Nearly identical allelic distributions of xanthine dehydrogenase in two populations of Drosophila pseudoobscura

The Selective Maintenance of Allelic Variation Under Generalized Dominance

Simple models of viability selection acting on variation at a single diploid locus only maintain multiple alleles for very restricted sets of fitnesses. Most of these models assume that fitnesses are independent, even if the genotypes share alleles. Here, we extend this result to a model with generalized dominance interactions, in which fitnesses are strongly affected by what we call the “primary effects” of the genotype’s component alleles, so that genotypes with shared alleles have correlated fitnesses. Nevertheless, in keeping with previously reported results, we also show that such fitness sets are easily constructed over time if recurrent mutation is occurring simultaneously. We find that such models maintain less variation over time than do (previous) models with independently sampled fitnesses, especially when the effects of genetic drift are taken into account. We also show that there is a weak tendency for greater weighting of primary effects to evolve over time.

The maintenance of single-locus polymorphism by maternal selection

Population geneticists have long been interested in the ability of natural selection to maintain the levels of standing variation observed in natural populations. Here, we study the polymorphism-maintaining properties of maternal selection, in which the fitness of an individual is a function of its own and its mother’s genotype. Using a model proposed by Gavrilets, we first estimate the proportion of parameter/state space that preserves allelic variation, before investigating the construction of polymorphism over time through the joint action of mutation and selection. These two methods, the “parameter-space” and “constructionist” approaches, respectively, enable us to draw some general conclusions. We argue that, even though the proportion of parameter-state space allowing multiallele polymorphism is greater under maternal selection than under the standard model of constant viability selection, the former is, in fact, less likely to maintain large numbers of alleles. Nevertheless, variation that is balanced by maternal selection is likely to show elements of heterozygous advantage and be resistant to depletion by genetic drift. We observe that the population mean fitness frequently decreases after the successful invasion of a new mutation, but such declines are usually temporary.

Models of frequency-dependent selection with mutation from parental alleles

Frequency-dependent selection (FDS) remains a common heuristic explanation for the maintenance of genetic variation in natural populations. The pairwise-interaction model (PIM) is a well-studied general model of frequency-dependent selection, which assumes that a genotype's fitness is a function of within-population intergenotypic interactions. Previous theoretical work indicated that this type of model is able to sustain large numbers of alleles at a single locus when it incorporates recurrent mutation. These studies, however, have ignored the impact of the distribution of fitness effects of new mutations on the dynamics and end results of polymorphism construction. We suggest that a natural way to model mutation would be to assume mutant fitness is related to the fitness of the parental allele, i.e., the existing allele from which the mutant arose. Here we examine the numbers and distributions of fitnesses and alleles produced by construction under the PIM with mutation from parental alleles and the impacts on such measures due to different methods of generating mutant fitnesses. We find that, in comparison with previous results, generating mutants from existing alleles lowers the average number of alleles likely to be observed in a system subject to FDS, but produces polymorphisms that are highly stable and have realistic allele-frequency distributions.

The generation and maintenance of genetic variation by frequency-dependent selection: constructing polymorphisms under the pairwise interaction model

Frequency-dependent selection remains the most commonly invoked heuristic explanation for the maintenance of genetic variation. For polymorphism to exist, new alleles must be both generated and maintained in the population. Here we use a construction approach to model frequency-dependent selection with mutation under the pairwise interaction model. The pairwise interaction model is a general model of frequency-dependent selection at the genotypic level. We find that frequency-dependent selection is able to generate a large number of alleles at a single locus. The construction process generates multiallelic polymorphisms with a wide range of allele-frequency distributions and genotypic fitness relationships. Levels of polymorphism and mean fitness are uncoupled, so constructed polymorphisms remain permanently invasible to new mutants; thus the model never settles down to an equilibrium state. Analysis of constructed fitness sets reveals signatures of heterozygote advantage and positive frequency dependence.

Frequency-dependent selection and the maintenance of genetic variation: exploring the parameter space of the multiallelic pairwise interaction model

When individuals' fitnesses depend on the genetic composition of the population in which they are found, selection is then frequency dependent. Frequency-dependent selection (FDS) is often invoked as a heuristic explanation for the maintenance of large numbers of alleles at a locus. The pairwise interaction model is a general model of FDS via intraspecific competition at the genotypic level. Here we use a parameter-space approach to investigate the full potential for the maintenance of multiallelic equilibria under the pairwise interaction model. We find that FDS maintains full polymorphism more often than classic constant-selection models and produces more skewed equilibrium allele frequencies. Fitness sets with some degree of rare advantage maintained full polymorphism most often, but a wide variety of nonobvious fitness patterns were also found to have positive potential for polymorphism. An example is put forth suggesting possible explanations for multiallelic polymorphisms maintained despite positive FDS on individual alleles.

