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1.
E. D. Özsoy 《Russian Journal of Genetics》2007,43(2):132-135
Small number of Drosophila melanogaster populations from two distinct geographical regions of Turkey, Central Anatolia and Black Sea, were studied. Populations sampled
were electrophoresed for a single locus, alcohol dehydrogenase (Adh) to assess population differentiation. Both the magnitude of genetic differentiation levels and the population structure
based on hierarchical F-statistics allow populations to be grouped on two genetically divergent area, Central Anatolian and Black Sea. One ecological
correlate, average yearly maximum rainfall, R
year, seems to track this Adh genetic variation pattern. The study also shows that a typical pattern of geographical Adh polymorphism can emerge with a handfull of populations sampled across a relatively small distance.
The text was submitted by the author in English. 相似文献
2.
Recent work has shown that Drosophila melanogaster genes with fast-evolving nonsynonymous sites have lower codon usage bias. This pattern has been attributed to interference between positive selection at nonsynonymous sites and weak selection on codon usage. Here we have looked for this correlation in a much larger and less biased dataset, comprising 630 gene pairs from D. melanogaster and D. yakuba. We confirmed that there is a negative correlation between the rate of nonsynonymous substitutions (dN) and codon bias in D. melanogaster. We then tested the interference hypothesis and other alternative explanations, including one involving gene expression. We found that dN indeed correlates with the level of gene expression. Given that gene expression is a strong determinant of codon bias, the relationship between dN and codon bias might be a by-product of gene expression. However, our tests show that none of the hypotheses we consider seem to explain the data fully.This article contains online supplementary material.Reviewing Editor: Dr. John Huelsenbeck 相似文献
3.
Soon-Jae Kwon Kyong-Cheul Park Jae-Han Son Thomas Bureau Cheul-Ho Park Nam-Soo Kim 《Molecules and cells》2009,27(4):459-465
MUG1 is a MULE transposon-related domesticated gene in plants. We assessed the sequence diversity, neutrality, expression, and
phylogenetics of the MUG1 gene among Oryza ssp. We found MUG1 expression in all tissues analyzed, with different levels in O. sativa. There were 408 variation sites in the 3886 bp of MUG1 locus. The nucleotide diversity of the MUG1 was higher than functionally known genes in rice. The nucleotide diversity (π) in the domains was lower than the average
nucleotide diversity in whole coding region. The π values in nonsynonymous sites were lower than those of synonymous sites.
Tajima D and Fu and Li D* values were mostly negative values, suggesting purifying selection in MUG1 sequences of Oryza ssp. Genome-specific variation and phylogenetic analyses show a general grouping of MUG1 sequences congruent with Oryza ssp. biogeography; however, our MUG1 phylogenetic results, in combination with separate B and D genome studies, might suggest an early divergence of the Oryza ssp. by continental drift of Gondwanaland. O. longistaminata MUG1 divergence from other AA diploids suggests that it might not be a direct ancestor of the African rice species.
These authors contributed equally to this work. 相似文献
4.
An understanding of the variation pattern in disease resistance (R) genes is essential for its use in breeding programs aimed at neutralizing the threat of pathogens. Although the variation
between populations is well known, there is little research about R-gene variation patterns within populations. Here, we investigate the polymorphism at three R-gene loci of 39 individual plants from nine populations of Arabidopsis thaliana. Our data suggest that alleles of each locus from individuals within a local population were either nearly identical, or
highly diverse as ones between populations. The vast majority (92.5%) of within-population variation was shared globally,
with high levels of allelic diversity (up to 11.7%) and abundant diverse-alleles. This unique pattern of within-population
variation at R-loci suggests that individual plants within a population had the great potential to maintain a high level of globally-shared
polymorphisms, and that the diversifying selection was the major force maintaining such polymorphisms. Consequently, the shared-polymorphism
became recyclable for new R-genes, as the corresponding avirulence re-emerges in pathogen populations.
Nucleotide sequence data reported are available in the GenBank databases under the accession numbers EF368054-EF368158. 相似文献
5.
6.
