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  • 1
    Electronic Resource
    Electronic Resource
    Determinants of Rate Variation in Mammalian DNA Sequence Evolution (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 610-621 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Molecular evolution — Molecular clock — Phylogeny — Metabolic rate — Generation time — Body size — Allometry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Attempts to analyze variation in the rates of molecular evolution among mammalian lineages have been hampered by paucity of data and by nonindependent comparisons. Using phylogenetically independent comparisons, we test three explanations for rate variation which predict correlations between rate variation and generation time, metabolic rate, and body size. Mitochondrial and nuclear genes, protein coding, rRNA, and nontranslated sequences from 61 mammal species representing 14 orders are used to compare the relative rates of sequence evolution. Correlation analyses performed on differences in genetic distance since common origin of each pair against differences in body mass, generation time, and metabolic rate reveal that substitution rate at fourfold degenerate sites in two out of three protein sequences is negatively correlated with generation time. In addition, there is a relationship between the rate of molecular evolution and body size for two nuclear-encoded sequences. No evidence is found for an effect of metabolic rate on rate of sequence evolution. Possible causes of variation in substitution rate between species are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02202109
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  • 2
    Electronic Resource
    Electronic Resource
    Testing the Extent of Sequence Similarity Among Viroids, Satellite RNAs, and Hepatitis Delta Virus (2000)
    Springer
    Journal of molecular evolution 50 (2000), S. 98-102 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Viroids — Satellite RNAs — Hepatitis delta virus — Monte Carlo simulation — Sequence similarity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. A Monte Carlo method was used to test the extent of sequence similarity among viroids, satellite RNAs, and hepatitis delta virus. This analysis revealed that there is insufficient sequence similarity among these pathogens to support the hypothesis that they have a common evolutionary origin. Furthermore, while definite patterns of sequence similarity were observed among some viroids, there was a clear lack of overall similarity, indicating that a monophyletic origin for even this group cannot be reliably supported from sequence data alone.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002399910011
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  • 3
    Electronic Resource
    Electronic Resource
    Recombination between sequences of hepatitis B virus from different genotypes (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 97-102 
    Details
    ISSN: 1432-1432
    Keywords: Hepatitis B virus ; Recombination ; Phylogeny ; Coinfection ; Genotypes ; Antigenic subtypes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A comparison of 25 hepatitis B virus (HBV) isolates for which complete genome sequences are available revealed two that occupied different positions in phylogenetic trees reconstructed from different open reading frames. Further analysis indicated that this incongruence was the result of recombination between viruses of different genomic and antigenic types. Both putative recombinants originated from geographic regions where multiple genotypes are known to cocirculate. A search of the sequence databases showed evidence of similar intergenotypic recombinants. These observations indicate that recombination between divergent strains may represent an important source of genetic variation in HBV.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02198834
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  • 4
    Electronic Resource
    Electronic Resource
    Elucidating the Population Histories and Transmission Dynamics of Papillomaviruses Using Phylogenetic Trees (1997)
    Springer
    Journal of molecular evolution 44 (1997), S. 199 -206 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Papillomaviruses — Phylogeny — Molecular clock — Population history — Transmission dynamics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Using gene genealogies constructed from gene sequence data, we show that both the mucosal and cutaneous papillomaviruses (PV)—supergroups A and B—appear to have been transmitted through susceptible populations faster than exponentially. The data and methods involved (1) examining the PV database for phylogenetic signal in an L1 open reading frame (ORF) fragment and an E1 ORF segment, (2) demonstrating that the same two fragments have evolved in a way consistent with a molecular clock, and (3) applying methods of phylogenetic tree analysis that test different scenarios for the dynamics of viral transmission within populations. The results indicate increases in PV populations of both supergroups A and B in the recent past. This form of the increases, which fit a null model of population growth with an exponent increasing in time, is compatible with the fact that human populations have grown at a faster than exponential rate, thus increasing the numbers of susceptible hosts for HPVs. There are, however, indications that the population of supergroup A has now stopped increasing in size.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006136
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  • 5
    Electronic Resource
    Electronic Resource
    The Power of Relative Rates Tests Depends on the Data (2000)
    Springer
