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  • Evolution  (245)
  • Springer  (245)
  • Blackwell Publishing Ltd
  • Annual Reviews
  • 2005-2009
  • 1990-1994  (178)
  • 1980-1984  (67)
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  • 1
    Electronic Resource
    Electronic Resource
    Cell lineage restrictions in the genital disc ofDrosophila revealed byMinute gynandromorphs (1983)
    Springer
    Development genes and evolution 192 (1983), S. 337-346 
    Details
    ISSN: 1432-041X
    Keywords: Drosophila ; Gynandromorphs ; Genital disc ; Compartments ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The genital imaginal disc ofDrosophila differentiates the terminalia, i.e. the genitalia and analia, of both sexes. It represents a composite anlage, containing a female genital primordium, a male genital primordium and an anal primordium. In normal males and females, only one of the two genital primordia differentiates; the other is developmentally repressed. Therefore, cell-lineage relationships between the male and female genital primordia can only be studied in sexual mosaics which differentiate female and male cells. We producedMinute (M)‖non-Minute(M+) gynandromorphs and selected those with sexually mosaic terminalia for a cell-lineage analysis. In these mosaics, either the male (XO) or female (XX) cells wereM + and thus had a growth advantage. The differential growth rates served as a tool to detect clonal restrictions. In control gynandromorphs (M +‖M +), the amount of female genitalia differentiated was largely independent of the amount of male genitalia present. In contrast, male and female anal structures, as a rule, added up to one full set. The same was true for the experimentalM‖M + gynandromorphs, but the contribution ofXX andXO cells to mosaic terminalia changed drastically due toM + cells competing successfully against the more slowly growingM cells. Specific subsamples ofM‖M + gynandromorphs showed thatM cells in a non-mosaic primordium are shielded from cell competition taking place in the neighbouring mosaic primordium. We conclude that the three primordia of the genital disc represent developmental compartments. In the genital primordia, even developmentally repressedM + cells compete successfully against developmentally activeM cells.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00848814
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  • 2
    Electronic Resource
    Electronic Resource
    Role of ooplasmic segregation in mammalian development (1994)
    Springer
    Development genes and evolution 203 (1994), S. 199-204 
    Details
    ISSN: 1432-041X
    Keywords: Cell differentiation ; Cytoplasm ; Micromanipulation ; Mouse embryo ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A new micromanipulation technique permitted the scrambling of the zygote cytoplasm. Such interference had no effect on preimplantation development, and when zygotes with scrambled cytoplasm were transfered to the pseudopregnant females, normal and fertile mice were born. This demonstrates that no morphogenetic factors are prelocalized in the egg cytoplasm. Cleavage characteristics of mouse embryos provide the evidence that zygote cytoplasm does not define any determinate type of cleavage. We conclude that the mechanism of ooplasmic segregation is not used in the mouse (and presumably mammalian) development. It is suggested that the turning point in the evolution of mammalian embryogenesis was the transition to the intrauterine development, that started the process leading among other changes, to the loss of the ooplasmic morphogenetic determinants.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00636335
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  • 3
    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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  • 4
    Electronic Resource
    Electronic Resource
    Adaptation ofDrosophila enzymes to temperature. III. Evolutionary conservatism in mitochondrial enzymes (1980)
    Springer
    Journal of molecular evolution 16 (1980), S. 37-46 
    Details
    ISSN: 1432-1432
    Keywords: Evolution ; Drosophila ; Temperature ; Mitochondrial enzymes ; Kinetic properties
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The evolutionary behavior of two mitochondrial enzymes (L-glycerol 3-phosphate:cytochrome c oxidoreductase E.C.1.1.1.95,αGPO, and L-malate: NAD+ oxidoreductase, E.C.1.1.1.37, m-MDH) obtained from several temperate and tropicalDrosophila species was examined by comparing their catalytic properties, which related to temperature (Km-Ea-Q10-Thermostability). MitochondrialαGPO or m-MDH obtained either from temperate or from tropical species was found to exhibit similar catalytic properties while for both cytosolic enzymes, theαGPDH and s-MDH, Km patterns were similar among species from the same thermal habitat and different between thermal habitats. In combination with other observations reported in the literature these facts support the view that the function, and probably the structure, of mitochondrial enzymes are better conserved in evolution than those of the corresponding enzymes found in the cytosol. It is proposed that the relative invariance of the mitochondrial enzymes structure is probably linked to a necessary relative invariance of molecular interactions inside the mitochondrion.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01732068
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  • 5
    Electronic Resource
    Electronic Resource
    Evolution of patterns of gene expression in Hawaiian picture-wingedDrosophila (1980)
    Springer
    Journal of molecular evolution 16 (1980), S. 73-94 
    Details
    ISSN: 1432-1432
    Keywords: Enzymes ; Evolution ; Gene regulation ; HawaiianDrosophila
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The tissue and stage specificity of expression of five enzymes was examined by electrophoretic analysis of relative enzyme levels in extracts of 13 larval and adult tissues in 27 species of Hawaiian picture-wingedDrosophila. The developmentally regulated patterns of enzyme expression thus characterized were compared to a modal standard phenotype. About 30% of the pattern features analyzed differed significantly from the standard in one or more species. Many of these regulatory differences are essentially qualitative, with tissue specific differences in enzyme activity in excess of 100 fold for some species pairs. The adaptive significance of these pattern differences is unknown, but the results provide strong direct evidence for rapid evolution of new patterns of gene regulation in this group of organisms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01731579
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  • 6
    Electronic Resource
    Electronic Resource
    The relationship between coding sequences and function in some heme binding proteins (1980)
    Springer
    Journal of molecular evolution 16 (1980), S. 149-150 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01731583
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  • 7
    Electronic Resource
    Electronic Resource
    Theoretical foundations for quantitative paleogenetics (1980)
    Springer
    Journal of molecular evolution 16 (1980), S. 211-267 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01804977
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  • 8
    Electronic Resource
    Electronic Resource
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01733911
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  • 9
    Electronic Resource
    Electronic Resource
    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 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01810829
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  • 10
    Electronic Resource
    Electronic Resource
    Tubulin evolution: Two major types of α-tubulin (1982)
    Springer
    Journal of molecular evolution 19 (1982), S. 80-86 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100226
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  • 11
    Electronic Resource
    Electronic Resource
    Evolution ofDrosophila repetitive-dispersed DNA (1983)
    Springer
    Journal of molecular evolution 19 (1983), S. 203-213 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02099967
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  • 12
    Electronic Resource
    Electronic Resource
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02099974
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  • 13
    Electronic Resource
    Electronic Resource
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101636
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  • 14
    Electronic Resource
    Electronic Resource
    Classification of elapid snake neurotoxins and cytotoxins according to chain length: Evolutionary implications (1984)
    Springer
    Journal of molecular evolution 20 (1984), S. 128-134 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02257373
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  • 15
    Electronic Resource
    Electronic Resource
    Prokaryotic and eukaryotic pyridoxal-dependent decarboxylases are homologous (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 325-329 
    Details
    ISSN: 1432-1432
