There are two known alleles of the mouse parotid secretory protein (PSP) gene: Pspa and Pspb. Pspa is carried by DBA/2J mice and Pspb is carried by C57BL/6J mice. Eighty-eight mice derived from a F1(C57BL/6J×DBA/2J) to DBA/2J backcross were analysed for PSP mRNA expression in the sublingual glands. Expression was found in heterozygous mice only. This indicates that only Pspb is expressed in this tissue. Furthermore, it maps the allele-specific sublingual gland determinant within 3·4 cM of Psp. Previous analysis of Pspb identified an enhancer-like region in position −4·6 to −3·1 kb that was necessary for transgene expression in the sublingual glands. Here it is shown that the corresponding region in Pspa enhances transgene expression in the sublingual glands as efficiently. The implications for regulation of PSP mRNA expression in the sublingual glands are discussed.

We use modifier theory to compare the evolution of recombination under mutation–selection and migration–selection balance models. Recombination between loosely linked loci subject to weak multilocus selection is controlled by the genotype at a selectively neutral modifier locus. We show that the success of a new modifier depends on the sign and amount of epistasis as well as on the linkage of the modifier locus to the loci under selection. With both migration and mutation, for recombination to increase requires negative (synergistic) epistasis. When epistasis is sufficiently weak, increased recombination is always favoured under mutation–selection balance and never under migration–selection balance. With stronger negative epistasis, there exists a critical recombination value. In this case, a recombination-increasing allele invades the population under mutation–selection balance if its recombination rate with the major loci is less than the critical recombination value, whereas with weak migration it must be above this value. These results are the same for haploid and diploid populations.

Rapid and divergent evolution of male genitalia represents one of the most general evolutionary patterns in animals with internal fertilization, but the causes of this evolutionary trend are poorly understood. Several hypotheses have been proposed to account for genitalic evolution, most prominent of which are the lock-and-key, sexual selection and pleiotropy hypotheses. However, insights into the evolutionary mechanisms of genitalic evolution are hindered by a lack of relevant in-depth studies of genital morphology. We used a biparental progenies breeding design to study the effects of food stress during ontogeny on phenotypic expression of a suite of genital and non-genital morphological traits, both linear traits and multivariate shape indices, in a natural population of the water strider Gerris incognitus. In general, genitalic traits were as variable as non-genital traits, both phenotypically and genotypically. Average narrow-sense heritability of genital traits was 0·47 (SE=0·05). Further, while food stress during development had a large impact on adult morphology, and expression of genitalic traits exhibited significant levels of condition dependence, different genotypes did not significantly differ in their ability to cope with food stress. Genitalic conformation was also both phenotypically and genetically correlated with general morphological traits. These patterns are in disagreement with certain predictions generated by the long-standing lock-and-key hypothesis, but are in general agreement with several other hypotheses of genital evolution. We failed to find any additive genetic components in fluctuating asymmetry of any bilaterally symmetrical traits and the effects on fluctuating asymmetry of food stress during development were very low and insignificant. Some methodological implications of our study are discussed, such as the bias introduced by the non-negativity constraint in restricted maximum likelihood estimation of variance components.

The question of loss of genetic diversity in spatially structured populations has been considered by many authors, who have either assumed symmetric migration between subpopulations or restricted the analysis to two subpopulations and allowed asymmetric migration. In this paper we briefly discuss the two-subpopulation case that has been dealt with by other authors and then find a general formula for fixation probabilities for a population divided into three and four subpopulations. The number of individuals in the subpopulations can be different, but the size of each subpopulation is constant over time. Migration between the subpopulations may be asymmetric, that is the number of migrants moving from subpopulation i to subpopulation j is not the same as the number of migrants moving from subpopulation j to subpopulation i. When migration is symmetric, the results of previous authors are confirmed. The result for asymmetric migration shows that the influence a subpopulation has on the fixation probability for the whole population is determined by its size and the net amount of gene flow out of the subpopulation, directly and indirectly, to the whole population. The position of a subpopulation relative to the other subpopulations (that is, edge versus centre) is only important in that it can determine the amount of net gene flow from a subpopulation. Some examples are given of how this result can be applied, and of applications to conservation genetics. We conclude that when considering a management plan with the intention of maintaining genetic diversity, the relative strength and direction of migration must be considered.

