Intraspecific and interspecific variation at the y-ac-sc region of Drosophila simulans and Drosophila melanogaster.

Abstract A 2.2-kb region including the ac gene of Drosophila simulans has been sequenced. Interspecific divergence between Drosophila melanogaster and D. simulans was estimated as 0.0695 and 0.0558 for silent and for all sites, respectively. Estimated silent site divergence for the ac region is comparable to that estimated for other regions of the genome between these species, indicating that silent sites of the ac region are not under significantly stronger functional constraint. Intraspecific variation in both species was also investigated. Restriction-site and length polymorphism in the ac region of D. simulans has been investigated for 103 X chromosome lines sampled from three natural populations in Spain using eight four-cutter restriction enzymes. Neither restriction-site nor length variation was detected in the three populations surveyed. In D. melanogaster restriction-site and length polymorphism in all major transcription units of the y-ac-sc region (23.1-kb region) has been studied using four four-cutter restriction enzymes for 245 X chromosome lines sampled from 10 natural populations (seven from Europe, two from North America and one from Japan). Fourteen restriction-site and 28 length polymorphisms were detected. There was some indication of population subdivision for North American vs. European samples of D. melanogaster. The frequency spectrum of restriction-site polymorphisms in European populations was skewed toward rarer frequencies than predicted by the neutral theory. Comparison of silent site variation at this telomeric region with that in the Adh 5'-flanking region showed a reduced level of heterozygosity in the y-ac-sc region. Since interspecific silent divergence is not reduced in the y-ac-sc region as compared to other regions, the reduction in standing levels of variation at this telomeric locus in both D. simulans and D. melanogaster is most easily explained by a hitchhiking effect of linked selected substitutions.

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Length Variation of CAG/CAA Trinucleotide Repeats in Natural Populations of Drosophila melanogaster and Its Relation to the Recombination Rate

Genetics ◽

10.1093/genetics/143.4.1713 ◽

1996 ◽

Vol 143 (4) ◽

pp. 1713-1725 ◽

Cited By ~ 1

Author(s):

Yannis Michalakis ◽

Michel Veuille

Keyword(s):

Drosophila Melanogaster ◽

Tandem Repeats ◽

Trinucleotide Repeat ◽

Natural Populations ◽

Population Subdivision ◽

Length Variation ◽

Unexpected Result ◽

Chromosome 2 ◽

Infinite Allele Model ◽

Selective Neutrality

Abstract Eleven genes distributed along the Drosophila melanogaster chromosome 2 and showing exonic tandem repeats of glutamine codons (CAG or CAA) were surveyed for length variation in a sample of four European and African populations. Only one gene was monomorphic. Eight genes were polymorphic in all populations, with a total number of alleles varying between five and 12 for 120 chromosomes. The average heterozygozity per locus and population was 0.41. Selective neutrality in length variation could not be rejected under the assumptions of the infinite allele model. Significant population subdivision was found though no geographical pattern emerged, all populations being equally different. Significant linkage disequilibrium was found in four out of seven cases where the genetic distance between loci was <1 cM and was negligible when the distance was larger. There is evidence that these associations were established after the populations separated. An unexpected result was that variation at each locus was independent of the coefficient of exchange, although the latter ranged from zero to the relatively high value of 6.7%. This would indicate that background selection and selective hitchhiking, which are thought to affect levels of nucleotide substitution polymorphism, have no effect on trinucleotide repeat variation.

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Molecular genetic variation in the centromeric region of the X chromosome in three Drosophila ananassae populations. I. Contrasts between the vermilion and forked loci.

Genetics ◽

10.1093/genetics/121.1.89 ◽

1989 ◽

Vol 121 (1) ◽

pp. 89-99 ◽

Cited By ~ 8

Author(s):

W Stephan ◽

C H Langley

Keyword(s):

X Chromosome ◽

Centromeric Region ◽

Molecular Genetic ◽

Natural Populations ◽

Restriction Enzymes ◽

Dna Polymorphisms ◽

Drosophila Ananassae ◽

Population Subdivision ◽

Frequency Distributions ◽

Evolutionary Force

Abstract We have surveyed three natural populations of Drosophila ananassae for restriction map variation at the forked (f) and vermilion (v) loci, using 6-cutter restriction enzymes. Both loci are located in the centromeric region of the X chromosome. Two major conclusions can be drawn from the data. First, we found strong evidence for population subdivision, i.e., significant differences in the frequency distributions of polymorphisms and/or haplotypes between the Burma, India, and Brazil populations. Secondly, the pattern of DNA sequence variation between the two loci is unexpectedly different. The level of nucleotide variation in the v locus region is reduced (relative to f), especially in the Burma population. Furthermore, in contrast to v, we found no insertions/deletions larger than 700 bp and no significant linkage disequilibrium at f. The genetic differentiation among subpopulations can readily be attributed to restricted migration as the predominant evolutionary force. According to population genetics theory, the differences in DNA polymorphisms between the two loci are in qualitative agreement with the hypothesis that recombination is reduced in the v locus region ("centromere effect") but not at f. In order to test this hypothesis directly, we determined the cytogenetic positions of several loci in the centromeric region by in situ hybridization and found by comparison with the genetic map that recombination at v is indeed very low, much lower than at f.