    Keywords: PLP-dependent decarboxylase ; Evolution ; Profile analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A database search has revealed significant and extensive sequence similarities among prokaryotic and eukaryotic pyridoxal phosphate (PLP)-dependent decarboxylases, includingDrosophila glutamic acid decarboxylase (GAD) and bacterial histidine decarboxylase (HDC). Based on these findings, the sequences of seven PLP-dependent decarboxylases from five different organisms have been aligned to derive a consensus sequence for this family of enzymes. In addition, quantitative methods have been employed to calculate the relative evolutionary distances between pairs of the decarboxylases comprising this family. The multiple sequence analysis together with the quantitative results strongly suggest an ancient and common origin for all PLP-dependent decarboxylases. This analysis also indicates that prokaryotic and eukaryotic HDC activities evolved independently. Finally, a sensitive search algorithm (PROFILE) was unable to detect additional members of this decarboxylase family in protein sequence databases.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101126
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  • 16
    Electronic Resource
    Electronic Resource
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101888
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  • 17
    Electronic Resource
    Electronic Resource
    Phylogeny of the major tetrapod groups: Morphological data and divergence dates (1990)
    Springer
    Journal of molecular evolution 30 (1990), S. 409-424 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101113
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  • 18
    Electronic Resource
    Electronic Resource
    Evolutionary origin of aminoglycoside phosphotransferase resistance genes (1990)
    Springer
    Journal of molecular evolution 30 (1990), S. 489-492 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101103
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  • 19
    Electronic Resource
    Electronic Resource
    The evolution of the thrombospondin gene family (1993)
    Springer
    Journal of molecular evolution 36 (1993), S. 509-516 
    Details
    ISSN: 1432-1432
    Keywords: Thrombospondin ; Evolution ; Adhesive glycoproteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Thrombospondin-1 is an adhesive glycoprotein that is involved in cellular attachment, spreading, migration, and proliferation. To date, four genes have been identified that encode for the members of the thrombospondin gene family. These four genes are homologous to each other in the EGF-like (type 2) repeats, the calcium-binding (type 3) motifs, and the COOH-terminal. The latter has been reported to be a cell-binding domain in thrombospondin-1. Phylogenetic trees have been constructed from the multisequence alignment of thrombospondin sequences from human, mouse, chicken, and frog. Two different algorithms generate comparable results in terms of the topology and the branch lengths. The analysis indicates that an early form of the thrombospondin gene duplicated about 925 million years ago. The gene duplication that produced the thrombospondin-1 and -2 branches of the family is predicted to have occurred 583 million years ago, whereas the gene duplication that produced the thrombospondin-3 and -4 branches of the family is predicted to have occurred 644 million years ago. These results indicate that the members of the thrombospondin gene family have existed throughout the evolution of the animal kingdom and thus probably participate in functions that are common to most of its members.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00556355
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  • 20
    Electronic Resource
    Electronic Resource
    The isochore patterns of mammalian genomes and their phylogenetic implications (1993)
    Springer
    Journal of molecular evolution 37 (1993), S. 93-108 
    Details
    ISSN: 1432-1432
    Keywords: DNA ; Base composition ; Vertebrates ; Eutheria ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The compositional distributions of high molecular weight DNA fragments from 20 species belonging to 9 out of the 17 eutherian orders were investigated by analytical CsCl density gradient centrifugation and by preparative fractionation in Cs2SO4/BAMD density gradients followed by analysis of the fractions in CsCl. These compositional distributions reflect those of the isochores making up the corresponding genomes. A “general distribution” was found in species belonging to eight mammalian orders. A “myomorph distribution” was found in Myomorpha, but not in the other rodent infraorders Sciuromorpha and Histricomorpha, which share the general distribution. Two other distributions were found in a megachiropteran (but not in microchiropteran, which, again, shares the general distribution) and in pangolin (a species from the only genus of the order Pholidota), respectively. The main difference between the general distribution and all other distributions is that the former contains sizable amounts (6–10%) of GC-rich isochores (detected as DNA fragments equal to, or higher than, 1.710 g/cm3 in modal buoyant density), which are scarce, or absent, in the other distributions. This difference is remarkable because gene concentrations in mammalian genomes are paralleled by GC levels, the highest gene concentrations being present in the GC-richest isochores. The compositional distributions of mammalian genomes reported here shed light on mammalian phylogeny. Indeed, all orders investigated, with the exception of Pholidota, seem to share a common ancestor. The compositional patterns of the megachiropteran and of Myomorpha may be derived from the general pattern or have independent origins.
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    URL: http://dx.doi.org/10.1007/BF02407344
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    On the mode of evolution of alpha satellite DNA in human populations (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 42-48 
    Details
    ISSN: 1432-1432
    Keywords: Satellite DNA ; Mouse ; Human chromosomes 13 and 21 ; Evolution ; Saltatory amplification ; Homogenization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The hypothesis that highly reiterated satellite DNAs in present-day populations evolve by molecular mechanisms that create, by saltatory amplification steps, new long arrays of satellite DNA, and that such long arrays are used for homogenization purposes, has been tested both in mouse and in humans. In mouse, the data obtained are consistent with this hypothesis. This was tested in more detail on chromosomes 13 and 21 of the human genome. A Centre d'Etudes du Polymorphisme Humain family, which in some individuals exhibits strong supplementary DNA bands following TaqI restriction endonuclease digestion and conventional gel electrophoresis, was analyzed by pulse field gel electrophoresis following restriction by BamHI. The supplementary bands on chromosome 13 (18 times the basic alpha satellite DNA repeat) and on chromosome 21 (a 9.5-mer) segregated with centromeric alpha satellite DNA blocks of 5 and 5.3 megabases, respectively. These are by far the largest alpha satellite block lengths seen in all chromosome 13 and chromosome 21 centrometric sequences so far analyzed in this manner. The possibility that these supplementary alpha satellite sequences were created in single individuals by saltatory amplification steps is discussed in light of our own data and that published by others. It is proposed that deletion events and unequal cross-overs, which both occur in large satellite DNA arrays, contribute to the homogenization of size and sequence of the alpha satellite DNA on most chromosomes of humans.
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    URL: http://dx.doi.org/10.1007/BF02100194
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    Genome variations in the transition from amphibians to reptiles (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 68-75 
    Details
    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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    URL: http://dx.doi.org/10.1007/BF02100197
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    Phylogeny and physiology of Drosophila opsins (1994)
    Springer
    Journal of molecular evolution 38 (1994), S. 250-262 
    Details
    ISSN: 1432-1432
    Keywords: Opsin ; Visual pigments ; Gene family ; Evolution ; Phylogeny ; Spectral sensitivity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Phylogenetic and physiological methods were used to study the evolution of the opsin gene family in Drosophila. A phylogeny based on DNA sequences from 13 opsin genes including representatives from the two major subgenera of Drosophila shows six major, well-supported clades: The “blue opsin” clade includes all of the Rhl and Rh2 genes and is separated into two distinct subclades of Rhl sequences and Rh2 sequences; the ultraviolet opsin clade includes all Rh3 and Rh4 genes and bifurcates into separate Rh3 and Rh4 clades. The duplications that generated this gene family most likely took place before the evolution of the subgenera Drosophila and Sophophora and their component species groups. Numerous changes have occurred in these genes since the duplications, including the loss and/or gain of introns in the different genes and even within the Rhl and Rh4 clades. Despite these changes, the spectral sensitivity of each of the opsins has remained remarkably fixed in a sample of four species representing two species groups in each of the two subgenera. All of the strains that were investigated had R1-6 (Rhl) spectral sensitivity curves that peaked at or near 480 nm, R7 (Rh3 and Rh4) peaks in the ultraviolet range, and ocellar (Rh2) peaks near 420 nm. Each of the four gene clades on the phylogeny exhibits very conservative patterns of amino acid replacement in domains of the protein thought to influence spectral sen sitivity, reflecting strong constraints on the spectrum of light visible to Drosophila.
