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  • 1
    Electronic Resource
    Electronic Resource
    Molecular evolution and phylogeny of the human AIDS viruses LAV, HTLV-III, and ARV (1987)
    Springer
    Journal of molecular evolution 24 (1987), S. 330-336 
    Details
    ISSN: 1432-1432
    Keywords: Human AIDS viruses ; Molecular evolution ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A phylogenetic tree for the human lymphadenopathy-associated virus (LAV), the human T-cell lymphotrophic virus type III (HTLV-III), and the acquired immune deficiency syndrome (AIDS)-associated retrovirus (ARV) has been constructed from comparisons of the amino acid sequences of their gag proteins. A method is proposed for estimating the divergence times among these AIDS viruses and the rates of nucleotide substitution for their RNA genomes. The analysis indicates that the LAV and HTLV-III strains diverged from one another after 1977 and that their common ancestor diverged from the ARV virus no more than 10 years earlier. Hence, the evolutionary diversity among strains of the AIDS viruses apparently has been generated within the last 20 years. It is estimated that the genome of the AIDS virus has a nucleotide substitution rate on the order of 10−3 per site per year, with the rate in the second half of the genome being double that in the first half.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02134131
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  • 2
    Electronic Resource
    Electronic Resource
    Molecular evolutionary rates of oncogenes (1987)
    Springer
    Journal of molecular evolution 26 (1987), S. 148-156 
    Details
    ISSN: 1432-1432
    Keywords: Oncogenes ; Retroviruses ; Evolutionary rates ; Nucleotide substitution ; Substitution pattern
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Using nine sets of viral and cellular oncogenes, the rates of nucleotide substitutions were computed by using Gojobori and Yokoyama's (1985) method. The results obtained confirmed our previous conclusion that the rates of nucleotide substitution for the viral oncogenes are about a million times higher than those for their cellular counterparts. For cellular oncogenes and most viral oncogenes, however, the rate of synonymous substitution is higher than that of nonsynonymous substitution. Moreover, the pattern of nucleotide substitutions for viral oncogenes is more similar to that for functional genes (such as cellular oncongenes) than for pseudogenes. This implies that nucleotide substitutions in viral oncogenes may be functionally constrained. Thus, our observation supports that nucleotide substitutions for the oncogenes in those DNA and RNA genomes are consistent with Kimura's neutral theory of molecular evolution (Kimura 1968, 1983).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02111288
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  • 3
    Electronic Resource
    Electronic Resource
    Different evolutionary histories of kringle and protease domains in serine proteases: A typical example of domain evolution (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 331-336 
    Details
    ISSN: 1432-1432
    Keywords: Kringle domain ; Protease domain ; Serine protease ; Domain evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract With the aim of elucidating the evolutionary processes of the kringle and protease domains in serine proteases which are involved with the system of blood coagulation and fibrinolysis, we constructed phylogenetic trees for the kringle and protease domains, separately, by use of amino acid sequence data. The phylogenetic trees constructed clearly showed that the topologies were different between the kringle and protease domains. Because both domains are coded by single peptides of serine proteases, this strongly suggests that the kringle and protease domains must have undergone different evolutionary processes. Thus, these observations imply that serine proteases evolve in a way such that each domain is a unit of evolution, exemplifying a typical mode of domain evolution. A possible relationship between the domain evolution and the exon shuffling theory is also discussed from the viewpoint of gene evolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00163238
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  • 4
    Electronic Resource
    Electronic Resource
    Evolutionary origin of a Kunitz-type trypsin inhibitor domain inserted in the amyloid β precursor protein of Alzheimer's disease (1992)
    Springer
    Journal of molecular evolution 34 (1992), S. 536-543 
    Details
    ISSN: 1432-1432
    Keywords: Serine protease inhibitor ; Kunitz type ; Evolutionary origin ; Alzheimer's disease ; Insertion sequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The Kunitz-type protease inhibitor is one of the serine protease inhibitors. It is found in blood, saliva, and all tissues in mammals. Recently, a Kunitz-type sequence was found in the protein sequence of the amyloid β precursor protein (βAPP). It is known that βAPP accumulates in the neuritic plaques and cerebrovascular deposits of patients with Alzheimer's disease. Collagen type VI in chicken also has an insertion of a Kunitz-type sequence. To elucidate the evolutionary origin of these insertion sequences, we constructed a phylogenetic tree by use of all the available sequences of Kunitz-type inhibitors. The tree shows that the ancestral gene of the Kunitz-type inhibitor appeared about 500 million years ago. Thereafter, this gene duplicated itself many times, and some of the duplicates were inserted into other protein-coding genes. During this process, the Kunitz-type sequence in the present βAPP gene diverged from its ancestral gene about 270 million years ago and was inserted into the gene soon after duplication. Although the function of the insertion sequences is unknown, our molecular evolutionary analysis shows that these insertion sequences in βAPP have an evolutionarily close relationship with the inter-α-trypsin inhibitor or trypstatin, which inhibits the activity of tryptase, a novel membrane-bound serine protease in human T4+ lymphocytes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00160466
