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  • 1
    Electronic Resource
    Electronic Resource
    Diversifying Selection Governs Sequence Polymorphism in the Major Adhesin Proteins FimA, PapA, and SfaA of Escherichia coli (1998)
    Springer
    Journal of molecular evolution 47 (1998), S. 258-267 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Diversifying selection —Escherichia coli— Major structural pilin proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Fimbriae or pili are essential adherence factors usually found in pathogenic bacteria to aid colonization of host cells. Three major structural pilin genes, fimA, sfaA, and papA, from Escherichia coli natural isolates were examined and nucleotide sequence data revealed elevated levels of both synonymous and nonsynonymous site variation at these loci. Examination of synonymous site variation shows a fivefold increase in fimA sites, relative to the housekeeping gene mdh; and similarly the sfaA and papA genes have increased synonymous sites variation relative to fimA. Nonsynonymous site variation is also elevated at all three loci but, in particular, at the papA locus (k N= 0.44). The k N/k S ratio for the three genes are among the highest yet reported for E. coli genes. Regional variation in nucleotide polymorphism within each of the genes reveal hypervariable segments where nonsynonymous substitutions exceed synonymous substitutions. We propose that at the fimA, papA, and sfaA genes, diversifying selection has brought about the increase levels of polymorphism.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006383
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  • 2
    Electronic Resource
    Electronic Resource
    Phylogeny and physiology of Drosophila opsins (1994)
    Springer
    Journal of molecular evolution 38 (1994), S. 250-262 
    Details
    ISSN: 1432-1432
    Keywords: Opsin ; Visual pigments ; Gene family ; Evolution ; Phylogeny ; Spectral sensitivity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Phylogenetic and physiological methods were used to study the evolution of the opsin gene family in Drosophila. A phylogeny based on DNA sequences from 13 opsin genes including representatives from the two major subgenera of Drosophila shows six major, well-supported clades: The “blue opsin” clade includes all of the Rhl and Rh2 genes and is separated into two distinct subclades of Rhl sequences and Rh2 sequences; the ultraviolet opsin clade includes all Rh3 and Rh4 genes and bifurcates into separate Rh3 and Rh4 clades. The duplications that generated this gene family most likely took place before the evolution of the subgenera Drosophila and Sophophora and their component species groups. Numerous changes have occurred in these genes since the duplications, including the loss and/or gain of introns in the different genes and even within the Rhl and Rh4 clades. Despite these changes, the spectral sensitivity of each of the opsins has remained remarkably fixed in a sample of four species representing two species groups in each of the two subgenera. All of the strains that were investigated had R1-6 (Rhl) spectral sensitivity curves that peaked at or near 480 nm, R7 (Rh3 and Rh4) peaks in the ultraviolet range, and ocellar (Rh2) peaks near 420 nm. Each of the four gene clades on the phylogeny exhibits very conservative patterns of amino acid replacement in domains of the protein thought to influence spectral sen sitivity, reflecting strong constraints on the spectrum of light visible to Drosophila.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00176087
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  • 3
    Electronic Resource
    Electronic Resource
    Molecular considerations in the evolution of bacterial genes (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 241-250 
    Details
    ISSN: 1432-1432
    Keywords: Enteric bacteria ; Codon usage bias ; Synonymous substitution ; Glyceraldehyde-3-phosphate dehydrogenase ; Outer membrane protein 3A
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Synonymous and nonsynonymous substitution rates at the loci encoding glyceraldehyde-3-phosphate dehydrogenase (gap) and outer membrane protein 3A (ompA) were examined in 12 species of enteric bacteria. By examining homologous sequences in species of varying degrees of relatedness and of known phylogenetic relationships, we analyzed the patterns of synonymous and nonsynonymous substitutions within and among these genes. Although both loci accumulate synonymous substitutions at reduced rates due to codon usage bias, portions of thegap andompA reading frames show significant deviation in synonymous substitution rates not attributable to local codon bias. A paucity of synonymous substitutions in portions of theompA gene may reflect selection for a novel mRNA secondary structure. In addition, these studies allow comparisons of homologous protein-coding sequences (gap) in plants, animals, and bacteria, revealing differences in evolutionary constraints on this glycolytic enzyme in these lineages.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100675
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  • 4
    Electronic Resource
    Electronic Resource
    Evidence for interspecific transfer of the transposable element mariner betweenDrosophila andZaprionus (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 514-524 
    Details
    ISSN: 1432-1432