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    URL: http://dx.doi.org/10.1007/BF00176087
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    Evolutionary origin of the class A and class C β-lactamases (1992)
    Springer
    Journal of molecular evolution 34 (1992), S. 345-350 
    Details
    ISSN: 1432-1432
    Keywords: Evolution ; β-Lactamase ; Phylogenetic tree ; Horizontal transfer
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The protein sequences of 18 class A β-lactamases and 2 class C β-lactamases were analyzed to produce a rooted phylogenetic tree using the DD peptidase of Streptomyces R61 as an outgroup. This tree supports the penicillin-binding proteins as the most likely candidate for the ancestoral origin of the class A and class C β-lactamases, these proteins diverging from a common evolutionary origin close to the DD peptidase. The actinomycetes are clearly shown as the origin of the class A β-lactamases found in other non-actinomycete species. The tree also divides the β-lactamases from the Streptomyces into two subgroups. One subgroup is closer to the DD peptidase root. The other Streptomyces subgroup shares a common branch point with the rest of the class A β-lactamases, showing this subgroup as the origin of the non-actinomycete class A β-lactamases. The non-actinomycete class A β-lactamase phylogenetic tree suggests a spread of these β-lactamases by horizontal transfer from the Streptomyces into the non-actinomycete gram-positive bacteria and thence into the gram-negative bacteria. The phylogenetic tree of the Streptomyces class A β-lactamases supports the possibility that horizontal transfer of class A β-lactamases occurred within the Streptomyces.
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    URL: http://dx.doi.org/10.1007/BF00160242
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    Organization and evolution of bacterial and bacteriophage primase-helicase systems (1992)
    Springer
    Journal of molecular evolution 34 (1992), S. 351-357 
    Details
    ISSN: 1432-1432
    Keywords: Primase-helicase systems ; Evolution ; Bacteria ; Bacteriophage
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Amino acid sequences of primases and associated helicases involved in the DNA replication of eubacteria and bacteriophages T7, T3, T4, P4, and P22 were compared by computer-assisted methods. There are two types of such systems, the first one represented by distinct helicase and primase proteins (e.g., DnaB and DnaG proteins of Escherichia coli), and the second one by single polypeptides comprising both activities (gp4 of bacteriophages T7 and T3, and alpha protein of bacteriophage P4). Pronounced sequence similarity was revealed between approximately 250 amino acid residue N-terminal domains of stand-alone primases and the primase-helicase proteins of T7(T3) and P4. All these domains contain, close to their N-termini, a conserved Zn-finger pattern that may be implicated in template DNA recognition by the primases. In addition, they encompass five other conserved motifs some of which may be involved in substrate (NTP) binding. Significant similarity was also observed between the primase-associated helicases (DnaB, gp12 of P22 and gp41 of T4) and the C-terminal domain of T7(T3) gp4. On the other hand the C-terminal domain of P-alpha of P4 is related to another group of DNA and RNA helicases. Tentative phylogenetic trees generated for the primases and the associated helicases showed no grouping of the phage proteins, with the exception of the primase domains of bacteriophages T4 and P4. This may indicate a common origin for one-component primase-helicase systems. Two scenarios for the evolution of primase-helicase systems are discussed. The first one involves fusion of the primase and helicase components (T7 and T3) or fusion of the primase component with a different type of helicase domain (P4). The second possibility is the duplication of an ancestral gene encoding a gp4-like bifunctional protein followed by divergence of the copies, one of which retains the primase and the other the helicase domain.
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    URL: http://dx.doi.org/10.1007/BF00160243
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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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    URL: http://dx.doi.org/10.1007/BF00178601
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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 
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    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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    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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    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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    URL: http://dx.doi.org/10.1007/BF02101786
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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.
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    URL: http://dx.doi.org/10.1007/BF01733893
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    Compartmentalized isozyme genes and the origin of introns (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 205-210 
    Details
    ISSN: 1432-1432
    Keywords: Isozyme ; Intron ; Phylogenetic tree ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Both the mouse cytosolic malate dehydrogenase gene and its mitochondrial counterpart contain eight introns, of which two are present at identical positions between the isozyme genes. The probability that the two intron positions coincide by chance between the two genes has been shown to be significantly small (=1.3×10−3), suggesting that the conservation of the intron positions has a biological significance. On the basis of a rooted phylogenetic tree inferred from a comparison of these isozymes and lactate dehydrogenases, we have shown that the origins of the conserved introns are very old, possibly going back to a date before the divergence of eubacteria, archaebacteria, and eukaryotes. In the aspartate aminotransferase isozyme genes, five of the introns are at identical places. The origins of the five conserved introns, however, are not obvious at present. It remains possible that some or all of the conserved introns have evolved after the divergence of eubacteria and eukaryotes.
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    URL: http://dx.doi.org/10.1007/BF02109497
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    Distribution of the salmonid Hpa 1 family in the salmonid species demonstrated by in vitro runoff transcription assay of total genomic DNA: A procedure to estimate repetitive frequency and sequence divergence of a certain repetitive family with a few known sequences (1991)
    Springer
    Journal of molecular evolution 32 (1991), S. 43-52 
    Details
    ISSN: 1432-1432
    Keywords: Retroposon ; Salmonid ; +RNA ; Evolution ; Average sequence divergence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary An in vitro runoff transcription assay of total genomic DNA was developed. As an example of use of this assay, analysis of a highly repetitive sequence in the cherry salmon (Oncorhynchus masou) is described. Total genomic DNA of the cherry salmon was completely digested with Hpa 1, whose site is known to be in the tRNA-unrelated region of the cherry salmon Hpa 1 family. On transcription of the digested DNA in a HeLa cell extract, a discrete-sized RNA of about 100 nucleotides, constituting 70% of the transcripts, was produced, whereas on transcription of the undigested total DNA, only smeared RNA was obtained. In a fingerprint, the oligonucleotides of the discrete transcript from the digested total DNA were very distinct and exactly corresponded to those of a transcript from an Hpa 1 digest of a cloned DNA, but with few extra oligonucleotides. These results showed that the cherry salmon Hpa 1 family constitutes a major repetitive family in the genome of the cherry salmon. For determination of the distribution of the salmonid Hpa 1 family in other salmonid species, the same analysis was applied to DNAs from the chum salmon (Oncorhynchus keta), brown trout (Salmo trutta), Japanese common charr (Salvelinus leucomaenis pluvius), and Japanese huchen (Hucho perryi). The results showed that the salmonid Hpa 1 family is widespread in the genomes of salmonid species. A method and equations are also presented for estimating the relationship between the ratio of a given repetitive family to all the Pol III genes and its average sequence divergence by calculating the molar ratio of the runoff transcript to all the in vitro Pol III transcripts.
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    URL: http://dx.doi.org/10.1007/BF02099928
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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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    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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    Evolution of proteins of the cystatin superfamily (1990)
    Springer
    Journal of molecular evolution 30 (1990), S. 60-71 
    Details
    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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    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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    URL: http://dx.doi.org/10.1007/BF00178245
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    Investigation of the human Rh blood group system in nonhuman primates and other species with serologic and Southern blot analysis (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 87-92 
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    ISSN: 1432-1432
    Keywords: Rh blood group ; Evolution ; Rh antibodies ; Restriction fragments ; Primates ; Chimpanzee ; Gorilla ; New World monkey ; Old World monkey
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract To investigate the evolution of the Rh blood-group system in anthropoid apes, New and Old World monkeys, and nonprimate animals, serologic typing of erythrocytes from these species with antibodies specific for the human Rh blood-group antigens was performed. In addition, genomic DNA from these animals was analyzed on Southern blots with a human Rh-specific cDNA. Consistent with earlier reports, serologic results showed that gorilla and chimpanzee erythrocytes had epitopes recognized by human Rh D and c antisera, and gibbon erythrocytes were recognized by the c antisera. Surprisingly, some Old and New World monkeys also expressed a Rh c epitope on their erythrocytes. No erythrocytes from the nonprimate animals reacted specifically with any of the human Rh antisera. Southern blot analysis with a human Rh-specific cDNA probe detected Rh-related sequences in anthropoid apes, all New and Old World monkeys, and in most nonprimate animals tested. Although some Rh-related restriction fragments were conserved across species lines in primates, the Rh locus was more polymorphic in chimpanzees and gorillas than in humans. In addition, restriction fragments segregating with the presence of the D antigen in humans were present in the primate species that expressed the D antigen.