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Molecular and phenotypic variation of the white locus region in Drosophila melanogaster.

Genetics ◽

10.1093/genetics/120.1.199 ◽

1988 ◽

Vol 120 (1) ◽

pp. 199-212

Author(s):

N Miyashita ◽

C H Langley

Keyword(s):

Drosophila Melanogaster ◽

X Chromosome ◽

Restriction Site ◽

Restriction Enzymes ◽

Transcriptional Unit ◽

X Chromosomes ◽

Linkage Disequilibria ◽

Restriction Sites ◽

White Locus ◽

Shock Locus

Abstract Restriction site and insertion/deletion polymorphism in a 45-kb region of the white locus on the X chromosome in Drosophila melanogaster was investigated for 64 X chromosome lines with six 6-cutter and ten 4-cutter restriction enzymes. A total of 109 polymorphisms were detected (54 restriction sites and 55 insertions/deletions). Estimated heterozygosity per nucleotide for this region (0.004-0.008) was similar to those of the Adh and 87A heat-shock locus regions located on the autosomes in D. melanogaster. This is contrary to a simple prediction based on the theory of mutation selection-balance of partially recessive deleterious mutants which predicts less variation on X chromosomes. Large linkage disequilibria between pairs of polymorphisms (including insertions and deletions) within the transcriptional unit (especially the 3' end of the 1st intron) were observed. As expected from population genetics theory, linkage disequilibria between these polymorphisms were greater for those pairs that are physically closer on the restriction map. Linkage equilibrium was typically observed when the pairs of sites were separated by 2 kb or more. Although significant between-line variation in eye pigment was observed (P less than 0.05), there is little evidence for strong associations between this phenotype and the polymorphisms at the DNA level.

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A comprehensive study of genic variation in natural populations of Drosophila melanogaster. IV. Mitochondrial DNA variation and the role of history vs. selection in the genetic structure of geographic populations.

Genetics ◽

10.1093/genetics/129.1.103 ◽

1991 ◽

Vol 129 (1) ◽

pp. 103-117

Author(s):

L R Hale ◽

R S Singh

Keyword(s):

Mitochondrial Dna ◽

Drosophila Melanogaster ◽

Restriction Site ◽

Far East ◽

Natural Populations ◽

Size Variation ◽

Restriction Enzymes ◽

Western Hemisphere ◽

Small Scale ◽

Coding Region

Abstract Preliminary studies with restriction fragment length polymorphisms of mitochondrial DNA (mtDNA) in natural populations of Drosophila melanogaster revealed considerable variation in terms of nucleotide sequence and overall size. In this report we present data from more isofemale lines and more restriction enzymes, and explore the utility of the data in inferring a colonization history of this species. Size variation in the noncoding A + T-rich region is particularly plentiful, with size variants occurring in all restriction site haplotypes in all populations. We report here classes of small-scale mobility polymorphisms (apparent range of 20 bp) in specific restriction fragments in the coding region. The variation in one such fragment appears to be generated even more rapidly than in the noncoding region. On the basis of the distribution of restriction site haplotypes, the species range can be divided into three major regions along longitudinal lines: Euro-African populations are the most diverse and are taken to be oldest; Far East populations have a complex distribution of haplotypes; Western Hemisphere populations are the least diverse and are interpreted to be the youngest. The history inferred from mtDNA alone is remarkably similar to one based on several nuclear markers. The mtDNA haplotype distribution is also very different from that of allozymes in these same populations. We interpret this as further evidence that natural selection is still the most parsimonious explanation for the parallel latitudinal allozyme clines in this species.

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Reduced variation in the yellow-achaete-scute region in natural populations of Drosophila melanogaster.

