scholarly journals The genetic structure of natural populations of Drosophila melanogaster. XXII. Comparative study of DNA polymorphisms in northern and southern natural populations.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 753-761
Author(s):  
T S Takano ◽  
S Kusakabe ◽  
T Mukai
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Drift ◽  
Nucleotide Diversity ◽  
Restriction Site ◽  
Natural Populations ◽  
Dna Polymorphisms ◽  
Restriction Map ◽  
Random Genetic Drift ◽  
Two Populations ◽  
Restriction Site Polymorphisms

Abstract Restriction map variation in four gene regions (Adh, Amy, Pu and Gpdh) was surveyed for 86 second chromosomes from northern (Aomori) and southern (Ogasawara) Japanese populations of Drosophila melanogaster (43 chromosomes from each population). The regions examined cover a total of 62 kilobases. Estimates of nucleotide diversity (pi) were approximately constant across the gene regions and populations examined. The distribution of restriction site polymorphisms was compatible with the expectation from the neutral mutation-random genetic drift hypothesis, but insertion/deletion polymorphisms were not consistent with it. While the two populations shared a majority of restriction site polymorphisms, frequencies of individual restriction site variants were significantly different between the two populations at 7 out of 35 segregating sites. In addition, an insertion in the Amy region was found in 15 chromosomes from the Ogasawara sample but absent in the Aomori sample. A considerable difference was observed in the number of rare insertions and deletions between the two populations. The numbers of aberrations uniquely represented were 16 in the Ogasawara sample and only 3 in the Aomori sample. These findings suggest that the two populations were differentiated from each other to some degree by means of random genetic drift and/or other factors.

scholarly journals Restriction map variation at the adh locus of Drosophila melanogaster in inverted and noninverted chromosomes.

Genetics ◽  
1988 ◽  
Vol 119 (1) ◽  
pp. 135-140
Author(s):  
M Aguade
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Population ◽  
Evolutionary History ◽  
Restriction Site ◽  
Restriction Enzymes ◽  
Restriction Map ◽  
Allozyme Polymorphism ◽  
Length Polymorphisms ◽  
History Of ◽  
Restriction Site Polymorphisms

Abstract Restriction map variation among 39 Standard and 40 In(2L)t chromosomes extracted from a Spanish natural population of Drosophila melanogaster was investigated for a 2.7-kb region encompassing the Adh locus with ten four-cutter restriction enzymes. A total of 20 polymorphisms were detected, representing 15 restriction site polymorphisms, 4 length polymorphisms and the allozyme polymorphism. Variation at the DNA level was compared among St-Adh(F), St-Adh(S) and t-Adh(S) chromosomes. t-Adh(S) chromosomes show a higher level of variation than St-Adh(F) chromosomes. This suggests that In(2L)t arose before the fast/slow allozyme divergence in the evolutionary history of D. melanogaster.

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

Genetics ◽  
1989 ◽  
Vol 122 (3) ◽  
pp. 607-615 ◽  
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.

scholarly journals DNA POLYMORPHISM DETECTABLE BY RESTRICTION ENDONUCLEASES

Genetics ◽  
1981 ◽  
Vol 97 (1) ◽  
pp. 145-163 ◽  
Author(s):  
Masatoshi Nei ◽  
Fumio Tajima
Keyword(s):  
Statistical Methods ◽  
Nucleotide Diversity ◽  
Restriction Site ◽  
Restriction Enzymes ◽  
Evolutionary Change ◽  
Restriction Endonucleases ◽  
Dna Polymorphisms ◽  
Effective Population ◽  
Mt Dna ◽  
Two Populations

ABSTRACT Data on DNA polymorphisms detected by restriction endonucleases are rapidly accumulating. With the aim of analyzing these data, several different measures of nucleon (DNA segment) diversity within and between populations are proposed, and statistical methods for estimating these quantities are developed. These statistical methods are applicable to both nuclear and non-nuclear DNAs. When evolutionary change of nucleons occurs mainly by mutation and genetic drift, all the measures can be expressed in terms of the product of mutation rate per nucleon and effective population size. A method for estimating nucleotide diversity from nucleon diversity is also presented under certain assumptions. It is shown that DNA divergence between two populations can be studied either by the average number of restriction site differences or by the average number of nucleotide differences. In either case, a large number of different restriction enzymes should be used for studying phylogenetic relationships among related organisms, since the effect of stochastic factors on these quantities is very large. The statistical methods developed have been applied to data of Shah and Langley on mitochondrial (mt)DNA from Drosophila melanogaster, simulans and virilis. This application has suggested that the evolutionary change of mtDNA in higher animals occurs mainly by nucleotide substitution rather than by deletion and insertion. The evolutionary distances among the three species have also been estimated.

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

Genetics ◽  
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.

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

Genetics ◽  
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.

scholarly journals Reduced levels of DNA polymorphism and fixed between-population differences in the centromeric region of Drosophila ananassae.

