A Comprehensive Study of Genic Variation in Natural Populations of Drosophila melanogaster. II. Estimates of Heterozygosity and Patterns of Geographic Differentiation

A study of genic variation in natural population of D. melanogaster was undertaken (1) to obtain a better estimate of heterozygosity by sampling a relatively large number of gene loci and (2) to identify different groups of polymorphic loci whose variation patterns might suggest different kinds of selection forces. A total of 117 gene loci (coding for 79 enzymes and 38 abundant proteins) were studied in 15 geographically distant populations originating from different continents. The findings of this study are as follows: (1) of the 117 gene loci studied, 61 are polymorphic and 56 are uniformly monomorphic everywhere. (2) An average population is polymorphic for 43% of its gene loci and an average individual is heterozygous for 10% of its gene loci. These estimates are remarkably similar among populations. (3) The average within-locality heterozygosity (H(S)) for polymorphic loci is uniformly distributed over the range of heterozygosity observed; i.e. , given that a locus has any local variation, it is nearly as likely to have a lot as a little. (4) The distribution of F(ST) (fixation index) is strongly skewed, with a prominent mode at 8-10% and a long tail of high values reaching a maximum of 58%. Two-thirds of all loci fall within the bell-shaped distribution centered on an F(ST) of 8-10%, a result compatible with the notion that they are experiencing a common tendency toward small interlocality differences owing to extensive gene flow among populations. (5) The distribution of total heterozygosity (H(T)) has a prominent bimodal distribution. The lower mode consists of loci with single prominent allele and a few uncommon ones and the upper mode consists of clinally varying loci with a high F(ST ) (e.g., Adh and G6-pd), loci with many alleles in high frequency (e.g., Ao and Xdh) and loci with two alleles in high frequency in all populations but, with little interpopulational differentiation (e.g., Est-6 and alpha-Fuc). The loci in the lower mode are probably under purifying selection; a large proportion of those in the latter mode may be under balancing selection. (6) Comparison of genic variation for loci located inside vs. outside inversions, comparison of F(ST) for inversions and their associated genes, and comparison of F(ST) and map position for pairs of loci all suggest that, while linkage has some influence, it does not seem to constrain the pattern of variation that a locus may develop. (7) Eighteen polymorphic loci show latitudinal variation in allele frequencies which are consistent in populations from different continents. (8) Estimates of Nei genetic distance between population pairs are generally low between populations on the same continent and high between populations on different continents. There are two important exceptions: population pairs for which both localities are in the temperate zone show no relationship to distance, and in cases where both populations are tropical or subtropical, the genetic distance is higher than for the temperate-tropical comparisons and seem even higher than one would expect from the geographic distance separating them. The latter observation suggests that either geographic separation outweighs differences in environment in determining the genetic composition of a population or that all tropical populations are not experiencing the same environment.-The results are discussed in relation to the neutralist-selectionist controversy of genic variation and two important conclusions are drawn: First, there is a negative correlation between the number of loci sampled and the resulting heterozygosity. This means that available estimates of heterozygosity, 85% of which are based on 30 or fewer loci, are high and hence not appropriate for making between-taxa comparisons. Secondly, there is a group of loci, comprising one-third of polymorphic loci (or about 15% of all loci studied), that is distinguishable by different patterns of variation within and among populations. Most of these loci have clinal variation which is consistent with the hypothesis that their genetic variation is maintained by balancing selection.     