Due to the tremendous cost of the traditional mutation-accumulation approach (the Bateman–Mukai technique), data are rare for deleterious mutation parameters such as genomic mutation rate, selection and dominance coefficients. Two alternative approaches have been developed (the Morton–Charlesworth and Deng–Lynch techniques). Except for the Deng–Lynch method, the statistical properties (bias and sampling variance) of these techniques are poorly understood; therefore we investigated them using computer simulation. With constant fitness effects of mutations, the Bateman–Mukai (assuming additive effects) and Deng–Lynch (assuming multiplicative effects) techniques are unbiased; the Morton–Charlesworth technique (assuming multiplicative effects) is very biased if fitness is used in the regression to estimate h, but slightly biased if the logarithm of fitness is used. With variable fitness effects, all techniques are biased. The Deng–Lynch technique is statistically better than the others except when fitness is used to estimate the average degree of dominance in selfing populations with the Morton–Charlesworth technique. If fitness effects are multiplicative but additivity is assumed, the Bateman–Mukai technique is biased under constant fitness effects, and less biased under variable fitness effects relative to when fitness effects are additive (as assumed by the technique). Our study not only quantifies the degree of bias under the biologically plausible situations investigated, thus forming a basis for correct inference of the true parameters by using these techniques, but also provides insights into the relative efficiencies of these techniques when the same number of genotypes are handled experimentally.

Methods to formulate and maximize response to selection for a quantitative trait over multiple generations when information on a quantitative trait locus (major gene) is available were developed to investigate and optimize response to selection in mixed inheritance models. Deterministic models with and without gametic phase disequilibrium between the major gene and other genes that affect the trait (polygenes) were considered. Genetic variance due to polygenes was assumed constant. Optimal control theory was used to formulate selection on an index of major gene effects and estimates of polygenic breeding values and to derive index weights that maximize cumulative response over multiple generations. Optimum selection strategies were illustrated using an example and compared with mass selection and with selection with full emphasis on the major gene (genotypic selection). The latter maximizes the single-generation response for a major gene with additive effects. For the example considered, differences between selection methods in cumulative response at the end of a planning horizon of 5, 10, or 15 generations were small but responses were greatest for optimum selection. Genotypic selection had the greatest response in the short term but the lowest response in the longer term. For optimum selection, emphasis on the major gene changed over generations. However, when accounting for variance contributed by the major gene, optimum selection resulted in approximately constant selection pressure on the major gene and polygenes over generations. Suboptimality of genotypic selection in the longer term was caused not so much by gametic phase disequilibrium but rather by unequal selection pressure on the major gene (and, therefore, on polygenes) over generations, as frequency and variance at the major gene changed. Extension of methods to more complex breeding structures, genetic models and objective functions is discussed.

The influence of mutation, selection and reproductive systems on within-population size variation at microsatellite loci was analysed using simulations. Mutation occurred through either (biased or unbiased) replication slippage, or unequal recombination between homologous chromosomes. Selection acted either on large allele size, or on the difference in size between the two homologous alleles of an individual. Reproduction was either sexual (panmictic) or clonal. Classical population genetics parameters, such as gene diversity or variance of allele size, were followed over (generally) 5000 generations for various sets of values of the mutation rate and strength of selection, in either clonally or sexually reproducing populations. The reproduction system had little influence on genetic parameters, either under neutral conditions or when selection acted on large allele size. Selection against difference in allele size strongly constrained variability in panmictic populations, whereas a limited influence was observed in clonal populations. Selection against the difference in allele size between the two alleles of an individual is an alternative explanation for the long life expectancy of microsatellite loci in sexual species. Whether this selection process actually occurs can therefore be tested by comparing the allele size distribution of microsatellite loci between regions/genomes exhibiting markedly different recombination rates.

A simulation study was performed to investigate methods for mapping single-dose (simplex) and double-dose (duplex) markers, and for identification of homologous chromosomes in an autotetraploid species, and to see how the map accuracy depends on the population size. An initial population of 1000 individuals was simulated, with 30 simplex and 10 duplex markers, and recombination fractions and lod scores were calculated between all pairs of markers. These were used to test the feasibility of mapping the simplex and duplex markers simultaneously. Smaller populations, from 500 to 75 individuals, were then simulated, and the estimates of the pairwise recombination fractions and the derived maps were compared with the true map. It was found that the accuracy of the estimates depended strongly on the type of markers involved, with simplex–simplex coupling pairs being most reliable and simplex–simplex repulsion pairs and duplex–duplex pairs in any configuration but coupling being least reliable. Maps can be assembled using recombination fractions and lod scores from pairs of simplex–simplex markers (coupling and repulsion), duplex–simplex (coupling and repulsion) and duplex–duplex (coupling). The agreement between the map order and the true order was good, although the map distance was generally underestimated at small sample sizes.

Three new dominant suppressor mutations of the C1 transcription regulator gene in maize – C1-IΔ1, C1-IΔ2 and C1-IΔ3 – are described that suppress anthocyanin colouration in kernels similar to the function of the C1-I standard inhibitor. The C1-IΔ mutations were induced by imprecise excision of an En/Spm transposon in the third exon of the C1 gene. These transposon footprints cause a frameshift in the C1 open reading frame that leads to truncated proteins due to an early stop codon 30 amino acids upstream of the wild-type C1 protein. Therefore, the C1-IΔ gene products lack the carboxy-terminal transcriptional activation domain of C1. The C1-I standard allele also lacks this domain and in addition differs in 17 amino acids from the wild-type C1 allele. The new C1-IΔ alleles provide evidence that deletion of the carboxy-terminal activation domain alone is sufficient to generate a dominant suppressive effect on the function of wild-type C1.