Genetics ◽  
1992 ◽  
Vol 132 (4) ◽  
pp. 1039-1045 ◽  
Author(s):  
W Stephan ◽  
S J Mitchell
Keyword(s):  
Dna Polymorphism ◽  
Restriction Site ◽  
Total Sample ◽  
Dna Polymorphisms ◽  
Drosophila Ananassae ◽  
Site Variation ◽  
V Region ◽  
Two Populations ◽  
Distal Gene

Abstract We have estimated DNA sequence variation within and between two populations of Drosophila ananassae, using six-cutter restriction site variation at vermilion (v) and furrowed (fw). These two gene regions are located close to the centromere on the left and right X chromosome arms, respectively. In the fw region, no DNA polymorphism was detected within each population. In the v region, average heterozygosity per nucleotide was very low in both populations (pi = 0.0005 in the Burma population, and 0.0009 in the India population). These estimates are significantly lower than those from loci in more distal gene regions. The distribution of DNA polymorphisms between both populations was also striking. At fw, three fixed differences between the Burma and India populations were detected (two restriction site differences and one insertion/deletion of approximately 2 kb). At v, each DNA polymorphism in high frequency in the total sample was nearly fixed in one or the other population, although none of them reached complete fixation. The observed pattern of reduced variation within populations and fixed differences between populations appears to correlate with recombination rate. We conclude that recent hitchhiking associated with directional selection is the best explanation for this pattern. The data indicate that different selective sweeps have occurred in the two populations. The possible role of genetic hitchhiking in rapid population differentiation in gene regions of restricted recombination is discussed.

scholarly journals Lack of underdominance in a naturally occurring pericentric inversion in Drosophila melanogaster and its implications for chromosome evolution.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 791-802
Author(s):  
J A Coyne ◽  
S Aulard ◽  
A Berry
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Selection ◽  
Genetic Drift ◽  
Related Species ◽  
Pericentric Inversion ◽  
Chromosome Evolution ◽  
Natural Populations ◽  
Crossing Over ◽  
Closely Related Species ◽  
Naturally Occurring

Abstract In(2LR)PL is a large pericentric inversion polymorphic in populations of Drosophila melanogaster on two Indian Ocean islands. This polymorphism is puzzling: because crossing over in female heterokaryotypes produces inviable zygotes, such inversions are thought to be underdominant and should be quickly eliminated from populations. The observed fixation for such inversions among related species has led to the idea that genetic drift can cause chromosome evolution in opposition to natural selection. We found, however, that In(2LR)PL is not underdominant for fertility, as heterokaryotypic females produce perfectly viable eggs. Genetic analysis shows that the lack of underdominance results from the nearly complete absence of crossing over in the inverted region. This phenomenon is probably caused by mechanical and not genetic factors, because crossing over is not suppressed in In(2LR)PL homokaryotypes. Our observations do not support the idea that the fixation of pericentric inversions among closely related species implies the action of genetic drift overcoming strong natural selection in very small populations. If chromosome arrangements vary in their underdominance, it is those with the least disadvantage as heterozygotes, like In(2LR)PL, that will be polymorphic or fixed in natural populations.

THE GENETIC STRUCTURE OF NATURAL POPULATIONS OF DROSOPHILA MELANOGASTER. XV. NATURE OF DEVELOPMENTAL HOMEOSTASIS FOR VIABILITY

Genetics ◽  
1982 ◽  
Vol 101 (2) ◽  
pp. 279-300
Author(s):  
Terumi Mukai ◽  
Sadao I Chigusa ◽  
Shin-Ichi Kusakabe
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Populations ◽  
Error Variance ◽  
Sampling Variance ◽  
Environmental Variance ◽  
Developmental Homeostasis ◽  
Relative Viability ◽  
The Difference ◽  
Two Populations ◽  
New Mutations

ABSTRACT Developmental homeostasis of relative viability was examined for homozygotes and heterozygotes using second chromosomes from two populations of Drosophila melanogaster. One was a chromosome population in which spontaneous mutations were allowed to accumulate since it was begun with a single near-normal second chromosome. The second was a natural population approximately at equilibrium. For the estimation of relative viability, the Cy method was employed (Wallace 1956), and environmental variance between simultaneously replicated cultures was used as the index of developmental homeostasis. A new method was used in the estimation of sampling variance for relative viability that was employed for the calculation of environmental variance (error variance between simultaneously replicated cultures — sampling variance). The following findings were obtained.: (1) The difference in environmental variance between homozygotes and heterozygotes could not be seen when a chromosome population with variation due to new mutations was tested. (2) When a chromosome group isolated from an approximate equilibrium population was examined, heterozygotes manifested a smaller environmental variance than the homozygotes if their relative viabilities were approximately the same. (3) There was a slight negative correlation between viability and environmental variance, although opposite results were found when the viabilities of individuals were high, especially when overdominance (coupling overdominance, Mukai 1969 a, b) was manifest. On the basis of these findings, it was concluded that developmental homeostasis was a product of natural selection, and its mechanism was discussed.

scholarly journals Isolation of the Drosophila melanogaster dunce chromosomal region and recombinational mapping of dunce sequences with restriction site polymorphisms as genetic markers.

1984 ◽  
Vol 4 (2) ◽  
pp. 358-367 ◽  
Author(s):  
R L Davis ◽  
N Davidson
Keyword(s):  
Drosophila Melanogaster ◽  
Salivary Gland ◽  
Meiotic Recombination ◽  
Restriction Site ◽  
Chromosomal Region ◽  
Nucleotide Metabolism ◽  
X Chromosomes ◽  
Chromosomal Walking ◽  
Chromosome Bands ◽  
Restriction Site Polymorphisms

Using the method of chromosomal walking, we have isolated a contiguous region of the Drosophila melanogaster X chromosome which corresponds to salivary gland chromosome bands 3C12 to 3D4. This five-band region contains approximately 100 kilobases of DNA, including those sequences comprising dunce, a gene which functions in memory and cyclic nucleotide metabolism. Genome blots of DNA from flies carrying several different chromosomal aberrations with breakpoints in the region have been probed with the isolated clones to map the breakpoints on the cloned DNA and to delimit dunce sequences. This has localized dunce to a 50-kilobase region. In addition, we have searched this 50-kilobase region for restriction site polymorphisms between X chromosomes from different Drosophila strains by genome blotting experiments, and we have followed the segregation of detected polymorphisms and dunce alleles after meiotic recombination. The data map one dunce mutation between two polymorphisms located 10 to 12 kilobases apart.

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