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Nucleotide sequence comparison of the rp49 gene region between Drosophila subobscura and D. melanogaster 总被引:5,自引:0,他引:5
A 1.6-kb fragment encompassing the rp49 gene, which codes for a ribosomal
protein, has been cloned and sequenced in Drosophila subobscura. The rp49
coding region has accumulated 46 nucleotide differences out of 402 bp since
D. subobscura diverged from D. melanogaster. Forty-three percent of the
effectively silent sites have changed since both species diverged. Both
silent and replacement differences are distributed at random between the
two exons of the gene. The frequency of silent differences in exons does
not differ from that observed in the 5' leader sequence and in the intron.
The frequency of silent differences in exon and intron sites is much
greater than the number of amino acid replacement differences. This
observation indicates strong purifying selection against amino acid
replacements.
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3.
The molecular evolution of the alcohol dehydrogenase and alcohol dehydrogenase-related genes in the Drosophila melanogaster species subgroup 总被引:5,自引:0,他引:5
The DNA sequences of the Adh genes of three members of the Drosophila
melanogaster species subgroup have been determined. This completes the Adh
sequences of the eight species of this subgroup. Two species, D. yakuba and
D. teissieri, possess processed Adh pseudogenes. In all of the species of
the subgroup, a gene of unknown function, Adhr, is located about 300 bp 3'
to Adh. Although this gene is experiencing a higher rate of synonymous
substitution than Adh, it is more constrained at the amino acid level.
Phylogenetic relationships between all eight members of the melanogaster
subgroup have been analyzed using a variety of methods. All analyses
suggested that the D. yakuba and D. teissieri pseudogenes have a single
common ancestor, rather than evolving independently in each species, and
that D. melanogaster is the sister species to D. simulans, D. sechellia,
and D. mauritiana. The evolutionary relationships of the latter three
species remain equivocal.
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4.
The evolutionary history of a region of DNA encompassing the Adh locus is studied by comparing patterns of variation in Drosophila melanogaster and its sibling species, D. simulans. An unexpectedly high level of silent polymorphism in the Adh coding region relative to the 5' and 3' flanking regions in D. melanogaster is revealed by a populational survey of restriction polymorphism using a four-cutter filter hybridization technique as well as by direct sequence comparisons. In both of these studies, a region of the Adh gene encompassing the three coding exons exhibits a frequency of polymorphism equal to that of a 4-kb 5' flanking region. In contrast, an interspecific sequence comparison shows a two-fold higher level of divergence in the 5' flanking sequence compared to the structural locus. Analysis of the patterns of variation suggest an excess of polymorphism within the D. melanogaster Adh locus, rather than lack of polymorphism in the 5' flanking region. An approach is outlined for testing neutral theory predictions about patterns of variation within and between species. This approach indicates that the observed patterns of variation are incompatible with an infinite site neutral model. 相似文献
5.
Conservation of alternative splicing and genomic organization of the myosin alkali light-chain (Mlc1) gene among Drosophila species 总被引:3,自引:0,他引:3
The Mlc1 gene of Drosophila melanogaster encodes two MLC1 isoforms via
developmentally regulated alternative pre-mRNA splicing. In larval muscle
and tubular and abdominal muscles of adults, all of the six exons are
included in the spliced mRNA, whereas, in the fibrillar indirect flight
muscle of adult, exon 5 is excluded from the mRNA. We show that this
tissue-specific pattern of alternative splicing of the Mlc1 pre-mRNA is
conserved in D. simulans, D. pseudoobscura, and D. virilis. Isolation and
sequencing of the Mlc1 genes from these three other Drosophila species have
revealed that the overall organization of the genes is identical and that
the genes have maintained a very high level of sequence identity within the
coding region. Pairwise amino acid identities are 94%-99%, and there are no
charge changes among the proteins. Total nucleotide divergence within the
coding region of the four genes supports the accepted genealogy of these
species, but the data indicate a significantly higher rate of amino acid
replacement in the branch leading to D. pseudoobscura. A comparison of
nucleotide substitutions in the coding portions of exon 5 and exon 6, which
encode the alternative carboxyl termini of the two MLC1 isoforms, suggests
that exon 5 is subject to greater evolutionary constraints than is exon 6.
In addition to the coding sequences, there is significant sequence
conservation within the 5' and 3' noncoding DNA and two of the introns,
including one that flanks exon 5. These regions are candidates for cis-
regulatory elements. Our results suggest that evolutionary constraints are
acting on both the coding and noncoding sequences of the Mlc1 gene to
maintain proper expression and function of the two MLC1 polypeptides.
