No association between sperm competition and sperm length variation across dung flies (Scathophagidae)

Sperm length is extremely variable across species, but a general explanation for this variation is lacking. However, when the risk of sperm competition is high, sperm length is predicted to be less variable within species, and there is some evidence for this in birds and social insects. Here, we examined intraspecific variation in sperm length, both within and between males, and its potential associations with sperm competition risk and variation in female reproductive tract morphology across dung flies. We used two measures of variation in sperm size, and testis size was employed as our index of sperm competition risk. We found no evidence of associations between sperm length variation and sperm competition or female reproductive tract variation. These results suggest that variation in sperm competition risk may not always be associated with variation in sperm morphology, and the cause(s) of sperm length variation in dung flies remains unclear.     

DEVELOPMENTAL PLASTICITY,GENETIC VARIATION,AND THE EVOLUTION OF ANDROMONOECY IN SOLANUM HIRTUM (SOLANACEAE)

Studies of andromonoecious species have shown that sex expression (proportions of hermaphrodite and staminate flowers) is quite variable. It is not known, however, whether this variation is due to variation among individuals for genetically fixed patterns of allocation to staminate and hermaphrodite flowers (population level variation) and/or to developmental plasticity of individuals in a heterogeneous environment (organismal level variation). Distinguishing between these two levels of variation is important for understanding the evolution of andromonoecy. This study investigates levels of variation in sex expression in the andromonoecious Solanum hirlum. Sex expression in this species is shown to be plastic among individuals of the same genotype (organismal level variation) and determined, in part, by the resource status of the individual. Among the genotypes examined there is also genetic variation for developmental plasticity. Thus, developmental plasticity can potentially respond to selection, and the evolution of this developmental system may have been instrumental in the establishment and maintenance of andromonoecy in S. hirtum.     

Phenotypic plasticity in leaf morphology of Crataegus monogyna (Rosaceae): an experimental study with taxonomic implications

Many leaf characters are considered in the taxonomy of Crataegus in Europe, and several have been used in studies of the extent of hybridization in populations of northwest Europe. In such analyses it is assumed that the environmental component of phenotypic variation in such characters is insignificant. We tested this assumption by analysing the variation in the size and shape of leaves borne on clone cuttings of Crataegus monogyna maintained under identical conditions apart from the availability of soil nutrients. The resulting variation among leaves from this single genotype was as great as that observed previously across populations. Furthermore, although most of this variation could not be explained, a part could be attributed to differences in nutrient availability; of nine leaf characters investigated, eight showed significant variation due to this source, and in seven, the variation covaried significantly with nutrient level. The systematic implications of this are briefly explored.     

Why intraspecific trait variation matters in community ecology

Natural populations consist of phenotypically diverse individuals that exhibit variation in their demographic parameters and intra- and inter-specific interactions. Recent experimental work indicates that such variation can have significant ecological effects. However, ecological models typically disregard this variation and focus instead on trait means and total population density. Under what situations is this simplification appropriate? Why might intraspecific variation alter ecological dynamics? In this review we synthesize recent theory and identify six general mechanisms by which trait variation changes the outcome of ecological interactions. These mechanisms include several direct effects of trait variation per se and indirect effects arising from the role of genetic variation in trait evolution.     

Quantifying phylogenetically structured environmental variation

Comparative analysis methods control for the variation linked to phylogeny before attempting to correlate the remaining variation of a trait to present-day conditions (i.e., ecology and/or environment). A portion of the phylogenetic variation of the trait may be related to ecology, however; this portion is called "phylogenetic niche conservatism." We propose a method of variation partitioning that allows users to quantify this portion of the variation, called the "phylogenetically structured environmental variation." The new method is applied to published data to study, in a phylogenetic framework, the link between body mass and population density in 79 species of mammals. The results suggest that an important part of the variation of mammal body mass is related to the common influence of phylogeny and population density.     

Difference mechanisms: explaining variation with mechanisms

Philosophers of science have developed an account of causal-mechanical explanation that captures regularity, but this account neglects variation. In this article I amend the philosophy of mechanisms to capture variation. The task is to explicate the relationship between regular causal mechanisms responsible for individual development and causes of variation responsible for variation in populations. As it turns out, disputes over this relationship have rested at the heart of the nature–nurture debate. Thus, an explication of the relationship between regular causal mechanisms and causes of variation and between individual development and variation offers both the necessary amendment to the philosophy of mechanisms and the resources to mediate the dispute.     

