EVIDENCE FOR LINKAGE DISEQUILIBRIUM MAINTAINED BY SELECTION IN TWO NATURAL POPULATIONS OF DROSOPHILA SUBOBSCURA

ABSTRACT One island and one mainland population of Drosophila subobscura were found polymorphic at the XDH (xanthine dehydrogenase) and the A0 (aldehyde oxidase) loci. It was observed that one allele at the XDH locus, which has a low frequency in both populations, is nonrandomly associated with the alleles at the A0 locus. Two lines of evidence support the thesis that this linkage disequilibrium is due to epistasis rather than random drift: (I)D or r, measures of the disequilibrium, have the same sign and magnitude in both populations. (2) The linkage disequilibrium is not due to inversions. Inversions segregating on the chromosome carrying XDH and A0 have been separated into two classes, between which exchange of alleles at the two loci is suppressed. Linkage disequilibrium for XDH and A0 was observed within each class. In the absence of any exchange of alleles, these disequilibria must have arisen and been maintained independently. The suggestion is made that the epistatic disequilibrium results from the close structural and physiological relationship which exists between the tn-o enzymes.

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Linkage disequilibrium in experimental populations of Drosophila simulans: a test of the random drift hypothesis

Genetics Research ◽

10.1017/s0016672300023685 ◽

1987 ◽

Vol 50 (3) ◽

pp. 187-193

Author(s):

Catherine Montchamp-Moreau ◽

Mariano Katz

Keyword(s):

Linkage Disequilibrium ◽

Genetic Drift ◽

Natural Populations ◽

Aldehyde Oxidase ◽

Drosophila Simulans ◽

Random Drift ◽

Esterase 6 ◽

Experimental Populations ◽

Experimental Values ◽

Neutralist Hypothesis

SummaryLinkage disequilibrium between five polymorphic enzymic loci of the third chromosome (Esterase-6, Phosphoglucomutase, Esterase-C, Aldehyde Oxidase and Acid Phosphatase) was studied in experimental populations of Drosophila simulans. Gametic data were obtained by mating sampled males with homozygous females at the five loci. Four cage populations were initiated with flies caught from natural populations. Extensive linkage disequilibrium was detected after 25 or 34 generations. The effective size of these populations was estimated about 400. Monte-Carlo simulations were performed in order to determine whether the observed disequilibria could be due to genetic drift. The observed probability distribution of the experimental values of r (the gametic correlation coefficient) was consistent with the distribution expected under random genetic drift. Our results are thus in accordance with the neutralist hypothesis.

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GENIC VERSUS CHROMOSOMAL VARIATION IN NATURAL POPULATIONS OF DROSOPHILA SUBOBSCURA

Genetics ◽

10.1093/genetics/78.4.1223 ◽

1974 ◽

Vol 78 (4) ◽

pp. 1223-1244

Author(s):

E Zouros ◽

C B Krimbas ◽

S Tsakas ◽

M Loukas

Keyword(s):

Linkage Disequilibrium ◽

Natural Populations ◽

Genetic Data ◽

Drosophila Subobscura ◽

Lower Degree ◽

Island Population ◽

Chromosomal Variation ◽

Random Drift ◽

Enzyme Loci ◽

High Degree

ABSTRACT Gametic frequencies in one mainland and one island population of D. subobscura were obtained by means of extracting wild chromosomes and subsequently analyzing them for inversions and allozymes. The high degree of cytological heterogeneity which characterizes these populations is not reflected in the genetic data. Two cases of non-random association were observed among eighteen pair-wise comparisons involving gene alleles and inversions to which the locus is linked. In both cases exchange of alleles at the locus is completely suppressed by the inversions. Four cases of linkage disequilibrium were detected among eighteen pairs of loci; two of them could best be explained as transient associations generated by random drift. The results suggest that disequilibria among enzyme loci are not widespread in natural populations—Populations with a lower degree of chromosomal variation are genetically as variable as populations with a higher degree of chromosomal variation. This observation does not support the hypothesis that selection in marginal homokaryotypic populations is for specialized homozygous genotypes.