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6.
Molecular Population Genetics of an Electrophoretically Monomorphic Protein in the Alcohol Dehydrogenase Region of Drosophila Pseudoobscura 下载免费PDF全文
Nucleotide sequence data from the alcohol dehydrogenase (Adh) region of 18 isochromosomal strains of Drosophila pseudoobscura were used to determine whether the lack of amino acid polymorphism in ADH results from a low neutral mutation rate or a recent directional selection event. We estimated the neutral mutation parameter, 4Nmu, in synonymous sites for 17 subregions of Adh. The nucleotide diversity data were tested for departures from an equilibrium neutral model with two statistical tests. The Tajima test and the Hudson, Kreitman and Aguade test each failed to reject a neutral model. These results suggest that the ADH enzyme of D. pseudoobscura lacks amino acid polymorphisms because the neutral mutation rate of nonsynonymous sites is low. The neutral mutation parameter for synonymous sites is heterogeneous between domains of the Adh region. These data indicate that selective constrains on synonymous sites can vary between functional domains. 相似文献
7.
The alcohol dehydrogenase (Adh) gene was isolated from Drosophila simulans
and D. mauritiana, and the DNA sequence of a 4.6-kb region, containing the
structural gene and flanking sequence, was determined for each. These
sequences were compared with the Adh region of D. melanogaster to
characterize changes that occur in the Drosophila genome during evolution
and to identify conserved sequences of functional importance. Drosophila
simulans and D. mauritiana Adh are organized in a manner similar to that of
D. melanogaster Adh, including the presence of two promoters for the single
Adh gene. This study identified conserved flanking elements that, in
conjunction with other studies, suggest regions that may be involved in the
control of Adh expression. Inter- and intraspecies comparisons revealed
differences in the kinds of sequence changes that have accumulated.
Sequence divergence in and around the Adh gene was used to assess inter-
and intraspecies evolutionary relationships. Finally, there appears to be
an unrelated structural gene located directly 3' of the Adh transcribed
region.
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The nucleotide sequences of the Adh and Adhr genes of Drosophila kuntzei were derived from combined overlapping sequences of clones isolated from a genomic library and from cloned PCR and inverse-PCR fragments. Only a proximal promoter was detected upstream of the Adh gene, indicating that D. kuntzei Adh is regulated by a one-promoter system. Further upstream of the Adh structural gene, an adult enhancer region (AAE) was found that contains most of the regulatory sequences described for AAEs of other Drosophila species. Analysis of the ADH protein showed an amino acid change from valine to threonine in the active site at position 189 which is also found in D. funebris but is otherwise unique among DROSOPHILA: This difference alone may be responsible for the very low ADH activity found in this species and may cause a difference in substrate usage pattern. Codon bias in Adh and Adhr was comparable and found to be very low compared with other species. Phylogenetic analysis showed that D. kuntzei is closest related to D. funebris and D. immigrans. The time of divergence between D. kuntzei and D. funebris was estimated to be 14.2-20.2 Myr and that between D. kuntzei-D. funebris and D. immigrans to be 30.8-44.0 Myr. An analysis of the genetic variation in the Adh gene and upstream sequences of four European strains showed that this gene was highly variable. Overall nucleotide diversity (pi) was 0.0139, which is two times higher than that in D. melanogaster. 相似文献
12.
The period gene of Drosophila carries species-specific behavioral instructions. 总被引:6,自引:5,他引:1 下载免费PDF全文
We have analyzed and compared the circadian locomotor activity rhythms of Drosophila melanogaster and D.pseudoobscura. The rhythms of D.pseudoobscura are stronger and the periods shorter than those of D.melanogaster. We have also transformed D.melanogaster flies with a hybrid gene containing the coding region of the D.pseudoobscura period (per) gene. Behavioral assays of flies containing this hybrid gene show that the per protein encoded by the D.pseudoobscura per gene is able to rescue the rhythmic deficiencies of arrhythmic, pero1 D.melanogaster. More important, the rhythms of some of these strains are stronger and the periods shorter than those of D.melanogaster (and those of transformants which carry the equivalent D.melanogaster per gene construct) and hence resemble those of D.pseudoobscura. The results suggest that the primary amino acid sequence of the per gene encodes species-specific behavioral instructions that are detectable when only the per gene is transferred to a different species. 相似文献
13.