The determination of empirical confidence intervals for the location of quantitative trait loci (QTLs) by interval mapping was investigated using simulation. Confidence intervals were created using a non-parametric (resampling method) and parametric (resimulation method) bootstrap for a backcross population derived from inbred lines. QTLs explaining 1%, 5% and 10% of the phenotypic variance were tested in populations of 200 or 500 individuals. Results from the two methods were compared at all locations along one half of the chromosome. The non-parametric bootstrap produced results close to expectation at all non-marker locations, but confidence intervals when the QTL was located at the marker were conservative. The parametric method performed poorly; results varied from conservative confidence intervals at the location of the marker, to anti-conservative intervals midway between markers. The results were shown to be influenced by a bias in the mapping procedure and by the accumulation of type 1 errors at the location of the markers. The parametric bootstrap is not a suitable method for constructing confidence intervals in QTL mapping. The confidence intervals from the non-parametric bootstrap are accurate and suitable for practical use.

The house mouse, Mus musculus, harbours a variable cluster of long-range repeats in chromosome 1. As shown in previous studies, some high-copy clusters such as the MUT cluster are cytogenetically apparent as a homogeneously staining region (HSR) and are associated with a distortion of the Mendelian recovery ratio when transmitted by heterozygous females. The effect is caused by a decreased viability of +/+ embryos. It is compensated by maternal or paternal MUT. In this study, a deletion derivative of MUT, MUTdel, shows normal transmission ratios and no compensating capability. In this respect, MUTdel behaves like a wild-type cluster. Hence, both properties – transmission ratio distortion and compensating capability – map to the deleted region. The deletion comprises three-quarters of the MUT HSR and does not extend to the nearest markers adjacent to the HSR.

A hybrid dysgenesis syndrome in Drosophila virilis is associated with the mobilization of at least four unrelated transposable elements designated Helena, Paris, Penelope and Ulysses. We carried out 42 crosses between eight strains differing in transposable element copy number in order to assess their contributions to hybrid dysgenesis. Linear regression and stepwise regression analysis was performed to estimate the correlation between the difference in euchromatic transposable element number between the parental flies of different strains involved in the crosses and the percentage, in the progeny of these crosses, of males with atrophic gonads. Male gonadal atrophy is a typical manifestation of the D. virilis hybrid dysgenesis syndrome. About half the variability in the level of male gonadal atrophy can be attributed to Penelope and Paris/Helena. Other factors also seem to play a significant role in hybrid dysgenesis in D. virilis, including maternally transmitted host factors and/or uncontrolled environmental variation. In the course of this work a novel transposable element named Telemac was found. Telemac is also mobilized in hybrid dysgenesis but does not appear to play a major causative role.

A fundamental assumption of models for the maintenance of genetic variation by environmental heterogeneity is that selection favours alternative alleles in different environments. It is not clear, however, whether such antagonistic pleiotropy is common. We mapped quantitative trait loci (QTLs) causing variation for reproductive performance in each of three environmental treatments among a set of 98 recombinant inbred (RI) lines derived from a cross between two D. melanogaster laboratory strains. The three treatments were standard medium at 25°C, ethanol-supplemented medium at 25°C, and standard medium at 18°C. The RI lines showed highly significant genotype–environment interaction for the fitness measure. Of six QTLs with significant effects on fitness in at least one of the environments, five had significantly different effects at the different temperatures. In each case, the QTL by temperature interaction arose because the QTL had stronger effects at one temperature than at the other. No evidence for QTLs with opposite fitness effects in different environments was found. These results, together with those of recent studies of crop plants, suggest that antagonistic pleiotropy is a relatively uncommon form of genotype–environment interaction for fitness, but additional studies of natural populations are needed to confirm this conclusion.

The problem of genetic hitch-hiking in a geographically subdivided population is analysed under the assumption that migration rates among populations are relatively small compared with the selection coefficient for a newly arising advantageous allele. The approximate method used in the paper is valid when the number of emigrants per generation (Nm) is less than one. The approximate analysis shows that hitch-hiking can result in substantial differences among populations in the frequencies of neutral alleles closely linked to the advantageous allele. Thus, in cases for which genetic hitch-hiking is thought to be responsible for low levels of genetic variability in regions of the genome with restricted crossing over, it might be possible to find confirmatory evidence for that hypothesis by finding unusual patterns of geographic differentiation in the same regions of the genome.