Genetics ◽

10.1093/genetics/122.3.607 ◽

1989 ◽

Vol 122 (3) ◽

pp. 607-615 ◽

Cited By ~ 9

Author(s):

M Aguade ◽

N Miyashita ◽

C H Langley

Keyword(s):

Drosophila Melanogaster ◽

Restriction Site ◽

Natural Populations ◽

Negative Relationship ◽

Relative Number ◽

Restriction Enzymes ◽

Crossing Over ◽

Length Polymorphisms ◽

Polymorphic Restriction ◽

Restriction Site Polymorphisms

Abstract Restriction map variation in 64 X chromosome lines extracted from three different populations of Drosophila melanogaster was investigated with seven six-nucleotide-recognizing restriction enzymes for a 106-kb region encompassing the yellow gene and the achaete-scute complex that is located in the region of reduced crossing over close to the telomere. Nine restriction site polymorphisms (out of 176 sites scored) and 19 length polymorphisms (15 insertions and 4 deletions) were detected. The estimated level of heterozygosity per nucleotide, H = 0.0003, is much lower than that reported for autosomal and sex-linked loci located in regions with normal levels of crossing over. The overall frequency of polymorphic restriction sites is reduced. Six out of nine restriction site polymorphisms are unique and the other three have frequencies less than 0.17. Some large insertions have reached relatively high frequencies, 0.08 to 0.17. Consistent with the theoretically predicted negative relationship between crossing over and the magnitude of linkage disequilibrium, an increase in the relative number of nonrandom associations was observed in the y-ac-sc region.

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Hybrid dysgenesis-induced quantitative variation on the X chromosome of Drosophila melanogaster.

Genetics ◽

10.1093/genetics/124.3.627 ◽

1990 ◽

Vol 124 (3) ◽

pp. 627-636

Author(s):

C Q Lai ◽

T F Mackay

Keyword(s):

Drosophila Melanogaster ◽

X Chromosome ◽

Quantitative Traits ◽

Natural Populations ◽

Quantitative Variation ◽

Hybrid Dysgenesis ◽

X Chromosomes ◽

Bristle Number ◽

Seven Generations ◽

Polygenic Variation

Abstract To determine the ability of the P-M hybrid dysgenesis system of Drosophila melanogaster to generate mutations affecting quantitative traits, X chromosome lines were constructed in which replicates of isogenic M and P strain X chromosomes were exposed to a dysgenic cross, a nondysgenic cross, or a control cross, and recovered in common autosomal backgrounds. Mutational heritabilities of abdominal and sternopleural bristle score were in general exceptionally high-of the same magnitude as heritabilities of these traits in natural populations. P strain chromosomes were eight times more mutable than M strain chromosomes, and dysgenic crosses three times more effective than nondysgenic crosses in inducing polygenic variation. However, mutational heritabilities of the bristle traits were appreciable for P strain chromosomes passed through one nondysgenic cross, and for M strain chromosomes backcrossed for seven generations to inbred P strain females, a result consistent with previous observations on mutations affecting quantitative traits arising from nondysgenic crosses. The new variation resulting from one generation of mutagenesis was caused by a few lines with large effects on bristle score, and all mutations reduced bristle number.

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MOLECULAR POPULATION GENETICS OF THE ALCOHOL DEHYDROGENASE GENE REGION OF DROSOPHILA MELANOGASTER

Genetics ◽

10.1093/genetics/114.4.1165 ◽

1986 ◽

Vol 114 (4) ◽

pp. 1165-1190

Author(s):

Charles F Aquadro ◽

Susan F Desse ◽

Molly M Bland ◽

Charles H Langley ◽

Cathy C Laurie-Ahlberg

Keyword(s):

Drosophila Melanogaster ◽

Alcohol Dehydrogenase ◽

Sequence Variation ◽

Natural Populations ◽

Restriction Map ◽

Length Variation ◽

Eastern United States ◽

Chromosome Inversion ◽

Frequency Spectra ◽

Adh Activity

ABSTRACT Variation in the DNA restriction map of a 13-kb region of chromosome ll including the alcohol dehydrogenase structural gene (Adh) was examined in Drosophila melanogaster from natural populations. Detailed analysis of 48 D. melanogaster lines representing four eastern United States populations revealed extensive DNA sequence variation due to base substitutions, insertions and deletions. Cloning of this region from several lines allowed characterization of length variation as due to unique sequence insertions or deletions [nine sizes; 21-200 base pairs (bp)] or transposable element insertions (several sizes, 340 bp to 10.2 kb, representing four different elements). Despite this extensive variation in sequences flanking the Adh gene, only one length polymorphism is clearly associated with altered Adh expression (a copia element approximately 250 bp 5′ to the distal transcript start site). Nonetheless, the frequency spectra of transposable elements within and between Drosophila species suggests they are slightly deleterious. Strong nonrandom associations are observed among Adh region sequence variants, ADH allozyme (Fast vs. Slow), ADH enzyme activity and the chromosome inversion ln(2L)t. Phylogenetic analysis of restriction map haplotypes suggest that the major twofold component of ADH activity variation (high vs. low, typical of Fast and Slow allozymes, respectively) is due to sequence variation tightly linked to and possibly distinct from that underlying the allozyme difference. The patterns of nucleotide and haplotype variation for Fast and Slow allozyme lines are consistent with the recent increase in frequency and spread of the Fast haplotype associated with high ADH activity. These data emphasize the important role of evolutionary history and strong nonrandom associations among tightly linked sequence variation as determinants of the patterns of variation observed in natural populations.

