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  • Evolution  (300)
  • Springer  (298)
  • UCL Press  (2)
  • Annual Reviews
  • Blackwell Publishing Ltd
  • 2020-2024  (3)
  • 2005-2009
  • 1990-1994  (178)
  • 1980-1984  (67)
  • 1975-1979  (52)
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  • 1
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    Bloomsbury Scientists (2021)
    UCL Press
    Details
    Publication Date: 2024-03-23
    Description: Bloomsbury Scientists is the story of the network of scientists and artists living in a square mile of London before and after the First World War. This inspired group of men and women viewed creativity and freedom as the driving force behind nature, and each strove to understand this in their own inventive way. Their collective energy changed the social mood of the era and brought a new synthesis of knowledge to ideas in science and art. Class barriers were threatened as power shifted from the landed oligarchy to those with talent and the will to make a difference. A time of unexpected opportunities, from the new disciplines of Genetics and Ecology to Post-Impressionism and beyond, Michael Boulter seamlessly weaves together the stories originating from Bloomsbury’s laboratories, libraries and studios. He narrates the breakthroughs of scientists such as Ray Lankester and Marie Stopes alongside the creative outputs of H. G. Wells and Virginia Woolf, among many others, and intricately connects them all through personal friendships, grievances, quarrels and affections. Bloomsbury Scientists offers a fresh and crucial perspective on this history at a time when the complex relationship between science and art continues to be debated.
    Keywords: london ; history of science ; bloomsbury ; scientists ; Biology ; Charles Darwin ; Evolution ; Francis Galton ; thema EDItEUR::1 Place qualifiers::1D Europe::1DD Western Europe::1DDU United Kingdom, Great Britain ; thema EDItEUR::N History and Archaeology::NH History::NHD European history ; thema EDItEUR::P Mathematics and Science::PD Science: general issues::PDX History of science
    Language: English
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  • 2
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    The Pangenome (2021)
    Springer Nature | Springer
    Details
    Publication Date: 2024-04-05
    Description: This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.
    Keywords: Microbial Genetics and Genomics ; Evolutionary Biology ; Genetics and Population Dynamics ; Microbial Ecology ; Human Genetics ; Genetics and Genomics ; Comparative genomics ; Metagenomics ; Microbial Population Analysis ; Pangenome Profile ; Supra-Genome Analysis ; Adaptive Evolution ; Computational Tools ; Bioinformatic Genomics ; Core Dispensable Genome ; Selection, Recombination, Composition ; Acquired Resistance ; Bacterial Species Concept ; Genomic Diversity ; Bacterial Ecology, Microevolution ; Open Access ; Pan-metagenomics ; Pan-microbiomics ; Pan-epigenome ; Gene Transfer ; Pan-phenomes ; Microbiology (non-medical) ; Genetics (non-medical) ; Evolution ; Applied mathematics ; Ecological science, the Biosphere ; Medical genetics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical) ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAJ Evolution ; thema EDItEUR::P Mathematics and Science::PB Mathematics::PBW Applied mathematics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAF Ecological science, the Biosphere ; thema EDItEUR::M Medicine and Nursing::MF Pre-clinical medicine: basic sciences::MFN Medical genetics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical)
    Language: English
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  • 3
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    The Origins of Self (2021)
    UCL Press
    Details
    Publication Date: 2024-03-24
    Description: The Origins of Self explores the role that selfhood plays in defining human society, and each human individual in that society. It considers the genetic and cultural origins of self, the role that self plays in socialisation and language, and the types of self we generate in our individual journeys to and through adulthood. Edwardes argues that other awareness is a relatively early evolutionary development, present throughout the primate clade and perhaps beyond, but self-awareness is a product of the sharing of social models, something only humans appear to do. The self of which we are aware is not something innate within us, it is a model of our self produced as a response to the models of us offered to us by other people. Edwardes proposes that human construction of selfhood involves seven different types of self. All but one of them are internally generated models, and the only non-model, the actual self, is completely hidden from conscious awareness. We rely on others to tell us about our self, and even to let us know we are a self.
    Keywords: Self ; Selfhood ; Anthropology ; Psychology ; Linguistics ; Evolution ; anthropology ; philosophy ; thema EDItEUR::C Language and Linguistics::CF Linguistics::CFA Philosophy of language ; thema EDItEUR::C Language and Linguistics::CF Linguistics::CFD Psycholinguistics and cognitive linguistics ; thema EDItEUR::J Society and Social Sciences::JH Sociology and anthropology ; thema EDItEUR::J Society and Social Sciences::JM Psychology::JMR Cognition and cognitive psychology ; thema EDItEUR::J Society and Social Sciences::JM Psychology::JMS Psychology: the self, ego, identity, personality ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues
    Language: English
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  • 4
    Electronic Resource
    Electronic Resource
    Can the theory of evolution be falsified? (1984)
    Springer
    Acta biotheoretica 33 (1984), S. 35-50 
    Details
    ISSN: 1572-8358
    Keywords: Evolution ; falsification ; Darwinism ; philosophy of science
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In this paper we discuss the epistemological positions of evolution theories. A sharp distinction is made between the theory that species evolved from common ancestors along specified lines of descent (here called “the theory of common descent”), and the theories intended as causal explanations of evolution (e.g. Lamarck's and Darwin's theory). The theory of common descent permits a large number of predictions of new results that would be improbable without evolution. For instance, (a) phylogenetic trees have been validated now; (b) the observed order in fossils of new species discovered since Darwin's time could be predicted from the theory of common descent; (c) owing to the theory of common descent, the degrees of similarity and difference in newly discovered properties of more or less related species could be predicted. Such observations can be regarded as attempts to falsify the theory of common descent. We conclude that the theory of common descent is an easily-falsifiable & often-tested & still-not-falsified theory, which is the strongest predicate a theory in an empirical science can obtain. Theories intended as causal explanations of evolution can be falsified essentially, and Lamarck's theory has been falsified actually. Several elements of Darwin's theory have been modified or falsified: new versions of a theory of evolution by natural selection are now the leading scientific theories on evolution. We have argued that the theory of common descent and Darwinism are ordinary, falsifiable scientific theories.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00045845
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  • 5
    Electronic Resource
    Electronic Resource
    On the possible role of montmorillonites in prebiotic peptide formation (1994)
    Springer
    Monatshefte für Chemie 125 (1994), S. 1033-1039 
    Details
    ISSN: 1434-4475
    Keywords: Prebiotic peptide formation ; Evolution ; Clay catalysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Description / Table of Contents: Zusammenfassung Die Fähigkeit von Tonmineralien der Montmorillonitklasse zur Katalyse von Peptidbildungsreaktionen aus Aminosäuren in wäßriger Lösung wurde am Beispiel von Glyzin und Kupfer sowie Kalzium und Morillonit untersucht. Experimente mit Verdampfungszyklen haben gezeigt, daß kleinere Mengen von Di- und Tripeptiden aus der Aminosäure gebildet werden. Die weitere Polymerisation von Dipeptiden hingegen scheint wesentlich leichter in diesem Reaktionssystem zu verlaufen als der Anfangsschritt der Bildung des Dipeptides. Eine mögliche Rolle von Tonmineralien in der präbiotischen Peptidevolution kann daher in der Verlängerung von Peptidketten gesehen werden. Kupferionen in der Tonmatrix zeigen keinerlei Vorteile gegenüber den üblichen Kalziumionen, die in natürlichem Montmorillonit vorkommen.
    Notes: Summary The ability of montmorillonite clay minerals for catalyzing peptide formation from amino acids in aqueous solution has been investigated using glycine and Cu2+ and Ca2+ containing montmorillonites as reaction systems. Evaporation cycle experiments showed that minor amounts of di- and tripeptide are formed from the amino acid. Further polymerization of dipeptide, however, seems to be more favoured by this reaction system than the initial step of dipeptide formation, and a possible role of clays in prebiotic peptide evolution could be seen therefore in the prolongation of peptide chains. Cu2+ ions in the clay matrix did not show any advantage over the usual Ca2+ ions embedded in natural montmorillonite.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00811510
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  • 6
    Electronic Resource
    Electronic Resource
    Die biotheoretischen Mängel der Evolutionären Erkenntnistheorie (1990)
    Springer
    Journal for general philosophy of science 21 (1990), S. 309-328 
    Details
    ISSN: 1572-8587
    Keywords: Evolution ; evolutionäre Erkenntnistheorie ; Organismus ; Autonomie ; Abbildungskritik
    Source: Springer Online Journal Archives 1860-2000
    Topics: Philosophy , Nature of Science, Research, Systems of Higher Education, Museum Science
    Notes: Summary The concept of evolutionary epistemology has been critically discussed by philosophers who have mainly pointed to unacceptable philosophical tenets (cf. Vittorio Hösle, this Journal, Vol. 19 (1988), pp. 348–377). However, as most philosophers are extremely reluctant to critically treat the biological theories on which the ideas of evolutionary epistemology are based, the invalid concepts of adaption escaped their critical scrutiny. Therefore the influence of preconceived biological theories on the biological basis of evolutionary epistemology and the distorting consequences on the philosophical level could not be elaborated. The following context sketches a new view of organismic reasoning and its impact on evolutionary aspects of epistemology. The basic theorem of adaptation is shown to be unacceptable and invalid if organisms are conceived as autonomous entities which can only evolve according to their specific internal organismic properties.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01801041
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  • 7
    Electronic Resource
    Electronic Resource
    Vesicular-arbuscular mycorrhizae of epiphytes (1993)
    Springer
    Mycorrhiza 4 (1993), S. 1-4 
    Details
    ISSN: 1432-1890
    Keywords: Tropics ; Mycotrophy ; Spore dispersal ; Community composition ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract This article introduces reports concerning the occurrence of mycorrhizae on epiphytes in Costa Rica, Ethiopia, Venezuela, Malaysia, and Mexico. Association of vesicular-arbuscular mycorrhizal fungi with the roots of epiphytes is not well known. Vesicular-arbuscular mycorrhizal fungi (VAM) do occur in the canopy, but are uncommon except in certain sites and host taxa. Occurrence of VAM on epiphytes may be constrained by mineral nutrient availability and spatial heterogeneity in the canopy. Nevertheless, epiphytes present unique opportunities to study influences of mycorrhizae on vascular plant community composition and on the evolution of mycorrhizal associations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00203242
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  • 8
    Electronic Resource
    Electronic Resource
    Kuehneltiella terricola gen. nov., sp. nov. — a carnivorous ciliate (Protozoa, Ciliophora) from a sandy soil in Australia (1990)
    Springer
    Biology and fertility of soils 9 (1990), S. 110-118 
    Details
    ISSN: 1432-0789
    Keywords: Kuehneltiella terricola gen. nov., sp. nov. ; Soil ciliates ; Colpodidae ; Systematics ; Evolution ; Australia
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary The morphology and biology of the colpodid ciliate Kuehneltiella terricola gen. nov., sp. nov. has been investigated using living organisms, various silver impregnation methods, and scanning electron microscopy. The new species has been isolated in soil from central Australia and might be endemic to this continent. The new genus Kuehneltiella differs from its nearest relative, Bresslaua, in having a right oral polykinetid composed of a single row of dikinetids. A reinvestigation of Lynn's slides of Bresslaua insidiatrix showed that, contrary to the statement of Lynn (1979), this species has a typic colpodid right oral polykinetid, i.e., composed of many short, disordered kineties. A brief review of the literature suggests that simple, single-rowed, right oral polykinetids are apomorphic in the colpodids s. str. Further, this special character has obviously evolved independently several times within the class Colpodea and even within the colpodids s. str. An illustrated key to the genera of the family Colpodidae is provided.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00335792
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  • 9
    Electronic Resource
    Electronic Resource
    Evolutionary studies on the Assulina-Valkanovia complex (Rhizopoda, Testaceafilosia) in Sphagnum and soil (1990)
    Springer
    Biology and fertility of soils 9 (1990), S. 95-100 
    Details
    ISSN: 1432-0789
    Keywords: Assulina-Valkanovia ; Testacea ; Polymorphism ; Genotypes ; Evolution ; Spruce forest ; Sphagnum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary The taxonomy and evolution of the Assulina-Valkanovia complex were investigated in a spruce forest soil which included a Sphagnum plot (GDR, Thuringia). In both habitats Assulina muscorum occurred in two colour forms (brown and colourless) and four shapes. A quantified phenospectrum from Assulina muscorum was obtained. The four shapes were distributed differently between the brown and the colourless forms in Sphagnum and soil. The shell measurements showed statistically significant differences between the brown and the colourless forms. Even between the two brown populations there were some significant differences. Each of the four shape types of brown and of colourless Assulina can be kept in clonal cultures for some time. However, without selection, single cultures eventually revert to mixed types. The four shape types show different degrees of stability. These colour and shape forms are genotypes, which can also occur for short periods in the natural habitats. The brown populations in Sphagnum and in the soil were dominated by different shape types during the period of investigation. Valkanovia elegans cannot be distinguished from Assulina muscorum type 4, but Valkanovia can inhabit both upper and lower soil horizons, whereas Assulina and its forms lives exclusively in the upper horizon (litter). Valkanovia from the lower horizon is constant in clonal culture. The conclusion of the present investigation is that there are stable and unstable constellations within a changeable genome, which give asexual groups both a taxonomic structure and a continuum of forms. Selection can increase stability, by polygenic control of features.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00335790
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  • 10
    Electronic Resource
    Electronic Resource
    Incremental growth of a large volume, chemically zoned magma body: a study of the tephra sequence beneath the Rainier Mesa ash flow sheet of the Timber Mountain Tuff (1994)
    Springer
    Bulletin of volcanology 56 (1994), S. 377-385 
    Details
    ISSN: 1432-0819
    Keywords: Key wordsZoned magma body ; Chemical variation ; ash-flow sheets ; Tephra sequence ; Differentiation ; time constraints ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences
    Notes: Abstract The Rainier Mesa ash-flow is a large (1200 km3), 11.6 My old, chemically zoned unit that ranges in composition from 55 to 76% SiO2– one of the largest chemical ranges ever observed in a large volume ash-flow sheet. Two chemical trends occur in this sheet, a low silica (55–66% SiO2) and a high silica (〉66% SiO2) trend. Ninety per cent of the Rainier Mesa sheet occurs in the high silica trend. Immediately beneath the Rainier Mesa sheet is a thick tephra sequence. The chemical variation of this sequence is nearly equivalent to the high silica portion of the Rainier Mesa ash-flow sheet (about 66–78% SiO2). Throughout the tephra sequence numerous small ash-flow layers occur, and each ash-flow layer is chemically zoned from more evolved at the base to less evolved at the top. This is consistent with having been erupted from a zoned magma body. The lowest silica tephra units are at the base of the sequence and the highest silica units are at the top – that is, the large-scale chemical trend of the entire sequence is opposite to that of the individual ash-flow layers. These ash-flow layers are of very small volume. The tephra sequence provides a unique record of the incremental development of the zoned, high silica portion of the Rainier Mesa magma body.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00326463
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  • 11
    Electronic Resource
    Electronic Resource
    Cloning of the PYR4 gene encoding orotidine-5′-phosphate decarboxylase in Cephalosporium acremonium (1990)
    Springer
    Current genetics 17 (1990), S. 223-227 
    Details
    ISSN: 1432-0983
    Keywords: Orotidine-5′-phosphate decarboxylase ; Cephalosporium acremonium ; Recombinant DNA ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have cloned the Cephalosporium acremonium pyr4 gene by cross-hybridization with the equivalent gene from Neurospora crassa, the closest relative from which this gene is available. The C. acremonium pyr4 gene complements an E. coli pyrF mutant lacking orotidine-5′-phosphate decarboxylase (OMPdecase), and most probably does not contain introns. Maxicell analysis in E. coli shows that it encodes a 46 kDa polypeptide. The C. acremonium OMPdecase contains a highly conserved pentadecapeptide characteristic for this category of enzyme. Extensive sequence comparison suggests an important role of this region in enzymatic activity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00312613
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  • 12
    Electronic Resource
    Electronic Resource
    Phylogenetic analysis of the RNA polymerases of Trypanosoma brucei, with special reference to class-specific transcription (1990)
    Springer
    Current genetics 18 (1990), S. 547-551 
    Details
    ISSN: 1432-0983
    Keywords: Trypanosomes ; RNA polymerase ; Transcription ; Evolution ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have sequenced the genes encoding te largest subunits of the three classes of DNA-dependent RNA polymerases of Trypanosoma brucei. The nucleotide and deduced amino acid sequences were compared and aligned with the corresponding sequences of other eukaryotes. Phylogenetic relationships were subsequently calculated with a distant matrix, a bootstrapped parsimony and a maximum-likelihood method. These independent calculations resulted in trees with very similar topologies. The analyses show that all the largest subunits of T. brucei are evolutionarily distant members within each of the three RNA polymerase classes. An early separation of the trypanosomal subunits from the eukaryotic lineage might from the fundamental basis for the unusual transcription process of this species. Finally, all dendrograms show a separate ramification for the largest subunit of RNA polymerase I, II and III. RNA polymerase II and/or III form a bifurcation with the archaebacterial lineage. RNA polymerase I, however, arises separately from the eubacterial β′ lineage. This suggests that the three eukaryotic RNA polymerase classes are not simply derived by two gene duplications of an ancestral gene with subsequent differentiation.
