It is now clear that the genetic basis of adaptation does not resemble that assumed by the infinitesimal model. Instead, adaptation often involves a modest number of factors of large effect and a greater number of factors of smaller effect. After reviewing relevant experimental studies, I consider recent theoretical attempts to predict the genetic architecture of adaptation from first principles. In particular, I review the history of work on Fisher's geometric model of adaptation, including recent studies which suggest that adaptation should be characterized by exponential distributions of gene effects. I also present the results of new simulation studies that test the robustness of this finding. I explore the effects of changes in the distribution of mutational effects (absolute versus relative) as well as in the nature of the character studied (total phenotypic effect versus single characters). The results show that adaptation towards a fixed optimum is generally characterized by an exponential effects trend.

The situation to which these studies point is not one of a large number of genes all with more or less equal effect. It seems, rather, that a small number of genes with large effects are responsible for most of the response, the remainder of the response being due to a larger number of loci with small effects.

D. S. Falconer (1981)

The phenomenon of transposition induction by heavy heat shock (HHS) was studied. Males of a Drosophila isogenic line with a mutation in the major gene radius incompletus (ri) were treated by HHS (37 °C for 1 h followed by 4 °C for 1 h, with the cycle repeated three times) and crossed to untreated females of the same line. The males were crossed 5 d after heat shock, and also 9 d after HHS. Many transpositions were seen in the F1 larvae by in situ hybridization. The rate of induced transposition was at least 2 orders of magnitude greater than that of the control sample, and was estimated to be 0·11 events per transposable element copy per sperm. Two ‘hot’ subdivisions for transpositions, induced probably during the post-meiotic stage of spermiogenesis, were found: 43B and 97DE. Three-quarters of all transpositions were localized in these positions. In other sites the rates of induced transpositions were (1·3–3·2)×10−2 events per occupied segment per sperm, 1 order of magnitude greater than those of the control.

Lysis inhibition is a mechanism of latent-period extension and burst-size increase that is induced by the T4 bacteriophage adsorption of T4-infected cells. Mutants of T4 genes imm, sp and 5 (specifically the ts1 mutant of 5) display some lysis inhibition. However, these mutants experience lysis-inhibition collapse, the lysis of lysis-inhibited cells, earlier than wild-type-infected cells (i.e. their collapse occurs prematurely). Lysis from without is a lysis induced by excessive T4 adsorption. Gp5 is an inducer of lysis from without while gpimm and gpsp effect resistance to lysis from without. This paper shows that interfering with the adsorption of phages to imm-, sp- or 5ts1-mutant-infected cells, in a variety of contexts, inhibits premature lysis-inhibition collapse. From these data it is inferred that wild-type T4-infected cells display resistance to lysis-inhibition collapse by a mechanism resembling resistance to lysis from without.

Fungi normally do not senesce, but in some species mitochondrial plasmids are known to occur that induce senescence. In this paper models for the dynamics of a senescence plasmid in a fungal population are developed and analysed. In the first model it is assumed that total fungal biomass density is constant, while in the second model the resource dynamics and its effect on fungal growth is modelled explicitly. An additional death rate describes the effect of the plasmid on the senescent subpopulation. Plasmids can be transferred to non-senescent fungus. Criteria for the coexistence of the non-senescent and senescent fungal strains are derived, all of which have a clear biological interpretation. It is shown that coexistence is not possible in the first model, but is possible in the second model for a large range of parameter values. We show that the interplay between resource dynamics, fungal growth and plasmid transmission is crucial for coexistence. We develop a biological interpretation of how these mechanisms have to interact to promote coexistence. A numerical study of the second model further clarifies the relations between the numerical value of several parameters and coexistence of non-senescent and senescent fungal strains.

Heart rate in pre-pupae of Drosophila melanogaster is shown to vary over a wide range from 2·5 to 3·7 beats per second. Quantitative genetic analysis of a sample of 11 highly inbred lines indicates that approaching one-quarter of the total variance in natural populations can be attributed to genetic differences between flies. A hypomorphic allele of the potassium channel gene ether-a-gogo, which is homologous to a human long-QT syndrome susceptibility gene (HERG), has a heart rate at the low end of the wild-type range, but this effect can be suppressed in certain wild-type genetic backgrounds. This study provides a baseline for investigation of pharmacological and other physiological influences on heart rate in the model organism, and implies that quantitative genetic dissection will provide insight into the molecular basis for variation in normal and arrhythmic heart function.

