Adjusting for selection bias in assessing treatment effect estimates from multiple subgroups

This paper discusses a number of methods for adjusting treatment effect estimates in clinical trials where differential effects in several subpopulations are suspected. In such situations, the estimates from the most extreme subpopulation are often overinterpreted. The paper focusses on the construction of simultaneous confidence intervals intended to provide a more realistic assessment regarding the uncertainty around these extreme results. The methods from simultaneous inference are compared with shrinkage estimates arising from Bayesian hierarchical models by discussing salient features of both approaches in a typical application.     

Fitness consequences of plants growing with siblings: reconciling kin selection, niche partitioning and competitive ability

Plant studies that have investigated the fitness consequences of growing with siblings have found conflicting evidence that can support different theoretical frameworks. Depending on whether siblings or strangers have higher fitness in competition, kin selection, niche partitioning and competitive ability have been invoked. Here, we bring together these processes in a conceptual synthesis and argue that they can be co-occurring. We propose that these processes can be reconciled and argue for a trait-based approach of measuring natural selection instead of the fitness-based approach to the study of sibling competition. This review will improve the understanding of how plants interact socially under competitive situations, and provide a framework for future studies.     

Field tests of density-and frequency-dependent selection in Erigeron annuus (Compositae)

Selection may maintain genetic diversity in natural populations if the physical or biotic environment is variable over space and-or time. Because density and genotype frequencies can be heterogeneous, and because genotypes may differ in competitive ability, both density-and frequency-dependent selection have been considered to be potentially important evolutionary processes. To address the possibility that intraspecific interactions among plants are a source of fitness variation in Erigeron annuus, we conducted field experiments over 2 yr that were designed to examine the potential of population density, genotype frequency, and their interaction to act as selective agents. In both experiments, apomictic genotypes of Erigeron were paired. Seedlings were planted into plots that differed in density and the identity of minority and majority genotype. There was evidence for a differential effect of density among genotypes for only one year's experiment, suggesting that density-dependent selection is either weak or temporally variable. Genotype frequency had no effect on fitness in either year, and thus there was no evidence for frequency-dependent selection. In addition, the lack of a frequency ;ts density interaction demonstrates that resource partitioning, one mechanism for frequency dependence, is not strong among Erigeron genotypes. If frequency-dependent selection does occur in this species, it is either too weak to detect even in large field experiments, or occurs only in the presence of a selective agent (e.g., pathogens) that was lacking in our experiments.     

Mortality costs of sexual selection and parental care in natural populations of birds

Abstract Is the cost of reproduction different between males and females? On the one hand, males typically compete intensely for mates, thus sexual selection theory predicts higher cost of reproduction for males in species with intense male‐male competition. On the other hand, care provisioning such as incubating the eggs and raising young may also be costly, thus parental care theory predicts higher mortality for the care‐giving sex, which is often the female. We tested both hypotheses of reproductive costs using phylogenetic comparative analyses of sex‐specific adult mortality rates of 194 bird species across 41 families. First, we show that evolutionary increases in male‐male competition were associated with male‐biased mortalities. This relationship is consistent between two measures of mating competition: social mating system and testis size. Second, as predicted by the parental cost hypothesis, females have significantly higher adult mortalities (mean ± SE, 0.364 ± 0.01) than males (0.328 ± 0.01). However, the mortality cost of parental care was only detectable in males, when the influence of mating competition was statistically controlled. Taken together, our results challenge the traditional explanation of female‐biased avian mortalities, because evolutionary changes in female care were unrelated to changes in mortality bias. The interspecific variation in avian mortality bias, as we show here, is driven by males, specifically via the costs of both mating competition and parental care. We also discuss alternative hypotheses for why most birds exhibit female‐biased mortalities, whereas in mammals male‐biased mortalities predominate.     

Evaluation of selection on cliff swallows

Abstract Estimates of the intensity of selection based on measurements of the living and the dead require knowledge of the fraction of the original population dying. We apply recently developed methods (Blanckenhorn et al. 1999) to estimate the intensity of selection in a population of cliff swallows. In this population the fraction of individuals dying was unknown, but certainly high. The inferred selection is very strong and impossible to achieve if the original population is assumed to have followed a normal distribution. We consider several alternative explanations for this result including measurement biases, undetected immigration, and sampling biases. Of these, sampling biases are perhaps the most likely. We conclude that the intensity of selection on the swallows was probably strong, but its absolute magnitude is unknown.     

