Despite their unmatched popularity in many research areas, microsatellites have not yet become a major tool for the inference of genealogical relationships of closely related species. Recent studies have successfully extended the repertoire of microsatellite analysis beyond population genetics and demonstrate that phylogenetic relationships of closely related species can be inferred accurately with fewer loci than previously assumed.

Map-based cloning has been considered problematic for isolating quantitative trait loci (QTLs) due to the confounding phenotypic effects of environment and other QTLs. However, five recent studies, all in plants, have succeeded in cloning QTLs using map-based methods. We review the important features of these studies and evaluate the prospects for broader application of the techniques. Successful map-based cloning requires that QTLs represent single genes that can be isolated in near-isogenic lines, and that genotypes can be unambiguously inferred by progeny testing. In plants or animals for which map-based cloning of genes with discrete phenotypes is feasible, the modified procedures required for QTLs should not be limiting in most cases. The choice between map-based cloning and alternative methods will depend on details of the species and traits being studied.

The mutant form of the intracellular asymmetrically localized Numb membrane-bound protein of Drosophila melanogaster suppresses the negative complementation of certain Abruptex (Ax) mutations of the Notch (N) locus encoding a transmembrane receptor protein in which the Ax mutations are mutations in the epidermal growth factor (EGF)-like repeats of the extracellular domain of the receptor. One model for how Ax mutants affect N function is that they are refractory to an antagonistic signal generated by an excess of N ligands. Genetically numb (nb) is an antagonist of N. In the absence of nb, cells follow the same fate as they would in the presence of a gain-of-function N allele, such as Ax. Numb has been shown to interact with the cytoplasmic domain of Notch. It is therefore suggested that numb counteracts the effect of Abruptex on Notch ligand binding, i.e. that Numb is an antagonist to the activation of the Notch signal generated by Notch ligands. Numb might accomplish this by interfering with the proteolytic cleavage of the Notch intracellular domain at the cell membrane. Thus, it seems possible that the mechanism of negative complementation of certain Ax mutants is the failure of this cleavage. Other possible mechanisms for negative complementation are also discussed.

The larvae of Drosophila sechellia are highly resistant to octanoic acid, a toxin found in D. sechellia's host plant, Morinda citrifolia. In contrast, close relatives of D. sechellia, D. simulans and D. melanogaster, are not resistant. In a series of interspecific backcrosses, 11 genetic markers were used to map factors affecting egg-to-adult (‘larval’) resistance in D. sechellia. The third chromosome harbours at least one partially dominant resistance factor. The second chromosome carries at least two mostly dominant resistance factors but no recessive factors. However, neither the X chromosome – which contains 20% of D. sechellia's genome – nor the fourth chromosome appear to affect resistance. These data suggest that larval resistance to Morinda toxin may involve only a handful of genes. These results, when compared with a previous analysis of adult resistance to Morinda toxin in D. sechellia, suggest that larval resistance may involve a subset of the genes underlying adult resistance.

We have investigated the role of the Antennapedia and Bithorax complexes (ANT-C and BX-C) on the production of cuticular hydrocarbons in Drosophila melanogaster. In males, there is little, if any, influence of these complexes on the hydrocarbon pattern. In females, there are large and opposite effects of these complexes on diene production: two ANT-C mutations cause an increase in diene production and a reduction of monoenes, whereas most BX-C mutations result in a decrease in dienes and an increase in monoenes, although their sum remains constant. The effect is the highest in Mcp and iab6 females. It is suggested that a factor originating from the prothorax might activate the conversion of monoenes to dienes in females. The abdomen seems to have a crucial role in the production or control of pheromones: abdominal segments four to seven have the main effects, with a most dramatic effect for segments four and five.

A pseudo maximum likelihood method is proposed to estimate effective population size (Ne) using temporal changes in allele frequencies at multi-allelic loci. The computation is simplified dramatically by (1) approximating the multi-dimensional joint probabilities of all the data by the product of marginal probabilities (hence the name pseudo-likelihood), (2) exploiting the special properties of transition matrix and (3) using a hidden Markov chain algorithm. Simulations show that the pseudo-likelihood method has a similar performance but needs much less computing time and storage compared with the full likelihood method in the case of 3 alleles per locus. Due to computational developments, I was able to assess the performance of the pseudo-likelihood method against the F-statistic method over a wide range of parameters by extensive simulations. It is shown that the pseudo-likelihood method gives more accurate and precise estimates of Ne than the F-statistic method, and the performance difference is mainly due to the presence of rare alleles in the samples. The pseudo-likelihood method is also flexible and can use three or more temporal samples simultaneously to estimate satisfactorily the Nes of each period, or the growth parameters of the population. The accuracy and precision of both methods depend on the ratio of the product of sample size and the number of generations involved to Ne, and the number of independent alleles used. In an application of the pseudo-likelihood method to a large data set of an olive fly population, more precise estimates of Ne are obtained than those from the F-statistic method.