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GENIC HETEROGENEITY WITHIN ELECTROPHORETIC "ALLELES" AND THE PATTERN OF VARIATION AMONG LOCI IN DROSOPHILA PSEUDOOBSCURA

Genetics ◽

10.1093/genetics/93.4.997 ◽

1979 ◽

Vol 93 (4) ◽

pp. 997-1018

Author(s):

Rama S Singh

Keyword(s):

Balancing Selection ◽

Natural Populations ◽

Aldehyde Oxidase ◽

Xanthine Dehydrogenase ◽

Drosophila Pseudoobscura ◽

Mainland Population ◽

Polymorphic Loci ◽

Genic Variation ◽

Pattern Of Variation

ABSTRACT An investigation, similar to our previously reported xanthine dehydrogenase study, was undertaken to examine the extent of hidden genic variation at nine loci (five larval proteins, three esterases and one aldehyde oxidase) by sequential application of various electrophoretic criteria employing pH, gel concentration and buffer variation. Polymorphic loci appear to fall into two distinct groups: weakly polymorphic, including larval protein 6, 7, 8, 10 and 13 and esterase-1 and -6; and highly polymorphic, including esterase-5, Xdh and possibly Ao. Monomorphic loci may belong to a third group different from all polymorphic lori. Bogota, a geographical isolate that is reproductively isolated from the mainland population, was found to be genetically distinct at four of the ten loci examined in detail so far, including Xdh, whereas previously it was found to be genetically distinct at none. These results are discussed in the light of balancing selection, neutral and mutation-selection hypotheses of genic variation in natural populations.

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Population dynamics of the 2 major mitochondrial DNA haplotypes in experimental populations of Drosophila subobscura

Genome ◽

10.1139/g05-077 ◽

2005 ◽

Vol 48 (6) ◽

pp. 1010-1018 ◽

Cited By ~ 10

Author(s):

Pedro Oliver ◽

Joan Balanyà ◽

Maria Misericòrdia Ramon ◽

Antònia Picornell ◽

Lluis Serra ◽

...

Keyword(s):

Mitochondrial Dna ◽

Natural Population ◽

Linear Trend ◽

Natural Populations ◽

Drosophila Subobscura ◽

Random Drift ◽

Significant Linear Trend ◽

Low Frequencies ◽

Mitochondrial Haplotypes ◽

Experimental Populations

The evolution of Drosophila subobscura mitochondrial DNA has been studied in experimental populations, founded with flies from a natural population from Calvià (Majorca, Balearic Islands, Spain). This population, like others founded in Europe, is characterized by the presence of 2 very common (>95%) mitochondrial haplotypes (named I and II) and rare and endemic haplotypes that appear at very low frequencies. Four experimental populations were established with flies having a heterogeneous nuclear genetic background, which was representative of the composition of the natural population. The populations were started with haplotypes I and II at an initial frequency of 50% each. After 33 generations, the 2 haplotypes coexisted. Random drift could be rejected as the only force responsible for the observed changes in haplotype frequencies. A slight but significant linear trend favouring a mtDNA (haploid) fitness effect has been detected, with a nonlinear deviation that could be due to a nuclear component. An analysis of chromosomal arrangements was made before the foundations of the cages and at generation 23. Our results indicated that the hypothesis that the maintenance of the frequencies of haplotypes I and II in natural populations could be due to their association with chromosomal arrangements remains controversial.Key words: natural selection, random drift, cytonuclear interactions, chromosomal arrangements, mtDNA haplotypes, Drosophila subobscura.

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

Genetics ◽

10.1093/genetics/123.2.359 ◽

1989 ◽

Vol 123 (2) ◽

pp. 359-369 ◽

Cited By ~ 3

Author(s):

M A Riley ◽

M E Hallas ◽

R C Lewontin

Keyword(s):

Genetic Variation ◽

Linkage Disequilibrium ◽

Base Pair ◽

Natural Populations ◽

Xanthine Dehydrogenase ◽

Drosophila Pseudoobscura ◽

Common Haplotype ◽

Coding Region ◽

Data Set ◽

Restriction Sites

Abstract 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.

