Assessing scales of variability in benthic diatom community structure

Sources of variability such as sampling method, sample preparation, and sample analysis (taxonomy) might affect our ability to measure differences in community structure between sites in environmental effects studies. It is therefore important to ensure that changes in community structure related to the physical or chemical differences between sites are not hidden by other sources of variability within a site. The goal of this study was to quantify the amount of variability in benthic diatom community structure related to sampling and laboratory procedures. Our results showed that variability in community structure was minimal among replicate microscope slides (< 1%) and among samples collected within a site (1.8%). Variability in community structure was substantially higher between sites located in one stream (16.6%), and highest across streams (59.6%). This suggests that field sampling and laboratory methods do not contribute a large amount of variation into our analyses of benthic diatom community structure across sites.     

Is assemblage variability related to environmental variability? An answer for riverine fish

We examine the variability of riverine fish assemblages in terms of assemblage stability (i.e. variability of numbers of individuals within species over time and variability of assemblage total density), assemblage persistence, and assemblage species richness using data from a 9-yr survey of 27 sites within 18 coastal streams of North-western France. To do so, we test a hypothesized directional model for the expected relationships between environmental variability, assemblage variability, assemblage persistence, and assemblage species richness: 1) environmental variability within a given system is likely to generate variable local population size within this system, thus increasing local assemblages variability; 2) environmental variability should increase extinction rates (or, under constant colonization rates, decrease persistence), because the more population sizes vary within an assemblage, the more likely they are to become zero in some period of time; 3) assemblage variability should reduce assemblage species richness by increasing extinction rates within populations composing these assemblages. Results are compatible with our starting hypotheses and show that assemblage variability increased with environmental variability (i.e. discharge variability), that assemblage persistence decreased with environmental variability, and that species richness decreased with assemblage variability after environmental factors were controlled for. Thus, disturbance regimes, in our case, can alter the stability properties of assemblages and extrinsic determinants of assemblage variability may be an important determinant of assemblage species richness. These results have important conservation and management implications, due to the strong impact of river regulation on flow regimes.     

Prioritizing key resilience indicators to support coral reef management in a changing climate

Managing coral reefs for resilience to climate change is a popular concept but has been difficult to implement because the empirical scientific evidence has either not been evaluated or is sometimes unsupportive of theory, which leads to uncertainty when considering methods and identifying priority reefs. We asked experts and reviewed the scientific literature for guidance on the multiple physical and biological factors that affect the ability of coral reefs to resist and recover from climate disturbance. Eleven key factors to inform decisions based on scaling scientific evidence and the achievability of quantifying the factors were identified. Factors important to resistance and recovery, which are important components of resilience, were not strongly related, and should be assessed independently. The abundance of resistant (heat-tolerant) coral species and past temperature variability were perceived to provide the greatest resistance to climate change, while coral recruitment rates, and macroalgae abundance were most influential in the recovery process. Based on the 11 key factors, we tested an evidence-based framework for climate change resilience in an Indonesian marine protected area. The results suggest our evidence-weighted framework improved upon existing un-weighted methods in terms of characterizing resilience and distinguishing priority sites. The evaluation supports the concept that, despite high ecological complexity, relatively few strong variables can be important in influencing ecosystem dynamics. This is the first rigorous assessment of factors promoting coral reef resilience based on their perceived importance, empirical evidence, and feasibility of measurement. There were few differences between scientists' perceptions of factor importance and the scientific evidence found in journal publications but more before and after impact studies will be required to fully test the validity of all the factors. The methods here will increase the feasibility and defensibility of including key resilience metrics in evaluations of coral reefs, as well as reduce costs. Adaptation, marine protected areas, priority setting, resistance, recovery.     

Characterization of noise and digitizer response variability in radiochromic film dosimetry. Impact on treatment verification

PurposeTo study how noise and scanner response variability affect radiochromic film dosimetry.MethodsFive treatment plans were analyzed in this work with two different multichannel protocols: the multichannel algorithm of Mayer et al. and the efficient protocol of Lewis et al.Results and conclusionThe multichannel protocol of Mayer et al. is not able to compensate variability in scanner response, which is an important issue for radiochromic film dosimetry. The efficient protocol compensates variations of scanner response, so dose values and gamma scores become more accurate and reproducible. The compensation of digitizer scan variability of the efficient protocol, together with time averaging improve radiochromic film dosimetry. Noise is related to selected resolution in the scanner, our results show that if high resolution measurements are required, de-noising should be considered.     