Molecular population genetics of X-linked genes in Drosophila pseudoobscura

This article presents a nucleotide sequence analysis of 500 bp determined in each of five X-linked genes, runt, sisterlessA, period, esterase 5, and Heat-shock protein 83, in 40 Drosophila pseudoobscura strains collected from two populations. Estimates of the neutral migration parameter for the five loci show that gene flow among D. pseudoobscura populations is sufficient to homogenize inversion frequencies across the range of the species. Nucleotide diversity at each locus fails to reject a neutral model of molecular evolution. The sample of 40 chromosomes included six Sex-ratio inversions, a series of three nonoverlapping inversions that are associated with a strong meiotic drive phenotype. The selection driven by the Sex-ratio meiotic drive element has not fixed variation across the X chromosome of D. pseudoobscura because, while significant linkage disequilibrium was observed within the sisterlessA, period, and esterase 5 genes, we did not find evidence for nonrandom association among loci. The Sex-ratio chromosome was estimated to be 25,000 years old based on the decomposition of linkage disequilibrium between esterase 5 and Heat-shock protein 83 or 1 million years old based on the net divergence of esterase 5 between Standard and Sex-ratio chromosomes. Genetic diversity was depressed within esterase 5 within Sex-ratio chromosomes, while the four other genes failed to show a reduction in heterozygosity in the Sex-ratio background. The reduced heterogeneity in esterase 5 is due either to its location near one of the Sex-ratio inversion breakpoints or that it is closely linked to a gene or genes responsible for the Sex-ratio meiotic drive system.

Sequential gel electrophoretic analysis of esterase-2 in two populations of Drosophila buzzatii

Sequential electrophoresis, using three different buffer systems on cellulose acetate gels, was used to characterize the allelic variation for esterase-2 in two populations of D. buzzatii in Australia that are separated by 550 km. Twenty-five alleles were detected, of which nine were unique to one population, eight unique to the other, and only eight were common to both populations. Allele frequencies within each population were significantly different between the two major chromosome sequences (standard and j inversion), and for each chromosome sequence allele frequencies were significantly different between populations. Observed allelic frequency distributions were not significantly different from those predicted for selective neutrality using the homozygosity test statistic. However, estimates of the effective sizes of the populations derived from their observed differentiation, together with the history of the species in Australia, provide support for some form of balancing selection affecting at least some of the alleles.

Estimates of gene flow in Drosophila pseudoobscura determined from nucleotide sequence analysis of the alcohol dehydrogenase region

The genetic structure of Drosophila pseudoobscura populations was inferred from a nucleotide sequence analysis of a 3.4-kb segment of the alcohol dehydrogenase (Adh) region. A total of 99 isochromosomal strains collected from 13 populations in North and South America were used to determine if any population departed from a neutral model and to estimate levels of gene flow between populations. This study also included the nucleotide sequences from two sibling species, D. persimilis and D. miranda. We estimated the neutral mutation parameter, 4N mu, in synonymous and noncoding sites for 17 subregions of Adh in each of nine populations with sample sizes greater than three. The nucleotide diversity data in the nine populations was tested for departures from an equilibrium neutral model with two statistical tests. The Tajima and the Hudson, Kreitman, Aguade tests showed that each population fails to reject a neutral model. Tests for genetic differentiation between populations fail to show any population substructure among the North American populations of D. pseudoobscura. The nucleotide diversity data is consistent with direct and indirect measures of gene flow that show extensive dispersal between populations of D. pseudoobscura.

Distinguishing the forces controlling genetic variation at the Xdh locus in Drosophila pseudoobscura

Fifty-eight isochromosomal lines sampled from two natural populations of Drosophila pseudoobscura in California and one from Bogota, Colombia, were examined using four-cutter restriction mapping. A 4.6-kb region of the xanthine dehydrogenase locus was probed and 66 of 135 restriction sites scored were polymorphic. This predicts that on average every 12th bp would be polymorphic in this region for the genes surveyed if polymorphism occurred randomly along the coding region. In addition, there were 12 insertion/deletion polymorphisms. Forty-nine distinct haplotypes were recognized in the 58 lines examined. The most common haplotype obtained a frequency of only 5%. Measures of base pair heterozygosity (0.0097) and linkage disequilibrium lead to a predicted population size in the range of 1.2-2.4 X 10(6) for the species. High levels of recombination (including gene conversion) can be inferred from the presence of all four gametic types in the data set.

Allelic variation in human mitochondrial genes based on patterns of restriction site polymorphism

Restriction maps of 145 human mtDNAs representing samples from five geographic regions were used to construct multilocus genotypes for 28 genetic loci of the mitochondrial genome. Alleles were defined as distinct combinations of the presence or absence of polymorphic restriction sites within each locus. The 28 loci included 13 genes encoding proteins, 10 genes specifying tRNAs, 2 genes specifying rRNAs, and 3 noncoding regions consisting of the D loop, the light strand origin of replication, and the 5' noncoding sequence. In 35 comparisons of allele frequency distributions to expected distributions predicted by neutral mutation theory (assuming an infinite alleles model), the results revealed that most genetic diversity values (71%) fell within the range predicted by the neutral model; however, excesses in the frequencies of common alleles and in the number of singleton alleles within populations were observed at specific loci. Departures from the neutral mutation model are most readily explained by the effects of the recent expansion of the human population and the action of purifying selection. Coefficients of population differentiation suggest that gene flow of mtDNA types between certain geographic regions may be limited.