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.     

Number of immunoreactive GnRH-containing neurons is heritable in a wild-derived population of white-footed mice (Peromyscus leucopus)

The evolution of mammalian brain function depends in part on levels of natural, heritable variation in numbers, location, and function of neurons. However, the nature and amount of natural genetic variation in neural traits and their physiological link to variation in function or evolutionary change are unknown. We estimated the level of within-population heritable variation in the number of gonadotropin-releasing hormone (GnRH) neurons, which play a major role in reproductive regulation, in an unselected outbred population recently derived (<10 generations) from a single natural population of white-footed mice (Peromyscus leucopus, Rafinesque). Young adult male mice exhibited an approximately threefold variation in the number of neurons immunoreactive for GnRH in the brain areas surveyed, as detected using SMI-41 antibody with a single-label avidin-biotin complex method. Consistent with earlier findings of selectable variation in GnRH neurons in this population, the level of genetic variation in this neuronal trait within this single population was high, with broadsense heritability using full-sib analysis estimated at 0.72 (P<0.05). Either weak selection on this trait or environmental variation that results in inconsistent selection on this trait might allow a high level of variation in this population.     

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.     

SOMACLONAL AND GAMETOCLONAL VARIATION

For several years it has been recognized that introduction of plant cells into culture results in genetic changes. These genetic alterations have been recovered in the plants regenerated from cell cultures. More recently it has been recognized that this method of introducing genetic changes into crop plants could be used to develop new breeding lines. The technology of introducing genetic variation by using cell culture has been termed somaclonal and gametoclonal variation. This paper reviews the history of this technology and offers genetic documentation of somaclonal variation in tomato. As this variation represents a new tool for the plant breeder, breeding strategies for the use of this variation are presented and discussed. Somaclonal and gametoclonal variation are new tools for the geneticist and plant breeder that permit reduction in the time period for new variety development and that permit access to new classes of genetic variation.     

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.     

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.     

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.     

云南红豆杉天然群体内同工酶遗传变异的研究

采用水平淀粉凝胶电泳技术,对分布于金沙江流域的云南红豆杉天然群体的10种酶系统同工酶的遗传变异进行了研究。在谱带遗传分析的基础上确定了15个酶基因座及其等位基因。其中有14个酶基因座属多态,只有一个单态基因座（ME－3）。14个多态基因座中,4个基因座遗传变异小,对该天然群体的遗传变异贡献不大,其余10个基因座遗传变异丰富,对该天然群体的遗传变异贡献大。该天然群体具有明显丰富的遗传变异性,多态基因座比率P=0.933,等位基因平均数A=2.90,平均期望杂合度He=0.290。紫杉醇含量与群体遗传变异有着密切的关系。 Abstract：Genetic variation of ten isoenzymes was studied within population of Taxus yun nanensis Cheng et L. K. Fu in the Jinsha River Valley using the method of hor izo ntal starch gel electrophoresis.On the basis of banding analysis,eight enzyme sy stems , presumablly coded by fifteen isoenzyme loci and their alleles were score d , and fourteen were polymorphic with only one monomorphic locus（ME－3）. Amon g them , four polymorphic loci with inevident genetic variation made little cont ribution to genetic variation of this population and other ten polymorphic loci with evident genetic variation made great contribution to genetic variation of this population . Isoenzyme data indicated high level of genetic variability in this population with P=0.933,A=2.90,He=0.290 . The taxol content had close r elation to genetic variation of population.     

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.     

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.     

Individual behavioral variation in predator–prey models

The role of individual behavioral variation in community dynamics was studied. Behavioral variation in this study does not refer to differences in average responses (e.g., average response between presence and absence of antipredator behavior). Rather it refers to the variation around the average response that is not explained by trivial experimental treatments. First, the effect of behavioral variation was examined based on Jensen’s inequality. In cases of commonly used modeling framework with type II functional response, neglecting behavioral variation (a component of encounter rate) causes overestimation of predation effects. The effect of this bias on community processes was examined by incorporating the behavioral variation in a commonly used consumer-resource model (Rosenzweig–MacArthur model). How such a consideration affects a model prediction (paradox of enrichment) was examined. The inclusion of behavioral variation can both quantitatively and qualitatively alter the model characteristics. Behavioral variation can substantially increase the stability of the community with respect to enrichment.     

Founder effects and phenotypic variation in Adelges cooleyi, an insect pest introduced to the eastern United States

Introduced organisms experience founder effects including genetic bottlenecks that result in significant reductions in genetic variation. Genetic bottlenecks may constrain the evolution of phenotypic traits that facilitate success in novel habitats. We examined the effect of introduction into novel environments on genetic diversity of an insect pest, Adelges cooleyi, which was introduced into the eastern United States during the mid nineteenth century. We compared variation in mitochondrial and nuclear genomes in native and introduced samples to determine the effect of introduction on genetic variation experienced by this insect. We also measured an ecologically important phenotype, variation in host preference, in both native and introduced samples to compare variation in that trait with molecular genetic variation. To further investigate the relationship between genetic and phenotypic variation, we examined the degree to which mtDNA haplotypes provide information about host preference. Adelges cooleyi in eastern North America has significantly reduced genetic and phenotypic variation, but this low variation does not appear to have prevented persistence in a novel environment. Introduced insects appear to have retained host preference phenotypes similar to those of insects found where introductions likely originated.     

