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  • 1
    Electronic Resource
    Electronic Resource
    Isolation and complete structure of the lymphocyte serine protease granzyme G, a novel member of the granzyme multigene family in murine cytolytic T lymphocytes. Evolutionary origin of lymphocyte proteases (1989)
    s.l. : American Chemical Society
    Biochemistry 28 (1989), S. 7953-7961 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00445a060
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  • 2
    Electronic Resource
    Electronic Resource
    The molecular clock runs more slowly in man than in apes and monkeys (1987)
    [s.l.] : Nature Publishing Group
    Nature 326 (1987), S. 93-96 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Wu and Li8 estimated that since the mammalian radiation the rate of synonymous substitution has been, on average, about two times higher in the rodent lineage than in the human and artiodactyl lineages. Because at the early stage of mammalian divergence the substitution rates in the three lineages ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/326093a0
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  • 3
    Electronic Resource
    Electronic Resource
    An evolutionary perspective on synonymous codon usage in unicellular organisms (1986)
    Springer
    Journal of molecular evolution 24 (1986), S. 28-38 
    Details
    ISSN: 1432-1432
    Keywords: Codon usage ; Synonymous substitution rate ; Codon Adaptation Index ; Enterobacterial genes ; G+C content ; Theoretical models
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Observed patterns of synonymous codon usage are explained in terms of the joint effects of mutation, selection, and random drift. Examination of the codon usage in 165Escherichia coli genes reveals a consistent trend of increasing bias with increasing gene expression level. Selection on codon usage appears to be unidirectional, so that the pattern seen in lowly expressed genes is best explained in terms of an absence of strong selection. A measure of directional synonymous-codon usage bias, the Codon Adaptation Index, has been developed. In enterobacteria, rates of synonymous substitution are seen to vary greatly among genes, and genes with a high codon bias evolve more slowly. A theoretical study shows that the patterns of extreme codon bias observed for someE. coli (and yeast) genes can be generated by rather small selective differences. The relative plausibilities of various theoretical models for explaining nonrandom codon usage are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02099948
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  • 4
    Electronic Resource
    Electronic Resource
    Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons (1987)
    Springer
    Journal of molecular evolution 24 (1987), S. 337-345 
    Details
    ISSN: 1432-1432
    Keywords: Single-site model ; Multisite model ; Additive selection ; Threshold selection ; Molecular evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The population dynamics of nearly neutral mutations are studied using a single-site and a multisite model. In the latter model, the nucleotides in a sequence are completely linked and the selection schemes employed are additive, multiplicative, and additive with a threshold. Although the third selection scheme is very different from the first two, the three schemes produce identical results for a wide range of parameter values. Thus the present study provides a general theory for the population dynamics of nearly neutral mutations because the results can also be used to draw inferences about other selection schemes such as stabilizing selection and synergistic selection. It is shown that the number of slightly deleterious mutations accumulated in a sequence can be considerably larger under the multisite model than under the single-site model, particularly if the sequence is long or if the mutation rate per site is high. The results show that even a very slight selective difference between synonymous codons can produce a strong bias in codon usage. Three alternative explanations for the strong bias in codon usage in bacterial and yeast genes are considered. The implications of the present results for molecular evolution are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02134132
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  • 5
    Electronic Resource
    Electronic Resource
    Rates of synonymous substitution in plant nuclear genes (1989)
    Springer
    Journal of molecular evolution 29 (1989), S. 208-211 
    Details
    ISSN: 1432-1432
    Keywords: Plant molecular evolution ; Molecular clock ; Chloroplast DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The rate of synonymous nucleotide substitution in nuclear genes of higher plants has been estimated. The rate varies among genes by a factor of up to two, in a manner that is not immediately explicable in terms of base composition or codon usage bias. The average rate, in both monocots and dicots, is about four times higher than that in chloroplast genes. This leads to an estimated absolute silent substitution rate of 6 × 10−9 substitutions per site per year that falls within the range of average rates (2−8 × 10−9) seen in different mammalian nuclear genomes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100204
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  • 6
    Electronic Resource
    Electronic Resource
    Deletions in processed pseudogenes accumulate faster in rodents than in humans (1989)