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Naturally occurring variation in the restriction map of the amy region of Drosophila melanogaster.

Genetics ◽

10.1093/genetics/119.3.619 ◽

1988 ◽

Vol 119 (3) ◽

pp. 619-629

Author(s):

C H Langley ◽

A E Shrimpton ◽

T Yamazaki ◽

N Miyashita ◽

Y Matsuo ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Restriction Site ◽

Natural Populations ◽

Alpha Amylase ◽

Low Frequencies ◽

Linkage Disequilibria ◽

Restriction Sites ◽

Site Variation ◽

Transcriptional Units ◽

Polymorphic Restriction

Abstract The restriction maps of 85 alleles of the Amy region of Drosophila melanogaster from natural populations were surveyed. A subset of these were also scored for allozyme phenotype and adult enzyme activity of alpha-amylase. Large insertions were found in 12% of the alleles in a 15-kb region surrounding the two transcriptional units of the duplicated Amy locus. The low frequencies at which each of these large insertions were found are consistent with earlier reports of variation in other loci. Four small deletions were found in the region 5' to the Amy genes. Each was also rare in the population. Restriction site variation provided an estimate of per nucleotide heterozygosity of 0.006. Several statistically significant linkage disequilibria were observed between four polymorphic restriction sites and the allozymes. Adult alpha-amylase activity was correlated with the allozymes and with the polymorphism at one restriction site close to the transcriptional units.

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Studies of esterase 6 in Drosophila melanogaster: XIV. Variation of esterase 6 levels controlled by unlinked genes in natural populations

Genetics Research ◽

10.1017/s0016672300025891 ◽

1984 ◽

Vol 43 (2) ◽

pp. 181-190 ◽

Cited By ~ 7

Author(s):

Craig S. Tepper ◽

Anne L. Terry ◽

James E. Holmes ◽

Rollin C. Richmond

Keyword(s):

Drosophila Melanogaster ◽

Structural Gene ◽

X Chromosome ◽

Genetic Background ◽

Natural Populations ◽

Regulatory Elements ◽

Regulatory Locus ◽

The Third ◽

Esterase 6 ◽

Activity Modifiers

SUMMARYThe esterase 6 (Est-6) locus in Drosophila melanogaster is located on the third chromosome and is the structural gene for a carboxylesterase (E.C.3.1.1.1) and is polymorphic for two major electromorphs (slow and fast). Isogenic lines containing X chromosomes extracted from natural populations and substituted into a common genetic background were used to detect unlinked factors that affect the activity of the Est-6 locus. Twofold activity differences of esterase 6 (EST 6) were found among males from these derived lines, which differ only in their X chromosome. These unlinked activity modifiers identify possible regulatory elements. Immunoelectrophoresis was used to estimate quantitatively the levels of specific cross-reacting material in the derived lines. The results show that the variation in activity is due to differences in the amount of EST 6 present. The data are consistent with the hypothesis that there is at least one locus on the X chromosome that regulates the synthesis of EST 6 and that this regulatory locus may be polymorphic in natural populations.

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Sex-ratio meiotic drive in Drosophila simulans: cellular mechanism, candidate genes and evolution

Biochemical Society Transactions ◽

10.1042/bst0340562 ◽

2006 ◽

Vol 34 (4) ◽

pp. 562-565 ◽

Cited By ~ 13

Author(s):

C. Montchamp-Moreau

Keyword(s):

Sex Ratio ◽

X Chromosome ◽

Natural Populations ◽

Meiotic Drive ◽

Female Offspring ◽

Drosophila Simulans ◽

X Chromosomes ◽

Individual Fitness ◽

Primary Sex Ratio ◽

Intragenomic Conflict

The sex-ratio trait, reported in a dozen Drosophila species, is a type of naturally occurring meiotic drive in which the driving elements are located on the X chromosome. Typically, as the result of a shortage of Y-bearing spermatozoa, males carrying a sex-ratio X chromosome produce a large excess of female offspring. The presence of sex-ratio chromosomes in a species can have considerable evolutionary consequences, because they can affect individual fitness and trigger extended intragenomic conflict. Here, I present the main results of the study performed in Drosophila simulans. In this species, the loss of Y-bearing spermatozoa is related to the inability of the Y chromosome sister-chromatids to separate properly during meiosis II. Fine genetic mapping has shown that the primary sex-ratio locus on the X chromosome contains two distorter elements acting synergistically, both of which are required for drive expression. One element has been genetically mapped to a tandem duplication. To infer the natural history of the trait, the pattern of DNA sequence polymorphism in the surrounding chromosomal region is being analysed in natural populations of D. simulans harbouring sex-ratio X chromosomes. Initial results have revealed the recent spread of a distorter allele.

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