Reducing environmental bias when measuring natural selection

Abstract.— Crucial to understanding the process of natural selection is characterizing phenotypic selection. Measures of phenotypic selection can be biased by environmental variation among individuals that causes a spurious correlation between a trait and fitness. One solution is analyzing genotypic data, rather than phenotypic data. Genotypic data, however, are difficult to gather, can be gathered from few species, and typically have low statistical power. Environmental correlations may act through traits other than through fitness itself. A path analytic framework, which includes measures of such traits, may reduce environmental bias in estimates of selection coefficients. We tested the efficacy of path analysis to reduce bias by re-analyzing three experiments where both phenotypic and genotypic data were available. All three consisted of plant species (Impatiens capensis, Arabidopsis thaliana , and Raphanus sativus) grown in experimental plots or the greenhouse. We found that selection coefficients estimated by path analysis using phenotypic data were highly correlated with those based on genotypic data with little systematic bias in estimating the strength of selection. Although not a panacea, using path analysis can substantially reduce environmental biases in estimates of selection coefficients. Such confidence in phenotypic selection estimates is critical for progress in the study of natural selection.     

Measuring spatial variation in natural selection using randomly-sown seeds of Arabidopsis thaliana

We describe a simple method of measuring spatial variation in fitness using randomly sown seeds. Given a random initial distribution of seeds, any spatial variation in the final distribution of genotypes must be the result of spatial variation in natural selection. Departures from spatial randomness are tested using a modification of join-count statistics, based on the probability that two randomly chosen plants separated by a given distance carry the same genetic marker. Monte Carlo simulations showed that for the randomly sown seeds design the join-count test had higher power to detect spatial variation in fitness than analysis of variance. The power was relatively independent of the number of genotypes used or the number of microsites sampled. The method was tested in the field using three standard lines of Arabidopsis thaliana. At the end of the life cycle, adjacent plants were significantly more likely to be the same line than randomly chosen pairs and the spatial dependence extended to distances of nearly 50 cm. Simple experiments like this may be especially useful for “comparative ecological genetics”, allowing systematic studies of natural selection among many species or habitats.     

MEASURING NATURAL SELECTION ON PHENOTYPIC PLASTICITY

To understand natural selection we need to integrate its measure across environments. We present a method for measuring phenotypic selection that combines the potential for both environmental variation and phenotypic plasticity. The method uses path analysis and a measure of selection that is analogous to selection on breeding values. For individuals growing in alternative environments, paths are created that represent potential changes in the environment. The probabilities for these changes are then multiplied by the path coefficients to calculate selection coefficients. Selection on plasticity is measured as the difference in selection within each environment. We illustrate these methods using data on selection in an experimental population of Arabidopsis thaliana. Individuals from 36 families were grown in one of four environments, a factorial combination of shaded/open and early/late shading. For final height of the inflorescence, there was positive selection in both the open and shaded environments and negative selection on plasticity of height. For bolting time, there was also positive selection in both environments, but no selection on plasticity. We show how to use this information to examine how selection would change with changes in environmental frequencies and their transition probabilities. These methods can be expanded to encompass continuous traits and continuous environments as well as other complexities of natural selection.     

Antagonistic multilevel selection on size and architecture in variable density settings

In some ecological settings, an individual's fitness depends on both its own phenotype (individual-level selection) as well as the phenotype of the individuals with which it interacts (group-level selection). Using contextual analysis to measure multilevel selection in experimental stands of Arabidopsis thaliana, we detected significant linear selection that reversed across individual versus group levels for two composite phenotypic traits, "size" and "elongation." In both cases, selection at the individual level acted to increase values of these traits, presumably due to their positive effect on resource acquisition. Group selection favored decreased values of the same traits. Nonlinear selection was weak but significant in several cases, including stabilizing selection on developmental rate; individuals with very rapid development likely had lower than average fitness due to their reduced resource level at reproduction, while very delayed reproduction may have resulted in lower fitness if prolonged competition for resources reduced overall environmental quality and fitness of all individuals in a group. Under this scenario, stabilizing selection on individual traits is evidence of selection at the group level. Significant density-dependent selection suggests that a threshold density must be reached before group selection acts. Below this threshold, selection at the individual level affects phenotypic evolution more strongly than group selection. A second experiment measured multilevel selection in progeny stands of the original experimental plants. Multilevel selection again acted antagonistically on a composite trait that included size and elongation as well as on an architectural trait, branch production. The magnitude of individual versus group selection was relatively similar in the progeny generation, and the observed balance of individual versus group selection across densities is generally consistent with the hypotheses that multilevel selection can contribute to phenotypic evolution and to important demographic phenomena, including soft selection and the "law of constant yield."     