Synonymous Substitutions in the Xdh Gene of Drosophila: Heterogeneous Distribution along the Coding Region 总被引:1,自引:1,他引:0 下载免费PDF全文
The Xdh (rosy) region of Drosophila subobscura has been sequenced and compared to the homologous region of D. pseudoobscura and D. melanogaster. Estimates of the numbers of synonymous substitutions per site (Ks) confirm that Xdh has a high synonymous substitution rate. The distributions of both nonsynonymous and synonymous substitutions along the coding region were found to be heterogeneous. Also, no relationship has been detected between Ks estimates and codon usage bias along the gene, in contrast with the generally observed relationship among genes. This heterogeneous distribution of synonymous substitutions along the Xdh gene, which is expression-level independent, could be explained by a differential selection pressure on synonymous sites along the coding region acting on mRNA secondary structure. The synonymous rate in the Xdh coding region is lower in the D. subobscura than in the D. pseudoobscura lineage, whereas the reverse is true for the Adh gene. 相似文献
14.
While developmentally regulated genes are generally conserved, transformer (tra), a key locus involved in the regulation of sexual differentiation, is highly diverged between species of Drosophila. With an aim to understand its divergence between sibling species, we investigated tra sequence variation among members of the Drosophila melanogaster species complex, D. melanogaster, D. simulans, D. mauritiana, and D. sechellia. In this species group, tra divergence is rapid yet clocklike and exhibits large differences in protein size. D. melanogaster contains a 13-amino acid tandem duplication, whereas D. sechellia possesses a 72-amino acid tandem duplication representing a 30% increase in total amino acid residues. We also found evidence of a nonrandom distribution of replacement substitutions and heterogeneity in substitution rates using clustering statistics and a codon substitution model. We show that tra's rapid divergence in this species complex is the result of generally lower selective constraints around regions that encode arginine-serine (RS) domains and a significantly higher rate of substitutions around the insertion site of D. sechellia's large duplication. The proximity of rapidly diverged regions to sites of nucleotide insertion suggests that higher local rates of mutation may provide a causal mechanism for TRA's rapid divergence in this subgroup. A comparison of tra orthologs across the genus Drosophila suggest that TRA maintains an assortment of RS domains for proper sex determining function while much of the protein evolves relatively unconstrained. 相似文献
15.
Historical Selection, Amino Acid Polymorphism and Lineage-Specific Divergence at the G6pd Locus in Drosophila Melanogaster and D. Simulans 总被引:2,自引:0,他引:2 下载免费PDF全文
W. F. Eanes M. Kirchner J. Yoon C. H. Biermann I. N. Wang M. A. McCartney B. C. Verrelli 《Genetics》1996,144(3):1027-1041
The nucleotide diversity across 1705 bp of the G6pd gene is studied in 50 Drosophila melanogaster and 12 D. simulans lines. Our earlier report contrasted intraspecific polymorphism and interspecific differences at silent and replacement sites in these species. This report expands the number of European and African lines and examines the pattern of polymorphism with respect to the common A/B allozymes. In D. melanogaster the silent nucleotide diversity varies 2.8-fold across localities. The B allele sequences are two- to fourfold more variable than the derived A allele, and differences between allozymes are twice as among B alleles. There is strong linkage disequilibrium across the G6pd region. In both species the level of silent polymorphism increases from the 5' to 3' ends, while there is no comparable pattern in level of silent site divergence or fixation. The neutral model is not rejected in either species. Using D. yakuba as an outgroup, the D. melanogaster lineage shows a twofold greater rate of silent fixation, but less than half the rate of amino acid replacement. Lineage-specific differences in mutation fixation are inconsistent with neutral expectations and suggest the interaction of species-specific population size differences with both weakly advantageous and deleterious selection. 相似文献
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Nucleotide sequence of the Xdh region in Drosophila pseudoobscura and an analysis of the evolution of synonymous codons 总被引:9,自引:0,他引:9
The nucleotide sequence of the Xdh region of Drosophila pseudoobscura is
presented. The Xdh gene structure and organization are compared with the
homologous region in D. melanogaster. This locus is shown to have similar
organization in the two species, although an additional intron and three
insertion/deletion events are described for the D. pseudoobscura coding
region. The encoded proteins are predicted to have very similar charges and
hydrophobic/hydrophilic domains even though 11% of the amino acids are
different. A gene 5' to Xdh, putative l(3)s12, is suggested from sequence
similarity between the species. Synonymous differences at the Xdh locus
between the two species are analyzed using a new method described in the
preceding paper by Lewontin. This analysis shows that synonymous positions
within the Xdh locus are evolving at very different rates, being dependent
on level of codon redundancy. A comparison of synonymous divergence between
D. melanogaster and D. pseudoobscura in five additional genes reveals
variation in the level of synonymous substitution.
