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  • 1
    ISSN: 1432-1432
    Keywords: Compositional patterns ; Compositional shifts ; Genome evolution ; Isochores ; Vertebrates ; Selection ; Neutral theory
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The evolution of vertebrate genomes can be investigated by analyzing their regional compositional patterns, namely the compositional distributions of large DNA fragments (in the 30–100-kb size range), of coding sequences, and of their different codon positions. This approach has shown the existence of two evolutionary modes. In the conservative mode, compositional patterns are maintained over long times (many million years), in spite of the accumulation of enormous numbers of base substitutions. In the transitional, or shifting, mode, compositional patterns change into new ones over much shorter times. The conservation of compositional patterns, which has been investigated in mammalian genomes, appears to be due in part to some measure of compositional conservation in the base substitution process, and in part to negative selection acting at regional (isochore) levels in the genome and eliminating deviations from a narrow range of values, presumably corresponding to optimal functional properties. On the other hand, shifts of compositional patterns, such as those that occurred between cold-blooded and warm-blooded vertebrates, appear to be due essentially to both negative and positive selection again operating at the isochore level, largely under the influence of changes in environmental conditions, and possibly taking advantage of mutational biases in the replication/repair enzymes and/or in the enzyme make-up of nucleotide precursor pools. Other events (like translocations and changes in chromosomal structure) also play a role in the transitional mode of genome evolution. The present findings (1) indicate that isochores, which correspond to the DNA segments of individual or contiguous chromatin domains, represent selection units in the vertebrate genome; and (2) shed new light on the selectionist-neutralist controversy.
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  • 2
    ISSN: 1432-1432
    Keywords: Xenopus laevis ; Xenopus tropicalis ; Adult α-globin genes ; Gene organization ; Conserved upstream sequences
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary To investigate the evolution of globin genes in the genusXenopus, we have determined the primary structure of the related adult α1- and αII genes ofX. laevis and of the adult α-globin gene ofX. tropicalis, including their 5′-flanking regions. All three genes are comprised of three exons and two introns at homologous positions. The exons are highly conserved and code for 141 amino acids. By contrast, the corresponding introns vary in length and show considerable divergence. Comparison of 900 bp of the 5′-flanking region revealed that theX. tropicalis gene contains a conserved proximal 310-bp promoter sequence, comprised of the canonical TATA and CCAAT motifs at homologous positions, and five conserved elements in the same order and at similar positions as previously shown for the corresponding genes ofX. laevis. We therefore conclude that these conserved upstream elements may represent regulatory sequences for cell-specific regulation of the adultXenopus globin genes.
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  • 3
    ISSN: 1432-1432
    Keywords: Genome evolution ; Rearrangement ; Inversion ; Brassica ; Base substitution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We examined the tempo and mode of mitochondrial DNA (mtDNA) evolution in six species of crucifers from two genera,Brassica andRaphanus. The six mtDNAs have undergone numerous internal rearrangements and therefore differ dramatically with respect to the sizes of their subgenomic circular chromosomes. Between 3 and 14 inversions must be postulated to account for the structural differences found between any two species. In contrast, these mtDNAs are extremely similar in primary sequence, differing at only 1–8 out of every 1000 bp. The point mutation rate in these plant mtDNAs is roughly 4 times slower than in land plant chloroplast DNA (cpDNA) and 100 times slower than in animal mtDNA. Conversely, the rate of rearrangements is extraordinarily faster in plant mtDNA than in cpDNA and animal mtDNA.
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  • 4
    ISSN: 1432-1432
    Keywords: rRNA ; Evolution ; Sequence comparison ; Parsimony ; Bootstrap
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Sequences of small subunit (SSU) and large subunit (LSU) ribosomal RNA genes from archaebacteria, eubacteria, and the nucleus, chloroplasts, and mitochondria of eukaryotes have been compared in order to identify the most conservative positions. Aligned sets of these positions for both SSU and LSU rRNA have been used to generate tree diagrams relating the source organisms/organelles. Branching patterns were evaluated using the statistical bootstrapping technique. The resulting SSU and LSU trees are remarkably congruent and show a high degree of similarity with those based on alternative data sets and/or generated by different techniques. In addition to providing insights into the evolution of prokaryotic and eukaryotic (nuclear) lineages, the analysis reported here provides, for the first time, an extensive phylogeny of the mitochondrial lineage.
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  • 5
    ISSN: 1432-1432
    Keywords: Actin ; Multigene family ; Nucleotide sequence ; Sea urchin ; Evolutionary divergence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The general organization and primary amino acid sequences of theS. purpuratus cytoskeletal actin genes CyIIb and CyIIIb have been determined from restriction enzyme analysis, DNA sequencing, and RNA mapping studies. As is the case with the other sea urchin cytoskeletal actin genes previously studied, the CyIIb and CyIIIb genes contain two introns that interrupt the coding DNA following codon 121 and within codon 204. An intron ending 26–27 nucleotides (nt) upstream of the initiation codon has also been localized in the 5′-flanking region of both genes. The CyIIb gene, which is part of a cluster of three genes linked in the order CyI-CyIIa-CyIIb, encodes a protein that differs from CyI by a single residue and from CyIIa by three residues. The substitutions observed within this linkage group are relatively conservative changes, and pairwise comparisons between genes indicate less than 5% mismatch in nucleotide sequence within the coding region. Nucleotide sequence comparisons of 5′-flanking region and intron DNA, however, indicate greater similarity between the CyI and CyIIb genes than the CyIIa gene that separates them, suggestive of a potential gene conversion event between the flanking genes in the CyI-CyIIa-CyIIb linkage. The CyIIIb gene, part of a separate cluster of two functional genes ordered CyIIIa-CyIIIb, shares little similarity outside of coding DNA with genes of the other linkage group. Although CyIIIb exhibits strong nucleotide sequence similarity outside of coding DNA with the neighboring CyIIIa gene, it differs from that gene at six codons. The CyIIIb gene encodes a protein considerably different from all cytoskeletal actins previously reported, with changes clustered in the latter 40% of the coding sequence. An 81-nt tandem duplication of the C-terminal coding region is located adjacent to the termination codon of the CyIIIb gene, a potential relic of a slipped mispairing and replication event.
