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  • Articles  (540)
  • wheat  (281)
  • Evolution  (259)
  • Springer  (540)
  • National Academy of Sciences
  • 1995-1999  (452)
  • 1975-1979  (88)
  • 1
    Electronic Resource
    Electronic Resource
    Comparison of the effect of hydroxamic acids from wheat on five species of cereal aphids (1995)
    Springer
    Entomologia experimentalis et applicata 74 (1995), S. 115-119 
    Details
    ISSN: 1570-7458
    Keywords: wheat ; aphids ; hydroxamic acids ; DIMBOA ; DIMBOA-glucoside ; EPG ; electrical penetration graph ; feeding deterrents ; antixenosis ; plant resistance
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Feeding behaviour of five species of cereal aphids in wheat seedlings differing in hydroxamic acid (Hx) levels, was monitored via electrical penetration graphs (EPG). Aphid species could be grouped as sensitive to the feeding deterrent effect of Hx in the seedlings (Rhopalosiphum padi, Schizaphis graminum, Sitobion avenae, andMetopolophium dirhodum) or insensitive to them (Rhopalosiphum maidis). However, when feeding behaviour was studied in artificial diets containing Hx, all species were equally sensitive to Hx. The behavour ofR. maidis was further compared with that ofR. padi through detailed EPG analysis. It was found that the insensitivity ofR. maidis to Hx in seedlings may be due to a feeding strategy avoiding contact with the compounds by decreasing the number of cellular punctures in live tissues other than sieve elements during its way to the phloem.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02383002
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  • 2
    Electronic Resource
    Electronic Resource
    Hypersensitive response of wheat to the Hessian fly (1995)
    Springer
    Entomologia experimentalis et applicata 74 (1995), S. 283-294 
    Details
    ISSN: 1570-7458
    Keywords: hypersensitivity ; Hessian fly ; plant resistance ; wheat
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Hessian flyMayetiola destructor (Say) larvae are able to obtain food from their host plant without inflicting mechanical damage to the plant surface, apparently by secreting substances which elicit release of nutrients from plant cells surrounding the feeding site. Cells of fully susceptible plants retain their normal appearances, while in resistant plants extensive areas of cellular collapse occur. These responses indicate that hypersensitivity is the basis of wheat's resistance to the Hessian fly. The fly's feeding mechanism more closely resembles that of a pathogen than of a phytophagous insect; correspondingly, both the genetic relationship and resistance mechanism of the host plant to the parasite are of the sorts commonly associated with bacterial and fungal pathogens.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02381793
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  • 3
    Electronic Resource
    Electronic Resource
    Some prerequisites for a study of the evolution of cognition in the animal kingdom (1996)
    Springer
    Acta biotheoretica 44 (1996), S. 37-57 
    Details
    ISSN: 1572-8358
    Keywords: Animal cognition ; Evolution ; Representation ; Computation ; Significance ; Phenomenology ; Autonomy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A distinction is made between two definitions of animal cognition: the one most frequently employed in cognitive sciences considers cognition as extracting and processing information; a more phenomenologically inspired model considers it as attributing to a form of the outside world a significance, linked to the state of the animal. The respective fields of validity of these two models are discussed along with the limitations they entail, and the questions they pose to evolutionary biologists are emphasized. This is followed by a presentation of a general overview of what might be the study of the evolution of knowledge in animals.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00046434
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  • 4
    Electronic Resource
    Electronic Resource
    Within-plant distribution of Rhopalosiphum padi on wheat seedlings is affected by induced responses (1999)
    Springer
    Entomologia experimentalis et applicata 93 (1999), S. 227-230 
    Details
    ISSN: 1570-7458
    Keywords: Rhopalosiphum padi ; cereal aphids ; wheat ; induced responses ; feeding site
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003874225681
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  • 5
    Electronic Resource
    Electronic Resource
    Comparison of Diuraphis noxia resistance in wheat isolines and plant introduction lines (1999)
    Springer
    Entomologia experimentalis et applicata 92 (1999), S. 157-164 
    Details
    ISSN: 1570-7458
    Keywords: plant resistance ; antibiosis ; tolerance ; antixenosis ; Russian wheat aphid ; wheat ; Homoptera ; Aphididae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The Russian wheat aphid, Diuraphis noxia (Mordvilko), is one of the most important aphid pests of wheat, Triticum aestivum L., worldwide. Among the various pest management options, plant resistance is an economical management tactic to control D. noxia in cereal crops such as wheat. Researchers have identified D. noxia resistant germplasm and it has been incorporated into wheat. This study compared D. noxia resistance between the ‘Betta’ wheat isolines Betta-Dn1, Betta-Dn2, and Betta-Dn5 and their corresponding donor gene plant introduction (PI) lines PI 137739 (Dn1), PI 262660 (Dn2), and PI 294994 (Dn5). Although the Betta isolines and PI lines showed D. noxia resistance when compared with Betta wheat, the degree of resistance in the isolines to D. noxia was different from their corresponding PI donors. Aphid number, aphid fecundity, and biomass per aphid were not different between Betta-Dn1 and PI 137739 or Betta-Dn2 and PI 262660; however, the same parameters were significantly lower on PI 294994 compared with Betta-Dn5. This indicated that aphid resistance in PI 137739 and PI 262660 was probably governed by a single dominant gene, while the resistance in PI 294994 was controlled by more than one gene. Additionally, plant biomass reduction was aphid density dependent, which suggested that use of appropriate aphid infestation level is important when using plant biomass reduction as an indicator of resistance. Plant resistance categorization showed that there was no detectable difference in antixenosis among the seven lines evaluated. However, the higher aphid fecundity observed on PI 262660 compared with PI 137739 and PI 294994, in addition to no significant differences among the three PIs in plant biomass reduction, suggested PI 262660 was a tolerant line, while PI 137739 and PI 294994 were antibiotic lines. Plant tolerance could not be elucidated among the three Betta isolines using aphid fecundity and plant biomass reduction as indicators.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003719325094
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  • 6
    Electronic Resource
    Electronic Resource
    Influence of cereal leaf epicuticular wax on Diuraphis noxia probing behavior and nymphoposition (1998)
    Springer
    Entomologia experimentalis et applicata 89 (1998), S. 111-118 
    Details
    ISSN: 1570-7458
    Keywords: leaf surface wax ; probing behavior ; nymphoposition ; Russian wheat aphid ; wheat ; barley ; oat ; Homoptera ; Aphididae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The effect of cereal leaf surface wax on Diuraphis noxia (Mordvilko), the Russian wheat aphid, probing behavior and nymphoposition was evaluated. Ultrastructure of leaf epicuticular wax from wheat (Triticum aestivum L.) c.v. ‘Arapahoe’ and ‘Halt’ was different from barley (Hordeum vulgare L.) c.v. ‘Morex’, and oat (Avena sativa L.) c.v. ‘Border’. Both wheat cultivars had similar rod-shaped epicuticular wax, while barley and oat plants had flakes. The chemical composition comparison of gas chromatograms also indicated that the extract of the two wheat cultivars had similar pattern of peaks, while the barley and oat leaves had similar peaks. Cereal variety significantly affected aphid probing behavior (P 〈 0.05), but wax removal using ethyl ether swab did not (P 〈 0.05). Aphids initiated significantly more probes on Border oat leaves than on Morex barley irrespective of wax removal, although total probing duration per aphid was not significantly different among the four cereals examined. Accumulative salivation duration per aphid on oat leaves with wax was significantly longer than other cereal leaves with wax, while accumulative ingestion duration per aphid on Arapahoe wheat and Morex barley was significantly longer than on oat. Nymphoposition of D. noxia on cereal leaves maintained on the benzimidazole-agar medium showed that aphids produced a greater number of nymphs on Morex barley and less on Border oat leaves, although wax removal did not affect aphid nymphoposition. Removal of leaf epicuticular waxes from the 4 cereal genotypes using ethyl ether swab indicated that the influence of wax on plant resistance to D. noxia probing and reproduction was limited. Morex barley was the most favorable, while Border oat was the least favorable cereal host of D. noxia.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003458406502
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  • 7
    Electronic Resource
    Electronic Resource
    Salivation into sieve elements in relation to plant chemistry: the case of the aphid Sitobion fragariae and the wheat, Triticum aestivum (1999)
    Springer
    Entomologia experimentalis et applicata 91 (1999), S. 111-114 
    Details
    ISSN: 1570-7458
    Keywords: sieve element ; salivation ; aphid ; plant resistance ; wheat ; Sitobion fragariae ; Triticum aestivum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Extended sieve element salivation (E1 waveform in the electrical penetration graph) is a characteristic activity during early sieve element punctures, particularly in resistant plants. In order to explore a chemically-mediated mechanism of resistance associated with sieve element salivation, we compared the pattern of feeding behaviour of the aphid, Sitobion fragariae (Walker), on two cultivars of the wheat Triticum aestivum L., with different concentrations of hydroxamic acids (Hx). During 24 h of electronic monitoring, aphids dedicated over 50% of the total time to phloem ingestion from the sieve elements. Total time allocated to E1 in the experiment, time to first E1 within the experiment, time allocated to E1 before a sustained phloem ingestion (E2) and the contribution of sieve element salivation to the phloem phase (E1/[E1+E2]) were significantly higher in the high-Hx cultivar. The increased salivation in plants with higher contents of Hx suggests the existence, at least in this system, of a chemically-mediated sieve element constraint.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003628703035
