Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome

The recent sequencing of several eukaryotic genomes has generated considerable interest in the study of gene duplication events. The classical model of duplicate gene evolution is that recurrent mutation ultimately results in one copy becoming a pseudogene, and only rarely will a beneficial new function evolve. Here, we study divergence between coding sequence duplications in Drosophila melanogaster as a function of the linkage relationship between paralogs. The mean K(a)/K(s) between all duplicates in the D. melanogaster genome is 0.2803, indicating that purifying selection is maintaining the structure of duplicate coding sequences. However, the mean K(a)/K(s) between duplicates that are both on the X chromosome is 0.4701, significantly higher than the genome average. Further, the distribution of K(a)/K(s) for these X-linked duplicates is significantly shifted toward higher values when compared with the distributions for paralogs in other linkage relationships. Two models of molecular evolution provide qualitative explanations of these observations-relaxation of selective pressure on the duplicate copies and, more likely, positive selection on recessive adaptations. We also show that there is an excess of X-linked duplicates with low K(s), suggesting a larger proportion of relatively young duplicates on the D. melanogaster X chromosome relative to autosomes.     

Genetic duplication in the white-split interval of the X chromosome in Drosophila melanogaster

A detailed cytogenetic study of male-viable and lethal deficiencies affecting the w-spl interval in Drosophila melanogaster has revealed the existence of genetic duplication such that, for example, the consequences of the loss of salivary chromosome band 3C3 are essentially compensated for by the presence of band 3C5-6, and vice versa. Although each of the duplicate elements possesses rst ⁺ and vt ⁺ activity, rst and vt phenotypes appear in males when 3C3 and part, but not all, of 3C5-6 are deleted. The degree of rst and vt expression can be correlated with the amount of material lost from 3C5-6. Deletions removing the entire 3C3-6 interval are male lethal. Despite the duplicate elements, at least one EMS-induced, presumptive point mutation expressing only rst is known; two others express both rst and vt. No loci other than rst and vt occur between W and spl. Band 3C2 appears to be associated with the w locus, which probably extends into the interband space between 3C1 and 3C2. The w locus is not involved in the rst-vt duplication in the 3C3-6 region. — The cytogenetic characteristics of the 3C region—a high coefficient of crossing over, frequent induced chromosome breakage, ectopic pairing, constriction, and an extended replication period—can be correlated with the fact that in 3C a relatively long stretch of DNA, nearly 2% of the entire X chromosome, is highly compacted into but few adjacent bands. These characteristics do not necessarily represent special properties of intercalary heterochromatin; they can be interpreted as reflecting the properties of any similarly organized euchromatic region.This investigation was aided by research grants from the U. S. Public Health Service (GM 13631) to G. Lefevre, Jr. and the National Science Foundation (GB 27599) to M. M. Green.     

Dynamic organization of the β-heterochromatin in the Drosophila melanogaster polytene X chromosome

Region 20 of the polytene X chromosome of Drosophila melanogaster was studied in salivary glands (SG) and pseudonurse cells (PNC) of otu mutants. In SG chromosomes the morphology of the region strongly depends on two modifiers of position effect variegation: temperature and amount of heterochromatin. It is banded in XYY males at 25°?C and β-heterochromatic in X0 males at 14°?C, i.e. it shows dynamic transitions. In PNC chromosomes region 20 is not heterochromatic, but demonstrates a clear banding pattern. Some molecular markers of mitotic heterochromatin were localized by means of in situ hybridization on PNC chromosomes: DNA of the gene su(f) in section 20C, the nucleolar organizer and 359-bp satellite in 20F. The 359-bp satellite, which has been considered to be specific for heterochromatin of the mitotic X chromosome, was found at two additional sites on chromosome 3L, proximally to 80C. The right arm of the X chromosome in SG chromosomes was localized in the inversion In(1LR)pn2b: the telomeric HeT-A DNA and AAGAG satellite from the right arm are polytenized, having been relocated from heterochromatin to euchromatin.     

