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  • 1
    Electronic Resource
    Electronic Resource
    Molecular systematics The platypus put in its place (1997)
    [s.l.] : Macmillan Magazines Ltd.
    Nature 387 (1997), S. 549-550 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The duck-billed platypus, an egglaying mammal, seems a contradiction in terms — not surprisingly, Richard Owen, a leading nineteenth-century anatomist, refused to believe the first reports from Australia that a platypus in captivity had laid eggs, because the animal is otherwise largely so ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/42352
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  • 2
    Electronic Resource
    Electronic Resource
    Gene transfer to the nucleus and the evolution of chloroplasts (1998)
    [s.l.] : Macmillan Magazines Ltd.
    Nature 393 (1998), S. 162-165 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Photosynthetic eukaryotes, particularly unicellular forms, possess a fossil record that is either wrought with gaps or difficult to interpret, or both. Attempts to reconstruct their evolution have focused on plastid phylogeny, but were limited by the amount and type of phylogenetic information ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/30234
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  • 3
    Electronic Resource
    Electronic Resource
    Phylogenetic Position of the Mitochondrion-Lacking Protozoan Trichomonas tenax, Based on Amino Acid Sequences of Elongation Factors 1α and 2 (1997)
    Springer
    Journal of molecular evolution 44 (1997), S. 98 -105 
    Details
    ISSN: 1432-1432
    Keywords: Key words:Trichomonas tenax— Elongation factor 1α— Elongation factor 2 — Mitochondrion-lacking protozoa — Protein evolution — Phylogenetic tree
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Major parts of amino-acid-coding regions of elongation factor (EF)-1α and EF-2 in Trichomonas tenax were amplified by PCR from total genomic DNA and the products were cloned into a plasmid vector, pGEM-T. The three clones from each of the products of the EF-1α and EF-2 were isolated and sequenced. The insert DNAs of the clones containing EF-1α coding regions were each 1,185 bp long with the same nucleotide sequence and contained 53.1% of G + C nucleotides. Those of the clones containing EF-2 coding regions had two different sequences; one was 2,283 bp long and the other was 2,286 bp long, and their G + C contents were 52.5 and 52.9%, respectively. The copy numbers of the EF-1α and EF-2 gene per chromosome were estimated as four and two, respectively. The deduced amino acid sequences obtained by the conceptual translation were 395 residues from EF-1α and 761 and 762 residues from the EF-2s. The sequences were aligned with the other eukaryotic and archaebacterial EF-1αs and EF-2s, respectively. The phylogenetic position of T. tenax was inferred by the maximum likelihood (ML) method using the EF-1α and EF-2 data sets. The EF-1α analysis suggested that three mitochondrion-lacking protozoa, Glugea plecoglossi, Giardia lamblia, and T. tenax, respectively, diverge in this order in the very early phase of eukaryotic evolution. The EF-2 analysis also supported the divergence of T. tenax to be immediately next to G. lamblia.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006127
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  • 4
    Electronic Resource
    Electronic Resource
    The Origin of Chlorarachniophyte Plastids, as Inferred from Phylogenetic Comparisons of Amino Acid Sequences of EF-Tu (1997)
    Springer
    Journal of molecular evolution 45 (1997), S. 682-687 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Chlorarachniophyceae — Endosymbiosis — Origin of plastids — Elongation factor Tu — Protein phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. A molecular phylogenetic analysis of elongation factor Tu (EF-Tu) proteins from plastids was performed in an attempt to identify the origin of chlorarachniophyte plastids, which are considered to have evolved from the endosymbiont of a photosynthetic eukaryote. Partial sequences of the genes for plastid EF-Tu proteins (1,080–1,089 bp) were determined for three algae that contain chlorophyll b, namely, Gymnochlora stellata (Chlorarachniophyceae), Bryopsis maxima (Ulvophyceae), and Pyramimonas disomata (Prasinophyceae). The deduced amino acid sequences were used to construct phylogenetic trees of the plastid and bacterial EF-Tu proteins by the maximum likelihood, the maximum parsimony, and the neighbor joining methods. The trees obtained in the present analysis suggest that all plastids that contain chlorophyll b are monophyletic and that the chlorarachniophyte plastids are closely related to those of the Ulvophyceae. The phylogenetic trees also suggest that euglenophyte plastids are closely related to prasinophycean plastids. The results indicate that the chlorarachniophyte plastids evolved from a green algal endosymbiont that was closely related to the Ulvophyceae and that at least two secondary endosymbiotic events have occurred in the lineage of algae with plastids that contain chlorophyll b.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006272
