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.

The red flour beetle, Tribolium castaneum, has been selected for whole genome shotgun sequencing in the next year. In this minireview, we discuss some of the genetic and genomic tools and biological properties of Tribolium that have established its importance as an organism for agricultural and biomedical research as well as for studies of development and evolution. A Tribolium genomic database, Beetlebase, is being constructed to integrate genetic, genomic and biological data as it becomes available.

We report here the consensus target sequence of transposons Tc1, Tc3 and Tc5 of Caenorhabditis elegans. These sequences were obtained by molecular analysis of 1008 random new insertions which have not been exposed to natural selection. This analysis reveals consensus target sites slightly different from those previously reported, and confirms that the mariner elements Tc1 and Tc3 insert in sites which are not preferentially palindromic.

The Triplo-lethal locus (Tpl) of Drosophila is both triplo-lethal and haploinsufficient, but the function of the locus is unknown. We have examined Tpl-aneuploid embryos and find that, in both trisomics and monosomics, the midgut shows extensive cell death and the tracheae are abnormal. Shortly thereafter, all tissues die. PCR-based genotyping of individual embryos and larvae show that this phenotype occurs in the trisomics after hatching and in the monosomics before hatching. Weak alleles of the interacting gene Su(Tpl) delay the death of Tpl trisomics, but they still show the same tracheal and midgut phenotypes before dying. Hyperoxia (45% oxygen) partially suppresses the phenotype of Tpl aneuploids, even though the use of a hypoxia reporter strain shows that dying Tpl aneuploids are not hypoxic. This is the first report of a phenotype associated with the Tpl locus and the first report of an environmental condition that suppresses the phenotype.

The MHC class II loci encoding cell surface antigens exhibit extremely high allelic polymorphism. There is considerable uncertainty in the literature over the relative roles of recombination and de novo mutation in generating this diversity. We studied class II sequence diversity and allelic polymorphism in two populations of Peromyscus maniculatus, which are among the most widespread and abundant mammals of North America. We find that intragenic recombination (or gene conversion) has been the predominant mode for the generation of allelic polymorphism in this species, with the amount of population recombination per base pair exceeding mutation by at least an order of magnitude during the history of the sample. Despite this, patchwork motifs of sites with high linkage disequilibrium are observed. This does not appear to be consistent with the much larger amount of recombination versus mutation in the history of the sample, unless the recombination rate is highly non-uniform over the sequence or selection maintains certain sites in linkage disequilibrium. We conclude that selection is most likely to be responsible for preserving sequence motifs in the presence of abundant recombination.

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.

We studied spatial and temporal variation in 20–23 Aedes aegypti samples collected in Phnom Penh and its suburbs to estimate the population genetic structure using allozymes and the susceptibility to a dengue-2 virus. Based on seven allozyme systems, we detected low levels of genetic exchanges (i.e. high, significant FST values) between populations collected in the city centre, and different patterns of genetic structure for samples collected in the suburbs, depending on the type of environment and the date of collection. In the southern suburbs and the Chroy Chang Var Peninsula, differentiation became highly significant at the end of the dry season, whereas the opposite situation was observed for collections from the northern suburbs. Vector competence assessed by oral infections with a dengue-2 virus was lower for samples collected in the city centre than in the suburbs. A significant decrease of dengue susceptibility was observed in populations during the dry season. This study allows a model of Ae. aegypti population functioning in Phnom Penh to be suggested. Dynamics of dengue virus diffusion depend on the population genetic structure of the vector and its evolution over space and time.

