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J Hey

Publications and source records attributed to J Hey.

34 records · Page 2Linked to original sources
PubMed1996

DNA sequence variation at the period locus reveals the history of species and speciation events in the Drosophila virilis group.

The virilis phylad of the Drosophila virilis group consists of five closely related taxa: D. virilis, D. lummei, D. novamexicana, D. americana americana and D. americana texana. DNA sequences from a 2.1-kb pair portion of the period locus were generated in four to eight individuals from each of the five taxa. We found evidence of recombination and high levels of variation within species. We found no evidence of recent natural selection. Surprisingly there was no evidence of divergence between D. a. americana and D. a. texana, and they collectively appear to have had a large historical effective population size. The ranges of these two taxa overlap in a large hybrid zone that has been delineated in the eastern U.S. on the basis of the geographic pattern of a chromosomal fusion. Also surprisingly, D. novamexicana appears to consist of two distinct groups each with low population size and no gene flow between them.

Animals↗
PubMed1996

The speciation history of Drosophila pseudoobscura and close relatives: inferences from DNA sequence variation at the period locus.

Thirty-five period locus sequences from Drosophila pseudoobscura and its siblings species, D. p. bogotana, D. persimilis, and D. miranda, were studied. A large amount of variation was found within D. pseudoobscura and D. persimilis, consistent with histories of large effective population sizes. D. p. bogotana, however, has a severe reduction in diversity. Combined analysis of per with two other loci, in both D. p. bogotana and D. pseudoobscura, strongly suggest this reduction is due to recent directional selection at or near per within D. p. bogotana. Since D. p. bogotana is highly variable and shares variation with D. pseudoobscura at other loci, the low level of variation at per within D. p. bogotana can not be explained by a small effective population size or by speciation via founder event. Both D. pseudoobscura and D. persimilis have considerable intraspecific gene flow. A large portion of one D. persimilis sequence appears to have arisen via introgression from D. pseudoobscura. The time of this event appears to be well after the initial separation of these two species. The estimated times since speciation are one mya for D. pseudoobscura and D. persimilis and 2 mya since the formation of D. miranda.

Amino Acid Sequence↗
PubMed1994

The effects of mutation and natural selection on codon bias in the genes of Drosophila.

Codon bias varies widely among the loci of Drosophila melanogaster, and some of this diversity has been explained by variation in the strength of natural selection. A study of correlations between intron and coding region base composition shows that variation in mutation pattern also contributes to codon bias variation. This finding is corroborated by an analysis of variance (ANOVA), which shows a tendency for introns from the same gene to be similar in base composition. The strength of base composition correlations between introns and codon third positions is greater for genes with low codon bias than for genes with high codon bias. This pattern can be explained by an overwhelming effect of natural selection, relative to mutation, in highly biased loci. In particular, this correlation is absent when examining fourfold degenerate sites of highly biased genes. In general, it appears that selection acts more strongly in choosing among fourfold degenerate codons than among twofold degenerate codons. Although the results indicate regional variation in mutational bias, no evidence is found for large scale regions of compositional homogeneity.

Animals↗
PubMed1993

DNA sequence variation at the period locus within and among species of the Drosophila melanogaster complex.

A 1.9-kilobase region of the period locus was sequenced in six individuals of Drosophila melanogaster and from six individuals of each of three sibling species: Drosophila simulans, Drosophila sechellia and Drosophila mauritiana. Extensive genealogical analysis of 174 polymorphic sites reveals a complex history. It appears that D. simulans, as a large population still segregating very old lineages, gave rise to the island species D. mauritiana and D. sechellia. Rather than considering these speciation events as having produced "sister" taxa, it seems more appropriate to consider D. simulans a parent species to D. sechellia and D. mauritiana. The order, in time, of these two phylogenetic events remains unclear. D. mauritiana supports a large number of polymorphisms, many of which are shared with D. simulans, and so appears to have begun and persisted as a large population. In contrast, D. sechellia has very little variation and seems to have experienced a severe population bottleneck. Alternatively, the low variation in D. sechellia could be due to recent directional selection and genetic hitchhiking at or near the per locus.

Animals↗
PubMed1993

Population genetics and phylogenetics of DNA sequence variation at multiple loci within the Drosophila melanogaster species complex.