    Journal of molecular evolution 50 (2000), S. 296-301 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Molecular clock — Substitution rate — Phylogeny — Molecular date estimates — Tajima test — Rate variation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. One of the most useful features of molecular phylogenetic analyses is the potential for estimating dates of divergence of evolutionary lineages from the DNA of extant species. But lineage-specific variation in rate of molecular evolution complicates molecular dating, because a calibration rate estimated from one lineage may not be an accurate representation of the rate in other lineages. Many molecular dating studies use a ``clock test'' to identify and exclude sequences that vary in rate between lineages. However, these clock tests should not be relied upon without a critical examination of their effectiveness at removing rate variable sequences from any given data set, particularly with regard to the sequence length and number of variable sites. As an illustration of this problem we present a power test of a frequently employed triplet relative rates test. We conclude that (1) relative rates tests are unlikely to detect moderate levels of lineage-specific rate variation (where one lineage has a rate of molecular evolution 1.5 to 4.0 times the other) for most commonly used sequences in molecular dating analyses, and (2) this lack of power is likely to result in substantial error in the estimation of dates of divergence. As an example, we show that the well-studied rate difference between murid rodents and great apes will not be detected for many of the sequences used to date the divergence between these two lineages and that this failure to detect rate variation is likely to result in consistent overestimation the date of the rodent–primate split.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002399910034
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  • 6
    Electronic Resource
    Electronic Resource
    Recombination Between Sequences of Hepatitis B Virus from Different Genotypes (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 97-102 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Hepatitis B virus — Recombination — Phylogeny — Coinfection — Genotypes — Antigenic subtypes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. A comparison of 25 hepatitis B virus (HBV) isolates for which complete genome sequences are available revealed two that occupied different positions in phylogenetic trees reconstructed from different open reading frames. Further analysis indicated that this incongruence was the result of recombination between viruses of different genomic and antigenic types. Both putative recombinants originated from geographic regions where multiple genotypes are known to cocirculate. A search of the sequence databases showed evidence of similar intergenotypic recombinants. These observations indicate that recombination between divergent strains may represent an important source of genetic variation in HBV.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02198834
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  • 7
    Electronic Resource
    Electronic Resource
    Determinants of rate variation in mammalian DNA sequence evolution (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 610-621 
    Details
    ISSN: 1432-1432
    Keywords: Molecular evolution ; Molecular clock ; Phylogeny ; Metabolic rate ; Generation time ; Body size ; Allometry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Attempts to analyze variation in the rates of molecular evolution among mammalian lineages have been hampered by paucity of data and by nonindependent comparisons. Using phylogenetically independent comparisons, we test three explanations for rate variation which predict correlations between rate variation and generation time, metabolic rate, and body size. Mitochondrial and nuclear genes, protein coding, rRNA, and nontranslated sequences from 61 mammal species representing 14 orders are used to compare the relative rates of sequence evolution. Correlation analyses performed on differences in genetic distance since common origin of each pair against differences in body mass, generation time, and metabolic rate reveal that substitution rate at fourfold degenerate sites in two out of three protein sequences is negatively correlated with generation time. In addition, there is a relationship between the rate of molecular evolution and body size for two nuclear-encoded sequences. No evidence is found for an effect of metabolic rate on rate of sequence evolution. Possible causes of variation in substitution rate between species are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02202109
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  • 8
    Electronic Resource
    Electronic Resource
    Human immunodeficiency virus Phylogeny and the origin of HIV-1 (2001)
    [s.l.] : Nature Publishing Group
    Nature 410 (2001), S. 1047-1048 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The origin of human immunodeficiency virus type 1 (HIV-1) is controversial. We show here that viruses obtained from the Democratic Republic of Congo in Africa have a quantitatively different phylogenetic tree structure from those sampled in other parts of the world. This indicates that the ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/35074179
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  • 9
    Electronic Resource
    Electronic Resource
    Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution (2001)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 409 (2001), S. 704-707 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The origin of the ratites, large flightless birds from the Southern Hemisphere, along with their flighted sister taxa, the South American tinamous, is central to understanding the role of plate tectonics in the distributions of modern birds and mammals. Defining the dates of ratite divergences ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/35055536
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  • 10
    Electronic Resource
    Electronic Resource
    Origin of AIDS Contaminated polio vaccine theory refuted (2004)
    [s.l.] : Nature Publishing Group
    Nature 428 (2004), S. 820-820 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Despite strong evidence to the contrary, speculation continues that the AIDS virus, human immunodeficiency virus type 1 (HIV-1), may have crossed into humans as a result of contamination of the oral polio vaccine (OPV). This ‘OPV/AIDS theory’ claims that chimpanzees from the ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/428820a
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