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  • 8
    Electronic Resource
    Electronic Resource
    Purification and characterization of an ADP-dependent phosphofructokinase from Thermococcus zilligii (1999)
    Springer
    Extremophiles 3 (1999), S. 121-129 
    Details
    ISSN: 1433-4909
    Keywords: Key words Thermococcus ; Pyrococcus ; Thermophilic ; Phosphofructokinase ; Evolution ; ADP ; Glycolysis ; ATP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The ADP-dependent phosphofructokinase (PFK) from Thermococcus zilligii has been purified 950 fold; it had a specific activity of 190 U mg−1. The enzyme required Mg2+ ions for optimal activity and was specific for ADP. The forward reaction kinetics were hyperbolic for both cosubstrates (pH optimum of 6.4), and the apparent K m values for ADP and fructose-6-phosphate were 0.6 mM (apparent V max of 243 U mg−1) and 1.47 mM (apparent V max of 197 U mg−1), respectively. Significantly, the enzyme is indicated to be nonallosteric but was slightly activated by some monovalent cations including Na+ and K+. The protein had a subunit size of 42.2 kDa and an estimated native molecular weight of 66 kDa (gel filtration). Maximal reaction rates for the reverse reaction were attained at pH 7.5–8.0, and the apparent K m values for fructose-1,6-bisphosphate and AMP were 0.56 mM (apparent V max of 2.9 U mg−1) and 12.5 mM, respectively. The biochemical characteristics of this unique ADP-dependent enzymatic activity are compared to ATP and pyrophosphate-dependent phosphofructokinases.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007920050107
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  • 9
    Electronic Resource
    Electronic Resource
    Isolation of a chymotrypsinogen B-like enzyme from the archaeon Natronomonas pharaonis and other halobacteria (1999)
    Springer
    Extremophiles 3 (1999), S. 153-161 
    Details
    ISSN: 1433-4909
    Keywords: Key wordsNatronomonas pharaonis ; Natronobacteria ; Archaea ; Serine protease ; Chymotrypsinogen ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A protease of a molecular mass of approximately 30 kDa was isolated and purified from the haloalkaliphilic archaeon Natronomonas (formerly Natronobacterium) pharaonis. The enzyme hydrolyzed synthetic peptides, preferentially at the carboxyl terminus of phenylalanine or leucine, as well as large proteins. Hydrolysis occurred over the range of pH from 6 to 12, with an optimum at pH 10. The temperature optimum was 61°C. The enzyme was nearly equally active over the range of salt concentration from 0.5 to 4 M (NaCl or KCl). A strong cross-reaction with a polyclonal antiserum against human chymotrypsin was observed. Enzymatic activity was inhibited by typical serine protease inhibitors. There was significant homology between N-terminal and internal sequences from autolytic fragments and the sequence of bovine chymotrypsinogen B; the overall amino acid composition was similar to that of vertebrate chymotrypsinogens. Evidence for a zymogen-like processing of the protease was obtained. Cell extracts from other halobacteria exhibited similar proteolytic activity and immunoreactivity. The data suggested a widespread distribution of a chymotrypsinogen B-like protease among halo- and haloalkaliphilic Archaea.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007920050111
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  • 10
    Electronic Resource
    Electronic Resource
    Multiple class I loci expressed by the quail Mhc (1999)
    Springer
    Immunogenetics 49 (1999), S. 456-460 
    Details
    ISSN: 1432-1211
    Keywords: Key words Antigen processing ; Evolution ; Cell surface molecules ; Mhc ; Class I antigens
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002510050519
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  • 11
    Electronic Resource
    Electronic Resource
    Identification and characterization of a fish natural resistance-associated macrophage protein (NRAMP) cDNA (1999)
    Springer
    Immunogenetics 50 (1999), S. 60-66 
    Details
    ISSN: 1432-1211
    Keywords: Key words NRAMP ; Fish ; Carp ; Evolution ; Expression
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  The mouse Lsh/Ity/Bcg locus regulates natural resistance to intracellular pathogens, and the Nramp1 gene was isolated as its candidate. Nramp is part of a small family of at least two genes, Nramp1 and Nramp2. In the present study, a full-length cDNA for carp NRAMP has been isolated and characterized. Nucleotide and predicted amino acid sequence analysis indicate that the carp NRAMP encodes a 548 amino acid membrane protein with 12 putative transmembrane domains, two N-linked glycosylation sites, and an evolutionarily conserved consensus transport motif. The peptide sequence identity among carp and human NRAMP2 is 78%, and 65% with human NRAMP1. Reverse transcription-polymerase chain reaction revealed that carp NRAMP is ubiquitously expressed. Phylogenetic analysis, using neigbor-joining, showed that the carp NRAMP protein clustered together with mammalian NRAMP2 proteins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002510050686
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  • 12
    Electronic Resource
    Electronic Resource
    Diversity and evolution of T-cell receptor variable region genes in mammals and birds (1999)
    Springer
    Immunogenetics 50 (1999), S. 301-308 
    Details
    ISSN: 1432-1211
    Keywords: Key words T-cell receptors ; Variable region genes ; Evolution ; Phylogeny ; Diversity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  The receptor of a T lymphocyte (TCR) recognizes nonself antigens in the company of major histocompatibility complex (MHC) molecules presented to it by the antigen-presenting cell. The variable region of TCR is encoded by either a concatenation of variable region (TCR-V), diversity region (TCR-D), and joining region (TCR-J) genes, or a concatenation of TCR-V and TCR-J genes. The TCR-V genes exist as a multigene family in vertebrate species. Here we study the evolutionary relationships of TCR-V genes from humans, sheep, cattle, rabbits, mice, and chicken. These six species can be classified into two groups according to the frequency of γδ T-cells in their peripheral T-cell populations. The "γδ low" group of species includes humans and mice, in which γδ T-cells constitute very limited portion of the T-cell population. The "γδ high" group includes sheep, cattle, rabbits, and chicken, in which γδ T-cells comprise up to 60% of the T-cell population. Here, we compiled TCR-V sequences from the six species and conducted a phylogenetic analysis. We identified various TCR-V gene subgroups based on the analysis. We found that humans and mice have representatives from nearly all of the subgroups identified, while other species have lost subgroups to different extent. Therefore, the γδ low species have a high degree of diversity of TCR-V genes, while γδ high species all have limited diversity of TCR-V genes. This pattern is similar to that found for immunoglobulin variable region (IGV) genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002510050606
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  • 13
    Electronic Resource
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    Marsupial light chains: IGK with four V families in the opossum Monodelphis domestica (1999)
    Springer
    Immunogenetics 50 (1999), S. 329-335 
    Details
    ISSN: 1432-1211
    Keywords: Key words Marsupials ; Light chains ; Variable regions ; IGK ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  A full-length and several partial cDNAs encoding IGK light chains from the marsupial South American opossum, Monodelphis domestica, were isolated and characterized. Using these clones as a starting point, the expressed IGKV repertoire was sampled by anchored polymerase chain reaction using an IGKC-specific primer. Based on nucleotide sequences of twenty unique, expressed IGKV-J combinations, there are at least four IGKV families and two J segments. Southern blot analysis revealed each IGK-V family contains multiple gene segments totaling at least thirty-five IGKV in the opossum genome. No evidence for particular, recurrent IGKV-J combinations in the opossum IGK repertoire was seen, rather the V-J combinations appeared random and diverse. Each of the four IGKV families appear more closely related to V segments from placental mammals than to each other, suggesting the duplication of the IGKV families prior to the separation of marsupials and placental mammals more than one-hundred-million years ago. Overall, the complexity of opossum light chain V segments appears greater than that found in the heavy chain, and light chains are likely to contribute significantly to Ig diversity in this species.With this report, the homologues encoding all three classes of eutherian Ig chains, IGH, IGL, and IGK, have been described in a non-placental mammal.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002510050609
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  • 14
    Electronic Resource
    Electronic Resource
    Major histocompatibility complex-linked MIC genes in rhesus macaques and other primates (1999)
    Springer
    Immunogenetics 50 (1999), S. 358-362 
    Details
    ISSN: 1432-1211
    Keywords: Key words MHC ; MIC ; Nonhuman primates ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002510050614
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  • 15
    Electronic Resource
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    Isolation and mapping of the rabbit DM genes (1999)
    Springer
    Immunogenetics 49 (1999), S. 295-302 
    Details
    ISSN: 1432-1211