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    The use of bonding between tRNAs to implement early peptide synthesis (1991)
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    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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    Evolutionary consequences of nonrandom damage and repair of chromatin domains (1992)
    Springer
    Journal of molecular evolution 35 (1992), S. 156-180 
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    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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    Conserved and nonconserved structures in the secretory proteins encoded in the Balbiani ring genes ofChironomus tentans (1984)
    Springer
    Journal of molecular evolution 20 (1984), S. 304-312 
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    ISSN: 1432-1432
    Keywords: Evolution ; Gene family ; Balbiani ring genes ; Repetitive sequences ; Structural proteins ; Protein conformation ; Polymerization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The large, repetitive Balbiani ring (BR) genes, BR 1, 2, and 6, inChironomus tentans originated from a short ancestral sequence and have all evolved according to analogous amplification schemes. We analyzed the structures of the BR-encoded secretory proteins and defined the parts that have been conserved during the evolutionary process. The BR products show striking similarities, with the BR 1 and BR 2 products being more similar to each other than to the BR 6 product. In the constant (C) region of the repeat units, 7 of the 30 amino acid residues are strictly conserved; 4 of these are the cysteine residues. The subrepeat (SR) regions of all the BR products are dominated by repeated tripeptide elements rich in proline and charged amino acid residues. Most of the amino acid replacements in both regions are conservative. Secondary structure predictions suggested that the C regions of the BR 1 and BR2 products have several elements of secondary structure: an α-helix, a β-strand, and one or two reverse turns, as in “globular structures.” The prediction for the C region of the BR 6 product is similar but lacks a β-strand. The predictions for the intervening SR regions appear less conclusive, but are clearly different from those for the C regions, and suggest regular structures not differing in their conformational elements. The SR regions evolved from an ancestor sequence similar to the C region; thus, the BR products seem to represent an example of evolution from one structure to two differently folded products. It is proposed that the alignment and polymerization of the long BR proteins could be promoted by the repetitive structure of the molecules, due to the possibility of forming disulfide bridges between half-cystine residues and electrostatic interactions between the charged residues of the SR regions. The divergence among the BR products is discussed in relation to possible functional differences among the members of the BR gene family.
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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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    Evolutionary trees from DNA sequences: A maximum likelihood approach (1981)
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    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
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    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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    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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    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 
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    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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    tRNA-rRNA sequence homologies: Evidence for a common evolutionary origin? (1983)
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    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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    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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    Regulatory DNA sequence conserved in the course of BK virus evolution (1990)
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    Journal of molecular evolution 31 (1990), S. 485-492 
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    ISSN: 1432-1432
    Keywords: BK virus ; Strains ; Regulatory region ; Late region ; Nucleotide sequence ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Within the genome of human polyomavirus BK (BKV), there exists a noncoding regulatory region toward the late region side of the origin of DNA replication. In most BKV strains isolated by viral culture, this regulatory region contains tandem repeats varying in size. Recently. however, several laboratories isolated new BKV strains (designated as archetypal strains) lacking such repeat sequences. To examine the genetic relationship between archetypal strains, a phylogenetic tree was constructed for seven BKV strains, including three archetypal strains, from DNA sequence data on the late genes, those for leader protein (agnoprotein), and those for structural proteins (VP1, VP2, and VP3). For three strains data previously reported were used, whereas for the others sequences were determined in this study. From total numbers of nucleotide substitutions in each pair of strains, a phylogenetic tree was constructed by the unweighted pair-group method. The phylogenetic tree obtained reveals that BKV strains containing the archetypal regulatory region do not constitute a cluster of closely related strains and that these strains, together with those carrying the major part of the archetypal regulatory region, are widespread in the BKV population. This finding suggests that the basic structure of the archetypal regulatory region has been conserved in the course of BKV evolution.
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    There appear to be conserved constraints on the distribution of nucleotide sequences in cellular genomes (1991)
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    Journal of molecular evolution 32 (1991), S. 24-30 
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    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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    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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    Interspecific comparison of the unusually repetitiveDrosophila locusmastermind (1991)
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    Journal of molecular evolution 32 (1991), S. 415-420 
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    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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    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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    The compositional patterns of the avian genomes and their evolutionary implications (1993)
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    Journal of molecular evolution 37 (1993), S. 544-551 
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    ISSN: 1432-1432
    Keywords: Isochores ; DNA ; Coding sequences ; Birds ; Mammals ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The compositional distributions of large (main-band) DNA fragments from eight birds belonging to eight different orders (including both paleognathous and neognathous species) are very broad and extremely close to each other. These findings, which are paralleled by the compositional similarity of homologous coding sequences and their codon positions, support the idea that birds are a monophyletic group. The compositional distribution of third-codon positions of genes from chicken, the only avian species for which a relatively large number of coding sequences is known, is very broad and bimodal, the minor GC-richer peak reaching 100% GC. The very high compositional heterogeneity of avian genomes is accompanied (as in the case of mammalian genomes) by a very high speciation rate compared to cold-blooded vertebrates which are characterized by genomes that are much less heterogeneous. The higher GC levels attained by avian compared to mammalian genomes might be correlated with the higher body temperature (41–43°C) of birds compared to mammals (37°C). A comparison of GC levels of coding sequences and codon positions from man and chicken revealed very close average GC levels and standard deviations. Homologous coding sequences and codon positions from man and chicken showed a surprisingly high degree of compositional similarity which was, however, higher for GC-poor than for GC-rich sequences. This indicates that GC-poor isochores of warm-blooded vertebrates reflect the composition of the isochores of the genome of the common reptilian ancestor of mammals and birds, which underwent only a small compositional change at the transition from cold- to warm-blooded vertebrates. In contrast, the GC-rich isochores of birds and mammals are the result of large compositional changes at the same evolutionary transition, where were in part different in the two classes of warm-blooded vertebrates.
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    URL: http://dx.doi.org/10.1007/BF00160434
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    Evolution of regulatory genes and patterns: Relationships to evolutionary rates and to metabolic functions (1993)
    Springer
    Journal of molecular evolution 37 (1993), S. 590-599 
    Details
    ISSN: 1432-1432
    Keywords: Evolution ; Gene regulation ; Drosophila ; Adaptation ; Enzymes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In an effort to understand the forces shaping evolution of regulatory genes and patterns, we have compared data on interspecific differences in enzyme expression patterns among the rapidly evolving Hawaiian picture-winged Drosophila to similar data on the more conservative virilis species group. Divergence of regulatory patterns is significantly more common in the former group, but cause and effect are difficult to discern. Random fixation of regulatory variants in small populations and/or during speciation may be somewhat more likely than divergence driven by selection. Within the picture-winged group, we also have compared enzymes that fulfill different metabolic roles. There are highly significant differences between individual enzymes, but no obvious correlations to functional categories.
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    URL: http://dx.doi.org/10.1007/BF00182745
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    Molecular evolution of the HSP70 multigene family (1994)
    Springer
    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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    URL: http://dx.doi.org/10.1007/BF00175490
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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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    Evolution and sequence analysis of a human Y-chromosomal DNA fragment (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 133-141 
    Details
    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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    URL: http://dx.doi.org/10.1007/BF02193627
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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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    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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    Cloning and characterization of the platypus mitochondrial genome (1994)
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    Journal of molecular evolution 39 (1994), S. 200-205 
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    ISSN: 1432-1432
    Keywords: Evolution ; Monotreme ; Platypus ; mtDNA ; tRNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The vertebrate mitochondrial genome is highly conserved in size and gene content. Among the chordates there appears to be one basic gene arrangement, but rearrangements in the mitochondrial gene order of the avian lineages have indicated that the mitochondrial genome may be more variable than once thought. Different gene orders in marsupials and eutherian mammals leave the ancestral mammalian order in some doubt. We have investigated the mitochondrial gene order in the platypus (Ornithorhynchus anatinus), a representative of the third major group of mammals, to determine which mitochondrial gene arrangement is ancestral in mammals. We have found that the platypus mtDNA conforms to the basic chordate gene arrangement, common to fish, amphibians, and eutherian mammals, indicating that this arrangement was the original mammalian arrangement, and that the unusual rearrangements observed in the avians and marsupials are probably lineage-specific.
