We analysed the distribution of transposable elements (TEs) in 100 aligned pairs of orthologous intergenic regions from the mouse and human genomes. Within these regions, conserved segments of high similarity between the two species alternate with segments of low similarity. Identifiable TEs comprise 40–60% of segments of low similarity. Within such segments, a particular copy of a TE found in one species has no orthologue in the other. Overall, TEs comprise only approximately 20% of conserved segments. However, TEs from two families, MIR and L2, are rather common within conserved segments. Statistical analysis of the distributions of TEs suggests that a majority of the MIR and L2 elements present in murine intergenic regions have human orthologues. These elements must have been present in the common ancestor of human and mouse and have remained under substantial negative selection that prevented their divergence beyond recognition. If so, recruitment of MIR- and L2-derived sequences to perform a function that increases host fitness is rather common, with at least two such events per host gene. The central part of the MIR consensus sequence is over-represented in conserved segments given its background frequency in the genome, suggesting that it is under the strongest selective constraint.

Rare, random mutations were induced in budding yeast by ethyl methanesulfonate (EMS). Clones known to bear a single non-neutral mutation were used to obtain mutant heterozygotes and mutant homozygotes that were later compared with wild-type homozygotes. The average homozygous effect of mutation was an approximately 2% decrease in the growth rate. In heterozygotes, the harmful effect of these relatively mild mutations was reduced approximately fivefold. In a test of epistasis, two heterozygous mutant loci were paired at random. Fitness of the double mutants was best explained by multiplicative action of effects at single loci, with little evidence for epistasis and essentially excluding synergism. In other experiments, the same mutations in haploid and heterozygous diploid clones were compared. Regardless of the haploid phenotypes, mildly deleterious or lethal, fitness of the heterozygotes was decreased by less than half a per cent on average. In general, the results presented here suggest that most mutations tend to exhibit small and weakly interacting effects in heterozygous loci regardless of how harmful they are in haploids or homozygotes.

The medaka fish transposable element, Tol2, is a member of the hAT family of transposons. It has been directly demonstrated to be active and two mRNAs, differing in length, have been isolated. They cover exons 1–4 and exons 2–4 and the longer form has already been proven to catalyse transposition reactions. However, the function of the shorter mRNA in medaka cells has hitherto remained unclear. In the present study, first we constructed a quantitative system to detect Tol2 excision using an indicator plasmid carrying a non-autonomous Tol2 within its lacZ gene; second we injected mRNAs with the plasmid into medaka eggs. Excision of Tol2 was detected as E. coli blue colonies caused by the recovery of lacZ activity. Addition of the longer mRNA increased excision, but the shorter did not. Moreover, co-injection of both mRNAs greatly lowered the frequency compared with the case of treatment with the longer mRNA alone. These results indicate that the shorter mRNA has an inhibitory effect on the excision reaction, and that the N-terminal region of the transposase encoded by exon 1, including a BED zinc finger, presumably plays an important role in excision. Here, we suggest a regulatory mechanism of Tol2 transposition involving the expression of these mRNAs.

New paradigms in genetics have increased the chance of finding genes that appear redundant but in fact may have been preserved due to a small level of positive selection potential acting during each generation. Monitoring changes in genotypic frequencies within and between generations allows the dissection of the fertility, viability and meiotic drive selection components acting on such genes in natural and experimental populations. Here, a formal maximum likelihood procedure is developed to identify and estimate these selection components in highly selfing populations by fitting the time-dependent solutions for genotypic frequencies to observed multigenerational counts. With adult census alone, we can not simultaneously estimate all three selection components considered. In such cases, we instead consider a hierarchy of 11 models with either fewer selection components, complete dominance, or multiplicative meiotic drive with a single parameter. We identify the best-fitting of these models by applying likelihood ratio tests to nested models and Akaike's Information Criterion (AIC) and the Bayesian Information Criterion (BIC) to non-nested models. With seed census, fertility and viability selection are not distinguishable and thus can only be estimated jointly. A combination of joint seed and adult census data allows us to estimate all three selection components simultaneously. Simulated data validate the estimation procedure and provide some practical guidelines for experimental design. An application to Arabidopsis data establishes that viability selection is the major selective force acting on the ACT2 actin gene in laboratory-grown Arabidopsis populations.

Simultaneous analysis of correlated traits that change with time is an important issue in genetic analyses. Several methodologies have already been proposed for the genetic analysis of longitudinal data on single traits, in particular random regression and character process models. Although the latter proved, in most cases, to compare favourably to alternative approaches for analysis of single function-valued traits, they do not allow a straightforward extension to the multivariate case. In this paper, another methodology (structured antedependence models) is proposed, and methods are derived for the genetic analysis of two or more correlated function-valued traits. Multivariate analyses are presented of fertility and mortality in Drosophila and of milk, fat and protein yields in dairy cattle. These models offer a substantial flexibility for the correlation structure, even in the case of complex non-stationary patterns, and perform better than multivariate random regression models, with fewer parameters.

Maternal effects play an important role in fitness and other aspects of individual performance in many species, particularly mammalian, yet their impact on genetic variation within species and its rate of loss during selection has been neglected. In this paper we extend the theory of expected long-term genetic contributions to include maternal effects, and tested the accuracy of predicted rates of inbreeding for populations under mass selection by comparison with simulations. The model includes selective advantages of direct and maternal additive genetic effects, and also the selective advantage of a common maternal environmental effect. The population structures investigated had a fixed number of dams per sire and fixed family size. Most prediction errors of the rate of inbreeding (ΔF) were less than 8% of the simulated means and were lower in magnitude than the prediction errors of genetic gain (ΔG). The predictions of ΔG from contributions equalled previously published predictions. A variation in maternal genetic effects resulted in a much larger ΔF than for an equally sized variation in common maternal environmental effects. For a fixed genetic gain, ΔF increased as the maternal heritability increased. The influence of family size, mating ratio and age structure on ΔF was greater with maternal effects than with only direct genetic effects included. In conclusion, maternal effects can be a very important aspect to consider when predicting ΔF in populations under selection, and the developed methodology gives good predictions.