A Comprehensive Study of Genic Variation in Natural Populations of Drosophila melanogaster. III. Variations in Genetic Structure and Their Causes between Drosophila melanogaster and Its Sibling Species Drosophila simulans

The natural populations of Drosophila melanogaster and Drosophila simulans were compared for their genetic structure. A total of 114 gene-protein loci were studied in four mainland (from Europe and Africa) and an island (Seychelle) populations of D. simulans and the results were compared with those obtained on the same set of homologous loci in fifteen worldwide populations of D. melanogaster. The main results are as follows: (1) D. melanogaster shows a significantly higher proportion of loci polymorphic than D. simulans (52% vs. 39%, P<0.05), (2) both species have similar mean heterozygosity and mean number of alleles per locus, (3) the two species share some highly polymorphic loci but they do not share loci that show high geographic differentiation, and (4) D. simulans shows significantly less geographic differentiation than D. melanogaster. The differences in genetic differentiation between the two species are limited to loci located on the X and second chromosomes only; loci on the third chromosome show similar level of geographic differentiation in both species. These two species have previously been shown to differ in their pattern of variation for chromosomal polymorphisms, quantitative and physiological characters, two-dimensional electrophoretic (2DE) proteins, middle repetitive DNA and mitochondrial DNA. Variation in niche-widths and/or genetic strategies of adaptation appear to be the main causes of differences in the genetic structure of these two species.     

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.     

Variation in Y Chromosome Segregation in Natural Populations of Drosophila melanogaster

Functional variation among Y chromosomes in natural populations of Drosophila melanogaster was assayed by a segregation study. A total of 36 Y chromosomes was extracted and ten generations of replacement backcrossing yielded stocks with Y chromosomes in two different genetic backgrounds. Eleven of the Y chromosomes were from diverse geographic origins, and the remaining 25 were from locally captured flies. Segregation of sexes in adult offspring was scored for the four possible crosses among the two backgrounds with each Y chromosome. Although the design confounds meiotic drive and effects on viability, statistical partitioning of these effects reveals significant variation among lines in Y chromosome segregation. Results are discussed in regards to models of Y-linked segregation and viability effects, which suggest that Y-linked adaptive polymorphism is unlikely.     

Metallothionein Gene Duplications and Metal Tolerance in Natural Populations of Drosophila melanogaster

A search for duplications of the Drosophila melanogaster metallothionein gene (Mtn) yielded numerous examples of this type of chromosomal rearrangement. These duplications are distributed widely--we found them in samples from four continents, and they are functional--larvae carrying Mtn duplications produce more Mtn RNA and tolerate increased cadmium and copper concentrations. Six different duplication types were characterized by restriction-enzyme analyses using probes from the Mtn region. The restriction maps show that in four cases the sequences, ranging in size between 2.2 and 6.0 kb, are arranged as direct, tandem repeats; in two other cases, this basic pattern is modified by the insertion of a putative transposable element into one of the repeated units. Duplications of the D. melanogaster metallothionein gene such as those that we found in natural populations may represent early stages in the evolution of a gene family.     

Genic VERSUS Chromosomal Variation in Natural Populations of DROSOPHILA SUBOBSCURA

Gametic frequencies in one mainland and one island population of D. subobscura were obtained by means of extracting wild chromosomes and subsequently analyzing them for inversions and allozymes. The high degree of cytological heterogeneity which characterizes these populations is not reflected in the genetic data. Two cases of non-random association were observed among eighteen pair-wise comparisons involving gene alleles and inversions to which the locus is linked. In both cases exchange of alleles at the locus is completely suppressed by the inversions. Four cases of linkage disequilibrium were detected among eighteen pairs of loci; two of them could best be explained as transient associations generated by random drift. The results suggest that disequilibria among enzyme loci are not widespread in natural populations—Populations with a lower degree of chromosomal variation are genetically as variable as populations with a higher degree of chromosomal variation. This observation does not support the hypothesis that selection in marginal homokaryotypic populations is for specialized homozygous genotypes.     