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POST-TRANSLATIONAL MODIFICATION AS A POTENTIAL EXPLANATION OF HIGH LEVELS OF ENZYME POLYMORPHISM: XANTHINE DEHYDROGENASE AND ALDEHYDE OXIDASE IN DROSOPHILA MELANOGASTER

Genetics ◽

10.1093/genetics/91.4.695 ◽

1979 ◽

Vol 91 (4) ◽

pp. 695-722

Author(s):

Victoria Finnerty ◽

George Johnson

Keyword(s):

Drosophila Melanogaster ◽

Natural Populations ◽

Aldehyde Oxidase ◽

Xanthine Dehydrogenase ◽

Enzyme Polymorphism ◽

The Body ◽

Post Translational Modification ◽

Heritable Variation ◽

Thermal Stabilities ◽

Partial Restoration

ABSTRACT Xanthine dehydrogenase (XDH) and aldehyde oxidase (AO) in Drosophila melanogaster require for their activity the action of another unlinked locus, maroon-like (mal), While the XDH and A 0 loci are on chromosome 3, mal maps to the X chromosome. Although functional mal gene product is required for XDH and A 0 activity, it is possible to examine the effects of mutant mal alleles in those cases when pairs of mutants complement to produce a partial restoration of activity. To test whether mal mediates a post-translational modification of the XDH and A0 proteins, we constructed several mal heteroallelic complementing stocks of Drosophila in which the third chromosomes were co-isogenic. Since all lines were co-isogenic for the XDH and A0 structural genes, any variation in these enzymes seen when comparing these stocks must have been produced by post-translational modification by mal. We examined the XDH and A 0 proteins in these stocks by gel-sieving electrophoresis, a procedure that permits independent characterization of a protein's charge and shape, and is capable of discriminating many variants not detected in routine electrophoresis. In every mal heteroallelic combination, there is a significant alteration in protein shape, when compared to wild type. The magnitude of differences in shape of XDH and AO is correlated both with differences in their enzyme activities and with differences in their thermal stabilities. As the body of this variation appears heritable, any functional differences resulting from these variants are of real genetic and evolutionary interest. A similar post-translational modification of XDH and A0 by yet another locus, lxd, was subsequently documented in an analogous manner. The pattern of electrophoretic differences produced by mal and lxd modification is similar to that reported for electrophoretic "alleles" of XDH in natural populations. The implication is that heritable variation in electrophoretic mobility at these two enzyme loci, and potentially at other loci, is not necessarily allelic to the structural gene loci.

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Absence of linkage disequilibria between chromosomal arrangements and mtDNA haplotypes in natural populations of Drosophila subobscura from the Balkan Peninsula

Genome ◽

10.1139/g2012-004 ◽

2012 ◽

Vol 55 (3) ◽

pp. 214-221 ◽

Cited By ~ 7

Author(s):

Mihailo Jelić ◽

José A. Castro ◽

Zorana Kurbalija Novičić ◽

Bojan Kenig ◽

Danica Dimitrijević ◽

...

Keyword(s):

Mitochondrial Dna ◽

Linkage Disequilibrium ◽

Natural Populations ◽

Balkan Peninsula ◽

Drosophila Subobscura ◽

Mitochondrial Haplotypes ◽

Linkage Disequilibria ◽

Mtdna Haplotypes ◽

Mitochondrial Dna Variability

The genetic structure of Drosophila subobscura from the Balkan Peninsula was studied with respect to restriction site polymorphism of mitochondrial DNA in populations from the Derventa River Gorge and Sicevo Gorge (Serbia). To investigate the role of cytonuclear interactions in shaping mitochondrial DNA variability in natural populations of this species, the study was complemented with the analysis of linkage disequilibria between mitochondrial haplotypes and chromosomal inversion arrangements. Similar to other populations of D. subobscura, two main haplotypes (I and II) were found, as well as a series of less common ones. The frequencies of haplotypes I and II accounted for 25.8% and 71.0%, respectively, in the population from the Derventa River Gorge, and for 32.4% and 58.1%, respectively, in the population from Sicevo Gorge. One of the haplotypes harbored a large insertion (2.7 kb) in the A+T rich region. The frequency distribution of both haplotypes did not depart from neutrality. Contrary to prior studies, we did not detect any significant linkage disequilibrium between the two most frequent mtDNA haplotypes and any of the chromosomal arrangements in either of the populations. We conclude that linkage disequilibrium is not a general occurrence in natural populations of D. subobscura, and we discuss how transient coadaptations, ecologically specific selective pressures, and demographics could contribute to population-specific patterns of linkage disequilibrium.