For neutral, additive quantitative characters, the amount of additive genetic variance within and among populations is predictable from Wright's FST, the effective population size and the mutational variance. The structure of quantitative genetic variance in a subdivided metapopulation can be predicted from results from coalescent theory, thereby allowing single-locus results to predict quantitative genetic processes. The expected total amount of additive genetic variance in a metapopulation of diploid individual is given by 2Neσ2m (1 + FST), where FST is Wright's among-population fixation index, Ne is the eigenvalue effective size of the metapopulation, and σ2m is the mutational variance. The expected additive genetic variance within populations is given by 2Neσ2e(1 − FST), and the variance among demes is given by 4FSTNeσ2m. These results are general with respect to the types of population structure involved. Furthermore, the dimensionless measure of the quantitative genetic variance among populations, QST, is shown to be generally equal to FST for the neutral additive model. Thus, for all population structures, a value of QST greater than FST for neutral loci is evidence for spatially divergent evolution by natural selection.

In Drosophila melanogaster, male courtship behaviour is genetically controlled and is influenced by sex pheromones. 7-tricosene (7-T) induces a dose-dependent inhibition of male–male courtship, whereas 7,11-dienes stimulate male courtship of females. There is a geographical quantitative variation in the production of two predominant male hydrocarbons, 7-T and 7-pentacosene (7-P). We have previously found that 7-P, the main hydrocarbon from males of West African strains, stimulates males that mainly produce 7-T. Using both ‘natural’ and genetically engineered strains, we find that genetic factors coding for low levels of 7-P in males have co-evolved with factor(s) coding for male responses to high levels of 7-P. These two phenotypes are coded by factors on different chromosomes: the intraspecific polymorphism for the production of 7-T and 7-P is largely controlled by chromosome 2, whereas the variation in courtship towards 7-P-rich males is largely controlled by chromosome 3. The polymorphism of male courtship towards 7-P-rich males shows no correlation with the variation in male responses to female flies.

Similarity between related genomes may carry information on selective constraint in each of them. We analysed patterns of similarity between several homologous regions of Caenorhabditis elegans and C. briggsae genomes. All homologous exons are quite similar. Alignments of introns and of intergenic sequences contain long gaps, segments where similarity is low and close to that between random sequences aligned using the same parameters, and segments of high similarity. Conservative estimates of the fractions of selectively constrained nucleotides are 72%, 17% and 18% for exons, introns and intergenic sequences, respectively. This implies that the total number of constrained nucleotides within non-coding sequences is comparable to that within coding sequences, so that at least one-third of nucleotides in C. elegans and C. briggsae genomes are under strong stabilizing selection.

This article outlines theoretical models of clines in additive polygenic traits, which are maintained by stabilizing selection towards a spatially varying optimum. Clines in the trait mean can be accurately predicted, given knowledge of the genetic variance. However, predicting the variance is difficult, because it depends on genetic details. Changes in genetic variance arise from changes in allele frequency, and in linkage disequilibria. Allele frequency changes dominate when selection is weak relative to recombination, and when there are a moderate number of loci. With a continuum of alleles, gene flow inflates the genetic variance in the same way as a source of mutations of small effect. The variance can be approximated by assuming a Gaussian distribution of allelic effects; with a sufficiently steep cline, this is accurate even when mutation and selection alone are better described by the ‘House of Cards’ approximation. With just two alleles at each locus, the phenotype changes in a similar way: the mean remains close to the optimum, while the variance changes more slowly, and over a wider region. However, there may be substantial cryptic divergence at the underlying loci. With strong selection and many loci, linkage disequilibria are the main cause of changes in genetic variance. Even for strong selection, the infinitesimal model can be closely approximated by assuming a Gaussian distribution of breeding values. Linkage disequilibria can generate a substantial increase in genetic variance, which is concentrated at sharp gradients in trait means.

The murine t complex on chromosome 17 contains a number of homozygous lethal and semi-lethal mutations that disrupt development of the mouse embryo. We recently characterized an embryonic lethality in the rat that results from a germ-line mutation in the tuberous sclerosis 2 (Tsc-2) tumour suppressor gene (the Eker mutation). Remarkably, mouse embryos homozygous for tw8 mutation display cranial defects reminiscent of those observed in rat embryos homozygous for the Eker mutation. To determine whether the Tsc-2 gene, which is in the t complex, is mutated in tw8 or other t haplotypes, we characterized this gene in a series of t haplotype mice. Four Tsc-2 polymorphisms were identified: three in the coding region and one intronic that appeared to be common to all t haplotypes analysed. No evidence was found to argue that the Tsc-2 gene is altered in tw8 haplotype mice. However, in the tw5 haplotype we found a G to T mutation in Tsc-2 that was present only in this t haplotype. In contrast to other polymorphisms within the Tsc-2 coding region which did not result in amino acid changes in Tsc-2 gene product tuberin, this mutation substituted a phenylalanine for a conserved cysteine in tw5 tuberin. Within the t complex, the Tsc-2 gene and the putative tw5 locus appeared to map to different positions, complicating identification of Tsc-2 as a candidate for the tw5 locus and suggesting that the G to T mutation in the Tsc-2 gene may have arisen independently of the tw5 functional mutation.

