The robustness of the weak selection approximation for the evolution of altruism against strong selection

The weak selection approximation of population genetics has made possible the analysis of social evolution under a considerable variety of biological scenarios. Despite its extensive usage, the accuracy of weak selection in predicting the emergence of altruism under limited dispersal when selection intensity increases remains unclear. Here, we derive the condition for the spread of an altruistic mutant in the infinite island model of dispersal under a Moran reproductive process and arbitrary strength of selection. The simplicity of the model allows us to compare weak and strong selection regimes analytically. Our results demonstrate that the weak selection approximation is robust to moderate increases in selection intensity and therefore provides a good approximation to understand the invasion of altruism in spatially structured population. In particular, we find that the weak selection approximation is excellent even if selection is very strong, when either migration is much stronger than selection or when patches are large. Importantly, we emphasize that the weak selection approximation provides the ideal condition for the invasion of altruism, and increasing selection intensity will impede the emergence of altruism. We discuss that this should also hold for more complicated life cycles and for culturally transmitted altruism. Using the weak selection approximation is therefore unlikely to miss out on any demographic scenario that lead to the evolution of altruism under limited dispersal.     

Weighing the evidence for adaptation at the molecular level

The abundance of genome polymorphism and divergence data has provided unprecedented insight into how mutation, drift and natural selection shape genome evolution. Application of the McDonald-Kreitman (MK) test to such data indicates a pervasive influence of positive selection, particularly in Drosophila species. However, evidence for positive selection in other species ranging from yeast to humans is often weak or absent. Although evidence for positive selection could be obscured in some species, there is also reason to believe that the frequency of adaptive substitutions could be overestimated as a result of epistatic fitness effects or hitchhiking of deleterious mutations. Based on these considerations it is argued that the common assumption of independence among sites must be relaxed before abandoning the neutral theory of molecular evolution.     

A Method for the Simultaneous Estimation of Selection Intensities in Overlapping Genes

Inferring the intensity of positive selection in protein-coding genes is important since it is used to shed light on the process of adaptation. Recently, it has been reported that overlapping genes, which are ubiquitous in all domains of life, seem to exhibit inordinate degrees of positive selection. Here, we present a new method for the simultaneous estimation of selection intensities in overlapping genes. We show that the appearance of positive selection is caused by assuming that selection operates independently on each gene in an overlapping pair, thereby ignoring the unique evolutionary constraints on overlapping coding regions. Our method uses an exact evolutionary model, thereby voiding the need for approximation or intensive computation. We test the method by simulating the evolution of overlapping genes of different types as well as under diverse evolutionary scenarios. Our results indicate that the independent estimation approach leads to the false appearance of positive selection even though the gene is in reality subject to negative selection. Finally, we use our method to estimate selection in two influenza A genes for which positive selection was previously inferred. We find no evidence for positive selection in both cases.     

Mating system and demographic constraints on the opportunity for sexual selection

In monogamous systems the fitness difference between males due to competition for mates is limited to one female. This constraint presumably impedes the action of sexual selection relative to polygynous systems. In this paper, we use formal selection theory to show how population size and the adult sex ratio constrain the force of sexual selection and phenotypic evolution under monogamy and polygyny. The force of sexual selection is ultimately constrained by the number of males in a population and the theoretical limit to the rate of male phenotypic evolution is realized if a single male mates with one or many females. These results imply that the force of sexual selection is not strictly constrained by monogamy. The constraint on female phenotypic evolution is typically higher than the constraint on males under polygyny and similar to selection on males in monogamous systems. The sexual asymmetry in the force of selection under polygyny--not necessarily weak sexual selection on males of monogamous systems--may explain the prominence of sexual dimorphism in polygynous systems.     

