Sources of uncertainty in assessment of marine phytoplankton communities

Characterisation of phytoplankton communities is important for classification of the ecological status of marine waters. In order to design a monitoring programme, it is important to know what degree of variation in the measurements occur at each level (water body, station and sample), so that resources can be spent in a way that maximise the precision of the measured parameters. Seven European water bodies were sampled to assess the variation in pigment concentrations and population densities attributed to water body, station and sample levels. It was found that the main proportion of the variation between pigment measurements was explained by the variation between stations (12–91% of variation) followed by the variation between water bodies (0–89% of variation). For measurements of population density, the main proportion of the variation between densities of cells recorded was explained by the variation between the taxonomists counting the samples (61%), whilst the main proportion of the variation between numbers of taxa recorded was explained by the variation between water bodies (83%). When the cell density of the nine dominant classes were analysed separately, the main proportion of variation was explained at the water body level for all but two class.     

群体基因组结构变异检测工作流

结构变异作为人类基因组上的一种大规模的变异类型,对分子与细胞进程、调节功能、基因表达调控、个体表型具有重要的影响,检测群体中基因组结构变异有助于绘制群体基因组变异图谱,刻画群体遗传进化特征,为疾病诊治、精准医疗的发展提供支撑。本研究提出一种面向高通量测序的群体基因组结构变异检测工作流,该工作流通过使用多种高性能基因组结构变异检测算法实现全面、精准的结构变异挖掘,使用多层融合与过滤获得高精度群体结构变异候选集合,利用基因型重新校正、变异修剪、类型校对,最终完整绘制群体基因组结构变异图谱。基于该工作流对由267个样本组成的人群进行群体结构变异检测,检测出了96 202个结构变异,其变异种类和频率分布与其他国际基因组计划相符,这些结果证明了本工作流具有良好的群体结构变异检测能力。同时,工作流通过并行的方式在内存可控的基础上显著降低了分析时间,为大规模人群基因组结构变异的高效检测提供了重要支撑。     

Patterns and causes of spatial variation in the reproductive success of a desert annual

Summary This study examines patterns and causes of variation in the reproductive success of the desert annual Stipa capensis. Three nested scales of variation were analyzed: variation between individuals of the same plot, variation between different plots of the same habitat, and variation between different habitats in the same region. Perturbation experiments (irrigation and neighbors removal) were performed to test the effects of heterogeneity in soil water and neighborhood competition on the magnitude of variation in each scale. The results demonstrate that variation of reproductive success was highest within plots, lowest between plots, and moderate between habitats. Soil water heterogeneity contributed to spatial variation in all scales but was most important for differences between habitats. Neighborhood competition increased the variation within plots, but decreased the variation between habitats. The results further demonstrate that water limitation was negatively correlated with the position of the habitat along the run-off/run-on gradient. An opposite trend was obtained for the effect of competition.     

Geographic variation of wing morphology of great fruit‐eating bats (Artibeus lituratus): environmental,genetic and spatial correlates of phenotypic differences

Responses of species to environmental gradients are important and frequent determinants of geographic phenotypic variation that can drive adaptive processes. Nonetheless, random genetic processes such as drift can also result in geographic variation in phenotypes, and should be evaluated before implicating selection as the process driving phenotypic change. We examined geographic variation in wing morphology of Artibeus lituratus among 18 different sites distributed across interior Atlantic Forest of Paraguay and Argentina. Moreover, we contrasted geographic variation with environmental, spatial, and genetic variation to test hypotheses related to selection and drift and their impacts on wing morphology. For A. lituratus distributed across interior Atlantic Forest, significant differences among sites characterized variation in wing morphology. Geographic variation was significantly related to climatic variables but not spatial or genetic distances. Such a pattern suggests that phenotypic variation is related to selection for particular environmental regimes, and not genetic drift. Four significant dimensions of phenotypic variation were determined. Three dimensions were related to variation among individuals in terms of wing tips, whereas one was related to overall body size. Wing tips are important for manoeuverability during flight and differences among sites likely reflect differences in forest and vegetation structure that must be managed during foraging. Although climate provides good surrogates for environmental variation, it is probably only an indirect cue of selection regimes that determine variation in wing morphology. Future studies should evaluate more direct environmental measures such as vegetation structure when attempting to interpret geographical variation in wing morphology.     

