Balancing Selection, Inversion Polymorphism and Adaptation in Ddt-Resistant Populations of DROSOPHILA MELANOGASTER

The modes of selection important in maintaining an inversion-allozyme polymorphism in two laboratory populations of Drosophila melanogaster were examined. The populations, 731R and J2, are highly resistant to DDT. The polymorphism involves the Standard and In(3R)P chromosomal arrangements in very strong linkage association with the AO ¹ and AO⁴ allozymes, respectively, of the aldehyde oxidase locus—The mean fertilities of the three karyotypes were not significantly different in 731R, but, in J2, In/In was significantly inferior to St/St and St/In. Egg-to-adult viability tests indicated very strong heterozygote advantage at all frequency combinations of the karyotypes in both populations when DDT was present. When DDT was excluded, the viabilities varied over the frequency combinations but were not inversely correlated with karyotype frequency, as predicted by balancing frequency-dependent selection. Discrete, multiple-generation experiments showed a rapid increase in heterozygote frequency to about 80% in both populations when DDT was present. Without DDT, 731R showed apparent directional selection favoring St, whereas J2 showed persistence of the polymorphism, although with extensive fluctuation.—Thus, the inversion-allozyme polymorphism is directly involved in the adaptation to a specific environmental component, DDT, and the selective advantage of the heterozygotes is the important balancing force. Balancing frequency-dependent selection was not observed, which suggests the hypothesis that this form of selection may not be involved in adaptation to novel environmental conditions.     

Targeted Selection Experiments and Enzyme Polymorphism: Negative Evidence for Octanoate Selection at the G6PD Locus in DROSOPHILA MELANOGASTER

Published studies have reported significant selection with respect to the G6pd locus for Drosophila melanogaster reared on Na-octanoate food. We have reexamined the selective effects of Na-octanoate on egg to adult viability with respect to the G6pd polymorphism using specially constructed X chromosomes. Four experiments were carried out using different 6Pgd backgrounds in two recombinant sets of chromosomes segregating for the G6pd locus but constructed so as to minimize variation over most of the X chromosome. In addition, two measures of viability were used, and the size of the experiments and their associated degrees of freedom are approximately double those reported in the former studies. Our results find no evidence for differential selection on G6pd genotypes (males and females) by Na-octanoate and, therefore, do not corroborate the positive results of selection reported by other investigators. The reasons for our different results are discussed.     

Polymorphism and Balancing Selection at Major Histocompatibility Complex Loci

Amino acid replacements in the peptide-binding region (PBR) of the functional major histocompatibility complex (Mhc) genes appear to be driven by balancing selection. Of the various types of balancing selection, we have examined a model equivalent to overdominance that confers heterozygote advantage. As discussed by A. Robertson, overdominance selection tends to maintain alleles that have more or less the same degree of heterozygote advantage. Because of this symmetry, the model makes various testable predictions about the genealogical relationships among different alleles and provides ways of analyzing DNA sequences of Mhc alleles. In this paper, we analyze DNA sequences of 85 alleles at the HLA-A, -B, -C, -DRB1 and -DQB1 loci with respect to the number of alleles and extent of nucleotide differences at the PBR, as well as at the synonymous (presumably neutral) sites. Theory suggests that the number of alleles that differ at the sites targeted by selection (presumably the nonsynonymous sites in the PBR) should be equal to the mean number of nucleotide substitutions among pairs of alleles. We also demonstrate that the nucleotide substitution rate at the targeted sites relative to that of neutral sites may be much larger than 1. The predictions of the presented model are in surprisingly good agreement with the actual data and thus provide means for inferring certain population parameters. For overdominance selection in a finite population at equilibrium, the product of selection intensity (s) against homozygotes and the effective population size (N) is estimated to be 350-3000, being largest at the B locus and smallest at the C locus. We argue that N is of the order of 10(5) and s is several percent at most, if the mutation rate per site per generation is 10(-8).     

Recombination Load in a Chromosomal Inversion Polymorphism of Drosophila subobscura

Chromosomal inversions suppress recombination in heterokaryotypes and may help to maintain positive epistatic interactions among groups of alleles at loci contained in the inversion. Here I evaluate the protective effect of inversions on recombination when different chromosomal segments, or even the whole chromosome O of Drosophila subobscura, can be effectively prevented from undergoing recombination in several naturally occurring heterokaryotypes. The fitness of flies made homozygous for recombinant chromosomes was generally lower when compared to their nonrecombinant counterparts, thus suggesting that segregating gene arrangements in this species hold together favorable combinations of alleles that interact epistatically.     

