vertical gradients in fecal coliform and enterococcus bacteria concentrations were present during summer stratification, with concentrations about 10×higher above the thermocline when compared with surface concentrations. In contrast, total bacteria, total virus and total coliform bacteria levels were unchanged with depth. Seasonal trends in bacteria concentrations were also present. This study shows that the choice of indicator bacteria and sampling depth can both strongly affect the apparent microbial water quality of a lake or reservoir.

Further support for the pain stages of change model: Suggestions for improved measurement

Recent efforts to operationalize persons’ readiness to adopt a self-management approach to chronic pain have met with promising, but somewhat limited, results. The current study describes the development and psychometric evaluation of a German version of Pain Stages of Change Questionnaire (PSOCQ). A new item pool was developed to attempt to improve in particular the discriminant validity of the scales and in order to obtain a shortened measure. The items were administered to 494 chronic pain patients who were split into two independent samples. Item- and factor-analysis performed on data from one half of the sample resulted in four scales: precontemplation, preparation, action, and maintenance. The scales of the new measure, called the “Freiburg Questionnaire-Stages of Chronic Pain Management (FQ-STAPM)”, showed good indices of reliability, homogeneity, and discriminant validity. Both the concurrent and divergent validity indices and the relationships between scale scores and pain related variables proved to be consistent with the transtheoretical model. Confirmatory factor analysis using LISREL performed on the second half of the sample supported the goodness-of-fit of the structure model. Implications of these findings for future research exploring the relevance of the pain stages of change model are discussed.

The radiation of the Seicercus burkii complex and its congeners (Aves: Sylviidae): molecular genetics and bioacoustics

Cryptic species of passerine birds lack notable morphological differentiation and can best be identified by molecular and bioacoustic markers. Here we investigate seven cryptic species of the golden-spectacled warbler ( Seicercus burkii complex) with respect to territorial song and cytochrome- b (cyt- b) sequences. Their phylogenetic relations to other Seicercus species and to members of the genus Phylloscopus are inferred by the same methods. Three separate lineages of Seicercus are nested within different branches of the molecular Phylloscopus tree. The S. burkii complex is a monophyletic unit comprising seven species ( S. burkii s. str., S. whistleri, S. valentini, S. soror, S. omeiensis, S. tephrocephalus and S. affinis). S. xanthoschistos turned out to be a close relative of Phylloscopus davisoni within the P. reguloides group. Two isolated sister taxa, S. grammiceps and S. castaniceps, also branch together with the P. reguloides group. Within the S. burkii complex the overall haplotype and nucleotide diversity is highest in taxa from the Chinese middle and upper mountain belt ( S. valentini, S. omeiensis and S. soror), indicating at least partially restricted gene flow in these species. This is explained by the fragmentation of high-altitude habitats in China while in the Himalayas the vicariant species S. whistleri inhabits a more continuous mountain belt at the same altitude. For the Chinese species from medium and high altitudes, past range expansion is indicated by significantly negative Tajima Ds. According to pairwise genetic distances, most species of the S. burkii complex have diverged 5 myr ago, the most recent split between S. burkii and S. tephrocephalus is dated 2 myr ago. Coalescence times for haplotype lineages of the different species range from 9 up to 12 myr, and between 5 and 6 myr for S. burkii and S. tephrocephalus. Within Seicercus divergence of song features such as frequency parameters and syntax structures correlate with genetic distances between taxa. The three cyt- b lineages of Seicercus correspond to different clusters in a discriminant analysis by acoustic parameters. Common syntax structures of territorial song in the Phylloscopus/ Seicercus assemblage are: (1) an introductory element derived from specific calls and (2) a syntax of trills and repeated element groups or a combination of both. There are clear indications that these song structures have repeatedly emerged, were lost or were altered in different branches of the phylogenetic tree at different times. Absolute differences between taxa in frequency parameters or in an acoustic divergence index increase significantly with growing genetic distances. However, due to multiple parallel evolution phylogenetic information provided by single acoustic traits decreases with increasing numbers of taxa involved in the investigation.

The role of inclination and part worth differences across segments in designing a price-discriminating product line

We consider a product line design problem with multiple quality-type attributes for a monopolist who serves multiple customer segments. We show that it is possible to get the first best solution (FBS) for this problem and develop a condition for it. We introduce the notion of inclination of a segment for a given bundle of attributes that measures the customer segment's overall preference for the bundle of attributes that are in the product category. We show that FBS implementability requires that the part worth between segments must be sufficiently separated. In fact, for a firm to price discriminate via a variety in the product line, this separation of parts worth between any pair of customer segments must be more than the separation in their inclinations. If inclination towards the product category varies vastly across segments, it will be harder to utilize the differences in part worth to offer separating products. We provide an elegant characterization of this condition in terms of divergence index between pairs of customers, which states that the divergence index must be less than one for FBS to be implementable. If inclination is equal across segments, then one can always design a differentiating product line no matter how many segments there are. We also provide a geometric interpretation of the FBS condition that is helpful in generating insights.