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  • 6
    ISSN: 1432-1432
    Keywords: rRNA ; Eucaryotes ; Phylogeny ; Sequences
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Due to their high information content and their particular mode of variation, large rRNA molecules potentially represent powerful indicators of phylogenetic relationships. Even partial sequences may suffice to generate reliable estimations, provided they correspond to well-chosen portions of the molecule. We have systematically analyzed a specific portion of the large rRNA (the region extending over nearly 400 nucleotides from the 5′ end) as a general index of eucaryotic phylogeny. By means of fast and direct rRNA sequencing, we have determined the sequence of this region for 20 additional eucaryotes, including several representatives of each vertebrate class, an invertebrate metazoan (mussel), a fungus (Schizosaccharomyces pombe), and three higher plants. Comparative treatment of these new data and previously reported rRNA sequences shows that this region can serve as an indicator of eucaryotic phylogeny for evaluating both long-range and short-range relationships. Its conservative domains appear to possess a rather uniform rate of nucleotide changes in all the eucaryotic lineages analyzed and the phylogenetic tree we derived agrees with classical views.
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  • 7
    ISSN: 1432-1432
    Keywords: Aspergillus nidulans ; 5S rRNA ; Pseudogenes ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary AllAspergillus nidulans 5S rRNA pseudogenes known so far are the result of integration of an approx. 0.2-kbp-long DNA sequence into the 5S rRNA genes. This sequence, called block C, is present in at least five copies in theA. nidulans genome and seems to be associated either with 5S rRNA genes or pseudogenes. In contrast to the 78% sequence conservation of the C-block in pseudogenes, the truncated 5′ halves of the pseudogenes are very highly conserved (96.9–100%). We postulate that the 5S rRNA pseudogenes are still a subject of concerted evolution. The C-block sequence shows similarity to the switch region of the mouse heavy chain immunoglobulin gene. A characteristic motif GGGTGAG is repeated several times in both sequences; the sequence conservation is 63%.
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  • 8
    ISSN: 1432-1432
    Keywords: α globin ; Crab-eating macaque ; Amino acid sequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We found two types of hemoglobin, T and R, from the crab-eating macaque and compared those to A and Q previously reported. The 22 animals studied showed six different phenotypes, A, R, QA, QT, QAT, and QAR. Analysis of the complete amino acid sequences for the α chains of hemoglobins Q, A, T, and R revealed that amino acids at four positions, 8, 55, 71, and 78 from the N-terminal, are variable. In the αA chain, Thr, Val, Gly, and Gln occupy these positions, and in the αQ chain the analogous amino acids are Thr, Val, Asp, and Gln, respectively. In the newly found αT chain they are Thr, Val, Gly, and His; and in the αR chain, they are Ser, Ile, Gly, and His, respectively. Two amino acids (α8 Thr and α79 Gln) in αA of the crab-eating macaque were found to be different from those in the α chain of the Japanese macaque.
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  • 9
    ISSN: 1432-1432
    Keywords: Rate of amino acid substitutions ; Amino acid composition ; Serine proteinase inhibitors ; Ovomucoids ; Spi-2 ; Neutral theory ; Positive Darwinian selection ; Serpins ; Kunitz-type inhibitors ; Kazal-type inhibitors
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary In at least two instances involving serine proteinase inhibitors it has been shown that functionally important sites evolve faster and exhibit more interspecific variability than functionally neutral sites. Because these phenomena are difficult to reconcile with the neutral theory of molecular evolution, it has been suggested that the accelerated rate of amino acid substitution at the reactive sites is brought about by positive Darwinian selection. We show that differences in the amino acid composition in the different regions of proteinase inhibitors can account for the differences in the rates of amino acid substitution. By using an index of protein mutability [D. Graur (1985) J Mol Evol 22∶53–62], we show that the amino acid composition of the reactive center in the ovomucoids andSpi-2 gene products is such that, regardless of function, they are expected to evolve more rapidly than any other polypeptide for which the rate of substitution is known. In addition, the reactive region in theSpi-2 proteins is shown to be free of compositional constraint. Positive Darwinian selection need not be invoked at the present time in these cases.
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 28 (1988), S. 161-169 
    ISSN: 1432-1432
    Keywords: Multiple protein sequence consensus ; Alignment ; Evolutionary tree ; Clustering
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A method for the alignment of two or more biological sequences is described. The method is a direct extension of the method of Taylor (1987) incorporating a consensus sequence approach and allows considerable freedom in the control of the clustering of the sequences. At one extreme this is equivalent to the earlier method (Taylor 1987), whereas at the other, the clustering approaches the binary method of Feng and Doolittle (1987). Such freedom allows the program to be adapted to particular problems, which has the important advantage of resulting in considerable savings in computer time, allowing very large problems to be tackled. Besides a detailed analysis of the alignment of the cytochrome c superfamily, the clustering and alignment of the PIR sequence data bank (3500 sequences approx.) is described.
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