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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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    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 
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    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.
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    Balbiani ring DNA: Sequence comparisons and evolutionary history of a family of hierarchically repetitive protein-coding genes (1984)
    Springer
    Journal of molecular evolution 20 (1984), S. 281-295 
    Details
    ISSN: 1432-1432
    Keywords: Balbiani ring ; Repeat ; Evolution ; Repetitive DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary All known types of Balbiani ring (BR) gene consist of multiple, tandemly arranged, ca. 180 to 300-bp repeat units that can be divided into a constant region and a subrepeat region. The latter region includes short tandem subrepeats (SRs). Comparison of all available BR sequences using computer methods has enabled us (a) to define more precisely the constant and subrepeat regions, (b) to infer the evolutionary relationships among the various types of BR repeats, (c) to derive a consensus approximation of an ancestral sequence from a small segment of which the highly diverse present-day SRs may have originated, and (d) to detect an underlying substructure in the constant region, evident in the consensus but not in the present-day sequences and possibly corresponding to an original 39-bp DNA segment from which the extant, giant BR sequences may have evolved. We discuss the processes of reduplication, diversification, and homogenization within the hierarchically repetitive BR sequences as examples of how a simple DNA element may evolve into a diverse family of large, protein-coding genes.
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    Evolution of RNA polymerases and branching patterns of the three major groups of archaebacteria (1991)
    Springer
    Journal of molecular evolution 32 (1991), S. 70-78 
    Details
    ISSN: 1432-1432
    Keywords: Phylogenetic tree ; Likelihood method ; RNA polymerase ; Archaebacteria ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The amino acid sequences of the largest subunits of the RNA polymerases I, II, and III from eukaryotes were compared with those of archaebacterial and eubacterial homologs, and their evolutionary relationships were analyzed in detail by a recently developed tree-making method, the likelihood method of protein phylogeny, as well as by the neighbor-joining method and the parsimony method, together with bootstrap analyses. It was shown that the best tree topologies predicted by the first two methods are identical, whereas the last one predicts a distinct tree. The maximum likelihood tree revealed that, after the separation from archaebacteria, the three eukaryotic RNA polymerases diverged from an ancestral precursor in the eukaryotic lineage. This result is contrasted with the published result showing multiple origins for the three eukaryotic polymerases. It was shown that eukaryotic RNA polymerase I evolved much more rapidly than RNA polymerases II and III: The N-terminal half of RNA polymerase I shows an extraordinarily high evolutionary rate, possibly due to relaxed functional constraints. In contrast the evolutionary rate of archaebacterial RNA polymerase is remarkably limited. In addition, including the second largest subunit of the RNA polymerase, a detailed analysis for the branching pattern of the three major groups of archaebacteria was carried out by the maximum likelihood method. It was shown that the three major groups of archaebacteria are likely to form a single cluster; that is, archaebacteria are likely to be monophyletic as originally proposed by Woese and his colleagues.
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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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    Prebiotic chemistry in clouds (1991)
    Springer
    Journal of molecular evolution 32 (1991), S. 296-303 
    Details
    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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    The sequence and expression pattern of the Calliphora erythrocephala yolk protein A and B genes (1994)
    Springer
    Journal of molecular evolution 38 (1994), S. 336-351 
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    ISSN: 1432-1432
    Keywords: Yolk protein genes ; Vitellogenesis ; Calliphora ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The yolk protein genes (yps) are expressed in a temporal, tissue- and sex-specific fashion in Drosophila melanogaster. Here we report the sequence of two related genes in Calliphora erythrocephala. The predicted Calliphora yolk protein (YP) sequences are well conserved, especially at the C-terminal end when compared to those of D. melanogaster and Ceratitis capitata. Database searches with the Calliphora yolk protein B (CeYPB) sequence identify the vertebrate lipase similarity reported for the YPs of Drosophila and Ceratitis. Moreover, sequences with identity to divalent ion-binding sites were observed, which colocalized with putative tyrosine sulfation sites. Calliphora oogenesis differs from Drosophila in that it is cyclic in response to a meat feed. The Calliphora yp genes are expressed in the follicle cells of the egg chamber during vitellogenesis, as shown by in situ hybridization, and the yp message levels correlate with YP synthesis. The synthesis of the yp transcripts in ovaries of Calliphora occurs in the same pattern as that for ovarian transcripts in Drosophila. In the carcass, yp transcript levels are correlated with the production of a batch of eggs.
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    Molecular phylogenies based on ribosomal protein L11, L1, L10, and L12 sequences (1994)
    Springer
    Journal of molecular evolution 38 (1994), S. 405-419 
    Details
    ISSN: 1432-1432
    Keywords: Molecular phylogeny ; Universal tree ; Ribosomal proteins ; Evolution ; Archaebacteria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Available sequences that correspond to the E. coli ribosomal proteins L11, L1, L10, and L12 from eubacteria, archaebacteria, and eukaryotes have been aligned. The alignments were analyzed qualitatively for shared structural features and for conservation of deletions or insertions. The alignments were further subjected to quantitative phylogenetic analysis, and the amino acid identity between selected pairs of sequences was calculated. In general, eubacteria, archaebacteria, and eukaryotes each form coherent and well-resolved nonoverlapping phylogenetic domains. The degree of diversity of the four proteins between the three groups is not uniform. For L11, the eubacterial and archaebacterial proteins are very similar whereas the eukaryotic L11 is clearly less similar. In contrast, in the case of the L12 proteins and to a lesser extent the L10 proteins, the archaebacterial and eukaryotic proteins are similar whereas the eubacterial proteins are different. The eukaryotic L1 equivalent protein has yet to be identified. If the root of the universal tree is near or within the eubacterial domain, our ribosomal protein-based phylogenies indicate that archaebacteria are monophyletic. The eukaryotic lineage appears to originate either near or within the archaebacterial domain.
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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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    Biogenesis as an evolutionary process (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 207-208 
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    ISSN: 1432-1432
    Keywords: Evolution ; Vesicle ; Biogenesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The earliest fossil stromatolites present evidence of a complex ecosystem of photosynthetic organisms. Because the origin of present life can be dated within a few hundred million years prior to these fossils, their complexity poses a problem. A heuristic model outlines the first radiation leading to the universal ancestor.
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    An analysis of retroposition in plants based on a family of SINEs from Brassica napus (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 378-386 
    Details
    ISSN: 1432-1432
    Keywords: CpG dinucleotides ; Evolution ; Repetitive sequences ; Reverse transcriptase ; S1Bn retroposons
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The identification of a family of SINE retroposons dispersed in the genome of oilseed rape Brassica napus has provided the basis for an evolutionary analysis of retroposition in plants. The repetitive elements (called S1Bn) are 170 by long and occupy roughly 500 loci by haploid genome. They present characteristic features of SINE retroposons such as a 3′ terminal A-rich region, two conserved polymerase III motifs (box A and B), flanking direct repeats of variable sizes, and a primary and secondary sequence homology to several tRNA species. A consensus sequence was made from the alignment of 34 members of the family. The retroposon population was divided into five subfamilies based on several correlated sets of mutations from the consensus. These precise separations in subfamilies based on “diagnostic” mutations and the random distribution of mutations observed inside each subfamily are consistent with the master sequence model proposed for the dispersion of mammalian retroposons. An independent analysis of each subfamily provides strong evidence for the coexpression of at least three subfamily master sequences (SMS). In contrast to mammalian retroposition, diagnostic positions are not shared between SMS. We therefore propose that SMS were all derived from a general master sequence (GMS) and independently activated for retroposition after a variable period of random drift. Possible models for plant retroposition are discussed.
