Natural Selection Shapes Variation in Genome-wide Recombination Rate in Drosophila pseudoobscura

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Linkage Disequilibrium in Natural and Experimental Populations of Drosophila Melanogaster

We have studied linkage disequilibrium in Drosophila melanogaster in two samples from a wild population and in four large laboratory populations derived from the wild samples. We have assayed four polymorphic enzyme loci, fairly closely linked in the third chromosome: Sod Est-6, Pgm, and Odh. The assay method used allows us to identify the allele associations separately in each of the two homologous chromosomes from each male sampled. We have detected significant linkage disequilibrium between two loci in 16.7% of the cases in the wild samples and in 27.8% of the cases in the experimental populations, considerably more than would be expected by chance alone. We have also found three-locus disequilibria in more instances than would be expected by chance. Some disequilibria present in the wild samples disappear in the experimental populations derived from them, but new ones appear over the generations. The effective population sizes required to generate the observed disequilibria by randomness range from 40 to more than 60,000 individuals in the natural population, depending on which locus pair is considered, and from 100 to more than 60,000 in the experimental populations. These population sizes are unrealistic; the fact that different locus-pairs yield disparate estimates within the same population argues against the likelihood that the disequilibria may have arisen as a consequence of population bottlenecks. Migration, or population mixing, cannot be excluded as the process generating the disequilibria in the wild samples, but can in the experimental populations. We conclude that linkage disequilibrium in these populations is most likely due to natural selection acting on the allozymes, or on loci very tightly linked to them.     

A Comprehensive Study of Genic Variation in Natural Populations of Drosophila Melanogaster. VI. Patterns and Processes of Genic Divergence between D. Melanogaster and Its Sibling Species, Drosophila Simulans

We present here an extensive set of data on allelic differences between homologous proteins of Drosophila melanogaster and its sibling species, Drosophila simulans, obtained by nondenaturing one-dimensional, and denaturing two-dimensional gel electrophoresis. The data suggest that, for these two species, (1) approximately 10% of protein-coding loci have no alleles in common in our sample, (2) the extent of genic variation at a locus (mean heterozygosity) within a species is not correlated with the extent of divergence (Nei's genetic distance) at that locus between species, and (3) significant heterogeneity of divergence rates exists for different structural/functional classes of loci. These results are discussed in the context of the dynamics of genetic variation within and between species.     

Structure of the Y Chromosomal Su(ste) Locus in Drosophila Melanogaster and Evidence for Localized Recombination among Repeats

The structure of the Suppressor of Stellate [Su(Ste)] locus on the Drosophila melanogaster Y chromosome was examined by restriction analysis of both native and cloned genomic DNA. The locus consists of short subarrays of tandem repeats separated by members of other moderately repeated families. Both size variants and restriction variants proved to be common. Most repeats fell into two size classes--2.8 and 2.5 kb--but other size variants were also observed. Restriction variants showed a strong tendency to cluster, both at the gross level where some variants were present in only one of three subintervals of the locus, and at the fine level, where repeats from the same phage clone were significantly more similar than repeats from different clones. Restriction variants were shared freely among repeats of different size classes; however, size variants appeared to be randomly distributed among phage clones. These data indicate that recombination among tandem Su(Ste) repeats occurs at much higher frequencies between close neighbors than distant ones. In addition, they suggest that gene conversion rather than sister chromatid exchange may be the primary recombinational mechanism for spreading variation among repeats at the Su(Ste) locus.     

Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster

Estimating fine-scale recombination maps of Drosophila from population genomic data is a challenging problem, in particular because of the high background recombination rate. In this paper, a new computational method is developed to address this challenge. Through an extensive simulation study, it is demonstrated that the method allows more accurate inference, and exhibits greater robustness to the effects of natural selection and noise, compared to a well-used previous method developed for studying fine-scale recombination rate variation in the human genome. As an application, a genome-wide analysis of genetic variation data is performed for two Drosophila melanogaster populations, one from North America (Raleigh, USA) and the other from Africa (Gikongoro, Rwanda). It is shown that fine-scale recombination rate variation is widespread throughout the D. melanogaster genome, across all chromosomes and in both populations. At the fine-scale, a conservative, systematic search for evidence of recombination hotspots suggests the existence of a handful of putative hotspots each with at least a tenfold increase in intensity over the background rate. A wavelet analysis is carried out to compare the estimated recombination maps in the two populations and to quantify the extent to which recombination rates are conserved. In general, similarity is observed at very broad scales, but substantial differences are seen at fine scales. The average recombination rate of the X chromosome appears to be higher than that of the autosomes in both populations, and this pattern is much more pronounced in the African population than the North American population. The correlation between various genomic features—including recombination rates, diversity, divergence, GC content, gene content, and sequence quality—is examined using the wavelet analysis, and it is shown that the most notable difference between D. melanogaster and humans is in the correlation between recombination and diversity.     

Stability of Tandem Repeats in the Drosophila Melanogaster HSR-Omega Nuclear RNA

The Drosophila melanogaster Hsr-omega locus produces a nuclear RNA containing >5 kb of tandem repeat sequences. These repeats are unique to Hsr-omega and show concerted evolution similar to that seen with classical satellite DNAs. In D. melanogaster the monomer is ~280 bp. Sequences of 191/2 monomers differ by 8 +/- 5% (mean +/- SD), when all pairwise comparisons are considered. Differences are single nucleotide substitutions and 1-3 nucleotide deletions/insertions. Changes appear to be randomly distributed over the repeat unit. Outer repeats do not show the decrease in monomer homogeneity that might be expected if homogeneity is maintained by recombination. However, just outside the last complete repeat at each end, there are a few fragments of sequence similar to the monomer. The sequences in these flanking regions are not those predicted for sequences decaying in the absence of recombination. Instead, the fragmentation of the sequence homology suggests that flanking regions have undergone more severe disruptions, possibly during an insertion or amplification event. Hsr-omega alleles differing in the number of repeats are detected and appear to be stable over a few thousand generations; however, both increases and decreases in repeat numbers have been observed. The new alleles appear to be as stable as their predecessors. No alleles of less than ~5 kb nor more than ~16 kb of repeats were seen in any stocks examined. The evidence that there is a limit on the minimum number of repeats is consistent with the suggestion that these repeats are important in the function of the unusual Hsr-omega nuclear RNA.     

Polymorphism and Locus-Specific Effects on Polymorphism at Microsatellite Loci in Natural Drosophila Melanogaster Populations

We have studied the natural variation at microsatellite loci in two African and five non-African populations of Drosophila melanogaster. Ten dinucleotide simple sequence loci were cloned from chromosomally mapped P1 clones and typed for single individuals from isofemale lines of the respective populations. We find that the African populations harbor the largest degree of diversity, while the non-African populations show a lower diversity. This supports previous results that D. melanogaster originated in Africa and spread across the rest of the world in historic times. Using genetic distance measures, we find also a distinct population subdivision between the non-African populations. Most interestingly, we find for some loci in some populations a strongly reduced variability, which cannot be explained by bottleneck effects. Employing a conservative test based on the variance in repeat number, we find that at least one locus in one population deviates significantly from the expectations of mutation-drift equilibrium. We suggest that this may be due to a recent selective sweep in this chromosomal region that may have been caused by a linked locus that was involved in local adaptation of the population.     

Molecular Variation of Adh and P6 Genes in an African Population of Drosophila Melanogaster and Its Relation to Chromosomal Inversions

Four-cutter molecular polymorphism of Adh and P6, and chromosome inversion polymorphism of chromosome II were investigated in 95 isogenic lines of an Ivory Coast population of Drosophila melanogaster, a species assumed to have recently spread throughout the world from a West African origin. The P6 gene showed little linkage disequilibrium with the In(2L)t inversion, although it is located within this inversion. This suggests that the inversion and the P6 locus have extensively exchanged genetic information through either double crossover or gene conversion. Allozymic variation in ADH was in linkage disequilibrium with In(2L)t and In(2R)NS inversions. Evidence suggests either that inversion linkage with the Fast allele is selectively maintained, or that this allele only recently appeared. Molecular polymorphism at the Adh locus in the Ivory Coast is not higher than in North American populations. New haplotypes specific to the African population were found, some of them connect the ``Wa(s)-like' haplotypes found at high frequencies in the United States to the other slow haplotypes. Their relation with In(2L)t supports the hypothesis that Wa(s) recently recombined away from an In(2L)t chromosome which may be the cause of its divergence from the other haplotypes.     