'Exceptional sons' from Drosophila melanogaster mothers carrying a balancer X chromosome

This study reports on exceptional males which are obtained by using Drosophila melanogaster mothers carrying the balancers In(1)FM6 or In(1)FM7 as one of their X chromosomes. The phenomenon was first observed in interspecific crosses between D. melanogaster females and males of its closest relatives which normally produce unisexual female hybrid progeny. Whereas hybrid sons from these crosses die as third instar larvae, the presence of the particular X balancers in the mother allows a low percentage of sons to survive. Similar sterile males are also observed among non-hybrid flies. Data are presented which suggest that the males thus generated could be hyperploid for part of their X chromosome as a result of a meiotic event in their mothers or else they could start life as female zygotes and change sex through a mitotic event at an early stage.     

Multiple signatures of positive selection downstream of notch on the X chromosome in Drosophila melanogaster

To identify genomic regions affected by the rapid fixation of beneficial mutations (selective sweeps), we performed a scan of microsatellite variability across the Notch locus region of Drosophila melanogaster. Nine microsatellites spanning 60 kb of the X chromosome were surveyed for variation in one African and three non-African populations of this species. The microsatellites identified an approximately 14-kb window for which we observed relatively low levels of variability and/or a skew in the frequency spectrum toward rare alleles, patterns predicted at regions linked to a selective sweep. DNA sequence polymorphism data were subsequently collected within this 14-kb region for three of the D. melanogaster populations. The sequence data strongly support the initial microsatellite findings; in the non-African populations there is evidence of a recent selective sweep downstream of the Notch locus near or within the open reading frames CG18508 and Fcp3C. In addition, we observe a significant McDonald-Kreitman test result suggesting too many amino acid fixations species wide, presumably due to positive selection, at the unannotated open reading frame CG18508. Thus, we observe within this small genomic region evidence for both recent (skew toward rare alleles in non-African populations) and recurring (amino acid evolution at CG18508) episodes of positive selection.     

The accumulation of P-elements on the tip of the X chromosome in populations of Drosophila melanogaster

Little information exists about the mechanisms that determine the fate of mobile elements in natural populations. In this study we catalogue the distribution of 638 P-elements across 114 X chromosomes in samples drawn from three natural populations of Drosophila melanogaster. There is an extremely high occurrence of elements at the tip relative to the rest of the euchromatic chromosome. We demonstrate that the distribution of de novo insertions of the P-element on a specific laboratory chromosome is markedly different; no P-elements were recovered at the tip in the 243 insertion events recorded. In contrast, insertion data for the pi2 chromosome suggests an elevated rate associated with the tip site although it does not appear sufficient to explain the large differential accumulation on wild chromosomes. This raises the issue of inter chromosome (or tip) variation in relative rates, as well as the possibility that rates of elimination are lower at the tip.     

Female Drosophila melanogaster gene expression and mate choice: the X chromosome harbours candidate genes underlying sexual isolation

Background

The evolution of female choice mechanisms favouring males of their own kind is considered a crucial step during the early stages of speciation. However, although the genomics of mate choice may influence both the likelihood and speed of speciation, the identity and location of genes underlying assortative mating remain largely unknown.

Methods and Findings

We used mate choice experiments and gene expression analysis of female Drosophila melanogaster to examine three key components influencing speciation. We show that the 1,498 genes in Zimbabwean female D. melanogaster whose expression levels differ when mating with more (Zimbabwean) versus less (Cosmopolitan strain) preferred males include many with high expression in the central nervous system and ovaries, are disproportionately X-linked and form a number of clusters with low recombination distance. Significant involvement of the brain and ovaries is consistent with the action of a combination of pre- and postcopulatory female choice mechanisms, while sex linkage and clustering of genes lead to high potential evolutionary rate and sheltering against the homogenizing effects of gene exchange between populations.