    Keywords: Key words Major histocompatibility complex ; Class II ; Antigen processing ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Proper peptide presentation by major histocompatibility complex (MHC)-encoded class II antigens is dependent on the products of the MHC DM loci. We identified the rabbit orthologues (RLA-DMA and -DMB) of human HLA-DMA and -DMB and found that they have 76.9% and 78.8% identity with HLA-DMA and -DMB, respectively. Like classical class II MHC genes, RLA-DM genes are more closely related to human HLA-DM genes than to mouse H2-DM. Among the DM family, there is a high degree of variability at the amino terminus of the DMa chains, and length variability in the cytoplasmic tails of both DMα and DMβ. The rabbit DM genes are coexpressed with class II genes in lymphoid tissues, as are the DM genes of other mammals. The RLA-DM locus maps to the class II region of the rabbit MHC, and is flanked by the DP and DOB loci. Despite having some similarities to class II genes of bony fishes, the DM family represents a separate branch of the MHC class II family.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002510050496
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  • 16
    Electronic Resource
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    New family of Mhc class II A genes identified from cDNA sequences in the cichlid fish Aulonocara hansbaenschi (1999)
    Springer
    Immunogenetics 49 (1999), S. 544-548 
    Details
    ISSN: 1432-1211
    Keywords: Key words Mhc ; Class II A ; Cichlid ; Fish ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002510050533
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  • 17
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    Characterization of beta2-microglobulin in a primitive fish, the Siberian sturgeon (Acipenser baeri) (1999)
    Springer
    Immunogenetics 50 (1999), S. 79-83 
    Details
    ISSN: 1432-1211
    Keywords: Key words Beta2-microglobulin ; Evolution ; Sturgeon ; cDNA ; Genomic
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
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    URL: http://dx.doi.org/10.1007/s002510050690
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  • 18
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    Crustal structure, evolution, and volcanic unrest of the Alban Hills, Central Italy (1997)
    Springer
    Bulletin of volcanology 59 (1997), S. 161-170 
    Details
    ISSN: 1432-0819
    Keywords: Key words Structure ; Evolution ; Uplift ; Geodetic modeling ; Alban Hills
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences
    Notes: Abstract  The Alban Hills, a Quaternary volcanic center lying west of the central Apennines, 15–25 km southeast of Rome, last erupted 19 ka and has produced approximately 290 km3 of eruptive deposits since the inception of volcanism at 580 ka. Earthquakes of moderate intensity have been generated there at least since the Roman age. Modern observations show that intermittent periods of swarm activity originate primarily beneath the youngest features, the phreatomagmatic craters on the west side of the volcano. Results from seismic tomography allow identification of a low-velocity region, perhaps still hot or partially molten, more than 6 km beneath the youngest craters and a high-velocity region, probably a solidified magma body, beneath the older central volcanic construct. Thirty centimeters of uplift measured by releveling supports the contention that high levels of seismicity during the 1980s and 1990s resulted from accumulation of magma beneath these craters. The volume of magma accumulation and the amount of maximum uplift was probably at least 40×106 m3 and 40 cm, respectively. Comparison of newer levelings with those completed in 1891 and 1927 suggests earlier episodes of uplift. The magma chamber beneath the western Alban Hills is probably responsible for much of the past 200 ka of eruptive activity, is still receiving intermittent batches of magma, and is, therefore, continuing to generate modest levels of volcanic unrest. Bending of overburden is the most likely cause of the persistent earthquakes, which generally have hypocenters above the 6-km-deep top of the magma reservoir. In this view, the most recent uplift and seismicity are probably characteristic and not precursors of more intense activity.
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    URL: http://dx.doi.org/10.1007/s004450050183
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  • 19
    Electronic Resource
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    Study of double and triple simultaneous substitutions of amino acids in cytochromes C (1975)
    Springer
    Journal of molecular evolution 5 (1975), S. 187-197 
    Details
    ISSN: 1432-1432
    Keywords: Evolution ; Cytochrome C ; Substitution ; Covarion ; Monte-Carlo Simulations
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A statistical analysis aimed at obtaining some informations on a possible correlation between simultaneous amino acid substitutions is proposed. This method is applied to a set of cytochromes C, at the level of tandem and triple substitutions separated along the peptide chain by 1 to 15 peptide bonds. Monte-Carlo simulations are performed and the results are compared. We find a significant occurence of three adjacent amino acid substitutions in which the first replacement requires a two nucleotide substitution. A possible explanation of this fact is proposed on the basis of covarions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01741241
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  • 20
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    Molecular phylogeny based on the κ-casein and cytochrome b sequences in the mammalian suborder Ruminantia (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 859-866 
    Details
    ISSN: 1432-1432
    Keywords: Evolution ; κ-Casein ; Cytochrome b ; Artiodactyla ; Ruminantia ; Caprinae ; Capricornis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Nucleotide sequences for the κ-casein precursor proteins have been determined from the genomic DNAs or hair roots of the Ruminantia. The coding regions, exons 2, 3, and 4, were amplified separately via the three kinds of PCRs and then directly sequenced. The primers were designed from the sequence of bovine κ-casein gene; they were applicable for the amplification of the κ-casein genes from the 13 species in the Ruminantia except exon 2 of the lesser mouse deer. These results permitted an easy phylogenetic analysis based on the sequences of an autosomal gene. A phylogenetic tree was constructed from the mature K-casein sequences and compared with the tree of the cytochrome b genes which were sequenced from the same individuals. The Cervidae (sika deer, Cervus nippon) were separated from the branch of the Bovidae on the tree of κ-casein genes with a relatively high confidence level of the bootstrap analysis, but included in the branch of the Bovidae on the tree of cytochrome b genes. The κ-casein tree indicated a monophyly of the subfamily Caprinae, although the internal branches were uncertain in the Caprinae. The tree based on the nucleotide sequences of cytochrome b genes clearly showed the relationships of the closely related species in the genus Capricornis consisting of serow (C. smatorensis), Japanese serow (C. crispus), and Formosan serow (C. swinhoei). These results would be explained by the difference of resolving power between the κ-casein and the cytochrome b sequences.
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    URL: http://dx.doi.org/10.1007/BF00173165
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  • 21
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    Frequency of insertion-deletion, transversion, and transition in the evolution of 5S ribosomal RNA (1976)
    Springer
    Journal of molecular evolution 7 (1976), S. 133-149 
    Details
    ISSN: 1432-1432
    Keywords: 5S rRNA ; Nucleotide Sequence Homology ; Evolution ; Mutation Frequencies
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The problem of choosing an alignment of two or more nucleotide sequences is particularly difficult for nucleic acids, such as 5S ribosomal RNA, which do not code for protein and for which secondary structure is unknown. Given a set of ‘costs’ for the various types of replacement mutations and for base insertion or deletion, we present a dynamic programming algorithm which finds the optimal (least costly) alignment for a set of N sequences simultaneously, where each sequence is associated with one of the N tips of a given evolutionary tree. Concurrently, protosequences are constructed corresponding to the ancestral nodes of the tree. A version of this algorithm, modified to be computationally feasible, is implemented to align the sequences of 5S RNA from nine organisms. Complete sets of alignments and proto-sequence reconstructions are done for a large number of different con-figurations of mutation costs. Examination of the family of curves of total replacements inferred versus the ratio of transitions/trans-versions inferred, each curve corresponding to a given number of in-sertions-deletions inferred, provides a method for estimating relative costs and relative frequencies for these different types of mutation.
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    URL: http://dx.doi.org/10.1007/BF01732471
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    The evolution of angiosperm seed proteins: A methionine-rich legumin subfamily present in lower angiosperm Clades (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 399-404 
    Details
    ISSN: 1432-1432
    Keywords: Asarum ; Dioscorea ; Angiosperms ; Evolution ; Legumins ; Seed proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Analysis of legumin-encoding cDNAs fromDioscorea caucasica Lipsky (Dioscoreaceae) and fromAsarum europaeum L. (Aristolochiaceae) shows that there is an especially methionine-rich legumin subfamily present in the lower angiosperm clades including the Monocotyledoneae. It is characterized by a methionine content of 3–4 mol% which is roughly triple the methionine proportion of most other legumins. These “MetR” legumins, if present, still have to be detected in the higher angiosperms including the important seed crops. Evolutionary analysis suggests that the MetR legumins are the result of a gene duplication allowing the differentiation of legumin genes according to their sulfur content. The duplication event must have taken place before the split into mono- and dicotyledonous plants but probably after the separation of angiosperms and gymnosperms.