    Keywords: Drosophila ; Zaprionus ; Mariner ; Transposable elements ; Horizontal gene transfer ; Alcohol dehydrogenase (Adh) ; Sequence divergence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The transposable element mariner occurs widely in themelanogaster species group ofDrosophila. However, in drosophilids outside of themelanogaster species group, sequences showing strong DNA hybridization with mariner are found only in the genusZaprionus. the mariner sequence obtained fromZaprionus tuberculatus is 97% identical with that fromDrosophila mauritiana, a member of themelanogaster species subgroup, whereas a mariner sequence isolated fromDrosophila tsacasi is only 92% identical with that fromD. mauritiana. BecauseD. tsacasi is much more closely related toD. mauritiana than isZaprionus, the presence of mariner inZaprionus may result from horizontal transfer. In order to confirm lack of a close phylogenetic relationship between the genusZaprionus and themelanogaster species group, we compared the alcohol dehydrogenase (Adh) sequences among these species. The results show that the coding region of Adh is only 82% identical betweenZ. tuberculatus andD. mauritiana, as compared with 90% identical betweenD. tsacasi andD. mauritiana. Furthermore, the mariner gene phylogeny obtained by maximum likelihood and maximum parsimony analyses is discordant with the species phylogeny estimated by using the Adh genes. The only inconsistency in the mariner gene phylogeny is in the placement of theZaprionus mariner sequence, which clusters with mariner fromDrosophila teissieri andDrosophila yakuba in themelanogaster species subgroup. These results strongly suggest horizontal transfer.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02102804
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  • 5
    Electronic Resource
    Electronic Resource
    Genetic variation in IncI1-co1Ib plasmids (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 129-133 
    Details
    ISSN: 1432-1432
    Keywords: Salmonella typhimurium ; Plasmid ; Colicin Ib ; Abortive infection gene (abi) ; Diversifying selection
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Nucleotide sequences of portions of three plasmid genes (cib, cir, and abi) present in IncI1-Co1Ib colicin plasmids obtained from strains of Salmonella typhimurium isolated in either 1974 (Barker strains) or between 1935 and 1941 (Murray strains) were examined along with sequences of the chromosomal gene for 6-phosphogluconate dehydrogenase (gnd). Our principal findings were: (1) The plasmid genes were virtually identical to those in IncI1-CoIIb plasmids from E. coli, suggesting that Salmonella and E. coli share overlapping pools of these plasmids. (2) The plasmid genes were much less polymorphic than gnd or any other known chromosomal gene from Salmonella, further suggesting horizontal transfer with rapid transmission and turnover. (3) No characteristic differences were found in either the plasmid genes or the chromosomal gene between the 1974 isolates and the Murray strains, indicating that these plasmids have been stable for at least several decades. (4) There was an excess of amino-acid replacement polymorphisms, relative to synonymous polymorphisms, in the plasmid genes, which is consistent with the hypothesis of diversifying selection among colicin-producing plasmid families. (5) The abi (abortive infection) gene present in each of the plasmids contained two single-nucleotide insertions relative to the published sequence. These result in a putative abi protein of 114 amino acids instead of 89.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00163801
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  • 6
    Electronic Resource
    Electronic Resource
    Insertion sites of the transposable elementmariner are fixed in the genome ofDrosophila sechellia (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 450-456 
    Details
    ISSN: 1432-1432
    Keywords: Drosophila ; Mariner ; Transposable elements
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The abundance of the transposable elementmariner differs dramatically in the genomes of the closely related speciesDrosophila simulans, D. mauritiana, D. sechellia, andD. melanogaster. Natural populations ofD. simulans andD. mauritiana have 1–10 and 20–30 copies per diploid genome, respectively, and the insertion sites are polymorphic. The element has not been found inD. melanogaster. In this paper we show thatD. sechellia, a species endemic to the Seychelles Islands, contains only twomariner elements that are at fixed sites in the genome. One element, inserted in chromosome 2R at 51A1–2, contains three deletions and is missing much of the 3′ end. The other element, inserted in chromosome 3L at 64A10–11, is the full length of 1286 bp. Although the sequence of the full-length element is polymorphic in populations ofD. sechellia, at least some of the sequences are closely related to elements fromD. simulans andD. mauritiana that are known to be active. However, judging from the progeny of crosses betweenD. sechellia andD. simulans, the biological activity of the full-lengthD. sechellia element appears to be low, either because of the nucleotide sequence of the element or because of its position in the genome, or both.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02103137
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  • 7
    Electronic Resource
    Electronic Resource
    P1 clones from Drosophila melanogaster as markers to study the chromosomal evolution of Muller's A element in two species of the obscura group of Drosophila (1995)
    Springer
    Chromosoma 104 (1995), S. 129-136 
    Details
    ISSN: 1432-0886