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    URL: http://dx.doi.org/10.1007/BF00327026
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  • 13
    Electronic Resource
    Electronic Resource
    Cyanellar Ferredoxin-NADP+-oxidoreductase of Cyanophora paradoxa is encoded by the nuclear genome and synthesized on cytoplasmatic 80S ribosomes (1990)
    Springer
    Current genetics 17 (1990), S. 265-267 
    Details
    ISSN: 1432-0983
    Keywords: Cyanophora paradoxa ; Ferredoxin-NADP+-oxidoreductase ; Protein-import ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Cyanophora paradoxa is an important model organism for the study of the transition from endocytobiontic cyanobacteria to factual eukaryotic cell organelles. The cyanelles of these organisms possess cyanobacterial, as well as plastidic, characteristics. Although the transfer of cyanellar proteins from cytosolic into cyanellar space has been shown, the process of translocation of a known protein across the peptidoglycan layer and the envelope membranes has not been characterized. In this study we demonstrate that a specific and obligate cyanelle protein —Ferredoxin-NADP+-oxidoreductase (FNR) — is coded on the nuclear genome, synthesized on 80S ribosomes and transported from the eukaryotic cell compartment into the cyanelles of Cyanophora paradoxa, an original intracellular host-guest relation. These results indicate a gene transfer from guest to host genome and support the view that, in spite of their cyanobacterial origin, cyanelles have been evolved to cell organelles comparable to plastids.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00312619
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  • 14
    Electronic Resource
    Electronic Resource
    Study of double and triple simultaneous substitutions of amino acids in cytochromes C (1975)
    Springer
    Journal of molecular evolution 5 (1975), S. 187-197 
    Details
    ISSN: 1432-1432
    Keywords: Evolution ; Cytochrome C ; Substitution ; Covarion ; Monte-Carlo Simulations
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A statistical analysis aimed at obtaining some informations on a possible correlation between simultaneous amino acid substitutions is proposed. This method is applied to a set of cytochromes C, at the level of tandem and triple substitutions separated along the peptide chain by 1 to 15 peptide bonds. Monte-Carlo simulations are performed and the results are compared. We find a significant occurence of three adjacent amino acid substitutions in which the first replacement requires a two nucleotide substitution. A possible explanation of this fact is proposed on the basis of covarions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01741241
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  • 15
    Electronic Resource
    Electronic Resource
    Frequency of insertion-deletion, transversion, and transition in the evolution of 5S ribosomal RNA (1976)
    Springer
    Journal of molecular evolution 7 (1976), S. 133-149 
    Details
    ISSN: 1432-1432
    Keywords: 5S rRNA ; Nucleotide Sequence Homology ; Evolution ; Mutation Frequencies
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The problem of choosing an alignment of two or more nucleotide sequences is particularly difficult for nucleic acids, such as 5S ribosomal RNA, which do not code for protein and for which secondary structure is unknown. Given a set of ‘costs’ for the various types of replacement mutations and for base insertion or deletion, we present a dynamic programming algorithm which finds the optimal (least costly) alignment for a set of N sequences simultaneously, where each sequence is associated with one of the N tips of a given evolutionary tree. Concurrently, protosequences are constructed corresponding to the ancestral nodes of the tree. A version of this algorithm, modified to be computationally feasible, is implemented to align the sequences of 5S RNA from nine organisms. Complete sets of alignments and proto-sequence reconstructions are done for a large number of different con-figurations of mutation costs. Examination of the family of curves of total replacements inferred versus the ratio of transitions/trans-versions inferred, each curve corresponding to a given number of in-sertions-deletions inferred, provides a method for estimating relative costs and relative frequencies for these different types of mutation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01732471
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  • 16
    Electronic Resource
    Electronic Resource
    Partial gene duplication and posterior pituitary peptide (1975)
    Springer
    Journal of molecular evolution 5 (1975), S. 47-55 
    Details
    ISSN: 1432-1432
    Keywords: Gene Duplication ; Dipeptides ; Posterior Pituitary Peptide ; Evolution ; Protein Sequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have compiled the dipeptide frequencies in 100 known protein sequences. We suggest that dipeptides which occur with low frequencies can be used to locate proteins where partial gene duplication may have taken place. The 48 residue sequence of posterior pituitary peptide contains two Cys Trp pairs. The adjacent portions of the sequence are compatible with a partial gene duplication in the evolutionary history of posterior pituitary peptide.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01732013
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  • 17
    Electronic Resource
    Electronic Resource
    Aminoacyl transfer from an adenylate anhydride to polyribonucleotides (1975)
    Springer
    Journal of molecular evolution 6 (1975), S. 309-320 
    Details
    ISSN: 1432-1432
    Keywords: Aminoacyl Transfer ; Amino Acid Adenylate ; Imidazole Catalysis ; Evolution ; Peptide
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Imidazole catalysis of phenylalanyl transfer from phenylalanine adenylate anhydride to the hydroxyl groups of homopolyribonucleotides was investigated as a chemical model of the biochemical aminoacylation of tRNA. Imidazole catalyzed transfer of phenylalanine to poly (U) increases from pH 6.5 to 7.7 and decreases above pH 7.7. At pH 7.7 approximately 10% of the phenylalanyl residues are transferred to poly (U). At pH 7.1, transfer to poly (U) was five times as great as to poly (A) and transfer to a poly (A) poly (U) double helix was negligible. At pH 7.1 approximately 45 mole percent linkages to poly (U) were monomeric phenylalanine; the remainder of the linkages were peptides of phenylalanine. The number of linkages and their lability to base and neutral hydroxylamine indicates that phenylalanine and its peptides are attached as esters to the 2′ hydroxyl groups throughout poly (U) and the 2′ (3) hydroxyl groups at the terminus of poly (U). These results do model the contemporary process of aminoacyl transfer to tRNA and continue to suggest that a histidine residue is in the active site of aminoacyl-tRNA-synthetases.
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    URL: http://dx.doi.org/10.1007/BF01794637
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  • 18
    Electronic Resource
    Electronic Resource
    Conservation of repeated DNA base sequences in theCrustacea: A molecular approach to decapod phylogeny (1976)
    Springer
    Journal of molecular evolution 7 (1976), S. 111-131 
    Details
    ISSN: 1432-1432
    Keywords: Crustacea ; Evolution ; Repeated DNA ; Molecular Hybridization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Analysis of data obtained from molecular hybridization of3H-labeled repetitious DNA has been utilized to reconstruct the broad outlines of phylogenetic relationships among decapod Crustacea. This molecular reconstruction agrees reasonably well with the paleontological record, and with other schemes obtained by comparative morphological and serological approaches. Preliminary evidence is in line with the hypothesis that continuous addition of new repeated sequence families to the genome over long periods of time may in part account for the correlation observed between percent repetitious DNA hybridized and divergence time. It is tentatively concluded that a core of DNA base sequence homology has been highly conserved throughout the evolution of theCrustacea. Demonstration of inter-species sequence homology has important implications to models which relegate a genetic regulatory function to repeated DNAs.
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    URL: http://dx.doi.org/10.1007/BF01732470
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    Counter-examples to a neutralist hypothesis (1976)
    Springer
    Journal of molecular evolution 7 (1976), S. 185-195 
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    ISSN: 1432-1432
    Keywords: Evolution ; Randomicity ; Counter-Example
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Specific counter-examples are derived theoretically to the hypothesis that a random amino acid composition signifies a random evolutionary process.
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    URL: http://dx.doi.org/10.1007/BF01731488
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    A comparison of the 16S ribosomal RNAs from mesophilic and thermophilic bacilli: Some modifications in the sanger method for RNA sequencing (1976)
    Springer
    Journal of molecular evolution 7 (1976), S. 197-213 
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    ISSN: 1432-1432
    Keywords: Bacilli, 16S rRNA ; Phylogeny ; Thermophile ; Evolution ; Oligonucleotide Fingerprint
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Two modifications in the Sanger two dimensional electrophoretic procedure for RNA analysis are reported. One increases resolution on the primary fingerprint to the point that digests of large RNAs, of the size 1500–3000 nucleotides yield well resolved fingerprint patterns. The other is a novel endonucleolytic procedure that proves useful in determining sequences of the large oligonucleotides produced by T1 ribonuclease. These modifications have been used in determining the catalogs of oligomers produced by T1 ribonuclease digestion of 16S rRNAs from three related organisms,Bacillus subtilis, B.pumilus andB.stearothermophilus. The possible effects of adaptation to a thermophilic niche on ribosomal RNA primary structure and the phylogenetic relatedness of the two mesophilic Bacilli are discussed.
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    URL: http://dx.doi.org/10.1007/BF01731489
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    The charge-state model of protein polymorphism in natural populations (1975)
    Springer
    Journal of molecular evolution 6 (1975), S. 149-163 
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    ISSN: 1432-1432
    Keywords: Electrophoretic Detectability ; Neutral Mutation Theory ; Evolution ; Mutation Rates
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Routine electrophoretic surveys for genetic variation in natural populations depend primarily upon detecting differences in the net charge carried by a protein. We have calculated the proportion of base substitutions which would yield an electrophoretically detectable mutant protein, and the relative mutation rates among different charge classes, under a variety of simplifying assumptions. These calculations indicate that: (i) only 25 per cent of all single base mutations would lead to a charge change on a protein molecule. (ii) five distinct classes of electrophoretic variants can be generated from a specified protein by single base substitutions. (iii) the relative mutation rates differ markedly among the different charge classes which can be generated by single base substitutions. The estimates of the proportion of electrophoretically detectable mutant proteins and relative mutation rates among charge classes were relatively robust to changes in assumptions concerned with the kind and site of base substitutions and the amino acid composition of the protein.
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    URL: http://dx.doi.org/10.1007/BF01732353
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    Basic chromosomal proteins in lower eukaryotes: Relevance to the evolution and function of histones (1976)
    Springer
    Journal of molecular evolution 8 (1976), S. 79-94 
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    ISSN: 1432-1432
    Keywords: Histones ; Evolution ; Prokaryotes ; Lower Eukaryotes ; Higher Eukaryotes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The occurrence of basic chromosomal proteins in lower eukaryotes provides a useful approach to the study of histone evolution and function in higher eukaryotes. The histones of higher plants and animals are very similar and some are nearly identical, suggesting a high degree of evolutionary conservation within this group of proteins. However, a literature survey reveals that in the lower eukaryotes the histone situation is quite variable. The ciliates, and the true and cellular slime molds possess basic chromosomal proteins that are very similar to the histones of higher plants and animals. Various other lower eukaryotes possess basic chromosomal proteins that resemble at least some of the major histone fractions, and some microorganisms possess basic chromosomal proteins that bear little or no relationship to higher plant and animal histones. Since histones play a major role in the control of gene expression and the maintenance of chromosome structure in higher organisms, the evolution of these proteins represents a major change in the packaging of DNA and the mode of regulating gene expression in eukaryotes.
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    URL: http://dx.doi.org/10.1007/BF01738884
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    Comment on E. Broda's recent publications (1976)
    Springer
    Journal of molecular evolution 8 (1976), S. 387-388 
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    ISSN: 1432-1432
    Keywords: Nitrate Respiration ; Fermentation ; Energy Metabolism ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary E. Broda's recent argument against our concept that nitrate respiration antedated oxygen respiration is criticized.
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    URL: http://dx.doi.org/10.1007/BF01739263
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    Evolutionary divergence and length of repetitive sequences in sea urchin DNA (1976)
    Springer
    Journal of molecular evolution 9 (1976), S. 1-23 
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    ISSN: 1432-1432
    Keywords: Evolution ; Repetitive DNA ; SI Nuclease ; Sequence Organization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The organization of repetitive and single copy DNA sequences in sea urchin DNA has been examined with the single strand specific nuclease Sl fromAspergillus. Conditions and levels of enzyme were established so that single strand DNA was effectively digested while reassociated divergent repetitive duplexes remained enzyme resistant. About 25% of sea urchin DNA reassociates with repetitive kinetics to form Sl resistant duplexes of two distinct size classes derived from long and short repetitive sequences in the sea urchin genome. Fragments 2,000 nucleotides long were reassociated to Cot 20 and subjected to controlled digestion with Sl nuclease. About half of the resistant duplexes (13% of the DNA) are short, with a mode size of about 300 nucleotide pairs. This class exhibits significant sequence divergence, and principally consists of repetitive sequences which were interspersed with single copy sequences. About one-third of the long duplexes (4% of the DNA) are reduced in size after extensive Sl nuclease digestion to about 300 nucleotide pairs. About two-thirds of the long resistant duplexes (8% of the DNA) remains long after extensive SI nuclease digestion. These long reassociated duplexes are precisely base paired. The short duplexes are imprecisely paired with a melting temperature about 9°C below that of precisely paired duplexes of the same length. The relationship between length of repetitive duplex and precision of repetition is confirmed by an independent method and has been observed in the DNA of a number of species over a wide phylogenetic area.