The impact of environment on ontogenesis variations in Ruggieria and Chrysocythere (Ostracoda).

The ontogenetic development of Ruggieria lekkii, Ruggieria triangulata, Ruggieria martinsoni and Chrysocythere ornata (Ostracoda) was investigated on two different continental shelves (Congo and Senegal). For one species, the ontogenetic trajectories obtained through length and height of valves differed considerably in distinct areas. In the first case, trajectories showing well-separated development stages and slight intraspecific variability in length and height were seen. In the second, trajectories showing valves which are difficult to relate to one stage or another and a high intraspecific variability were noted. In the latter, the uncertainties in the determination of the development stages were resolved by using a statistical method. Furthermore, this allowed for the comparison of the variations in ontogenesis (augmentation or reduction in the development), in relation to abiotic (detrital supply and upwelling processes) and biotic ecological factors (faunal density and interspecific competition). Comparisons were also made with ornamental variations observed on Chrysocythere ornata, which are directly linked with bioprecipitation (environmental) conditions. This comparison highlights the role played by abiotic and trophic factors on the developmental variations of ostracods in some continental shelves areas. This work shows that ontogenetic variations depend either on biotic or abiotic factors. They can act in different ways on distinct species and one can be predominant in a particular biota. Once the architectural characters have appeared, their variations no more depend on ontogenetic development. The study of ontogenesis reveals the adaptation capacities of one species in an environment with variable conditions.     

A characterization model with spatial and temporal resolution for life cycle impact assessment of photochemical precursors in the United States

Background, aim, and scope  Traditional life cycle impact assessment methodologies have used aggregated characterization factors, neglecting spatial and temporal variations in regional impacts like photochemical oxidant formation. This increases the uncertainty of the LCA results and diminishes the ease of decision-making. This study compares four common impact assessment methods, CML2001, Eco-indicator 99, TRACI, and EDIP2003, on their underlying models, spatial and temporal resolution, and the level at which photochemical oxidant impacts are calculated. A new characterization model is proposed that incorporates spatial and temporal differentiation. Materials and methods  A photochemical air quality modeling system (CAMx-MM5-SMOKE) is used to simulate the process of formation, transformation, transport, and removal of photochemical pollutants. Monthly characterization factors for individual US states are calculated at three levels along the cause–effect chain, namely, fate level, human and ecosystem exposure level, and human effect level. Results and discussion  The results indicate that a spatial variability of one order of magnitude and a temporal variability of two orders of magnitude exist in both the fate level and human exposure and effect level characterization factors for NO_x. The summer time characterization factors for NO_x are higher than the winter time factors. However, for anthropogenic VOC, the summer time factors are lower than the winter time in almost half of the states. This is due to the higher emission rates of biogenic VOCs in the summer. The ecosystem exposure factors for NO_x and VOC do not follow a regular pattern and show a spatial variation of about three orders of magnitude. They do not show strong correlation with the human exposure factors. Sensitivity analysis has shown that the effect of meteorology and emission inputs is limited to a factor of three, which is several times smaller than the variation seen in the factors. Conclusions  Uncertainties are introduced in the characterization of photochemical precursors due to a failure to consider the spatial and temporal variations. Seasonal variations in photochemical activity influence the characterization factors more than the location of emissions. The human and ecosystem exposures occur through different mechanisms, and impacts calculated at the fate level based only on ozone concentration are not a good indicator for ecosystem impacts. Recommendations and perspectives  Spatial and temporal differentiation account for fate and transport of the pollutant, and the exposure of and effect on the sensitive human population or ecosystem. Adequate resolution for seasonal and regional processes, like photochemical oxidant formation, is important to reduce the uncertainty in impact assessment and improve decision-making power. An emphasis on incorporating some form of spatial and temporal information within standard LCI databases and using adequately resolved characterization factors will greatly increase the fidelity of a standard LCA. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Human F7 sequence is split into three deep clades that are related to FVII plasma levels