Consequences of ignoring spatial variation in population trend when conducting a power analysis

Long‐term, large‐scale monitoring programs are becoming increasingly common to document status and trends of wild populations. A successful program for monitoring population trend hinges on the ability to detect the trend of interest. Power analyses are useful for quantifying the sample size needed for trend detection, given expected variation in the population. Four components of variation (within‐year variation at a given site, interannual variation within a site, variation among sites in the interannual variation, and variation among sites in mean abundance or density) are commonly considered in power analyses for population trend, but a fifth is rarely considered: variation among sites in the local trend. Spatial variation in trend is expected to reduce statistical power, but the magnitude of this reduction has not been fully explored. We used computer simulations to evaluate the consequences of ignoring spatial variation in trend under a variety of sampling designs and wide ranges of other components of variation. The effect of spatial variation in trend on power was minor when other input parameters took extreme values that made the trend either very difficult or very easy to detect. However, at moderate values of the other parameters, spatial variation in trend had a strong effect, reducing statistical power by up to 60%. In some cases, ignoring spatial variation in trend resulted in an 80% probability of a type I error (falsely detecting a trend in a stable population). Spatial variation in trend is therefore an important consideration when designing a long‐term monitoring program for many species, especially those affected by local conditions at sites that are repeatedly surveyed. If variation in trend is ignored, as in many previous power analyses, the recommended sampling design will likely be insufficient to detect the trend of interest and lead to potentially false conclusions of a stable population.     

Approaching the Lower Limits of Transgene Variability

The inclusion of chicken lysozyme matrix-associated regions (MARs) in T-DNA has been demonstrated to reduce the variation in [beta]-glucuronidase (GUS) gene expression among first-generation transformed plants. The residual variation observed between transgenic plant lines with MARs at the T-DNA borders was investigated. By definition, any phenotypic variance between or within genetically identical plants is caused by random or environmental variation. This variation therefore sets a lower limit to the variation in GUS activities. The variance of GUS activity in offspring plant populations of genetically identical individuals was used as an estimate of environmental variation. For transgenic plants with MARs at the T-DNA borders, the variation between independent transformants could not be distinguished from the environmental variation. The variation could be attributed mainly to the variation in the GUS activity measurement. Therefore, the MAR element approached the maximal possible reduction of transgene variability given current technology and sample sizes. The role of MARs in offspring plants was evaluated by comparing such populations of transgenic plants for the magnitude of and variation in GUS activity. Pairwise comparisons showed that the presence of MARs reduced variation in offspring generations in the same manner as demonstrated for primary transformants. The populations carrying a doubled cauliflower mosaic virus 35S promoter-GUS gene tended to be more variable than the Lhca3.St.1 promoter-GUS gene-carrying populations. This tendency indicated an intrinsic susceptibility of the doubled cauliflower mosaic virus 35S promoter to variation. Homozygous plants were approximately twice as active as the corresponding hemizygous plants and tended to be more variable than the hemizygous plants. We hypothesized that the magnitude of environmental variations is related to a higher susceptibility to transgene silencing.     

The causes of variation in tree seedling traits: the roles of environmental selection versus chance

A key aspect of biodiversity is the great quantitative variation in functional traits observed among species. One perspective asserts that trait values should converge on a single optimum value in a particular selective environment, and consequently trait variation would reflect differences in selective environment, and evolutionary outcomes would be predictable. An alternative perspective asserts that there are likely multiple alternative optima within a particular selective environment, and consequently different lineages would evolve toward different optima due to chance. Because there is evidence for both of these perspectives, there is a long-standing controversy over the relative importance of convergence due to environmental selection versus divergence due to chance in shaping trait variation. Here, I use a model of tree seedling growth and survival to distinguish trait variation associated with multiple alternative optima from variation associated with environmental differences. I show that variation in whole plant traits is best explained by environmental differences, whereas in organ level traits variation is more affected by alternative optima. Consequently, I predict that in nature variation in organ level traits is most closely related to phylogeny, whereas variation in whole plant traits is most closely related to ecology.     