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18.
Origin and Evolution of a New Gene Descended from Alcohol Dehydrogenase in Drosophila 总被引:3,自引:1,他引:2 下载免费PDF全文
D. J. Begun 《Genetics》1997,145(2):375-382
Drosophila alcohol dehydrogenase (Adh) is highly conserved in size, organization, and amino acid sequence. Adh-ψ was hypothesized to be a pseudogene derived from an Adh duplication in the repleta group of Drosophila; however, several results from molecular analyses of this gene conflict with currently held notions of molecular evolution. Perhaps the most difficult observations to reconcile with the pseudogene hypothesis are that the hypothetical replacement sites of Adh-ψ evolve only slightly more quickly than replacement sites of closely related, functional Adh genes, and that the replacement sites of the pseudogenes evolve considerably more slowly than neighboring silent sites. The data have been presented as a paradox that challenges our understanding of the mechanisms underlying DNA sequence divergence. Here I show that Adh-ψ is actually a new, functional gene recently descended from an Adh duplication. This descendant recruited ~60 new N-terminal amino acids, is considerably more basic than ADH, and is evolving at a faster rate than Adh. Furthermore, though the descendant is clearly functional, as inferred from molecular evolution and population genetic data, it retains no obvious ADH activity. This probably reflects functional divergence from its Adh ancestor. 相似文献
19.
The Drosophila subobscura Adh genomic region contains valuable evolutionary markers. 总被引:3,自引:0,他引:3
We have sequenced 4 kb of the genomic region comprising the Adh (Alcohol dehydrogenase) gene of Drosophila subobscura. In agreement with other species which belong to the same subgenus, two structural genes, Adh and Adh-dup, are contained in this region. The main features of these two genes of D. subobscura have been inferred from the sequence data and compared with the homologous region of D. ambigua and D. pseudoobscura. Drosophila subobscura Adh and Adh-dup differ from those of D. ambigua at a corrected estimation of 10.1% and 12.5%, respectively, while from those of D. pseudoobscura they differ by 9.5% and 8.1%, respectively. Our data suggest that Adh and Adh-dup are evolving independently, showing a species-specific pattern. Moreover, particular features of some regions of these genes make them valuable evolutionary hallmarks. For instance, replacement substitutions in the third exon of Adh may indicate the branching of the melanogaster-obscura groups, whereas replacement substitutions in the third exon of the Adh-dup could be used to assess speciation within the obscura group. 相似文献
20.
Intraspecific nuclear DNA variation in Drosophila 总被引:18,自引:6,他引:12
We have summarized and analyzed all available nuclear DNA sequence
polymorphism studies for three species of Drosophila, D. melanogaster (24
loci), D. simulans (12 loci), and D. pseudoobscura (5 loci). Our major
findings are: (1) The average nucleotide heterozygosity ranges from about
0.4% to 2% depending upon species and function of the region, i.e., coding
or noncoding. (2) Compared to D. simulans and D. pseudoobscura (which are
about equally variable), D. melanogaster displays a low degree of DNA
polymorphism. (3) Noncoding introns and 3' and 5' flanking DNA shows less
polymorphism than silent sites within coding DNA. (4) X-linked genes are
less variable than autosomal genes. (5) Transition (Ts) and transversion
(Tv) polymorphisms are about equally frequent in non-coding DNA and at
fourfold degenerate sites in coding DNA while Ts polymorphisms outnumber Tv
polymorphisms by about 2:1 in total coding DNA. The increased Ts
polymorphism in coding regions is likely due to the structure of the
genetic code: silent changes are more often Ts's than are replacement
substitutions. (6) The proportion of replacement polymorphisms is
significantly higher in D. melanogaster than in D. simulans. (7) The level
of variation in coding DNA and the adjacent noncoding DNA is significantly
correlated indicating regional effects, most notably recombination. (8)
Surprisingly, the level of polymorphism at silent coding sites in D.
melanogaster is positively correlated with degree of codon usage bias. (9)
Three proposed tests of the neutral theory of DNA polymorphisms have been
performed on the data: Tajima's test, the HKA test, and the
McDonald-Kreitman test. About half of the loci fail to conform to the
expectations of neutral theory by one of the tests. We conclude that many
variables are affecting levels of DNA polymorphism in Drosophila, from
properties of nucleotides to population history and, perhaps, mating
structure. No simple, all encompassing explanation satisfactorily accounts
for the data.
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