It is widely accepted that FVII levels are strongly, consistently, and independently related to cardiovascular risk. These levels are influenced by genetic and environmental factors. Among the genetic factors, only a limited number of polymorphisms in the F7 gene have been reported, and they explain only a small proportion of the genetic variability. Recently, we have accomplished the complete dissection of the F7 quantitative trait locus responsible for all of the genetic variability observed in FVII levels. Now, we present the thorough study of the haplotype organization of F7 DNA sequence variation among individuals and the evolutionary processes that produced this variation, by sequencing 15 kb of genomic DNA sequence from the F7 locus in 40 unrelated individual (80 chromosomes) from the genetic analysis of idiopathic thrombophilia (GAIT) project as well as four non-human primate species. Our study revealed 49 polymorphisms, of which 39 SNPs were further considered. Genotyping of these DNA variations in the whole family-based GAIT sample helped resolve linkage phases, and a total of 37 distinct haplotypes were identified. Tajima’s D was significantly positive in this sample, suggesting balancing selection. This parameter was a reflection of the phylogenetic structure of F7 haplotype, which was deeply split into three well-supported clades or haplogroups, suggesting that functional differences among F7 variants do not depend on a few single-site variations. Moreover, haplogroup 2 was associated with high FVII levels and haplogroup 3 with low levels. In this study, we have for the first time established a clear relation between genotypic variability structure and phenotypic variability of a particular quantitative trait involved in a complex disease. Electronic Supplementary Material Supplementary material is available for this article at     

Minimizing creatine kinase variability in rats for neuromuscular research purposes

Rat serum or plasma creatine kinase (CK) activity is widely used to evaluate myopathic processes, to test the myotoxicity of different drugs, or to analyse the benefits of emerging gene therapies in some neuromuscular disorders. However, great variability is found in this determination. The aim of this study has been to control some factors of variation in order to reduce variability and increase the reproducibility of analytical data. 8-10-week-old Wistar-Han rats were used. The study consisted of four sequential phases. Phase I aimed to analyse the effect of ether and isoflurane as anaesthetic drugs. The objective of Phase II was to evaluate bleeding rats via retro-orbital sinus vs. tail vein. Phases III and IV were designed as two separate, repeated measure experiments on two factors: habituation to laboratory handling procedures in Phase III and gender in Phase IV. The repeated factor was the storage temperature of blood sample prior to centrifugation. Ether did not significantly increased the CK value. Using isoflurane, getting rats accustomed to laboratory handling procedures and whole blood refrigeration prior to centrifugation and serum separation resulted in statistically significant reduction in CK value and variability. Male rats showed significantly higher values than female rats. In the light of our findings, CK value and variability in rats may be minimized by choosing tail vein as site of bleeding, getting rats accustomed to laboratory handling procedures and maintaining whole blood refrigerated until centrifugation and serum separation.     

Characterization and Compensation of Network-Level Anomalies in Mixed-Signal Neuromorphic Modeling Platforms

Advancing the size and complexity of neural network models leads to an ever increasing demand for computational resources for their simulation. Neuromorphic devices offer a number of advantages over conventional computing architectures, such as high emulation speed or low power consumption, but this usually comes at the price of reduced configurability and precision. In this article, we investigate the consequences of several such factors that are common to neuromorphic devices, more specifically limited hardware resources, limited parameter configurability and parameter variations due to fixed-pattern noise and trial-to-trial variability. Our final aim is to provide an array of methods for coping with such inevitable distortion mechanisms. As a platform for testing our proposed strategies, we use an executable system specification (ESS) of the BrainScaleS neuromorphic system, which has been designed as a universal emulation back-end for neuroscientific modeling. We address the most essential limitations of this device in detail and study their effects on three prototypical benchmark network models within a well-defined, systematic workflow. For each network model, we start by defining quantifiable functionality measures by which we then assess the effects of typical hardware-specific distortion mechanisms, both in idealized software simulations and on the ESS. For those effects that cause unacceptable deviations from the original network dynamics, we suggest generic compensation mechanisms and demonstrate their effectiveness. Both the suggested workflow and the investigated compensation mechanisms are largely back-end independent and do not require additional hardware configurability beyond the one required to emulate the benchmark networks in the first place. We hereby provide a generic methodological environment for configurable neuromorphic devices that are targeted at emulating large-scale, functional neural networks.     