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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 
    Details
    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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    URL: http://dx.doi.org/10.1007/BF00160151
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    Interspecific sequence comparison of the muscle-myosin heavy-chain genes from Drosophila hydei and Drosophila melanogaster (1994)
    Springer
    Journal of molecular evolution 39 (1994), S. 357-368 
    Details
    ISSN: 1432-1432
    Keywords: Drosophila ; Muscle-myosin heavy-chain gene ; Alternative exons ; Synonymous substitutions ; Amino acid substitutions ; Evolution ; Testis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The muscle-myosin heavy-chain (mMHC) gene of Drosophila hydei has been sequenced completely (size 23.3 kb). The sequence comparison with the D. melanogaster mMHC gene revealed that the exonintron pattern is identical. The protein coding regions show a high degree of conservation (97%). The alternatively spliced exons (3a-b, 7a-d, 9a-c, 11a-e, and 15a-b) display more variations in the number of nonsynonymous and synonymous substitutions than the common exons (2, 4, 5, 6, 8, 10, 12, 13, 14, 16, 17, and 19). The base composition at synonymous sites of fourfold degenerate codons (third position) is not biased in the alternative exons. In the common exons there exists a bias for C and against A. These findings imply that the alternative exons of the Drosophila mMHC gene evolve at a different, in several cases higher, rate than the common ones. The 5′ splice junctions and 5′ and 3′ untranslated regions show a high level of similarity, indicating a functional constraint on these sequences. The intron regions vary considerably in length within one species, but the corresponding introns are very similar in length between the two species and all contain stretches of sequence similarity. A particular example is the first intron, which contains multiple regions of similarity. In the conserved regions of intron 12 (head-tail border) sequences were found which have the potential to direct another smaller mMHC transcript.
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    URL: http://dx.doi.org/10.1007/BF00160268
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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 
    Details
    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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    Higher selection processes in evolutionary economic change (1992)
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    Journal of evolutionary economics 2 (1992), S. 1-16 
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    ISSN: 1432-1386
    Keywords: Evolution ; Innovation ; Selection ; Technology ; JEL classification numbers: 036, 112
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract Virtually all models of economic change are based on a Darwinian picture of a world where change is gradual, smooth, and where economic survival depends on being more efficient. This paper, drawing from current controversies in evolutionary biology, presents a broader interpretation of evolutionary change in which competitive selection is only one possible reason for economic survival. Economic change is presented as a hierarchical process. At one level, change takes place through the accumulation of small changes based on competitive selection at the margin, as described by standard economic theory. At higher levels, survival depends on processes over which the agent being selected has no control.
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    Technological change and institutional inertia: a game-theoretic approach (1993)
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    Journal of evolutionary economics 3 (1993), S. 199-224 
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    ISSN: 1432-1386
    Keywords: Technological change ; Institutions ; Evolution ; Games ; C71 ; 017 ; 031
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract In this paper, we study a co-evolutionary model of economic change at two hierarchical levels. At the lower level, “institutions” are given and the focus is on how resources are allocated and innovation produced in response to the pay-off structure induced by prevailing institutions. At the higher level, it is the institutions themselves that change as the outcome of a process of social bargaining. The main objective of the paper is to study the interaction between these two levels of change, attempting to provide some insight on issues like technological/institutional divergence, technological dead-end, institutional inertia, etc.
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    URL: http://dx.doi.org/10.1007/BF01200868
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    Firm selection and industry evolution: the post-entry performance of new firms (1994)
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    Journal of evolutionary economics 4 (1994), S. 243-260 
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    ISSN: 1432-1386
    Keywords: Innovation ; Evolution ; Survival and growth ; O ; O3
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract A dynamic framework based on the process of firm selection and industry evolution is used to analyse the post-entry performance of new firms. In particular, it is hypothesized that, based on the stylized fact that virtually all new firms start at a very small scale of output, firm growth and survival are shaped by the need to attain an efficient level of output. The post-entry performance of more than 11,000 U.S. manufacturing firms established in 1976 is tracked throughout the subsequent tenyear period. Firm growth is found to be negatively influenced by firm size but positively related to the extent of scale economies, capital intensity, innovative activity, and market growth. By contrast, the likelihood of survival is identified as being positively influenced by firm size, market growth, and capital intensity, but negatively affected by the degree of scale economies in the industry. When viewed through the dynamic framework of firm selection and industry evolution, the empirical results shed considerable light on several paradoxes in the industrial organization literature, such as the continued persistence over time of an asymmetrical firm-size distribution consisting predominantely of suboptimal scale firms, and the failure of capital intensity and scale economies to substantially deter the entry and start-up of new firms.
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    A mathematical model of biological evolution (1982)
    Springer
    Journal of mathematical biology 14 (1982), S. 327-353 
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    ISSN: 1432-1416
    Keywords: Evolution ; Molecular evolution ; Dynamical system ; Neo-Darwinian evolution ; Non-Darwinian evolution ; Neutral theory
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract In order to understand generally how the biological evolution rate depends on relevant parameters such as mutation rate, intensity of selection pressure and its persistence time, the following mathematical model is proposed: dN n (t)/dt=(m n (t-μ)N n (t)+μN n-1(t) (n=0,1,2,3...), where N n (t) and m n (t) are respectively the number and Malthusian parameter of replicons with step number n in a population at time t and μ is the mutation rate, assumed to be a positive constant. The step number of each replicon is defined as either equal to or larger by one than that of its parent, the latter case occurring when and only when mutation has taken place. The average evolution rate defined by $$\upsilon _\infty \equiv {\text{ lim}}_{t \to \infty } \sum _{n = 0}^\infty nN_n (t)/t\sum _{n = 0}^\infty N_n (t)$$ is rigorously obtained for the case (i) m n (t)=m n is independent of t (constant fitness model), where m n is essentially periodic with respect to n, and for the case (ii) $$m_n (t) = {\text{ }}s( - 1)^{n + [1/\tau ]} $$ (periodic fitness model), together with the long time average m ∞ of the average Malthusian parameter $$\bar m \equiv \sum _{n = 0}^\infty m_n (t)N_n (t)/\sum _{n = 0}^\infty N_n (t)$$ . The biological meaning of the results is discussed, comparing them with the features of actual molecular evolution and with some results of computer simulation of the model for finite populations.
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    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 
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    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.
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    Evolutionary relationships of superoxide dismutases and glutamine synthetases from marine species of Alteromonas, Oceanospirillum, Pseudomonas and Deleya (1984)
    Springer
    Archives of microbiology 138 (1984), S. 170-178 
    Details
    ISSN: 1432-072X
    Keywords: Superoxide dismutase ; Glutamine synthetase ; Evolution ; Marine bacteria ; Alcaligenes ; Alteromonas ; Deleya ; Oceanospirillum ; Pseudomonas
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Evolutionary relationships among marine species assigned to the genera Alteromonas, Oceanospirillum, Pseudomonas, and Alcaligenes were determined by an immunological study of their Fe-containing superoxide dismutases (FeSOD) and glutamine synthetases (GS), two enzymes with differentially conserved amino acid sequences which are useful for determining intermediate and distant relationships, respectively. Five reference antisera were prepared against the FeSODs from Alteromonas macleodii, A. haloplanktis, Oceanospirillum commune, Pseudomonas stanieri, and Deleya pacifica. For GS, a previously prepared antiserum to the enzyme from Escherichia coli was employed. Amino acid sequence similarities for both enzymes were determined by the quantitative microcomplement fixation technique and the Ouchterlony double diffusion procedure. Six evolutionary groups were detected by FeSOD sequence similarities: three subgroups within the genus Alteromonas, the genera Oceanospirillum and Pseudomonas, and a new genus, Deleya (to accommodate marine Alcaligenes). Only four groupings were delineated by the GS data: the latter three genera and one group composed of all the species of Alteromonas. Evidence that all of these subgroups are derived from the evolutionary lineage defined by the purple sulfur photosynthetic bacteria is presented.