Galium catalinense (Rubiaceae) is a perennial shrub consisting of two subspecies endemic to California’s Channel Islands: Galium catalinense subsp. catalinense on Santa Catalina Island, and G. catalinense subsp. acrispum, a state-endangered taxon on San Clemente Island. A long history of overgrazing by introduced herbivores has contributed
to population declines in G. catalinense subsp. acrispum. We surveyed 12 populations throughout the taxon’s range for genetic variation using eight polymorphic microsatellite loci
to determine the genetic impact of this demographic bottleneck. At the taxon level, 65 alleles were identified with an average
of 8.1 alleles per locus, although many alleles were rare; the effective number of alleles per locus averaged 2.6. Expected
heterozygosity was 0.550. Individual populations had between six and eight polymorphic loci, with expected heterozygosities
ranging from 0.36 to 0.60, and effective numbers of alleles ranging from 1.8 to 3.5 per locus. Populations fell into three
or four genetic clusters, depending on type of analysis, which may represent refugia where the populations persisted during
intense herbivory. There is little evidence of genetic bottlenecks or substantial inbreeding within populations. These findings,
coupled with indications of recent migration between populations, suggest that G. catalinense subsp. acrispum is currently unlikely to be endangered by genetic factors, but small population sizes make the taxon vulnerable to future
loss of genetic diversity. Management strategies based on these genetic data, population sizes, and the spatial distribution
of populations are discussed. 相似文献
7.
Yoshida K Miyashita NT Ishii T 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2004,109(7):1406-1416
Nucleotide variation in the alcohol dehydrogenase (Adh1) locus region of the wild rice Oryza rufipogon and its related species was analysed to clarify the maintenance mechanism of DNA variation in Oryza species. The estimated nucleotide diversity in the Adh1 locus region of O. rufipogon was 0.002, which was one of the lowest values detected in nuclear loci of plant species investigated so far. Tests of neutrality detected significantly negative deviation from the neutral mutation model for the coding region, especially for replacement sites. When each of the ADH1 domains was considered, significance was detected only for the catalytic domain 1. These results suggest purifying selection in the Adh1 coding region. In the phylogenetic tree of Oryza species based on Adh1 variation, cultivated rice O. sativa subspp. japonica and indica were included in the cluster of O. rufipogon. The genetic distance of the Adh1 region between O. rufipogon and O. sativa was as low as the nucleotide diversity of O. rufipogon. These results imply that O. rufipogon and O. sativa cannot be classified based on the nucleotide variation of Adh1. No replacement divergence between O. rufipogon and the other three A-genome species (O. glumaepatula, O. barthii and O. meridionalis) were detected, indicating that ADH1 is conserved in the A-genome species. On the other hand, between O. rufipogon and the E-genome species O. australiensis, replacement changes were detected only in the catalytic domain 1. The difference in replacement substitutions between the A- and E-genome species may be related to adaptive changes in the ADH1 domains, reflecting environmental differences where the species encounter anaerobic stress. 相似文献
8.
The evolution and patterns of selection of genes encoding 10 Drosophila odorant receptors (Or) and the sex pheromone receptor Gr68a were investigated by comparing orthologous sequences across five
to eight ecologically diverse species of Drosophila. Using maximum likelihood estimates of dN/dS ratios we show that all 11 genes sampled are under purifying selection, indicating
functional constraint. Four of these genes (Or33c, Or42a, Or85e, and Gr68a) may be under positive selection, and if so, there is good evidence that 12 specific amino acid sites may be under positive
selection. All of these sites are predicted to be located either in loop regions or just inside membrane spanning regions,
and interestingly one of the two sites in Gr68a is in a similar position to a previously described polymorphism in Gr5a that causes a shift in sensitivity to its ligand trehalose. For three Ors, possible evidence for positive selection was detected along a lineage. These include Or22a in the lineage leading to D. mauritiana and Or22b in the lineage leading to D. simulans. This is of interest in light of previous data showing a change in ligand response profile for these species in the sensory
neuron (ab3A) which expresses both Or22a and Or22b in D. melanogaster. In summary, while the main chemosensory function and/or structural integrity of these 10 Or genes and Gr68a are evolutionarily preserved, positive selection appears to be acting on some of these genes, at specific sites and along
certain lineages, and provides testable hypotheses for further functional experimentation.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
[Reviewing Editor: Dr. David Pollock] 相似文献
9.
Matthieu F Faure Patrice David François Bonhomme Nicolas Bierne 《BMC evolutionary biology》2008,8(1):164
Background
Few models of genetic hitchhiking in subdivided populations have been developed and the rarity of empirical examples is even more striking. We here provide evidences of genetic hitchhiking in a subdivided population of the marine mussel Mytilus edulis. In the Bay of Biscay (France), a patch of M. edulis populations happens to be separated from its North Sea conspecifics by a wide region occupied only by the sister species M. galloprovincialis. Although genetic differentiation between the two M. edulis regions is largely non-significant at ten marker loci (average FST~0.007), a strong genetic differentiation is observed at a single locus (FST = 0.25). We validated the outlier status of this locus, and analysed DNA sequence polymorphism in order to identify the nature of the selection responsible for the unusual differentiation. 相似文献10.