Phylogenetic Relationships of the Sparidae Family (Pisces, Perciformes) Inferred from Satellite-DNA

The phylogenetic relationships within the taxonomically controversial Sparidae family of fish are inferred using two satellite-DNA families as phylogenetic markers. The cross-hybridization, strength and restriction patterns of hybridizing the monomer units of these two satellite-DNA families to the DNAs of ten sparid species, served as an index of taxonomic divergence. The results indicate the existence of two separate lineages from a common ancestor, each one clearly defined by either satellite-DNA family. The results also indicate a closeness between Sparus and Diplodus, and a divergence between Spams and Pagrus. These data agree with the currently. Accepted opinion considering Sparus a monotypic genus which should include only Sparus aurata, and recommending the separation of the genus Pagrus to include the common seabream Pagrus pagrus and the red-banded seabream Pagrus auriga, among others.

The effect of neutral nonadditive gene action on the quantitative index of population divergence.

For neutral additive genes, the quantitative index of population divergence (Q(ST)) is equivalent to Wright's fixation index (F(ST)). Thus, divergent or convergent selection is usually invoked, respectively, as a cause of the observed increase (Q(ST) > F(ST)) or decrease (Q(ST) < F(ST)) of Q(ST) from its neutral expectation (Q(ST) = F(ST)). However, neutral nonadditive gene action can mimic the additive expectations under selection. We have studied theoretically the effect of consecutive population bottlenecks on the difference F(ST) - Q(ST) for two neutral biallelic epistatic loci, covering all types of marginal gene action. With simple dominance, Q(ST) < F(ST) for only low to moderate frequencies of the recessive alleles; otherwise, Q(ST) > F(ST). Additional epistasis extends the condition Q(ST) < F(ST) to a broader range of frequencies. Irrespective of the type of nonadditive action, Q(ST) < F(ST) generally implies an increase of both the within-line additive variance after bottlenecks over its ancestral value (V(A)) and the between-line variance over its additive expectation (2F(ST)V(A)). Thus, both the redistribution of the genetic variance after bottlenecks and the F(ST) - Q(ST) value are governed largely by the marginal properties of single loci. The results indicate that the use of the F(ST) - Q(ST) criterion to investigate the relative importance of drift and selection in population differentiation should be restricted to pure additive traits.

An index of divergence from species to life-form diversity based on the notion of intrinsic diversity ordering

In this paper, we propose a measure of divergence from species tolife-form diversity based on the notion of intrinsic diversity ordering. First,species and life-form relative abundances within the analyzed community aredetermined. Next, community intrinsic diversity profile is computed both fromspecies and life-form relative abundances. Finally, the speed of decrease fromspecies to life-form diversity is obtained by comparing the area under thespecies diversity profile with the area under the corresponding life-formdiversity profile. Since life-forms classify plants into ecologically relevantgroups irrespective of their systematics, the proposed measure might be usefulto quantify the ecological similarity of different communities without loosinginformation on traditional taxonomic diversity figures. As an application fordemonstration, a small data set from a garigue community on ultramafic soils ofTuscany (central Italy) is used.

Prospects for reconstruction of seasonal environment from tree-ring δ 13C: baseline findings from the Great Lakes area, USA

Plant δ 13C and discrimination (Δ≈δ 13C air−δ 13C plant) embody ecophysiological response to environmental conditions influencing rates of carbon fixation and stomatal conductance. This study scrutinizes the seasonal variation of δ 13C and Δ in growth rings developed in 1990, as represented in trees of 11 species at three sites along a 5° latitude transect in Illinois and Wisconsin, USA. Radial stem xylem growth of the trees was monitored with monthly punch cores, and the resulting growth curves precisely identified the growth period represented in the five segments into which each growth ring was subdivided. Seasonal δ 13C variation of cellulose was usually 1–1.5‰, and the seasonal patterns were similar among angiosperm and conifer trees at a site, with angiosperms generally 13C-depleted by 0.5–1.5‰. Seasonal δ 13C (and Δ) patterns was different among sites, however, and regression with several environmental parameters revealed most frequent significant correlation with soil moisture (Palmer Drought Severity Index [PDSI]). The site-averaged seasonal Δ patterns track each of their divergent local seasonal drought index chronologies very well, even when isotopic curves of the different trees are simply averaged without adjustment for different growth rates. Seasonal tree-ring δ 13C analysis is affirmed as a valuable method for assessing seasonal moisture status. Furthermore, results favor successful extension to ancient tree rings where different species and slope aspects may be represented in wood samples at a collection site, and where rates of ring development and seasonal δ 13C air are not likely to be known.