Fluctuating mate preferences in a marine fish

According to theory, directional female choice for male sexual ornaments is expected to erode underlying genetic variation. Considerable attention, in this regard, has been given to understanding the ubiquity of heritable genetic variation in both female choice and male sexual traits. One intriguing possibility emerging from this work is that persistent genetic variation could be maintained, over time, by variation in female mate preferences. Here, we report the results of a four-year study showing significant year-to-year fluctuations in mate preferences in a small marine fish, the sand goby, Pomatoschistus minutus. Although the average size of mature fish varied across years, we were unable to find direct evidence linking this variation to differences in female preferences among years. Our results, nevertheless, underscore the importance of temporal fluctuations in female mate preferences, as these can have important consequences for understanding variation in sexual traits and the intensity of sexual selection.     

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.     

Variation in female mate choice within guppy populations: population divergence,multiple ornaments and the maintenance of polymorphism

The evolutionary significance of variation in mate choice behaviour is currently a subject of some debate and considerable empirical study. Here, I review recent work on variation within and among guppy (Poecilia reticulata) populations in female mate choice and mating preferences. Empirical results demonstrate that there is substantial variation within and among populations in female responsiveness and choosiness, and much of this variation is genetic. Evidence for variation in preference functions also exists, but this appears to be more equivocal and the relative importance of genetic variation is less clear cut. In the second half of this review I discuss the potential significance of this variation to three important evolutionary issues: the presence of multiple male ornaments, the maintenance of polymorphism and divergence in mate recognition among populations. Studies of genetic variation in mate choice within populations indicate that females have complex, multivariate preferences that are able to evolve independently to some extent. These findings suggest that the presence of multiple male ornaments may be due to multiple female mating preferences. The extreme polymorphism in male guppy colour patterns demands explanation, yet no single satisfactory explanation has yet emerged. I review several old ideas and a few new ones in order to identify the most promising potential explanations for future empirical testing. Among these are negative frequency dependent selection, environmental heterogeneity coupled with gene flow, and genetic constraints. Last, I review the relative extent of within and among-population variation in mate choice and mating preferences in order to assess why guppies have not speciated despite a history of isolation and divergence. I argue that variation within guppy populations in mate choice and enhanced mating success of new immigrants to a pool are major impediments to population divergence of the magnitude that would be required for speciation to occur.     

Somaclonal variation--genetic basis and breeding applications

Somaclonal variation, the recovery of genetic changes in plants regenerated from tissue culture, offers an opportunity to uncover natural variability and to use this variability for the development of new varieties. This review focuses on the unique variation generated by this technique and the current use of somaclonal variation to develop new plant varieties.     

Non‐Salient Geographic Variation in Birdsong in a Species That Learns by Improvisation

Geographic variation in birdsong and differential responses of territorial males to local and non‐local song variants have been documented in a number of songbird species in which males learn their songs through imitation. Here, we investigated geographic song variation and responses to local and non‐local song in the grasshopper sparrow (Ammodramus savannarum), a species in which males develop song by improvisation rather than imitation, as a first step toward understanding how the extent and salience of geographic song variation is related to the mode of song development. To describe the geographic variation in song, we compared songs from populations in eastern Maryland and central Ohio, USA, using multiple acoustic analysis techniques. We then conducted a playback experiment in Maryland using local and non‐local (Ohio) songs to test how territorial males responded to this geographic variation. We found acoustic differences between songs from the two sites. However, males responded similarly to playback of these songs, suggesting that this geographic variation is not behaviorally salient in a territorial context. Together with previous studies, our results suggest that across species, geographic song variation and the extent to which this variation functions in communication may be correlated with the accuracy with which song models are imitated during song development.     

Geographic variation in the status signals of Polistes dominulus paper wasps

Understanding intraspecific geographic variation in animal signals poses a challenging evolutionary problem. Studies addressing geographic variation typically focus on signals used in mate-choice, however, geographic variation in intrasexual signals involved in competition is also known to occur. In Polistes dominulus paper wasps, females have black facial spots that signal dominance: individuals wasps with more complex 'broken' facial patterns are better fighters and are avoided by rivals. Recent work suggests there is dramatic geographic variation in these visual signals of quality, though this variation has not been explicitly described or quantified. Here, we analyze variation in P. dominulus signals across six populations and explore how environmental conditions may account for this variation. Overall, we found substantial variation in facial pattern brokenness across populations and castes. Workers have less broken facial patterns than gynes and queens, which have similar facial patterns. Strepsipteran parasitism, body size and temperature are all correlated with the facial pattern variation, suggesting that developmental plasticity likely plays a key role in this variation. First, the extent of parasitism varies across populations and parasitized individuals have lower facial pattern brokenness than unparasitized individuals. Second, there is substantial variation in body size across populations and a weak but significant relationship between facial pattern brokenness and body size. Wasps from populations with smaller body size (e.g. Italy) tend to have less broken facial patterns than wasps from populations with larger body size (e.g. New York, USA). Third, there is an apparent association between facial patterns and climate, with wasp from cooler locations tending to have higher facial pattern brokenness than wasps from warmer locations. Additional experimental work testing the causes and consequences of facial pattern variation will be important, as geographic variation in signals has important consequences for the evolution of communication systems and social behavior.     

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.