Historicity and the Population Genetics of Drosophila Melanogaster and D. Simulans

We summarize data showing that there is population structure in African populations of Drosophila from the melanogaster-simulans complex. In D. melanogaster, population structuring is found at individual loci, but is obscured by population structuring for large inversions that simultaneously affect several loci. In D. simulans, molecular polymorphism at the X-linked vermilion locus suggests that different groups of populations have been geographically isolated for some time. Invading populations are probably derived from different areas in Africa. European populations originate from an east African population that was probably not at a demographic equilibrium. The origin of the Antilles population is apparently different and is as yet unknown. In south-western France, populations from these two species undergo different population structuring at the scale of a few kilometres: D. melanogaster makes up a large panmictic population, whereas D. simulans forms a metapopulation that is divided into smaller demes.     

Drosophila Melanogaster, Drosophila Simulans: so Similar yet so Different

During the last two decades, the two cosmopolitan species Drosophila melanogaster and Drosophila simulans have been compared with regard to numerous characteristics, ranging from their geographic distribution and ecology to their DNA polymorphism. Various traits have been compared, including morphology, physiology, sexual behavior, allozymes and other proteins, chromosomal inversions, mitochondrial and nuclear DNA, transposable elements, wolbachia etc. Such comparisons reveal similarities and differences between the two species, depending on the trait considered. In most cases, the between-population variability of D. simulans is lower than that of D. melanogaster, but the two species exhibit similar levels of within-population variability. One of the main exceptions is the nucleotide polymorphism of several nuclear regions. Although several hypotheses have been proposed to explain these observations, the evolutionary dynamics of these two species are far from being understood. How have two species sharing a common ancestor in the recent past accumulated so many differences? A brief history of comparisons of the two species, from the first in 1919 by A.H. Sturtevant, and a summary of the hypotheses proposed to explain the similarities and the differences between these species are presented and discussed.     

Sexual Isolation Between Drosophila Melanogaster, D. Simulans and D. Mauritiana: Sex and Species Specific Discrimination

The sexual isolation among the related species Drosophila melanogaster, D. simulans and D. mauritiana is asymmetrical. While D. mauritiana males mate well with both D. melanogaster and D. simulans females, females of D. mauritiana discriminate strongly against males of these two species. Similarly, D. simulans males mate with D. melanogaster females but the reciprocal cross is difficult. Interspecific crosses between several populations of the three species were performed to determine if (i) males and females of the same species share a common sexual isolation genetic system, and (ii) males (or females) use the same genetic system to discriminate against females (or males) of the other two species. Results indicate that although differences in male and female isolation depend on the populations tested, the isolation behaviour between a pair of species is highly correlated despite the variations. However, the rank order of the isolation level along the populations was not correlated in both sexes, which suggests that different genes act in male and female sexual isolation. Neither for males nor for females, the isolation behaviour of one species was paralleled in the other two species, which indicates that the genetic systems involved in this trait are species-pair specific. The implications of these results are discussed. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetics of Differences in Pheromonal Hydrocarbons between Drosophila Melanogaster and D. Simulans

Females of Drosophila melanogaster and its sibling species D. simulans have very different cuticular hydrocarbons, with the former bearing predominantly 7,11-heptacosadiene and the latter 7-tricosene. This difference contributes to reproductive isolation between the species. Genetic analysis shows that this difference maps to only the third chromosome, with the other three chromosomes having no apparent effect. The D. simulans alleles on the left arm of chromosome 3 are largely recessive, allowing us to search for the relevant regions using D. melanogaster deficiencies. At least four nonoverlapping regions of this arm have large effects on the hydrocarbon profile, implying that several genes on this arm are responsible for the species difference. Because the right arm of chromosome 3 also affects the hydrocarbon profile, a minimum of five genes appear to be involved. The large effect of the thrid chromosome on hydrocarbons has also been reported in the hybridization between D. simulans and its closer relative D. sechellia, implying either an evolutionary convergence or the retention in D. sechellia of an ancestral sexual dimorphism.     