适合度的相对性与路径依赖的自然选择

自然选择理论认为生物个体或者种群在进化的过程中, 其基因或者性状、行为策略的选择一定是能够提高其适合度或者达到某个可期的“目标”。然而, 随着某个突变基因或者性状特征、行为策略在种群中扩散, 其期望收益将随着其在种群中分布的密度变化或环境改变而发生改变, 这就是适合度景观的悖论, 即静态的、固定可期望的收益可能因此而不存在。基于动态而非静态适合度景观的概念, 我们提出路径依赖的自然选择概念。路径依赖的自然选择过程中, 一个突变的基因或表型在某种环境下随机产生, 但是该基因或表型在某些特定环境下会产生正反馈。尤其是在正反馈与随机漂变的共同作用下, 多条路径的演化就可能发生, 并且其路径的形成将同时受到其种群进化历史过程和空间特征分布等因素的强烈影响。而在不同路径下, 由于观测维度、角度和尺度的不同, 适合度意义将因此而存在不同。在此意义下, 自然选择更可能选择路径频率而不是适合度大小。基于上述概念, 我们借鉴现代物理学中复函数的方法, 来描述多重动力对物种形成或者生物特征、种群进化等路径依赖的演化过程, 以期为同域物种、隐存种形成以及生物多样性演化提供解释机制。     

Intragenic Hill-Robertson interference influences selection intensity on synonymous mutations in Drosophila

Natural selection influences synonymous mutations and synonymouscodon usage in many eukaryotes to improve the efficiency oftranslation in highly expressed genes. Recent studies of genecomposition in eukaryotes have shown that codon usage also variesindependently of expression levels, both among genes and atthe intragenic level. Here, we investigate rates of evolution(Ks) and intensity of selection (_s) on synonymous mutationsin two groups of genes that differ greatly in the length oftheir exons, but with equivalent levels of gene expression andrates of crossing-over in Drosophila melanogaster. We estimate_s using patterns of divergence and polymorphism in 50 Drosophilagenes (100 kb of coding sequence) to take into account possiblevariation in mutation trends across the genome, among genesor among codons. We show that genes with long exons exhibithigher Ks and reduced _s compared to genes with short exons.We also show that Ks and _s vary significantly across long exons,with higher Ks and reduced _s in the central region comparedto flanking regions of the same exons, hence indicating thatthe difference between genes with short and long exons can bemostly attributed to the central region of these long exons.Although amino acid composition can also play a significantrole when estimating Ks and _s, our analyses show that the differencesin Ks and _s between genes with short and long exons and acrosslong exons cannot be explained by differences in protein composition.All these results are consistent with the Interference Selection(IS) model that proposes that the Hill-Robertson (HR) effectcaused by many weakly selected mutations has detectable evolutionaryconsequences at the intragenic level in genomes with recombination.Under the IS model, exon size and exon-intron structure influencethe effectiveness of selection, with long exons showing reducedeffectiveness of selection when compared to small exons andthe central region of long exons showing reduced intensity ofselection compared to flanking coding regions. Finally, ourresults further stress the need to consider selection on synonymousmutations and its variation—among and across genes andexons—in studies of protein evolution.     

Quantifying episodes of sexual selection: Insights from a transparent worm with fluorescent sperm

Sexual selection operates through consecutive episodes of selection that ultimately contribute to the observed variance in reproductive success between individuals. Understanding the relative importance of these episodes is challenging, particularly because the relevant postcopulatory fitness components are often difficult to assess. Here, we investigate different episodes of sexual selection on the male sex function, by assessing how (precopulatory) mating success, and (postcopulatory) sperm‐transfer efficiency and sperm‐fertilizing efficiency contribute to male reproductive success. Specifically, we used a transgenic line of the transparent flatworm, Macrostomum lignano, which expresses green fluorescent protein (GFP) in all cell types, including sperm cells, enabling in vivo sperm tracking and paternity analysis. We found that a large proportion of variance in male reproductive success arose from the postcopulatory episodes. Moreover, we also quantified selection differentials on 10 morphological traits. Testis size and seminal vesicle size showed significant positive selection differentials, which were mainly due to selection on sperm‐transfer efficiency. Overall, our results demonstrate that male reproductive success in M. lignano is not primarily limited by the number of matings achieved, but rather by the ability to convert matings into successful fertilizations, which is facilitated by producing many sperm.     

Lifetime selection on adult body size and components of body size in a waterstrider: opposing selection and maintenance of sexual size dimorphism

Abstract.— Sexual size dimorphism (SSD), the difference in body size between males and females, is common in almost all taxa of animals and is generally assumed to be adaptive. Although sexual selection and fecundity selection alone have often been invoked to explain the evolution of SSD, more recent views indicate that the sexes must experience different lifetime selection pressures for SSD to evolve and be maintained. We estimated selection acting on male and female adult body size (total length) and components of body size in the waterstrider Aquarius remigis during three phases of life history. Opposing selection pressures for overall body size occurred in separate episodes of fitness for females in both years and for males in one year. Specific components of body size were often the targets of the selection on overall body size. When net adult fitness was estimated by combining each individual's fitnesses from all episodes, we found stabilizing selection in both sexes. In addition, the net optimum overall body size of males was smaller than that of females. However, even when components of body size had experienced opposing selection pressures in individual episodes, no components appeared to be under lifetime stabilizing selection. This is the first evidence that contemporary selection in a natural population acts to maintain female size larger than male size, the most common pattern of SSD in nature.     