Selection and Endpoint Distribution of Bacterial Inversion Mutations

This paper describes the isolation and characterization of spontaneous inversion mutants of Salmonella typhimurium. The mutants are selected by demanding that an unexpressed hisD gene acquire a new promoter. Chromosome rearrangements that juxtapose the hisD gene and a foreign promoter are obtained by this selection. Although a number of inversions are found, the frequency was lower than expected. The breakpoint of these inversions are not distributed randomly either in the his operon or on the chromosome. The his breakpoint lies in the hisG-hisD intercistronic region, a sequence known to occur at several places on the bacterial chromosome. In most of the inversions, the 'non-his' breakpoint lies across the chromosome, so that the inverted region includes the origin or terminus of DNA replication. The significance of these results is discussed.     

Two Modes of Balancing Selection in Drosophila Melanogaster: Overcompensation and Overdominance

Overdominance is often invoked to account for the extensive polymorphisms found in natural populations of organisms; overcompensation, however, may be equally or more important. Overcompensation occurs when limiting resources are better exploited by a genetically mixed than by a uniform population, and is often causally related to frequency-dependent selection. We have designed experiments to test whether overcompensation occurs in Drosophila melanogaster, using the Sod locus as a marker. Tests are made at each of two densities and two temperatures for cultures with desired genetic compositions. Both temperature and density have statistically significant effects on the per-female productivity of the cultures. More important, there are strong effects due to overcompensation. Cultures that are more polymorphic are also more productive than less polymorphic ones even when the level of individual heterozygosity is the same in all. There is also overdominance for the Sod locus: the heterozygotes are more productive than either homozygote at every temperature and density, and the differences are statistically significant in several cases. These results corroborate previous studies showing that overdominance may contribute to the maintenance of the Sod polymorphisms. Moreover, our results indicate that the significance of overcompensation as a mechanism to account for polymorphism in natural populations deserves further investigation.     

Modes of Selection Maintaining an Inversion Polymorphism in DROSOPHILA PAULISTORUM

The possibility that fitness relationships associated with an inversion polymorphism in D. paulistorum were frequency dependent was investigated. Using allozymes of tetrazolium oxidase to mark inversions, the effects of genotype frequency, larval density, and culture conditions on fitness were assessed. The proportions of genotypes among egg-laying females were varied, thus changing the expected proportions of progeny produced in the absence of fecundity or viability selection. The genotypes of progeny were determined by electrophoresis and comparisons of the ratio of the numbers of the different genotypes produced to the expected ratio was used to evaluate fitness relationships. Fitness relationships were dependent on genotype frequency, larval density, and culture conditions. Selection was either absent, directional, frequency dependent (favoring rare types), or heterotic depending on density and culture conditions. It is implied that the adaptive value of genetic variants need not be apparent in all environments, or may change with changing conditions. There is evidence for different criteria for selection in the two sexes. These results add to the evidence supporting the importance of frequency-dependent selection. It is argued that for frequency dependence to be of general importance, selection must act on genes in groups, either as an inversion or as lengths of chromosome with integrity maintained by disequilibrium.     

Time-Series Analysis of Seasonal Changes of the O Inversion Polymorphism of Drosophila Subobscura

We have studied seasonal variation (spring, early summer, last summer and autumn) of inversion polymorphisms of the O chromosome of Drosophila subobscura in a natural population over 15 years. The length of the study allowed us to investigate the temporal behavior (short-term seasonal changes and long-term directional trends) of the O arrangements by the powerful statistical method of time series analysis. It is shown that the O inversion polymorphisms varied on two different time scales: short-term seasonal changes repeated over the years superimposed on long-term directional trends. All the common arrangements (O(3+4+7), O(ST), O(3+4) and O(3+4+8)) showed significant cyclic seasonal changes, and all but one of these arrangements (O(3+4+7)) showed significant long-term trends. Moreover, the degree of seasonality was different for different arrangements. Thus, O(3+4+7) and O(ST) showed the highest seasonality, which accounted for ~61 and 47% of their total variances, respectively. The seasonal changes in the frequencies of chromosome arrangements were significantly associated with the seasonal variation of the climate (temperature, rainfall, humidity and insolation). In particular, O(3+4+7) and O(ST), the arrangements with the greatest seasonal component, showed the strongest association with all climatic factors investigated, especially to the seasonal changes of extreme temperature and humidity.     