Arguments for the use of physiological criteria for improving the salt tolerance in crops

Efforts to develop new crop varieties with improved salt tolerance have been intensified over the past 15–20 years. Despite the existence of genetic variation for salt tolerance within species, and many methods available for expanding the source of genetic variation, there is only a limited number of varieties that have been developed with improved tolerance. These new varieties have all been based upon selection for agronomic characters such as yield or survival in saline conditions. That is, based upon characters that integrate the various physiological mechanisms responsible for tolerance. Yet over the same time period, knowledge of physiological salt responses has increased substantially.Selection and breeding to increase salt tolerance might be more successful if selection is based directly on the physiological mechanisms or characters conferring tolerance. Basic questions associated with using physiological selection criteria are discussed in the paper. These are centred around the need for genetic variation, the importance of the targeted mechanism, the ease of detection of the physiological mechanism (including the analytical requirements) and the breeding strategy. Many mechanisms, including ion exclusion, ion accumulation, compatible solute production and osmotic adjustment have been associated with genetic variation in salt tolerance. Yet their successful use in improving salt tolerance, via physiological selection criteria, is largely non-existent. Consideration is given to the role of physiological criteria in the short and long term in improving salt tolerance. In several glycophytic species, particularly legumes, physiological selection based on ion exclusion from the shoots shows promise. Recent results for white clover indicate the potential for using a broad physiological selection criterion of restricted Cl accumulation in the shoots, with scope for future refinement based upon the specific physiological characters that combined result in ion exclusion.     

Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level

Recent years have seen an explosion of interest in evidence for positive Darwinian selection at the molecular level. This quest has been hampered by the use of statistical methods that fail adequately to rule out alternative hypotheses, particularly the relaxation of purifying selection and the effects of population bottlenecks, during which the effectiveness of purifying selection is reduced. A further problem has been the assumption that positive selection will generally involve repeated amino-acid changes to a single protein. This model was derived from the case of the vertebrate major histocompatibility complex (MHC), but the MHC proteins are unusual in being involved in protein-protein recognition and in a co-evolutionary process of pathogens. There is no reason to suppose that repeated amino-acid changes to a single protein are involved in selectively advantageous phenotypes in general. Rather adaptive phenotypes are much more likely to result from other causes, including single amino-acid changes; deletion or silencing of genes or changes in the pattern of gene expression.     

Genetic versus census estimators of the opportunity for sexual selection in the wild

Abstract The existence of a direct link between intensity of sexual selection and mating-system type is widely accepted. However, the quantification of sexual selection has proven problematic. Several measures of sexual selection have been proposed, including the operational sex ratio (OSR), the breeding sex ratio (BSR), and the opportunity for sexual selection (I(mates)). For a wild population of pronghorn (Antilocapra americana), we calculated OSR and BSR. We estimated I(mates) from census data on the spatial and temporal distribution of receptive females in rut and from a multigenerational genetic pedigree. OSR and BSR indicated weak sexual selection on males, but census and pedigree I(mates) suggested stronger sexual selection on males than on females. OSR and BSR correlated with census but not pedigree estimates of I(mates), and census I(mates) did not correlate with pedigree estimates. This suggests that the behavioral mating system, as deduced from the spatial and temporal distribution of females, does not predict the genetic mating system of pronghorn. The differences we observed between estimators were primarily due to female mate sampling and choice and to the sex ratio. For most species, behavioral data are not perfectly accurate and therefore will be an insufficient alternative to using multigenerational pedigrees to quantify sexual selection.     

Selection for cheating across disparate environments in the legume‐rhizobium mutualism

The primary dilemma in evolutionarily stable mutualisms is that natural selection for cheating could overwhelm selection for cooperation. Cheating need not entail parasitism; selection favours cheating as a quantitative trait whenever less‐cooperative partners are more fit than more‐cooperative partners. Mutualisms might be stabilised by mechanisms that direct benefits to more‐cooperative individuals, which counter selection for cheating; however, empirical evidence that natural selection favours cheating in mutualisms is sparse. We measured selection on cheating in single‐partner pairings of wild legume and rhizobium lineages, which prevented legume choice. Across contrasting environments, selection consistently favoured cheating by rhizobia, but did not favour legumes that provided less benefit to rhizobium partners. This is the first simultaneous measurement of selection on cheating across both host and symbiont lineages from a natural population. We empirically confirm selection for cheating as a source of antagonistic coevolutionary pressure in mutualism and a biological dilemma for models of cooperation.     

