scholarly journals Analysis of linkage disequilibria between allozyme loci in natural populations of Drosophila melanogaster

1978 ◽  
Vol 32 (3) ◽  
pp. 215-229 ◽  
Author(s):  
Charles H. Langley ◽  
Diana B. Smith ◽  
F. M. Johnson
Keyword(s):  
Drosophila Melanogaster ◽  
Linkage Disequilibrium ◽  
Natural Population ◽  
Analysis Of Variance ◽  
Natural Populations ◽  
Correlation Coefficients ◽  
Absolute Value ◽  
Linkage Disequilibria ◽  
Enzyme Loci ◽  
Allozyme Loci

SUMMARYLinkage disequilibria between pairs of 8 polymorphic enzyme loci (αGpdh, Mdh, Adh, Est-6, Pgm, Odh, Est-C and Acph) in some 100 natural population samples of Drosophila melanogaster were examined. The estimates of linkage disequilibrium were made from zygotic frequencies. The magnitude of linkage disequilibria are small and similar to those in previous reports. Variation in linkage disequilibrium among related subpopulations was analysed by analysis of variance of the correlation coefficients. Despite the small absolute value of linkage disequilibrium there is a suggestion of a correlation among related subpopulations. The magnitude of linkage disequilibrium was observed to be positively correlated with linkage. Two cage populations were observed to demonstrate large amounts of linkage disequilibrium between closely linked loci in contrast to the situation in natural populations. This is attributable to the finite sizes of these cage populations.

scholarly journals LINKAGE DISEQUILIBRIUM IN NATURAL POPULATIONS OF DROSOPHILA MELANOGASTER. SEASONAL VARIATION

Genetics ◽  
1977 ◽  
Vol 86 (2) ◽  
pp. 447-454
Author(s):  
Charles H Langley ◽  
Kazuko Ito ◽  
Robert A Voelker
Keyword(s):  
Drosophila Melanogaster ◽  
Seasonal Variation ◽  
Linkage Disequilibrium ◽  
Natural Population ◽  
Natural Populations ◽  
The Other ◽  
Allozyme Loci

ABSTRACT Linkage disequilibrium among ten polymorphic allozyme loci and polymorphic inversions on chromosomes 2 and 3 in a natural population of Drosophila melanogaster was examined early and late in the annual season. Similar to previous studies, little linkage disequilibrium was observed among allozymes. The two significant cases that were observed in the first sample behaved in a contradictory way. One declined much more rapidly than expected due simply to recombination; the other declined slowly as expected. There was little change in allozyme or inversion frequencies during the season.

scholarly journals LINKAGE DISEQUILIBRIUM IN NATURAL POPULATIONS OF DROSOPHILA MELANOGASTER

Genetics ◽  
1974 ◽  
Vol 78 (3) ◽  
pp. 921-936
Author(s):  
Charles H Langley ◽  
Yoshiko N Tobari ◽  
Ken-Ichi Kojima
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
Natural Populations ◽  
Chromosomal Gene ◽  
Gene Frequencies ◽  
Linkage Disequilibria ◽  
Allozyme Loci ◽  
Two Populations ◽  
Stable Populations

ABSTRACT Two large, stable populations (Texas and Japan) of Drosophila melanogaster were surveyed at 21 allozyme loci on the second and third chromosomes and for chromosomal gene arrangements on those two chromosomes. Over 220 independent gametes were sampled from each population. The types and frequencies of the surveyed genetic variation are similar to those observed previously and suggest only slight differentiation among geographically distant populations. Linkage disequilibrium among linked allozymes loci is only slightly, if at all, detectable with these sample sizes. Linkage disequilibrium between linked inversions and allozymes loci is common especially when located in the same arm. These disequilibria appear to be in the same direction for most comparisons in the two population samples. This result is interpreted as evidence of similar selective environments (ecological and genetic) in the two populations. It is also noted that the direction of these linkage disequilibria appears to be oriented with respect to the gene frequencies at the component loci.

scholarly journals Extensive linkage disequilibrium in the achaete-scute complex of Drosophila melanogaster.