Overcoming technical variation and biological variation in quantitative proteomics

Quantitative proteomics investigates physiology at the molecular level by measuring relative differences in protein expression between samples under different experimental conditions. A major obstacle to reliably determining quantitative changes in protein expression is to overcome error imposed by technical variation and biological variation. In drug discovery and development the issue of biological variation often rises in concordance with the developmental stage of research, spanning from in vitro assays to clinical trials. In this paper we present case studies to raise awareness to the issues of technical variation and biological variation and the impact this places on applying quantitative proteomics. We defined the degree of technical variation from the process of two-dimensional electrophoresis as 20-30% coefficient of variation. On the other hand, biological variation observed experiment-to-experiment showed a broader degree of variation depending upon the sample type. This was demonstrated with case studies where variation was monitored across experiments with bacteria, established cell lines, primary cultures, and with drug treated human subjects. We discuss technical variation and biological variation as key factors to consider during experimental design, and offer insight into preparing experiments that overcome this challenge to provide statistically significant outcomes for conducting quantitative proteomic research.     

Towards plant pangenomics

As an increasing number of genome sequences become available for a wide range of species, there is a growing understanding that the genome of a single individual is insufficient to represent the gene diversity within a whole species. Many studies examine the sequence diversity within genes, and this allelic variation is an important source of phenotypic variation which can be selected for by man or nature. However, the significant gene presence/absence variation that has been observed within species and the impact of this variation on traits is only now being studied in detail. The sum of the genes for a species is termed the pangenome, and the determination and characterization of the pangenome is a requirement to understand variation within a species. In this review, we explore the current progress in pangenomics as well as methods and approaches for the characterization of pangenomes for a wide range of plant species.     

Genetic basis for colonial variation in Neisseria gonorrhoeae.

When the piliated colony types of Neisseria gonorrhoeae, which predominate in recent isolates, were nonselectively subcultured in vitro, they gave rise to large numbers of nonpiliated, avirulent colonial variants. Evidence is presented to show that most of this variation occurs after active growth has ceased and that the variation is sensitive to the action of deoxyribonuclease. We suggest that this variation is a result of transformation. A second variation in colonial morphology involved differing levels of "colony opacity-associated proteins" in the outer membrane. This variation was also inhibited by the presence of deoxyribonuclease, but the genetic basis for it is not as yet clear.     

Evaluation of the Variation in Calculated Human Exposure to Soil Contaminants Using Seven Different European Models

Calculations using seven European exposure models were performed for 20 different exposure scenarios. The objective of this article is to understand the variation in the resulting calculated human exposures due to soil contamination. To this purpose, the variation in calculated exposures has been compared with the variation in calculated concentrations in contact media and in the soil compartments and with the variation in the input parameters. This led to the conclusion that most of the variation in Exposure through soil ingestion is explained by differences in the input parameter average daily soil intake. When model-specific input parameters are used the variation in Exposure through crop consumption is explained by differences in the product of total consumption rate and fraction of total consumption rate that is home-grown. When standardized input parameters are used, this variation is comparable with the variation in Concentration in root vegetables and in Concentration in leafy vegetables. The variation in Exposure through indoor air inhalation is comparable with the variation in Concentration in indoor air. This suggests that the parameters that control the variation in Concentration in the indoor air, that is, surface and volume of the building and, to a lesser extent, ventilation frequency of the building, also control the variation in Exposure through indoor air inhalation.     

Strong environmental determination of a carotenoid-based plumage trait is not mediated by carotenoid availability

Carotenoid-based colours are recognized as having an important signalling function, yet the nature of the mechanisms that maintain their honesty is not well understood. By combining a carotenoid-feeding experiment with a quantitative genetic experiment in a wild population of blue tits (Parus caeruleus), we were able to test predictions that differentiate between proposed mechanisms. If variation in carotenoid ingestion underlies variation in carotenoid-based colour expression, then carotenoid-supplemented birds should have reduced variance in colour. In this study, carotenoid supplementation produced a small but significant change in plumage colouration, but no significant change in variation. These results suggest that variation in carotenoid acquisition is not an important source of variation for this colour trait, and that variation in post-ingestion processes are likely to be more important. The low heritability of this colour trait suggests environmental factors are likely to underlie the majority of variation in these processes.     