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    URL: http://dx.doi.org/10.1007/BF02339013
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    Integration of retroposable elements in mammals: Selection of target sites (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 685-689 
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    ISSN: 1432-1432
    Keywords: Retroposons ; Integration targets ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Genomic DNA fragments generated by the reverse transcription of cellular RNA are called retroposons. Because they are flanked by short repeats, mammalian retroposons are believed to integrate at staggered chromosomal breaks. Recently, a significant sequence pattern associated with the integration of Alu and ID repeats was identified (Jurka 1996). It is represented by the 5′ TTAAAA consensus sequence around the 5′ ends of flanking repeats of Alu, ID, as well as, of B1 and B2 retroposed elements as shown in this paper. This consensus is a potential target for enzymatic nicking which probably occurs in the complementary strand between 3′ AA and the following 3′ TTTT bases. The first four bases of the flanking repeats corresponding to the 3′ TTTT consensus sequence show some sequence variations that may be affected by complementary base pairing between the A-rich RNA tails and the DNA target sequences prior to nicking and reverse transcription. We discuss potential evidence for such base pairing based on correlated variations in nucleotide composition of different tail and target regions.
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    URL: http://dx.doi.org/10.1007/BF02202117
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    Caenorhabditis Globin genes: Rapid intronic divergence contrasts with conservation of silent exonic sites (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 101-108 
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    ISSN: 1432-1432
    Keywords: Alleles ; Evolution ; Gene conversion ; Introns ; Nematode
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Globin genes from theCaenorhabditis speciesbriggsae andremanei were identified and compared with a previously describedC. elegans globin gene. The encoded globins share between 86% and 93% amino acid identity, with most of the changes in or just before the putative B helix.C. remanei was found to have two globin alleles,Crg1-1 andCrgl-2. The coding sequence for each is interrupted by a single intron in the same position. The exons of the two genes are only 1 % divergent at the nucleotide level and encode identical polypeptides. In contrast, intron sequence divergence is 16% and numerous insertions and deletions have significantly altered the size and content of both introns. Genetic crosses show thatCrg1-1 andCrgl-2 segregate as alleles. Homozygous lines for each allele were constructed and northern analysis confirmed the expression of both alleles. These data reveal an unusual situation wherein two alleles encoding identical proteins have diverged much more rapidly in their introns than the silent sites of their coding sequences, suggesting multiple gene conversion events.
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    URL: http://dx.doi.org/10.1007/BF02337354
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    Partial gene duplication and posterior pituitary peptide (1975)
    Springer
    Journal of molecular evolution 5 (1975), S. 47-55 
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    ISSN: 1432-1432
    Keywords: Gene Duplication ; Dipeptides ; Posterior Pituitary Peptide ; Evolution ; Protein Sequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have compiled the dipeptide frequencies in 100 known protein sequences. We suggest that dipeptides which occur with low frequencies can be used to locate proteins where partial gene duplication may have taken place. The 48 residue sequence of posterior pituitary peptide contains two Cys Trp pairs. The adjacent portions of the sequence are compatible with a partial gene duplication in the evolutionary history of posterior pituitary peptide.
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    URL: http://dx.doi.org/10.1007/BF01732013
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    Aminoacyl transfer from an adenylate anhydride to polyribonucleotides (1975)
    Springer
    Journal of molecular evolution 6 (1975), S. 309-320 
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    ISSN: 1432-1432
    Keywords: Aminoacyl Transfer ; Amino Acid Adenylate ; Imidazole Catalysis ; Evolution ; Peptide
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Imidazole catalysis of phenylalanyl transfer from phenylalanine adenylate anhydride to the hydroxyl groups of homopolyribonucleotides was investigated as a chemical model of the biochemical aminoacylation of tRNA. Imidazole catalyzed transfer of phenylalanine to poly (U) increases from pH 6.5 to 7.7 and decreases above pH 7.7. At pH 7.7 approximately 10% of the phenylalanyl residues are transferred to poly (U). At pH 7.1, transfer to poly (U) was five times as great as to poly (A) and transfer to a poly (A) poly (U) double helix was negligible. At pH 7.1 approximately 45 mole percent linkages to poly (U) were monomeric phenylalanine; the remainder of the linkages were peptides of phenylalanine. The number of linkages and their lability to base and neutral hydroxylamine indicates that phenylalanine and its peptides are attached as esters to the 2′ hydroxyl groups throughout poly (U) and the 2′ (3) hydroxyl groups at the terminus of poly (U). These results do model the contemporary process of aminoacyl transfer to tRNA and continue to suggest that a histidine residue is in the active site of aminoacyl-tRNA-synthetases.
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    URL: http://dx.doi.org/10.1007/BF01794637
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    Conservation of repeated DNA base sequences in theCrustacea: A molecular approach to decapod phylogeny (1976)
    Springer
    Journal of molecular evolution 7 (1976), S. 111-131 
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    ISSN: 1432-1432
    Keywords: Crustacea ; Evolution ; Repeated DNA ; Molecular Hybridization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Analysis of data obtained from molecular hybridization of3H-labeled repetitious DNA has been utilized to reconstruct the broad outlines of phylogenetic relationships among decapod Crustacea. This molecular reconstruction agrees reasonably well with the paleontological record, and with other schemes obtained by comparative morphological and serological approaches. Preliminary evidence is in line with the hypothesis that continuous addition of new repeated sequence families to the genome over long periods of time may in part account for the correlation observed between percent repetitious DNA hybridized and divergence time. It is tentatively concluded that a core of DNA base sequence homology has been highly conserved throughout the evolution of theCrustacea. Demonstration of inter-species sequence homology has important implications to models which relegate a genetic regulatory function to repeated DNAs.
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    URL: http://dx.doi.org/10.1007/BF01732470
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    Counter-examples to a neutralist hypothesis (1976)
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    Journal of molecular evolution 7 (1976), S. 185-195 
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    ISSN: 1432-1432
    Keywords: Evolution ; Randomicity ; Counter-Example
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Specific counter-examples are derived theoretically to the hypothesis that a random amino acid composition signifies a random evolutionary process.
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    URL: http://dx.doi.org/10.1007/BF01731488
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    A comparison of the 16S ribosomal RNAs from mesophilic and thermophilic bacilli: Some modifications in the sanger method for RNA sequencing (1976)
    Springer
    Journal of molecular evolution 7 (1976), S. 197-213 
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    ISSN: 1432-1432
    Keywords: Bacilli, 16S rRNA ; Phylogeny ; Thermophile ; Evolution ; Oligonucleotide Fingerprint
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Two modifications in the Sanger two dimensional electrophoretic procedure for RNA analysis are reported. One increases resolution on the primary fingerprint to the point that digests of large RNAs, of the size 1500–3000 nucleotides yield well resolved fingerprint patterns. The other is a novel endonucleolytic procedure that proves useful in determining sequences of the large oligonucleotides produced by T1 ribonuclease. These modifications have been used in determining the catalogs of oligomers produced by T1 ribonuclease digestion of 16S rRNAs from three related organisms,Bacillus subtilis, B.pumilus andB.stearothermophilus. The possible effects of adaptation to a thermophilic niche on ribosomal RNA primary structure and the phylogenetic relatedness of the two mesophilic Bacilli are discussed.
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    The charge-state model of protein polymorphism in natural populations (1975)
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    Journal of molecular evolution 6 (1975), S. 149-163 
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    ISSN: 1432-1432
    Keywords: Electrophoretic Detectability ; Neutral Mutation Theory ; Evolution ; Mutation Rates
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Routine electrophoretic surveys for genetic variation in natural populations depend primarily upon detecting differences in the net charge carried by a protein. We have calculated the proportion of base substitutions which would yield an electrophoretically detectable mutant protein, and the relative mutation rates among different charge classes, under a variety of simplifying assumptions. These calculations indicate that: (i) only 25 per cent of all single base mutations would lead to a charge change on a protein molecule. (ii) five distinct classes of electrophoretic variants can be generated from a specified protein by single base substitutions. (iii) the relative mutation rates differ markedly among the different charge classes which can be generated by single base substitutions. The estimates of the proportion of electrophoretically detectable mutant proteins and relative mutation rates among charge classes were relatively robust to changes in assumptions concerned with the kind and site of base substitutions and the amino acid composition of the protein.