Genetics ◽  
1990 ◽  
Vol 126 (1) ◽  
pp. 121-129
Author(s):  
J N Macpherson ◽  
B S Weir ◽  
A J Leigh Brown
Keyword(s):  
Drosophila Melanogaster ◽  
Linkage Disequilibrium ◽  
Natural Population ◽  
Nucleotide Diversity ◽  
Single Site ◽  
Restriction Map ◽  
X Chromosomes ◽  
Linkage Disequilibria ◽  
Restriction Sites ◽  
Gametic Association

Abstract We have analyzed the level of gametic association between restriction map variants in a sample of 44 X chromosomes from a natural population of Drosophila melanogaster. Of 21 pairwise tests involving 7 restriction map polymorphisms in the yellow-achaete-scute complex, 17 were found to be significant, including some between restriction sites over 80 kb apart. Three-way linkage disequilibria and their variances were also estimated for all 35 three-way comparisons between these loci. Twelve such tests were found to be significant, again spanning distances of up to 80 kb on the restriction map. Only 9 of a possible 128 haplotypes were represented in the sample and 8 of these could be linked together by changes at a single site. The strength of these associations at y-ac-sc is unusual by comparison with studies on other regions of the genome of D. melanogaster, and is consistent with the very low level of recombination which has been reported for the complex. However, our estimate of nucleotide diversity in the region is not significantly different from those made for some other loci in this species.

scholarly journals THE GENETIC STRUCTURE OF NATURAL POPULATIONS OF DROSOPHILA MELANOGASTER XIII. FURTHER STUDIES ON LINKAGE DISEQUILIBRIUM

Genetics ◽  
1977 ◽  
Vol 86 (1) ◽  
pp. 175-185
Author(s):  
Terumi Mukai ◽  
Robert A Voelker
Keyword(s):  
Drosophila Melanogaster ◽  
Linkage Disequilibrium ◽  
Natural Populations ◽  
Linkage Disequilibria ◽  
Two Factors ◽  
Carolina Population ◽  
Recombination Value ◽  
Significant Linkage ◽  
Octanol Dehydrogenase ◽  
Double Crossovers

ABSTRACT The Raleigh, North Carolina, population of Drosophila melanogaster was examined for linkage disequilibrium in 1974, several years after previous analyses in 1968, 1969, and 1970. αglycerol-3-phosphate dehydrogenase-1 (αGpdh-1), malate dehydrogenase-1 (Mdh-1), alcohol dehydrogenase (Adh), and hexokinase-C (Hex-C, tentative name, F. M. Johnson, unpublished; position determined by the present authors to be 2-74.5) were assayed for 617 second chromosomes, and esterase-C (Est-C) and octanol dehydrogenase (Odh) were assayed for 526 third chromosomes. In addition, two polymorphic inversions in the second chromosomes [In(2L)t and In(2R)NS] were examined, and the following findings were obtained: (1) No linkage disequilibrium between isozyme genes was detected. Significant linkage disequilibria were found only between the polymorphic inversions and isozyme genes [In(2L)t vs. Adh, and In(2R)NS vs. Hex-C]. Significant disequilibrium was not detected between In(2L)t and αGpdh-1, which is included in the inversion, but a tendency toward disequilibrium was consistently found from 1968 to 1974. The frequency of two-strand double crossovers within inversion In(2L)t involving a single crossover on each side of αGpdh-1 was estimated to be 0.00022. Thus, the consistent but not significant linkage disequilibrium between the two factors can be explained by recombination after the inversion occurred. (2) Previously existing linkage disequilibrium between Adh and In(2R)NS (the distance is about 30 cM, but the effective recombination value is about 1.75%) was found to have disappeared. (3) No higher-order linkage disequilibrium was detected. (4) Linkage disequilibrium between Odh and Est-C (the distance of which was estimated to be 0.0058 ± 0.002) could not be detected (χ2  df=1 = 0.9).—From the above results, it was concluded that linkage disequilibria among isozyme genes are very rare in D. melanogaster, so that the Franklin-Lewontin model (Franklin and Lewontin 1970) is not applicable to these genes. The linkage disequilibria between some isozyme genes and polymorphic inversions may be explained by founder effect.