Orientation of the genetic variance-covariance matrix and the fitness surface for multiple male sexually selected traits

Stabilizing selection has been predicted to change genetic variances and covariances so that the orientation of the genetic variance-covariance matrix (G) becomes aligned with the orientation of the fitness surface, but it is less clear how directional selection may change G. Here we develop statistical approaches to the comparison of G with vectors of linear and nonlinear selection. We apply these approaches to a set of male sexually selected cuticular hydrocarbons (CHCs) of Drosophila serrata. Even though male CHCs displayed substantial additive genetic variance, more than 99% of the genetic variance was orientated 74.9 degrees away from the vector of linear sexual selection, suggesting that open-ended female preferences may greatly reduce genetic variation in male display traits. Although the orientation of G and the fitness surface were found to differ significantly, the similarity present in eigenstructure was a consequence of traits under weak linear selection and strong nonlinear (convex) selection. Associating the eigenstructure of G with vectors of linear and nonlinear selection may provide a way of determining what long-term changes in G may be generated by the processes of natural and sexual selection.     

Experimental evidence for the role of sexual selection in the evolution of cuticular hydrocarbons in the dung beetle,Onthophagus taurus

A role for sexual selection in the evolution of insect cuticular hydrocarbons (CHCs) is suggested by observations of selection acting on male CHCs during female mate choice. However, evidence that CHCs evolve in response to sexual selection is generally lacking, and there is a need to extend our understanding beyond well‐studied taxa. Experimental evolution offers a powerful approach to investigate the effect of sexual selection on the evolution of insect CHCs. We conducted such an experiment using the dung beetle, Onthophagus taurus. After six, 12 and 21 generations of experimental evolution, we measured the CHCs of beetles from three populations subject to sexual selection and three populations within which sexual selection had been removed via enforced monogamy. We found that the male CHC profile responded to the experimental removal of sexual selection. Conversely, the CHC profile of females responded to the presence of sexual selection but not to its removal. These results show that sexual selection can be an important mechanism affecting the evolution of insect CHCs and that male and female CHCs can evolve independently.     

On the opportunity for polymorphism with sex-linkage or haplodiploidy

This paper addresses the assertion that X-linked and haplodiploid genetic systems are inherently limited with respect to the potential for selectively maintained genetic polymorphisms. Using a variation of Haldane and Jayakar's (1964) parameterization of selection on an X-linked locus, analytical expressions are derived for the proportion of the total parameter space (P) in which stable diallelic polymorphism is attained. P is a function of the ratio of selection coefficients (r) associated with homozygous and hemizygous genotypes, and the intensity of selection (s). Analytical expressions for the opportunity for polymorphism at an autosomal locus (P(a)) are also derived for comparison to the X-linked case. P and P(a) are maximal and equal if the ratios of selection coefficients are -1 and selection is intense. Otherwise, P is slightly less than P(a), but the difference between autosomal and sex-linked loci is less than the range of values of P obtained over the range of r. Several arguments are presented suggesting that polymorphism arising from differential selection in the sexes (r < 0) is probabilistically and biologically feasible.     

Differential selection between the sexes and selection for sex

Anisogamy is known to generate an important cost for sexual reproduction (the famous "twofold cost of sex"). However, male-female differences may have other consequences on the evolution of sex, due to the fact that selective pressures may differ among the sexes. On the one hand, intralocus sexual conflict should favor asexual females, which can fix female-beneficial, male-detrimental alleles. On the other hand, it has been suggested repeatedly that sexual selection among males may help to purge the mutation load, providing an advantage to sexual females. However, no analytical model has computed the strength of selection acting on a modifier gene affecting the frequency of sexual reproduction when selection differs between the sexes. In this article, we analyze a two-locus model using two approaches: a quasi-linkage-equilibrium (QLE) analysis and a local stability analysis, whose predictions are verified using a multilocus simulation. We find that costly sex can be maintained when selection is stronger in males than in females, but acts in the same direction in both. Complete asexuality, however, evolves under any other form of selection. Finally, we discuss how experimental measurements of fitness variances and covariances between sexes could be used to determine the overall direction and strength on selection for sex arising from differences in selection between males and females.     