Single-locus equilibrium frequencies of a partially recessive deleterious mutation under the mutation–selection balance model are derived for partially selfing autotetraploid populations. Assuming multiplicative fitness interactions among loci, approximate solutions for the mean fitness and inbreeding depression values are also derived for the multiple locus case and compared with expectations for the diploid model. As in diploids, purging of deleterious mutations through consanguineous matings occurs in autotetraploid populations, i.e. the equilibrium mutation load is a decreasing function of the selfing rate. However, the variation of inbreeding depression with the selfing rate depends strongly on the dominance coefficients associated with the three heterozygous genotypes. Inbreeding depression can either increase or decrease with the selfing rate, and does not always vary monotonically. Expected issues for the evolution of the selfing rate consequently differ depending on the dominance coefficients. In some cases, expectations for the evolution of the selfing rate resemble expectations in diploids; but particular sets of dominance coefficients can be found that lead to either complete selfing or intermediate selfing rates as unique evolutionary stable state.

Most of the major genetic concerns in conservation biology, including inbreeding depression, loss of evolutionary potential, genetic adaptation to captivity and outbreeding depression, involve quantitative genetics. Small population size leads to inbreeding and loss of genetic diversity and so increases extinction risk. Captive populations of endangered species are managed to maximize the retention of genetic diversity by minimizing kinship, with subsidiary efforts to minimize inbreeding. There is growing evidence that genetic adaptation to captivity is a major issue in the genetic management of captive populations of endangered species as it reduces reproductive fitness when captive populations are reintroduced into the wild. This problem is not currently addressed, but it can be alleviated by deliberately fragmenting captive populations, with occasional exchange of immigrants to avoid excessive inbreeding. The extent and importance of outbreeding depression is a matter of controversy. Currently, an extremely cautious approach is taken to mixing populations. However, this cannot continue if fragmented populations are to be adequately managed to minimize extinctions. Most genetic management recommendations for endangered species arise directly, or indirectly, from quantitative genetic considerations.

Patterns of synonymous codon usage are determined by the forces of mutation, selection and drift. We elaborate on previous population genetic models of codon usage to incorporate parameters of population polymorphism, and demonstrate that the degree of codon bias expected in a single sequence picked at random from the population is accurately predicted by previous models, irrespective of population polymorphism. This new model is used to explore the relationships between synonymous codon usage, nucleotide site diversity and the rate of substitution. We derive the equilibrium frequency distribution of weakly selected segregating sites under the infinite-sites model, and the expected nucleotide site diversity. Contrary to intuition, levels of silent-site diversity can increase with the strength of selection acting on codon usage. We also predict the effects of background selection on statistics of synonymous codon usage and derive simple formulae to predict patterns of codon usage at amino acids with more than two synonymous codons, and the effects of variation in selection coefficient between sites within a gene. We show that patterns of silent-site variation and synonymous codon usage on the X chromosome and autosomes in Drosophila are compatible with recessivity of the fitness effects of unpreferred codons. Finally, we suggest that there still exist considerable discrepancies between current models and data.

Correlated responses to artificial selection on body size in Drosophila melanogaster were investigated, to determine how the changes in size were produced during development. Selection for increased thorax length was associated with an increase in larval development time, an extended growth period, no change in growth rate, and an increased critical larval weight for pupariation. Selection for reduced thorax length was associated with reduced growth rate, no change in duration of larval development and a reduced critical larval weight for pupariation. In both lines selected for thorax length and lines selected for wing area, total body size changed in the same direction as the artificially selected trait. In large selection lines of both types, the increase in size was achieved almost entirely by an increase in cell number, while in the small lines the decrease in size was achieved predominantly by reduced cell size, and also by a reduction in cell number. The implications of the results for evolutionary-genetic change in body size in nature are discussed.

Hypertrophied sexually dimorphic eye stalks have evolved independently in several families of Diptera, with the eyespan of males exceeding their total body length in some species. These structures function in intermale contests for territories and in mate attraction, the classical mechanisms of sexual selection. In the family Diopsidae, species with extremely exaggerated eye stalks and marked sexual dimorphism in relative eyespan also usually have strongly female-biased sex ratios in nature caused by X-linked meiotic drive, whereas species with relatively small eye stalks have little or no sexual dimorphism, often lack meiotic drive and have even sex ratios. We investigate the possible connection between sexual selection and sex-ratio meiotic drive by analysing a three-locus model for the evolution of female choice for a male character associated with meiotic drive. Both meiotic drive and the male character are X-linked and the female preference is autosomal. Our model shows that suppressed recombination between meiotic drive and the male character, e.g. by inversion of the X chromosome, is necessary for sex-ratio selection to promote the origin of female mating preferences and exaggerated secondary sexual characters. With complete suppression of recombination, sexual selection reduces the frequency of meiotic drive, and may eliminate it. Very rare recombination, gene conversion or mutation, at rates characteristic of chromosome inversions in Drosophila, restores the meiotic drive polymorphism to its original equilibrium. Sex-ratio meiotic drive may thus act as a catalyst accelerating the origin of female mating preference and exaggerated male traits.

