The effect of repeated cycles of selection on genetic variance,heritability, and response

Summary The genetic variance of a quantitative trait decreases under directional selection due to generation of linkage disequilibrium. After a few cycles of selection on individual phenotype, a limit is reached where there is no further reduction in the genetic variance. Bulmer's model is extended to an animal breeding situation where selection is on information on relatives rather than on the individual's own performance. Algebraic expressions are derived to predict the decrease in genetic variance and associated reductions in heritability and response in the limit. Consequences of the results are discussed in the context of breeding strategies.     

Societies to genes: can we get there from here?

Understanding the organization and evolution of social complexity is a major task because it requires building an understanding of mechanisms operating at different levels of biological organization from genes to social interactions. I discuss here, a unique forward genetic approach spanning more than 30 years beginning with human-assisted colony-level selection for a single social trait, the amount of pollen honey bees (Apis mellifera L.) store. The goal was to understand a complex social trait from the social phenotype to genes responsible for observed trait variation. The approach combined the results of colony-level selection with detailed studies of individual behavior and physiology resulting in a mapped, integrated phenotypic architecture composed of correlative relationships between traits spanning anatomy, physiology, sensory response systems, and individual behavior that affect individual foraging decisions. Colony-level selection reverse engineered the architecture of an integrated phenotype of individuals resulting in changes in the social trait. Quantitative trait locus (QTL) studies combined with an exceptionally high recombination rate (60 kb/cM), and a phenotypic map, provided a genotype–phenotype map of high complexity demonstrating broad QTL pleiotropy, epistasis, and epistatic pleiotropy suggesting that gene pleiotropy or tight linkage of genes within QTL integrated the phenotype. Gene expression and knockdown of identified positional candidates revealed genes affecting foraging behavior and confirmed one pleiotropic gene, a tyramine receptor, as a target for colony-level selection that was under selection in two different tissues in two different life stages. The approach presented here has resulted in a comprehensive understanding of the structure and evolution of honey bee social organization.     

Patterns of fluctuating asymmetry in sexual ornaments predict female choice

Extravagant secondary sexual characters are assumed to have arisen and be maintained by sexual selection. While traits like horns, antlers and spurs can be ascribed to intrasexual competition, other traits such as extravagant feather ornaments, displays and pheromones have to be ascribed to mate choice. A number of studies have tested whether females exert selection on the size of male ornaments, but only some of these have recorded female preferences for the most extravagantly ornamented males. Here I demonstrate that female choice can be directly predicted from the relationship between the degree of fluctuating asymmetry and the size of a secondary sexual character. Fluctuating asymmetry is an epigenetic measure of the ability of individuals to cope with stress, and it occurs when an individual is unable to undergo identical development of an otherwise bilaterally symmetric trait on both sides of its body. There is a negative relationship between the degree of fluctuating asymmetry and the absolute size of an ornament in those bird species with a female preference for the largest male sex trait, while there is a flat or U-shaped relationship among species without a female preference. These results suggest that females prefer exaggerated secondary sexual characters if they reliably demonstrate the ability of males to cope with genetic and environmental stress. Some species may demonstrate a flat or U-shaped relationship between the degree of fluctuating asymmetry and the absolute size of an ornament because (i) the genetic variance in viability signalled by the secondary sex trait has been depleted; (ii) the secondary sex trait is not particularly costly and therefore does not demonstrate condition dependence; or because (iii) the sex traits can be considered arbitrary traits rather than characters reflecting good genes.     

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."     

Selection explanations of token traits

The “negative view” is the claim that natural selection cannot explain why a particular individual has one trait, rather than another. Here, I modify an example from Lewens (2001) to show that this claim is sometimes false. I then advance a variation on the negative view. It is the claim that selection at the organism level within a lineage cannot explain why a particular individual in that lineage has one allele, rather than another. This formulation better describes the explanatory role of selection.     