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  • 5
    Electronic Resource
    Electronic Resource
    Six strains of human immunodeficiency virus type 1 isolated in Japan and their molecular phylogeny (1992)
    Springer
    Journal of molecular evolution 35 (1992), S. 329-336 
    Details
    ISSN: 1432-1432
    Keywords: AIDS ; HIV-1 isolate ; Japanese hemophiliac ; Restriction map ; Phylogenetic tree
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Five strains of human immunodeficiency virus type 1 (HIV-1) were isolated from five Japanese hemophilia patients. Two isolates, HIV1[GUN-1] and HIV-1[GUN-2], were from brother patients with hemophilia B and the other three isolates, HIV-I[GUN-3], HIV-1[GUN-4], and HIV1[GUN-5], were from hemophilia A patients. Another HIV-1 strain, HIV-1[GUN-6], was isolated from a Canadian male homosexual with AIDS. The restriction endonuclease cleavage maps of the proviral genomes of these six HIV-1 strains revealed that they were apparently different from each other. The phylogenetic trees constructed using restriction maps and nucleotide sequences were quite similar, indicating that phylogenetic analyses of Japanese HIV-1 isolates can be done using restriction maps of the proviruses. Phylogenetic analyses showed that they were more closely related to HIV-1s which had been reported to be isolated from homosexual patients in the United States than those isolated from African patients. In particular, GUN-1 and GUN-2 isolates were on the branch of a San Francisco isolate, ARV2, while GUN-5 and GUN-6 isolates were on the branch of HTLV-IIIB-related isolates.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00161170
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  • 6
    Electronic Resource
    Electronic Resource
    Genome Plasticity as a Paradigm of Eubacteria Evolution (1997)
    Springer
    Journal of molecular evolution 44 (1997), S. S057 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Genome evolution — Eubacteria — Rearrangement — S10 region
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. To test the hypotheses that eubacterial genomes leave evolutionarily stable structures and that the variety of genome size is brought about through genome doubling during evolution, the genome structures of Haemophilus influenzae, Mycoplasma genitalium, Escherichia coli, and Bacillus subtilis were compared using the DNA sequences of the entire genome or substantial portions of genome. In these comparisons, the locations of orthologous genes were examined among different genomes. Using orthologous genes for the comparisons guaranteed that differences revealed in physical location would reflect changes in genome structure after speciation. We found that dynamic rearrangements have so frequently occurred in eubacterial genomes as to break operon structures during evolution, even after the relatively recent divergence between E. coli and H. influenzae. Interestingly, in such eubacterial genomes of high plasticity, we could find several highly conservative regions with the longest conserved region comprising the S10, spc, and α operons. This suggests that such exceptional conservative regions have undergone strong structural constraints during evolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00000052
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  • 7
    Electronic Resource
    Electronic Resource
    Constrained Evolution with Respect to Gene Overlap of Hepatitis B Virus (1997)
    Springer
    Journal of molecular evolution 44 (1997), S. S083 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Hepatitis B virus — Genetic classification — Constrained evolution — Overlapping gene
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. With the aim of elucidating the evolution of a hepadnavirus family, we constructed molecular phylogenetic trees for 27 strains of hepatitis B virus (HBV) using both the unweighted pair-grouping and neighbor-joining methods. All five gene regions, P, C, S, X, and preS, were used to construct the phylogenetic trees. Using the phylogenetic trees obtained, we classified these strains into five major groups in which the strains were closely related to each other. Our classification reinforced our previous view that genetic classification is not always compatible with conventional classification determined by serological subtypes. Moreover, constraints on the evolutionary process of HBV were analyzed for amino-acid-altering (nonsynonymous) and silent (synonymous) substitutions, because two-thirds of the open reading frame (ORF), P, contains alternating overlapping ORFs. In our unique analysis of this interesting gene structure of HBV, the most frequent synonymous substitutions were observed in the nonoverlapped parts of the P and C genes. On the other hand, the number of synonymous substitutions per nucleotide site for the S gene was quite low and appeared a strongly constrained evolution. Because the P gene overlaps the S gene in a different frame, the low rate of synonymous substitution for the S gene can be explained by the evolutionary constraints which are imposed on the overlapping gene region. In other words, synonymous substitutions in the S gene can cause amino acid changes in its overlapping region in a different frame. Thus, the evolution of HBV is constrained evolutionarily by the overlapping genes. We propose calling this mode of viral evolution ``constrained evolution.'' The evolution of HBV represents a typical constrained evolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00000061
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  • 8
    Electronic Resource