The evolution of dispersal under demographic stochasticity

Temporal and spatial variations of the environment are important factors favoring the evolution of dispersal. With few exceptions, these variations have been considered to be exclusively fluctuations of habitat quality. However, since the presence of conspecifics forms part of an individual's environment, demographic stochasticity may be a component of this variability as well, in particular when local populations are small. To study this effect, we analyzed the evolution of juvenile dispersal in a metapopulation model in which habitat quality is constant in space and time but occupancy fluctuates because of demographic stochasticity. Our analysis extends previous studies in that it includes competition of resources and competition for space. Also, juvenile dispersal is not given by a fixed probability but is made conditional on the presence of free territories in a patch, whereas individuals born in full patches will always disperse. Using a combination of analytical and numerical approaches, we show that demographic stochasticity in itself may provide enough variability to favor dispersal even from patches that are not fully occupied. However, there is no simple relationship between the evolution of dispersal and various indicators of demographic stochasticity. Selected dispersal depends on all aspects of the life-history profile, including kin selection.     

Conserved patterns of incomplete reporting in pre-vaccine era childhood diseases

Incomplete observation is an important yet often neglected feature of observational ecological timeseries. In particular, observational case report timeseries of childhood diseases have played an important role in the formulation of mechanistic dynamical models of populations and metapopulations. Yet to our knowledge, no comprehensive study of childhood disease reporting probabilities (commonly referred to as reporting rates) has been conducted to date. Here, we provide a detailed analysis of measles and whooping cough reporting probabilities in pre-vaccine United States cities and states, as well as measles in cities of England and Wales. Overall, we find the variability between locations and diseases greatly exceeds that between methods or time periods. We demonstrate a strong relationship within location between diseases and within disease between geographical areas. In addition, we find that demographic covariates such as ethnic composition and school attendance explain a non-trivial proportion of reporting probability variation. Overall, our findings show that disease reporting is both variable and non-random and that completeness of reporting is influenced by disease identity, geography and socioeconomic factors. We suggest that variations in incomplete observation can be accounted for and that doing so can reveal ecologically important features that are otherwise obscured.     

Evolution of genome size in Drosophila. is the invader's genome being invaded by transposable elements?

Genome size varies considerably between species, and transposable elements (TEs) are known to play an important role in this variability. However, it is far from clear whether TEs are involved in genome size differences between populations within a given species. We show here that in Drosophila melanogaster and Drosophila simulans the size of the genome varies among populations and is correlated with the TE copy number on the chromosome arms. The TEs embedded within the heterochromatin do not seem to be involved directly in this phenomenon, although they may contribute to differences in genome size. Furthermore, genome size and TE content variations parallel the worldwide colonization of D. melanogaster species. No such relationship exists for the more recently dispersed D. simulans species, which indicates that a quantitative increase in the TEs in local populations and fly migration are sufficient to account for the increase in genome size, with no need for an adaptation hypothesis.     

Is the polymorphism of protein amounts related to phenotypic variability? A comparison of two-dimensional electrophoresis data with morphological traits in maize

Summary The hypothesis that the quantitative variations in gene product levels could be a more important basis for morphological and adaptative change than the classical qualitative variability revealed by electrophoretic techniques was studied by comparing five maize lines from three sets of variables: (i) qualitative variations of proteins (presence/absence) revealed by two-dimensional polyacrylamide gel electrophoresis (2D PAGE), at a physiological seedling stage; (ii) quantitative variations in proteins (spots more or less intense) revealed by 2D PAGE, at the same physiological stage; (iii) general combining abilities of fourteen heritable, morphological or agronomical characters measured at various juvenile and adult stages. Distances between lines were defined, based on qualitative and quantitative variations of proteins. These distances do not appear to be correlated and do not give the same patterns of divergence between lines, as shown by principal coordinate analyses. Mahalanobis distances computed from the general combining abilities of the morphological characters are significantly correlated (r=0.75) to quantitative but not to qualitative distances. The comparison of the first planes of the principal coordinate analyses performed on the three kinds of distances clearly confirms this finding. Our results are discussed in connection with the possible genetic meaning of the two molecular distances and with the hypothesis that regulatory processes are primarily implicated in morphological variation.     