    Springer
    Journal of molecular evolution 28 (1989), S. 279-285 
    Details
    ISSN: 1432-1432
    Keywords: Processed pseudogenes ; Rate of substitution ; Deletions ; Insertions ; Genome size
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The relative rates of point nucleotide substitution and accumulation of gap events (deletions and insertions) were calculated for 22 human and 30 rodent processed pseudogenes. Deletion events not only outnumbered insertions (the ratio being 7∶1 and 3∶1 for human and rodent pseudogenes, respectively), but also the total length of deletions was greater than that of insertions. Compared with their functional homologs, human processed pseudogenes were found to be shorter by about 1.2%, and rodent pseudogenes by about 2.3%. DNA loss from processed pseudogenes through deletion is estimated to be at least seven times faster in rodents than in humans. In comparison with the rate of point substitutions, the abridgment of pseudogenes during evolutionary times is a slow process that probably does not retard the rate of growth of the genome due to the proliferation of processed pseudogenes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02103423
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  • 7
    Electronic Resource
    Electronic Resource
    Evolution of protein inhibitors of serine proteinases: Positive Darwinian selection or compositional effects? (1988)
    Springer
    Journal of molecular evolution 28 (1988), S. 131-135 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02143504
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  • 8
    Electronic Resource
    Electronic Resource
    Evolutionary change of restriction sites under unequal rates of nucleotide substitution among the three positions of codons (1986)
    Springer
    Journal of molecular evolution 23 (1986), S. 205-210 
    Details
    ISSN: 1432-1432
    Keywords: Restriction maps ; Nucleotide substitution ; Unequal rates ; Evolutionary distance ; Underestimation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Under the assumption of unequal rates of nucleotide substitution among the three positions of codons, mathematical formulas are derived for the probability that a restriction site observed at time 0 in a DNA sequence will be present at time t, the probability that a new restriction site will emerge at a particular place in two descendant sequences, and the proportion of identical restriction sites between two such sequences. All three quantitites are shown to be larger for the case of unequal rates than for the case of equal rates. As a consequence, estimates of nucleotide divergence (2λt) between two sequences based on restriction-site data tend to be lower than the actual values of the assumption of equal rates is made but actually does not hold. However, the degree of underestimation is slight if 2λt is 0.10 or smaller. The underestimation can be serious when 2λt becomes 0.20 or larger, particularly if the substitution rates at the three codon positions are very different or if transitional substitution occurs more frequently than transversional substitution. The underestimation is more serious for four-base enzymes than for sixbase enzymes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02115577
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  • 9
    Electronic Resource
    Electronic Resource
    Ubiquitin genes as a paradigm of concerted evolution of tandem repeats (1987)
    Springer
    Journal of molecular evolution 25 (1987), S. 58-64 
    Details
    ISSN: 1432-1432
    Keywords: Molecular evolution ; Protein sequence conservation ; Synonymous substitution ; Unequal crossover ; Gene conversion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Ubiquitin is remarkable for its ubiquitous distribution and its extreme protein sequence conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences of several ubiquitin repeats from each of humans, chicken,Xenopus, Drosophila, barley, and yeast have recently been determined. By analysis of these data we show that ubiquitin is evolving more slowly than any other known protein, and that this (together with its gene organization) contributes to an ideal situation for the occurrence of concerted evolution of tandem repeats. By contrast, there is little evidence of between-cluster concerted evolution. We deduce that in ubiquitin genes, concerted evolution involves both unequal crossover and gene conversion, and that the average time since two repeated units within the polyubiquitin locus most recently shared a common ancestor is approximately 38 million years (Myr) in mammals, but perhaps only 11 Myr inDrosophila. The extreme conservatism of ubiquitin evolution also allows the inference that certain synonymous serine codons differing at the first two positions were probably mutated at single steps.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100041
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  • 10
    Electronic Resource
    Electronic Resource
    Angiosperm origins (1989)
    [s.l.] : Nature Publishing Group
    Nature 342 (1989), S. 131-132 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] SIRá€"Our recent analysis12 of extensive chloroplast and nuclear DNA sequence data firmly supports Martin et á«/.'s evidence for a pre-Cretaceous origin of angiosperms. But our estimate of the monocot-dicot divergence at 200 million years (Myr) ago (with an uncertainty ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/342131c0
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