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    Basic chromosomal proteins in lower eukaryotes: Relevance to the evolution and function of histones (1976)
    Springer
    Journal of molecular evolution 8 (1976), S. 79-94 
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    ISSN: 1432-1432
    Keywords: Histones ; Evolution ; Prokaryotes ; Lower Eukaryotes ; Higher Eukaryotes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The occurrence of basic chromosomal proteins in lower eukaryotes provides a useful approach to the study of histone evolution and function in higher eukaryotes. The histones of higher plants and animals are very similar and some are nearly identical, suggesting a high degree of evolutionary conservation within this group of proteins. However, a literature survey reveals that in the lower eukaryotes the histone situation is quite variable. The ciliates, and the true and cellular slime molds possess basic chromosomal proteins that are very similar to the histones of higher plants and animals. Various other lower eukaryotes possess basic chromosomal proteins that resemble at least some of the major histone fractions, and some microorganisms possess basic chromosomal proteins that bear little or no relationship to higher plant and animal histones. Since histones play a major role in the control of gene expression and the maintenance of chromosome structure in higher organisms, the evolution of these proteins represents a major change in the packaging of DNA and the mode of regulating gene expression in eukaryotes.
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    Evolution of the response patterns to dietary carbohydrates and the developmental differentiation of gene expression of α-amylase in Drosophila (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 1076-1084 
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    ISSN: 1432-1432
    Keywords: Evolution ; Expression patterns ; α-Amylase ; Glucose repression ; Starch induction ; Intra- and interspecific variation ; Drosophila ; Gene expression ; Regulatory genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Intraspecific variation of α-amylase activity in D. melanogaster and D. immigrans, which is distantly related to D. melanogaster, and interspecific variation of α-amylase activity in 18 Drosophila species were examined. The amount of intraspecific variation of α-amylase activities measured in terms of coefficient of variation in D. melanogaster and D. immigrans was one-half and one-tenth or less, respectively, of the interspecific variation in 18 Drosophila species. We also surveyed the response patterns of α-amylase activity to dietary carbohydrates at the larval and adult stages. The levels of α-amylase activity depended on both repression by dietary glucose (glucose repression) and induction by dietary starch (starch induction). In general, our data suggest that glucose repression was conserved among species at both stages while starch induction was mainly observed in larvae, although the degree of the response depended on species. In D. lebanonensis lebanonensis and D. serrata, larvae expressed electrophoretically different α-amylase variants (isozymes) from those of adult flies. These results may suggest that the regulatory systems responsible both for the response to environment and developmental expression are different among species in Drosophila.
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    URL: http://dx.doi.org/10.1007/BF00173189
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    Ferritin gene organization: Differences between plants and animals suggest possible kingdom-specific selective constraints (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 325-336 
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    ISSN: 1432-1432
    Keywords: Soybean ; Ferritin ; Plant-animal ; Monocotyledons ; Dicotyledons ; Plastid ; Gene organization ; Evolution ; Intron
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Ferritin, a protein widespread in nature, concentrates iron −1011−1012-fold above the solubility within a spherical shell of 24 subunits; it derives in plants and animals from a common ancestor (based on sequence) but displays a cytoplasmic location in animals compared to the plastid in contemporary plants. Ferritin gene regulation in plants and animals is altered by development, hormones, and excess iron; iron signals target DNA in plants but mRNA in animals. Evolution has thus conserved the two end points of ferritin gene expression, the physiological signals and the protein structure, while allowing some divergence of the genetic mechanisms. Comparison of ferritin gene organization in plants and animals, made possible by the cloning of a dicot (soy-bean) ferritin gene presented here and the recent cloning of two monocot (maize) ferritin genes, shows evolutionary divergence in ferritin gene organization between plants and animals but conservation among plants or among animals; divergence in the genetic mechanism for iron regulation is reflected by the absence in all three plant genes of the IRE, a highly conserved, noncoding sequence in vertebrate animal ferritin mRNA. In plant ferritin genes, the number of introns (n = 7) is higher than in animals (n = 3). Second, no intron positions are conserved when ferritin genes of plants and animals are compared, although all ferritin gene introns are in the coding region; within kingdoms, the intron positions in ferritin genes are conserved. Finally, secondary protein structure has no apparent relationship to intron/exon boundaries in plant ferritin genes, whereas in animal ferritin genes the correspondence is high. The structural differences in introns/exons among phylogenetically related ferritin coding sequences and the high conservation of the gene structure within plant or animal kingdoms suggest that kingdom-specific functional constraints may exist to maintain a particular intron/exon pattern within ferritin genes. In the case of plants, where ferritin gene intron placement is unrelated to triplet codons or protein structure, and where ferritin is targeted to the plastid, the selection pressure on gene organization may relate to RNA function and plastid/nuclear signaling.
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    Sequence divergence in a family of variant surface glycoprotein genes from trypanosomes: Coding region hypervariability and downstream recombinogenic repeats (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 500-511 
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    ISSN: 1432-1432
    Keywords: Evolution ; Multigene family ; Recombination ; Trypanosome ; Variant surface glycoprotein
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The surface of the parasitic protozoanTrypanosoma brucei spp. is covered with a dense coat consisting of a single type of glycoprotein molecule, the variant surface glycoprotein (VSG). There may be as many as 1,000 genes for VSG within the genome ofT. brucei, and the switch of expression from one to another is the phenomenon of antigenic variation. As an approach to understanding the evolution of VSG genes we have determined the genomic DNA sequences of the eight genes encoding the variant surface glycoprotein 117 (VSG) family. From these data we have observed a number of features concerning the relationships between these genes: (1) there is a region of high variability confined to the N-terminus of the coding sequence, and comparison of the sequences with the available X-ray diffraction crystal structures suggests that two of the most variable stretches within the N-terminal domain are present on surface-exposed loops, indicating a role for epitope selection in evolution of these genes; (2) the 29 nucleotides surrounding the splice acceptor site are absolutely conserved in all eight 117 VSG genes; (3) numerous insertion/deletion mutations are located within or immediately downstream of the C-terminal protein-coding sequences: (4) within 500 by downstream of the insertion/deletion mutations are one or two copies of a repeat motif highly homologous to the recombinogenic 76-bp repeat sequences present upstream of many VSG basic copy genes and the expression-linked copy.
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    Evolution of disintegrin cysteine-rich and mammalian matrix-degrading metalloproteinases: Gene duplication and divergence of a common ancestor rather than convergent evolution (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 263-269 
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    ISSN: 1432-1432
    Keywords: Metalloproteinase ; Disintegrin ; Evolution ; Venom ; Phylogeny ; Gene duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The evolution of the Metalloproteinase Disintegrin Cysteine-rich (MDC) gene family and that of the mammalian Matrix-degrading Metalloproteinases (MMPs) are compared. The alignment of snake venom and mammalian MDC and MMP precursor sequences generated a phylogenetic tree that grouped these proteins mainly according to their function. Based on this observation, a common ancestry is suggested for mammalian and snake venom MDCs; it is also possible that gene duplication of the already-assembled domain structure, followed by divergence of the copies, may have significantly contributed to the evolution of the functionally diverse MDC proteins. The data also suggest that the structural resemblance of the zinc-binding motif of venom MDCs and MMPs may best be explained by common ancestry and conservation of the proteolytic motifs during the divergence of the proteins rather than through convergent evolution.
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    The puzzle of the Krebs citric acid cycle: Assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 293-303 
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    ISSN: 1432-1432
    Keywords: Krebs cycle ; Evolution ; Metabolism ; Citric acid cycle ; Chemical design
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The evolutionary origin of the Krebs citric acid cycle has been for a long time a model case in the understanding of the origin and evolution of metabolic pathways: How can the emergence of such a complex pathway be explained? A number of speculative studies have been carried out that have reached the conclusion that the Krebs cycle evolved from pathways for amino acid biosynthesis, but many important questions remain open: Why and how did the full pathway emerge from there? Are other alternative routes for the same purpose possible? Are they better or worse? Have they had any opportunity to be developed in cellular metabolism evolution? We have analyzed the Krebs cycle as a problem of chemical design to oxidize acetate yielding reduction equivalents to the respiratory chain to make ATP. Our analysis demonstrates that although there are several different chemical solutions to this problem, the design of this metabolic pathway as it occurs in living cells is the best chemical solution: It has the least possible number of steps and it also has the greatest ATP yielding. Study of the evolutionary possibilities of each one-taking the available material to build new pathways-demonstrates that the emergence of the Krebs cycle has been a typical case of opportunism in molecular evolution. Our analysis proves, therefore, that the role of opportunism in evolution has converted a problem of several possible chemical solutions into asingle-solution problem, with the actual Krebs cycle demonstrated to be the best possible chemical design. Our results also allow us to derive the rules under which metabolic pathways emerged during the origin of life.
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    Comment on E. Broda's recent publications (1976)
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    Journal of molecular evolution 8 (1976), S. 387-388 
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    ISSN: 1432-1432
    Keywords: Nitrate Respiration ; Fermentation ; Energy Metabolism ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary E. Broda's recent argument against our concept that nitrate respiration antedated oxygen respiration is criticized.