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    URL: http://dx.doi.org/10.1007/BF01796119
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    The evolution of muscular parvalbumins investigated by the maximum parsimony method (1977)
    Springer
    Journal of molecular evolution 9 (1977), S. 131-158 
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    ISSN: 1432-1432
    Keywords: Parvalbumins ; Evolution ; Maximum parsimony ; Troponin-C ; Myosin alkali light chain
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Phylogenetic trees requiring the lowest sum of nucleotide replacements and gene duplicative events were constructed from the amino acid sequence data on ten gnathostome parvalbumins (PAR) and two related myofibrillar proteins troponin-C (TNC) and myosin alkali-light-chain (ALC). The origin and differentiation of the structural domains within these proteins were also investigated by the maximum parsimony method and by an alignment statistic for identifying evolutionarily related protein sequences. The results suggest, in agreement with the Weeds-McLachlan model, that tandem duplications in a precursor gene caused a primordial one-domain polypeptide (consisting of two helices with a calcium binding region in between) to double and then quadruple in size. Duplications of the gene coding for this four domain (I–II–III–IV) protein in an early metazoan, pre-gnathostome lineage gave rise to the separate loci for TNC, ALC, and PAR. TNC, which alone retained the Ca-binding function in each of its four domains, evolved much more slowly than either the ALC or PAR lineages. In the PAR lineage the I–II–III–IV structure was degraded, presumably by a partial gene deletion, to the II–III–IV structure during descent to the gnathostome ancestor of parvalbumins. Also during this period the mid region in domain II lost its Ca-binding function and, as it did so, evolved at an accelerated rate over other regions, a pattern indicative of positive selection for a change in function. In turn, from the gnathostome ancestor to the present, the mid regions of domains III and IV, which each retained Ca-bindung function, evolved much more slowly than other regions, a pattern indicative of stabilizing selection for preservation of function. Between the gnathostome and teleost-tetrapod ancestor a gene duplication separated the parvalbumins into anα-lineage and aβ-lineage. During this early vertebrate period PAR genes evolved at the extremely fast rate of 89 nucleotide replacements per 100 codons per 108 years (i.e. 89 NR %), but from the teleost-tetrapod ancestor to the present, bothα- andβ-PAR lineages evolved at a much slower rate, about 8 NR %. The use ofβ-parvalbumins as phylogenetic markers was complicated by presumptive evidence that paralogous (i.e. duplication dependent) gene lineages occur within this group. As a final point, in the genealogy of TNC, ALC, and PAR lineages, a non-random pattern of nucleotide replacements was observed between the reconstructed ancestral and descendant mRNA sequences. The pattern was similar to that observed for other protein genealogies and seems to reflect a bias in the genetic code for guanine to adenine and adenine to guanine transitions (especially at the first nucleotide position of the RNA codons) to produce amino acid substitutions which are compatible with the preservation of protein three-dimensional structure.
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    URL: http://dx.doi.org/10.1007/BF01732745
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    The architecture of 5S rRNA and its relation to function (1975)
    Springer
    Journal of molecular evolution 6 (1975), S. 61-76 
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    ISSN: 1432-1432
    Keywords: 5S ribosomal RNA ; Translation ; Evolution ; Molecular Architecture ; Conformational Changes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary An extensive comparative analysis of the available primary sequence data on 5S rRNA has been made. A universal secondary structure is presented for procaryotic 5S rRNA which contains four helical regions. Eucaryotic 5S rRNAs are found to have only three of these helices and thus have a somewhat different architecture. In addition, a highly conserved segment of more than thirty nucleotides is identified in the 5′ half of the procaryotic molecule. This segment includes the oligonucleotide-CGAAC- which presumably binds to the t-RNA “common” sequence-GTΨCG-. Among the eucaryotes, the plants display a procaryotic nature in this region, but no eucaryote has the sequence -CGAAC- in this segment. A functional role for the procaryotic 5S rRNA molecule is discussed in which it is envisioned to undergo conformational change, i.e., coiling and uncoiling of one of the helices, which can result in a cyclic interaction of the 5S rRNA molecule with two t-RNA molecules. A general principle also emerges: the natural rotational motion inherent in coiling and uncoiling of nucleic acid helices can be converted quite simply to linear mechanical motion.
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    URL: http://dx.doi.org/10.1007/BF01732674
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    Mutagenic topography of theE. Coli chromosome (1975)
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    Journal of molecular evolution 5 (1975), S. 279-290 
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    ISSN: 1432-1432
    Keywords: E.coli ; Mutagenesis ; Evolution ; Gene Transposition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The lactose fermenting genes inE.coli have been transposed to various chromosomal locations. The bacterial strains were mutagenized with different chemical mutagens and the frequency of Lac negative mutant colonies was measured as a function of lactose gene location in the chromosome. There appears to be a highly mutable location between 58–60 minutes on theE.coli map. This region does not appear to be correlated with the origin of DNA replication or with the terminus. The possible significance of this mutable region in the evolution of new bacterial genes is discussed.
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    URL: http://dx.doi.org/10.1007/BF01732215
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    Sequence characterization of 5S ribosomal RNA from eight gram positive procaryotes (1976)
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    Journal of molecular evolution 8 (1976), S. 143-153 
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    ISSN: 1432-1432
    Keywords: 5S rRNA ; Comparative Analysis ; Secondary Structure ; Evolution ; Tuned Helix
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The available comparative data on procaryotic 5S rRNA was extended through sequencing studies of eight gram positive procaryotes. Complete nucleotide sequences were presented for 5S rRNA fromBacillus subtilis, B. firmus, B.pasteurii, B.brevis, Lactobacillus brevis andStreptococcus faecalis. In addition, 5S rRNA oligonucleotide catalogs and partial sequence data were provided forB.cereus andSporosarcina ureae. These sequences and catalogs were discussed in terms of known features of procaryotic 5S rRNA architecture.
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    Organization and evolution of the mitochondrial genome of yeast (1976)
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    Journal of molecular evolution 9 (1976), S. 25-35 
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    ISSN: 1432-1432
    Keywords: Genome organization ; Evolution ; Mitochondria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The mitochondrial genome of yeast (S. cerevisiae orS. carlsbergensis) appears to be formed by 60–70 genetic units, each one of which is formed by (1) a GC-rich sequence, possibly having a regulatory role; (2) a gene, and (3) an AT-rich spacer, which probably is not transcribed. Recombination in this genome appears to underlie a number of important phenomena. The organization of the mitochondrial genome of yeast and these recombinational events are discussed in relationship with the organization and evolution of the nuclear genome of eukaryotes.
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    URL: http://dx.doi.org/10.1007/BF01796120
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    Primitive haemoglobin (1977)
    Springer
    Journal of molecular evolution 9 (1977), S. 343-347 
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    ISSN: 1432-1432
    Keywords: Evolution ; Haemoglobin ; Cooperativity ; Lamprey ; Maximum parsimony
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The sequences ofPetromyzon andAplysia globins are compared with the postulated vertebrate and mollusc-vertebrate ancestors to see if differences exist in the rates of evolution of different types of residue positions. Between the mollusc-vertebrate ancestor andAplysia globin there is no very striking pattern of changes except that the interior positions are relatively conserved. In the evolution ofPetromyzon haemoglobin, theα 1 β 2 contact area is relatively conserved. The homopolymeric binding of lamprey Hb seems to be a primitive function.
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    URL: http://dx.doi.org/10.1007/BF01796097
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    A comment on methanogenic bacteria and the primitive ecology (1977)
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    Journal of molecular evolution 9 (1977), S. 369-371 
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    ISSN: 1432-1432
    Keywords: Methanogenic bacteria ; Primitive atmosphere ; Evolution ; Ecology ; Methane-carbon dioxide cycle
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The phenotype and antiquity of methanogenic bacteria suggest them to have been one of the major factors determining a dynamic balance between CO2 and CH4 in the primitive atmosphere.
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    URL: http://dx.doi.org/10.1007/BF01796101
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    Partial enzyme digestion studies onescherichia coli, pseudomonas, chlorella, drosophila, HeLa and yeast 5S RNAs support a general class of 5S RNA models (1977)
    Springer
    Journal of molecular evolution 10 (1977), S. 77-86 
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    ISSN: 1432-1432
    Keywords: Ribosome ; 5S RNA ; Conformation ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Fox and Woese (1975a) have shown that a model of 5S RNA secondary structure similar to the one originally derived forChlorella 5S RNA can be generalized with relatively minor variations to all sequenced 5S RNA molecules, i.e. that corresponding base paired regions can be formed at approximately the same positions. We present experimental data in favour of this hypothesis and show that the points at which ribonucleases T1, T2 and pancreatic ribonuclease cleave six different 5S RNA molecules under ‘mild’ conditions (high ionic strength, low temperature, low RNAase concentration) nearly always fall in the proposed single-stranded regions. We conclude that this model is a good approximation to the conformation of 5S RNA in solution.
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    Evolutionary changes ofα-crystallin and the phylogeny of mammalian orders (1977)
    Springer
    Journal of molecular evolution 10 (1977), S. 123-135 
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    ISSN: 1432-1432
    Keywords: Ancestral sequence ; Eye lens protein ; Evolution ; Phylogenetic tree
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The sequences of the A chains of the eye lens proteinα-crystallin from seventeen mammalian species were compared. They showed a generally slow rate of evolution, but with marked variations in different lineages. Most substitutions have occurred in the C-terminal part of the chain, which probably forms part of the surface of theα-crystallin aggregate. The ancestral sequence method of Dayhoff revealed interesting indications about the phylogenetic relationships between the eleven mammalian orders that were represented by the investigated species. Most evident was the divergence of marsupial and placental orders. A notable resemblance between the hyrax and elephant sequences was observed, setting them apart from the ungulates, including whale. Primates, rodents, lagomorphs, insectivores and tupaiids seem to derive from a common stem group. These phylogenetic inferences are discussed in relation to current palaeontological and taxonomical opinions, and compared to evidence from other protein sequence data.
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    Amino acid-directed nucleic acid synthesis (1978)
    Springer
    Journal of molecular evolution 11 (1978), S. 109-120 
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    ISSN: 1432-1432
    Keywords: Origin of Life ; Genetic code ; Protein synthesis ; Evolution ; Prebiotic reactions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The fact that proteins contain onlya-amino acids and that protein structure is determined by 3′ → 5′ linked ribonucleotides is postulated to be the result of the copolymerization of these molecules in the prebiotic environment. Ribonucleotides therefore represent partial degradation products and proteins represent a side reaction developing from copolymerization. The basic structural unit of copolymerization is a nucleotide substituted with an amino acid at the 2′ position. Characteristics of modern amino and ribonucleic acid structure are all consistent with and necessary for this hypothesis. The characteristics and individual base assignments of the code also provide strong support for origin from the postulated copolymers. All characteristics of the code can be accounted for by this single hypothesis.
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    A measure of the denseness of a phylogenetic network (1978)
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    Journal of molecular evolution 11 (1978), S. 225-231 
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    ISSN: 1432-1432
    Keywords: Phylogenetic denseness ; Phylogenetic trees ; Topology ; Molecular reconstructions ; Evolution ; Paleogenetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The concept of phylogenetic denseness bears critically on the accuracy of evolutionary pathways inferred from experimentally sequenced proteins isolated from extant species. In this paper I develop an objective measure,ρ, of denseness to supplement previous intuitive concepts and which permits one to use this concept in comparing the quality of different evolutionary reconstructions. This measure is used to examine several published phylogenetic trees: insulin, a-hemoglobin,β-hemoglobin, myoglobin, cytochromec, and the parvalbumin family. The paper emphasizes 1) the importance of denseness in accurately estimating the number of nucleotide replacements which separate homologous sequences when this estimation is made by the method of parsimony, 2) the value of this concept in assessing the quality of those estimates, and 3) the use of this concept as a biologically practical heuristic method for identifying poorly studied regions in a phylogenetic tree, whether or not the tree was obtained by the parsimony method.
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    A proposal concerning the origin of life on the planet earth (1979)
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    Journal of molecular evolution 13 (1979), S. 95-101 
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    ISSN: 1432-1432
    Keywords: Oparin Ocean ; Origin of Life ; Evolution ; Runaway greenhouse ; Photosynthesis ; Methanogenesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The widely accepted Oparin thesis for the origin and early evolution of life seems sufficiently far from the true state of affairs as to be considered incorrect. It is proposed that life on earth actually arose in the planet's atmosphere, however an atmosphere very different from the present one. Because of an extremely warm surface, the early earth may have possessed no liquid surface water, its water being partitioned between a molten crust and a fairly dense atmosphere. Early preliving systems are taken to arise in the droplet phase in such an atmosphere. The early earth, which resembled Venus then and to some extent now, underwent a transition to its present condition largely as a result of the evolution of methanogenic metabolism.
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    The relationship between coding sequences and function in some heme binding proteins (1980)
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    Journal of molecular evolution 16 (1980), S. 149-150 
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    ISSN: 1432-1432
    Keywords: Exons ; Evolution ; Heme-binding proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary It is known that globin genes contain three exons with the middle exon coding for a four-helical supersecondary structure responsible for heme binding. Since this portion of the globin peptide chain can be structurally superimposed onto the cytochromec and cytochromeb 5 chains (Argos and Rossmann 1979), it can be inferred that the cytochromec gene will contain only one coding sequence while the cytochromeb 5 gene will be composed of three exons as found in the globin gene.
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    Theoretical foundations for quantitative paleogenetics (1980)
    Springer
    Journal of molecular evolution 16 (1980), S. 211-267 
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    ISSN: 1432-1432
    Keywords: Nucleic acids ; Proteins ; Natural selection ; Genetics ; Nonrandom molecular divergence ; Nonrandom REH theory ; Evolution ; mRNA ; DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary REH theory is extended by deriving the theoretical equations that permit one to analyze the nonrandom molecular divergence of homologous genes and proteins. The nonrandomicities considered are amino acid and base composition, the frequencies with which each of the four nucleotides is replaced by one of the other three, unequal usage of degenerate codons, distribution of fixed base replacements at the three nucleotide positions within codons, and distributions of fixed base replacements among codons. The latter two distributions turn out to dominate the accuracy of genetic distance estimates. The negative binomial density is used to allow for the unequal mutability of different codon sites, and the implications of its two limiting forms, the Poisson and geometric distributions, are considered. It is shown that the fixation intensity — the average number of base replacements per variable codon - is expressible as the simple product of two factors, the first describing the asymmetry of the distribution of base replacements over the gene and the second defining the ratio of the average probability that a codon will fix a mutation to the probability that it will not. Tables are given relating these features to experimentally observable quantities inα hemoglobin,β hemoglobin, myoglobin, cytochromec, and the parvalbumin group of proteins and to the structure of their corre-sponding genes or mRNAs. The principal results are (1) more accurate methods of estimating parameters of evolutionary interest from experimental gene and protein sequence data, and (2) the fact that change in gene and protein structure has been a much less efficient process than previously believed in the sense of requiring many more base replacements to effect a given structural change than earlier estimation procedures had indicated. This inefficiency is directly traceable to Darwinian selection for the nonrandom gene or protein structures necessary for biological function. The application of these methods is illustrated by detailed consideration of the rabbitα -andβ hemoglobin mRNAs and the proteins for which they code. It is found that these two genes are separated by about 425 fixed base replacements, which is a factor of two greater than earlier estimates. The replacements are distributed over approximately 114 codon sites that were free to accept base mutations during the divergence of these two genes.