Wolbachia Infections in Drosophila Melanogaster and D. Simulans: Polymorphism and Levels of Cytoplasmic Incompatibility

Wolbachia are endosymbiotic bacteria, widespread in terrestrial Arthropods. They are mainly transmitted vertically, from mothers to offspring and induce various alterations of their hosts' sexuality and reproduction, the most commonly reported phenomenon being Cytoplasmic Incompatibility (CI), observed in Drosophila melanogaster and D. simulans. Basically, CI results in a more or less intense embryonic mortality, occurring in crosses between males infected by Wolbachia and uninfected females. In D. simulans, Wolbachia and CI were observed in 1986. Since then, this host species has become a model system for investigating the polymorphism of Wolbachia infections and CI. In this review we describe the different Wolbachia infections currently known to occur in D. melanogaster and D. simulans. The two species are highly contrasting with regard to symbiotic diversity: while five Wolbachia variants have been described in D. simulans natural populations, D. melanogaster seems to harbor one Wolbachia variant only. Another marked difference between these two Drosophila species is their permissiveness with regard to CI, which seems to be fully expressed in D. simulans but partially or totally repressed in D. melanogaster, demonstrating the involvement of host factors in the control of CI levels. The potential of the two host species regarding the understanding of CI and its evolution is also discussed.     

Molecular Evolution between Drosophila Melanogaster and D. Simulans: Reduced Codon Bias, Faster Rates of Amino Acid Substitution, and Larger Proteins in D. Melanogaster

Both natural selection and mutational biases contribute to variation in codon usage bias within Drosophila species. This study addresses the cause of codon bias differences between the sibling species, Drosophila melanogaster and D. simulans. Under a model of mutation-selection-drift, variation in mutational processes between species predicts greater base composition differences in neutrally evolving regions than in highly biased genes. Variation in selection intensity, however, predicts larger base composition differences in highly biased loci. Greater differences in the G+C content of 34 coding regions than 46 intron sequences between D. melanogaster and D. simulans suggest that D. melanogaster has undergone a reduction in selection intensity for codon bias. Computer simulations suggest at least a fivefold reduction in N(e)s at silent sites in this lineage. Other classes of molecular change show lineage effects between these species. Rates of amino acid substitution are higher in the D. melanogaster lineage than in D. simulans in 14 genes for which outgroup sequences are available. Surprisingly, protein sizes are larger in D. melanogaster than in D. simulans in the 34 genes compared between the two species. A substantial fraction of silent, replacement, and insertion/deletion mutations in coding regions may be weakly selected in Drosophila.     

A Reanalysis of Protein Polymorphism in Drosophila Melanogaster, D. Simulans, D. Sechellia and D. Mauritiana: Effects of Population Size and Selection

Comparison of synonymous and nonsynonymous variation/substitution within and between species at individual genes has become a widely used general approach to detect the effect of selection versus drift. The sibling species group comprised of two cosmopolitan (Drosophila melanogaster and Drosophila simulans) and two island (Drosophila mauritiana and Drosophila sechellia) species has become a model system for such studies. In the present study we reanalyzed the pattern of protein variation in these species, and the results were compared against the patterns of nucleotide variation obtained from the literature, mostly available for melanogaster and simulans. We have mainly focused on the contrasting patterns of variation between the cosmopolitan pair. The results can be summarized as follows: (1) As expected the island species D. mauritiana and D. sechellia showed much less variation than the cosmopolitan species D. melanogaster and D. simulans. (2) The chromosome 2 showed significantly less variation than chromosome 3 and X in all four species which may indicate effects of past selective sweeps. (3) In contrast to its overall low variation, D. mauritiana showed highest variation for X-linked loci which may indicate introgression from its sibling, D. simulans. (4) An average population of D. simulans was as heterozygous as that of D. melanogaster (14.4% v.s. 13.9%) but the difference was large and significant when considering only polymorphic loci (37.2% v.s. 26.1%). (5) The species-wise pooled populations of these two species showed similar results (all loci = 18.3% v.s. 20.0%, polymorphic loci = 47.2% v.s. 37.6%). (6) An average population of D. simulans had more low-frequency alleles than D. melanogaster, and the D. simulans alleles were found widely distributed in all populations whereas the D. melanogaster alleles were limited to local populations. As a results of this, pooled populations of D. melanogaster showed more polymorphic loci than those of D. simulans (48.0% v.s. 32.0%) but the difference was reduced when the comparison was made on the basis of an average population (29.1% v.s. 21.4%). (7) While the allele frequency distributions within populations were nonsignificant in both D. melanogaster and D. simulans, melanogaster had fewer than simulans, but more than expected from the neutral theory, low frequency alleles. (8) Diallelic loci with the second allele with a frequency less than 20% had similar frequencies in all four species but those with the second allele with a frequency higher than 20% were limited to only melanogaster the latter group of loci have clinal (latitudinal) patterns of variation indicative of balancing selection. (9) The comparison of D. simulans/D. melanogaster protein variation gave a ratio of 1.04 for all loci and 1.42 for polymorphic loci, against a ratio of approximately 2-fold difference for silent nucleotide sites. This suggests that the species ratios of protein and silent nucleotide polymorphism are too close to call for selective difference between silent and allozyme variation in D. simulans. In conclusion, the contrasting levels of allozyme polymorphism, distribution of rare alleles, number of diallelic loci and the patterns of geographic differentiation between the two species suggest the role of natural selection in D. melanogaster, and of possibly ancient population structure and recent worldwide migration in D. simulans. Population size differences alone are insufficient as an explanation for the patterns of variation between these two species.     