Evolution of variation in presence and absence of genes in bacterial pathways

ABSTRACT: BACKGROUND: Bacterial genomes exhibit a remarkable degree of variation in the presence and absence of genes, which probably extends to the level of individual pathways. This variation may be a consequence of the significant evolutionary role played by horizontal gene transfer, but might also be explained by the loss of genes through mutation. A challenge is to understand why there would be variation in gene presence within pathways if they confer a benefit only when complete. RESULTS: Here, we develop a mathematical model to study how variation in pathway content is produced by horizontal transfer, gene loss and partial exposure of a population to a novel environment. CONCLUSIONS: We discuss the possibility that variation in gene presence acts as cryptic genetic variation on which selection acts when the appropriate environment occurs. We find that a high level of variation in gene presence can be readily explained by decay of the pathway through mutation when there is no longer exposure to the selective environment, or when selection becomes too weak to maintain the genes. In the context of pathway variation the role of horizontal gene transfer is probably the initial introduction of a complete novel pathway rather than in building up the variation in a genome without the pathway.     

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.     

Individual size variation reduces spatial variation in abundance of tree community assemblage,not of tree populations

Research on individual trait variation has gained much attention because of its implication for ecosystem functions and community ecology. The effect of individual variation on population and community abundance (number of individuals) variation remains scarcely tested. Using two established ecological scaling laws (Taylor's law and abundance–size relationship), we derived a new scaling relationship between the individual size variation and spatial variation of abundance. Tested against multi‐plot tree data from Diaoluo Mountain tropical forest in Hainan, China, the new scaling relationship showed that individual size variation reduced the spatial variation of community assemblage abundance, but not of taxon‐specific population abundance. The different responses of community and population to individual variation were reflected by the validity of the abundance–size relationship. We tested and confirmed this scaling framework using two measures of individual tree size: aboveground biomass and diameter at breast height. Using delta method and height‐diameter allometry, we derived the analytic relation of scaling exponents estimated under different individual size measures. In addition, we used multiple regression models to analyze the effect of taxon richness on the relationship between individual size variation and spatial variation of population or community abundance, for taxon‐specific and taxon‐mixed data, respectively. This work offers empirical evidence and a scaling framework for the negative effect of individual trait variation on spatial variation of plant community. It has implications for forest ecosystem and management where the role of individual variation in regulating population or community spatial variation is important but understudied.     

Identifying Sources of Variation in Sheet Metal Stamping

Manufacturers using traditional process control charts to monitor their sheet metal stamping processes often encounter out-of-control signals indicating that the process mean has changed. Unfortunately, a sheet metal stamping process does not have the necessary adjustability in its process variable input settings to allow easily correcting the mean response in an out-of-control condition. Hence the signals often go ignored. Accordingly, manufacturers are unaware of how much these changes in the mean inflate the variance in the process output. We suggest using a designed experiment to quantify the variation in stamped panels attributable to changing means. Specifically, we suggest classifying stamping variation into three components: part-to-part, batch-to-batch, and within batch variation. The part-to-part variation represents the short run variability about a given stable or trending batch mean. The batch-to-batch variation represents the variability of the individual batch mean between die setups. The within batch variation represents any movement of the process mean during a given batch run. Using a two-factor nested analysis of variance model, a manufacturer may estimate the three components of variation. After partitioning the variation, the manufacturer may identify appropriate countermeasures in a variation reduction plan. In addition, identifying the part-to-part or short run variation allows the manufacturer to predict the potential process capability and the inherent variation of the process given a stable mean. We demonstrate the methodology using a case study of an automotive body side panel.     

Historic and contemporary levels of genetic variation in two New Zealand passerines with different histories of decline

We compared historic and contemporary genetic variation in two threatened New Zealand birds (saddlebacks and robins) with disparate bottleneck histories. Saddlebacks showed massive loss of genetic variation when extirpated from the mainland, but no significant loss of variation following a severe bottleneck in the 1960s when the last population was reduced from approximately 1000 to 36 birds. Low genetic variation was probably characteristic of this isolated island population: considerably more genetic variation would exist in saddlebacks today if a mainland population had survived. In contrast to saddlebacks, contemporary robin populations showed only a small decrease in genetic variation compared with historical populations. Genetic variation in robins was probably maintained because of their superior ability to disperse and coexist with introduced predators. These results demonstrate that contemporary genetic variation may depend more greatly on the nature of the source population and its genetic past than it does on recent bottlenecks.     