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  • 5
    Electronic Resource
    Electronic Resource
    Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders (1998)
    Springer
    Journal of molecular evolution 47 (1998), S. 307-322 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Mammalian phylogeny — Mitochondrial proteins — Trees of individual proteins — Maximum-likelihood method — ND1 — Convergent evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The phylogenetic relationship among primates, ferungulates (artiodactyls + cetaceans + perissodactyls + carnivores), and rodents was examined using proteins encoded by the H strand of mtDNA, with marsupials and monotremes as the outgroup. Trees estimated from individual proteins were compared in detail with the tree estimated from all 12 proteins (either concatenated or summing up log-likelihood scores for each gene). Although the overall evidence strongly suggests ((primates, ferungulates), rodents), the ND1 data clearly support another tree, ((primates, rodents), ferungulates). To clarify whether this contradiction is due to (1) a stochastic (sampling) error; (2) minor model-based errors (e.g., ignoring site rate variability), or (3) convergent and parallel evolution (specifically between either primates and rodents or ferungulates and the outgroup), the ND1 genes from many additional species of primates, rodents, other eutherian orders, and the outgroup (marsupials + monotremes) were sequenced. The phylogenetic analyses were extensive and aimed to eliminate the following artifacts as possible causes of the aberrant result: base composition biases, unequal site substitution rates, or the cumulative effects of both. Neither more sophisticated evolutionary analyses nor the addition of species changed the previous conclusion. That is, the statistical support for grouping rodents and primates to the exclusion of all other taxa fluctuates upward or downward in quite a tight range centered near 95% confidence. These results and a site-by-site examination of the sequences clearly suggest that convergent or parallel evolution has occurred in ND1 between primates and rodents and/or between ferungulates and the outgroup. While the primate/rodent grouping is strange, ND1 also throws some interesting light on the relationships of some eutherian orders, marsupials, and montremes. In these parts of the tree, ND1 shows no apparent tendency for unexplained convergences.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006389
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  • 6
    Electronic Resource
    Electronic Resource
    Model of Amino Acid Substitution in Proteins Encoded by Mitochondrial DNA (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 459-468 
    Details
    ISSN: 1432-1432
    Keywords: Key words: General reversible Markov model — Amino acid substitution — Maximum likelihood method
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Mitochondrial DNA (mtDNA) sequences are widely used for inferring the phylogenetic relationships among species. Clearly, the assumed model of nucleotide or amino acid substitution used should be as realistic as possible. Dependence among neighboring nucleotides in a codon complicates modeling of nucleotide substitutions in protein-encoding genes. It seems preferable to model amino acid substitution rather than nucleotide substitution. Therefore, we present a transition probability matrix of the general reversible Markov model of amino acid substitution for mtDNA-encoded proteins. The matrix is estimated by the maximum likelihood (ML) method from the complete sequence data of mtDNA from 20 vertebrate species. This matrix represents the substitution pattern of the mtDNA-encoded proteins and shows some differences from the matrix estimated from the nuclear-encoded proteins. The use of this matrix would be recommended in inferring trees from mtDNA-encoded protein sequences by the ML method.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00013324
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  • 7
    Electronic Resource
    Electronic Resource
    Novel Phylogeny of Whales Supported by Total Molecular Evidence (1997)
    Springer
    Journal of molecular evolution 44 (1997), S. S117 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Cetacean evolution — Molecular phylogeny — Total evidence — Maximum likelihood — Sperm whale