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    Sequence divergence of the murB and rrfB genes from Escherichia coli and Salmonella typhimurium (1994)
    Springer
    Archives of microbiology 161 (1994), S. 501-507 
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    ISSN: 1432-072X
    Keywords: Escherichia coli ; Salmonella typhimurium ; murB ; rrfB ; Repetitive extragenic palindrome ; Evolution ; Mutation rate
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The murB gene of Salmonella typhimurium was cloned and found to be 75% and 82% identical to the DNA and protein sequences, respectively, of the same gene in Escherichia coli. These identities are among the lowest recorded between the two bacteria. Nevertheless, wild-type S. typhimurium murB complemented the known temperature-sensitive E. coli mutant, and wild-type E. coli murB complemented three temperature-sensitive mutants of S. typhimurium. The 5S rRNA gene, rrfB, and the region between murB and rrfB were also cloned and sequenced. The rrfB gene of S. typhimurium differs from rrfB of E. coli in only 2 of 120 nt, but the region between murB and rrfB has diverged greatly and includes a sequence that elosely resembles a repetitive extragenic palindrome of the type normally associated with E. coli. Previous comparisons of gene divergence have suggested that the chromosomal mutation rate is lower in the vicinity of the origin of replication. However, the S. typhimurium murB gene, located 6 map minutes from the origin of replication, is highly substituted at synonymous sites and the sequence between murB and rrfB is significantly modified as well. Thus, murB is an exception to the general observation that genes near the origin of replication show less divergence than do genes elsewhere in the bacterial chromosome.
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    Evolutionary relationships in Vibrio and Photobacterium as determined by immunological studies of superoxide dismutase (1981)
    Springer
    Archives of microbiology 130 (1981), S. 111-120 
    Details
    ISSN: 1432-072X
    Keywords: Evolution ; Vibrio ; Photobacterium ; Alteromonas ; Aeromonas ; Marine bacteria ; Superoxide dismutase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The amino acid sequence divergence of superoxide dismutases (SODs) from 22 species and five groups of Vibrio, Photobacterium, and a number of related organisms was determined by means of the microcomplement fixation technique and the Ouchterlony double diffusion procedure. Five reference antisera were used which had been prepared against the purified SODs from V. alginolyticus, V. splendidus II, V. fischeri, V. cholerae, and P. leiognathi. With a few exceptions the results were in agreement with past studies of other informational molecules and provided a comprehensive overview of evolutionary relationships in Vibrio and Photobacterium. The genus Vibrio was found to consist of a major group of primarily marine species which included V. fischeri, V. logei, V. splendidus, V. pelagius, V. nereis, V. campbellii, V. harveyi, V. natriegens, V. alginolyticus, V. parahaemolyticus, V. proteolyticus, V. fluvialis, V. vulnificus, V. nigripulchritudo, and V. anguillarum. On the outskirts of this large and relatively heterogeneous group were the fresh water and estuarine species V. cholerae and V. metschnikovii as well as the marine species V. gazogenes. A considerable distance from Vibrio were the related species of Photobacterium: P. phosphoreum, P. leiognathi, and P. angustum. Both genera were distant from species of Aeromonas as well as from Plesiomonas shigelloides, Escherichia coli, and Alteromonas hanedai, a luminous strict aerobe. The agreement between these and previous studies of evolution of informational molecules in Vibrio and Photobacterium is best explained by vertical evolution (involving no genetic exchange between species) rather than by its opposite — horizontal evolution.
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    Glycogen in thermoacidophilic archaebacteria of the genera Sulfolobus, Thermoproteus, Desulfurococcus and Thermococcus (1982)
    Springer
    Archives of microbiology 132 (1982), S. 297-303 
    Details
    ISSN: 1432-072X
    Keywords: Glycogen ; Archaebacteria ; Thermoacidophiles ; Sulfolobus ; Thermoproteales ; Glucosyl transferase ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Glycogen has been found in thermoacidophilic archaebacteria of the genera Sulfolobus, Thermoproteus, Desulfurococcus and Thermococcus. Thermoplasma acidophilum yielded a related, though less defined compound. Glycogen was identified by elementary analysis, infrared spectroscopy, the nature of the hydrolysis products, the iodine reaction, and the nature of the products of periodate oxydation and reduction. The average chain length was 7. From crude extracts of Sulfolobus and Thermoproteus complexes of glycogen with 4 respectively 2 proteins have been isolated by CsCl density gradient centrifugation. In either case, one of the proteins was identified as glucosyl transferase. The glucosyl transferase of Sulfolobus acidocaldarius strain B 12 utilizes UDP-glucose as well as ADP-glucose as substrates, with K m values of 0.42 and 0.2 mM respectively and turnover numbers of 4.6 and 5.2 per second respectively. In electron micrographs the isolated glycogen protein complex appears as scale like aggregates, whereas in cell sections amorphous bodies fill large portions of the cells.
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    Evolutionary relationship of some stalked and budding bacteria (genera Caulobacter, “Hyphobacter”, Hyphomonas and Hyphomicrobium) as studied by the new integral taxonomical method (1990)
    Springer
    Archives of microbiology 153 (1990), S. 123-128 
    Details
    ISSN: 1432-072X
    Keywords: Oligotrophic bacteria ; Caulobacter ; “Hyphobacter” ; Hyphomonas ; Hyphomicrobium ; Antibiotic sensitivity ; Evolution ; Fatty acids ; Lipids ; Taxonomy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A new approach was developed for the determination of taxonomic and evolutional relationships among four genera of oligotrophic bacteria. The main idea of this approach is the algorithmized integrative analysis of the morphological and physiological specificity of these bacteria, their 5S rRNA sequences, fatty acid and lipid composition of their membranes, as well as their sensitivity to a large variety of antibiotics. It was shown that the genera Caulobacter and Hyphomonas are closely related to each other, but they are both distant from Hyphomicrobium species. The new genus, “Hyphobacter”, is placed between Caulobacter and Hyphomonas. Taxonomic heterogeneity was found to exist within the genera Caulobacter and Hyphomicrobium. Evolutional pathways from Caulobacter to Hyphomicrobium are proposed on the basis of the present data. No correlations were found between the cell morphology of the organisms and their geno-and chemotaxonomy.
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    Fervidobacterium islandicum sp. nov., a new extremely thermophilic eubacterium belonging to the “Thermotogales” (1990)
    Springer
    Archives of microbiology 154 (1990), S. 105-111 
    Details
    ISSN: 1432-072X
    Keywords: Eubacterium ; Thermophile ; Evolution ; Fervidobacterium ; Lipids ; Thermotoga
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract An extremely thermophilic anaerobic fermentative eubacterium growing at temperatures between 50 and 80°C (opt.: 65°C) was isolated from an Icelandic hot spring. The cells were Gram-negative motile rods, about 1.8 μm in length, and 0.6 μm in width occurring singly and in pairs. About 50% of the cells formed large spheroids at one end similar to Fervidobacterium nodosum. The new isolate H 21 differed from Fervidobacterium nodosum by a 6 mol % higher GC-content of its DNA (41 mol %), its ability to grow on cellulose, and insignificant DNA homology. The lipids of isolate H 21 were similar to that of members of “Thermotogales”. 16S rRNA sequencing of isolate H 21 and Fervidobacterium nodosum indicated (a) that isolate H 21 represents a new species of the genus Fervidobacterium which we name Fervidobacterium islandicum and (b) that the genus Fervidobacterium belongs to the “Thermotogales” branch.