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    Evolutionary divergence and length of repetitive sequences in sea urchin DNA (1976)
    Springer
    Journal of molecular evolution 9 (1976), S. 1-23 
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    ISSN: 1432-1432
    Keywords: Evolution ; Repetitive DNA ; SI Nuclease ; Sequence Organization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The organization of repetitive and single copy DNA sequences in sea urchin DNA has been examined with the single strand specific nuclease Sl fromAspergillus. Conditions and levels of enzyme were established so that single strand DNA was effectively digested while reassociated divergent repetitive duplexes remained enzyme resistant. About 25% of sea urchin DNA reassociates with repetitive kinetics to form Sl resistant duplexes of two distinct size classes derived from long and short repetitive sequences in the sea urchin genome. Fragments 2,000 nucleotides long were reassociated to Cot 20 and subjected to controlled digestion with Sl nuclease. About half of the resistant duplexes (13% of the DNA) are short, with a mode size of about 300 nucleotide pairs. This class exhibits significant sequence divergence, and principally consists of repetitive sequences which were interspersed with single copy sequences. About one-third of the long duplexes (4% of the DNA) are reduced in size after extensive Sl nuclease digestion to about 300 nucleotide pairs. About two-thirds of the long resistant duplexes (8% of the DNA) remains long after extensive SI nuclease digestion. These long reassociated duplexes are precisely base paired. The short duplexes are imprecisely paired with a melting temperature about 9°C below that of precisely paired duplexes of the same length. The relationship between length of repetitive duplex and precision of repetition is confirmed by an independent method and has been observed in the DNA of a number of species over a wide phylogenetic area.
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    The evolution of muscular parvalbumins investigated by the maximum parsimony method (1977)
    Springer
    Journal of molecular evolution 9 (1977), S. 131-158 
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    ISSN: 1432-1432
    Keywords: Parvalbumins ; Evolution ; Maximum parsimony ; Troponin-C ; Myosin alkali light chain
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Phylogenetic trees requiring the lowest sum of nucleotide replacements and gene duplicative events were constructed from the amino acid sequence data on ten gnathostome parvalbumins (PAR) and two related myofibrillar proteins troponin-C (TNC) and myosin alkali-light-chain (ALC). The origin and differentiation of the structural domains within these proteins were also investigated by the maximum parsimony method and by an alignment statistic for identifying evolutionarily related protein sequences. The results suggest, in agreement with the Weeds-McLachlan model, that tandem duplications in a precursor gene caused a primordial one-domain polypeptide (consisting of two helices with a calcium binding region in between) to double and then quadruple in size. Duplications of the gene coding for this four domain (I–II–III–IV) protein in an early metazoan, pre-gnathostome lineage gave rise to the separate loci for TNC, ALC, and PAR. TNC, which alone retained the Ca-binding function in each of its four domains, evolved much more slowly than either the ALC or PAR lineages. In the PAR lineage the I–II–III–IV structure was degraded, presumably by a partial gene deletion, to the II–III–IV structure during descent to the gnathostome ancestor of parvalbumins. Also during this period the mid region in domain II lost its Ca-binding function and, as it did so, evolved at an accelerated rate over other regions, a pattern indicative of positive selection for a change in function. In turn, from the gnathostome ancestor to the present, the mid regions of domains III and IV, which each retained Ca-bindung function, evolved much more slowly than other regions, a pattern indicative of stabilizing selection for preservation of function. Between the gnathostome and teleost-tetrapod ancestor a gene duplication separated the parvalbumins into anα-lineage and aβ-lineage. During this early vertebrate period PAR genes evolved at the extremely fast rate of 89 nucleotide replacements per 100 codons per 108 years (i.e. 89 NR %), but from the teleost-tetrapod ancestor to the present, bothα- andβ-PAR lineages evolved at a much slower rate, about 8 NR %. The use ofβ-parvalbumins as phylogenetic markers was complicated by presumptive evidence that paralogous (i.e. duplication dependent) gene lineages occur within this group. As a final point, in the genealogy of TNC, ALC, and PAR lineages, a non-random pattern of nucleotide replacements was observed between the reconstructed ancestral and descendant mRNA sequences. The pattern was similar to that observed for other protein genealogies and seems to reflect a bias in the genetic code for guanine to adenine and adenine to guanine transitions (especially at the first nucleotide position of the RNA codons) to produce amino acid substitutions which are compatible with the preservation of protein three-dimensional structure.
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    Sequence simplicity and evolution of the 3′ untranslated region of the histone H1° Gene (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 125-134 
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    ISSN: 1432-1432
    Keywords: Histone H1° ; 3′ untranslated region ; Slippage ; Sequence simplicity ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The H1° gene has a long 3′ untranslated region (3′UTR) of 1,125 nucleotides in the rat and 1,310 in humans. Analysis of the sequences shows that they have features of simple DNA that suggest involvement of replication slippage in their evolution. These features include the length imbalance between the rat and human sequences; the abundance of single-base repeats, two-base runs and other simple motifs clustered along the sequence; and the presence of single-base repeat length polymorphisms in the rat and mouse sequences. Pairwise comparisons show numerous short insertions/deletions, often flanked by direct repeats. In addition, a proportion of short insertions/deletions results from length differences in conserved single-base repeats. Quantification of the sequence simplicity shows that simple sequences have been more actively incorporated in the human lineage than in the rodent lineage. The combination of insertions/deletions and nucleotide substitutions along the sequence gives rise to three main regions of homology: a highly variable central region flanked by more conserved regions nearest the coding region and the polyA addition site.
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    The architecture of 5S rRNA and its relation to function (1975)
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    Journal of molecular evolution 6 (1975), S. 61-76 
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    ISSN: 1432-1432
    Keywords: 5S ribosomal RNA ; Translation ; Evolution ; Molecular Architecture ; Conformational Changes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary An extensive comparative analysis of the available primary sequence data on 5S rRNA has been made. A universal secondary structure is presented for procaryotic 5S rRNA which contains four helical regions. Eucaryotic 5S rRNAs are found to have only three of these helices and thus have a somewhat different architecture. In addition, a highly conserved segment of more than thirty nucleotides is identified in the 5′ half of the procaryotic molecule. This segment includes the oligonucleotide-CGAAC- which presumably binds to the t-RNA “common” sequence-GTΨCG-. Among the eucaryotes, the plants display a procaryotic nature in this region, but no eucaryote has the sequence -CGAAC- in this segment. A functional role for the procaryotic 5S rRNA molecule is discussed in which it is envisioned to undergo conformational change, i.e., coiling and uncoiling of one of the helices, which can result in a cyclic interaction of the 5S rRNA molecule with two t-RNA molecules. A general principle also emerges: the natural rotational motion inherent in coiling and uncoiling of nucleic acid helices can be converted quite simply to linear mechanical motion.
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    Mutagenic topography of theE. Coli chromosome (1975)
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    Journal of molecular evolution 5 (1975), S. 279-290 
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    ISSN: 1432-1432
    Keywords: E.coli ; Mutagenesis ; Evolution ; Gene Transposition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The lactose fermenting genes inE.coli have been transposed to various chromosomal locations. The bacterial strains were mutagenized with different chemical mutagens and the frequency of Lac negative mutant colonies was measured as a function of lactose gene location in the chromosome. There appears to be a highly mutable location between 58–60 minutes on theE.coli map. This region does not appear to be correlated with the origin of DNA replication or with the terminus. The possible significance of this mutable region in the evolution of new bacterial genes is discussed.
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    Sequence characterization of 5S ribosomal RNA from eight gram positive procaryotes (1976)
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    Journal of molecular evolution 8 (1976), S. 143-153 
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    ISSN: 1432-1432
    Keywords: 5S rRNA ; Comparative Analysis ; Secondary Structure ; Evolution ; Tuned Helix
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The available comparative data on procaryotic 5S rRNA was extended through sequencing studies of eight gram positive procaryotes. Complete nucleotide sequences were presented for 5S rRNA fromBacillus subtilis, B. firmus, B.pasteurii, B.brevis, Lactobacillus brevis andStreptococcus faecalis. In addition, 5S rRNA oligonucleotide catalogs and partial sequence data were provided forB.cereus andSporosarcina ureae. These sequences and catalogs were discussed in terms of known features of procaryotic 5S rRNA architecture.
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    Organization and evolution of the mitochondrial genome of yeast (1976)
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    Journal of molecular evolution 9 (1976), S. 25-35 
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    ISSN: 1432-1432
    Keywords: Genome organization ; Evolution ; Mitochondria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The mitochondrial genome of yeast (S. cerevisiae orS. carlsbergensis) appears to be formed by 60–70 genetic units, each one of which is formed by (1) a GC-rich sequence, possibly having a regulatory role; (2) a gene, and (3) an AT-rich spacer, which probably is not transcribed. Recombination in this genome appears to underlie a number of important phenomena. The organization of the mitochondrial genome of yeast and these recombinational events are discussed in relationship with the organization and evolution of the nuclear genome of eukaryotes.