From genotype to phenotype: buffering mechanisms and the storage of genetic information

DNA sequence variation is abundant in wild populations. While molecular biologists use genetically homogeneous strains of model organisms to avoid this variation, evolutionary biologists embrace genetic variation as the material of evolution since heritable differences in fitness drive evolutionary change. Yet, the relationship between the phenotypic variation affecting fitness and the genotypic variation producing it is complex. Genetic buffering mechanisms modify this relationship by concealing the effects of genetic and environmental variation on phenotype. Genetic buffering allows the build-up and storage of genetic variation in phenotypically normal populations. When buffering breaks down, thresholds governing the expression of previously silent variation are crossed. At these thresholds, phenotypic differences suddenly appear and are available for selection. Thus, buffering mechanisms modulate evolution and regulate a balance between evolutionary stasis and change. Recent work provides a glimpse of the molecular details governing some types of genetic buffering.     

Variation of shell shape in the clonal snail Melanoides tuberculata and its consequences for the interpretation of fossil series

Interpreting paleontological data is difficult because the genetic nature of observed morphological variation is generally unknown. Indeed, it is hardly possible to distinguish among several sources of morphological variation including phenotypic plasticity, sexual dimorphism, within-species genetic variation or differences among species. This can be addressed using fossil organisms with recent representatives. The freshwater snail Melanoides tuberculata ranks in this category. A fossil series of this and other species have been studied in the Turkana Basin (Kenya) and is presented as one of the best examples illustrating the punctuated pattern of evolution by the tenants of this theory. Melanoides tuberculata today occupies most of the tropics. We studied variation of shell shape in natural populations of this parthenogenetic snail using Raup's model of shell coiling. We considered different sources of variation on estimates of three relevant parameters of Raup's model: (1) variation in shell shape was detected among clones, and had both genetic and environmental bases; (2) sexual dimorphism, in those clones in which males occur, appeared as an additional source of shell variation; and (3) ecophenotypic variation was detected by comparing samples from different sites and years within two clones. We then tested the performance of discriminant function analyses, a classical tool in paleontological studies, using several datasets. Although the three sources of variation cited above contributed significantly to the observed morphological variance, they could not be detected without a priori knowledge of the biological entities studied. However, it was possible to distinguish between M. tuberculata and a related thiarid species using these analyses. Overall, this suggests that the tools classically used in paleontological studies are poorly efficient when distinguishing between important sources of within-species variation. Our study also gives some empirical bases to the doubts cast on the interpretation of the molluscan series of the Turkana Basin.     

Patterns of tooth crown size and shape variation in great apes and humans and species recognition in the hominid fossil record

It has been suggested that patterns of craniodental variation in living hominids (Gorilla, Homo, Pan, and Pongo) may be useful for evaluating variation in fossil hominid assemblages. Using this approach, a fossil sample exhibiting a pattern of variation that deviates from one shared among living taxa would be regarded as taxonomically heterogeneous. Here we examine patterns of tooth crown size and shape variation in great apes and humans to determine 1) if these taxa share a pattern of dental variation, and 2) if such a pattern can reliably discriminate between samples that contain single species and those that contain multiple species. We use parametric and nonparametric correlation methods to establish the degree of pattern similarity among taxa, and randomization tests to assess their statistical significance. The results of this study show that extant hominids do not share a pattern of dental size variation, and thus these taxa cannot be used to generate expectations for patterns of size variation in fossil hominid species. The hominines (Gorilla, Homo, and Pan) do share a pattern of shape variation in the mandibular dentition; however, Pongo is distinct, and thus it is unclear which, if either, pattern should be expected in fossil hominids. Moreover, in this case, most combined-species samples exhibit patterns of shape variation that are similar to those for single hominine species samples. Thus, although a common pattern of shape variation is present in the mandibular dentition, it is not useful for recognizing taxonomically mixed paleontological samples.     