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Given that the analysis of a single gene does not necessarily provide unambiguous phylogenetic information, it is important to scrutinize as many genes as possible. Using the maximum likelihood method, particularly suitable for a total evidence approach, we evaluated the phylogenetic information provided by the 12S and 16S rRNA, cytochrome b, and myoglobin sequence data in order to resolve one of the most debated phylogenetic questions: the relationships among the major groups of cetaceans. Our analysis strongly supports the hypothesis that sperm whales are closer to baleen whales than to dolphins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00000062
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  • 8
    Electronic Resource
    Electronic Resource
    Maximum likelihood inference of protein phylogeny and the origin of chloroplasts (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 151-160 
    Details
    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
    URL: http://dx.doi.org/10.1007/BF02109483
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  • 9
    Electronic Resource
    Electronic Resource
    Toward a more accurate time scale for the human mitochondrial DNA tree (1993)
    Springer
    Journal of molecular evolution 37 (1993), S. 347-354 
    Details
    ISSN: 1432-1432
    Keywords: Third positions of codons ; Control region ; Heterogeneity among sites ; Molecular clock
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Several estimates of the time of occurrence of the most recent common mitochondrial DNA (mtDNA) ancestor of modern humans have been made. Estimates derived from noncoding regions based on a model that classifies sites into two categories (variable and invariable) have been consistently older than those derived from the third positions of codons. This discrepancy can be attributed to a violation of the assumption of rate homogeneity among variable sites when analyzing the noncoding regions. Additional data from the partial control region sequences allow us to take into account some of this further heterogeneity. By assigning the sites to three classes (highly variable, moderately variable, and invariable) and by assuming that the last common mtDNA ancestor of humans and chimpanzees lived 4 million years ago, the most recent common mtDNA ancestor of humans is estimated to have occurred 211,000 ±111,000 years ago (±1 SE), consistent with the estimate, 101,000 ± 52,000 years, made from third positions of codons and also with those proposed previously. We used the same technique to estimate when a putative expansion of modern humans out of Africa took place and estimated a time of 89,000 ± 69,000 years ago. Even though the standard errors of these estimates are large, they allow us to reject the multiregional hypothesis of modern human origin.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00178865
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  • 10
    Electronic Resource
    Electronic Resource
    Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: Rapid evolution in warm-blooded vertebrates (1993)
    Springer
    Journal of molecular evolution 36 (1993), S. 270-281 
    Details
    ISSN: 1432-1432
    Keywords: Protein phylogeny ; Maximum likelihood ; Dayhoff model ; Change of evolutionary rate ; Relaxation of selective constraint
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary By using complete sequence data of mitochondrial DNAs, three Markov models (Day-hoff, Proportional, and Poisson models) for amino acid substitutions during evolution were applied in maximum likelihood analyses of mitochondrially encoded proteins to estimate a phylogenetic tree depicting human, cow, whale, and murids (mouse and rat), with chicken, frog, and carp as outgroups. A cow/whale clade was confirmed with a more than 99.8% confidence level by any of the three models, but the branching order among human, murids, and the cow/whale clade remained uncertain. It turned out that the Dayhoff model is by far the most appropriate model among the alternatives in approximating the amino acid substitutions of mitochondrially encoded proteins, which is consistent with a previous analysis of a more limited data set. It was shown that the substitution rate of mitochondrially encoded proteins has increased in the order of fishes, amphibians, birds, and mammals and that the rate in mammals is at least six times, probably an order of magnitude, higher than that in fishes. The higher evolutionary rate in birds and mammals than in amphibians and fishes was attributed to relaxation of selective constraints operating on proteins in warm-blooded vertebrates and to high mutation rate of bird and mammalian mitochondrial DNAs.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00160483
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