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  • Computer simulation  (1)
  • DNA hybridization  (1)
  • Geometric density  (1)
  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 11 (1978), S. 75-85 
    ISSN: 1432-1432
    Keywords: Maximum parsimony ; Populous path algorithm ; Computer simulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Goodman et al.'s (1974) populous path algorithm for estimating hidden mutational change in protein evolution is designed to be used as an adjunct to the maximum parsimony method. When the algorithm is so used, the augmented maximum parsimony distances, far from being overestimates, are underestimates of the actual number of nucleotide substitutions which occur in Tateno and Nei's (1978) computer simulation by the Poisson process model, even when the simulation is carried out at two and a half times the sequence density. Although underestimates, our evidence shows that they are nevertheless more accurate than estimates obtained by a Poisson correction. In the maximum parsimony reconstruction, there is a bias towards overrepresenting the number of shared nucleotide identities between adjacent ancestral and descendant nodal sequences with the bias being stronger in those portions of the evolutionary tree sparser in sequence data. Because of this particular property of maximum parsimony reconstructed sequences, the conclusions of Tateno and Nei concerning the statistical properties of the populous path algorithm are invalid. We conclude that estimates of protein evolutionary rates by the maximum parsimony - populous path approach will become more accurate rather than less as larger numbers of closely related species are included in the analysis.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular evolution 19 (1983), S. 437-448 
    ISSN: 1432-1432
    Keywords: Base substitution patterns ; Mutability ; Poisson density ; Geometric density ; Negative binomial density ; Natural selection ; Amino acids ; Proteins ; Genes ; Nucleotides
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have examined the extensive amino acid sequence data now available for five protein families — the α crystallin A chain, myoglobin, alpha and beta hemoglobin, and the cytochromesc — with the goal of estimating the true spatial distribution of base substitutions within genes that code for proteins. In every case the commonly used Poisson density failed to even approximate the experimental pattern of base substitution. For the 87 species of beta hemoglobin examined, for example, the probability that the observed results were from a Poisson process was the minuscule 10−44. Analogous results were obtained for the other functional families. All the data were reasonably, but not perfectly, described by the negative binomial density. In particular, most of the data were described by one of the very simple limiting forms of this density, the geometric density. The implications of this for evolutionary inference are discussed. It is evident that most estimates of total base substitutions between genes are badly in need of revision.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1432-1432
    Keywords: Noncoding nucleotide sequences ; DNA hybridization ; Primate phylogeny ; Maximum parsimony ; Cladistic classification
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The genetic distances among primate lineages estimated from orthologous noncoding nucleotide sequences of β-type globin loci and their flanking and intergenic DNA agree closely with the distances (delta T50H values) estimated by cross hybridization of total genomic single-copy DNAs. These DNA distances and the maximum parsimony tree constructed for the nucleotide sequence orthologues depict a branching pattern of primate lineages that is essentially congruent with the picture from phylogenetic analyses of morphological characters. The molecular evidence, however, resolves ambiguities in the morphological picture and provides an objective view of the cladistic position of humans among the primates. The molecular data group humans with chimpanzees in subtribe Hominina, with gorillas in tribe Hominini, orangutans in subfamily Homininae, gibbons in family Hominidae, Old World monkeys in infraorder Catarrhini, New World monkeys in semisuborder Anthropoidea, tarsiers in suborder Haplorhini, and strepsirhines (lemuriforms and lorisiforms) in order Primates. A seeming incongruency between organismal and molecular levels of evolution, namely that morphological evolution appears to have speeded up in higher primates, especially in the lineage to humans, while molecular evolution has slowed down, may have the trivial explanation that relatively small genetic changes may sometimes result in marked phenotypic changes.
    Type of Medium: Electronic Resource
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