Effects of egg size on Double-crested Cormorant (Phalacrocorax auritus) egg composition and hatchling phenotype

Maternal investment of yolk and albumen in avian eggs varies with egg mass and contributes to variation in hatchling mass. Here we use the natural variation in mass and composition of Double-crested Cormorant (Phalacrocorax auritus) eggs to examine consequences of variation in yolk and albumen mass on hatchling phenotype. The Double-crested Cormorant, a large bird with altricial young, lays eggs ranging in mass from 40 to 60 g and containing an average of 82% albumen and 18% yolk. Variation in Cormorant egg mass arises primarily from variation in the amount of albumen and water in the eggs; yolk mass remains relatively constant, contributing only 10% to egg mass variation. Likewise, variation in hatchling mass correlates positively with albumen mass and albumen solids contribute to hatchling dry mass. Thus, variation in Cormorant egg mass is primarily the result of variation in the amount of egg albumen, which contributes most to variation in hatchling mass. Similarities in egg composition of altricial birds, along with data presented here, suggest that variation in hatchling mass of all altricial birds may depend most on the amount of egg albumen, unlike species with precocial young that hatch from eggs with substantially more yolk.     

Role of FRIGIDA and FLOWERING LOCUS C in determining variation in flowering time of Arabidopsis

Arabidopsis (Arabidopsis thaliana) accessions provide an excellent resource to dissect the molecular basis of adaptation. We have selected 192 Arabidopsis accessions collected to represent worldwide and local variation and analyzed two adaptively important traits, flowering time and vernalization response. There was huge variation in the flowering habit of the different accessions, with no simple relationship to latitude of collection site and considerable diversity occurring within local regions. We explored the contribution to this variation from the two genes FRIGIDA (FRI) and FLOWERING LOCUS C (FLC), previously shown to be important determinants in natural variation of flowering time. A correlation of FLC expression with flowering time and vernalization was observed, but it was not as strong as anticipated due to many late-flowering/vernalization-requiring accessions being associated with low FLC expression and early-flowering accessions with high FLC expression. Sequence analysis of FRI revealed which accessions were likely to carry functional alleles, and, from comparison of flowering time with allelic type, we estimate that approximately 70% of flowering time variation can be accounted for by allelic variation of FRI. The maintenance and propagation of 20 independent nonfunctional FRI haplotypes suggest that the loss-of-function mutations can confer a strong selective advantage. Accessions with a common FRI haplotype were, in some cases, associated with very different FLC levels and wide variation in flowering time, suggesting additional variation at FLC itself or other genes regulating FLC. These data reveal how useful these Arabidopsis accessions will be in dissecting the complex molecular variation that has led to the adaptive phenotypic variation in flowering time.     

Evolution of anuran brains: disentangling ecological and phylogenetic sources of variation

Variation in ecological selection pressures has been implicated to explain variation in brain size and architecture in fishes, birds and mammals, but little is known in this respect about amphibians. Likewise, the relative importance of constraint vs. mosaic hypotheses of brain evolution in explaining variation in brain size and architecture remains contentious. Using phylogenetic comparative methods, we studied interspecific variation in brain size and size of different brain parts among 43 Chinese anuran frogs and explored how much of this variation was explainable by variation in ecological factors (viz. habitat type, diet and predation risk). We also evaluated which of the two above‐mentioned hypotheses best explains the observed patterns. Although variation in brain size explained on average 80.5% of the variation in size of different brain parts (supporting the constraint hypothesis), none of the three ecological factors were found to explain variation in overall brain size. However, habitat and diet type explained a significant amount of variation in telencephalon size, as well in three composite measures of brain architecture. Likewise, predation risk explained a significant amount of variation in bulbus olfactorius and optic tecta size. Our results show that evolution of anuran brain accommodates features compatible with both constraint (viz. strong allometry among brain parts) and mosaic (viz. independent size changes in response to ecological factors in certain brain parts) models of brain size evolution.     

Nonclinality of molecular variation implicates selection in maintaining a morphological cline of Drosophila melanogaster

One general approach for assessing whether phenotypic variation is due to selection is to test its correlation with presumably neutral molecular variation. Neutral variation is determined by population history, the most likely alternative explanation of spatial genetic structure, whereas phenotypic variation may be influenced by the spatial pattern of selection pressure. Several methods for comparing the spatial apportionment of molecular and morphological variation have been used. Here, we present an analysis of variance framework that compares the magnitudes of latitudinal effects for molecular and morphological variation along a body size cline in Australian Drosophila populations. Explicit incorporation of the relevant environmental gradient can result in a simple and powerful test of selection. For the Australian cline, our analysis provides strong internal evidence that the cline is due to selection.     

