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.     

Genomics and conservation genetics

In large part, the relevance of genetics to conservation rests on the premise that neutral marker variation in populations reflects levels of detrimental and adaptive genetic variation. Despite its prominence, this tenet has been difficult to evaluate, until now. As we discuss here, genome sequence information and new technological and bioinformatics platforms now enable comprehensive surveys of neutral variation and more direct inferences of detrimental and adaptive variation in species with sequenced genomes and in 'genome-enabled' endangered taxa. Moreover, conservation schemes could begin to consider specific pathological genetic variants. A new conservation genetic agenda would utilize data from enhanced surveys of genomic variation in endangered species to better manage functional genetic variation.     

Gene-expression variation within and among human populations

Understanding patterns of gene-expression variation within and among human populations will provide important insights into the molecular basis of phenotypic diversity and the interpretation of patterns of expression variation in disease. However, little is known about how gene-expression variation is apportioned within and among human populations. Here, we characterize patterns of natural gene-expression variation in 16 individuals of European and African ancestry. We find extensive variation in gene-expression levels and estimate that approximately 83% of genes are differentially expressed among individuals and that approximately 17% of genes are differentially expressed among populations. By decomposing total gene-expression variation into within- versus among-population components, we find that most expression variation is due to variation among individuals rather than among populations, which parallels observations of extant patterns of human genetic variation. Finally, we performed allele-specific quantitative polymerase chain reaction to demonstrate that cis-regulatory variation in the lymphocyte adaptor protein (SH2B adapter protein 3) contributes to differential expression between European and African samples. These results provide the first insight into how human population structure manifests itself in gene-expression levels and will help guide the search for regulatory quantitative trait loci.     

Evolutionary relationships between gene-structure and gene-regulation variation inDrosophila melanogaster

The evolutionary relationship between gene-structure and gene-regulation variation was examined by using data on allozyme and activity variation for a group of enzyme loci inDrosophila melanogaster. No significant correlation between the two kinds of variation was found, although the present data set is small and probably not sensitive for tests of association. Various hypotheses of association between the two types of variation are discussed and it is shown that any association between gene-structure and gene-regulation variation (positive or negative) would be sensitive to distortion by repeated bottlenecks and genetic drift. Furthermore, random forces would affect gene-structure (allozyme) variation, which is often controlled by one gene, more severely than enzyme activity variation, which is usually controlled by many genes. Measurements of activity variation would appear to provide an evolutionarily more stable and reliable estimate of. loci-specific ‘molecular flexibility’ than measurements of structural variation. It is suggested that locus-specific gene regulation studies employing a set of major alleles would provide a better test of association between gene-structure and gene-regulation variation. The relationship between gene regulation and quantitative variation is discussed and a number of population-genetic questions related to regulatory gene variation are formulated.     

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.     

Individual variation in bark beetle and moth pheromones - a comparison and an evolutionary background

The presently published data of variation in pheromone content in bark beetles (Coleoptera: Scolytidae) and moths (Lepidoptera) are reviewed. In both taxa high coefficients of variation, often up to around 100% for amount of pheromone, seem to be the rule. The contribution to the variation from errors in the chemical methods was small in most studies compared with the intrinsic biological variation. Examples arc given of variation in both absolute amounts, proportions of geometric isomers and in enantiomeric composition. Ratios of isomers often had lower coefficients of variation (25% or less). A lower average variation among sex pheromone in moths could relate to a mating system involving singly calling females, compared with the aggregation pheromone of bark beetles, which often call in large groups. The origin of a resource-based aggregation pheromone system by evolution working via individual selection is outlined.     

