Molecular organization of the Drosophila melanogaster Adh chromosomal region in D. repleta and D. buzzatii, two distantly related species of the Drosophila subgenus.

The molecular organization of a 1.944-Mb chromosomal region of Drosophila melanogaster around the Adh locus has been analyzed in two repleta group species: D. repleta and D. buzzatii. The extensive genetic and molecular information about this region in D. melanogaster makes it a prime choice for comparative studies of genomic organization among distantly related species. A set of 26 P1 phages from D. melanogaster were successfully hybridized using fluorescence in-situ hybridization (FISH) to the salivary gland chromosomes of both repleta group species. The results show that the Adh region is distributed in D. repleta and D. buzatii over six distant sites of chromosome 3, homologous to chromosomal arm 2L of D. melanogaster (Muller's element B). This observation implies a density of 2.57 fixed breakpoints per Mb in the Adh region and suggests a considerable reorganization of this chromosomal element via the fixation of paracentric inversions. Nevertheless, breakpoint density in the Adh region is three times lower than that estimated for D. repleta chromosome 2, homologous to D. melanogaster 3R (Muller's element E). Differences in the rate of evolution among chromosomal elements are seemingly persistent in the Drosophila genus over long phylogenetic distances.

Duplication, dicistronic transcription, and subsequent evolution of the Alcohol dehydrogenase and Alcohol dehydrogenase-related genes in Drosophila.

It has recently been discovered that the Alcohol dehydrogenase and Alcohol dehydrogenase-related genes of Drosophila melanogaster and closely related species constitute a single transcription unit and that the Alcohol dehydrogenase-related gene is exclusively expressed from a dicistronic mRNA. Here, we show that in Drosophila lebanonensis, subgenus Scaptodrosophila, Adhr: is also transcribed as a dicistronic transcript with Adh Using degenerate primers designed on the sequence of the known Adhr proteins, we have been able to amplify and sequence a partial sequence of Adhr: in species representative of the whole subgenus Drosophila. This has allowed the study of the organization and expression of Adhr: in Drosophila buzzatii. We find that in D. buzzatii Adhr is transcribed as a monocistronic transcript. Adh and Adhr are believed to originate by duplication, and our data suggest that the cotranscription of these two genes was the primitive state, and that their independent transcription in the subgenus Drosophila is derived. We can rationalize the D. buzzatii condition as being correlated with the two genes evolving independent transcriptional control. However, why these two genes with clear divergence in the functions of their proteins should remain cotranscribed in groups as divergent as the subgenus Sophophora and the subgenus Scaptodrosophila remains a mystery.

Recombination and gene flux caused by gene conversion and crossing over in inversion heterokaryotypes.

A theoretical analysis of the effects of inversions on recombination and gene flux between arrangements caused by gene conversion and crossing over was carried out. Two different mathematical models of recombination were used: the Poisson model (without interference) and the Counting model (with interference). The main results are as follows. (1) Recombination and gene flux are highly site-dependent both inside and outside the inverted regions. (2) Crossing over overwhelms gene conversion as a cause of gene flux in large inversions, while conversion becomes relatively significant in short inversions and in regions around the breakpoints. (3) Under the Counting model the recombination rate between two markers depends strongly on the position of the markers along the inverted segment. Two equally spaced markers in the central part of the inverted segment have less recombination than if they are in a more extreme position. (4) Inversions affect recombination rates in the univerted regions of the chromosome. Recombination increases in the distal segment and decreases in the proximal segment. These results provide an explanation for a number of observations reported in the literature. Because inversions are ubiquitous in the evolutionary history of many Drosophila species, the effects of inversions on recombination are expected to influence DNA variation patterns.

The estimation of the number and the length distribution of gene conversion tracts from population DNA sequence data.

DNA sequence variation studies report the transfer of small segments of DNA among different sequences caused by gene conversion events. Here, we provide an algorithm to detect gene conversion tracts and a statistical model to estimate the number and the length distribution of conversion tracts for population DNA sequence data. Two length distributions are defined in the model: (1) that of the observed tract lengths and (2) that of the true tract lengths. If the latter follows a geometric distribution, the relationship between both distributions depends on two basic parameters: psi, which measures the probability of detecting a converted site, and phi, the parameter of the geometric distribution, from which the average true tract length, 1/(1-phi), can be estimated. Expressions are provided for estimating phi by the method of the moments and that of the maximum likelihood. The robustness of the model is examined by computer simulation. The present methods have been applied to the published rp49 sequences of Drosophila subobscura. Maximum likelihood estimate of phi for this data set is 0.9918, which represents an average conversion tract length of 122 bp. Only a small percentage of extant conversion events is detected.

Dynamics of gametic disequilibria between loci linked to chromosome inversions: the recombination-redistributing effect of inversions.

The total gametic disequilibrium between two loci linked to polymorphic inversions can be partitioned into two types of components: within and between chromosome arrangements. The within components depend on the gametic disequilibrium within each chromosome arrangement. The between components depend on the locus-inversion disequilibria. This partitioning has practical applications and is indispensable for studying the dynamics of these systems because inversions greatly reduce recombination in the heterokaryotypes while allowing free, and sometimes different, recombination in each of the homokaryotypes. We provide equations for the per generation change of the various disequilibria for systems with two and three chromosome arrangements, and the general recursive equations predicting the disequilibria after any number of generations for the case of two arrangements. Simulation studies were carried out using different values of the recombination parameters and all possible initial conditions. The results show a complex convergence to linkage equilibrium in inversion systems. The various disequilibria can have local maxima and minima while approaching equilibrium and, moreover, their dynamics cannot be described, in general, using a single parameter, i.e. an effective recombination rate. We conclude that the effects of inversions on gametic disequilibria must be carefully considered when dealing with disequilibria in inversion systems. The formulae provided in this paper can be used for such purpose.

The evolutionary history of Drosophila buzzatii. XXXII. Linkage disequilibrium between allozymes and chromosome inversions in two colonizing populations.

Chromosome polymorphism in Drosophila buzzatii is under selection but the genes responsible for the effect of the inversions of fitness are unknown. On the other hand, there is evidence for selection on several allozyme loci but the presence of paracentric inversions on the second chromosome, where most of the polymorphic loci are located, complicates the interpretation. Studies of the associations between allozymes and inversions are thus necessary to help understand the effect of selection at both the chromosomal and allozymic level. Until now this kind of information has only been available in D. buzzatii for two loci, Est-1 and Est-2, in Australian populations. Here we describe the genetic constitution of two Old World populations, Carboneras and Colera. Emphasis has been placed on the analysis of the linkage disequilibria between the second chromosome arrangements and three allozyme loci, Est-2, Pept-2 and Aldox, located on this chromosome. In addition, the recombination frequencies between the loci, and between the loci and the inversion breakpoints, have been estimated and a genetic map of the three loci has been produced. The two populations differ in allele and arrangement frequencies, as well as in the pattern of one-locus disequilibria. Est-2 and Aldox are associated with the second chromosome arrangements in both populations. On the other hand, Pept-2 is associated with the inversions in Colera but not in Carboneras. The gametic associations among the three loci are discussed taking into account the position of these loci on the chromosome map and the lack of recombination in the heterokaryotypes.