The Alhambra ( Alh) gene is the Drosophila homologue of the human AF10 gene. AF10 has been identified as a fusion partner of MLL, a human homologue of the fly gene trithorax, in infant leukemias. The endogenous function of human AF10 is not known, but may be vital to its role in acute leukemia. This prompted us to analyse Alh function. We describe here the genetic organisation of the Alh locus in D. melanogaster. We show that an independent lethal complementation group encoding a muscle protein ( Mlp84B) is located within an Alh intron. We have already shown that the leucine zipper (LZ) domain of ALH activates several Polycomb group-responsive elements. We further demonstrate that the LZ domain on its own bears the Alh vital function, since it is necessary and sufficient for rescue of Alh mutant lethality. Finally, we demonstrate that, in contrast to a previous report, Alh does not affect position-effect variegation.Communicated by G. Reuter 相似文献
11.
James D. Fry 《Journal of genetics》2008,87(4):355-362
A fundamental assumption of models for the maintenance of genetic variation by environmental heterogeneity is that selection
favours different genotypes in different environments. Here, I use a method for measuring total fitness of chromosomal heterozygotes
in Drosophila melanogaster to assess genotype-environment interaction for fitness across two ecologically relevant environments, medium with and without
added ethanol. Two-third chromosomes are compared, one from a population selected for ethanol tolerance, and the other from
a control population. The results show strong crossing of reaction norms for outbred, total fitness, with the chromosome from
the ethanol-adapted population increasing fitness on ethanol-supplemented food, but decreasing fitness on regular food, relative
to the chromosome from the control population. Although I did not map the fitness effects below the chromosome level, the
method could be adapted for quantitative trait locus mapping, to determine whether a substantial proportion of fitness variation
is contributed by loci at which different alleles are favoured in different environments. 相似文献
12.
Sophie Marion de Procé Daniel L. Halligan Peter D. Keightley Brian Charlesworth 《Journal of molecular evolution》2009,69(6):601-611
Contrary to the classical view, a large amount of non-coding DNA seems to be selectively constrained in Drosophila and other
species. Here, using Drosophila miranda BAC sequences and the Drosophila pseudoobscura genome sequence, we aligned coding and non-coding sequences between D. pseudoobscura and D. miranda, and investigated their patterns of evolution. We found two patterns that have previously been observed in comparisons between
Drosophila melanogaster and its relatives. First, there is a negative correlation between intron divergence and intron length, suggesting that longer
non-coding sequences may contain more regulatory elements than shorter sequences. Our other main finding is a negative correlation
between the rate of non-synonymous substitutions (d
N) and codon usage bias (F
op), showing that fast-evolving genes have a lower codon usage bias, consistent with strong positive selection interfering with
weak selection for codon usage. 相似文献
13.
Stefanie Kimbacher Ingrid Gerstl Branko Velimirov Sylvia Hagemann 《Molecular genetics and genomics : MGG》2009,282(2):165-172
P transposons belong to the eukaryotic DNA transposons, which are transposed by a cut and paste mechanism using a P-element-coded transposase. They have been detected in Drosophila, and reside as single copies and stable homologous sequences in many vertebrate species. We present the P elements Pcin1, Pcin2 and Pcin3 from Ciona intestinalis, a species of the most primitive chordates, and compare them with those from Ciona savignyi. They showed typical DNA transposon structures, namely terminal inverted repeats and target site duplications. The coding
region of Pcin1 consisted of 13 small exons that could be translated into a P-transposon-homologous protein. C. intestinalis and C. savignyi displayed nearly the same phenotype. However, their P elements were highly divergent and the assumed P transposase from C. intestinalis was more closely related to the transposase from Drosophila melanogaster than to the transposase of C. savignyi. The present study showed that P elements with typical features of transposable DNA elements may be found already at the base of the chordate lineage.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
14.