Craniofacial variation in Homo habilis: an analysis of the evidence for multiple species

The question of heterogeneity in the Homo habilis sample continues to be controversial. Various lines of evidence have been used to reject the null hypothesis of intraspecific variation. This evidence derives from analyses of endocranial volume variation, probability estimates of sexual dimorphism, facial variation, cranial angles, CV analysis of craniofacial variation, the multivariate pattern of sexual dimorphism, the pattern of variability (CV) profiles, distance data using exact randomization methods, and various kinds of quantitative ordinations of fossils. Although consensus is lacking as to how the H. habilis sample is to be split, there is a growing perception that the degree of variation among the fossils is too great and the pattern of variation is too different to be explained by intraspecific variation. This has resulted in the recognition of new species such as "Homo rudolfensis." The present study critically examines the evidence commonly cited as the basis for recognizing multiple species in the extended H. habilis hypodigm. Reanalysis and reinterpretation of these data indicates that: (1) the degree of variation in the H. habilis sample is typical of modern hominoids, and (2) the pattern of variation among specimens of the H. habilis sample is consistent with intraspecific variation. Thus, at present, there is no sound basis to reject the null hypothesis of intraspecific variation as an adequate explanation of the morphological variation seen among specimens of the extended H. habilis sample. If multiple species are indeed represented, then their presence has not yet been satisfactorily demonstrated.     

The effect of genetic and environmental variation on metabolic gene expression

What is the relationship between genetic or environmental variation and the variation in messenger RNA (mRNA) expression? To address this, microarrays were used to examine the effect of genetic and environmental variation on cardiac mRNA expression for metabolic genes in three groups of Fundulus heteroclitus: (i) individuals sampled in the field (field), (ii) field individuals acclimated for 6 months to laboratory conditions (acclimated), or (iii) individuals bred for 10 successive generations in a laboratory environment (G10). The G10 individuals have significantly less genetic variation than individuals obtained in the field and had a significantly lower variation in mRNA expression across all genes in comparison to the other two groups (P = 0.001). When examining the gene specific variation, 22 genes had variation in expression that was significantly different among groups with lower variation in G10 individuals than in acclimated individuals. Additionally, there were fewer genes with significant differences in expression among G10 individuals vs. either acclimated or field individuals: 66 genes have statistically different levels of expression vs. 107 or 97 for acclimated or field groups. Based on the permutation of the data, these differences in the number of genes with significant differences among individuals within a group are unlikely to occur by chance (P < 0.01). Surprisingly, variation in mRNA expression in field individuals is lower than in acclimated individuals. Relative to the variation among individual within a group, few genes have significant differences in expression among groups (seven, 2.3%) and none of these are different between acclimated and field individuals. The results support the concept that genetic variation affects variation in mRNA expression and also suggests that temporal environmental variation associated with estuarine environments does not increase the variation among individuals or add to the differences among groups.     

Coexistence of competitors in spatially and temporally varying environments: A look at the combined effects of different sorts of variability

A stochastic model is developed for competition among organisms living in a patchy and varying environment. The model is designed to be suitable for species with sedentary adults and widely dispersing larvae or propagules, and applies best to marine systems but may also be adequate for some terrestrial systems. Three kinds of environmental variation are incorporated simultaneously in the model. These are pure spatial variation, pure temporal variation, and the space × time interaction. All three kinds of variation can promote coexistence, and when variation is restricted to immigration rates, all three kinds act very similarly. Moreover, for long-lived organisms their action is nearly identical, and their effects, when present together, combine equivalently. For short-lived organisms, however, pure temporal variation is a less effective promoter of coexistence. Variation in death rates acts quite differently from variation in birth rates for it may demote coexistence in some circumstances, while promoting coexistence in other circumstances. Furthermore, pure spatial variation in death rates has quite different effects than other kinds of death-rate variation. In addition to conditions for coexistence, information is given on population fluctuations, convergence to stationary distributions, and asymptotic distributions for long-lived organisms. While the model is presented as an ecological model, a genetical interpretation is also possible. This leads to new suggested mechanisms for the maintenance of polymorphisms in populations.