Conclusion

Taken together our results imply favourable genomic conditions for the evolution of reproductive isolation through mate choice in Zimbabwean D. melanogaster and suggest that mate choice may, in general, act as an even more important engine of speciation than previously realized.     

Molecular and genetic studies on the euchromatin-heterochromatin transition region of the X chromosome of Drosophila melanogaster

A recombinant Charon 4 bacteriophage has been isolated on the basis of RNAs which are enriched in the head of the adult Drosophila melanogaster and hence are likely to be of neural origin. The cloned insert maps to the near vicinity of the uncoordinated locus in polytene chromosome band 19E8. This band is within the transition zone between the euchromatic and heterochromatic regions of the X chromosome, a region which has been well characterized cytogenetically. The insert contains both repetitious and low copy number sequences, some of which vary extensively in both frequency and restriction fragment size between different laboratory strains. One particular family of moderately repeated sequences occurs predominantly in divisions 19 and 20 of the X chromosome and perhaps the distally located X heterochromatin. The molecular landscape surrounding the initial entry point contains many repeated sequences and is thus unlike those observed in most published chromosomal walks. The possible significance of the presence of repeated sequence families in the distinct properties of this region are discussed.     

Recombination in the X chromosome of Drosophila melanogaster females heterozygous for two autosomal translocations

X chromosome recombination was measured in females carrying two 2; 3-translocations. Total X chromosome recombination values varied according to the amount of structural heterozygosity between the two translocations. The results support the hypothesis that the observed effects of autosomal translocation homozygosity on recombination in the X chromosome are due to homozygosity for position effects of the translocation breakpoints and are not due to chromosome discontinuity.     

Feminization of complex traits in Drosophila melanogaster via female-limited X chromosome evolution*

A handful of studies have investigated sexually antagonistic constraints on achieving sex-specific fitness optima, although exclusively through male-genome-limited evolution experiments. In this article, we established a female-limited X chromosome evolution experiment, where we used an X chromosome balancer to enforce the inheritance of the X through the matriline, thus removing exposure to male selective constraints. This approach eliminates the effects of sexually antagonistic selection on the X chromosome, permitting evolution toward a single sex-specific optimum. After multiple generations of selection, we found strong evidence that body size and development time had moved toward a female-specific optimum, whereas reproductive fitness and locomotion activity remained unchanged. The changes in body size and development time are consistent with previous results, and suggest that the X chromosome is enriched for sexually antagonistic genetic variation controlling these particular traits. The lack of change in reproductive fitness and locomotion activity could be due to a number of mutually nonexclusive explanations, including a lack of sexually antagonistic variance on the X chromosome for those traits or confounding effects of the use of the balancer chromosome. This study is the first to employ female-genome-limited selection and adds to the understanding of the complexity of sexually antagonistic genetic variation.     

The effect of X chromosome heterozygosity on the structure of the ribosomal genes in Drosophila melanogaster.

Sucrose gradient analysis of DNA isolated from detergent-pronase lysates of adult flies has been used to look for ribosomal genes not integrated into the DNA of the chromosome in genotypes containing various combinations of inversions having breakpoints in the proximal heterochromatin of the X chromosome. Unintegrated genes are found in females heterozygous for inversions which have one breakpoint between the nucleolus organizer and the centromere. Homozygotes and males do not have unintegrated genes. The results suggest that unintegrated ribosomal genes result from an interaction between homologues having different arrangements of the proximal heterochromatin. In addition, data from a series of stocks carrying duplications of the X heterochromatin provide independent evidence for the size of the DNA on our gradients.     

Digest: Female‐limited X chromosome evolution in Drosophila melanogaster*

Sexual dimorphism can cause sexual antagonism of phenotypic traits. Lund‐Hansen and colleagues (2020) investigated female‐limited X chromosome evolution in Drosophila melanogaster using forced matrilineal inheritance. Body size and developmental time evolved toward their female optima, but reproductive fitness and locomotion remained unchanged. These findings imply that some sexually antagonized loci may be distributed across the genome and that some phenotypes may have already reached their female optima in nature.     