Phenotypic and Genetic Analysis of Clock, a New Circadian Rhythm Mutant in Drosophila Melanogaster

Clock is a semidominant X-linked mutation that results in shortening the period of Drosophila melanogaster's free-running locomotor activity rhythm from ca. 24.0 to ca. 22.5 hr. This mutation similarly shortened the phase response curve, determined by resetting activity rhythms with light pulses. Eclosion peaks for Clk cultures were separated by only 22.5 hr instead of the normal 24 hr. Clk was mapped close to, but separable from, another rhythm mutation--period01--by recombination. The estimated distance between these two mutations was short enough to suggest that Clk could be a per allele. If this is the case, the new mutant is unique in that it, unlike other per variants, is associated with essentially normal 1-min courtship song rhythms when Clk is expressed in males. Also, the new rhythm variant could not, in contrast to a short-period per mutation, have its effects on free-running activity rhythms uncovered by deletions. This result, and the lack of coverage of Clk's effects by duplications, suggest that it is not a simple hypomorphic or amorphic mutation.     

Transposable Element Dynamics in Two Sibling Species: Drosophila Melanogaster and Drosophila Simulans

Transposable elements (TEs) in the two sibling species, Drosophila melanogaster and D. simulans, differ considerably in amount and dynamics, with D. simulans having a smaller amount of TEs than D. melanogaster. Several hypotheses have been proposed to explain these differences, based on the evolutionary history of the two species, and claim differences either in the effective size of the population or in genome characteristics. Recent data suggest, however, that the higher amount of TEs in D. melanogaster could be associated with the worldwide invasion of D. melanogaster a long time ago while D. simulans is still under the process of such geographical spread. Stresses due to new environmental conditions and crosses between migrating populations could explain the mobilization of TEs while the flies colonize. Colonization and TE mobilization may be strong evolutionary forces that have shaped and are still shaping the eukaryote genomes.     

Molecular Variation at the Vermilion Locus in Geographically Diverse Populations of Drosophila Melanogaster and D. Simulans

We surveyed nucleotide variation at vermilion in population samples of Drosophila melanogaster from Africa, Asia and the Americas to test the hypothesis that the vermilion gene was a target of balancing selection and to improve our understanding of geographic differentiation. Patterns of polymorphism and divergence showed no evidence for non-neutral evolution. However, the frequency spectrum of polymorphic sites in some non-African samples departed from the neutral equilibrium expectation. Furthermore, there were high levels of linkage disequilibrium in non-African samples, despite apparently high rates of crossing over in the vermilion region. In the absence of comparable data from other loci in these same population samples, we cannot determine whether the unusual patterns of variation at vermilion reflect demographic as opposed to locus-specific events. We found surprisingly high levels of differentiation at vermilion between U.S. and Congo samples of D. simulans. In light of previously published allozyme and mtDNA data that provided no evidence for significant differentiation between African and non-African D. simulans populations, the vermilion data raise the possibility that both mtDNA and allozymes have been influenced by selection.     

Genetic Variability and Fluctuating Asymmetry of Morphological Traits in Drosophila melanogasterReared on a Pesticide-Containing Medium

The effects of chlorine-organic insecticide endosulfane (thiodan) on phenotypic and genetic variation in four morphological traits of Drosophila melanogaster(wing length, thorax length, the number of orbital bristles and the number of sternopleural bristles) were examined. In addition, the effect of this pesticide on stability of development measured as fluctuating asymmetry of bilateral traits was estimated. On the medium with endosulfane, phenotypic variation of morphometric traits was significantly higher. No difference in fluctuating asymmetry between the stressed and the control samples was found. The among-line variance of morphometric traits of flies reared on the endosulfane-containing medium was significantly higher as compared to the corresponding variance under control conditions. The efficiency of using fluctuating asymmetry and phenotypic variation of morphometric and meristic traits as indicators of environmental stress in insect populations is discussed.     

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.