We studied the population genetics of two antimicrobial peptide (AMP) loci, called Mytilin B and Mytilus galloprovincialis defensin 2 (MGD2), in the secondary contact mosaic hybrid zone between Mytilus edulis and M. galloprovincialis. The isolation period between the two species was estimated to be ~1 million years (range, 0.5 million to 2 million years)
long. During this period, coevolution between microbes and the immune system has likely occurred. The secondary contact, which
would date back to ~25,000 (0–200,000) years, recently allowed these coadaptations to be rearranged through hybridization.
Distinctive polymorphisms were uncovered in coding sequences of the two AMP loci such as insertion/deletion of codons or bisubstituted
codons. Very low levels of differentiation were observed between populations of the two species at both loci, while other
nuclear loci often showed marked structure among the same samples. The absence of population differentiation proved to be
the consequence of secondary introgression of highly divergent alleles. While only a few recombinants were observed at the
Mytilin B locus, the MGD2 locus showed a high intragenic recombination rate, which increased in the exon coding for the mature peptide. In addition,
standard neutrality tests revealed significant deviations from the mutation-drift equilibrium at both loci. These results
suggest that either balancing or directional selection is likely to play a role in the evolution of the two AMPs and introgression
would be adaptive. However, evidence accumulated at the Mytilin B locus allows neither for identification of the direction of selection nor for any conclusions on whether selection acted
directly on the antimicrobial peptide itself. At the MGD2 locus, a spatial variation of polymorphism patterns along the sequence suggests that selection was direct, although the precise
nature of the selection (directional vs. balancing) remains unclear. This study concurs with previous reports of an effect
of slight selection on AMP genes evolution in other invertebrates, although selection does not necessarily act on the mature
peptides.
E. Boon and M. F. Faure contributed equally to this work. 相似文献
15.
Polycomb group (PcG) proteins are required to maintain a stable repression of the homeotic genes during Drosophila development. Mutants in the PcG gene Supressor of zeste 12 (Su(z)12) exhibit strong homeotic transformations caused by widespread misexpression of several homeotic genes in embryos and larvae.
Su(z)12 has also been suggested to be involved in position effect variegation and in regulation of the white gene expression in combination with zeste. To elucidate whether SU(Z)12 has any such direct functions we investigated the binding pattern to polytene chromosomes and
compared the localization to other proteins. We found that SU(Z)12 binds to about 90 specific eukaryotic sites, however, not
the white locus. We also find staining at the chromocenter and the nucleolus. The binding along chromosome arms is mostly in interbands
and these sites correlate precisely with those of Enhancer-of-zeste and other components of the PRC2 silencing complex. This
implies that SU(Z)12 mainly exists in complex with PRC2. Comparisons with other PcG protein-binding patterns reveal extensive
overlap. However, SU(Z)12 binding sites and histone 3 trimethylated lysine 27 residues (3meK27 H3) do not correlate that well.
Still, we show that Su(z)12 is essential for tri-methylation of the lysine 27 residue of histone H3 in vivo, and that overexpression of SU(Z)12 in somatic
clones results in higher levels of histone methylation, indicating that SU(Z)12 is rate limiting for the enzymatic activity
of PRC2. In addition, we analyzed the binding pattern of Heterochromatin Protein 1 (HP1) and found that SU(Z)12 and HP1 do
not co-localize. 相似文献
16.
Prevalence of <Emphasis Type="Italic">Wolbachia</Emphasis> Infection in <Emphasis Type="Italic">Bemisia tabaci</Emphasis> 总被引:1,自引:0,他引:1
Wolbachia are obligate intracellular bacteria present in reproductive tissues of many arthropod species. It has been reported that
few silverleafing populations of Bemisia tabaci were positive for Wolbachia, whereas non-silverleafing populations were more likely infected with Wolbachia and all that infect B. tabaci are Wolbachia belonging to supergroup B. However, current detection methods were shown to be not sensitive enough to uncover all infections.
Herein, a protocol based on polymerase chain reaction–restriction fragment length polymorphism analysis of Wolbachia 16S ribosomal DNA is presented. A systematic survey for the prevalence of Wolbachia infection in natural populations of B. tabaci using this method revealed that (1) all populations of B. tabaci tested positive for Wolbachia and the overall infection rate reached 80.5% (293 positives in 364 tests); (2) both single infection and superinfection existed
within individual whiteflies tested; and (3) silverleafing populations of B. tabaci most likely harbored A Wolbachia as single infection, whereas non-silverleafing populations tend to carry B Wolbachia as superinfection. It is clear that the Wolbachia infection pattern is closely related to the genetic races of B. tabaci, and the infection frequencies are apparently much higher than those described previously. This study shows that detection
methods can significantly influence estimation of Wolbachia infection. It is supposed that Wolbachia may be acting as a biotic agent promoting rapid differentiation and speciation of B. tabaci. This is the most systematic survey of Wolbachia infection within B. tabaci. 相似文献
17.