Seasonal change in the opportunity for sexual selection

Environmental and population parameters that influence the strength of sexual selection may vary considerably over the course of the reproductive season. However, the potential for sexual selection frequently fails to translate into variation in reproductive success among individuals. We investigated seasonal changes in variation in reproductive success, measured as the opportunity for sexual selection, using parentage analysis in 20 experimental populations of the European bitterling (Rhodeus amarus, Cyprinidae), a small freshwater fish with a promiscuous, resource-based mating system. We showed that although the largest males sired most offspring over the entire reproductive season, variation in reproductive success and hence the opportunity for sexual selection was low at the start of the season but increased significantly at its end. This seasonal difference probably arose from the superior competitive endurance of large males and from a higher temporal clustering of reproductively active females at the start of the breeding season than later in the season. The spatial distribution of oviposition sites had a negligible effect on the variation in reproductive success. We discuss the potential implications of our results for the importance and strength of sexual selection in natural populations.     

Variation in natural selection for growth and phlorotannins in the brown alga Fucus vesiculosus

Directional selection for plant traits associated with resistance to herbivory tends to eliminate genetic variation in such traits. On the other hand, balancing selection arising from trade-offs between resistance and growth or spatially variable selection acts against the elimination of genetic variation. We explore both the amount of genetic variation and variability of natural selection for growth and concentration of phenolic secondary compounds, phlorotannins, in the brown alga Fucus vesiculosus. We measured variation in selection at two growing depths and two levels of nutrient availability in algae that had faced two kinds of past growing environments. Genetic variation was low for growth but high for phlorotannins. The form and strength of selection for both focal traits depended on the past growing environment of the algae. We found strong directional selection for growth rate in algae previously subjected to higher ultraviolet radiation, but not in algae previously subjected to higher nutrient availability. Stabilizing selection for growth occurred especially in the deep growing environment. Selection for phlorotannins was generally weak, but in some past-environment-current-environment combinations we detected either directional selection against phlorotannins or stabilizing selection. Thus, phlorotannins are not selectively neutral but affect the fitness of F. vesiculosus. In particular, there may be a fitness cost of producing phlorotannins, but the realization of such a cost varies from one environment to another. Genetic correlations between selective environments were high for growth but nonexistent for phlorotannins, emphasizing the high phenotypic plasticity of phlorotannin production. The highly heterogeneous selection, including directional, stabilizing, and spatially variable selection as well as temporal change in selection due to responses to past environmental conditions, probably maintains a high amount of genetic variation in phlorotannins. Such variation provides the potential for rapid evolutionary response of phlorotannins under directional selection.     

Monitoring the efficacy of hybrid selection during positional cloning: the search for BRCA1

Positional cloning often requires isolation of candidate genes from a large, genetically defined region. Hybrid selection (direct cDNA selection, solution hybrid capture) is a rapid, simple procedure that has been used to identify expressed sequence tags (ESTs) from cloned genomic DNA. We used hybrid selection to screen a 600-kb region that includes the BRCA1 gene. From a set of 931 sequenced clones, we obtained 118 nonoverlapping candidate ESTs from ovary and lymphocyte cDNA. We analyzed the results of our hybrid selection experiments with particular attention to the overall completeness, efficiency, and background noise of the experiment. We introduce simple parameters that serve as measures of important aspects of the hybrid selection process in the context of positional cloning.     

Sex ratio represents a unique context for selection on attractive traits: consequences for the evolution of sexual dimorphism

We explored the idea that sex ratio represents a unique context for selection on attractive traits by manipulating sex ratio and pollinator abundance in experimental populations of a gender-dimorphic wild strawberry Fragaria virginiana. We found that increasing the frequency of functional males (the pollen-bearing morph) increased the frequency of pollen-collecting syrphid flies in the pollinator assemblage, decreased pollinator visitation to less preferred morph (females), and decreased the degree of pollen limitation of females. Moreover, sex ratio influenced the strength of selection on petal size through female fitness but did not alter the strength of selection through male fitness components, suggesting that sex ratio can alter the gender bias of selection on an attractive trait. This study of context-dependent selection has important implications for the evolution of sexual dimorphism in attractive traits. First, it suggests that only certain conditions generate male-biased selection and, thus, could lead to selection-driven male-biased petal size dimorphism. Second, it suggests that flexible pollinator foraging may be an important mechanism by which sex ratio influences selection on attractive traits. Finally, it implies that variation in sex ratio could limit the evolution of sexual dimorphism and/or could maintain genetic variation in attractive traits.     