Genetic variation and fitness in salmonids

Over the last quarter century, many studieshave attempted to clarify the relationshipbetween genetic variability and fitness, butfew of these have involved salmonid fishes. Examination of studies of salmonids revealsthat such a relationship varies both among andwithin species. A correlation between geneticvariability and fitness can be affected bygenetic background, environment, and age, andit also depends upon the genetic markers andphenotypes evaluated. The relationshipsbetween molecular genetic variation,quantitative genetic variation, and phenotypicvariation may be more relevant to conservationissues than those between genetic variation andaverage fitness or performance. Consequently,future work in salmonids should include moreintensive investigation of the correspondenceof molecular genetic variation within and amongpopulations to quantitative genetic andphenotypic variation for traits affectingfitness. In the absence of a more completeunderstanding of the relationship betweengenetic variation and fitness, maintenance ofgenetic and phenotypic variation within andamong conspecific populations should beconsidered a primary goal of conservingsalmonid fishes.     

The Good,the Bad,and the Ugly: The Influence of Skull Reconstructions and Intraspecific Variability in Studies of Cranial Morphometrics in Theropods and Basal Saurischians

Several studies investigating macroevolutionary skull shape variation in fossil reptiles were published recently, often using skull reconstructions taken from the scientific literature. However, this approach could be potentially problematic, because skull reconstructions might differ notably due to incompleteness and/or deformation of the material. Furthermore, the influence of intraspecific variation has usually not been explored in these studies. Both points could influence the results of morphometric analyses by affecting the relative position of species to each other within the morphospace. The aim of the current study is to investigate the variation in morphometric data between skull reconstructions based on the same specimen, and to compare the results to shape variation occurring in skull reconstructions based on different specimens of the same species (intraspecific variation) and skulls of closely related species (intraspecific variation). Based on the current results, shape variation of different skull reconstructions based on the same specimen seems to have generally little influence on the results of a geometric morphometric analysis, although it cannot be excluded that some erroneous reconstructions of poorly preserved specimens might cause problems occasionally. In contrast, for different specimens of the same species the variation is generally higher than between different reconstructions based on the same specimen. For closely related species, at least with similar ecological preferences in respect to the dietary spectrum, the degree of interspecific variation can overlap with that of intraspecific variation, most probably due to similar biomechanical constraints.     

Genetic Variation Underlying Sexual Behavior and Reproduction

Selection depletes additive genetic variation underlying traitsimportant in fitness. Intense mating competition and femalechoice may result in negligible heritability in males. Femalesoften appear to choose mates, however, suggesting genetic variationin males which is important to females. Evidence is reviewedon allelic substitutions, karyotypic variation, and especiallythe heritable variation of continuous traits involved in sexualbehavior and reproduction. Phenotypic variation in male matingspeed and courtship intensity, female mating and ovipositionbehavior, egg size and number, body size, parthenogenesis, andthe sex ratio generally have heritable variation. The maintenanceof genetic variation, and the meaning of heritability estimatesfor natural populations is considered.     

Ornament and body size variation and their measurement in natural populations

Measurement of intrapopulation variation in secondary sexual traits is a priority in the testing of sexual selection models. However, it is important to take care in the choice of materials and delimitation of populations. The use of museum skins to study variation in male tail ornaments may substantially underrepresent the real degree of intrapopulation variation. Data from live animals in specific areas provide more realistic estimates, and should be used whenever possible. I use as an example field data on male ornament length and body size in Vidua macroura (Aves: Ploceidae), a promiscuous, parasitic African finch with elongated tail plumes. Individual males differ in the timing and rate of ornament growth, and females are therefore faced with a large degree of phenotypic variation in male ornament size, even though genetic variation may not be great. By correcting for seasonal variation in the ornament lengths of males caught at different times, I show that mid-season coefficients of variation in ornament length of breeding males in two populations are as high as 18% and 55%. By contrast, tarsus, wing and unornamented tail lengths of the same males vary from 2 to 4%.     