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    Ancient repeated sequences in the pea and mung bean genomes and implications for genome evolution (1981)
    Springer
    Journal of molecular evolution 17 (1981), S. 31-42 
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    ISSN: 1432-1432
    Keywords: Pea ; Mung bean ; Genome organization ; Evolution ; Amplification ; Repetitive DNA ; Single copy DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Essentially all of the sequences in the pea (Pisum sativum) genome which reassociate with single copy kinetics at standard (Tm -25°C) criterion follow repetitive kinetics at lower temperatures (about Tm-35°C). Analysis of thermal stability profiles for presumptive single copy duplexes show that they contain substantial mismatch even when formed at standard criterion. Thus most of the sequences in the pea genome which are conventionally defined as “single copy” are actually “fossil repeats” — that is, they are members of extensively diverged (mutuated) and thus presumably ancient families of repeated sequences. Coding sequences as represented by a cDNA probe prepared from poly-somal poly(A) + mRNA reassociate with single copy kinetics regardless of criterion and do not form mismatched duplexes. The coding regions thus appear to be composed of true single copy sequences but they cannot represent more than a few percent of the pea genome. Ancient diverged repeats are present, but not a prominent feature of the smaller mung bean (Vigna radiata) genome. An extension of a simple evolutionary model is proposed in which these and other differences in genome organization are considered to reflect different rates of sequence amplification or genome turnover during evolution. The model accounts for some of the differences between typical plant and animal genomes.
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    URL: http://dx.doi.org/10.1007/BF01792422
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    Evolutionary trees from DNA sequences: A maximum likelihood approach (1981)
    Springer
    Journal of molecular evolution 17 (1981), S. 368-376 
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    ISSN: 1432-1432
    Keywords: Evolution ; Phylogeny ; Maximum likelihood ; Parsimony ; Estimation ; DNA sequences
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of the estimate of the tree.
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    Amino acid codes in mitochondria as possible clues to primitive codes (1981)
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    Journal of molecular evolution 18 (1981), S. 15-17 
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    ISSN: 1432-1432
    Keywords: Amino acid code ; Evolution ; Primitive codes ; Mitochondria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Differences between mitochondrial codes and the universal code indicate that an evolutionary simplification has taken place, rather than a return to a more primitive code. However, these differences make it evident that the universal code is not the only code possible, and therefore earlier codes may have differed markedly from the previous code. The present universal code is probably a “frozen accident.” The change in CUN codons from leucine to threonine (Neurospora vs. yeast mitochondria) indicates that neutral or near-neutral changes occurred in the corresponding proteins when this code change took place, caused presumably by a mutation in a tRNA gene.
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    Studies on the evolutionary relationships between hemoglobins inChironomus pallidivittatus andC. Tentans (1981)
    Springer
    Journal of molecular evolution 18 (1981), S. 9-14 
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    ISSN: 1432-1432
    Keywords: Monomeric hemoglobins ; Dimeric hemoglobins ; Chironomus ; Antibodies ; Evolution ; Gene duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The monomeric hemoglobins ofChironomus tentans andC. pallidivittatus have been isolated and separated into their respective components by gel chromatography on Sephadex G-75 and ion-exchange chromatography on DEAE-Sephacel. The amino acid compositions of the purified components are given. The sequence of the 30 N-terminal amino acid residues of one of the monomeric components (Hb I fromC. pallidivittatus) was determined and found to be identical in almost all of its parts with the monomeric hemoglobins ofC. thummi (CTT III and CTT IV). Antibodies against the monomeric hemoglobins Hb I and Hb IIc and the dimeric fraction were highly specific and no cross reaction between dimeric and monomeric hemoglobins could be demonstrated. The antibodies against the monomers crossreact with the monomeric hemoglobins CTT III and CTT IV ofC. thummi. Taken together with genetic data, the immunological results indicate that divergence of monomeric from dimeric forms was an early event in the evolution of the various hemoglobins inChironomus.
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    Evolutionary origin of aminoglycoside phosphotransferase resistance genes (1990)
    Springer
    Journal of molecular evolution 30 (1990), S. 489-492 
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    ISSN: 1432-1432
    Keywords: Actinomyces ; Phosphotransferase ; Aminoglycoside ; Phylogenetic tree ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The protein sequences of seven 3′-aminoglycoside phosphotransferases falling into the six identified types and three 6′-aminoglycoside phosphotransferases were analyzed to give a rooted phylogenetic tree. This tree supports the origin of these groups of enzymes in an ancestor closely related to the actinomycetes, and that horizontal transfer of the resistance genes occurred, possibly via transposons. The implications for genetic engineering of a novel antibiotic are discussed.
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    Endosymbionts and mitochondrial origins (1977)
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    Journal of molecular evolution 10 (1977), S. 93-96 
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    ISSN: 1432-1432
    Keywords: Evolution ; Endosymbiosis ; Mitochondrion ; Photosynthetic
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The possibility is put forth that the mitochondrion did not originate from an endosymbiosis, 1–2 billion years ago, involving an aerobic bacterium. Rather, it arose by endosymbiosis in a much early, anaerobic period, and was initially a photosynthetic organelle, analogous to the modern chloroplast. This suggestion arises from a reconsideration of the nature of endosymbiosis. It ex-plains the remarkable diversity in mitochondrial information storage and processing systems.
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    Nucleotide sequence of nine protein-coding genes and 22 tRNAs in the mitochondrial DNA of the sea starPisaster ochraceus (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 195-204 
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    ISSN: 1432-1432
    Keywords: Mitochondrial DNA ; Evolution ; Echinoderms ; Sea stars ; DNA sequence ; Mitochondrial proteins ; Mitochondrial tRNA genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have cloned and sequenced over 9 kb of the mitochondrial genome from the sea starPisaster ochraceus. Within a continuous 8.0-kb fragment are located the genes for NADH dehydrogenase subunits 1, 2, 3, and 4L (ND1, ND2, ND3, and ND4L), cytochrome oxidase subunits I, II, and III (COI, COII, and COIII), and adenosine triphosphatase subunits 6 and 8 (ATPase 6 and ATPase 8). This large fragment also contains a cluster of 13 tRNA genes between ND1 and COI as well as the genes for isoleucine tRNA between ND1 and ND2, arginine tRNA between COI and ND4L, lysine tRNA between COII and ATPase 8, and the serine (UCN) tRNA between COIII and ND3. The genes for the other five tRNAs lie outside this fragment. The gene for phenylalanine tRNA is located between cytochrome b and the 12S ribosomal genes. The genes for tRNAglu and tRNAthr are 3′ to the 12S ribosomal gene. The tRNAs for histidine and serine (AGN) are adjacent to each other and lie between ND4 and ND5. These data confirm the novel gene order in mitochondrial DNA (mtDNA) of sea stars and delineate additional distinctions between the sea star and other mtDNA molecules.
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    Globular proteins, GU wobbling, and the evolution of the genetic code (1982)
    Springer
    Journal of molecular evolution 19 (1982), S. 20-27 
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    ISSN: 1432-1432
    Keywords: GU base pairing ; RNA replication ; Globular proteins ; Genetic code ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary It has previously been shown that the formation of GU base pairs in RNA copying processes leads to an accumulation of G and U in both strands of the replicating RNA, which results in a non-random distribution of base triplets. In the present paper, this distribution is calculated, and, using the χ2-test, a correlation between the distribution of triplets and the amino acid composition of the evolutionarily conservative interior regions of selected globular proteins is established. It is suggested that GU wobbling in early replication of RNA could have led to the observed amino acid composition of present-day protein interiors. If this hypothesis is correct, the GU wobbling must have been very extensive in the imprecisely replicating RNA, even reaching values close to the critical for stability of its double-helical structure. Implications of the hypothesis both for the evolution of the genetic code and of proteins are discussed.
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    Evolution ofDrosophila repetitive-dispersed DNA (1983)
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    Journal of molecular evolution 19 (1983), S. 203-213 
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    ISSN: 1432-1432
    Keywords: Evolution ; Phylogenetic distribution ; Repetitive-dispersed DNAs ; Speciation ; Transposons
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have examined the phylogenetic distribution of a spectrum ofDrosophila repetitive-dispersed DNAs ranging from structurally complex transposable elements to scrambled middle repetitive sequences. Our data suggest that unlike typical “genes” these DNAs are unstable components of the drosophilid genome. The unusual behavior of these repetitive-dispersed DNAs raises the possibility that this type of sequence may have an important role in the evolution of the family Drosophilidae.
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    Genome variations in the transition from amphibians to reptiles (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 68-75 
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    ISSN: 1432-1432
    Keywords: DNA ; Genome size ; Repetitive DNA ; Amphibians ; Reptiles ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Many characters differentiate amphibian from reptilian genomes. The former have, on the average, larger and more variable genome sizes, a greater repetitive DNA percentage, and a higher interspersion level among DNAs with different degrees of repetitivity. Reptiles have more reduced and uniform genome sizes, a repetitive DNA percentage generally lower than 50%, and a lower interspersion level. Other differences can be observed in the chromosome banding and in the correlations between genome size and other morphometric and functional parameters of the cell. The differences found in amphibians and reptiles seem to indicate that in these two vertebrate classes there is a different tendency toward or tolerance of the accumulation and preservation of genetically dispensable DNA fractions. This might depend either on a different propensity toward genic amplification or on the appearance, in reptiles, of stricter and more efficient constraints regulating genome size.
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    Evolution and sequence analysis of a human Y-chromosomal DNA fragment (1991)
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    Journal of molecular evolution 33 (1991), S. 133-141 
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    ISSN: 1432-1432
    Keywords: Y-chromosome ; DNA ; Human ; Primate ; Evolution ; PUPPY sequence ; Alu element
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A Y-chromosomal DNA fragment has been isolated from a human Y-Charon 21A recombinant library. Evolutionary analysis of 1F5 indicates that the size and sequence of this fragment have been conserved in higher primates. Deletion mapping and in situ hybridization analysis have localized 1F5 to the middle euchromatic portion of the long arm of the human Y chromosome at Yq11.2. Sequence analysis revealed the presence of an atypical Alu element and two regions rich in polypyrimidine-polypurine residues.
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    Evolutionary relationships among the permease proteins of the bacterial phosphoenolpyruvate: Sugar phosphotransferase system. Construction of phylogenetic trees and possible relatedness to proteins of eukaryotic mitochondria (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 179-193 
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    ISSN: 1432-1432
    Keywords: Bacteria ; Sugars ; Phosphotransferase system ; Transport proteins ; Evolution ; Sequence comparisons ; NADH dehydrogenase ; Mitochondria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The amino acid sequences of 15 sugar permeases of the bacterial phosphoenolpyruvatedependent phosphotransferase system (PTS) were divided into four homologous segments, and these segments were analyzed to give phylogenetic trees. The permease segments fell into four clusters: the lactose-cellobiose cluster, the fructose-mannitol cluster, the glucose-N-acetylglucosamine cluster, and the sucrose-β-glucoside cluster. Sequences of the glucitol and mannose permeases (clusters 5 and 6, respectively) were too dissimilar to establish homology with the other permeases, but short regions of statistically significant sequence similarities were noted. The functional and structural relationships of these permease segments are discussed. Some of the homologous PTS permeases were found to exhibit sufficient sequence similarity to subunits 4 and 5 of the eukaryotic mitochondrial NADH dehydrogenase complex to suggest homology. Moreover, subunits 4 and 5 of this complex appeared to be homologous to each other, suggesting that these PTS and mitochondrial proteins comprise a superfamily. The integral membrane subunits of the evolutionarily divergent mannose PTS permease, the P and M subunits, exhibited limited sequence similarity to subunit 6 of the mitochondrial F1F0-ATPase and subunit 5b of cytochrome oxidase, respectively. These results suggest that PTS sugar permeases and mitochondrial proton-translocating proteins may be related, although the possibility of convergent evolution cannot be ruled out.
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    Insect lysozymes from three species of lepidoptera: Their structural relatedness to the c (chicken) type lysozyme (1979)
    Springer
    Journal of molecular evolution 14 (1979), S. 267-271 
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    ISSN: 1432-1432
    Keywords: Lysozyme ; Insect ; Lepidoptera ; Evolution ; Sequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Sequence studies of the N-terminal halves of the lysozymes isolated fromBombyx mori, Galleria mellonella andSpodoptera littoralis (Lepidoptera) allow us to classify these enzymes among the c (chicken) type lysozymes.
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    Evolution of methionine initiator and phenylalanine transfer RNAs (1979)
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    Journal of molecular evolution 14 (1979), S. 287-300 
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    ISSN: 1432-1432
    Keywords: Phenylalanine tRNA ; Methionine initiator tRNA ; Evolution ; Mutations ; Conformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Sequence data from methionine initiator and phenylalanine transfer RNAs were used to construct phylogenetic trees by the maximum parsimony method. Although eukaryotes, prokaryotes and chloroplasts appear related to a common ancestor, no firm conclusion can be drawn at this time about mitochondrial-coded transfer RNAs. tRNA evolution is not appropriately described by random hit models, since the various regions of the molecule differ sharply in their mutational fixation rates. ‘Hot’ mutational spots are identified in the TψC, the amino acceptor and the upper anticodon stems; the D arm and the loop areas on the other hand are highly conserved. Crucial tertiary interactions are thus essentially preserved while most of the double helical domain undergoes base pair interchange. Transitions are about half as costly as transversions, suggesting that base pair interchanges proceed mostly through G-U and A -C intermediates. There is a preponderance of replacements starting from G and C but this bias appears to follow the high G + C content of the easily mutated base paired regions.
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    Evolutionary analysis ofα andβ hemoglobin genes by reh theory under the assumption of the equiprobability of genetic events (1980)
    Springer
    Journal of molecular evolution 15 (1980), S. 149-159 
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    ISSN: 1432-1432
    Keywords: Genes ; REH theory ; Genetic distance ; Evolution ; mRNA ; Nucleic acids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary It is shown how REH theory in conjunction with mRNA or gene sequence data can be used to obtain estimates of the fixation intensity, the number of varions, and the total mutations fixed between homologous pairs of nucleic acids. These estimates are more accurate than those that can be derived from amino acid sequence data. The method is illustrated forα andβ hemoglobin genes and these improved estimates are compared with those made from the amino acid sequences for which those genes code. Significant differences are found between the estimates made by these two methods. For theβ hemoglobin gene sequences examined here, the fixation intensity is some-what less than the protein data had suggested, and the number of rations is considerably greater. Depending on the gene sequences examined, between 62 and 83% of the codons appear able to fix mutations during the divergences considered. This reflects the constraints of natural selection on acceptable mutations. The total number of base replacements separating the genes for human, mouse, and rabbitβ hemoglobin varies from 61 to 105 depending on the pair examined. Rabbitα andβ hemoglobin are separated by at least 290 fixed mutations. For such distantly related sequences estimates made from protein and mRNA data differ less, reflecting the higher quality of information from the many observed changes in primary structure. The effects of nonrandom gene structure on these evolutionary estimates and the fact that various genetic events are not equiprobable are discussed.