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The detection of geographical substructuring of Trypanosoma brucei populations by the analysis of minisatellite polymorphisms

Parasitology ◽

10.1017/s0031182001008666 ◽

2001 ◽

Vol 123 (5) ◽

pp. 475-482 ◽

Cited By ~ 11

Author(s):

A. MacLEOD ◽

C. M. R. TURNER ◽

A. TAIT

Keyword(s):

Linkage Disequilibrium ◽

Trypanosoma Brucei ◽

Natural Populations ◽

Geographical Location ◽

Low Frequency ◽

Genetic Exchange ◽

Rapid Expansion ◽

Isolated Populations ◽

Single Population ◽

Multilocus Genotypes

Analysis of natural populations of Trypanosoma brucei has shown that there is linkage disequilibrium between alleles at pairs of loci in isolates taken from the field. This disequilibrium can occur as a result of a low frequency of genetic exchange, the masking of frequent genetic exchange by the rapid expansion of a few genotypes or by the treatment of 2 (or more) genetically isolated populations as a single population. We have analysed stocks from 2 geographically separate locations using 3 minisatellite markers to determine the frequencies of the alleles in each area and the frequency and nature of the multilocus genotypes. The results show that many alleles and multilocus genotypes are unique to each geographical location, supporting the conclusion that these populations are genetically isolated with limited or no gene flow between them. This geographical substructuring needs to be taken into account in considering the origins of the linkage disequilibrium in a number of populations.

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Development of associative overdominance through linkage disequilibrium in finite populations

Genetics Research ◽

10.1017/s0016672300002391 ◽

1970 ◽

Vol 16 (2) ◽

pp. 165-177 ◽

Cited By ~ 60

Author(s):

Tomoko Ohta ◽

Motoo Kimura

Keyword(s):

Linkage Disequilibrium ◽

Population Size ◽

Effective Population Size ◽

Natural Populations ◽

Approximation Formula ◽

Effective Population ◽

Finite Populations ◽

Random Drift ◽

Neutral Locus ◽

Image Position

SUMMARYAssociative overdominance arises at an intrinsically neutral locus through its non-random association with overdominant loci. In finite populations, even if fitness is additive between loci, non-random association will be created by random genetic drift.The magnitude of such associative overdominance is roughly proportional to the sum of between the neutral and the surrounding over-dominant loci, where is the squared standard linkage deviation, defined between any two loci by the relationin which p and 1 – p are frequencies of alleles A1 and A2 in the first locus, q and 1 – q are frequencies of alleles B1 and B2 in the second locus, and D is the coefficient of linkage disequilibrium. A theory was developed based on diffusion models which enables us to obtain formulae for under various conditions, and Monte Carlo experiments were performed to check the validity of those formulae.It was shown that if A1 and A2 are strongly overdominant while B1 and B2 are selectively neutral, we have approximatelyprovided that 4Nec ≫ 1, where Ne is the effective population size and c is the recombination fraction between the two loci. This approximation formula is also valid between two strongly overdominant as well as weakly overdominant loci, if 4Nec ≫ 1.The significance of associative overdominance for the maintenance of genetic variability in natural populations was discussed, and it was shown that Nes′, that is, the product between effective population size and the coefficient of associative overdominance, remanis constant with varying Ne, if the total segregational (overdominant) load is kept constant.The amount of linkage disequilibrium expected due to random drift in experimental populations was also discussed, and it was shown that in the first generation, if it is produced by extracting n chromosomes from a large parental population in which D = 0.

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EXPECTED LINKAGE DISEQUILIBRIUM FOR A NEUTRAL LOCUS LINKED TO A CHROMOSOMAL ARRANGEMENT

Genetics ◽

10.1093/genetics/103.3.545 ◽

1983 ◽

Vol 103 (3) ◽

pp. 545-555

Author(s):

Curtis Strobeck

Keyword(s):

Linkage Disequilibrium ◽

Balancing Selection ◽

Natural Populations ◽

Transient Behavior ◽

Random Drift ◽

Strong Linkage ◽

Linkage Disequilibria ◽

Chromosomal Arrangement ◽

Neutral Locus ◽

Selection For

ABSTRACT The expected value of the squared linkage disequilibrium is derived for a neutral locus associated with a chromosomal arrangement that is maintained in the population by strong balancing selection. For a given value of recombination, the expected squared linkage disequilibrium is shown to decrease as the intensity of selection maintaining the arrangement increases. The transient behavior of the expected square linkage disequilibrium is also derived. This theory applies to loci that are closely linked to inversions in Drosophila species and to loci closely linked to the differential segments of the translocation complexes in ring-forming species of Oenothera. In both cases the strong linkage disequilibria that have been observed in natural populations can be explained by random drift.

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