Normative and Psychometric Data from the Body Image Assessment - Revised in a Population of French-Speaking Women

This article concerns the creation of norms and the validation in French of the Body Image Assessment - Revised (BIA-R; Beebe, Holmbeck, & Grzeskiewicz, 1999). The sample comprised 100 normal female subjects They completed questionnaires assessing body experience, eating pathology, psychological functioning, general perception and the BIA-R (Beebe et al.. 1999). This test consists of nine silhouettes from which the subject has to choose the somatotype corresponding to her actual shape (cognitive response), the way she feels (affective response) and the way she would like to look (optative response). The results show a good concurrent validity for the cognitive and affective indices and the affective/ cognitive vs. optative divergences. On the other hand, we were not able to demonstrate such validity for the optative index and the affective vs. cognitive divergence index.

Multilocus isozyme systems in African lungfish, Protopterus annectens: distribution, differential expression and variation in dipnoans

Distribution of ADH, ALP, FBALD, GAPDH, G3PDH, G6PDH, GPI, LDH, MDH, PGM, and SOD was identified in retina, heart, muscle, liver, kidney, gills, brain, gut, lung and ovary of the African lungfish. Data are compared with patterns previously described in dipnoans and other vertebrates. The number of loci expressed for all enzymes was found to be similar to those of diploid Actinopterygii. Differences in the number of loci expressed in Amphibia were found for ALP, sG3PDH, GPI, LDH, MDH and SOD. Differences in tissue distribution were noted in ALP due to the absence of an intestinal-specific form typical of teleostean fish, amphibians, reptiles and birds, and in GPI and MDH, due to the tissue expression, as in primitive fish. There were also differences in LDH, where a third locus ( LDH-C*) was expressed in the gills of Protopterus annectens and not in the retina or liver tissues, as in teleosts. LDH-A 4 was most common in all the tissues. Major differences were noted in the tissue patterns of protein expression in the three dipnoans compared. As expected, the least divergence was found between the two species belonging to the same family (Lepidosirenidae). The highest index of divergence was observed between Neoceratodus forsteri and Lepidosiren paradoxa, belonging to the families Ceratontidae and Lepidosirenidae, respectively. The divergence is revealed by changes at the enzyme and morphological levels. These results suggest that P. annectens occupies an interesting systematic position, its biochemical characteristics distinguishing it from N. forsteri, L. paradoxa, the advanced fish and amphibians.

Political Denials: The Policy Effect of Intercameral Partisan Differences in Bicameral Parliamentary Systems

Bicameralism in legislatures affects both the legislative process and partisan competition. In the United States, divided partisan control of Congress has been found to lead to interparty logrolls and increased budget deficits. In parliamentary systems, it is generally assumed that similarly divided legislatures have little effect on policy. I argue, by contrast, that party discipline means that divided control of the legislature has the opposite effect: because cooperation dilutes party labels, parties have an interest in passing and claiming credit for policy, but also in preventing their counterparts from doing the same. The result is a game in which chamber majorities balance the desire to make policy with the need to differentiate themselves from each other (to the extent that they are different). I test the hypothesis of an inverse relationship between divergence and policy making in a nine-country, TSCS regression of deficits on an index of chamber divergence. Copyright 2001 by Oxford University Press.

Algorithms for quantitation of protein expression variation in normal versus tumor tissue as a prognostic factor in cancer: Met oncogene expression, and breast cancer as a model

Immunohistochemistry and immunofluorescence (IF) assays frequently rely on subjective observer evaluation for grading. The aim of our study was to develop an objective quantitative index based on confocal laser scanning microscopy (CLSM) and image analysis of an IF assay to determine alteration in protein expression levels in normal versus tumor tissue. The relative levels of Met expression, a prognostic factor in breast cancer, were used as a model for evaluating image analysis algorithms. Primary human breast cancer biopsies were collected. Sections containing tumor and adjacent uninvolved normal regions were immunostained for Met and digital images were acquired by CLSM. Subsequently, the digital data were manipulated using several different algorithms to calculate prognostic indexes. The results were correlated with the clinical outcome to determine the prognostic value of these indexes. Different algorithms were used to obtain quantitative indexes to evaluate the relative levels of Met expression. We report a statistical correlation between patient prognosis and relative Met level in normal versus tumor tissue as determined by three distinct algorithms using Kaplan-Meier analysis (log-rank): calculations based on intensity levels differences DV (P = 0.002), DIntensity (P = 0.014), and entropy divergence (Dentropy; P = 0.0023). Using adjacent normal tissue as an internal reference, a quantitative index of tumor Met level divergence can be objectively determined to have a prognostic value. Moreover, this methodology can be used for other proteins in a variety of different diseases.

Seasonal microbial community dynamics in a flowerpot-using personal composting system for disposal of household biowaste.