The genetic consequences of selection in natural populations

The selection coefficient, s, quantifies the strength of selection acting on a genetic variant. Despite this parameter's central importance to population genetic models, until recently we have known relatively little about the value of s in natural populations. With the development of molecular genetic techniques in the late 20th century and the sequencing technologies that followed, biologists are now able to identify genetic variants and directly relate them to organismal fitness. We reviewed the literature for published estimates of natural selection acting at the genetic level and found over 3000 estimates of selection coefficients from 79 studies. Selection coefficients were roughly exponentially distributed, suggesting that the impact of selection at the genetic level is generally weak but can occasionally be quite strong. We used both nonparametric statistics and formal random‐effects meta‐analysis to determine how selection varies across biological and methodological categories. Selection was stronger when measured over shorter timescales, with the mean magnitude of s greatest for studies that measured selection within a single generation. Our analyses found conflicting trends when considering how selection varies with the genetic scale (e.g., SNPs or haplotypes) at which it is measured, suggesting a need for further research. Besides these quantitative conclusions, we highlight key issues in the calculation, interpretation, and reporting of selection coefficients and provide recommendations for future research.     

Exploring natural selection to guide breeding for agriculture

Climate change threatens reduced crop production and poses major challenges to food security. The breeding of climate‐resilient crop varieties is increasingly urgent. Wild plant populations evolve to cope with changes in their environment due to the forces of natural selection. This adaptation may be followed over time in populations at the same site or explored by examining differences between populations growing in different environments or across an environmental gradient. Survival in the wild has important differences to the objective of agriculture to maximize crop yields. However, understanding the nature of adaptation in wild populations at the whole genome level may suggest strategies for crop breeding to deliver agricultural production with more resilience to climate variability.     

Natural selection. VI. Partitioning the information in fitness and characters by path analysis

Three steps aid in the analysis of selection. First, describe phenotypes by their component causes. Components include genes, maternal effects, symbionts and any other predictors of phenotype that are of interest. Second, describe fitness by its component causes, such as an individual's phenotype, its neighbours’ phenotypes, resource availability and so on. Third, put the predictors of phenotype and fitness into an exact equation for evolutionary change, providing a complete expression of selection and other evolutionary processes. The complete expression separates the distinct causal roles of the various hypothesized components of phenotypes and fitness. Traditionally, those components are given by the covariance, variance and regression terms of evolutionary models. I show how to interpret those statistical expressions with respect to information theory. The resulting interpretation allows one to read the fundamental equations of selection and evolution as sentences that express how various causes lead to the accumulation of information by selection and the decay of information by other evolutionary processes. The interpretation in terms of information leads to a deeper understanding of selection and heritability, and a clearer sense of how to formulate causal hypotheses about evolutionary process. Kin selection appears as a particular type of causal analysis that partitions social effects into meaningful components.     