Interpretations arising from Wrightian and Malthusian fitness under strong frequency dependent selection

Fitness is the central concept in evolutionary theory. It measures a phenotype's ability to survive and reproduce. There are different ways to represent this measure: Malthusian fitness and Wrightian fitness. One can go back and forth between the two, but when we characterize model properties or interpret data, it can be important to distinguish between them. Here, we discuss a recent experiment to show how the interpretation changes if an alternative definition is used.     

On the standardization of fitness and traits in comparative studies of phenotypic selection

Comparisons of the strength and form of phenotypic selection among groups provide a powerful approach for testing adaptive hypotheses. A central and largely unaddressed issue is how fitness and phenotypes are standardized in such studies; standardization across or within groups can qualitatively change conclusions whenever mean fitness differs between groups. We briefly reviewed recent relevant literature, and found that selection studies vary widely in their scale of standardization, but few investigators motivated their rationale for chosen standardization approaches. Here, we propose that the scale at which fitness should be relativized should reflect whether selection is likely to be hard or soft; that is, the scale at which populations (or hypothetical populations in the case of a contrived experiment) are regulated. We argue that many comparative studies of selection are implicitly or explicitly focused on soft selection (i.e., frequency and density‐dependent selection). In such studies, relative fitness should preferably be calculated using within‐group means, although this approach is taken only occasionally. Related difficulties arise for the standardization of phenotypes. The appropriate scale at which standardization should take place depends on whether groups are considered to be fixed or random. We emphasize that the scale of standardization is a critical decision in empirical studies of selection that should always warrant explicit justification.     

Translational selection on SHH genes

Codon usage bias has been observed in various organisms. In this study, the correlation between SHH genes expression in some tissues and codon usage features was analyzed by bioinformatics. We found that translational selection may act on compositional features of this set of genes.     

Cultural selection drives the evolution of human communication systems

Human communication systems evolve culturally, but the evolutionary mechanisms that drive this evolution are not well understood. Against a baseline that communication variants spread in a population following neutral evolutionary dynamics (also known as drift models), we tested the role of two cultural selection models: coordination- and content-biased. We constructed a parametrized mixed probabilistic model of the spread of communicative variants in four 8-person laboratory micro-societies engaged in a simple communication game. We found that selectionist models, working in combination, explain the majority of the empirical data. The best-fitting parameter setting includes an egocentric bias and a content bias, suggesting that participants retained their own previously used communicative variants unless they encountered a superior (content-biased) variant, in which case it was adopted. This novel pattern of results suggests that (i) a theory of the cultural evolution of human communication systems must integrate selectionist models and (ii) human communication systems are functionally adaptive complex systems.     

Phenotypic selection in hawkmoth-pollinated Platanthera bifolia: targets and fitness surfaces

Abstract.— The present study explored phenotypic selection on phenological and morphological reproductive traits in hawkmoth-pollinated Platanthera bifolia (Orchidaceae), a Eurasian perennial herb displaying bisexual, long-spurred flowers. The work was carried out during three flowering seasons (1993–1995) in a Swedish population. Fitness was estimated as the number of pollinia removed (male fitness) and fruits produced (female fitness). Targets and patterns of selection were compared between years and sex functions by the use of multiple linear regression (including correlational selection estimates, i.e., of combination of traits), analysis of covariance, and projection pursuit regression (PPR). Results from the nonparametric surface-fitting-method PPR showed that selection was mostly linear, thus justifying the use of the parametric methods. In all study years, male and female fitness were highest in plants with many flowers. This reflects that flower number sets an upper limit to fitness and that a large inflorescence attracts more pollinators. In 1994, the summer was dry and the average spur length of P. bifolia was shorter than in the other years. In this year, male and female fitness were positively related to spur length, apparently because the spur of short-spurred plants was somewhat too short relative to the tongue length of the local pollinator for optimal pollen export and import. Additionally, the dry weather in 1994 caused a tendency for correlational selection, which was not found in the other years of study. Among small individuals (apparently more sensitive to drought than large ones), early-flowering plants had higher male and female fitness. The results show that patterns of selection may vary both between years and between sex functions in perennial hermaphroditic plants. The present study is one of the first to consider correlational selection in plants, which probably is of common occurrence and deserves to be investigated more.     