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    The case for a polyphyletic origin of mitochondria: Morphological and molecular comparisons (1984)
    Springer
    Journal of molecular evolution 21 (1984), S. 54-57 
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    ISSN: 1432-1432
    Keywords: Mitochondrion ; Cytochrome C ; Rhodospirillaceae ; Endosymbiosis ; rRNA ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The comparative morphology and pigmentation of protists suggest that those with tubular mitochondrial cristae belong to a different lineage than those with lamellar cristae and that the evolutionary divergence might have been very early. We propose that the difference in cristal morphology is the result of separate origins of the mitochondria from endosymbionts related to the Rhodospirillaceae (purple nonsulfur bacteria) but differing in the morphology of their internal membranes. Comparisons of the cytochromes c of protists and the Rhodospirillaceae and of 16s rRNA T1 oligonucleotide catalogs in the Rhodospirillaceae do not contradict, and in fact provide support for, the idea. More extensive evidence may be lacking simply because cytochromes c have been studied in very few protists with tubular mitochondrial cristae.
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    Temperature as a determinative factor in the evolution of genetic systems (1984)
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    Journal of molecular evolution 21 (1984), S. 72-75 
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    ISSN: 1432-1432
    Keywords: Heat ; Rates of copy error ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Heat induces a number of premutational lesions (for example, the deamination of cytosine to uracil) in DNA and RNA. These kinds of errors occur in resting as well as replicating polynucleotides. However, an increase in temperature also raises the probability of copying error occurring in nucleic acids because of increased thermal noise in the replicative machinery. In most modern genetic systems, the majority of heat-induced lesions are efficiently repaired. It follows that the importance of heat-induced error increases as the effectiveness of repair declines. We show in this paper that the error rate of enzymatic polynucleotide copying is expected to increase monotonically with temperature. We also explore the effects of temperature variations on the early evolution of biological information transmission mechanisms.
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    Evolution of proteins of the cystatin superfamily (1990)
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    Journal of molecular evolution 30 (1990), S. 60-71 
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    ISSN: 1432-1432
    Keywords: Cysteine endopeptidase ; Cysteine proteinase ; Inhibitor ; Cystatin ; Kininogen ; Evolution ; Amino acid sequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have examined the amino acid sequences of a number of proteins that have been suggested to be related to chicken cystatin, a protein from chicken egg white that inhibits cysteine proteinases. On the basis of statistical analysis, the following proteins were found to be members of the cystatin superfamily: human cystatin A, rat cystatin A(α), human cystatin B, rat cystatin B(β), rice cystatin, human cystatin C, ox colostrum cystatin, human cystatin S, human cystatin SA, human cystatin SN, chicken cystatin, puff adder cystatin, human kininogen, ox kininogen, rat kininogen, rat T-kininogens 1 and 2, human α2HS-glycoprotein, and human histidine-rich glycoprotein. Fibronectin is shown not to be a member of this superfamily, and the c-Ha-ras oncogene protein p21(Val-12) probably is not a member also. It was convenient to divide members of the superfamily into four types on the basis of the presence of one, two, or three copies of cystatin-like segments and the presence or absence of disulfide bonds. Evolutionary dendrograms were calculated by three methods, and from these we have constructed a scheme depicting the sequence of events in the evolution of these proteins. We suggest that about 1000 million years ago a precursor containing disulfide loops appeared, and that all disulfide-containing cystatins are derived from this. We follow the evolution of the proteins of the superfamily along four main lineages, with special attention to the part that duplication of segments has played in the development of the more complex molecules.
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    Evolution of protamine P1 genes in primates (1993)
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    Journal of molecular evolution 37 (1993), S. 426-434 
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    ISSN: 1432-1432
    Keywords: Primate ; Evolution ; Protamine ; Polymerase chain reaction ; Sperm proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Protamine P1 genes have been sequenced by PCR amplification and direct DNA sequencing from 9 primates representing 5 major families, Cebidae (new world monkeys), Cercopithecidae (old world monkeys), Hylobatidae (gibbons), Pongidae (gorilla, orangutan, and chimpanzee), and Hominidae (human). In this recently diverged group of primates these genes are clearly orthologous but very variable, both at the DNA level and in their expressed amino acid sequences. The rate of variation amongst the protamine Pls indicates that they are amongst the most rapidly diverging polypeptides studied. However, some regions are conserved both in primates and generally in other placental mammals. These are the 13 N-terminal residues (including a region of alternating serine and arginine residues (the motif SRSR, res. 10–13) susceptible to Ser phosphorylation), a tract of six Arg residues (res. 24–29) in the center of the molecule, and a six-residue region (RCCRRR, res. 39–44), consisting of a pair of cysteines flanked by arginines. Detailed consideration of nearest neighbor matrices and trees based on maximum parsimony indicates that PI genes from humans, gorillas, and chimpanzees are very similar. The amino acid and nucleotide differences between humans and gorillas. are fewer than those between humans and chimpanzees. This finding is at variance with data from DNA-DNA hybridization and extensive globin and mitochondrial DNA sequences which place human and chimpanzee as closest relatives in the super family, Hominoidea. This may be related to the fact that protamine Pls are expressed in germ line rather than somatic cells. In contrast to the variability of the exon regions of the protamine P1 genes, the sequence of the single intron is highly conserved.
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    Molecular evolution of the HSP70 multigene family (1994)
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    Journal of molecular evolution 38 (1994), S. 1-17 
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    ISSN: 1432-1432
    Keywords: HSP70 ; Heat shock ; Evolution ; Phylogeny ; Yeast ; Multigene family ; Subcellular compartmentalization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Eukaryotic genomes encode multiple 70-kDa heat-shock proteins (HSP70s). The Saccharomyces cerevisiae HSP70 family is comprised of eight members. Here we present the nucleotide sequence of the SSA3 and SSB2 genes, completing the nucleotide sequence data for the yeast HSP70 family. We have analyzed these yeast sequences as well as 29 HSP70s from 24 additional eukaryotic and prokaryotic species. Comparison of the sequences demonstrates the extreme conservation of HSP70s; proteins from the most distantly related species share at least 45% identity and more than one-sixth of the amino acids are identical in the aligned region (567 amino acids) among all proteins analyzed. Phylogenetic trees constructed by two independent methods indicate that ancient molecular and cellular events have given rise to at least four monophyletic groups of eukaryotic HSP70 proteins. Each group of evolutionarily similar HSP70s shares a common intracellular localization and is presumed to be comprised of functional homologues; these include heat-shock proteins of the cytoplasm, endoplasmic reticulum, mitochondria, and chloroplasts. HSP70s localized in mitochondria and plastids are most similar to the DnaK HSP70 homologues in purple bacteria and cyanobacteria, respectively, which is consistent with the proposed prokaryotic origin of these organelles. The analyses indicate that the major eukaryotic HSP70 groups arose prior to the divergence of the earliest eukaryotes, roughly 2 billion years ago. In some cases, as exemplified by the SSA genes encoding the cytoplasmic HSP70s of S. cerevisiae, more recent duplication events have given rise to subfamilies within the major groups. The S. cerevisiae SSB proteins comprise a unique subfamily not identified in other species to date. This subfamily appears to have resulted from an ancient gene duplication that occurred at approximately the same time as the origin of the major eukaryotic HSP70 groups.
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    Molecular characteristics of the heterochromatic I elements from a reactive strain ofDrosophila melanogaster (1990)
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    Journal of molecular evolution 31 (1990), S. 424-431 
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    ISSN: 1432-1432
    Keywords: Drosophila melanogaster ; Evolution ; Hybrid dysgenesis ; I elements ; Transposons
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary There are two categories of strains inDrosophila melanogaster with respect to the I-R system of hybrid dysgenesis. The inducer strains contain particular transposable elements named I factors. They are not present in the strains of the other category called reactive (R) strains. Defective I elements are present in the pericentromeric regions of both categories of strains. This last subfamily of I sequences has not yet been described in detail and little is known about its origin. In this paper, we report that the defective I elements display an average of 94% of sequence identity with each other and with the transposable I factor. The results suggest that they cannot be the progenitors of the present day I factors, but that each of these two subfamilies started to evolve independently several million years ago. Furthermore, the sequence comparison of these I elements with an active I factor fromDrosophila teissieri provides useful information about when the deleted I elements became immobilized.
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    Characterization of a species-specific satellite DNA family of Dolichopoda schiavazzii (Orthoptera, Rhaphidophoridae) cave crickets (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 274-281 
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    ISSN: 1432-1432
    Keywords: Repetitive DNA ; Tandem repeats ; Sequence analysis ; Recombination ; Isolated populations ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The satellite DNA family pDoP102 is species specific for the cave cricket Dolichopoda schiavazzii, an endemic species of mainland and insular Tuscany. It consists of numerous tandemly arranged repeats, 102 bp in length, and evolved most probably after cladogenesis of D. schiavazzii from the D. baccettii-aegilion group within the last 2.3 ± 0.8 million years. A sequence comparison of 31 clones (53 repetition units) from three isolated populations reveals a very high degree of sequence homogeneity within the species with no evidence for any specific population features. This appears to be in contrast to the results of allozyme analyses which account for a relatively old evolutionary divergence of the Elba island population from the mainland ones. Since the assumption of actual gene flow and recent colonization is rejected, the observed sequence homogeneity is hypothesized to be maintained by recombination processes preventing fixation of newly introduced mutations on pDoP102 sequence clusters.
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    Prebiotic chemistry in clouds (1991)
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    Journal of molecular evolution 32 (1991), S. 296-303 
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    ISSN: 1432-1432
    Keywords: Prebiotic chemistry ; Primordial soup ; Oparin hypothesis ; Evolution ; Impact catastrophism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary In the traditional concept for the origin of life as proposed by Oparin and Haldane in the 1920s, prebiotic reactants became slowly concentrated in the primordial oceans and life evolved slowly from a series of highly protracted chemical reactions during the first billion years of Earth's history. However, chemical evolution may not have occurred continuously because planetesimals and asterioids impacted the Earth many times during the first billion years, may have sterilized the Earth, and required the process to start over. A rapid process of chemical evolution may have been required in order that life appeared at or before 3.5 billion years ago. Thus, a setting favoring rapid chemical evolution may be required. A chemical evolution hypothesis set forth by Woese in 1979 accomplished prebiotic reactions rapidly in droplets in giant atmospheric reflux columns. However, in 1985 Scherer raised a number of objections to Woese's hypothesis and concluded that it was not valid. We propose a mechanism for prebiotic chemistry in clouds that satisfies Scherer's concerns regarding the Woese hypothesis and includes advantageous droplet chemistry. Prebiotic reactants were supplied to the atmosphere by comets, meteorites, and interplanetary dust or synthesized in the atmosphere from simple compounds using energy sources such as ultraviolet light, corona discharge, or lightning. These prebiotic monomers would have first encountered moisture in cloud drops and precipitation. We propose that rapid prebiotic chemical evolution was facilitated on the primordial Earth by cycles of condensation and evaporation of cloud drops containing clay condensation nuclei and nonvolatile monomers. For example, amino acids supplied by, or synthesized during entry of, meteorites, comets, and interplanetary dust would have been scavenged by cloud drops containing clay condensation nuclei. Polymerization would have occurred within cloud systems during cycles of condensation, freezing, melting, and evaporation of cloud drops. We suggest that polymerization reactions occurred in the atmosphere as in the Woese hypothesis, but life originated in the ocean as in the Oparin-Haldane hypothesis. The rapidity with which chemical evolution could have occurred within clouds accommodates the time constraints suggested by recent astrophysical theories.
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    URL: http://dx.doi.org/10.1007/BF02102187
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    Interspecific comparison of the unusually repetitiveDrosophila locusmastermind (1991)
    Springer
    Journal of molecular evolution 32 (1991), S. 415-420 
    Details
    ISSN: 1432-1432
    Keywords: Drosophila melanogaster ; Drosophila virilis ; mastermind ; Gene comparison ; Repetitive sequences ; Homopolymers ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Themastermind gene ofDrosophila melanogaster encodes a novel, highly repetitive nuclear protein required for neural development. To identify functionally important regions we have initiated an interspecific comparison of the gene inDrosophila virilis. Mastermind transcription and genomic organization are similar in both species and sequence analysis reveals significant conservation in a major cluster of charged amino acids. In contrast, extensive variation is noted in homopolymer domains that immediately flank the acidic cluster. Distinct patterns of evolutionary change can be identified: the major difference between unique regions are occasional amino acid substitutions whereas the repetitive areas are characterized by numerous large in-frame insertions/deletions and a nearly threefold higher rate of amino acid replacement. Conservation of the acidic domain suggests that it has an important functional role whereas the hypervariable homopolymer regions appear to be under less selective constraints than adjacent unique areas.
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    URL: http://dx.doi.org/10.1007/BF02101281
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    Divergent evolution may link human immunodeficiency virus GP41 to human CD4 (1993)
    Springer
    Journal of molecular evolution 36 (1993), S. 448-457 
    Details
    ISSN: 1432-1432
    Keywords: Retrovirus ; HIV ; CD4 ; Minus strand ; Alternate reading frame ; Frameshift ; Divergence ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A local sequence similarity of HIV envelope proteins (gp120 and gp41) to immunoglobulins suggests that a mimicry phenomenon may form the basis of the HIV-cell membrane interaction and of HIV-induced autoimmune reaction. We explored the hypothesis of any deeper relationship between HIV env proteins and immunoglobulin family members. An overall DNA sequence similarity between gp41 coding region of env gene and the HIV-receptor CD4 gene was observed and a 14-base-long oligonucleotide, almost unique in the GenBank, was found in gp41 and CD4 genes. The alignment of env gene to CD4 gene and to 84 different sequences showed a significantly higher homology score and a nonrandom similarity in the CD4-env alignment. A significant similarity was also found between the env protein and the sequence encoded by an alternate reading frame of CD4 gene. Our observations suggest that gp41 coding region might have a different origin than the gp120 coding region of the env gene, and that a divergent evolution might link gp41 to CD4 or immunoglobulin family members. In this study the analysis of alternate-reading-frame products is also proposed as a novel approach to investigate evolutionary links and structure-function relationships.