Genetic and Evolutionary Correlates of Fine-Scale Recombination Rate Variation in Drosophila persimilis

Recombination is fundamental to meiosis in many species and generates variation on which natural selection can act, yet fine-scale linkage maps are cumbersome to construct. We generated a fine-scale map of recombination rates across two major chromosomes in Drosophila persimilis using 181 SNP markers spanning two of five major chromosome arms. Using this map, we report significant fine-scale heterogeneity of local recombination rates. However, we also observed “recombinational neighborhoods,” where adjacent intervals had similar recombination rates after excluding regions near the centromere and telomere. We further found significant positive associations of fine-scale recombination rate with repetitive element abundance and a 13-bp sequence motif known to associate with human recombination rates. We noted strong crossover interference extending 5–7 Mb from the initial crossover event. Further, we observed that fine-scale recombination rates in D. persimilis are strongly correlated with those obtained from a comparable study of its sister species, D. pseudoobscura. We documented a significant relationship between recombination rates and intron nucleotide sequence diversity within species, but no relationship between recombination rate and intron divergence between species. These results are consistent with selection models (hitchhiking and background selection) rather than mutagenic recombination models for explaining the relationship of recombination with nucleotide diversity within species. Finally, we found significant correlations between recombination rate and GC content, supporting both GC-biased gene conversion (BGC) models and selection-driven codon bias models. Overall, this genome-enabled map of fine-scale recombination rates allowed us to confirm findings of broader-scale studies and identify multiple novel features that merit further investigation.     

Cytoplasmic Incompatibility in Australian Populations of Drosophila Melanogaster

In Drosophila melanogaster, weak incompatibility in crosses between infected and uninfected strains is associated with a Wolbachia microorganism. Crosses between infected males and uninfected females show a reduction (15-30%) in egg hatch. Progeny tests indicated that the infection is widespread in Australian D. melanogaster populations and that populations are polymorphic for the presence of the infection. The infection status of 266 lines from 12 populations along the eastern coast of Australia was determined by 4',6-diamidino-2-phenylindole (DAPI) staining of embryos. All populations contained both infected and uninfected flies. Infection frequencies varied between populations but there was no discernible geographical pattern. Laboratory experiments indicated that the infection was not associated with a reduction in fecundity as in Drosophila simulans. Incompatibility levels could not be increased by laboratory selection on isofemale lines. Factors contributing to the persistence of the infection in D. melanogaster populations are discussed.     

A Comprehensive Study of Genic Variation in Natural Populations of Drosophila Melanogaster. IV. Mitochondrial DNA Variation and the Role of History Vs. Selection in the Genetic Structure of Geographic Populations

Preliminary studies with restriction fragment length polymorphisms of mitochondrial DNA (mtDNA) in natural populations of Drosophila melanogaster revealed considerable variation in terms of nucleotide sequence and overall size. In this report we present data from more isofemale lines and more restriction enzymes, and explore the utility of the data in inferring a colonization history of this species. Size variation in the noncoding A + T-rich region is particularly plentiful, with size variants occurring in all restriction site haplotypes in all populations. We report here classes of small-scale mobility polymorphisms (apparent range of 20 bp) in specific restriction fragments in the coding region. The variation in one such fragment appears to be generated even more rapidly than in the noncoding region. On the basis of the distribution of restriction site haplotypes, the species range can be divided into three major regions along longitudinal lines: Euro-African populations are the most diverse and are taken to be oldest; Far East populations have a complex distribution of haplotypes; Western Hemisphere populations are the least diverse and are interpreted to be the youngest. The history inferred from mtDNA alone is remarkably similar to one based on several nuclear markers. The mtDNA haplotype distribution is also very different from that of allozymes in these same populations. We interpret this as further evidence that natural selection is still the most parsimonious explanation for the parallel latitudinal allozyme clines in this species.