Adaptive Role of Inversion Polymorphism of Drosophila subobscura in Lead Stressed Environment

Local adaptation to environmental stress at different levels of genetic polymorphism in various plants and animals has been documented through evolution of heavy metal tolerance. We used samples of Drosophila subobscura populations from two differently polluted environments to analyze the change of chromosomal inversion polymorphism as genetic marker during laboratory exposure to lead. Exposure to environmental contamination can affect the genetic content within a particular inversion and produce targets for selection in populations from different environments. The aims were to discover whether the inversion polymorphism is shaped by the local natural environments, and if lead as a selection pressure would cause adaptive divergence of two populations during the multigenerational laboratory experiment. The results showed that populations retain signatures from past contamination events, and that heavy metal pollution can cause adaptive changes in population. Differences in inversion polymorphism between the two populations increased over generations under lead contamination in the laboratory. The inversion polymorphism of population originating from the more polluted natural environment was more stable during the experiment, both under conditions with and without lead. Therefore, results showed that inversion polymorphism as a genetic marker reflects a strong signature of adaptation to the local environment, and that historical demographic events and selection are important for both prediction of evolutionary potential and long-term viability of natural populations.     

Natural Selection and the Frequency Distributions of ``silent' DNA Polymorphism in Drosophila

In Escherichia coli, Saccharomyces cerevisiae, and Drosophila melanogaster, codon bias may be maintained by a balance among mutation pressure, genetic drift, and natural selection favoring translationally superior codons. Under such an evolutionary model, silent mutations fall into two fitness categories: preferred mutations that increase codon bias and unpreferred changes in the opposite direction. This prediction can be tested by comparing the frequency spectra of synonymous changes segregating within populations; natural selection will elevate the frequencies of advantageous mutations relative to that of deleterious changes. The frequency distributions of preferred and unpreferred mutations differ in the predicted direction among 99 alleles of two D. pseudoobscura genes and five alleles of eight D. simulans genes. This result confirms the existence of fitness classes of silent mutations. Maximum likelihood estimates suggest that selection intensity at silent sites is, on average, very weak in both D. pseudoobscura and D. simulans (|N(e)s| & 1). Inference of evolutionary processes from within-species sequence variation is often hindered by the assumption of a stationary frequency distribution. This assumption can be avoided when identifying the action of selection and tested when estimating selection intensity.     

Lack of Polymorphism on the Drosophila Fourth Chromosome Resulting from Selection

Evolutionary processes can be inferred from comparisons of intraspecific polymorphism and interspecific divergence. We sequenced a 1.1-kb fragment of the cubitus interruptus Dominant (ciD) locus located on the nonrecombining fourth chromosome for ten natural lines of Drosophila melanogaster and nine of Drosophila simulans. We found no polymorphism within D. melanogaster and a single polymorphism within D. simulans; divergence between the species was about 5%. Comparison with the alcohol dehydrogenase gene and its two flanking regions in D. melanogaster, for which comparable data are available, revealed a statistically significant departure from neutrality in all three tests. This lack of polymorphism in the ciD locus may reflect recent positive selective sweeps on the fourth chromosome with extreme hitchhiking generated by the lack of recombination. By simulation, we estimate there to be a 50% chance that the selective sweeps occurred within the past 30,000 years in D. melanogaster and 75,000 in D. simulans.     

Background Selection as Baseline for Nucleotide Variation across the Drosophila Genome

The constant removal of deleterious mutations by natural selection causes a reduction in neutral diversity and efficacy of selection at genetically linked sites (a process called Background Selection, BGS). Population genetic studies, however, often ignore BGS effects when investigating demographic events or the presence of other types of selection. To obtain a more realistic evolutionary expectation that incorporates the unavoidable consequences of deleterious mutations, we generated high-resolution landscapes of variation across the Drosophila melanogaster genome under a BGS scenario independent of polymorphism data. We find that BGS plays a significant role in shaping levels of variation across the entire genome, including long introns and intergenic regions distant from annotated genes. We also find that a very large percentage of the observed variation in diversity across autosomes can be explained by BGS alone, up to 70% across individual chromosome arms at 100-kb scale, thus indicating that BGS predictions can be used as baseline to infer additional types of selection and demographic events. This approach allows detecting several outlier regions with signal of recent adaptive events and selective sweeps. The use of a BGS baseline, however, is particularly appropriate to investigate the presence of balancing selection and our study exposes numerous genomic regions with the predicted signature of higher polymorphism than expected when a BGS context is taken into account. Importantly, we show that these conclusions are robust to the mutation and selection parameters of the BGS model. Finally, analyses of protein evolution together with previous comparisons of genetic maps between Drosophila species, suggest temporally variable recombination landscapes and, thus, local BGS effects that may differ between extant and past phases. Because genome-wide BGS and temporal changes in linkage effects can skew approaches to estimate demographic and selective events, future analyses should incorporate BGS predictions and capture local recombination variation across genomes and along lineages.     