Genetic variability at five microsatellite loci was analysed in three hatchery-propagated populations of the flat oyster, Ostrea edulis. These populations were part of a selection programme for resistance to the protozoan parasite Bonamia ostreae and were produced by mass spawns, without control of the genealogy. Evidence for population bottlenecks and inbreeding was sought. A reduction in the number of alleles, mainly due to the loss of rare alleles, was observed in all selected populations, relative to the natural population from which they were derived. Heterozygote excesses were observed in two populations, and were attributed to substructuring of the population into a small number of families. Pedigree reconstruction showed that these two populations were produced by at most two spawning events involving a limited number of parents. Most individuals within these populations are half or full-sib, as shown by relatedness coefficients. The occurrence of population bottlenecks was supported by estimates of effective number of breeders derived by three methods: temporal variance in allelic frequencies, heterozygote excess, and a new method based on reduction in the number of alleles. The estimates from the different methods were consistent. The evidence for bottleneck and small effective number of breeders are expected to lead to increasing inbreeding, and have important consequences for the future management of the three O. edulis selected populations.

The rate and distance of instantaneous pollen flow in a population are parameters of considerable current interest for plant population geneticists and conservation biologists. We have recently developed an estimator (Φft) of differentiation between the inferred pollen clouds that fertilize several females, sampled within a single population. We have shown that there is a simple relation between Φft and the average pollen dispersal distance (δ) for the case of a population with no geographic structure. Though forest trees usually show considerable pollen flow, assuming an absence of spatially distributed genetic structure is not always wise. Here, we develop analytical theory for the relation between Φft and δ, for the case where the probability of Identity by Descent (IBD) for two individuals decreases with the physical distance between them. This analytical theory allows us to provide an effective method for estimating pollen dispersal distance in a population with adult genetic structure. Using real examples, we show that estimation errors can be large if genetic structure is not taken into account, so it is wise to evaluate adult genetic structure simultaneously with estimation of Φft for the pollen clouds. We show that the results are only moderately affected by changes in the decay function, a result of some importance since no completely established theory is available for this function.

A method for estimating genotypic and identity-by-descent probabilities in complex pedigrees is described. The method consists of an algorithm for drawing independent genotype samples which are consistent with the pedigree and observed genotype. The probability distribution function for samples obtained using the algorithm can be evaluated up to a normalizing constant, and combined with the likelihood to produce a weight for each sample. Importance sampling is then used to estimate genotypic and identity-by-descent probabilities. On small but complex pedigrees, the genotypic probability estimates are demonstrated to be empirically unbiased. On large complex pedigrees, while the algorithm for obtaining genotype samples is feasible, importance sampling may require an infeasible number of samples to estimate genotypic probabilities with accuracy.

The transmission disequilibrium test (TDT) customarily uses affected children and their parents (often case–parent trios, TDTD). Control–parent trios are necessary to guard against spurious significant results due to segregation distortion but are not generally utilized in the identification of disease susceptibility loci (DSL). Controls are often easy to recruit and the TDT can easily be extended to include control–parent trios into the analyses with unrelated case–parent trios. We present an extension of the TDT (TDTDC) that incorporates unrelated cases and controls and their parents into a single analysis. We develop a simple and accurate analytical method for computing the statistical power of various TDT (e.g. the TDTD, TDTDC, TDTDC and TDTC that employ control–parent trios only) under any genetic model. We investigated the power of these TDT, and particularly compared the relative power of the TDTD and TDTDC. We found that the TDTDC is almost always more powerful than the TDTC and TDTD. The relative power of the TDTDC and TDTD depends largely upon a number of parameters identified in the study. This study provides a basis for efficient use of control–parent trios in DSL identification.

Most QTL mapping methods assume that phenotypes follow a normal distribution, but many phenotypes of interest are not normally distributed, e.g. bacteria counts (or colony-forming units, CFU). Such data are extremely skewed to the right and can present a high amount of zero values, which are ties from a statistical point of view. Our objective is therefore to assess the efficiency of four QTL mapping methods applied to bacteria counts: (1) least-squares (LS) analysis, (2) maximum-likelihood (ML) analysis, (3) non-parametric (NP) mapping and (4) nested ANOVA (AN). A transformation based on quantiles is used to mimic observed distributions of bacteria counts. Single positions (1 marker, 1 QTL) as well as chromosome scans (11 markers, 1 QTL) are simulated. When compared with the analysis of a normally distributed phenotype, the analysis of raw bacteria counts leads to a strong decrease in power for parametric methods, but no decrease is observed for NP. However, when a mathematical transformation (MT) is applied to bacteria counts prior to analysis, parametric methods have the same power as NP. Furthermore, parametric methods, when coupled with MT, outperform NP when bacteria counts have a very high proportion of zeros (70·8%). Our results show that the loss of power is mainly explained by the asymmetry of the phenotypic distribution, for parametric methods, and by the existence of ties, for the non-parametric method. Therefore, mapping of QTL for bacterial diseases, as well as for other diseases assessed by a counting process, should focus on the occurrence of ties in phenotypes before choosing the appropriate QTL mapping method.