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    Primitive haemoglobin (1977)
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    Journal of molecular evolution 9 (1977), S. 343-347 
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    ISSN: 1432-1432
    Keywords: Evolution ; Haemoglobin ; Cooperativity ; Lamprey ; Maximum parsimony
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The sequences ofPetromyzon andAplysia globins are compared with the postulated vertebrate and mollusc-vertebrate ancestors to see if differences exist in the rates of evolution of different types of residue positions. Between the mollusc-vertebrate ancestor andAplysia globin there is no very striking pattern of changes except that the interior positions are relatively conserved. In the evolution ofPetromyzon haemoglobin, theα 1 β 2 contact area is relatively conserved. The homopolymeric binding of lamprey Hb seems to be a primitive function.
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    A comment on methanogenic bacteria and the primitive ecology (1977)
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    Journal of molecular evolution 9 (1977), S. 369-371 
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    ISSN: 1432-1432
    Keywords: Methanogenic bacteria ; Primitive atmosphere ; Evolution ; Ecology ; Methane-carbon dioxide cycle
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The phenotype and antiquity of methanogenic bacteria suggest them to have been one of the major factors determining a dynamic balance between CO2 and CH4 in the primitive atmosphere.
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    Partial enzyme digestion studies onescherichia coli, pseudomonas, chlorella, drosophila, HeLa and yeast 5S RNAs support a general class of 5S RNA models (1977)
    Springer
    Journal of molecular evolution 10 (1977), S. 77-86 
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    ISSN: 1432-1432
    Keywords: Ribosome ; 5S RNA ; Conformation ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Fox and Woese (1975a) have shown that a model of 5S RNA secondary structure similar to the one originally derived forChlorella 5S RNA can be generalized with relatively minor variations to all sequenced 5S RNA molecules, i.e. that corresponding base paired regions can be formed at approximately the same positions. We present experimental data in favour of this hypothesis and show that the points at which ribonucleases T1, T2 and pancreatic ribonuclease cleave six different 5S RNA molecules under ‘mild’ conditions (high ionic strength, low temperature, low RNAase concentration) nearly always fall in the proposed single-stranded regions. We conclude that this model is a good approximation to the conformation of 5S RNA in solution.
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    Evolutionary changes ofα-crystallin and the phylogeny of mammalian orders (1977)
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    Journal of molecular evolution 10 (1977), S. 123-135 
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    ISSN: 1432-1432
    Keywords: Ancestral sequence ; Eye lens protein ; Evolution ; Phylogenetic tree
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The sequences of the A chains of the eye lens proteinα-crystallin from seventeen mammalian species were compared. They showed a generally slow rate of evolution, but with marked variations in different lineages. Most substitutions have occurred in the C-terminal part of the chain, which probably forms part of the surface of theα-crystallin aggregate. The ancestral sequence method of Dayhoff revealed interesting indications about the phylogenetic relationships between the eleven mammalian orders that were represented by the investigated species. Most evident was the divergence of marsupial and placental orders. A notable resemblance between the hyrax and elephant sequences was observed, setting them apart from the ungulates, including whale. Primates, rodents, lagomorphs, insectivores and tupaiids seem to derive from a common stem group. These phylogenetic inferences are discussed in relation to current palaeontological and taxonomical opinions, and compared to evidence from other protein sequence data.
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    Amino acid-directed nucleic acid synthesis (1978)
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    Journal of molecular evolution 11 (1978), S. 109-120 
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    ISSN: 1432-1432
    Keywords: Origin of Life ; Genetic code ; Protein synthesis ; Evolution ; Prebiotic reactions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The fact that proteins contain onlya-amino acids and that protein structure is determined by 3′ → 5′ linked ribonucleotides is postulated to be the result of the copolymerization of these molecules in the prebiotic environment. Ribonucleotides therefore represent partial degradation products and proteins represent a side reaction developing from copolymerization. The basic structural unit of copolymerization is a nucleotide substituted with an amino acid at the 2′ position. Characteristics of modern amino and ribonucleic acid structure are all consistent with and necessary for this hypothesis. The characteristics and individual base assignments of the code also provide strong support for origin from the postulated copolymers. All characteristics of the code can be accounted for by this single hypothesis.
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    A measure of the denseness of a phylogenetic network (1978)
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    Journal of molecular evolution 11 (1978), S. 225-231 
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    ISSN: 1432-1432
    Keywords: Phylogenetic denseness ; Phylogenetic trees ; Topology ; Molecular reconstructions ; Evolution ; Paleogenetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The concept of phylogenetic denseness bears critically on the accuracy of evolutionary pathways inferred from experimentally sequenced proteins isolated from extant species. In this paper I develop an objective measure,ρ, of denseness to supplement previous intuitive concepts and which permits one to use this concept in comparing the quality of different evolutionary reconstructions. This measure is used to examine several published phylogenetic trees: insulin, a-hemoglobin,β-hemoglobin, myoglobin, cytochromec, and the parvalbumin family. The paper emphasizes 1) the importance of denseness in accurately estimating the number of nucleotide replacements which separate homologous sequences when this estimation is made by the method of parsimony, 2) the value of this concept in assessing the quality of those estimates, and 3) the use of this concept as a biologically practical heuristic method for identifying poorly studied regions in a phylogenetic tree, whether or not the tree was obtained by the parsimony method.
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    A proposal concerning the origin of life on the planet earth (1979)
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    Journal of molecular evolution 13 (1979), S. 95-101 
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    ISSN: 1432-1432
    Keywords: Oparin Ocean ; Origin of Life ; Evolution ; Runaway greenhouse ; Photosynthesis ; Methanogenesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The widely accepted Oparin thesis for the origin and early evolution of life seems sufficiently far from the true state of affairs as to be considered incorrect. It is proposed that life on earth actually arose in the planet's atmosphere, however an atmosphere very different from the present one. Because of an extremely warm surface, the early earth may have possessed no liquid surface water, its water being partitioned between a molten crust and a fairly dense atmosphere. Early preliving systems are taken to arise in the droplet phase in such an atmosphere. The early earth, which resembled Venus then and to some extent now, underwent a transition to its present condition largely as a result of the evolution of methanogenic metabolism.
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    Endosymbionts and mitochondrial origins (1977)
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    Journal of molecular evolution 10 (1977), S. 93-96 
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    ISSN: 1432-1432
    Keywords: Evolution ; Endosymbiosis ; Mitochondrion ; Photosynthetic
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    Topics: Biology
    Notes: Summary The possibility is put forth that the mitochondrion did not originate from an endosymbiosis, 1–2 billion years ago, involving an aerobic bacterium. Rather, it arose by endosymbiosis in a much early, anaerobic period, and was initially a photosynthetic organelle, analogous to the modern chloroplast. This suggestion arises from a reconsideration of the nature of endosymbiosis. It ex-plains the remarkable diversity in mitochondrial information storage and processing systems.
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    Insect lysozymes from three species of lepidoptera: Their structural relatedness to the c (chicken) type lysozyme (1979)
    Springer
    Journal of molecular evolution 14 (1979), S. 267-271 
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    ISSN: 1432-1432
    Keywords: Lysozyme ; Insect ; Lepidoptera ; Evolution ; Sequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Sequence studies of the N-terminal halves of the lysozymes isolated fromBombyx mori, Galleria mellonella andSpodoptera littoralis (Lepidoptera) allow us to classify these enzymes among the c (chicken) type lysozymes.
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    Evolution of methionine initiator and phenylalanine transfer RNAs (1979)
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    Journal of molecular evolution 14 (1979), S. 287-300 
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    ISSN: 1432-1432
    Keywords: Phenylalanine tRNA ; Methionine initiator tRNA ; Evolution ; Mutations ; Conformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Sequence data from methionine initiator and phenylalanine transfer RNAs were used to construct phylogenetic trees by the maximum parsimony method. Although eukaryotes, prokaryotes and chloroplasts appear related to a common ancestor, no firm conclusion can be drawn at this time about mitochondrial-coded transfer RNAs. tRNA evolution is not appropriately described by random hit models, since the various regions of the molecule differ sharply in their mutational fixation rates. ‘Hot’ mutational spots are identified in the TψC, the amino acceptor and the upper anticodon stems; the D arm and the loop areas on the other hand are highly conserved. Crucial tertiary interactions are thus essentially preserved while most of the double helical domain undergoes base pair interchange. Transitions are about half as costly as transversions, suggesting that base pair interchanges proceed mostly through G-U and A -C intermediates. There is a preponderance of replacements starting from G and C but this bias appears to follow the high G + C content of the easily mutated base paired regions.
