scholarly journals 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 ◽  
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.

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

Genetics ◽  
1992 ◽  
Vol 130 (4) ◽  
pp. 805-816 ◽  
Author(s):  
J M Martín-Campos ◽  
J M Comerón ◽  
N Miyashita ◽  
M Aguadé
Keyword(s):  
Drosophila Melanogaster ◽  
X Chromosome ◽  
Length Polymorphism ◽  
Restriction Site ◽  
Natural Populations ◽  
Restriction Enzymes ◽  
Drosophila Simulans ◽  
Population Subdivision ◽  
Telomeric Region ◽  
Length Variation

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.

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 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.

Ribosomal DNA variation in the grasshopper, Dichroplus elongatus

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1125-1133 ◽  
Author(s):  
M Clemente ◽  
M I Remis ◽  
J C Vilardi
Keyword(s):  
Ribosomal Dna ◽  
Fragment Size ◽  
Natural Populations ◽  
Size Variation ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Genetic Distances ◽  
Climatic Variables ◽  
Dna Variation ◽  
And Migration

We report an RFLP analysis of ribosomal DNA variation in natural populations of the grasshopper, Dichroplus elongatus, previously analyzed for mitochondrial DNA variation. DNA samples were digested with five restriction enzymes, BamHI, EcoRI, HindIII, PstI, andXbaI.BamHI was the only enzyme that showed no variation. The remaining enzymes showed fragment size variation at both intra- and interpopulation levels. Stepwise regression analysis revealed that the average number of length variants per individual is significantly associated with altitude. Moreover, the same analysis indicated that the frequency of some restriction variants exhibits a significant regression on both geographic and climatic variables. The intra- and interpopulation variability of rDNA was analysed by Lynch's and Hedrick's similarity indices using presence or absence of a fragment and band intensities, respectively. The corresponding neighbour-joining (N-J) trees based on Lynch's and Hedrick's genetic distances resulted in similar topologies. However, these trees were not in agreement with the N-J dendrogram obtained from mtDNA data previously reported by Clemente et al. (2000). The disagreement between mtDNA and rDNA phenograms along with the observed correlation between rDNA variability and geographical and climatic variables suggest some form of selection, besides genetic drift and migration, is involved in the pattern of rDNA variation.Key words: Dichroplus elongatus, ribosomal DNA, RFLP, environmental variables.

scholarly journals Drosophila melanogaster mitochondrial DNA: gene organization and evolutionary considerations.

Genetics ◽  
1988 ◽  
Vol 118 (4) ◽  
pp. 649-663
Author(s):  
R Garesse
Keyword(s):  
Mitochondrial Dna ◽  
Drosophila Melanogaster ◽  
Mitochondrial Genome ◽  
Gene Organization ◽  
Coding Region ◽  
Similar Frequency ◽  
Predominant Type ◽  
Drosophila Yakuba ◽  
Very High ◽  
Type Of Transition

Abstract The sequence of a 8351-nucleotide mitochondrial DNA (mtDNA) fragment has been obtained extending the knowledge of the Drosophila melanogaster mitochondrial genome to 90% of its coding region. The sequence encodes seven polypeptides, 12 tRNAs and the 3' end of the 16S rRNA and CO III genes. The gene organization is strictly conserved with respect to the Drosophila yakuba mitochondrial genome, and different from that found in mammals and Xenopus. The high A + T content of D. melanogaster mitochondrial DNA is reflected in a reiterative codon usage, with more than 90% of the codons ending in T or A, G + C rich codons being practically absent. The average level of homology between the D. melanogaster and D. yakuba sequences is very high (roughly 94%), although insertion and deletions have been detected in protein, tRNA and large ribosomal genes. The analysis of nucleotide changes reveals a similar frequency for transitions and transversions, and reflects a strong bias against G + C on both strands. The predominant type of transition is strand specific.

scholarly journals Recombination can initiate and terminate at a large number of sites within the rosy locus of Drosophila melanogaster.

Genetics ◽  
1988 ◽  
Vol 118 (2) ◽  
pp. 261-266
Author(s):  
S H Clark ◽  
A J Hilliker ◽  
A Chovnick
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Markers ◽  
Restriction Site ◽  
Intragenic Recombination ◽  
Dna Homology ◽  
Coding Region ◽  
Heterozygous Genotype ◽  
Order Of Magnitude ◽  
Dna Restriction ◽  
Restriction Site Polymorphisms

Abstract This report presents the results of a recombination experiment designed to question the existence of special sites for the initiation or termination of a recombination heteroduplex within the region of the rosy locus. Intragenic recombination events were monitored between two physically separated rosy mutant alleles ry301 and ry2 utilizing DNA restriction site polymorphisms as genetic markers. Both ry301 and ry2 are known from previous studies to be associated with gene conversion frequencies an order of magnitude lower than single site mutations. The mutations are associated with large, well defined insertions located as internal sites within the locus in prior intragenic mapping studies. On the molecular map, they represent large insertions approximately 2.7 kb apart in the second and third exons, respectively, of the XDH coding region. The present study monitors intragenic recombination in a mutant heterozygous genotype in which DNA homology is disrupted by these large discontinuities, greater than the region of DNA homology and flanking both sides of the locus. If initiation/or termination requires separate sites at either end of the locus, then intragenic recombination within the rosy locus of the heterozygote should be eliminated. Contrary to expectation, significant recombination between these sites is seen.