Adaptive divergence in flowering time among natural populations of Arabidopsis thaliana: Estimates of selection and QTL mapping

To identify the ecological and genetic mechanisms of local adaptation requires estimating selection on traits, identifying their genetic basis, and evaluating whether divergence in adaptive traits is due to conditional neutrality or genetic trade‐offs. To this end, we conducted field experiments for three years using recombinant inbred lines (RILs) derived from two ecotypes of Arabidopsis thaliana (Italy, Sweden), and at each parental site examined selection on flowering time and mapped quantitative trait loci (QTL). There was strong selection for early flowering in Italy, but weak selection in Sweden. Eleven distinct flowering time QTL were detected, and for each the Italian genotype caused earlier flowering. Twenty‐seven candidate genes were identified, two of which (FLC and VIN3) appear under major flowering time QTL in Italy. Seven of eight QTL in Italy with narrow credible intervals colocalized with previously reported fitness QTL, in comparison to three of four in Sweden. The results demonstrate that the magnitude of selection on flowering time differs strikingly between our study populations, that the genetic basis of flowering time variation is multigenic with some QTL of large effect, and suggest that divergence in flowering time between ecotypes is due mainly to conditional neutrality.     

天山北部拟南芥自然居群表型变化的环境依赖特征

拟南芥(Arabidopsis thaliana)是植物生物学的模式植物, 在分子遗传学方面已经积累了丰富的研究成果, 但目前对拟南芥自然分布的生境特点、表型变化的环境依赖特征等研究很少, 极大地限制了对拟南芥进化动力和机制的理解。为了了解在微环境下拟南芥种群分布和表型性状的变化特点, 对天山北部分布于塔尔巴哈台山、阿尔泰山和天山的10个拟南芥种群的分布特征、表型的变化特点, 以及与综合环境因子的相互关系进行了分析。结果表明: 除分枝数外, 株高、株重、根重、单个果实重量、单株果数、单株果重、果长、果实开裂力度、单株果重/总重9个特征在种群间变化显著, 可塑性能力较强; 但方差分析和变异系数结果显示, 角果长度、果实开裂力度在种群内和种群间的变化相对较小。表型特征在山系间、经纬度和海拔间的变化规律不明显。拟南芥主要分布于pH值和HCO₃ ^-含量低, 有机质丰富, 且有一定坡度的沙土地块上。种群内拟南芥分布频度很低, 在1.56%-10.69%之间, 空间自相关距离在15.4-46.7 cm之间变化较大, 10个种群均呈现极显著集群分布, 分布的集群性受果实开裂力度的影响显著, 而果实开裂力度随环境胁迫而极显著增加。总结认为: 天山北部拟南芥生长和分布主要受微环境的影响, 在干旱环境下, 拟南芥主要通过增加繁殖分配比例, 产生难开裂的果实, 促使种子短距离扩散于母株周围, 确保子代利用原适宜生境来生存繁衍。     

Using human demographic history to infer natural selection reveals contrasting patterns on different families of immune genes

Detecting regions of the human genome that are, or have been, influenced by natural selection remains an important goal for geneticists. Many methods are used to infer selection, but there is a general reliance on an accurate understanding of how mutation and recombination events are distributed, and the well-known link between these processes and their evolutionary transience introduces uncertainty into inferences. Here, we present and apply two new, independent approaches; one based on single nucleotide polymorphisms (SNPs) that exploits geographical patterns in how humans lost variability as we colonized the world, the other based on the relationship between microsatellite repeat number and heterozygosity. We show that the two methods give concordant results. Of these, the SNP-based method is both widely applicable and detects selection over a well-defined time interval, the last 50 000 years. Analysis of all human genes by their Gene Ontology codes reveals how accelerated and decelerated loss of variability are both preferentially associated with immune genes. Applied to 168 immune genes used as the focus of a previous study, we show that members of the same gene family tend to yield similar indices of selection, even when located on different chromosomes. We hope our approach will provide a useful tool with which to infer where selection has acted to shape the human genome.     

Assortment and the analysis of natural selection on social traits

A central problem in evolutionary biology is to determine whether and how social interactions contribute to natural selection. A key method for phenotypic data is social selection analysis, in which fitness effects from social partners contribute to selection only when there is a correlation between the traits of individuals and their social partners (nonrandom phenotypic assortment). However, there are inconsistencies in the use of social selection that center around the measurement of phenotypic assortment. Here, we use data analysis and simulations to resolve these inconsistencies, showing that: (i) not all measures of assortment are suitable for social selection analysis; and (ii) the interpretation of assortment, and how to detect nonrandom assortment, will depend on the scale at which it is measured. We discuss links to kin selection theory and provide a practical guide for the social selection approach.     