Apparent Selection of Enzyme Alleles in Laboratory Populations of Drosophila

Twelve laboratory populations of recently collected Drosophila willistoni were begun with different frequencies of alleles at three enzyme loci, six populations at 25 degrees and six at 19 degrees . Periodic sampling of the populations allowed monitoring of the frequency changes in allozymes over time.-At Lap-5 (a locus coding for leucine amino peptidase), three alleles converged to the same frequencies in all populations at both temperatures. The apparent equilibrium frequency of the major allele was about.75; this is different from the frequency (.57) found in the natural population from which the experimental populations were begun. Allele frequency changes at the esterase-5 locus (Est-5) were slower but consistent in all cages. It is difficult to determine if an equilibrium has been reached. However, the frequency of the rare allele in all cages is about the same as in wild populations, 5%. Alleles at both Lap-5 and Est-5 are non-randomly associated with inversions in the chromosomes onto which they map. Because of these associations, it is impossible to unambiguously attribute the change in allele frequencies to selection at the loci being observed.-After one year, no significant gene frequency changes were detected at Est-7, the third locus studied.     

Ancestral Polymorphism of Mhc Class II Genes in Mice: Implications for Balancing Selection and the Mammalian Molecular Clock

To investigate the evolutionary dynamics at Mhc class II DR genes of mice (genus Mus), we sequenced the peptide binding regions (PBRs) of 41 DRB (=Eβ) genes and eight DRA (=Eα) genes from 15 strains representing eight species. As expected trees of these PBR sequences imply extensive maintenance of ancestral DRB alleles across species. We use a coalescent simulation model to show that the number of interspecific coalescent events (c) observed on these trees was higher than the number expected for neutral genealogies and similar sample sizes and is more consistent with balancing selection than with neutrality. Patterns of ancestral polymorphism in mouse DRB alleles were also used to examine the tempo of synonymous substitution in the PBR of mouse class II genes. Both absolute and relative rate tests on DRA and DRB genes imply increased substitution rates at two- and fourfold degnerate sites of mice and rats relative to primates, and decreased rates for the DRB genes of primates relative to ungulate and carnivore relatives. Thus rates of synonymous substitution at Mhc DR genes in mammals appear to be subject to generation time effects in ways similar to those found at other mammalian genes.     

Drosophila Alcohol Dehydrogenase Polymorphism and Carbon-13 Fluxes: Opportunities for Epistasis and Natural Selection

The influence of genetic variations in Drosophila alcohol dehydrogenase (ADH) on steady-state metabolic fluxes was studied by means of (13)C NMR spectroscopy. Four pathways were found to be operative during 8 hr of ethanol degradation in third instar larvae of Drosophila. Seven strains differed by 18-25% in the ratio between two major pathway fluxes, i.e., into glutamate-glutamine-proline vs. lactate-alanine-trehalose. In general, Adh genotypes with higher ADH activity exhibit a twofold difference in relative carbon flux from malate into lactate and alanine vs. α,α-trehalose compared to low ADH activity genotypes. Trehalose was degraded by the pentose-phosphate shunt. The pentose-phosphate shunt and malic enzyme could supply NADPH necessary for lipid synthesis from ethanol. Lactate and/or proline synthesis may maintain the NADH/NAD(+) balance during ethanol degradation. After 24 hr the flux into trehalose is increased, while the flux into lipids declines in Adh(F) larvae. In Adh(S) larvae the flux into lipids remains high. This co-ordinated nature of metabolism and the genotype-dependent differences in metabolic fluxes may form the basis for various epistatic interactions and ultimately for variations in organismal fitness.     

The Chromosomal Distribution of CpG Islands in the Mouse: Evidence for Genome Scrambling in the Rodent Lineage

We have prepared a library of mouse whole CpG islands using a methyl-CpG binding domain column. The distribution of CpG islands in the mouse genome was determined by FISH, using the library as a probe. Unlike in other vertebrate genomes that have been examined (human and chicken), extreme clustering of CpG islands was not seen in the mouse genome. No individual murine chromosome stood out as being either very gene-rich or very gene-poor. Despite the more even distribution of CpG islands in the mouse at a gross chromosomal level, at finer resolution concentrations of CpG islands are seen to correspond to the R-band early replicating regions of the genome.     

Genome,Evolution, Drosophila and Beyond: The New Dimensions

A century ago, a little fly with red eyes was first used for genetic studies. That insignificant fly called at that time, Drosophila ampelophila, was going to revolutionize biology while becoming the model we know today as Drosophila melanogaster. Since then, its study has never ceased, but the field of interest has somewhat changed over the century. Drosophila meetings are exceptional opportunities to gather biologists of diverse backgrounds to not only learn about the latest improvements in our field of interest, but also to appreciate learning another bit of biology. From this biological melting pot a culture very specific to the fly community has emerged. Thus, besides neurobiology, cell biology and development a diversity of other fields of research exist, and they all have their own place in the cultural and historical dimension of the "Drosophila" model. Several communications from these diverse fields of research were presented at the 8th Japanese Drosophila Research Conference (JDRC8) and they are briefly reported here.