    Electronic Resource
    Patterns of nucleotide substitutions inferred from the phylogenies of the class I major histocompatibility complex genes (1992)
    Springer
    Journal of molecular evolution 35 (1992), S. 196-204 
    Details
    ISSN: 1432-1432
    Keywords: Major histocompatibility complex (MHC) ; HLA ; Antigen recognition site (ARS) ; Patterns of nucleotide substitutions ; Natural selection ; Functional constraint ; Pseudogene ; Neutrality
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Patterns of nucleotide substitutions in human major histocompatibility complex (MHC) class I genes were estimated by using phylogenetic trees of DNA sequences. The pattern is defined as a set of 12 parameters, each of which represents the relative frequency of substitutions from a particular nucleotide to another. The pattern at the antigen recognition sites (ARS) in functional MHC genes was remarkably different from that at the remaining coding region (non-ARS). In particular, the proportion of transitions among all the nucleotide substitutions (P s) was extremely low at the third codon positions of ARS. In the HLA-A genes, P s at the third codon positions was only 6% in ARS, whereas it was 69% in non-ARS. In HLA-B, the corresponding values were 30% in ARS and 80% in non-ARS, respectively. On the other hand, P s in a class I pseudogene (HLA-H) was 57%, which was in good agreement with P s in other pseudogenes. Because pseudogenes are selectively neutral, the pattern in pseudogenes is regarded as the pattern of spontaneous substitution mutations. In general, the pattern in functional genes that are subject to selective forces deviates from the pattern in pseudogenes. At the third codon positions in coding regions, transitions scarcely cause amino acid replacements, whereas about half of transversions do cause replacements. Accordingly, P s at the third codon positions decreases if amino acid replacements are accelerated by natural selection but increases if amino acids are conserved by functional constraint. Our observations imply that the ARS region is subject to natural selection favoring amino acid replacements, whereas the non-ARS region is subject to functional constraint.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00178595
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  • 9
    Electronic Resource
    Electronic Resource
    Patterns of nucleotide substitution in pseudogenes and functional genes (1982)
    Springer
    Journal of molecular evolution 18 (1982), S. 360-369 
    Details
    ISSN: 1432-1432
    Keywords: Neutral mutation ; Transitions and transversions ; Functional constraints ; Base content ; Substitution mutagenesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The pattern of point mutations is inferred from nucleotide substitutions in pseudogenes. The pattern obtained suggests that transition mutations occur somewhat more frequently than transversion mutations and that mutations result more often in A or T than in G or C. Our results are discussed with respect to the predictions from Topal and Fresco's model for the molecular basis of point (substitution) mutations (Nature 263:285–289, 1976). The pattern of nucleotide substitution at the first and second positions of codons in functional genes is quite similar to that in pseudogenes, but the relative frequency of the transition C→T in the sense strand is drastically reduced and those of the transversions C→G and G→C are doubled. The differences between the two patterns can be explained by the observation that in the protein evolution amino acid substitutions occur mainly between amino acids with similar biochemical properties (Grantham, Science 185:862–864, 1974). Our results for the patterns of nucleotide substitutions in pseudogenes and in functional genes lead to the prediction that both the coding and non-coding regions of protein coding genes should have high frequencies of A and T. Available data show that the non-coding regions are indeed high in A and T but the coding regions are low in T, though high in A.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01733904
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  • 10
    Electronic Resource
    Electronic Resource
    Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide (1982)
    Springer
    Journal of molecular evolution 18 (1982), S. 414-422 
    Details
    ISSN: 1432-1432
    Keywords: Molecular evolution ; Nucleotide substitution ; Evolutionary distance
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A formal mathematical analysis of Kimura's (1981) six-parameter model of nucleotide substitution for the case of unequal substitution rates among different pairs of nucleotides is conducted, and new formulae for estimating the number of nucleotide substitutions and its standard error are obtained. By using computer simulation, the validities and utilities of Jukes and Cantor's (1969) one-parameter formula, Takahata and Kimura's (1981) four-parameter formula, and our sixparameter formula for estimating the number of nucleotide substitutions are examined under three different schemes of nucleotide substitution. It is shown that the one-parameter and four-parameter formulae often give underestimates when the number of nucleotide substitutions is large, whereas the six-parameter formula generally gives a good estimate for all the three substitution schemes examined. However, when the number of nucleotide substitutions is large, the six-parameter and four-parameter formulae are often inapplicable unless the number of nucleotides compared is extremely large. It is also shown that as long as the mean number of nucleotide substitutions is smaller than one per nucleotide site the three formulae give more or less the same estimate regardless of the substitution scheme used.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01840889
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