Quantification and decomposition of environment‐selection relationships

In nature, selection varies across time in most environments, but we lack an understanding of how specific ecological changes drive this variation. Ecological factors can alter phenotypic selection coefficients through changes in trait distributions or individual mean fitness, even when the trait‐absolute fitness relationship remains constant. We apply and extend a regression‐based approach in a population of Soay sheep (Ovis aries) and suggest metrics of environment‐selection relationships that can be compared across studies. We then introduce a novel method that constructs an environmentally structured fitness function. This allows calculation of full (as in existing approaches) and partial (acting separately through the absolute fitness function slope, mean fitness, and phenotype distribution) sensitivities of selection to an ecological variable. Both approaches show positive overall effects of density on viability selection of lamb mass. However, the second approach demonstrates that this relationship is largely driven by effects of density on mean fitness, rather than on the trait‐fitness relationship slope. If such mechanisms of environmental dependence of selection are common, this could have important implications regarding the frequency of fluctuating selection, and how previous selection inferences relate to longer term evolutionary dynamics.     

The concept of correlated progression as the basis of a model for the evolutionary origin of major new taxa

Understanding the evolutionary processes responsible for the long treks through morphospace associated with the origin of new higher taxa is hampered by the lack of a realistic and usable model that accounts for long-term phenotypic evolvability. The systems-related concept of correlated progression, in which all the traits are functionally linked and so constrained to evolve by small increments at a time in parallel with each other, provides the basis for such a model. Implications for the process of evolution at high taxonomic level are that: the evolving traits must be considered together as a system, and the exact sequence of incremental changes in characters is indeterminable; there are no identifiable key innovations; selection acts on the phenotype as a whole rather than on individual traits; and the selection force is therefore multidimensional. Application of the model to the pattern of evolution of traits and trait states as revealed by the fossil record of the stem groups of such taxa as mammals, turtles and tetrapods generates realistic testable hypotheses about how such groups evolved.     

Pleiotropic Models of Polygenic Variation, Stabilizing Selection, and Epistasis

We show that in polymorphic populations many polygenic traits pleiotropically related to fitness are expected to be under apparent ``stabilizing selection' independently of the real selection acting on the population. This occurs, for example, if the genetic system is at a stable polymorphic equilibrium determined by selection and the nonadditive contributions of the loci to the trait value either are absent, or are random and independent of those to fitness. Stabilizing selection is also observed if the polygenic system is at an equilibrium determined by a balance between selection and mutation (or migration) when both additive and nonadditive contributions of the loci to the trait value are random and independent of those to fitness. We also compare different viability models that can maintain genetic variability at many loci with respect to their ability to account for the strong stabilizing selection on an additive trait. Let V(m) be the genetic variance supplied by mutation (or migration) each generation, V(g) be the genotypic variance maintained in the population, and n be the number of the loci influencing fitness. We demonstrate that in mutation (migration)-selection balance models the strength of apparent stabilizing selection is order V(m)/V(g). In the overdominant model and in the symmetric viability model the strength of apparent stabilizing selection is approximately 1/(2n) that of total selection on the whole phenotype. We show that a selection system that involves pairwise additive by additive epistasis in maintaining variability can lead to a lower genetic load and genetic variance in fitness (approximately 1/(2n) times) than an equivalent selection system that involves overdominance. We show that, in the epistatic model, the apparent stabilizing selection on an additive trait can be as strong as the total selection on the whole phenotype.     

EXPERIMENTAL STUDIES OF COMMUNITY EVOLUTION I: THE RESPONSE TO SELECTION AT THE COMMUNITY LEVEL

Coevolution generally refers to the process of two or more organisms adapting to each other as a result of individual selection. Another possibility, however, is that coevolution may result from selection acting directly at the community level. Certain types of multispecies associations, such as lichens, which are a symbiotic association between an alga and a fungus, are examples of simple two species communities that may be units of selection. The study presented here uses two species communities of Tribolium castaneum and T. confusum in an investigation of selection acting at the community level. Selection at the community level is performed on one trait measured in one species and correlated responses in other traits measured both within species and among species are monitored. I demonstrate that community selection, defined as the differential survival and or reproduction of communities, can result in significant changes in the phenotype of a community. The observed changes in the phenotype of a community as a result of community selection included changes in the trait under selection (direct effects of selection), as well as changes in traits that are not under selection (correlated responses to selection). Furthermore, two types of correlated responses to selection were observed. The first, within-species correlated responses to selection, are changes in a trait measured in one species as a result of community selection acting on another trait measured in the same species. The second, between-species correlated responses to selection, are changes in a trait measured in one species as a result of community selection acting on a trait measured in another species. Between species correlated responses to selection are of particular interest because they cannot be mediated by pathways of gene action that are internal to an individual, rather they can be mediated only through ecological pathways. In other words, between-species correlated responses to selection suggest that genetically based interactions among individuals are contributing to the response to community selection. These among species ecological pathways of gene action cannot contribute to a response to selection at a lower level; thus community selection may be able to bring about a response to selection that is qualitatively different from the response selection that would occur as a result of selection acting at a lower level.     