Two regions of the genome, a 1-kbp portion of the zeste locus and a 1.1-kbp portion of the yolk protein 2 locus, were sequenced in six individuals from each of four species: Drosophila melanogaster, D. simulans, D. mauritiana, and D. sechellia. The species and strains were the same as those of a previous study of a 1.9-kbp region of the period locus. No evidence was found for recent balancing or directional selection or for the accumulation of selected differences between species. Yolk protein 2 has a high level of amino acid replacement variation and a low level of synonymous variation, while zeste has the opposite pattern. This contrast is consistent with information on gene function and patterns of codon bias. Polymorphism levels are consistent with a ranking of effective population sizes, from low to high, in the following order: D. sechellia, D. melanogaster, D.mauritiana, and D. simulans. The apparent species relationships are very similar to those suggested by the period locus study. In particular, D. simulans appears to be a large population that is still segregating variation that arose before the separation of D. mauritiana and D. sechellia. It is estimated that the separation of ancestral D. melanogaster from the other species occurred 2.5-3.4 Mya. The separations of D. sechellia and D. mauritiana from ancestral D. simulans appear to have occurred 0.58-0.86 Mya, with D. mauritiana having diverged from ancestral D. simulans 0.1 Myr more recently than D. sechellia.

Animals↗
PubMed1993

Reduced natural selection associated with low recombination in Drosophila melanogaster.

Synonymous codons are not used equally in many organisms, and the extent of codon bias varies among loci. Earlier studies have suggested that more highly expressed loci in Drosophila melanogaster are more biased, consistent with findings from several prokaryotes and unicellular eukaryotes that codon bias is partly due to natural selection for translational efficiency. We link this model of varying selection intensity to the population-genetics prediction that the effectiveness of natural selection is decreased under reduced recombination. In analyses of 385 D. melanogaster loci, we find that codon bias is reduced in regions of low recombination (i.e., near centromeres and telomeres and on the fourth chromosome). The effect does not appear to be a linear function of recombination rate; rather, it seems limited to regions with the very lowest levels of recombination. The large majority of the genome apparently experiences recombination at a sufficiently high rate for effective natural selection against suboptimal codons. These findings support models of the Hill-Robertson effect and genetic hitchhiking and are largely consistent with multiple reports of low levels of DNA sequence variation in regions of low recombination.

Animals↗
PubMed1991

A multi-dimensional coalescent process applied to multi-allelic selection models and migration models.

For a sample of two genes from a population divided into an arbitrary number of allele classes, a general mathematical framework is developed to address the expectation and variance of the time of the most recent common ancestor. Depending on the meaning of allele classes and the manner in which genes can change among them, this framework can be applied to a diversity of population genetic models. By adoption of the infinite sites model, the effect on heterozygosity is modelled for balancing selection among allele classes, mutation between allele classes, migration among populations, and gene conversion between loci. Most results are described for a continuous time approximation to a discrete generation model. It is also shown how the discrete generation model can be used to study the hitch-hiking effect of favorable mutations.

Alleles↗
PubMed1991

Hemorrhage following mandibular osteotomies: a report of 21 cases.

Hemorrhage associated with mandibular osteotomies, especially to the extent that it becomes life threatening, is a rare occurrence and its risk is less than that following maxillary orthognathic surgery. Twenty-one cases of significant bleeding following mandibular sagittal split ramus osteotomies, vertical and oblique ramus osteotomies, and genioplasties are presented. Life-threatening hemorrhage associated with mandibular osteotomies is primarily an intraoperative problem and the incidence of major postoperative and recurrent hemorrhage is not as great as following maxillary osteotomies. Suggestions for the avoidance and treatment of these bleeding complications are discussed.

Adolescent↗
PubMed1991

The structure of genealogies and the distribution of fixed differences between DNA sequence samples from natural populations.

When two samples of DNA sequences are compared, one way in which they may differ is in the presence of fixed differences, which are defined as sites at which all of the sequences in one sample are different from all of the sequences in a second sample. The probability distribution of the number of fixed differences is developed. The theory employs Wright-Fisher genealogies and the infinite sites mutation model. For the case when both samples are drawn randomly from the same population it is found that genealogies permitting fixed differences are very unlikely. Thus the mere presence of fixed differences between samples is statistically significant, even for small samples. The theory is extended to samples from populations that have been separated for some time. The relationship between a simple Poisson distribution of mutations and the distribution of fixed differences is described as a function of the time since populations have been isolated. It is shown how these results may contribute to improved tests of recent balancing or directional selection.

Base Sequence↗
PubMed1990

Effect of aging on kinetic parameters of 3 alpha(beta)-hydroxysteroid oxidoreductases in epithelium and stroma of human normal and hyperplastic prostate.