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    URL: http://dx.doi.org/10.1007/BF02406721
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    Evolutionary consequences of nonrandom damage and repair of chromatin domains (1992)
    Springer
    Journal of molecular evolution 35 (1992), S. 156-180 
    Details
    ISSN: 1432-1432
    Keywords: DNA damage ; DNA repair ; Chromatin ; Evolution ; Nucleosomes ; Nuclear matrix ; Active genes ; Z-DNA ; Sperm ; Mutation ; Molecular clock
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Some evolutionary consequences of different rates and trends in DNA damage and repair are explained. Different types of DNA damaging agents cause nonrandom lesions along the DNA. The type of DNA sequence motifs to be preferentially attacked depends upon the chemical or physical nature of the assaulting agent and the DNA base composition. Higher-order chromatin structure, the nonrandom nucleosome positioning along the DNA, the absence of nucleosomes from the promoter regions of active genes, curved DNA, the presence of sequence-specific binding proteins, and the torsional strain on the DNA induced by an increased transcriptional activity all are expected to affect rates of damage of individual genes. Furthermore, potential Z-DNA, H-DNA, slippage, and cruciform structures in the regulatory region of some genes or in other genomic loci induced by torsional strain on the DNA are more prone to modification by genotoxic agents. A specific actively transcribed gene may be preferentially damaged over nontranscribed genes only in specific cell types that maintain this gene in active chromatin fractions because of (1) its decondensed chromatin structure, (2) torsional strain in its DNA, (3) absence of nucleosomes from its regulatory region, and (4) altered nucleosome structure in its coding sequence due to the presence of modified histones and HMG proteins. The situation in this regard of germ cell lineages is, of course, the only one to intervene in evolution. Most lesions in DNA such as those caused by UV or DNA alkylating agents tend to diminish the GC content of genomes. Thus, DNA sequences not bound by selective constraints, such as pseudogenes, will show an increase in their AT content during evolution as evidenced by experimental observations. On the other hand, transcriptionally active parts may be repaired at rates higher than inactive parts of the genome, and proliferating cells may display higher repair activities than quiescent cells. This might arise from a tight coupling of the repair process with both transcription and replication, all these processes taking place on the nuclear matrix. Repair activities differ greatly among species, and there is a good correlation between life span and repair among mammals. It is predicted that genes that are transcriptionally active in germ-cell lineages have a lower mutation rate than bulk DNA, a circumstance that is expected to be reflected in evolution. Exception to this rule might be genes containing potential Z-DNA, H-DNA, or cruciform structures in their coding or regulatory regions that appear to be refractory to repair. This study supports the molecular clock hypothesis when applied to one gene within a group of related species and contends that evolutionary rates might vary between genes and gene segments not only as a result of differences in selective constraints but also as a result of differences in the rate of damage minus rate of repair among different segments of chromatin DNA.
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    URL: http://dx.doi.org/10.1007/BF00183227
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    The phylogeny of echinoderm classes based on mitochondrial gene arrangements (1993)
    Springer
    Journal of molecular evolution 36 (1993), S. 545-554 
    Details
    ISSN: 1432-1432
    Keywords: Echinoderms ; Evolution ; Phylogeny ; mtDNA ; Mitochondrial gene arrangements
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Previous analyses have demonstrated that, among the echinoderms, the sea star (class: Asteroidea) mitochondrial genome contains a large inversion in comparison to the mitochondrial DNA of sea urchins (class: Echinoidea). Polymerase chain reaction amplification, DNA cloning, and sequencing have been used to examine the relationships of the brittle stars (class: Ophiuroidea) and sea cucumbers (class: Holothuroidea) to the sea stars and sea urchins. The DNA sequence of the regions spanning potential inversion junctions in both brittle stars and sea cucumbers has been determined. This study has also revealed a highly modified tRNA cluster in the ophiuroid mitochondrial genome. Our data indicate mitochondrial gene arrangement patterns that group the sea cucumbers with sea urchins and sea stars with brittle stars. This use of molecular characters clarifies the relationships among these classes.
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    URL: http://dx.doi.org/10.1007/BF00556359
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    Characterization of two abundant satellite DNAs from the mealworm Tenebrio obscurus (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 489-495 
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    ISSN: 1432-1432
    Keywords: Repetitive sequences ; Sequence variability ; Evolution ; Heterochromatin ; DNA curvature
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Two highly abundant satellite DNAs comprise 36% of the Tenebrio obscurus (Tenebrionidae, Coleoptera) genome. They are designated as satellite I and satellite II with the monomer length of 344 and 142 base pairs (bp), respectively. Both satellites differ in their nucleotide (nt) sequences, but the frequency of point mutations, well-conserved length of monomer variants, stretches of shared mutations characteristic for the process of gene conversion, and distribution of both satellites in regions of centromeric heterochromatin of all chromosomes indicate that the same evolutionary processes act on both of them with the same, or similar, rate. While satellite I shares no sequence similarity with any other known nt sequence, satellite II is 79.7% homologous with the highly abundant satellite from closely related Tenebrio molitor. Difference in the frequency of point mutations and absence of shared mutations indicating gene conversion strongly suggest that in these two closely related species mutational processes affecting satellite DNAs seem to be changed. Retarded electrophoretic mobility, due to sequence-induced curvature of DNA helix axis, was observed for T. obscurus satellite II, but not for satellite I. Although evolutionary processes act with different rates in T. obscurus and T. molitor satellites the monomer length and sequence-induced curvature are well preserved in both 142-bp satellites, as well as in, at the nt sequence level completely divergent, Palorus ratzeburgii (Tenebrionidae) satellite, indicating potential importance of these parameters in their evolution.
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    URL: http://dx.doi.org/10.1007/BF00173418
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    Convergent evolution of crystallin gene regulation in squid and chicken: The AP-1/ARE connection (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 134-143 
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    ISSN: 1432-1432
    Keywords: Lens ; Crystallin ; Squid ; Chicken ; Gene ; Regulation ; AP-1 ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Previous experiments have shown that the minimal promoters required for function of the squid SL20-1 and SL11 crystallin genes in transfected rabbit lens epithelial cells contain an overlapping AP-1/antioxidant responsive element (ARE) upstream of the TATA box. This region resembles the PL-1 and PL-2 elements of the chicken βB 1-cry stallin promoter which are essential for promoter function in transfected primary chicken lens epithelial cells. Here we demonstrate by site-directed mutagenesis that the AP-1/ARE sequence is essential for activity of the squid SL20-1 and SL11 promoters in transfected embryonic chicken lens cells and fibroblasts. Promoter activity was higher in transfected lens cells than in fibroblasts. Electrophoretic mobility shift and DNase protection experiments demonstrated the formation of numerous complexes between nuclear proteins of the embryonic chicken lens and the AP-1/ARE sequences of the squid SL20-1 and SL11 crystallin promoters. One of these complexes comigrated and cross-competed with that formed with the PL-1 element of the chicken βB1-crystallin promoter. This complex formed with nuclear extracts from the lens, heart, brain, and skeletal muscle of embryonic chickens and was eliminated by competition with a consensus AP-1 sequence. The nonfunctional mutant AP-1/ ARE sequences did not compete for complex formation. These data raise the intriguing possibility that entirely different, nonhomologous crystallin genes of the chicken and squid have convergently evolved a similar cis-acting regulatory element (AP-1/ARE) for high expression in the lens.
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    URL: http://dx.doi.org/10.1007/BF00163802
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    Procaryote phylogeny IV: Concerning the phylogenetic status of a photosynthetic bacterium (1975)
    Springer
    Journal of molecular evolution 5 (1975), S. 25-34 
    Details
    ISSN: 1432-1432
    Keywords: Rhodopseudomonas spheroides ; 16S Ribosomal RNA ; T1 Ribonuclease Digest ; Phylogeny ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The 16S ribosomal RNA (30S subunit) ofRhodopseudomonas spheroides has been characterized in terms of T1 ribonuclease digestion products. This “fingerprint” ultimately permits the placement ofR. spheroides into a detailed procaryotic phylogenetic tree. Given the number of major procaryotic lines that have been characterized in these terms to date, one can tentatively place the Athiorhodaceae closer to the Vibrio-Enteric group than to the Bacillaceae or Cyanophyta.
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    The nucleotide sequence of the 5S ribosomal RNA from a photobacterium (1975)
    Springer
    Journal of molecular evolution 5 (1975), S. 35-46 
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    ISSN: 1432-1432
    Keywords: Photobacter Strain 8265 ; 5S Ribosomal RNA ; Primary Structure ; Comparative Characterization ; Evolution ; Energetically Constrained Helix
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Comparative sequencing studies provide powerful insights into molecular function and evolution. The sequence for 5S ribosomal RNA from Photobacter strain 8265 is eighteen base replacements removed from that ofEscherichia coli. Of these, the vast majority involve a G or C becoming an A or U. These variations also define unequivocally a hexanucleotide base paired region, which appears to be a universal feature of the 5S RNA molecule. The base composition of this helix seems to be under rather stringent, and so unusual, energetic constraints. The possible implications of this are discussed - in particular the prospect of a 5S RNA molecule that undergoes conformational transitions as a part of the overall state changes that constitute the function of the ribosome.
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    Sequence ofDrosophila 5S RNA synthesized by cultured cells and by the insect at different developmental stages (1977)
    Springer
    Journal of molecular evolution 9 (1977), S. 279-298 
    Details
    ISSN: 1432-1432
    Keywords: 5S RNA ; Drosophila ; Evolution ; Secondary structure ; Development
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The nucleotide sequence ofDrosophila melanogaster 5S RNA has been determined and appears to be homogeneous both in the KC cell line and in the insect at different developmental stages. Experimental evidence on the conformation of this molecule is in agreement with a general class of 5S RNA models.
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    An ancient divergence among the bacteria (1977)
    Springer
    Journal of molecular evolution 9 (1977), S. 305-311 
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    ISSN: 1432-1432
    Keywords: Comparative cataloging ; Methanogenic bacteria ; Phylogeny ; 16S ribosomal RNA ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The 16S ribosomal RNAs from two species of methanogenic bacteria, the mesophileMethanobacterium ruminantium and the thermophileMethanobacterium thermoautotropbicum, have been characterized in terms of the oligonucleotides produced by digestion withT 1 ribonuclease. These two organisms are found to be sufficiently related that they can be considered members of the same genus or family. However, they bear only slight resemblance to “typical” Procaryotic genera; such asEschericbia, Bacillus andAnacystis. The divergence of the methanogeinc bacteria from other bacteria may be the most ancient phylogenetic event yet detected — antedating considerably the divergence of the blue green algal line for example, from the main bacterial line.
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    URL: http://dx.doi.org/10.1007/BF01796092
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    Chemical and physical microenvironments at the Viking landing sites (1979)
    Springer
    Journal of molecular evolution 14 (1979), S. 13-31 
    Details
    ISSN: 1432-1432
    Keywords: Mars ; Evolution ; Planetary geochemistry ; Soil ; Ionizing radiation ; Exobiology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Physical and chemical considerations permit the division of the near-surface regolith on Mars into at least six zones of distinct microenvironments. The zones are euphotic, duricrust/peds, tempofrost, permafrost, endolithic, and interfacial/transitional. Microenvironments vary significantly in temperature extremes, mean temperature, salt content, relative pressure of water vapor, UV and visible light irradiance, and exposure to ionizing radiation events (100 Mrad) and oxidative molecular species. From what is known of the chemistry of the atmossphere and regolith fines (soil), limits upon the aqueous chemistry of soil pastesmay be estimated. Heat of wetting could reach 45 cal/g dry soil; initial pH is indeterminate between 1 and 10; ionic strength and salinity are predicted to be extremely high; freezing point depression is inadequate to provide quantities of liquid water except in special cases. The prospects for biotic survival are grim by terrestrial standards, but the extremes of biological resiliency are inaccessible to evaluation. Second-generation in situ experiments which will better define Martian microenvironments are clearly possible. Antarctic dry valleys are approximations to Martian conditions, but deviate significantly by at least half-a-dozen criteria.
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    URL: http://dx.doi.org/10.1007/BF01732364
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    The estimation of genetic divergence (1981)
    Springer
    Journal of molecular evolution 17 (1981), S. 167-181 
    Details
    ISSN: 1432-1432
    Keywords: Evolution ; Genetics ; REH theory ; Mutations ; Natural selection ; Nucleic acids ; Proteins ; Paleogenetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have independently repeated the computer simulations on which Nei and Tateno (1978) base their criticism of REH theory and have extended the analysis to include mRNAs as well as proteins. The simulation data confirm the correctness of the REH method. The high average value of the fixation intensity μ2 found by Nei and Tateno is due to two factors: 1) they reported only the five replications in which μ2 was high, excluding the forty-five replications containing the more representative data;and 2) the lack of information, inherent to protein sequence data, about fixed mutations at the third nucleotide position within codons, as the values are lower when the estimate is made from the mRNAs that code for the proteins. REH values calculated from protein or nucleic acid data on the basis of the equiprobability of genetic events underestimate, not overestimate, the total fixed mutations. In REH theory the experimental data determine the estimate T2 of the time average number of codons that have been free to fix mutations during a given period of divergence. In the method of Nei and Tateno it is assumed, despite evidence to the contrary, that every amino acid position may fix a mutation. Under the latter assumption, the measure X2 of genetic divergence suggested by Nei and Tateno is not tenable: values of X2 for theα hemoglobin divergences are less than the minimum number of fixed substitutions known to have occurred. Within the context of REH theory, a paradox, first posed by Zuckerkandl, with respect to the high rate of covarion turnover and the nature of general function sites in proteins is resolved.
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    Vertebrate protamine gene evolution I. Sequence alignments and gene structure (1990)
    Springer
    Journal of molecular evolution 30 (1990), S. 333-346 
    Details
    ISSN: 1432-1432
    Keywords: Protamine ; Evolution ; Nuclear protein ; DNA condensation ; Sperm proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The availability of the amino acid sequence for nine different mammalian P1 family protamines and the revised amino acid sequence of the chicken protamine galline (Oliva and Dixon 1989) reveals a much close relationship between mammalian and avian protamines than was previously thought (Nakano et al. 1976). Dot matrix analysis of all protamine genes for which genomic DNA or cDNA sequence is available reveals both marked sequence similarities in the mammalian protamine gene family and internal repeated sequences in the chicken protamine gene. The detailed alignments of the cis-acting regulatory DNA sequences shows several consensus sequence patterns, particularly the conservation of a cAMP response element (CRE) in all the protamine genes and of the regions flanking the TATA box, CAP site, N-terminal coding region, and polyadenylation signal. In addition we have found a high frequency of the CA dinucleotide immediately adjacent to the CRE element of both the protamine genes and the testis transition proteins, a feature not present in other genes, which suggests the existence of an extended CRE motif involved in the coordinate expression of protamine and transition protein genes during spermatogenesis. Overall these findings suggest the existence of an avian-mammalian P1 protamine gene line and are discussed in the context of different hypotheses for protamine gene evolution and regulation.
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    Phylogeny of the major tetrapod groups: Morphological data and divergence dates (1990)
    Springer
    Journal of molecular evolution 30 (1990), S. 409-424 
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    ISSN: 1432-1432
    Keywords: Phylogeny ; Tetrapods ; Morphology ; Cladistics ; Divergence ; Evolution ; Amphibians ; Reptiles ; Birds ; Mammals
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The phylogeny of the major groups of tetrapods (amphibians, reptiles, birds, and mammals) has until recently been poorly understood. Cladistic analyses of morphological data are producing new hypotheses concerning the relationships of the major groups, with a focus on the identification of monophyletic groups. Molecular phylogenies support some of these views and dispute others. Geological dates of the major evolutionary branching points are recalculated on the basis of the cladograms and new fossil finds.