Sources and consequences of seed size variation in Lupinus perennis (Fabaceae): adaptive and non-adaptive hypotheses

Seed size variation within species and individuals is common. This variation may be adaptive in heterogeneous landscapes if the fitness consequences of seed size differ among environments or through time. Variation may also arise from constraints that limit control of seed size. I manipulated resource availability in both maternal and offspring environments to test conditions underlying these explanations for seed size variation in the herbaceous perennial Lupinus perennis. A fivefold variation in seed size arose primarily from differences among individuals and within-plant variability rather than from environmental conditions manipulated in the experiment. Environmental conditions had little effect on mean seed size; in contrast, within-plant variation in seed size increased with reduced resources. Fitness benefits from large seed size were similar across offspring environments, suggesting that environmental heterogeneity alone may not maintain seed size variation in this species. Surprisingly, seed size affected long-term fitness measures, including a plant's size and probability of flowering through its second year. These results are consistent with non-adaptive but not adaptive explanations for seed size variation. They also suggest that offspring size variation per se may contribute to variation in maternal fitness.     

Expression variation and covariation impair analog and enable binary signaling control

Due to noise in the synthesis and degradation of proteins, the concentrations of individual vertebrate signaling proteins were estimated to vary with a coefficient of variation (CV) of approximately 25% between cells. Such high variation is beneficial for population‐level regulation of cell functions but abolishes accurate single‐cell signal transmission. Here, we measure cell‐to‐cell variability of relative protein abundance using quantitative proteomics of individual Xenopus laevis eggs and cultured human cells and show that variation is typically much lower, in the range of 5–15%, compatible with accurate single‐cell transmission. Focusing on bimodal ERK signaling, we show that variation and covariation in MEK and ERK expression improves controllability of the percentage of activated cells, demonstrating how variation and covariation in expression enables population‐level control of binary cell‐fate decisions. Together, our study argues for a control principle whereby low expression variation enables accurate control of analog single‐cell signaling, while increased variation, covariation, and numbers of pathway components are required to widen the stimulus range over which external inputs regulate binary cell activation to enable precise control of the fraction of activated cells in a population.     

Evolutionary and plastic rescue in multitrophic model communities

Under changing environmental conditions, intraspecific variation can potentially rescue populations from extinction. There are two principal sources of variation that may ultimately lead to population rescue: genetic diversity and phenotypic plasticity. We compared the potential for evolutionary rescue (through genetic diversity) and plastic rescue (through phenotypic plasticity) by analysing their differential ability to produce dynamical stability and persistence in model food webs. We also evaluated how rescue is affected by the trophic location of variation. We tested the following hypotheses: (i) plastic communities are more likely to exhibit stability and persistence than communities in which genetic diversity provides the same range of traits. (ii) Variation at the lowest trophic level promotes stability and persistence more than variation at higher levels. (iii) Communities with variation at two levels have greater probabilities of stability and persistence than communities with variation at only one level. We found that (i) plasticity promotes stability and persistence more than genetic diversity; (ii) variation at the second highest trophic level promotes stability and persistence more than variation at the autotroph level; and (iii) more than variation at two trophic levels. Our study shows that proper evaluation of the rescue potential of intraspecific variation critically depends on its origin and trophic location.     

Environmental variation, stochastic extinction, and competitive coexistence

Understanding how environmental fluctuations affect population persistence is essential for predicting the ecological impacts of expected future increases in climate variability. However, two bodies of theory make opposite predictions about the effect of environmental variation on persistence. Single-species theory, common in conservation biology and population viability analyses, suggests that environmental variation increases the risk of stochastic extinction. By contrast, coexistence theory has shown that environmental variation can buffer inferior competitors against competitive exclusion through a storage effect. We reconcile these two perspectives by showing that in the presence of demographic stochasticity, environmental variation can increase the chance of extinction while simultaneously stabilizing coexistence. Our stochastic simulations of a two-species storage effect model reveal a unimodal relationship between environmental variation and coexistence time, implying maximum coexistence at intermediate levels of environmental variation. The unimodal pattern reflects the fact that the stabilizing influence of the storage effect accumulates rapidly at low levels of environmental variation, whereas the risk of extinction due to the combined effects of environmental variation and demographic stochasticity increases most rapidly at higher levels of variation. Future increases in environmental variation could either increase or decrease an inferior competitor's expected persistence time, depending on the distance between the present level of environmental variation and the optimal level anticipated by this theory.     