Theoretical considerations and probability models for the somatic development of the T-cell repertoire

A theory about the somatic development of the T-cell repertoire is described which explains the high proportion of alloreactive T lymphocytes as a side effect resulting from two biologically important selection processes. It is assumed that the T-cell receptors contain two binding sites X and Y similar to the two V regions of the B-cell receptors and immunoglobulin molecules, but with a different specificity repertoire as a result of the two selection processes. The first selection process is mediated by T-lineage inducer cells, which have already been postulated by Zinkernagel. They are believed to induce only cells with a binding site Y that can bind to major histocompatibility antigens (MHA) on the inducer cells. This selection forces the T-cell system to recognize preferentially cell-bound antigens; and it introduces under certain circumstances a high degree of self-MHA restriction and self-reactivity, and also a low degree of alloreactivity on the basis of cross-reactivity. The subsequent second selection process serves the purpose of self-tolerance induction. This process is expected under certain circumstances to result in a loss self-reactivity combined with a partial loss of self-restriction and selective enrichment of alloreactive T cells. Probability models are presented to illustrate how the two selection processes shape the T-cell repertoire and how the proportion of alloreactive cells is increased under special circumstances. It is possible that some T-cell subclasses are not affected by the second selection and maintain the primary repertoire. The theory is, in contrast to major competing theories, compatible with the assumption that the original V gene repertoires for the T-cell receptors are random.     

A variable selection index for the compensation of correlated genetic change

Summary A selection index for two traits has been constructed which allows partial restriction for one of the traits. The index is used in a situation where correlated response to selection in one sex is compenstated for by selection for other traits in the opposite sex. A numerical example is given.     

Inference on the strength of balancing selection for epistatically interacting loci

Existing inference methods for estimating the strength of balancing selection in multi-locus genotypes rely on the assumption that there are no epistatic interactions between loci. Complex systems in which balancing selection is prevalent, such as sets of human immune system genes, are known to contain components that interact epistatically. Therefore, current methods may not produce reliable inference on the strength of selection at these loci. In this paper, we address this problem by presenting statistical methods that can account for epistatic interactions in making inference about balancing selection. A theoretical result due to Fearnhead (2006) is used to build a multi-locus Wright-Fisher model of balancing selection, allowing for epistatic interactions among loci. Antagonistic and synergistic types of interactions are examined. The joint posterior distribution of the selection and mutation parameters is sampled by Markov chain Monte Carlo methods, and the plausibility of models is assessed via Bayes factors. As a component of the inference process, an algorithm to generate multi-locus allele frequencies under balancing selection models with epistasis is also presented. Recent evidence on interactions among a set of human immune system genes is introduced as a motivating biological system for the epistatic model, and data on these genes are used to demonstrate the methods.     

A migration-selection model for the morph frequency variation in the peppered moth over England and Wales

A migration-selection model for the spatial and temporal variation of morph frequencies over England and Wales for the peppered moth has been constructed. The morph frequencies have been obtained by computer simulation using the model for various assumptions regarding selection and migration within the boundaries of experimental observation. The selection, in this case, has been assumed to be wholly caused by bird predation and non-visual selection is taken to be same for all phenotypes. The results are compared with available experimental data along three transects. Reasonable agreement with the data is obtained for the Manchester-North Wales transect and the South Wales-London transect. The simulation fails, on the other hand, to reproduce observations along the Central Wales-Birmingham-East Anglia transect. Thus it is concluded that the hypothesis ol balance of selection and migration is untenable as it stands. Either the visual selection pressures are incorrectly or incompletely specified, or else non-visual selection is also operating.