Genes required for embryonic muscle development in Drosophila melanogaster A survey of the X chromosome

We have begun a genetic analysis to dissect the process of myogenesis by surveying the X chromosome of Drosophila melanogaster for mutations that affect embryonic muscle development. Using polarised light microscopy and antibody staining techniques we analysed embryos hemizygous for a series of 67 deletion mutations that together cover an estimated 85% of the X chromosome, or 16.5% of the genome. Whereas the mature wild type embryo has a regular array of contractile muscles that insert into the epidermis, 31 of the deletion mutants have defects in muscle pattern, contractility or both, that cannot be attributed simply to epidermal defects and identify functions required for wild type muscle development. We have defined mutant pattern phenotypes that can be described in terms of muscle absences, incomplete myoblast fusion, failure of attachment of the muscle to the epidermis or mispositioning of attachment sites. Thus muscle development can be mutationally disrupted in characteristic and interpretable ways. The areas of overlap of the 31 deletions define 19 regions of the X chromosome that include genes whose products are essential for various aspects of myogenesis. We conclude that our screen can usefully identify loci coding for gene products essential in muscle development.     

A 5.9-kb tandem repeat at the euchromatin-heterochromatin boundary of the X chromosome of Drosophila melanogaster

We present an analysis of a chromosomal walk in the region of the euchromatin-heterochromatin transition at the base of the X chromosome of Drosophila melanogaster. This region is difficult to analyse because of the presence of repeated sequences, and we have used cosmids to walk from the last euchromatic gene, suppressor of forked, towards the pericentric heterochromatin. The proximal 30-kb sequence we have isolated consists of repetitive DNA, including four tandem copies of a 5.9-kb sequence. This tandem repeat is itself a mosaic of other, mostly repeated, sequences, including part of a retrotransposon without long terminal repeats, a simple-sequence region of TAA repeats and part of a retrotransposon with long terminal repeats that has not been previously described. Although sequences homologous to these components are found elsewhere in the genome, this arrangement of repeated sequences is only found at the base of the X chromosome. It is conserved in D. melanogaster strains of different geographic origin, but is not conserved in even closely related species.     

Sex-specific Trans-regulatory Variation on the Drosophila melanogaster X Chromosome

The X chromosome constitutes a unique genomic environment because it is present in one copy in males, but two copies in females. This simple fact has motivated several theoretical predictions with respect to how standing genetic variation on the X chromosome should differ from the autosomes. Unmasked expression of deleterious mutations in males and a lower census size are expected to reduce variation, while allelic variants with sexually antagonistic effects, and potentially those with a sex-specific effect, could accumulate on the X chromosome and contribute to increased genetic variation. In addition, incomplete dosage compensation of the X chromosome could potentially dampen the male-specific effects of random mutations, and promote the accumulation of X-linked alleles with sexually dimorphic phenotypic effects. Here we test both the amount and the type of genetic variation on the X chromosome within a population of Drosophila melanogaster, by comparing the proportion of X linked and autosomal trans-regulatory SNPs with a sexually concordant and discordant effect on gene expression. We find that the X chromosome is depleted for SNPs with a sexually concordant effect, but hosts comparatively more SNPs with a sexually discordant effect. Interestingly, the contrasting results for SNPs with sexually concordant and discordant effects are driven by SNPs with a larger influence on expression in females than expression in males. Furthermore, the distribution of these SNPs is shifted towards regions where dosage compensation is predicted to be less complete. These results suggest that intrinsic properties of dosage compensation influence either the accumulation of different types of trans-factors and/or their propensity to accumulate mutations. Our findings document a potential mechanistic basis for sex-specific genetic variation, and identify the X as a reservoir for sexually dimorphic phenotypic variation. These results have general implications for X chromosome evolution, as well as the genetic basis of sex-specific evolutionary change.