Eye-Size Variability in Deep-Sea Lanternfishes (Myctophidae): An Ecological and Phylogenetic Study

One of the most common visual adaptations seen in the mesopelagic zone (200–1000 m), where the amount of light diminishes exponentially with depth and where bioluminescent organisms predominate, is the enlargement of the eye and pupil area. However, it remains unclear how eye size is influenced by depth, other environmental conditions and phylogeny. In this study, we determine the factors influencing variability in eye size and assess whether this variability is explained by ecological differences in habitat and lifestyle within a family of mesopelagic fishes characterized by broad intra- and interspecific variance in depth range and luminous patterns. We focus our study on the lanternfish family (Myctophidae) and hypothesise that lanternfishes with a deeper distribution and/or a reduction of bioluminescent emissions have smaller eyes and that ecological factors rather than phylogenetic relationships will drive the evolution of the visual system. Eye diameter and standard length were measured in 237 individuals from 61 species of lanternfishes representing all the recognised tribes within the family in addition to compiling an ecological dataset including depth distribution during night and day and the location and sexual dimorphism of luminous organs. Hypotheses were tested by investigating the relationship between the relative size of the eye (corrected for body size) and variations in depth and/or patterns of luminous-organs using phylogenetic comparative analyses. Results show a great variability in relative eye size within the Myctophidae at all taxonomic levels (from subfamily to genus), suggesting that this character may have evolved several times. However, variability in eye size within the family could not be explained by any of our ecological variables (bioluminescence and depth patterns), and appears to be driven solely by phylogenetic relationships.     

Intra-Site Variability in the Still Bay Fauna at Blombos Cave: Implications for Explanatory Models of the Middle Stone Age Cultural and Technological Evolution

To explain cultural and technological innovations in the Middle Stone Age (MSA) of southern Africa, scholars invoke several factors. A major question in this research theme is whether MSA technocomplexes are adapted to a particular set of environmental conditions and subsistence strategies or, on the contrary, to a wide range of different foraging behaviours. While faunal studies provide key information for addressing these factors, most analyses do not assess intra-technocomplex variability of faunal exploitation (i.e. variability within MSA phases). In this study, we assess the spatial variability of the Still Bay fauna in one phase (M1) of the Blombos Cave sequence. Analyses of taxonomic composition, taphonomic alterations and combustion patterns reveal important faunal variability both across space (lateral variation in the post-depositional history of the deposits, spatial organisation of combustion features) and over time (fine-scale diachronic changes throughout a single phase). Our results show how grouping material prior to zooarchaeological interpretations (e.g. by layer or phase) can induce a loss of information. Finally, we discuss how multiple independent subdivisions of archaeological sequences can improve our understanding of both the timing of different changes (for example in technology, culture, subsistence, environment) and how they may be inter-related.     

Importance of complete DNA digestion in minimizing variability of 8-oxo-dG analyses.

Estimates of 8-oxo-2'-deoxyguanosine (8-oxo-dG) in DNA vary at least one order of magnitude using different quantitative methods or even the same method. Our hypothesis is that an incomplete DNA hydrolysis to nucleosides by the conventional nuclease P1 (NP1) and alkaline phosphatase (AP) digestion system plays an important role in contributing to the variability of measurements using HPLC coupled with UV and electrochemical (EC) detection. We show here that factors, such as the amount of DNA, choice of enzymes, their activities, and incubation time, can affect DNA digestion and, thus, cause variability in 8-oxo-dG levels. The addition of DNase I and phosphodiesterases I and II to the NP1 + AP system improves the DNA digestion by completely releasing normal nucleosides and 8-oxo-dG, thereby reducing the interday variations of 8-oxo-dG levels. Diethylenetriamine pentaacetic acid (DTPA), an iron chelator, prevented background increases of 8-oxo-dG during DNA digestion, as well as during the waiting period in the autosampler when a batch of DNA samples is analyzed by HPLC. After optimization of the DNA digestion conditions, the interday variability of 8-oxo-dG measurements using commercially available salmon testes DNA (ST DNA) were 26% over a period of 2 years. Under these optimal conditions, our laboratory variability may contribute as little as 13% to the overall variability as shown by assessment of oxidative DNA damage in a population of smokers. Based on our results, we believe that the modified DNA digestion conditions will provide much more accurate 8-oxo-dG determinations and, thus, more reliable estimates of cancer risk.     