The accumulation of 5 alpha-dihydrotestosterone (DHT), particularly in stroma, is a possible etiological factor in regard of the age-dependent development of benign prostatic hyperplasia (BPH). In this context, we have recently demonstrated age-dependent alterations of 5 alpha-reductase, which is responsible for the irreversible conversion of testosterone to DHT. Therefore, it was also of interest to study possible age-dependent alterations of those enzymes mainly involved in the reversible metabolism of DHT to 5 alpha-androstanediols. Thus, we determined, in the presence of NADPH/NADP+, kinetic parameters [Km and maximum velocity (Vmax)] of 3-hydroxysteroid oxidoreductases (3 alpha-HSORred, 3 beta-HSORred, and 3 alpha-HSORox) in separated epithelium and stroma of 10 normal (NPR) and 20 hyperplastic prostates (BPH) and correlated the data with the age of the donors (15-86 yr). The mean Km (nanomolar concentrations +/- SEM) of 3 alpha-HSORred was significantly (P less than 0.01) higher in epithelium (NPR, 1391 +/- 181; BPH, 2150 +/- 157) than in stroma (NPR, 778 +/- 22; BPH, 749 +/- 62), indicating the presence of epithelial and stromal enzymes. The mean Km values of 3 beta-HSORred and 3 alpha-HSORox were similar. Concerning 3 alpha-HSORred, the mean potential capacity, i.e. the quotient of Vmax/Km (+/- SEM), was significantly (P less than 0.01) higher in epithelium (0.56 +/- 0.08) than in stroma (0.19 +/- 0.02) of NPR, while in BPH nearly identical mean potential capacities were found in epithelium (0.33 +/- 0.04) and stroma (0.26 +/- 0.02). The respective Vmax/Km of 3 beta-HSORred and 3 alpha-HSORox were significantly (P less than 0.05) lower. In addition, the potential capacity of all three enzymes was distinctly lower than the potential DHT-forming capacity of 5 alpha-reductase. With advancing age, the Vmax/Km decreased significantly (P less than 0.001; 3 alpha-HSORred and 3 beta-HSORred) or tendentiously (3 alpha-HSORox) in epithelium, while in stroma a significant (P less than 0.001; 3 alpha-HSORred and 3 alpha-HSORox) or tendentious (3 beta-HSORred) increase with age was found. Our results indicate that aging has a significant impact on DHT-removing enzymes. However, these enzymes counterbalance only in part the strong potential capacity of 5 alpha-reductase.

3-Hydroxysteroid Dehydrogenases↗
PubMed1989

The transposable portion of the genome of Drosophila algonquin is very different from that in D. melanogaster.

Four clones containing different transposable elements were isolated from a genomic library of Drosophila algonquin. Each clone was hybridized to salivary-gland chromosomes of three lines of D. algonquin and two lines of D. affinis. The estimated copy number in D. algonquin of the four element families varied from 59 to 333. The occupancy per site varied from 0.64 to 0.75. Thus the transposable portion of the D. algonquin genome is dominated by a few high-copy-number elements, each characterized by high occupancies. The copy number and occupancy values were very similar in D. affinis. This differs from the situation in D. melanogaster mobile middle-repetitive DNA, which has at least 30 and perhaps as many as 100 different families of mobile elements, with copy numbers ranging from 5 to 100. When several lines have been examined, elements in D. melanogaster are revealed to have very low occupancies. The four D. algonquin elements do not hybridize with D. melanogaster DNA, but they did hybridize with 15 obscura-group species, thereby revealing a pattern that is consistent with concerted evolution.

Animals↗
PubMed1989

Restriction-map variation associated with the G6PD polymorphism in natural populations of Drosophila melanogaster.

Restriction-map variation was studied in 126 copies of the G6pd region in X chromosome lines of Drosophila melanogaster from North America, Europe, and Africa. Special attention was focused on the distribution of variation relative to the geographically variable polymorphism for two electrophoretic variants. Nucleotide heterozygosity as determined by eight six-cutter restriction enzymes for the 13-kb region is estimated, on the basis of the worldwide sample, to be 0.065%, which is the lowest value reported for any comparable region in the D. melanogaster genome. Significant linkage disequilibrium between electrophoretic alleles and restriction-site variation is observed for several sites. In contrast to published studies of other genetic regions, there are large insertions that reach significant frequencies and are found across considerable geographic distances. There is a clustering of this variation inside the first large intervening sequence of the G6PD gene.

Africa↗
PubMed1985

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.

Animals↗
PubMedDate not supplied

Parasite populations: the puzzle of Plasmodium.

The issue of whether the malaria parasite Plasmodium falciparum is effectively clonal, as some argue, or undergoes outcrossing at a high rate, as many others believe, has been controversial. Recent data support the latter view, though no doubt the puzzle has not yet been laid to rest.

Animals↗