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  • Amino acid substitution  (1)
  • Eukaryotic kingdoms  (1)
  • Evolutionary tree  (1)
  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 31 (1990), S. 151-160 
    ISSN: 1432-1432
    Keywords: Evolutionary tree ; Amino acid sequence ; Insertion/deletion ; Bootstrap probability ; psbA ; Prochlorothrix
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A maximum likelihood method for inferring protein phylogeny was developed. It is based on a Markov model that takes into account the unequal transition probabilities among pairs of amino acids and does not assume constancy of rate among different lineages. Therefore, this method is expected to be powerful in inferring phylogeny among distantly related proteins, either orthologous or parallogous, where the evolutionary rate may deviate from constancy. Not only amino acid substitutions but also insertion/deletion events during evolution were incorporated into the Markov model. A simple method for estimating a bootstrap probability for the maximum likelihood tree among alternatives without performing a maximum likelihood estimation for each resampled data set was developed. These methods were applied to amino acid sequence data of a photosynthetic membrane protein,psbA, from photosystem II, and the phylogeny of this protein was discussed in relation to the origin of chloroplasts.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1432-1432
    Keywords: Entamoeba histolytica ; Protozoa lacking mitochondria ; Eukaryotic kingdoms ; Elongation factor-1α ; Maximum likelihood ; Protein phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Phylogenetic analyses of ribosomal RNA sequences have played an important role in the study of early evolution of life. However, Loomis and Smith suggested that the ribosomal RNA tree is sometimes misleading—especially when G+C content differs widely among lineages—and that a protein tree from amino acid sequences may be more reliable. In this study, we analyzed amino acid sequence data of elongation factor-1α by a maximum likelihood method to clarify branching orders in the early evolution of eukaryotes. Contrary to Sogin et al.'s tree of small-subunit ribosomal RNA, a protozoan species, Entamoeba histolytica, that lacks mitochondria was shown to have diverged from the line leading to eukaryotes with mitochondria before the latter separated into several kingdoms. This indicates that Entamoeba is a living relic of the earliest phase of eukaryotic evolution before the symbiosis of protomitochondria occurred. Furthermore, this suggests that, among eukaryotic kingdoms with mitochondria, Fungi is the closest relative of Animalia, and that a cellular slime mold, Dictyostelium discoideum, had not diverged from the line leading to Plantae-Fungi-Animalia before these three kingdoms separated.
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 12 (1979), S. 219-236 
    ISSN: 1432-1432
    Keywords: Amino acid substitution ; Physico-chemical difference ; Conservative ; Low-constraint ; Protein evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The frequency of amino acid substitutions, relative to the frequency expected by chance, decreases linearly with the increase in physico-chemical differences between amino acid pairs involved in a substitution. This correlation does not apply to abnormal human hemoglobins. Since abnormal hemoglobins mostly reflect the process of mutation rather than selection, the correlation manifest during protein evolution between substitution frequency and physico-chemical difference in amino acids can be attributed to natural selection. Outside of ‘abnormal’ proteins, the correlation also does not apply to certain regions of proteins characterized by rapid rates of substitution. In these cases again, except for the largest physico-chemical differences between amino acid pairs, the substitution frequencies seem to be independent of the physico-chemical parameters. The limination of the substituents involving the largest physicochemical differences can once more be attributed to natural selection. For smaller physico-chemical differences, natural selection, if it is operating in the polypeptide regions, must be based on parameters other than those examined.
    Type of Medium: Electronic Resource
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