Latitudinal Variation in Starvation Resistance is Explained by Lipid Content in Natural Populations of Drosophila melanogaster

One of the most common environmental stressors is a shortage or suboptimal quality of food, thus all animals deal with periods of starvation. In the present study we examine variation in starvation resistance, longevity and body lipid content and the correlations between traits along an environmental gradient using isofemale lines recently derived from natural populations of Drosophila melanogaster from South America. The use of isofemale lines and controlled rearing laboratory conditions allows us to investigate within and among population components of genetic variation and the potential associations among starvation resistance, longevity and body lipid content. All these traits were analyzed separately in females and males, improving our understanding of sexual dimorphism. Our results revealed significant differences among populations in starvation resistance and longevity. Actually, the opposing latitudinal cline detected for starvation resistance suggests that natural selection played an essential role in shaping the pattern of geographic variation in this trait. Moreover, we also detected a positive relationship between starvation resistance and body lipid content in both sexes, providing evidence for a physiological and/or evolutionary association between these traits. Conversely, starvation resistance was not correlated with longevity indicating that these traits might be enabled to evolve independently. Finally, our study reveals that there is abundant within population genetic variation for all traits that may be maintained by sex-specific effects.     

Cytoplasmic Incompatibility in Drosophila Simulans: Dynamics and Parameter Estimates from Natural Populations

In Drosophila simulans, cytoplasmically transmitted Wolbachia microbes cause reduced egg hatch when infected males mate with uninfected females. A Wolbachia infection and an associated mtDNA variant have spread northward through California since 1986. PCR assays show that Wolbachia infection is prevalent throughout the continental US and Central and South America, but some lines from Florida and Ecuador that are PCR-positive for Wolbachia do not cause incompatibility. We estimate from natural populations infection frequencies and the transmission and incompatibility parameter values that affect the spread of the infection. On average, infected females from nature produce 3-4% uninfected ova. Infected females with relatively low fidelity of maternal transmission show partial incompatibility with very young infected laboratory males. Nevertheless, crosses between infected flies in nature produce egg-hatch rates indistinguishable from those produced by crosses between uninfected individuals. Incompatible crosses in nature produce hatch rates 30-70% as high as those from compatible crosses. Wild-caught infected and uninfected females are equally fecund in the laboratory. Incompatibility decreases with male age, and age-specific incompatibility levels suggest that males mating in nature may often be 2 or 3 weeks old. Our parameter estimates accurately predict the frequency of Wolbachia infection in California populations.     

Gene Flow and Adaptive Potential in Drosophila melanogaster

Gene flow among historically isolated populations is expected to increase genetic diversity and consequently the ability of populations to adapt to environmental changes. Few experimental studies, however, have examined the relationship between gene flow and the adaptive potential of populations. The increase in adaptive potential that occurs as a result of gene flow is expected to depend on the genetic variance among populations that undergo genetic exchange. In the present study, we compared observed and expected changes in adaptive potential (as measured by the selection response of sternopleural bristle number) that occur as a result of gene flow among experimental populations of Drosophila melanogaster. We examined the effect of limited immigration (m = 0.05 over 3 generations) among a set of experimentally isolated lineages, in addition to the effect of complete hybridization among lineages. As expected, we found that limited immigration and hybridization both yielded increases in adaptive potential. However, whereas the effect of limited immigration agreed well with theoretical expectations, the increase in adaptive potential following complete hybridization of lineages was significantly less than expected. We discuss these findings in relation to endangered species conservation efforts, particularly with respect to the goal of maximizing the retention of adaptive potential within managed populations.     

Enzyme Variability in the DROSOPHILA WILLISTONI Group. IV. Genic Variation in Natural Populations of DROSOPHILA WILLISTONI

We describe allelic variation at 28 gene loci in natural populations of D. willistoni. Seventy samples were studied from localities extending from Mexico and Florida, through Central America, the West Indies, and tropical South America, down to South Brazil. At least several hundred, and often several thousand, genomes were sampled for each locus. We have discovered a great deal of genetic variation. On the average, 58% loci are polymorphic in a given population. (A locus is considered polymorphic when the frequency of the most common allele is no greater than 0.95). An individual fly is heterozygous, on the average, at 18.4% loci.-Concerning the pattern of the variation, the most remarkable finding is the similarity of the configuration of allelic frequencies from locality to locality throughout the distribution of the species. Our observations support the conclusion that balancing natural selection is the major factor responsible for the considerable genetic variation observed in D. willistoni.