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    Taxonomic relations between archaebacteria including 6 novel genera examined by cross hybridization of DNAs and 16S rRNAs (1982)
    Springer
    Journal of molecular evolution 18 (1982), S. 109-114 
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    ISSN: 1432-1432
    Keywords: Archaebacteria ; Taxonomy ; Evolution ; DNA ; 16S rRNA ; Hybridization ; Phylogeny ; Thermoproteales
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary DNAs from 16 species of archaebacteria including 6 novel isolates were hybridized with 16S rRNAs from 7 species representing different orders or groups of the urkingdom of archaebacteria. The yields, normalized for the number of genes perµg of DNA, and the temperature stabilities of all hybrids were determined and related to each other. A taxonomic tree constructed from such fractional stability data reveals the same major divisions as that derived from comparative cataloging of 16S rRNA sequences. The extreme halophiles appear however as a distinct order besides the three known divisions of methanogens. The methanogens, the halophiles andThermoplasma form one of two clearly recognizable branches of the archaebacterial urkingdom. The order represented bySulfolobus and the related novel orderThermoproteales form the other branch. Three novel genera,Thermoproteus, Desulfurococcus and the “stiff filaments” represent three families of this order. The extremely thermophilic methanogenMethanothermus fervidus belongs to theMethanobacteriales. SN1, a methanogen from Italy, appears as another species of the genusMethanococcus. Another novel methanogen, M3, represents a genus or family of the orderMethanomicrobiales.
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    On the cysteine and cystine content of proteins (1977)
    Springer
    Journal of molecular evolution 10 (1977), S. 155-160 
    Details
    ISSN: 1432-1432
    Keywords: Cysteine ; Cystine ; Protein ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Analysis of published data on the cysteine and half-cystine content of proteins indicates that most intracellular proteins may be classified as sulfhydryl proteins (those containing cysteine but little or no half-cystine) and that such sulf-hydryl proteins have a low cysteine content. The mean cysteine content found for 32 intracellular mammalian proteins was 1.6 % and intracellular proteins of many bacteria have similar or lower values. Extracellular mammalian proteins are primarily disulfide proteins (those containing half-cystine but little or no cysteine) and have a high half-cystine content, the mean value found for some 34 extracellular mammalian proteins being 4.1 %. This is contrasted with many of the extracellular proteins from facultative bacteria which are cyst(e)ine-free proteins, being lacking in both cysteine and half-cystine. These and related observations are interpreted in terms of the evolution of life in a reducing atmosphere and the subsequent transition to an oxidizing environment. It is suggested that disulfide proteins evolved primarily after the accumulation of oxygen in the atmosphere.
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    URL: http://dx.doi.org/10.1007/BF01751808
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    There appear to be conserved constraints on the distribution of nucleotide sequences in cellular genomes (1991)
    Springer
    Journal of molecular evolution 32 (1991), S. 24-30 
    Details
    ISSN: 1432-1432
    Keywords: Short sequence distribution ; Sequence constraints ; Averaged sequence ; Sequence structure ; Asymmetric nucleotide sequences ; GC content ; Evolution ; Evolutionary constraints
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The data from a genomic library can be sorted into the frequencies of every possible tetranucleotide in the sequence. This tabulation, a short sequence distribution, contains the frequency of occurrence of the 256 tetranucleotides and thus seems to serve as a vehicle for averaging sequence information. Two such distributions can be readily compared by correlation. Reported here are correlations (Spearmanr s) of the distributions from all of the genomic libraries in GenBank 44.0 with sizes equal to or larger than that ofSalmonella typhimurium, except for the data for mouse and humans. All of the organisms examined showed highly significant correlations between the two DNA strands (not the complementarity expected from base pairing). Of 155 comparisons between libraries, 132 showed significant correlations at the 99% confidence level. Application of the correlation coefficients as a similarity matrix clustered most organisms in a phenogram in a pattern consistent with other hypotheses. This suggests a highly conserved pattern underlying all other genetic information in cellular DNA and affecting both DNA strands, perhaps caused by interaction with conserved factors necessary for DNA packaging.
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    Tubulin evolution: Two major types of α-tubulin (1982)
    Springer
    Journal of molecular evolution 19 (1982), S. 80-86 
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    ISSN: 1432-1432
    Keywords: Microtubules ; Tubulin ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Tubulin subunits have been isolated from a variety of protists and marine invertebrates. The sources were: sperm tails of a tunicate (Ciona intestinalis), an abalone (Haliotis rufescens) and a sea anemone (Tealia crassicornis), the gill cilia of a clam (Mercenaria mercenaria), the cilia of a ciliate (Tetrahymena pyriformis) and the cytoplasm of a slime mold (Physarum polycephalum). All the β-tubulins, as characterised by their electropherograms after limited proteolytic cleavage withStaphylococcus aureus protease, were fairly similar. In contrast, two markedly different peptide patterns were found for the α-tubulins of (a) metazoan axonemes and (b) protistan axonemes, plant axonemes and slime mold cytoplasm. Metazoan axonemal α-tubulin peptide patterns could be further divided into two similar but distinct subtypes which did not correlate with the taxonomic divisions of deuterostomia and protostomia, or to different tubulins within an axoneme, or to different tubulins of flagella and cilia. We have postulated that these small differences may be accounted for by a simple glutamicaspartic acid exchange at a particular position in the α-tubulin sequence. Identical peptide patterns were observed for sea urchin and sea anemone sperm tail tubulins, proving that the metazoan type of axonemal tubulin arose before the divergence of bilateral and radial symmetric organisms. The close similarity of the slime mold cytoplasmic α-tubulin peptide pattern to protistan and plant axonemal α-tubulin patterns suggests that the same type of tubulin might be used to form both axonemal and cytoplasmic types of microtubules in protists and plants. The large structural constraints imposed upon this tubulin molecule probably allowed very little change in its primary structure, thus explaining the similarity of tubulins from organisms which diverged at such an early time in eukaryote history. Duplication and modification of the tubulin gene may then have led to the development of specific axonemal and cytoplasmic microtubules during the evolution of the metazoa.
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    URL: http://dx.doi.org/10.1007/BF02100226
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    The evolutionary pattern of aromatic amino acid biosynthesis and the emerging phylogeny of pseudomonad bacteria (1983)
    Springer
    Journal of molecular evolution 19 (1983), S. 272-282 
    Details
    ISSN: 1432-1432
    Keywords: Microbial phylogeny ; Evolution ; Aromatic biosynthesis ; Regulatory enzymes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Pseudomonad bacterial are a phylogenetically diverse assemblage of species named within contemporary genera that includePseudomonas, Xanthomonas andAlcaligenes. Thus far, five distinct rRNA homology groups (Groups I through V) have been established by oligonucleotide cataloging and by rRNA/DNA hybridization. A pattern of enzymic features of aromatic amino acid biosynthesis (enzymological patterning) is conserved at the level of rRNA homology, five distinct and unambiguous patterns therefore existing in correspondence with the rRNA homology groups. We sorted 87 pseudomonad strains into Groups (and Subgroups) by aromatic pathway patterning. The reliability of this methodology was tested in a blind study using coded cultures of diverse pseudomonad organisms provided by American Type Culture Collection. Fourteen of 14 correct assignments were made at the Group level (the level of rRNA homology), and 12 of 14 correct assignments were made at the finer-tuned Subgroup levels. Many strains of unknown rRNA-homology affiliation had been placed into tentative rRNA groupings based upon enzymological patterning. Positive confirmation of such strains as members of the predicted rRNA homology groups was demonstrated by DNA/rRNA hybridization in nearly every case. It seems clear that the combination of these molecular approaches will make it feasible to deduce the evolution of biochemical-pathway construction and regulation in parallel with the emerging phylogenies of microbes housing these pathways.
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    URL: http://dx.doi.org/10.1007/BF02099974
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    Order and orientation of genic sequences in circular mitochondrial DNA fromSaccharomyces exiguus: Implications for evolution of yeast mtDNAs (1983)
    Springer
    Journal of molecular evolution 19 (1983), S. 333-341 
    Details
    ISSN: 1432-1432
    Keywords: mtDNA ; Gene mapping ; Evolution ; Yeasts
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Mapping of sequences specifying the large and small ribosomal RNAs and six polypeptides in the circular 23.7 kbp mitochondrial DNA ofSaccharomyces exiguus has shown that these genes have the same orientation and that a 5 gene cluster is common to this DNA and the 18.9 kbp mtDNA fromTorulopsis glabrata. Included in the preserved region are juxtaposed sequences specifying ATPase subunits 6 and 9 which have the same order and orientation as analogous genes in theEscherichia coli unc operon. The above data, together with knowledge that these two sequences are dispersed in larger yeast mtDNAs, leads us to suggest that larger forms are derived from a smaller ancestral molecule that would have had some resemblance to the mtDNAs ofS. exiguus andT. glabrata.
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    URL: http://dx.doi.org/10.1007/BF02101636
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    Analysis of a five gene cluster and unique orientation of large genic sequences inTorulopsis glabrata mitochondrial DNA (1983)
    Springer
    Journal of molecular evolution 19 (1983), S. 342-345 
    Details
    ISSN: 1432-1432
    Keywords: mtDNA ; Gene mapping ; Evolution ; Yeasts
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Analysis of gene order and orientation in the circular 18.9 kbp mitochondrial DNA molecule ofTorulopsis glabrata has shown that the eight large genic sequences have the same orientation and that a five gene cluster which runs — cytochrome b, cytochrome oxidase subunit 1, ATPase subunits 6 and 9 and cytochrome oxidase subunit 2 — is common to this DNA andSaccharomyces exiguus mtDNA (see accompanying paper).
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    URL: http://dx.doi.org/10.1007/BF02101637
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    Mitochondrial DNA evolution in lagomorphs: Origin of systematic heteroplasmy and organization of diversity in European rabbits (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 92-102 
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    ISSN: 1432-1432
    Keywords: Lagomorphs ; Rabbit ; Mitochondrial DNA ; Heteroplasmy ; Restriction site polymorphism ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A characterization was conducted on mitochondrial DNA (mtDNA) molecules extracted separately from 107 European rabbits (Oryctolagus cuniculus) both wild and domestic, 13 European hares (Lepus capensis), and 1 eastern cottontail (Sylvilagus floridanus). Experimentally this study took into account restriction site polymorphism, overall length variation of the noncoding region, and numbers of repeated sequences. Nucleotide divergences indicate that the mtDNAs from the three species derived from a common ancestor some 6–8 million years (Myr) ago. Every animal appeared heteroplasmic for a set of molecules with various lengths of the noncoding region and variable numbers of repeated sequences that contribute to them. This systematic heteroplasmy, most probably generated by a rate of localized mtDNA rearrangements high enough to counterbalance the cellular segregation of rearranged molecules, is a shared derived character of leporids. The geographic distribution of mtDNA polymorphism among wild rabbit populations over the western European basin shows that two molecular lineages are represented, one in southern Spain, the second over northern Spain, France, and Tunisia. These two lineages derived from a common ancestor some 2 Myr ago. Their present geographical distribution may be correlated to the separation of rabbits into two stocks at the time of Mindel glaciation. Finally the distribution of mtDNA diversity exhibits a mosaic pattern both at inter- and intrapopulation levels.
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    URL: http://dx.doi.org/10.1007/BF02100200
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    Structure and evolution of 5S rRNA genes and pseudogenes in the genusAspergillus (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 175-178 
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    ISSN: 1432-1432
    Keywords: Aspergillus ; 5S rRNA genes ; 5S rRNA pseudogenes ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have cloned and determined the nucleotide sequence of 18 DNA fragments hybridizing to 5S rRNA from twoAspergillus species-A. wentii andA. awamori. Four of the analyzed sequences were pseudogenes. The gene sequences of these two species were very similar and differed fromAspergillus nidulans at both constant and microheterogeneous sites.
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    URL: http://dx.doi.org/10.1007/BF02193632
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    tRNA-rRNA sequence homologies: Evidence for a common evolutionary origin? (1983)
    Springer
    Journal of molecular evolution 19 (1983), S. 420-428 
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    ISSN: 1432-1432
    Keywords: Yeast ; E. coli ; tRNA ; rRNA ; Sequence homologies ; Evolution ; Origins ; Coding mechanism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Many tRNAs ofE. coli and yeast contain stretches whose base sequences are similar to those found in their respective rRNAs. The matches are too frequent and extensive to be attributed to coincidence. They are distributed without discernible pattern along and among the RNAs and between the two species. They occur in loops as well as in stems, among both conserved and non-conserved regions. Their distributions suggest that they reflect common ancestral origins rather than common functions, and that they represent true homologies.
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    URL: http://dx.doi.org/10.1007/BF02102317
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    Classification of elapid snake neurotoxins and cytotoxins according to chain length: Evolutionary implications (1984)
    Springer
    Journal of molecular evolution 20 (1984), S. 128-134 
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    ISSN: 1432-1432
    Keywords: Snake venom ; Neurotoxin ; Cytotoxin ; Evolution ; Circular dichroism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The amino acid sequences of the 139 homologous “short” neurotoxins, “long” neurotoxins and cytotoxins so far characterised from elapid snake venoms were compared on the basis of the amino acid deletion/insertion events that have occurred during evolution. Systematic grouping of the toxins according to similarity suggests that the short neurotoxins resemble the cytotoxins more closely than they do the long neurotoxins. The significance of this finding is discussed in relation to the methodology, the conformations of the toxins (as represented by circular dichroism spectra) and the outcome of the study that would have been obtained had more traditional methods been used. It appears probable that the cytotoxins evolved relatively recently from neurotoxic ancestors.
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    The use of bonding between tRNAs to implement early peptide synthesis (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 464-469 
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    ISSN: 1432-1432
    Keywords: Evolution ; tRNA ; Ribosome ; Peptide bond ; Catalytic RNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Continuation of early evolutionary bonding between tRNAs would provide a solution to residence time problems between peptidyl-tRNA and mRNA. It could also improve the speed of peptide bond formation by holding the amino acid close to the growing peptide. The tRNA clover leaf structure would allow each tRNA to from a TΨC(GA)-loop bond to one side and a D-loop bond to the other, hence fixing itself within a group of tRNAs, all attached to the mRNA. This can be developed into a system for peptide elongation in which bonds are made and broken in an ordered sequence, with each step triggering the next. This leads to a model system that fits with some recent propsals for a three-site ribosome.
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    URL: http://dx.doi.org/10.1007/BF02103139
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    Two independent mutational events in the loss of urate oxidase during hominoid evolution (1992)
    Springer
    Journal of molecular evolution 34 (1992), S. 78-84 
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    ISSN: 1432-1432
    Keywords: Urate oxidase ; Evolution ; Mechanism of inactivation ; Mutations ; Hominoids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Urate oxidase was lost in hominoids during primate evolution. The mechanism and biological reason for this loss remain unknown. In an attempt to address these questions, we analyzed the sequence of urate oxidase genes from four species of hominoids: human (Homo sapiens), chimpanzee (Pan troglodytes), orangutan (Pongo pygmaeus), and gibbon (Hylobates). Two nonsense mutations at codon positions 33 and 187 and an aberrant splice site were found in the human gene. These three deleterious mutations were also identified in the chimpanzee. The nonsense mutation at codon 33 was observed in the orangutan urate oxidase gene. None of the three mutations was present in the gibbon; in contrast, a 13-bp deletion was identified that disrupted the gibbon urate oxidase reading frame. These results suggest that the loss of urate oxidase during the evolution of hominoids could be caused by two independent events after the divergence of the gibbon lineage; the nonsense mutation at codon position 33 resulted in the loss of urate oxidase activity in the human, chimpanzee, and orangutan, whereas the 13-bp deletion was responsible for the urate oxidase deficiency in the gibbon. Because the disruption of a functional gene by independent events in two different evolutionary lineages is unlikely to occur on a chance basis, our data favor the hypothesis that the loss of urate oxidase may have evolutionary advantages.