scholarly journals GENETIC LOAD IN NATURAL POPULATIONS: IS IT COMPATIBLE WITH THE HYPOTHESIS THAT MANY POLYMORPHISMS ARE MAINTAINED BY NATURAL SELECTION?

Genetics ◽  
1974 ◽  
Vol 77 (3) ◽  
pp. 569-589
Author(s):  
Martin L Tracey ◽  
Francisco J Ayala
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Selection ◽  
Natural Population ◽  
Natural Populations ◽  
Genetic Load ◽  
Structural Genes ◽  
Invertebrate Species ◽  
Average Proportion ◽  
Mean Fitness ◽  
The Mean

ABSTRACT Recent studies of genetically controlled enzyme variation lead to an estimation that at least 30 to 60% of the structural genes are polymorphic in natural populations of many vertebrate and invertebrate species. Some authors have argued that a substantial proportion of these polymorphisms cannot be maintained by natural selection because this would result in an unbearable genetic load. If many polymorphisms are maintained by heterotic natural selection, individuals with much greater than average proportion of homozygous loci should have very low fitness. We have measured in Drosophila melanogaster the fitness of flies homozygous for a complete chromosome relative to normal wild flies. A total of 37 chromosomes from a natural population have been tested using 92 experimental populations. The mean fitness of homozygous flies is 0.12 for second chromosomes, and 0.13 for third chromosomes. These estimates are compatible with the hypothesis that many (more than one thousand) loci are maintained by heterotic selection in natural populations of D. melanogaster.

scholarly journals Joint Linkage and Linkage Disequilibrium Mapping in Natural Populations

Genetics ◽  
2001 ◽  
Vol 157 (2) ◽  
pp. 899-909
Author(s):  
Rongling Wu ◽  
Zhao-Bang Zeng
Keyword(s):  
Linkage Disequilibrium ◽  
Complex Traits ◽  
Positional Cloning ◽  
Genome Structure ◽  
Natural Populations ◽  
Linkage Disequilibrium Mapping ◽  
Linkage Disequilibria ◽  
Time Simulation ◽  
New Strategy ◽  
Fisher Scoring Algorithm

Abstract A new strategy for studying the genome structure and organization of natural populations is proposed on the basis of a combined analysis of linkage and linkage disequilibrium using known polymorphic markers. This strategy exploits a random sample drawn from a panmictic natural population and the open-pollinated progeny of the sample. It is established on the principle of gene transmission from the parental to progeny generation during which the linkage between different markers is broken down due to meiotic recombination. The strategy has power to simultaneously capture the information about the linkage of the markers (as measured by recombination fraction) and the degree of their linkage disequilibrium created at a historic time. Simulation studies indicate that the statistical method implemented by the Fisher-scoring algorithm can provide accurate and precise estimates for the allele frequencies, recombination fractions, and linkage disequilibria between different markers. The strategy has great implications for constructing a dense linkage disequilibrium map that can facilitate the identification and positional cloning of the genes underlying both simple and complex traits.

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.