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Thirty P1 clones from the X chromosome (Muller's A element) of Drosophila melanogaster were cross-hybridized in situ to Drosophila subobscura and Drosophila pseudoobscura polytene chromosomes. An additional recombinant phage λDsuby was also used as a marker. Twenty-three (77%) of the P1 clones gave positive hybridization on D. pseudoobscura chromosomes bat only 16 (53%) did so with those of D. subobscura. Eight P1 clones gave more than one hybridization signal on D. pseudoobscura and/or D. subobscura chromosomes. All P1 clones and λDsuby hybridized on Muller's A element (X chromosome) of D. subobscura. In contrast, only 18 P1 clones and λDsuby hybridized on Muller's D element (XR chromosomal arm) of D. pseudoobscura; 4 additional P1 clones hybridized on Muller's D element (XR chromosomal arm) of this species and the remaining P1 clone gave on hybridization signal on each arm of the X chromosome. This latter clone may contain one breakpoint of a pericentric inversion that may account for the interchange of genetic material between Muller's A and D elements in D. pseudoobscura. In contrast to the rare interchange of genetic material between chromosomal elements, profound differences in the order and spacing of markers were detected between D. melanogaster, D. pseudoobscura and D. subobscura. In fact, the number of chromosomal segments delimited by identical markers and conserved between pairwise comparisons is small. Therefore, extensive reorganization within Muller's A element has been produced during the divergence of the three species. Rough estimates of the number of cytologically detectable inversions contributing to differentiation of Muller's A element were obtained. The most reliable of these estimates is that obtained from the D. pseudoobscura and D. melanogaster comparison since a greater number of markers have been mapped in both species. Tentatively, one inversion breakpoint about every 200 kb has been produced and fixed during the divergence of D. pseudoobscura and D. melanogaster.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00347695
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  • 8
    Electronic Resource
    Electronic Resource
    reply: How was the Sdic gene fixed? (1999)
    [s.l.] : Macmillan Magazines Ltd.
    Nature 400 (1999), S. 520-520 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Nurminsky and Hartl reply — One hallmark of persistent strong background selection is a severe diminution of codon usage bias,. An example is the Drosophila gene rolled (gene 1 in Fig. 1), which is located in the centromeric heterochromatin of chromosome 2, where recombination is ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/22924
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  • 9
    Electronic Resource
    Electronic Resource
    High intrinsic rate of DNA loss in Drosophila (1996)
    [s.l.] : Nature Publishing Group
    Nature 384 (1996), S. 346-349 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Non-LTR retrotransposable elements comprise a distinct group in the retroid lineage10. These elements are on average 4-5 kilobases (kb) long, have no introns, lack terminal repeats, have a dA-rich tail at the 3' end, and contain 1-2 open reading frames, one of which encodes the reverse ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/384346a0
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  • 10
    Electronic Resource
    Electronic Resource
    MODERN THOUGHTS ON AN ANCYENT MARINERE:Function, Evolution, Regulation (1997)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Genetics 31 (1997), S. 337-358 
    Details
    ISSN: 0066-4197
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract The mariner/Tc1 superfamily of transposable elements is one of the most diverse and widespread Class II transposable elements. Within the larger assemblage, the mariner-like elements (MLEs) and the Tc1-like elements (TLEs) are distinct families differing characteristically in the composition of the "D,D(35)E" cation-binding domain. Based on levels of sequence similarity, the elements in each family can be subdivided further into several smaller subfamilies. MLEs and TLEs both have an extraordinarily wide host range. They are abundant in insect genomes and other invertebrates and are found even in some vertebrate species including, in the case of mariner, humans, in which one element on chromosome 17p has been implicated as a hotspot of recombination. In spite of the extraordinary evolutionary success of the elements, virtually nothing is known about their mode of regulation within genomes. There is abundant evidence that the elements are disseminated to naive host genomes by horizontal transmission, and there is a substantial base of evidence for inference about the subsequent population dynamics. Studies of engineered mariner elements and induced mutations in the transposase have identified two mechanisms that may be operative in mariner regulation. One mechanism is overproduction inhibition, in which excessive wild-type transposase reduces the rate of excision of a target element. A second mechanism is dominant-negative complementation, in which certain mutant transposase proteins antagonize the activity of the wild-type transposase. The latter process may help explain why the vast majority of MLEs in nature undergo "vertical inactivation" by multiple mutations and, eventually, stochastic loss. There is also evidence that mariner/Tc1 elements can be mobilized in hybrid dysgenesis; in particular, certain dysgenic crosses in Drosophila virilis result in mobilization of a TLE designated Paris as well as the mobilization of other unrelated transposable elements.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.genet.31.1.337
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