Effects on phenotypic variability of directional selection arising through genetic differences in residual variability

In standard models of quantitative traits, genotypes are assumed to differ in mean but not variance of the trait. Here we consider directional selection for a quantitative trait for which genotypes also confer differences in variability, viewed either as differences in residual phenotypic variance when individual loci are concerned or as differences in environmental variability when the whole genome is considered. At an individual locus with additive effects, the selective value of the increasing allele is given by ia/sigma + 1/2 ixb/sigma2, where i is the selection intensity, x is the standardized truncation point, sigma2 is the phenotypic variance, and a/sigma and b/sigma2 are the standardized differences in mean and variance respectively between genotypes at the locus. Assuming additive effects on mean and variance across loci, the response to selection on phenotype in mean is isigma2(Am)/sigma + 1/2 ixcov(Amv)/sigma2 and in variance is icov(Amv)/sigma + 1/2 ixsigma2(Av)/sigma2, where sigma2(Am) is the (usual) additive genetic variance of effects of genes on the mean, sigma2(Av) is the corresponding additive genetic variance of their effects on the variance, and cov(Amv) is the additive genetic covariance of their effects. Changes in variance also have to be corrected for any changes due to gene frequency change and for the Bulmer effect, and relevant formulae are given. It is shown that effects on variance are likely to be greatest when selection is intense and when selection is on individual phenotype or within family deviation rather than on family mean performance. The evidence for and implications of such variability in variance are discussed.     

Stabilizing Selection,Purifying Selection,and Mutational Bias in Finite Populations

Genomic traits such as codon usage and the lengths of noncoding sequences may be subject to stabilizing selection rather than purifying selection. Mutations affecting these traits are often biased in one direction. To investigate the potential role of stabilizing selection on genomic traits, the effects of mutational bias on the equilibrium value of a trait under stabilizing selection in a finite population were investigated, using two different mutational models. Numerical results were generated using a matrix method for calculating the probability distribution of variant frequencies at sites affecting the trait, as well as by Monte Carlo simulations. Analytical approximations were also derived, which provided useful insights into the numerical results. A novel conclusion is that the scaled intensity of selection acting on individual variants is nearly independent of the effective population size over a wide range of parameter space and is strongly determined by the logarithm of the mutational bias parameter. This is true even when there is a very small departure of the mean from the optimum, as is usually the case. This implies that studies of the frequency spectra of DNA sequence variants may be unable to distinguish between stabilizing and purifying selection. A similar investigation of purifying selection against deleterious mutations was also carried out. Contrary to previous suggestions, the scaled intensity of purifying selection with synergistic fitness effects is sensitive to population size, which is inconsistent with the general lack of sensitivity of codon usage to effective population size.     

Multilevel selection and the partitioning of covariance: a comparison of three approaches

Where the evolution of a trait is affected by selection at more than one hierarchical level, it is often useful to compare the magnitude of selection at each level by asking how much of the total evolutionary change is attributable to each level of selection. Three statistical partitioning techniques, each designed to answer this question, are compared, in relation to a simple multilevel selection model in which a trait's evolution is affected by both individual and group selection. None of the three techniques is wholly satisfactory: one implies that group selection can operate even if individual fitness is determined by individual phenotype alone, whereas the other two imply that group selection can operate even if there is no variance in group fitness. This has significant implications both for our understanding of what the term "multilevel selection" means and for the traditional concept of group selection.     