HORDEIN VARIATION IN WILD (HORDEUM SPONTANEUM) AND CULTIVATED (H. VULGARE) BARLEY

1979 ◽  
Vol 21 (3) ◽  
pp. 391-404 ◽  
Author(s):  
Hans Doll ◽  
A. H. D. Brown
Keyword(s):  
Linkage Disequilibrium ◽  
Wild Species ◽  
Storage Protein ◽  
Natural Populations ◽  
Hordeum Spontaneum ◽  
Allele Frequencies ◽  
Evolutionary Processes ◽  
Highly Correlated ◽  
The Individual ◽  
Allozyme Loci

The storage protein hordein contains two major groups of polypeptides which are highly polymorphic in barley, and in its evolutionary progenitor Hordeum spontaneum Koch. Crosses between the two species showed that the complex electrophoretic phenotypes within the two groups of polypeptides are governed by codominant alleles at two corresponding loci, Hor-1 and Hor-2, which are moderately linked (11% ± 2). In natural populations of the wild species, the two complex hordein loci were much more polymorphic than the allozyme loci. Furthermore, the variation at these two loci was highly correlated so that individuals differ from one another at both loci much more frequently than expected from the allele frequencies at the individual loci. Considerable hordein variation was also present in Composite Cross XXI, and there was evidence of reassortment of patterns by the seventeenth generation. Thus the complex hordein loci, with their extreme diversity and linkage disequilibrium, are ideal markers for monitoring evolutionary processes in both natural, or composite cross populations.

scholarly journals GENETIC ANALYSIS OF NATURAL POPULATIONS OF DROSOPHILA MELANOGASTER IN JAPAN. II. THE MEASUREMENT OF FITNESS AND FITNESS COMPONENTS IN HOMOZYGOUS LINES

Genetics ◽  
1984 ◽  
Vol 108 (1) ◽  
pp. 213-221 ◽  
Author(s):  
Tsuneyuki Yamazaki ◽  
Yasuko Hirose
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Analysis ◽  
Natural Population ◽  
Natural Populations ◽  
Distribution Patterns ◽  
Developmental Time ◽  
Fitness Components ◽  
Isogenic Lines ◽  
Genetic Structures

ABSTRACT Fifty lethal-free, sterility-free isogenic lines of Drosophila melanogaster that were randomly sampled from a natural population were tested for net fitness and other components of fitness by competition with D. hydei. Larval viability and developmental time were also measured using the balanced marker method. Distribution patterns of these fitness components were similar, but correlation between the fitness components varied depending on the combinations used. The highest correlations were obtained between net fitness and productivity (rp = 0.6987, rg = 0.9269). The correlation between net fitness and total larval viability was much lower (rp = 0.1473 and rg = 0.2171). These results indicate that measuring net fitness, not just a component of fitness, is necessary for the good understanding of the genetic structures of natural populations.

scholarly journals THE EFFECT OF COMBINING ALLELES INTO ELECTROPHORETIC CLASSES ON DETECTING LINKAGE DISEQUILIBRIUM

Genetics ◽  
1977 ◽  
Vol 85 (3) ◽  
pp. 543-556
Author(s):  
E Zouros ◽  
G B Golding ◽  
Trudy F C MacKay
Keyword(s):  
Linkage Disequilibrium ◽  
Sample Size ◽  
Natural Populations ◽  
Epistatic Interactions ◽  
Detection Power ◽  
Linkage Disequilibria ◽  
Allelic Distribution ◽  
Order Of Magnitude ◽  
Actual Degree

ABSTRACT When alleles are combined into few detectable classes, linkage correlations are underestimated most of the time. The probability that the linkage correlation will be underestimated is a function of the actual degree of correlation and the evenness of the allelic distribution, but is mainly determined by the distribution of alleles into distinguishable classes. With only two alleles per class this probability will usually be higher than 0.7. Also, the consistency in the sign of the linkage disequilibrium over many populations may escape detection. An increase of sample size by one order of magnitude or more may be required to compensate for the loss in detection power. It follows that the available electrophoretic studies of linkage correlations, although negative in their majority, do not suggest that epistatic interactions and linkage disequilibria are rare in natural populations.

Sign in / Sign up

Export Citation Format

Share Document