We have investigated the pattern of DNA sequence variation at the exuperantia2 locus in Drosophila pseudoobscura. This adds to the increasing dataset of genetic variation in D. pseudoobscura, a useful model species for evolutionary genetic studies. The level of silent site nucleotide diversity and the divergence from an outgroup Drosophila miranda are comparable with those for other X-linked loci. One peculiar pattern at the exu2 locus of D. pseudoobscura is a complete linkage disequilibrium between two SNPs, one of which is a replacement site. As a result, there are two distinct haplotype groups in our dataset. Based upon the comparisons with the outgroup sequences from D. miranda and Drosophila persimilis, we show that the newly derived haplotype group has lower diversity than the ancestral haplotype group. The pattern of protein evolution at exu2 shows some deviation from the neutral model. Together, these and other characteristics of the exu2 locus suggest the action of selection on the pattern of SNP variation, consistent with a partial selective sweep associated with the newly derived haplotype.

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.

In asexual eukaryotes, the two allelic gene copies at a locus are expected to become highly divergent as a result of the independent accumulation of mutations in the absence of segregation. If sexual reproduction was abandoned millions of generations ago, intra-individual allelic divergences can be significantly larger than in species that reproduce sexually. Owing to the disputed existence of truly ancient asexual species, this so-called ‘Meselson effect’ has been put forward as a means of confirming the complete loss of sexual reproduction. Very few attempts have, however, been made at quantifying the effect of sexual reproduction on the degree of divergence between gene copies in an asexual population. Here, I describe how asexual reproduction can be regarded as a special case of population subdivision. Using a slightly modified version of the standard two-deme structured coalescent, I derive the expected coalescence time for a pair of gene copies in an asexual population and show that the Meselson effect is compatible with low rates of sexual reproduction.

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.

In the Australian red-claw crayfish Cherax quadricarinatus (von Martens) (Decapoda, Parastacidae), a gonochoristic species, seven different combinations of intersex individuals (with both male and female genital openings) have been described. However, to date, the genetic basis for this phenomenon has not been investigated. This study was designed to test a simple chromosome-based sex-determination model for C. quadricarinatus that assumes the male to be the homogametic (ZZ) sex. According to our model, intersex individuals that are functionally males are genetically females (WZ). Individual crosses were performed between intersex and female crayfish, with control crosses being performed between normal males and females. The control crosses yielded, in most cases, the expected 1[ratio ]1 sex ratio in the F1 progeny. Crosses between intersex individuals and females yielded a 1[ratio ]3 (male[ratio ]female) sex ratio in most crosses. According to our hypothesis, one-third of the females produced in a cross of a female with an intersex animal should be WW females. The hypothesis was tested by crossing normal males with F1 females, which were progeny of intersex fathers. These crosses yielded almost 100% females, a finding that conforms to the above-suggested sex determination model for C. quadricarinatus and the female WZ genotype of intersex individuals.

Inbred lines of the nematode Caenorhabditis elegans containing independent EMS-induced mutations were crossed to the ancestral wild-type strain (N2). Replicated inbred sublines were generated from the F1 offspring under conditions of minimal selection and, along with the N2 and mutant progenitor lines, were assayed for several fitness correlates including relative fitness (w). A modification of the Castle–Wright estimator and a maximum-likelihood (ML) method were used to estimate the numbers and effects of detectable mutations affecting these characters. The ML method allows for variation in mutational effects by fitting either one or two classes of mutational effect, and uses a Box–Cox power transformation of residual values to account for a skewed distribution of residuals. Both the Castle–Wright and the ML analyses suggest that most of the variation among sublines was due to a few (~1·5–2·5 on average) large-effect mutations. Under ML, a model with two classes of mutational effects, including a class with small effects, fitted better than a single mutation class model, although not significantly better. Nonetheless, given that we expect there to be many mutations induced per line, our results support the hypothesis that mutations vary widely in their effects.