Modern concepts of socialisation for dogs: implications for their behaviour, welfare and use in scientific procedures

The provision of a socialisation and training programme for dogs can lead to an improvement in the quality of the data that are produced from scientific procedures, and also to an improvement in animal welfare. A reduction in the number of animals needed to produce statistically significant data can result from decreasing the variability of the experimental data. The effects of a dog's behaviour can be a major source of random variability. A well socialised, habituated and trained dog should be calm during experimental procedures and, for example, during an ECG measurement, thus providing good quality data. A fearful, poorly socialised dog may also appear to be well-behaved on an examination table, and during an ECG measurement, because of the freezing response. However, there is likely to be a difference in the level of stress that these two individuals experience during the procedures. The stress response can have an impact on vital physiological parameters, such as heart rate. The variability in these parameters and the behaviour exhibited within a group of socialised, habituated and trained dogs that have been well prepared for experimental procedures, should be less than the variability present within a similar group of dogs that have not been prepared for these procedures. This paper describes two socialisation programmes, which were designed in order to compare the heart rates and behaviour of dogs which had received different degrees of socialisation, habituation and training. The behaviour of small groups of dogs from this study was compared with that of dogs on a standard socialisation programme, by using a simple, reproducible behavioural score scheme. The heart rate of the dogs was also measured. The results showed that there was little difference in heart rate between the groups, but that there were significant differences in the scores for key behaviours. There was evidence of a decrease in the variability of the behavioural scores for the groups of dogs that had undergone an intensive socialisation programme. Therefore, a socialisation programme can have a significant effect on behaviour and welfare, and has the potential to improve the quality of the data that are recorded.     

Causes and consequences of variation in competitive ability in plant communities

Abstract. Several factors may define the cause and pattern of variation in competitive ability among individuals within a plant community. Variation may be a consequence of genetic or environmental variability. These two sources of variation may vary in their relative magnitudes. The relevant scale of genetic variation may occur at the individual genotype level or at the species level. The relevant scale of environmental variation may occur at the individual plant level or at the neighbourhood (or community) level. Relative competitive abilities may be effected by genotype-environment interaction or by genotype-genotype (or species-species) interaction. The complex relationship among these factors reveals the mechanistic basis for establishing a clear distinction among five specific hypotheses for species coexistence and diversity that are all variations of the general hypothesis that competitive abilities do not differ sufficiently among coexisting species to cause any competitive exclusion at the community level. These hypotheses are compared in terms of the degree to which they are restricted by assumptions and supported by existing data, and in the extent to which they involve evolutionary consequences of competition.     

Hypervariable genes--experimental error or hidden dynamics

In a homogeneous group of samples, not all genes of high variability stem from experimental errors in microarray experiments. These expression variations can be attributed to many factors including natural biological oscillations or metabolic processes. The behavior of these genes can tease out important clues about naturally occurring dynamic processes in the organism or experimental system under study. We developed a statistical procedure for the selection of genes with high variability denoted hypervariable (HV) genes. After the exclusion of low expressed genes and a stabilizing log-transformation, the majority of genes have comparable residual variability. Based on an F-test, HV genes are selected as having a statistically significant difference from the majority of variability stabilized genes measured by the 'reference group'. A novel F-test clustering technique, further noted as 'F-means clustering', groups HV genes with similar variability patterns, presumably from their participation in a common dynamic biological process. F-means clustering establishes, for the first time, groups of co-expressed HV genes and is illustrated with microarray data from patients with juvenile rheumatoid arthritis and healthy controls.