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31.
Sequence evolution and phylogenetic signal in control-region and cytochrome b sequences of rainbow fishes (Melanotaeniidae) 总被引:3,自引:0,他引:3
The nucleotide sequences of segments of the cytochrome b gene (351 bp), the
tRNA(Pro) gene (49 bp), and the control region (approximately 313 bp) of
mitochondrial DNA were obtained from 26 fish representing different
populations and species of Melanotaenia and one species of Glossolepis,
freshwater rainbow fishes confined to Australia and New Guinea. The purpose
was to investigate relative rates and patterns of sequence evolution.
Overall levels of divergence were similar for the cytochrome b and tRNA
control-region sequences, both ranging from < 1% within subspecies to
15%-19% between genera. However, the patterns of sequence evolution
differed. For the cytochrome b gene, transitions consistently exceeded
transversions, the bias ranging from 4.2:1 to 2:1, depending on the level
of sequence divergence. However, in the control-region sequence, a bias
toward transitions (2:1) was observed only in comparisons between very
similar sequences, and transversions outnumbered transitions in comparisons
of divergent sequences. Graphic comparisons suggested that the control
region was saturated for transitions at relatively low levels of sequence
divergence but accumulated transversions at a greater rate than did the
cytochrome b sequence. These distinct patterns of base substitution are
associated with differences in A+T content, which is 70% for the tRNA
control- region segment versus 50% for cytochrome b. A test for skewness in
the distribution of lengths of random trees indicated that both segments
contained phylogenetic signal. Parsimony analyses of the data from the two
regions, with or without weighting schemes appropriate to the respective
patterns of sequence evolution, identified the same five groupings of
sequences, but the relationships among the groups differed. However, in
most cases the branches uniting different combinations of groups were
poorly supported, and the differences among topologies were insignificant.
Considering the observed patterns of base substitution and the results of
the phylogenetic analyses, we deduce that both the control region and
cytochrome b are appropriate for population genetic studies but that the
control region is less effective than cytochrome b for resolving
relationships among divergent lineages of rainbow fishes.
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32.
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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33.
A nearly universal feature of intron sequences is that even closely related
species exhibit a large number of insertion/deletion differences. The goal
of the analysis described here is to test whether the observed pattern of
insertion/deletion events in the genealogy of the myosin alkali light chain
(Mlc1) gene is consistent with neutrality, and if not, to determine the
underlying forces of evolutionary change. Mlc1 pre-mRNA is alternatively
spliced, and one constraint is that signals necessary for
tissue-specificity of directed splicing must be conserved. If the total
length of an intron is functionally constrained, then the distribution of
indels on branches of the gene genealogy should reflect a departure from
randomness. Here we perform a phylogenetic analysis, inferring ancestral
states wherever possible on a phylogeny of 29 alleles of Mlc1 from six
species of Drosophila. Observed patterns of indels on the genealogy were
compared to those from simulated data, with the result that we cannot
reject the null hypothesis of neutrality. A clear departure from a neutral
prediction was seen in the excess folding free energy predicted for the
introns flanking the alternatively spliced exon. Relative rate tests also
suggest a retardation in the rate of Mlc1 sequence evolution in the
simulans clade.
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34.
35.
Widespread distribution of deletions of the bgl operon in natural isolates of Escherichia coli 总被引:2,自引:0,他引:2
A deletion that includes the bgl (beta-glucoside utilization) operon of
Escherichia coli was originally detected in several rarely occurring
natural isolates that utilize cellobiose. Here I show that bgl deletions
are present in 95% of the Cel+ isolates obtained from diverse sources. They
are also present in 29% of the Cel- strains in two different collections of
natural isolates of E. coli. At least three versions of bgl deletions are
present in E. coli populations. In the most common version approximately 8
kb of DNA around the bgl region of E. coli K12 is replaced by a specific
6.5-kb DNA fragment. In another version a deletion of similar length is not
replaced by the same sequence. A third version involves deletion of
approximately 14 kb without the replacement fragment being present. The
distribution of these deletions suggests that the version 1 deletion
occurred very early in the history of E coli. It also appears likely that
there is selection for bgl deletions in Cel+ strains of E. coli. The
presence of the version 1 deletion within distantly related phylogenetic
groups of E. coli provides evidence for recombination within natural
populations of E coli.
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