Son preference among Filipino Muslims: A causal analysis

Abstract

A social selection model for deleterious genes has been studied by considering two alleles at one locus. The model allows for the fitness of an individual to be determined by parental phenotypes as well as by his/her own phenotype. We show that the equilibrium gene frequency depends on the loss of fitness of an individual due to the trait (γ) and due to affected parents (P), and the probability that the heterozygote develops the trait (h). We show that whenever an interior equilibrium point exists for given values of γ and β, it is unique and that the sufficient condition for the existence of the equilibrium point is given by     

Mendelian Factors Underlying Quantitative Traits in Tomato: Comparison across Species, Generations, and Environments

As part of ongoing studies regarding the genetic basis of quantitative variation in phenotype, we have determined the chromosomal locations of quantitative trait loci (QTLs) affecting fruit size, soluble solids concentration, and pH, in a cross between the domestic tomato (Lycopersicon esculentum Mill.) and a closely-related wild species, L. cheesmanii. Using a RFLP map of the tomato genome, we compared the inheritance patterns of polymorphisms in 350 F2 individuals with phenotypes scored in three different ways: (1) from the F2 progeny themselves, grown near Davis, California; (2) from F3 families obtained by selfing each F2 individual, grown near Gilroy, California (F3-CA); and (3) from equivalent F3 families grown near Rehovot, Israel (F3-IS). Maximum likelihood methods were used to estimate the approximate chromosomal locations, phenotypic effects (both additive effects and dominance deviations), and gene action of QTLs underlying phenotypic variation in each of these three environments. A total of 29 putative QTLs were detected in the three environments. These QTLs were distributed over 11 of the 12 chromosomes, accounted for 4.7-42.0% of the phenotypic variance in a trait, and showed different types of gene action. Among these 29 QTLs, 4 were detected in all three environments, 10 in two environments, and 15 in only a single environment. The two California environments were most similar, sharing 11/25 (44%) QTLs, while the Israel environment was quite different, sharing 7/20 (35%) and 5/26 (19%) QTLs with the respective California environments. One major goal of QTL mapping is to predict, with maximum accuracy, which individuals will produce progeny showing particular phenotypes. Traditionally, the phenotype of an individual alone has been used to predict the phenotype of its progeny. Our results suggested that, for a trait with low heritability (soluble solids), the phenotype of F3 progeny could be predicted more accurately from the genotype of the F2 parent at QTLs than from the phenotype of the F2 individual. For a trait with intermediate heritability (fruit pH), QTL genotype and observed phenotype were about equally effective at predicting progeny phenotype. For a trait with high heritability (mass per fruit), knowing the QTL genotype of an individual added little if any predictive value, to simply knowing the phenotype. The QTLs mapped in the L. esculentum X L. cheesmanii F2 appear to be at similar locations to many of those mapped in a previous cross with a different wild tomato (L. chmielewskii).(ABSTRACT TRUNCATED AT 400 WORDS)     

Simulation of marker-assisted selection utilizing linkage disequilibrium: the effects of several additional factors

Use was made of our published model and methods to investigate the effects of several additional factors on marker-assisted selection (MAS) utilizing linkage disequilibrium. The additional factors were: size of the sample used to estimate the marker quantitative trait locus (MQTL) association effects, the method used to estimate the MQTL effects, use of the average of the top MQTL estimates in selection rather than individual estimates, size of the selection population, and the crossing of duplicate selection lines to generate further linkage disequilibrium and further selection response. The average map distance between the quantitative trait loci (QTLs) and their nearest marker was 0.15 Morgans. Use of estimates of MQTL effects derived by least squares yielded smaller selection responses than estimates derived by mixed-model methods. Selection responses were also reduced by using a smaller sample for estimating the associations because MQTL effects were less well estimated. This applied to selection on the MQTL effects themselves and to selection combining the MQTL with phenotypic information. Thus, poorly estimated MQTL effects added noise to the system and reduced selection response in combined selection. Using the average of the top MQTL estimates, rather than individual estimates, also reduced selection response. New linkage disequilibrium, generated by crossing two lines selected from the same population, did not lead to additional selection response in the cross line. These results show limitations to MAS using linkage disequilibrium until close linkages of markers and QTLs are available.     

