The copia element is a retrotransposon that is hypothesized to have been horizontally transferred from Drosophila melanogaster to some populations of Drosophila willistoni in Florida. Here we have used PCR and Southern blots to screen for sequences similar to copia element in South American populations of D. willistoni, as well as in strains previously shown to be carriers of the element. We have not found the canonical copia element in any of these populations. Unlike the P element, which invaded the D. melanogaster genome from D. willistoni and quickly spread worldwide, the canonical copia element appears to have transferred in the opposite direction and has not spread. This may be explained by differences in the requirements for transposition and in the host control of transposition.

The rate of insertion of transposable elements (TEs) is a fundamental parameter to understand both their dynamics and role in the evolution of the eukaryotic genome. Nonetheless, direct estimates of insertion rates are scarce because transposition is in general a rare phenomenon. A great deal of our previous work on transposition was based on a set of long-term mutation accumulation (MA) lines of Drosophila melanogaster started in 1987 (Oviedo lines), where roo was found highly active, with a rate of insertion of 7×10−4 insertions per element and generation, as compared with other 15 TE families that presented transposition rates around 10−5. Here, we study the evolution of the roo transposition rate, by in situ hybridization, after 60–75 additional generations of MA in two subsets of the Oviedo lines, O and O′, which had achieved average numbers of roo insertions of 77 and 84, respectively. In the O lines, insertions accumulated at a rate that remained constant (7×10−4 insertions per element and generation); however, the subset of lines O′ showed a lower accumulation rate of 4×10−4 insertions per element per generation, suggesting a regulation of transposition that depends on the number of elements. However, one of the O′ lines reached a number of 103 insertions, departing from the group mean by 4·6 sd, and showing that it escapes regulation. Hence, ‘de novo’ mutations affecting the regulation of transposition are relatively common. These results are discussed in relation to the possible mechanisms of containment of TEs.

Bayesian regularization of artificial neural networks (BRANNs) were used to predict body mass index (BMI) in mice using single nucleotide polymorphism (SNP) markers. Data from 1896 animals with both phenotypic and genotypic (12 320 loci) information were used for the analysis. Missing genotypes were imputed based on estimated allelic frequencies, with no attempt to reconstruct haplotypes based on family information or linkage disequilibrium between markers. A feed-forward multilayer perceptron network consisting of a single output layer and one hidden layer was used. Training of the neural network was done using the Bayesian regularized backpropagation algorithm. When the number of neurons in the hidden layer was increased, the number of effective parameters, γ, increased up to a point and stabilized thereafter. A model with five neurons in the hidden layer produced a value of γ that saturated the data. In terms of predictive ability, a network with five neurons in the hidden layer attained the smallest error and highest correlation in the test data although differences among networks were negligible. Using inherent weight information of BRANN with different number of neurons in the hidden layer, it was observed that 17 SNPs had a larger impact on the network, indicating their possible relevance in prediction of BMI. It is concluded that BRANN may be at least as useful as other methods for high-dimensional genome-enabled prediction, with the advantage of its potential ability of capturing non-linear relationships, which may be useful in the study of quantitative traits under complex gene action.

Genetic resistance to gastrointestinal worms is a complex trait of great importance in both livestock and humans. In order to gain insights into the genetic architecture of this trait, a mixed breed population of sheep was artificially infected with Trichostrongylus colubriformis (n=3326) and then Haemonchus contortus (n=2669) to measure faecal worm egg count (WEC). The population was genotyped with the Illumina OvineSNP50 BeadChip and 48 640 single nucleotide polymorphism (SNP) markers passed the quality controls. An independent population of 316 sires of mixed breeds with accurate estimated breeding values for WEC were genotyped for the same SNP to assess the results obtained from the first population. We used principal components from the genomic relationship matrix among genotyped individuals to account for population stratification, and a novel approach to directly account for the sampling error associated with each SNP marker regression. The largest marker effects were estimated to explain an average of 0·48% (T. colubriformis) or 0·08% (H. contortus) of the phenotypic variance in WEC. These effects are small but consistent with results from other complex traits. We also demonstrated that methods which use all markers simultaneously can successfully predict genetic merit for resistance to worms, despite the small effects of individual markers. Correlations of genomic predictions with breeding values of the industry sires reached a maximum of 0·32. We estimate that effective across-breed predictions of genetic merit with multi-breed populations will require an average marker spacing of approximately 10 kbp.

Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual, the extreme progeny may be selected by multiple generations of asexual reproduction and selection. We analyse this method of measuring phenotype in asexual progeny and examine the changes in marker allele frequency due to selection over many generations. Stochasticity in marker frequency in the selected population arises due to the finite initial population size. We derive the distribution of marker frequency as a result of selection at a single major locus, and show that in order to avoid spurious changes in marker allele frequency in the selected population, the initial population size should be in the low to mid hundreds.

Crow et al. (1990) and Barton (1992) have examined the critical migration rate for swamping selection in the nuclear system. Here, I use the same methodology to examine the critical migration rate in the cytonuclear system for hermaphrodite plants with a mixed mating system. Two selection schemes for a nuclear gene (heterozygote disadvantage and directional selection) and the directional selection scheme for organelle genes are considered. Results show that under random mating, the previous results are applicable to plant species by appropriate re-parameterization of the migration rate for nuclear and paternal organelle genes. A simple complementary relationship exists between seed and pollen flow in contributing to the critical migration rate. Under the mixed mating system, the critical migration rate of seeds and pollen for nuclear and paternal organelle genes can be changed due to the effects of selection and the cytonuclear linkage disequilibrium generated by migration and inbreeding. A negative but not complementary relationship exists between seed and pollen flow in contributing to the critical migration rate, varying with the mating system. Partial selfing can also adjust the critical seed flow for the maternal organelle gene, with a small critical migration rate for species of a high selfing rate. Both concordance and discordance among cytonuclear genes can occur under certain conditions during the process of swamping selection. This theory predicts the presence of various contributions of seed versus pollen flow to genetic swamping for plants with diverse mating systems.