scholarly journals POLYMORPHIC SITES AND THE MECHANISM OF EVOLUTION IN HUMAN MITOCHONDRIAL DNA

Genetics ◽  
1984 ◽  
Vol 106 (3) ◽  
pp. 479-499
Author(s):  
Rebecca L Cann ◽  
Wesley M Brown ◽  
Allan C Wilson
Keyword(s):  
Mitochondrial Dna ◽  
Ribosomal Proteins ◽  
Restriction Site ◽  
Restriction Enzymes ◽  
Mitochondrial Genes ◽  
Rrna Genes ◽  
Exact Nature ◽  
Sequence Comparisons ◽  
Functional Regions ◽  
Mtdna Sequence

ABSTRACT Twelve restriction enzymes were used to screen for the presence or absence of cleavage sites at 441 locations in the mitochondrial DNA of 112 humans from four continents. Cleavage maps were constructed by comparison of DNA fragment sizes with those expected from the published sequence for one human mtDNA. One hundred and sixty-three of the sites were polymorphic, i.e., present in some individuals but absent from others, 278 sites being invariant. These polymorphisms probably result from single base substitutions and occur in all functional regions of the genome.—In 77 cases, it was possible to specify the exact nature and location (within a restriction site) of the mutation responsible for the absence of a restriction site in a known human mtDNA sequence and its presence in another human mtDNA. Fifty-two of these 77 gain mutations occur in genes coding for proteins, 34 being silent and 18 causing amino acid replacements; moreover, nine of the replacements are radical.—Notable also is the anomalous ratio of transitions to transversions required to account for these 77 restriction site differences between the known human mtDNA sequences and other human mtDNAs. This ratio is lower for most groups of restriction sites than has been reported from sequence comparisons of limited parts of the mtDNA genome in closely related mammals, perhaps indicating a special functional role or sensitivity to mutagenesis for palindromic regions containing high levels of guanine and cytosine.—From the genomic distribution of the 163 polymorphic sites, it is inferred that the level of point mutational variability in tRNA and rRNA genes is nearly as high as in protein-coding genes but lower than in noncoding mtDNA. Thus, the functional constraints operating on components of the protein-synthetic apparatus may be lower for mitochondria than for other systems. Furthermore, the mitochondrial genes for tRNAs that recognize four codons are more variable than those recognizing only two codons.—Among the more variable of the human mitochondrial genes coding for proteins is that for subunit 2 of cytochrome oxidase; this polypeptide appears to have been evolving about five times faster in primates than in other mammals. Cytochrome c, a nuclearly encoded protein that interacts directly with the oxidase 2 subunit in electron transport, has also evolved faster in primates than in rodents or ungulates. This example, along with that for the mitochondrial rRNA genes and the nuclear genes coding for mitochondrial ribosomal proteins, provides evidence for coevolution between specific nuclear and mitochondrial genes.

scholarly journals Linkage disequilibrium in the white locus region of Drosophila melanogaster

1993 ◽  
Vol 62 (2) ◽  
pp. 101-109 ◽  
Author(s):  
Naohiko T. Miyashita ◽  
Montserrat Aguadé ◽  
Charles H. Langley
Keyword(s):  
Drosophila Melanogaster ◽  
Linkage Disequilibrium ◽  
Natural Populations ◽  
Restriction Enzymes ◽  
Transcriptional Unit ◽  
Similar Degree ◽  
Significant Linkage Disequilibrium ◽  
White Locus ◽  
Different Populations ◽  
Significant Linkage

SummaryLinkage disequilibrium between molecular polymorphisms in a 10 kb region in the white locus of Drosophila melanogaster, revealed with a battery of four-cutter restriction enzymes, was investigated in 266 lines sampled from seven natural populations around the world. A total of 73 (35 restriction site, 37 insertion/deletion and 1 inversion) polymorphisms were detected, of which 55 non-unique polymorphisms were analysed for linkage disequilibrium. Clustering of significant linkage disequilibrium was observed in the transcriptional unit of the white locus as in Miyashita & Langley (1988). It was shown that about two thirds of the 2-locus combinations showing significant linkage disequilibrium have similar degree and direction of association over different populations. Despite lower divergence in allelic frequencies of molecular polymorphisms among populations, an increase in the proportion of 2-locus pairs showing significant linkage disequilibrium is observed in the transcriptional unit. Large values of Ohta's D measure ratio (1982 a, b) cluster in the transcriptional unit, and correspond to significant linkage disequilibria. Although the exact molecular mechanism is not clear, these results suggest that epistatic selection is responsible for significant linkage disequilibrium in the transcriptional unit of this locus

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