A truly ecological epigenetics study

Until a few years ago, epigenetics was a field of research that had nothing to do with ecology and that virtually no ecologist had ever heard of. This is now changing, as more and more ecologists learn about epigenetic processes and their potential ecological and evolutionary relevance, and a new research field of ecological epigenetics is beginning to take shape. One question that is particularly intriguing ecologists is to what extent epigenetic variation is an additional, and hitherto overlooked, source of natural variation in ecologically important traits. In this issue of Molecular Ecology, Herrera & Bazaga (2011) provide one of the first attempts to truly address this question in an ecological setting. They study variation of DNA methylation in a wild population of the rare, long-lived violet Viola cazorlensis, and they use these data to explore interrelations between environmental, genetic and epigenetic variation, and in particular the extent to which these factors are related to long-term differences in herbivore damage among plants. They find substantial epigenetic variation among plant individuals. Interestingly, this epigenetic variation is significantly correlated with long-term differences in herbivory, but only weakly with herbivory-related DNA sequence variation, which suggests that besides habitat, substrate and genetic variation, epigenetic variation may be an additional, and at least partly independent, factor influencing plant–herbivore interactions in the field. Although the study by Herrera & Bazaga (2011) raises at least as many new questions as it answers, it is a pioneering example of how epigenetics can be incorporated into ecological field studies, and it illustrates the value and potential novel insights to be gained from such efforts.     

ANOVA Method for Variance Component Decomposition and Diagnosis in Batch Manufacturing Processes

In batch manufacturing processes, the total process variation is generally decomposed into batch-by-batch variation and within-batch variation. Since different variation components may be caused by different sources, separation, testing, and estimation of each variance component are essential to the process improvement. Most of the previous SPC research emphasized reducing variations due to assignable causes by implementing control charts for process monitoring. Different from this focus, this article aims to analyze and reduce inherent natural process variations by applying the ANOVA method. The key issue of using the ANOVA method is how to develop appropriate statistical models for all variation components of interest. The article provides a generic framework for decomposition of three typical variation components in batch manufacturing processes. For the purpose of variation root causes diagnosis, the corresponding linear contrasts are defined to represent the possible site variation patterns and the statistical nested effect models are developed accordingly. The article shows that the use of a full factor decomposition model can expedite the determination of the number of nested effect models and the model structure. Finally, an example is given for the variation reduction in the screening conductive gridline printing process for solar battery fabrication.     

C-terminal lysine variants in fully human monoclonal antibodies: investigation of test methods and possible causes

The C-terminal lysine variation is commonly observed in biopharmaceutical monoclonal antibodies. This modification can be important since it is found to be sensitive to the production process. The methods commonly used to probe this charge variation, including IEF, cIEF, ion-exchange chromatography, and LC-MS, were evaluated for their ability to effectively approximate relative percentages of lysine variants. A monoclonal antibody produced in a B cell hybridoma versus a CHO cell transfectoma was examined and it was determined that the relative amount of incorporated C-terminal lysine can vary greatly between these two production schemes. Another case study is shown whereby a different monoclonal antibody is subject to some minor process changes and the extent of lysine variation also exhibits a significant difference. During these studies the different methods for determining the extent of variation were evaluated and it was determined that LC-MS after trypsin digestion provides reproducible relative percentage information and has significant advantages over other methods. The final section of this work investigates the possible origins of this modification and evidence is shown that carboxypeptidase B or another basic carboxypeptidase causes this variation.     

Cuticular hydrocarbons are heritable in the cricket Teleogryllus oceanicus

The ability of individuals to respond differentially to conspecifics depending on their genetic relatedness is a widespread phenomenon across the animal kingdom. Despite this, little is known about the selection processes that act on the phenotypic variation of traits used during recognition. Here we use a quantitative genetic approach to examine the patterns of genetic variation in cuticular hydrocarbon (CHC) profiles, a pheromonal system used extensively in insect communication. Using gas chromatography, we found family specificity in the CHC profiles of male crickets, Teleogryllus oceanicus. Across CHC peaks, our mean coefficient of additive genetic variation was 10.8%. Multivariate principal component analysis showed that most axes of variation were weighted by CHC peaks with significant additive genetic variation. Our results provide evidence that variation in CHC profiles can reflect genetic relatedness, supporting the widely held belief that this phenotypic trait is used as a mechanism for chemosensory kin recognition.