Using genetic markers to directly estimate male selection gradients

We present an analysis of Raphanus raphanistrum and simulations illustrating the utility of directly estimating male phenotypic selection gradients using genetic markers. The method offers a much more refined characterization of selection than attempting to assign paternity to individual progeny. Our analysis of R. raphanistrum reveals selection on remarkably fine features of floral morphology, including anther exsertion, that were opaque to previous approaches. The new results also undermine a previous conclusion that selection on wild radish floral morphology acts primarily through female fitness. Simulation results show that selection gradients on the order of beta = 0.1-0.2 can be readily detected with allozyme markers in moderate-sized (< 200 paternal individuals) populations. Highly polymorphic (e.g., microsatellite) markers will likely detect fine scale selection (beta < 0.1) in larger populations (> or = 400 individuals). Increased progeny sample size, by sampling either additional maternal families or more progeny per maternal parent, partly compensates for low exclusion probability. Increasing the number of possible fathers without changing progeny sample size decreases the ability to detect selection, especially at lower exclusion probabilities. Sampling only some male genotypes reduces the power to detect selection and biases (underestimates) the magnitude of the selection gradient estimate.     

A non-destructive selection method for resistance to fusicoccin in Arabidopsis thaliana

A mutagenised population of seeds of Arabidopsis thaliana was allowed to germinate in the presence of the positively charged aminoglycoside hygromycin (4 μg/ml) and the fungal toxin fusicoccin (5×10^–6 m). This hygromycin concentration, which is non-toxic by itself, becomes toxic when used together with fusicoccin, which stimulates cation uptake. Seeds that had germinated after 3–5 days and produced seedlings with green cotyledons were potentially resistant to fusicoccin and were therefore transferred into sterile Magenta vessels containing 1/2-strength Murashige and Skoog medium. This selection procedure is non-destructive, i.e. it allows the recovery of viable seedlings and their growth into adult plants thus permitting direct physiological characterisation. Received: 16 February 1998 / Revision received: 11 August 1998 / Accepted: 13 August 1998     

天山北麓中段拟南芥（Arabidopsis thaliana）与相邻物种的分布格局及相互关系

天山山脉是世界拟南芥(Arabidopsis thaliana)及其近缘种的分布中心之一,资源优势明显.在北天山中段浅山地带选择拟南芥分布的典型样地50m×50m,分析了样地物种的结构、组成和土壤理化性质,用Ripley's K(d)函数分析了拟南芥与相邻物种的空间特征和相互关系.发现样地由7科23个物种组成,以新疆绢蒿(Seriphidium kaschgaricum)为建群种,短命植物物种占近70%.拟南芥仅分布于北坡,在3m内聚集强度高于所有分析物种,在5m范围内与新疆绢蒿中株呈显著正关联,与十字花科的涩芥(Malcolmia africana)、藜科的散枝猪毛菜(Salsola brachiata)、木碱蓬(Suaeda dendroides)、角果藜(Ceratocarpus arenarius)呈一定尺度显著负关联.分析认为拟南芥空间分布依赖于新疆绢蒿大株、中株生长塑造的遮阴、保湿和丰富土壤有机质,生态位与藜科物种差异极大,生境特异性高于同属近缘种小鼠耳芥(Arabidopsis pumila),以及涩芥(M. africana)、庭芥(Alyssum desertorum)、四齿芥(Tetracme quadricornis)、丝叶芥(Leptaleum filifolium)、狭果鹤虱(Lappula semiglabra)等短命植物.在干旱胁迫下,拟南芥环境选择强度大于种内作用,密度依赖的种子扩散表现不明显.扩散对策是通过大量生产种子,依靠果实不易开裂控制种子短距离扩散,充分利用原适宜生境来维持种群繁衍.     