Microbial community dynamics in a flowerpot-using solid biowaste composting (FUSBIC) process were monitored seasonally by quinone profiling and conventional microbiological methods. The FUSBIC system, which consisted of three flowerpots (14 L or 20 L capacity) with 5-6 kg each of a soil-compost mixture (SCM) as the primary reactors, was loaded daily with household biowaste from November 1998 to October 1999. The monthly average waste reduction rate was 88.2% for the 14-L system and 92.5% for the 20-L system on a wet weight basis. The direct total microbial count detected in the 14-L primary reactors ranged from 4.5 to 9.6x10(11) cells.g(-1) of dry wt of SCM, and the viable count of aerobic heterotrophic bacteria recovered on agar plates at 28 degrees C varied from 1.9 to 5.7x10(11) CFU.g(-1) of dry wt. The quinone content of SCM samples from the 14-L and 20-L systems ranged from 160 to 353 nmol.g(-1) of dry SCM. Ubiquinones, unsaturated menaquinones, and partially saturated menaquinones constituted 15.0-36.4, 14.8-22.0, and 41.8-61.6 mol% of the total content, respectively. The major quinone types detected were usually MK-8(H(2)), MK-9(H(2)), and Q-10. Variations in quinone profiles were evaluated numerically by using two parameters, the dissimilarity index (D) and microbial divergence index (MD(q)). The upper limit of seasonal changes in the microbial community structure was about 30% as expressed by D values. The MD(q) values calculated ranged from 18 to 22. A significant positive correlation was found between seasonal temperature and bacterial populations containing partially saturated menaquinones. These results indicated that the FUSBIC system contained highly diverse microbial populations that fluctuated to some extent depending on seasonal temperature. Members of the Actinobacteria were suggested to be the major constituents of the total population present.

Analysis of fragment homology among DNA sequences from cytochrome P450 families 4 and 6.

Cytochrome P450s comprise a diverse superfamily of proteins that often share as little as 12% amino acid identity. Accordingly, the identification of novel gene families, subfamilies and alleles has been based primarily on 'benchmark' levels of global amino acid identity and, more recently, phylogenetic relatedness has been used to resolve ambiguous relationships. However, PCR-based cloning strategies have resulted in a large increase in the number of short DNA sequences, particularly among insects. Many of these fragments remain unnamed and even their gene family membership remains unknown due to the uncertainty as to whether these fragments accurately reflect the levels of sequence identity or patterns of evolutionary divergence exhibited by groups of full-length P450 sequences. As a result, the nature of P450 diversity among insects remains obscure. In this paper, P450 sequences belonging to the two major gene families, that is, families CYP4 and CYP6, are analyzed by comparing segments to full-length sequences. A parameter called the Segmental Divergence Index is used to characterize segments of P450s with respect to the degree to which they mirror the divergence of full-length sequences. The reliability of these fragments in phylogenetic analyses is also tested. The results of these analyses support the use of some commonly amplified P450 gene fragments for naming new P450 genes and for studies of P450 diversity and evolution.

Changes in quinone profiles of hot spring microbial mats with a thermal gradient

The respiratory and photosynthetic quinones of microbial mats which occurred in Japanese sulfide-containing neutral-pH hot springs at different temperatures were analyzed by spectrochromatography and mass spectrometry. All of the microbial mats that developed at high temperatures (temperatures above 68 degreesC) were so-called sulfur-turf bacterial mats and produced methionaquinones (MTKs) as the major quinones. A 78 degreesC hot spring sediment had a similar quinone profile. Chloroflexus-mixed mats occurred at temperatures of 61 to 65 degreesC and contained menaquinone 10 (MK-10) as the major component together with significant amounts of either MTKs or plastoquinone 9 (PQ-9). The sunlight-exposed biomats growing at temperatures of 45 to 56 degreesC were all cyanobacterial mats, in which the photosynthetic quinones (PQ-9 and phylloquinone) predominated and MK-10 was the next most abundant component in most cases. Ubiquinones (UQs) were not found or were detected in only small amounts in the biomats growing at temperatures of 50 degreesC and above, whereas the majority of the quinones of a purple photosynthetic mat growing at 34 degreesC were UQs. A numerical analysis of the quinone profiles was performed by using the following three parameters: dissimilarity index (D), microbial divergence index (MDq), and bioenergetic divergence index (BDq). A D matrix tree analysis showed that the hot spring mats consisting of the sulfur-turf bacteria, Chloroflexus spp., cyanobacteria, and purple phototrophic bacteria formed distinct clusters. Analyses of MDq and BDq values indicated that the microbial diversity of hot spring mats decreased as the temperature of the environment increased. The changes in quinone profiles and physiological types of microbial mats in hot springs with thermal gradients are discussed from evolutionary viewpoints.