Natural selection and non-metric traits in skeletal populations

The hypothesis of this article is that the frequency of non-metric traits varies at different reproductive periods because of differential mortality associated with non-metric traits. 450 male and 203 female crania were examined. Mortality in the reproduction period is connected with the elimination of individuals with certain variants of non-metric traits. It seems that key genes which perform the stimulating function in the appearance of traits in a given category of formation are under selective pressure. It is assumed that natural selection acts both on the morphology of organisms and on developmental process through environmental conditions. Selection not only optimises the fitness of morphological features but also the processes leading to the formation of features during ontogeny. Both these mechanisms influence the interpopulational variability of non-metric traits.     

Index of opportunity for natural selection among the Gowdas of Kodagahalli village,Karnataka, India

BACKGROUND:

In order to understand how selection is operating in the Gowda population, the index of opportunity for selection was calculated and the present findings were compared with some related findings from other South Indian (SI) populations.

MATERIALS AND METHODS:

Crow (1958) and the modified method by Johnston and Kensinger (1971) were used for the present purpose.

RESULTS AND DISCUSSION:

The index of total selection intensity (I) was found to be moderate taking into consideration the range for many Indian populations. Considering certain differences in fertility and mortality heritable, it appears that natural selection play an important role in shaping the genetic constitution of the Gowda population. Analysis of data indicates that the index due to fertility seems to contribute more towards selection than mortality. This trend might be because of better living condition and health-care system among the Gowdas which have a positive impact on the lower contribution of mortality for the evolution mechanism of the Gowda population through natural selection.     

Estimating evolutionary parameters when viability selection is operating

Some individuals die before a trait is measured or expressed (the invisible fraction), and some relevant traits are not measured in any individual (missing traits). This paper discusses how these concepts can be cast in terms of missing data problems from statistics. Using missing data theory, I show formally the conditions under which a valid evolutionary inference is possible when the invisible fraction and/or missing traits are ignored. These conditions are restrictive and unlikely to be met in even the most comprehensive long-term studies. When these conditions are not met, many selection and quantitative genetic parameters cannot be estimated accurately unless the missing data process is explicitly modelled. Surprisingly, this does not seem to have been attempted in evolutionary biology. In the case of the invisible fraction, viability selection and the missing data process are often intimately linked. In such cases, models used in survival analysis can be extended to provide a flexible and justified model of the missing data mechanism. Although missing traits pose a more difficult problem, important biological parameters can still be estimated without bias when appropriate techniques are used. This is in contrast to current methods which have large biases and poor precision. Generally, the quantitative genetic approach is shown to be superior to phenotypic studies of selection when invisible fractions or missing traits exist because part of the missing information can be recovered from relatives.     

植物的亲缘选择

亲缘选择是指在一个随机交配群体中的个体基于亲缘关系而以一种非随机性的方式相互作用,其作用结果是亲缘个体得到更大的广义适合度。综述了亲缘选择和亲缘竞争两种观点以及各自的试验支持证据;分析了导致亲缘选择试验结果出现分歧的原因,认为这主要是由于对亲缘选择理解上的模糊以及试验设计的不严谨所致。植物间的亲缘选择研究不仅相对较少,对亲缘选择的机制研究更为欠缺,这就造成了目前对此问题在科学认识上出现不少盲点。综合前期研究,提出今后对亲缘选择的研究应该首先界定"亲缘"程度,同时改良试验设计方案,选择多种不同生境下的物种对亲缘选择进行深入研究,并且考虑环境因子对植物亲缘选择的影响。同时,对植物亲缘识别机制的研究应该从生理生化方面出发,通过定性定量地分析探索植物根系分泌物在植物亲缘识别中的作用和作用途径。     

The total opportunity for sexual selection and the integration of pre‐ and post‐mating episodes of sexual selection in a complex world

It is well known that sexual selection can target reproductive traits during successive pre‐ and post‐mating episodes of selection. A key focus of recent studies has been to understand and quantify how these episodes of sexual selection interact to determine overall variance in reproductive success. In this article, we review empirical developments in this field but also highlight the considerable variability in patterns of pre‐ and post‐mating sexual selection, attributable to variation in patterns of resource acquisition and allocation, ecological and social factors, genotype‐by‐environment interaction and possible methodological factors that might obscure such patterns. Our aim is to highlight how (co)variances in pre‐ and post‐mating sexually selected traits can be sensitive to changes in a range of ecological and environmental variables. We argue that failure to capture this variation when quantifying the opportunity for sexual selection may lead to erroneous conclusions about the strength, direction or form of sexual selection operating on pre‐ and post‐mating traits. Overall, we advocate for approaches that combine measures of pre‐ and post‐mating selection across contrasting environmental or ecological gradients to better understand the dynamics of sexual selection in polyandrous species. We also discuss some directions for future research in this area.