EVOLUTION AND EXTINCTION IN A CHANGING ENVIRONMENT: A QUANTITATIVE-GENETIC ANALYSIS

Because of the ubiquity of genetic variation for quantitative traits, virtually all populations have some capacity to respond evolutionarily to selective challenges. However, natural selection imposes demographic costs on a population, and if these costs are sufficiently large, the likelihood of extinction will be high. We consider how the mean time to extinction depends on selective pressures (rate and stochasticity of environmental change, and strength of selection), population parameters (carrying capacity, and reproductive capacity), and genetics (rate of polygenic mutation). We assume that in a randomly mating, finite population subject to density-dependent population growth, individual fitness is determined by a single quantitative-genetic character under Gaussian stabilizing selection with the optimum phenotype exhibiting directional change, or random fluctuations, or both. The quantitative trait is determined by a finite number of freely recombining, mutationally equivalent, additive loci. The dynamics of evolution and extinction are investigated, assuming that the population is initially under mutation-selection-drift balance. Under this model, in a directionally changing environment, the mean phenotype lags behind the optimum, but on the average evolves parallel to it. The magnitude of the lag determines the vulnerability to extinction. In finite populations, stochastic variation in the genetic variance can be quite pronounced, and bottlenecks in the genetic variance temporarily can impair the population's adaptive capacity enough to cause extinction when it would otherwise be unlikely in an effectively infinite population. We find that maximum sustainable rates of evolution or, equivalently, critical rates of environmental change, may be considerably less than 10% of a phenotypic standard deviation per generation.     

Selection on skewed characters and the paradox of stasis

Observed phenotypic responses to selection in the wild often differ from predictions based on measurements of selection and genetic variance. An overlooked hypothesis to explain this paradox of stasis is that a skewed phenotypic distribution affects natural selection and evolution. We show through mathematical modeling that, when a trait selected for an optimum phenotype has a skewed distribution, directional selection is detected even at evolutionary equilibrium, where it causes no change in the mean phenotype. When environmental effects are skewed, Lande and Arnold's (1983) directional gradient is in the direction opposite to the skew. In contrast, skewed breeding values can displace the mean phenotype from the optimum, causing directional selection in the direction of the skew. These effects can be partitioned out using alternative selection estimates based on average derivatives of individual relative fitness, or additive genetic covariances between relative fitness and trait (Robertson–Price identity). We assess the validity of these predictions using simulations of selection estimation under moderate sample sizes. Ecologically relevant traits may commonly have skewed distributions, as we here exemplify with avian laying date — repeatedly described as more evolutionarily stable than expected — so this skewness should be accounted for when investigating evolutionary dynamics in the wild.     

Spatial patterns of polygenic variation in Impatiens capensis,a species with an environmentally controlled mixed mating system

Impatiens capensis displays a mixed mating system in which individual out-crossing rate is expected to increase with light and resource availability. We investigated the amount and spatial distribution of polygenic variation for 15 morphological traits within and among six natural populations of I. capensis growing in three distinct light habitats (shaded, mixed, full sun). We grew individuals from each population in uniform greenhouse conditions and detected significant genetic variation among families within populations for all the quantitative traits examined. However, only the features related to the vegetative characteristics of seedlings and sexually mature plants show also differentiation at the population level. Surprisingly, even though light availability is likely to be the most important factor affecting the mating system of I. capensis, we find that: (1) trait means of individuals from similar light environments are not more similar than those from different light environments; (2) partitioning of polygenic variance within and among families differs both among populations from the same light habitat and among characters within each population. If natural selection is maintaining such variation, it must operate primarily through heterogeneous selection pressure within, rather than between, populations.     

Some important physiological selection criteria for salt tolerance in plants

Undoubtedly, plant breeders have made a significant achievement in the past few years, improving salinity tolerance in a number of potential crops using artificial selection and conventional breeding approaches, although molecular biology approaches are currently being intensively pursued for achieving this goal. However, most of the selection procedures used so far, were based merely on differences in agronomic characters. Agronomic characters represent the combined genetic and environmental effects on plant growth, and include the integration of the physiological phenomena conferring salinity tolerance. In fact, physiological criteria are able to supply more reliable information than agronomic characters. Although there are large numbers of reports in the literature mainly dealing with water relations, photosynthesis, and accumulation of various inorganic ions and organic metabolites in individual crops, there is little information available on the use of these attributes as selection criteria for improving salt tolerance through selection and breeding programs. In this review, the major adaptive components of salt tolerance such as osmotic adjustment, photosynthesis, water relations and ion relations are reviewed. In view of the complexity of salt tolerance and its great variation at intra-specific and inter-specific levels, it is difficult to identify single criteria, which could be used as effective selection targets. Rather it is most meaningful if physiological and biochemical indicators for individual species are determined rather than generic indicators.