We examine an analytical model of selection against the deleterious effects of transposable element (TE) insertions in Drosophila, focusing attention on the asymptotic and dynamic characteristics. With strong selection the only asymptotically stable equilibrium point corresponds to extinction of the TEs. With very weak selection a stable and realistic equilibrium point can be obtained. The dynamics of the system is fast for strong selection and slow, on the human time scale, for weak selection. Hence weak selection acts as a force that contributes to the stabilization of mean TE copy number. The consequence is that under weak selection, and ‘out-of-equilibrium’ situation can be maintained for a long time in populations, with mean TE copy number appearing stabilized.

Information on the genetic correlation between traits provides fundamental insight into the constraints on the evolutionary process. Estimates of such correlations are conventionally obtained by raising individuals of known relatedness in artificial environments. However, many species are not readily amenable to controlled breeding programmes, and considerable uncertainty exists over the extent to which estimates derived under benign laboratory conditions reflect the properties of populations in natural settings. Here, non-invasive methods that allow the estimation of genetic correlations from phenotypic measurements derived from individuals of unknown relatedness are introduced. Like the conventional approach, these methods demand large sample sizes in order to yield reasonably precise estimates, and special precautions need to be taken to eliminate bias from shared environmental effects. Provided the sample consists of at least 20% or so relatives, informative estimates of the genetic correlation are obtainable with sample sizes of several hundred individuals, particularly if supplemental information on relatedness is available from polymorphic molecular markers.

This research reports analyses of correlated response in reproductive onset in ICR mice after 23 generations of restricted index selection for divergent body weight gain, early (birth–10 days) or later (28–56 days) in life. Long-term selection altered growth trajectories and 56 day body weight of individuals under different selection regimes in this study. Mice in lines under early selection have the same percentage mature weight at vaginal opening as controls (63%). Vaginal opening is delayed in mice selected for slow early growth, which take longer to reach what appears to be a weight threshold. In contrast, individuals in lines selected for later slow growth undergo vaginal opening at the same age as controls, but at a lower weight and increased percentage mature weight. Pre-compensation or ‘counter-balance growth’ is observed in these lines, with mice selected for late enhanced growth reaching 52% of mature weight at vaginal opening while mice with late slow growth attain 71% of mature weight prior to vaginal opening. Only 42% of mice with late slow growth attain first oestrus by 56 days. We speculate this is a function of growth rate and fat/lean ratio. Mice with early slow growth show compensatory growth, reaching first oestrus at a similar time to controls. We conclude that selection for growth rate has asymmetrically affected reproductive onset, with lines selected for suppressed gains experiencing delays in the reproductive onset traits measured.

Many phenotypes respond physiologically or developmentally to continuously distributed environmental variables such as temperature and nutritional quality. Information about phenotypic plasticity can be used to improve the efficiency of artificial selection. Here we show that the quantitative genetic theory for ‘infinite-dimensional’ traits such as reaction norms provides a natural framework to accomplish this goal. It is expected to improve selection responses by making more efficient use of information about environmental effects than do conventional methods. The approach is illustrated by deriving an index for mass selection of a phenotypically plastic trait. We suggest that the same approach could be extended directly to more general and efficient breeding schemes, such as those based on general best linear unbiased prediction. Methods for estimating genetic covariance functions are reviewed.

Two new test statistics were constructed to detect departures from the equilibrium neutral theory that tend to produce genealogies with longer internal branches (e.g. population subdivision or balancing selection). The new statistics are based on a measure of linkage disequilibrium between adjacent pairs of segregating sites. Simulations were run to determine the power of these and previously proposed test statistics to reject an island model of geographic subdivision. Unlike previous power studies, this one uses a coalescent model with recombination. It is found that recombination rates on the order of the mutation rate substantially reduce the power of most test statistics, and that one of the new test statistics is generally more powerful than the others. Two suggestions are made for increasing the power of the statistical tests examined here. First, they can be made more powerful if critical values are obtained from simulations that condition on a lower bound for the population recombination rate. Secondly, for the same total length sequenced, power is increased if independent loci are considered instead of a single contiguous stretch.