Several predatory mites have been found in association with the coconut mite, Aceria guerreronis Keifer, in northeast Brazil. However, the latter still causes damage to coconut in that region. The objectives of this work
were to compare the frequencies of occurrence of Neoseiulus (Phytoseiidae) and Proctolaelaps (Melicharidae) species on standing and aborted coconuts in coastal Pernambuco State, northeast Brazil and to analyze their
possible limitations as control agents of the coconut mite, based on evaluations of the restrictions they may have to access
the microhabitat inhabited by the pest and their functional and reproductive responses to increasing densities of the latter.
Neoseiulus baraki (Athias-Henriot) was found mostly on standing coconuts whereas Proctolaelaps bickleyi (Bram) was found mostly on aborted coconuts. Measurements of the entrance to the microhabitat occupied by the coconut mite,
between the bracts and the subjacent fruit surface, showed that this different pattern of predator prevalence could be related
to predator sizes, although other environmental factors could not be disregarded. Progressively higher predation rate of N. baraki was observed up to an experimental density that corresponded to 1,200 coconut mites per fruit, which is close to the average
number determined in northeast Brazil, reducing slightly afterwards. Predation rate of P. bickleyi reduced consistently but slightly with increasing prey densities, but in absolute values, rates were always much higher than
determined for N. baraki. The excessively high killing capacity of P. bickleyi, probably related to its high feeding requirement, may be detrimental in terms of stability. In fact, such high requirement
for food suggests that P. bickleyi might not have a strong relation with the coconut mite and that the latter may not be its main food source under natural
conditions. It is concluded that body sizes of both predators and the exceedingly high feeding requirement of P. bickleyi may limit their performance as control agents of the coconut mite. 相似文献
18.
Gene expression variation in African and European populations of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>
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Background
Differences in levels of gene expression among individuals are an important source of phenotypic variation within populations. Recent microarray studies have revealed that expression variation is abundant in many species, including Drosophila melanogaster. However, previous expression surveys in this species generally focused on a small number of laboratory strains established from derived populations. Thus, these studies were not ideal for population genetic analyses. 相似文献19.
Eric P. Caragata Kathryn M. Real Myron P. Zalucki Elizabeth A. McGraw 《Symbiosis (Philadelphia, Pa.)》2011,54(1):55-60
Wolbachia pipientis is a commonly occurring endosymbiont with well-characterised effects on host reproductive biology associated with its infection
of the gonads. Wolbachia infections are also widespread in somatic tissues and consequently they have the potential to play a much broader role in
host biology. Recently, Wolbachia was shown to alter the locomotion of Drosophila melanogaster in response to food cues in the laboratory. To determine whether this laboratory-based phenotype might translate to real
differences for insects in the field, we performed a simple mark-release-recapture experiment with Wolbachia-infected D. melanogaster in a forested habitat. We demonstrate that infected flies are recaptured at twice the rate of uninfected flies, although
infection does not affect the distance traveled by those flies recaptured. The differences in recapture could be explained
by infection-induced changes in physiology or behavior. If generalizable, such changes may affect the interpretation of behavioral
studies for Wolbachia-infected insects and have potential implications for the dynamics of Wolbachia infections in natural populations, including situations where Wolbachia-infected insects are being released for biological control. 相似文献
20.
We have studied the molecular characteristics of the yellow locus (y; 1–0.0), which determines the body color of phenotypically wild-type and mutant alleles isolated in different years from geographically distant populations of Drosophila melanogaster. According to the Southern blot, data restriction maps of the yellow locus of all examined strains differ from one another, as well as from Oregon stock. FISH analysis shows that, in the neighborhood of the yellow locus in the X chromosome, neither P nor hobo elements are found in y1–775 stock, while only hobo is found in these region in y1–859 and y1–866 stocks, only the P element is found in y+sn849 stock, and both elements are found in y1–719 stock. Thus, all yellow mutants studied are of independent origin. Locus yellow located on the end of X chromosome (region 1A5–8 on the cytologic map) carries significantly more transposon than retrotransposon induced mutations compared to the white locus (region 3C2). It is possible that, at the ends of Drosophila melanogaster chromosomes, transposons are more active than retrotransposons. 相似文献