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    URL: http://dx.doi.org/10.1007/BF00163854
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    Estimating the fraction of invariable codons with a capture-recapture method (1992)
    Springer
    Journal of molecular evolution 35 (1992), S. 253-260 
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    ISSN: 1432-1432
    Keywords: Protein-coding sequences ; DNA sequences ; Evolution ; Evolutionary rates ; Rate heterogeneity ; Maximum likelihood ; Statistical testing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A codon-based approach to estimating the number of variable sites in a protein is presented. When first and second positions of codons are assumed to be replacement positions, a capture-recapture model can be used to estimate the number of variable codons from every pair of homologous and aligned sequences. The capture-recapture estimate is compared to a maximum likelihood estimate of the number of variable codons and to previous approaches that estimate the number of variable sites (not codons) in a sequence. Computer simulations are presented that show under which circumstances the capture-recapture estimate can be used to correct biases in distance matrices. Analysis of published sequences of two genes, calmodulin and serum albumin, shows that distance corrections that employ a capture-recapture estimate of the number of variable sites may be considerably different from corrections that assume that the number of variable sites is equal to the total number of positions in the sequence.
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    Molecular analysis of ependymins from the cerebrospinal fluid of the orders clupeiformes and salmoniformes: no indication for the existence of an euteleost infradivision (1993)
    Springer
    Journal of molecular evolution 36 (1993), S. 578-585 
    Details
    ISSN: 1432-1432
    Keywords: Evolution ; Teleostei ; Clupea harengus ; Esox lucius ; Fish ; Polymerase chain reaction ; Calcium binding
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Ependymins represent the predominant protein constituents in the cerebrospinal fluid of many teleost fish and they are synthesized in meningeal fibroblasts. Here, we present the ependymin sequences from the herring (Clupea harengus) and the pike (Esox lucius). A comparison of ependymin homologous sequences from three different orders of teleost fish (Salmoniformes, Cypriniformes, and Clupeiformes) revealed the highest similarity between Clupeiformes and Cypriniformes. This result is unexpected because it does not reflect current systematics, in which Clupeiformes belong to a separate infradivision (Clupeomorpha) than Salmoniformes and Cypriniformes (Euteleostei). Furthermore, in Salmoniformes the evolutionary rate of ependymins seems to be accelerated mainly on the protein level. However, considering these inconstant rates, neither neighbor joining trees nor DNA parsimony methods gave any indication that a separate euteleost infradivision exists.
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    Sequences related to the ox pancreatic ribonuclease coding region in the genomic DNA of mammalian species (1993)
    Springer
    Journal of molecular evolution 37 (1993), S. 29-35 
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    ISSN: 1432-1432
    Keywords: Ribonuclease ; Evolution ; Gene duplication ; Ruminants
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Mammalian pancreatic ribonucleases form a family of homologous proteins that has been extensively investigated. The primary structures of these enzymes were used to derive phylogenetic trees. These analyses indicate that the presence of three strictly homologous enzymes in the bovine species (the pancreatic, seminal, and cerebral ribonucleases) is due to gene duplication events which occurred during the evolution of ancestral ruminants. In this paper we present evidence that confirms this finding and that suggests an overall structural conservation of the putative ribonuclease genes in ruminant species. We could also demonstrate that the sequences related to ox ribonuclease coding regions present in genomic DNA of the giraffe species are the orthologues of the bovine genes encoding the three ribonucleases mentioned above.
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    Molecular evolutionary analysis based on the amino acid sequence of catalase (1993)
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    Journal of molecular evolution 37 (1993), S. 71-76 
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    ISSN: 1432-1432
    Keywords: Evolution ; Catalase ; Phylogenetic tree
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Heme-containing catalase sequences from 20 different organisms representing prokaryotes, fungi, animals, and plants have been compiled for phylogenetic reconstruction. Phylogenies based on distance and parsimony analysis show that fungal and animal catalases can be derived from one ancestor, whereas bacterial catalases fail to form a monophyletic group. Plant catalases appear to form a second class of catalases that arose independently from a possible prokaryotic ancestor.
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    Conservation of human Y chromosome sequences among male great apes: Implications for the evolution of Y chromosomes (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 13-21 
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    ISSN: 1432-1432
    Keywords: Y chromosome ; Great ape ; Human ; Evolution ; DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Nine newly described single-copy and lowcopy-number genomic DNA sequences isolated from a flow-sorted human Y chromosome library were mapped to regions of the human Y chromosome and were hybridized to Southern blots of male and female great ape genomic DNAs (Gorilla gorilla, Pan troglodytes, Pongo pygmaeus). Eight of the nine sequences mapped to the euchromatic Y long arm (Yq) in humans, and the ninth mapped to the short arm or pericentromeric region. All nine of the newly identified sequences and two additional human Yq sequences hybridized to restriction fragments in male but not female genomic DNA from the great apes, indicating Y chromosome localization. Seven of these 11 human Yq sequences hybridized to similarly-sized restriction endonuclease fragments in all the great ape species analyzed. The five human sequences that mapped to the most distal subregion of Yq (deletion of which region is associated with spermatogenic failure in humans) were hybridized to Southern blots generated by pulsed-field gel electrophoresis. These sequences define a region of approximately 1 Mb on human Yq in which HpaII tiny fragment (HTF) islands appear to be absent. The conservation of these human Yq sequences on great ape Y chromosomes indicates a greater stability in this region of the Y than has been previously described for most anonymous human Y chromosomal sequences. The stability of these sequences on great ape Y chromosomes seems remarkable given that this region of the Y does not undergo meiotic recombination and the sequences do not appear to encode genes for which positive selection might occur.
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    The neuroethology of sound production in tiger moths (Lepidoptera, Arctiidae) (1992)
    Springer
    Journal of comparative physiology 170 (1992), S. 575-588 
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    ISSN: 1432-1351
    Keywords: Moth ; Sensorimotor integration ; Neuroethology ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary 1. Certain species of tiger moths emit clicks when stimulated by bat-like sounds. These clicks are generated by modified thoracic episterna (tymbals) (Fig. 1) and constitute a rhythmic behaviour activated by simple sensory input. 2. Tymbal periods are indirectly related to stimulus intensity and periods (Fig. 3). Moths initiate sounds with the tymbal opposite to the stimulated ear and once a sequence commences it continues in an undisrupted fashion. 3. The tymbal is innervated by a pleural branch (IIIN2a) of the metathoracic leg nerve, a similar anatomy to that in the unmodified episterna of silent moths (Fig. 5). Backfills of the IIIN2a in Cycnia tenera reveal sensory fibres and a cluster of 5–9 motor neurons with densely overlying dendritic fields (Fig. 6). 4. Extracellular recordings of the IIIN2a reveal a large impulse preceding each tymbal sound (Fig. 7). I suggest that this impulse results from the synchronous firing of 2–3 motor neurons and is the motor output of the tymbal central pattern generator (CPG). The spikes alternate (Figs. 9, 10) and are bilaterally co-related (Fig. 11) but with an phase asymmetry of 2–3 ms (Fig. 12). 5. Normal motor output continues in the absence of tymbal sounds (Fig. 13) and when all nerve-tymbal connections are severed (Fig. 14, Table 1) therefore this CPG operates independent of sensory feedback. A model is proposed for the tymbal circuitry based upon the present data and the auditory organization of related noctuid moths (Fig. 15). I propose that the tymbal response in modern arctiids evolved from either flight or walking CPGs and that preadaptive circuitry ancestral to tymbal movements still exists in modern silent Lepidoptera.
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    The evolutionary adaptation of flower colours and the insect pollinators' colour vision (1992)
    Springer
    Journal of comparative physiology 171 (1992), S. 171-181 
    Details
    ISSN: 1432-1351
    Keywords: Colour vision ; Flower colours ; Evolution ; Hymenoptera ; Pollination ecology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary The evolutionary tuning between floral colouration and the colour vision of flower-visiting Hymenoptera is quantified by evaluating the informational transfer from the signalling flower to the perceiving pollinator. The analysis of 180 spectral reflection spectra of angiosperm blossoms reveals that sharp steps occur precisely at those wavelengths where the pollinators are most sensitive to spectral differences. Straight-forward model calculations determine the optimal set of 3 spectral photoreceptor types for discrimination of floral colour signals on the basis of perceptual difference values. The results show good agreement with the sets of photoreceptors characterized electrophysiologically in 40 species of Hymenoptera.
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    URL: http://dx.doi.org/10.1007/BF00188925
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    Did neural pooling for night vision lead to the evolution of neural superposition eyes? (1994)
    Springer
    Journal of comparative physiology 175 (1994), S. 289-302 
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    ISSN: 1432-1351
    Keywords: Compound eye ; Open rhabdom ; Neural superposition ; Visual ecology ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Observations of the infrared deep pseudopupil, optical determinations of the corneal nodal point, and histological methods were used to relate the visual fields of individual rhabdomeres to the array of ommatidial optical axes in four insects with open rhabdoms: the tenebrionid beetle Zophobas morio, the earwig Forficula auricularia, the crane fly Tipula pruinosa, and the backswimmer Notonecta glauca. The open rhabdoms of all four species have a central pair of rhabdomeres surrounded by six peripheral rhabdomeres. At night, a distal pigment aperture is fully open and the rhabdom receives light over an angle approximately six times the interommatidial angle. Different rhabdomeres within the same ommatidium do not share the same visual axis, and the visual fields of the peripheral rhabdomeres overlap the optical axes of several near-by ommatidia. During the day, the pigment aperture is considerably smaller, and all rhabdomeres share the same visual field of about two interommatidial angles, or less, depending on the degree of light adaptation. The pigment aperture serves two functions: (1) it allows the circadian rhythm to switch between the night and day sampling patterns, and (2) it works as a light driven pupil during the day. Theoretical considerations suggest that, in the night eye, the peripheral retinula cells are involved in neural pooling in the lamina, with asymmetric pooling fields matching the visual fields of the rhabdomeres. Such a system provides high sensitivity for nocturnal vision, and the open rhabdom has the potential of feeding information into parallel spatial channels with different tradeoffs between resolution and sensitivity. Modification of this operational principle to suit a strictly diurnal life, makes the contractile pigment aperture superfluous, and decreasing angular sensitivities together with decreasing pooling fields lead to a neural superposition eye.
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    Functional elements and domains inferred from sequence comparisons of a heat shock gene in two nematodes (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 3-9 
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    ISSN: 1432-1432
    Keywords: Caenorhabditis elegans ; Caenorhabditis briggsae ; hsp70 ; grp78 ; Gene comparison ; Evolution ; Regulatory elements
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Caenorhabditis elegans andCaenorhabditis briggsae are two closely related nematode species that are nearly identical morphologically. Interspecific cross-hybridizing DNA appears to be restricted primarily to coding regions. We compared portions of thehsp-3 homologs two grp 78-like genes, fromC. elegans andC. briggsae and detected regions of DNA identity in the coding region, the 5′ flanking DNAs, and the introns. Thehsp-3 homologs share approximately 98% and 93% identity at the amino acid and nucleotide levels, respectively. Using the nucleotide substitution rate at the silent third position of the codons, we have estimated a lower limit for the date of divergence betweenC. elegans andC. briggsae to be approximately 23–32 million years ago. The 5′ flanking DNAs and one of the introns contain elements that are highly conserved betweenC. elegans andC. briggsae. Some of the regions of nucleotide identity in the 5′ flanking DNAs correspond to previously detected identities including viral enhancer sequences, a heat shock element, and an element present in the regulatory regions of mammalian grp78 and grp94 genes. We propose that a comparison ofC. elegans andC. briggsae sequences will be useful in the detection of potential regulatory and structural elements.
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    Secondary structural elements exclusive to the sequences flanking ribosomal RNAs lend support to the monophyletic nature of the archaebacteria (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 25-32 
    Details
    ISSN: 1432-1432
    Keywords: Archaebacteria ; rRNA operons ; Secondary structure ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Several sequences flanking the large rRNA genes of several transcripts from extreme thermophiles, extreme halophiles, and methanogens were aligned and analyzed for the presence of common primary and secondary structural features, which would bear on the concept of monphyletic archaebacteria. Few sequences were common to all the archaebacterial transcripts, and these were confined to short regions generally flanking putative double helices. At a secondary structural level, however, in addition to the previously characterized processing stems of the 16S and 23S RNAs, four helices were detected that were common to the archaebacterial transcripts: two in the 16S RNA leader sequence and two in the 16S-23S RNA spacer. Although all of these helices vary in size and form from organism to organism, three of them contain double helical segments that are strongly supported by compensating base changes among the three archaebacterial groups. Three extreme halophiles exhibited two additional helices in their relatively large spacers and a further helix preceding the 5S RNA, which are also supported by compensating base changes. Ribosomal RNA transcripts from eubateria/chloroplasts and eukaryotes were also examined for secondary structural features with locations and forms corresponding to those of the archaebacteria, but none were detected. The analysis provides support for the monophyletic nature of the archaebacteria and reinforces their differences from eubacteria/chloroplasts and eukaryotes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101789
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    Biochemical and genetic consequences of gene transfer from endosymbiont to host genome (1982)
    Springer
    Journal of molecular evolution 18 (1982), S. 287-292 
    Details
    ISSN: 1432-1432
    Keywords: Evolution ; Endosymbiosis ; Gene transfer ; Transmembrane movement of proteins ; Receptors
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary In the origin of the mitochondrion and plastid, gene transfer from the ancestral endosymbiont to the host was proposed to be a crucial event. For this genic integration to proceed, products of transferred genes had to return to and enter the endosymbionts. The limiting event was the crossing of the barrier presented by the two semipermeable membranes bounding the proto-organelle. In this paper it is suggested that spontaneous transport allowed transferred gene encoded proteins to enter the endosymbionts before receptors evolved. The effects of these events, including the degeneration of the endosymbiont genome, are discussed. Although the presumed gene transfer had profound effects on the metabolic relationships between host and endosymbionts it probably cannot account for all examples of organelle/cytoplasmic isozyme pairs or the absence of amino acid synthetic enzymes in animal cells.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01733893
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  • 100
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    Electronic Resource
    The concept of cellular evolution (1977)
    Springer
    Journal of molecular evolution 10 (1977), S. 1-6 
    Details
    ISSN: 1432-1432
    Keywords: Evolution ; Ribosomes ; Genotype-Phenotype ; Cytoplasm ; Endosymbiosis ; Procaryote ; Eucaryote ; Progenote
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A central evolutionary question is whether the eucaryotic cytoplasm represents a line of descent that is separate from the typical bacterial line. It is argued on the basis of differences between their respective translation mechanisms that the two lines do represent separate phylogenetic trees in the sense that each line of descent independently evolved to a level of organization that could be called procaryotic. The two lines of descent, nevertheless shared a common ancestor, that was far simpler than the procaryote. This primitive entity is called a progenote, to recognize the possibility that it had not yet completed evolving the link between genotype and phenotype. This concept changes considerably the view one takes toward cellular evolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01796132
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