During courtship, visual and chemical signals are often exchanged between the sexes. The proper exchange of such signals ensures intraspecific recognition. We have examined the genetic basis of interspecific differences in male mating behaviour and pheromone concentration between Drosophila simulans and D. sechellia by using Drosophila simulans/D. sechellia introgression lines. Our results show a majority of quantitative trait loci (QTLs) explaining variation in both male mating behaviour and pheromone concentration to be located on the third chromosome. One QTL found on the third chromosome explains variation in time needed to start courtship and copulation as well as time spent courting. The position of such QTL (approximately 84A–88B) with effects on courtship and copulation aspects of mating includes the candidate sex determination gene doublesex (84E5–6) and Voila (86E1–2), a gene that affects male courtship in D. melanogaster. One additional third chromosome QTL explained variation in 7-tricosene pheromone concentrations among males. The interval mapping position of this QTL (approximately 68E–76E) did not overlap with the position detected for differences in mating behaviour and the intervals did not include candidate genes previously identified as having an effect on D. melanogaster cuticular hydrocarbon production. We did not detect any directionality of the effect of Drosophila sechellia allele introgressions in male mating recognition.

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.

Many diseases show dichotomous phenotypic variation but do not follow a simple Mendelian pattern of inheritance. Variances of these binary diseases are presumably controlled by multiple loci and environmental variants. A least-squares method has been developed for mapping such complex disease loci by treating the binary phenotypes (0 and 1) as if they were continuous. However, the least-squares method is not recommended because of its ad hoc nature. Maximum Likelihood (ML) and Bayesian methods have also been developed for binary disease mapping by incorporating the discrete nature of the phenotypic distribution. In the ML analysis, the likelihood function is usually maximized using some complicated maximization algorithms (e.g. the Newton–Raphson or the simplex algorithm). Under the threshold model of binary disease, we develop an Expectation Maximization (EM) algorithm to solve for the maximum likelihood estimates (MLEs). The new EM algorithm is developed by treating both the unobserved genotype and the disease liability as missing values. As a result, the EM iteration equations have the same form as the normal equation system in linear regression. The EM algorithm is further modified to take into account sexual dimorphism in the linkage maps. Applying the EM-implemented ML method to a four-way-cross mouse family, we detected two regions on the fourth chromosome that have evidence of QTLs controlling the segregation of fibrosarcoma, a form of connective tissue cancer. The two QTLs explain 50–60% of the variance in the disease liability. We also applied a Bayesian method previously developed (modified to take into account sex-specific maps) to this data set and detected one additional QTL on chromosome 13 that explains another 26% of the variance of the disease liability. All the QTLs detected primarily show dominance effects.

Normal mixed models with different levels of heterogeneity in the residual variance are fitted to pig litter size data. Exploratory analysis and model assessment is based on examination of various posterior predictive distributions. Comparisons based on Bayes factors and related criteria favour models with a genetically structured residual variance heterogeneity. There is, moreover, strong evidence of a negative correlation between the additive genetic values affecting litter size and those affecting residual variance. The models are also compared according to the purposes for which they might be used, such as prediction of ‘future’ data, inference about response to selection and ranking candidates for selection. A brief discussion is given of some implications for selection of the genetically structured residual variance model.

This paper examines the properties of likelihood maps generated by interval mapping (IM) and composite interval mapping (CIM), two widely used methods for detecting quantitative trait loci (QTLs). We evaluate the usefulness of interpretations of entire maps, rather than only evaluating summary statistics that consider isolated features of maps. A simulation study was performed in which traits with varying genetic architectures, including 20–40 QTLs per chromosome, were examined with both IM and CIM under different marker densities and sample sizes. IM was found to be an unreliable tool for precise estimation of the number and locations of individual QTLs, although it has greater power for simply detecting the presence of QTLs than CIM. The ability of CIM to resolve the correct number of QTLs and to estimate their locations correctly is good if there are three or fewer QTLs per 100 centiMorgans, but can lead to erroneous inferences for more complex architectures. When the underlying genetic architecture of a trait consists of several QTLs with randomly distributed effects and locations likelihood profiles were often indicative of a few underlying genes of large effect. Studies that have detected more than a few QTLs per chromosome should be interpreted with caution.