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    Nucleotide sequence of the clustered genes for apocytochrome b6 and subunit 4 of the cytochrome b/f complex in the spinach plastid chromosome (1984)
    Springer
    Current genetics 8 (1984), S. 543-549 
    Details
    ISSN: 1432-0983
    Keywords: Plastid DNA ; Cytochrome b6 gene ; Amino acid sequence ; Hydropathy ; Thylakoid membrane ; Transcript modification ; Evolution ; Spinach
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A 2.4 kilobase-pair segment of the spinach plastid chromosome carrying the genes for apocytochrome b6 and subunit 4 of the thylakoid membrane cytochrome b/f complex has been analysed by DNA sequencing and Northern blot analysis. The nucleotide sequence reveals two uninterrupted open reading frames of 211 and 139 triplets coding for two hydrophobic proteins of 23.7 kd (cytochrome b6) and 15.2 kd (subunit 4). The genes are located on the same strand and are separated from each other by 1018 untranslated base pairs. They map adjacent to the gene for the P680 chlorophyll α apoprotein of the photosystem II reaction center. The three genes appear to be under common transcriptional control and the transcripts post-transcriptionally modified. The deduced amino acid sequences of cytochrome b6 and subunit 4 both exhibit significant homology with published sequences from mitochondrial b cytochromes (42 kd) suggesting that these functionally equivalent polypeptides in photosynthetic and respiratory electron transport chains arose monophyletically.
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    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: Zoned 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.
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    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.
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    Interactive evolution of equations for procedural models (1993)
    Springer
    The visual computer 9 (1993), S. 466-476 
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    ISSN: 1432-2315
    Keywords: Evolution ; Genetic algorithms ; Procedural models
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science
    Notes: Abstract This paper describes how the evolutionary mechanisms of variation and selection can be used to “evolve” complex equations used by procedural models for computer graphics and animation. An interactive process between the user and the computer allows the user to guide evolving equations by observing results and providing aesthetic information at each step of the process. The computer automatically generates random mutations of equations and combinations between equations to create new generations of results. This repeated interaction between user and computer allows the user to search hyperspaces of posible equations without being required to design the equations by hand or even understand them. Three examples of these techniques have been implemented and are described: procedurally generated pictures and textures, three-dimensional shapes represented by parametric equations, and two-dimensional dynamical systems described by sets of differential equations. It is proposed that these methods have potential as powerful tools for exploring procedural models and achieving flexible complexity with a minimum of user input and knowledge of details.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01888721
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    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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    Contribution of abdominal commissures in the bilateral coordination of the hindlegs during stridulation in the grasshopper Chorthippus dorsatus (1991)
    Springer
    Journal of comparative physiology 169 (1991), S. 191-200 
    Details
    ISSN: 1432-1351
    Keywords: Insect ; Behaviour ; Pattern generation ; Grasshopper ; Stridulation ; Bilateral coordination ; Abdominal ganglia ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Stridulation of grasshoppers is controlled by hemisegmental pattern generator subunits which probably are restricted to the metathoracic ganglion complex (TG3-complex). The coordination of left and right pattern generator subunits depends on commissures of the TG3-complex (Ronacher 1989). The coordination of the stridulatory movements was studied in Chorthippus dorsatus males with partial mediosagittal incisions in the TG3-complex. Animals bearing anterior incisions in the TG3-complex, by which all commissures of the metathoracic neuromere and the first abdominal neuromere were transected, were still able to produce bilaterally coordinated species-specific stridulatory movements. Commissures of the T3- and A1-neuromere, thus, are not necessary, and the A2-, A3-commissures are sufficient for this coordination (Figs. 3, 4). Animals with partial posterior incisions, extending until A1, had deficits in their stridulation pattern; the coordination between the hindlegs was impaired though not completely lost (Fig. 6). This is discussed in view of the structure of ‘stridulation interneurons’ identified in a related grasshopper species (Omocestus viridulus). These results indicate an unexpected substantial contribution of the abdominal neuromeres A2 and A3 to the control of stridulatory movements. This constitutes an interesting parallel to the flight control system of locusts where interneurons located in the first 3 abdominal neuromeres also appear to contribute to the flight pattern generator (Robertson et al. 1982).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00215866
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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 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00199334
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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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    Three unexpected cases of refracting superposition eyes in crustaceans (1990)
    Springer
    Journal of comparative physiology 167 (1990), S. 71-78 
    Details
    ISSN: 1432-1351
    Keywords: Compound eye ; Optics ; Crustacea ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Compound eyes of the decapod shrimp Gennadas, the hermit crab Dardanus, and the syncarid crustacean Anaspides are studied histologically and with optical experiments. The results demonstrate that these three crustaceans all have refracting superposition eyes. The conclusion is based on the following observations: 1. There is a wide clear-zone, which allows for a superposition image to be formed. 2. Dark-adapted eyes display a large eye-glow, and the ommatidia are not optically isolated. 3. The crystalline cones have the shape typical for refracting superposition eyes, and they contain the required lens-cylinder gradient of refractive index. Euphausiids and mysids were previously thought to be the only crustaceans with refracting superposition eyes, whereas the species investigated here were assumed to have reflecting superposition eyes (decapod shrimps) or apposition eyes (hermit crabs and syncarids). The present findings increase more than twofold the number of crustacean groups that are known to have developed refracting superposition optics. It also provides insight into the evolutionary mechanisms that may have led to the development of this type of imaging optics.
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    URL: http://dx.doi.org/10.1007/BF00192407
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    Discrimination of the sign of frequency differences bySternopygus, an electric fish without a jamming avoidance response (1991)
    Springer
    Journal of comparative physiology 168 (1991), S. 461-467 
    Details
    ISSN: 1432-1351
    Keywords: Electric fish ; Sternopygus ; Jamming avoidance ; Electrolocation conditioning ; Preadaptation ; Temporal filtering ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Several species of weakly electric fish reflexively change their frequency of electric organ discharge (EOD) in response to sensing signals of similar frequency from conspecifics; that is, they exhibit jamming avoidance responses (JAR).Eigenmannia increases its EOD frequency if jammed by a signal of lower frequency and decreases its EOD frequency if jammed by a signal of higher frequency. This discrimination is based on an analysis of the patterns of amplitude modulations and phase differences resulting from signal interference. Fish of the closely related genus,Sternopygus, however, do not exhibit a JAR. Here we show that despite lacking this behavior,Sternopygus shares many sensory processing capacities withEigenmannia: 1. Fish could be conditioned to discriminate the sign of the frequency difference (Df) between an exogenous sinusoidal signal and its own EODs with as few as 300 training trials. 2. Fish can discriminate the sign of Df for jamming signals with an amplitude as low as 2 μV/cm (p-p); which is approximately 40 dB below the amplitude of the fish's EOD, as measured lateral to the operculum. 3. Fish appear to discriminate the sign of Df by evaluating modulations in signal amplitude and differences in the timing of signals received by different areas of the body surface. 4. Sternopygus processes electrosensory information through band-pass modulation filters. Tuning to modulation rates over at least 4–16 Hz exists.
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    URL: http://dx.doi.org/10.1007/BF00199605
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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 
    Details
    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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    URL: http://dx.doi.org/10.1007/BF00192988
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