An experimental test of the adaptive evolution of phototropins: blue-light photoreceptors controlling phototropism in Arabidopsis thaliana

Phototropins are blue-light photoreceptor molecules mediating the capacity for phototropism or bending toward or away from directional light. Like the red-light sensing phytochromes that control shade avoidance, phototropins modulate developmental plasticity in plant architecture. Yet, unlike phytochromes, the adaptive significance of phototropins has been largely a topic of conjecture. In Arabidopsis thaliana, phototropism of seedling and plant stems is under the control of two paralogous genes, PHOT1 and PHOT2, that encode different phototropins with partially redundant light response qualities. The PHOT1 gene product interacts with the NPH3 gene product to cause phototropic bending over a broad range of light intensity, from very weak light in the soil to stronger light in the aerial environment. The PHOT2 gene product modulates shoot bending in response to light of higher intensity only. We compared the fitness of wild-type, phot1, phot2, and nph3 genotypes over a range of light conditions in the field. Seeds were sown in the field on the soil surface and left bare or covered with either gravel or bark mulch chips. Plantings were made under full sun and dense canopy cover. Rates of seedling emergence, survival to flowering, and total seed set were measured. All mutant genotypes had significantly reduced lifetime fitness compared to wild-type. Consistent with their different fluence rate sensitivities, phot1 and phot2 signaling pathways affected fitness at discrete life-cycle stages. Fitness costs of phot1 and nph3 were expressed mainly during seedling emergence from the soil whereas that of phot2 was expressed solely after emergence. Surprisingly, the only significant genotype-by-environment interaction for fitness occurred during emergence: genotypes blind to dim blue light (phot1 and nph3) had poor emergence in the open, but not in the shade. Possibly, the loss of negative phototropism in seedling roots of mutant genotypes reduced establishment success in open (dry soil) conditions. Results show that phototropin-modulated pathways are adaptive and that their evolution has involved functional specialization. However, mechanism(s) of selection on these pathways remain a mystery.     

Phenotypic selection and response to selection in Lobularia maritima: importance of direct and correlational components of natural selection

By using selection differentials, gradients and structural equation modelling (SEM), I have quantified the phenotypic selection acting on Lobularia maritima (Cruciferae) flower size, display, colour and density, using data on lifetime female fitness. Furthermore, by analysing the resulting F₁ generation in field and greenhouse conditions, I estimated the actual intergenerational change in the value of these traits. Both pollinators preferred plants with many and large flowers. Strong directional selection for increased flower display was found in all years of the study, regardless of the technique used. Indirect selection due to a high significant correlation with flower display occurred on flower colour and size. SEM showed that pollinators played only a minor role in this observed phenotypic selection. The analysis of the phenotypes of F₁ plants showed that flower display actually increased across generations. In addition, white flowers were significantly more frequent in the offspring population than in the parental one, mostly due to the association between flower display and white coloured flowers. This suggests that both direct and indirect selection can play a role in the evolution of correlated traits in this crucifer.     

Viability selection prior to trait expression is an essential component of natural selection

Natural selection operates throughout the life cycle of an organism. Correlative studies typically fail to consider the effects of viability selection prior to trait expression. A 3-year field experiment on the wildflower Mimulus guttatus demonstrates that this unmeasured component of selection can be very strong. As in previous studies, we find that fecundity is positively related to flower size. However, survival to flowering is much lower in large-flowered genotypes than in small-flowered genotypes. Aggregating viability and fecundity, lifetime fitness through female function generally favoured smaller flowered genotypes. This result differs from the great majority of field studies, which suggest strong positive selection on flower size. It has important cautionary implications for studies of natural and sexual selection on adult characters generally, in both plants and animals.     

Patrick Matthew's law of natural selection

Patrick Matthew is the little‐known first originator of macroevolution by natural selection. I review his ideas, and introduce some previously unnoticed writings (catalogued at a new website: http://smarturl.it/patrickmatthew ) that clarify how they differ from Darwin's and Wallace's. Matthew's formulation emphasized natural selection as an axiomatic ‘law’ rather than a ‘theory’, a distinction that could still be of use to us today. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●● , ●●–●●.