Genomic copy numbers and the rates of movement of nine families of transposable elements (TEs) of Drosophila melanogaster were estimated in two sets of mutation accumulation lines: Beltsville and Madrid. Southern blotting was used to screen a large number of samples from both genetic backgrounds for TEs. The Madrid lines were also screened by in situ hybridization of TEs to polytene chromosomes, in order to obtain more detailed information about the behaviour of TEs in the euchromatin. Southern blotting data provided evidence of insertions and excision events in both genetic backgrounds, occurring at rates of approximately 10−5 and 10−6 per element copy per generation, respectively. In contrast, in situ data from the Madrid background presented a completely different picture, with no evidence for excisions, and a significantly higher rate of transposition (1·01×10−4). Direct comparison of the two data sets suggests that the Southern blotting technique had serious deficiencies: (i) it underestimated element abundance; (ii) it revealed less than 30% of the new insertions detected by in situ hybridization; and (iii) changes in the size of restriction fragments from any source were spuriously identified as simultaneous insertion–excision events. Our in situ data are consistent with previous studies, and suggest that selection is the main force controlling element spread by transposition.

Members of the Polycomb group (Pc-G) and trithorax group (trx-G) of genes, as well as the enhancers of trx-G and Pc-G (ETP), function together to maintain segment identity during Drosophila development. In order to obtain new marked P mutations in these genes, we screened for dominant modifiers of the extra-sex-combs phenotype displayed by males mutant for the polyhomeotic (ph) gene, a member of the Pc-G group. Five P{lacW} insertions in four different genes were found to stably suppress ph: two are allelic to trithorax, one is the first allele specific to the Minute(2)21C gene, and the remaining two define new trx-G genes, toutatis (tou) in 48A and taranis (tara) in 89B10-13. tou is predicted to encode a 3109 amino acid sequence protein (TOU), which contains a TAM DNA-binding domain, a WAKZ motif, two PHD zinc fingers and a C-terminal bromodomain, and as such is likely to be involved in regulation of chromatin structure as a subunit of a novel chromatin remodelling complex. In a previous study, we found that insertion of a P{ph} transposable element containing ph regulatory sequences creates a high frequency of mutations modifying ph homeotic phenotypes. One such insertion enhanced the ph phenotype and we show that it is a new allele of UbcD1/eff, a gene encoding a ubiquitin-conjugating enzyme that is involved in telomere association and potentially in chromatin remodelling.

The rate of accumulation of deleterious mutations by Muller's ratchet is investigated in large asexual haploid populations, for a range of parameters with potential biological relevance. The rate of this process is studied by considering a very simple model in which mutations can have two types of effect: either strongly deleterious or mildly deleterious. It is shown that the rate of accumulation of mildly deleterious mutations can be greatly increased by the presence of strongly deleterious mutations, and that this can be predicted from the associated reduction in effective population size (the background selection effect). We also examine the rate of the ratchet when there are two classes of mutation of similar but unequal effects on fitness. The accuracy of analytical approximations for the rate of this process is analysed. Its possible role in causing the degeneration of Y and neo-Y chromosomes is discussed in the light of our present knowledge of deleterious mutation rates and selection coefficients.

Parentage studies often estimate the number of parents contributing to half-sib progeny arrays by counting the number of alleles attributed to unshared parents. This approach is compromised when an offspring has the same heterozygous genotype as the shared parent, for then the contribution of the unshared parent cannot be unambiguously deduced. To determine how often such cases occur, formulae for co-dominant markers with n alleles are derived here for Ph, the probability that a given heterozygous parent has an offspring with the same heterozygous genotype, and Pa, the probability that a randomly chosen offspring has the same heterozygous genotype as the shared parent. These formulae have been derived assuming Mendelian segregation with either (1) an arbitrary mating system, (2) random mating or (3) mixed mating. The maximum value of Pa under random mating is 0·25 and occurs with any two alleles each at a frequency of 0·5. The behaviour with partial selfing (where reproduction is by selfing with probability s, and random mating otherwise) is more complex. For n [les ] 3 alleles, the maximum value of Pa occurs with any two alleles each at a frequency of 0·5 if s < 0·25, and with three equally frequent alleles otherwise. Numerically, the maximum value of Pa for n [ges ] 4 alleles occurs with n* [les ] n alleles at equal frequencies, where the maximizing number of alleles n* is an increasing function of the selfing rate. Analytically, the maximum occurs with all n alleles present and equally frequent if s [ges ] 2/3. In addition, the potential applicability of these formulae for evolutionary studies is briefly discussed.

The evolution of molecular quantitative traits, such as codon usage bias or base frequencies, can be explained as the result of mutational biases alone, or as the result of mutation and selection. Whereas mutation models can be investigated easily, realistic modelling of selection-directed genome evolution is analytically intractable, and numerical calculations require substantial computer resources. We investigated the evolution of optimal codon frequency under additive and multiplicative effects of selected linked codons. We show that additive selective effects of many linked sites cannot be effective in genomes when the number of selected sites is greater than the effective population size, a realistic assumption according to current molecular data. We then discuss the implications of these results for isochore evolution in vertebrates.

Haseman and Elston (1972) developed a robust regression method for the detection of linkage between a marker and a quantitative trait locus (QTL) using sib pair data. The principle underlying this method is that the difference in phenotypes between pairs of sibs becomes larger as they share a decreasing number of alleles at a particular QTL identical by descent (IBD) from their parents. In this case, phenotypically very different sibs will also on average share a proportion of alleles IBD at any marker linked to the QTL that is lower than the expected value of 0·5. Thus, the deviation of the proportion of marker alleles IBD from the expected value in pairs of sibs selected to be phenotypically different (i.e. discordant) can provide a test for the presence of a QTL. A simple regression method for QTL detection in sib pairs selected for high phenotypic differences is presented here. The power of the analytical method was found to be greater than the power obtained using the standard analysis when samples of sib pairs with high phenotypic differences were used. However, the use of discordant sib pairs was found to be less powerful for QTL detection than alternative selective genotyping schemes based on the phenotypic values of the sibs except with intense selection, when its advantage was only marginal. The most effective selection scheme overall was the use of sib pairs from entire families selected on the basis of high within-family variance for the trait in question. There is little effect of selection on QTL position estimates, which are in good agreement with the simulated values. However, QTL variance estimates are biased to a greater or lesser degree, depending on the selection method.

Xie & Xu (2000) present a model for mapping quantitative trait loci in an autotetraploid population. However, one aspect of their model, namely gamete formation, does not properly represent the biological process in autotetraploid species. This paper gives a more realistic formulation for this part of the model, and discusses the consequences for multipoint mapping.