Female guppies agree to differ: phenotypic and genetic variation in mate-choice behavior and the consequences for sexual selection

Variation among females in mate choice may influence evolution by sexual selection. The genetic basis of this variation is of interest because the elaboration of mating preferences requires additive genetic variation in these traits. Here we measure the repeatability and heritability of two components of female choosiness (responsiveness and discrimination) and of female preference functions for the multiple ornaments borne by male guppies (Poecilia reticulata). We show that there is significant repeatable variation in both components of choosiness and in some preference functions but not in others. There appear to be several male ornaments that females find uniformly attractive and others for which females differ in preference. One consequence is that there is no universally attractive male phenotype. Only responsiveness shows significant additive genetic variation. Variation in responsiveness appears to mask variation in discrimination and some preference functions and may be the most biologically relevant source of phenotypic and genetic variation in mate-choice behavior. To test the potential evolutionary importance of the phenotypic variation in mate choice that we report, we estimated the opportunity for and the intensity of sexual selection under models of mate choice that excluded and that incorporated individual female variation. We then compared these estimates with estimates based on measured mating success. Incorporating individual variation in mate choice generally did not predict the outcome of sexual selection any better than models that ignored such variation.     

The Conservation Value of Peripheral Populations and a Relationship Between Quantitative Trait and Molecular Variation

The adaptive potential of populations and therefore their ability to cope with rapid environmental changes is a question of paramount fundamental and applied importance. However, what is still not clear is the effect of population position within the species range (i.e. core vs. edge) on population adaptive potential, and whether the adaptive potential can be predicted from extent of neutral molecular variation. In this study, we compared the extent and structure of neutral (SSR) and presumably adaptive quantitative trait genetic variation in populations of Triticum dicoccoides sampled at the species range core and two opposite edges, and related this information to multigenerational performance of plants experimentally introduced beyond the range edge. The plants from the species arid edge performed worse than plants from the more mesic core in extreme desert conditions. The core and edge populations did not differ in extent of SSR variation. In contrast to the neutral genetic variation, there was lower quantitative trait variation in the two edge as compared with the core population for many traits, and no trait in any edge population had higher variation than the core population or either of its habitats. Reduced variation in selectively important traits indicates a lower adaptive potential of the two edge as compared with the core population. Our results imply (1) that extent of variation in quantitative traits can predict plant performance in novel environments while extent of variation in molecular markers can not; and (2) caution in usage of peripheral populations in such conservation actions as relocation and creation of new populations. We also warn against usage of neutral molecular variation as a surrogate for selectively important quantitative variation in conservation decisions.     

云南滇龙胆居群表型多样性及其与环境关系研究

为揭示滇龙胆天然居群表型变异程度和变异规律,以云南省5个区域天然分布的20个野生居群400个单株20个表型性状指标为调查研究对象,并用变异系数、Shannon-Weiner多样性指数和巢式方差分析对滇龙胆居群间和居群内的表型变异进行分析,用相关性分析对滇龙胆表型性状与地理气象因子间的变异格局进行分析,用类平均聚类法对20个滇龙胆居群进行分类.结果表明:5个区域的滇龙胆以楚雄地区变异最大,变异系数为39.8%,变异最小的是昆明地区,为31.4%;不同居群的20个表型性状变异程度差异明显,变异系数在14.4%～91.8%之间,平均为40.4%,20个居群的平均变异为26.8%～37.0%;滇龙胆地理居群的表型分化较高,20个性状居群间的分化系数平均为73.14%,变化范围为36.03%～91.94%,居群间变异高于居群内;滇龙胆20个表型性状的总的多样性指数平均为2.547,5个不同分布区域多样性指数存在差异,最大为楚雄(1.271 4),最小为玉溪(1.266 7);表型性状变异受经度和降雨量影响较大,与纬度、海拔和温度相关性不显著;通过UPGMA聚类,滇龙胆被分成3个组,性状的表型特征并没有依地理距离而聚类....