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    Investigating hypothetical products from noncoding frames (HyPNoFs) (1995)
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    Journal of molecular evolution 40 (1995), S. 570-577 
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    ISSN: 1432-1432
    Keywords: Alternate reading frames ; Evolution ; Overlapping frames ; Homology search ; Primary sequence analysis ; Polycistronic genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Hypothetical Products from Noncoding Frames (i.e., HyPNoFs) are hypothetical, not-coded proteins, translated from alternate reading frames (i.e., coding+1 and coding+2) of cDNAs. HyPNoFs of CD4, PKC, oncostatin, bcl-2 proto-oncogene, tumor suppressor p53, cystic fibrosis transmembrane regulator (CFTR), and tumor necrosis factors a and β were searched as query sequences vs the SWISS-PROT data bank. Homology searches carried out revealed that hypothetical products (i.e., HyPNoFs) may share high similarity with real protein products actually coded. Sequence similarity of hypothetical products to real proteins is sometimes very high, suggesting common conformational features, according to the Sander and Schneider cutoff value. This finding supports the hypothesis that eukaryotic DNA, currently considered to be monocistronic, might occasionally have polycistronic regions, carrying different protein messages on overlapping frames. As yet, polycistronic genes have been observed in viral genomes only. The presence of polycistronic regions in eukaryotic genes is likely reminiscent of an ancient strategy, rather than a present feature of the genome in eukaryotes. These data suggest that thorough investigation of HyPNoFs is likely to improve our ability to trace genes' evolution and to investigate structure-function relationships of protein and DNA sequences.
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    Evolution of protamine P1 genes in mammals (1995)
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    Journal of molecular evolution 40 (1995), S. 601-607 
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    ISSN: 1432-1432
    Keywords: Prolamine ; Sperm proteins ; Evolution ; Mammals
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Prolamine P1 genes have been sequenced following PCR amplification from 11 mammals representing five major mammalian orders: Rodentia (rat and guinea pig), Carnivora (cat and bear), Proboscidea (elephant), Perissodactyla (horse), and Artiodactyla (camel, deer, elk, moose, and gazelle). The predicted amino acid sequence for these genes together with previously reported sequences results in a data set of 25 different P1 genes and 30 different P1 amino acid sequences. The alignment of all these sequences reveals that prolamines are amongst the most rapidly diverging proteins studied. In spite of the large number of differences there are conserved motifs that are also common to birds such as the N-terminal ARYR followed by the triple alternating SRSRSR phosphorylation site. The central region contains 3 arginine clusters consisting of 5–6 arginines each. The C-terminus appears to be the most variable region of the protamines. Overall the molecular evolution of P1 genes is in agreement with the expected species evolution supporting that these genes have evolved vertically.
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    The molecular cloning of a phospholipase A2 from Bothrops jararacussu snake venom: Evolution of venom group II phospholipase A2's may imply gene duplications (1995)
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    Journal of molecular evolution 41 (1995), S. 174-179 
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    ISSN: 1432-1432
    Keywords: Snake venom ; Bothrops ; Phospholipase ; Myotoxin ; Evolution ; cDNA ; Gene duplication ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The sequence coding for a snake venom phospholipase A2 (PLA2), BJUPLA2, has been cloned from a Bothrops jararacussu venom gland cDNA library. The cDNA sequence predicts a precursor containing a 16-residue signal peptide followed by a molecule of 122 amino acid residues with a strong sequence similarity to group II snake venom PLA2's. A striking feature of the cDNA is the high sequence conservation of the 5′ and 3′ untranslated regions in cDNAs coding for PLA2's from a number of viper species. The greatest sequence variation was observed between the regions coding for the mature proteins, with most substitutions occurring in nonsynonymous sites. The phylogenetic tree constructed by alignment of the amino acid sequence of BJUPLA2 with group II PLA2's in general groups them according to current taxonomical divisions and/or functional activity. It also suggests that gene duplications may have occurred at a number of different points during the evolution of snake venom group II PLA2's.
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    Phylogenetic position of Dictyostelium inferred from multiple protein data sets (1995)
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    Journal of molecular evolution 41 (1995), S. 238-246 
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    ISSN: 1432-1432
    Keywords: Cellular slime molds ; Animals ; Fungi ; Plantae ; Maximum-likelihood method ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The phylogenetic position of Dictyostelium inferred from 18S rRNA data contradicts that from protein data. Protein trees always show the close affinity of Dictyostelium with animals, fungi, and plants, whereas in 18S rRNA trees the branching of Dictyostelium is placed at a position before the massive radiation of protist groups including the divergence of the three kingdoms. To settle this controversial issue and to determine the correct position of Dictyostelium, we inferred the phylogenetic relationship among Dictyostelium and the three kingdoms Animalia, Fungi, and Plantae by a maximum-likelihood method using 19 different protein data sets. It was shown at the significance level of 1 SE that the branching of Dictyostelium antedates the divergence of Animalia and Fungi, and Plantae is an outgroup of the Animalia-Fungi-Dictyostelium clade.
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    The β-tubulin gene family evolution in theDrosophila montium subgroup of themelanogaster species group (1995)
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    Journal of molecular evolution 41 (1995), S. 293-298 
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    ISSN: 1432-1432
    Keywords: β-tubulin ; Evolution ; Gene cluster ; Gene dispersion ; Drosophila montium subgroup
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The β1-, β2-, and β3-tubulin genes have been mapped by in situ hybridization on the polytene chromosomes of 11 selected species (15 strains) belonging to theDrosophila montium subgroup. Although the hybridization pattern among the strains of the same species does not differ, this pattern is significantly different among the species. The β-tubulin genes in themontium subgroup seem to be organized in a cluster, or in a semi-cluster, or are completely dispersed. The clustered arrangement is found in the North-Oriental sibling speciesD. auraria, D. triauraria, andD. quadraria. The semi-clustered arrangement, wherein the β1 and β2 genes are located at the same locus while β3 is at a different one, appears in the South-Oriental speciesD. bicomuta, D. serrata, andD. birchii, as well as in the Afrotropical speciesD. diplacantha andD. seguyi. The complete separation of the genes is observed in the Indian speciesD. kikkawai andD. jambulina and in the Afrotropical speciesD. vulcana. Based on the above results, a possible mode of evolution of the β-tubulin genes in the montium subgroup is attempted. In addition, phylogenetic relationships among themontium species are discussed.
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    The β-tubulin gene family evolution in the Drosophila montium subgroup of the melanogaster species group (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 293-298 
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    ISSN: 1432-1432
    Keywords: β-tubulin ; Evolution ; Gene cluster ; Gene dispersion ; Drosophila montium subgroup
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The β1-, β2-, and β3-tubulin genes have been mapped by in situ hybridization on the polytene chromosomes of 11 selected species (15 strains) belonging to the Drosophila montium subgroup. Although the hybridization pattern among the strains of the same species does not differ, this pattern is significantly different among the species. The β-tubulin genes in the montium subgroup seem to be organized in a cluster, or in a semi-cluster, or are completely dispersed. The clustered arrangement is found in the North-Oriental sibling species D. auraria, D. triauraria, and D. quadraria. The semi-clustered arrangement, wherein the β1 and β2 genes are located at the same locus while β3 is at a different one, appears in the South-Oriental species D. bicomuta, D. serrata, and D. birchii, as well as in the Afrotropical species D. diplacantha and D. seguyi. The complete separation of the genes is observed in the Indian species D. kikkawai and D. jambulina and in the Afrotropical species D. vulcana. Based on the above results, a possible mode of evolution of the β-tubulin genes in the montium subgroup is attempted. In addition, phylogenetic relationships among the montium species are discussed.
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    Molecular and phylogenetic analysis of PCR-amplified cyclin-dependent kinase (CDK) family sequences from representatives of the earliest available lineages of eukaryotes (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 407-413 
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    ISSN: 1432-1432
    Keywords: Giardia ; Trichomonas ; CDK ; CDC ; Unicellular ; Metazoa ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Cyclin-dependent kinase (CDK) and cell division control (CDC2) sequences are strongly conserved among eukaryotes and may complement the use of other sequence families in eukaryotic phylogenetic inference. We synthesized degenerate PCR primers to amplify the catalytic region of CDK homologs in representatives of the earliest available lineages of eukaryotes. CDK family sequence-based, maximum-likelihood distance measurements with neighbor joining, and Fitch-Margoliash least-squares analyses produced unrooted dendrograms that included protists, yeasts, and higher eukaryotes. Bootstrap confidence estimates supported CDK-based phylogenetic groupings among the protists, fungi, and vertebrates although resolution within these groups was often insignificant. However, Trichomonas vaginalis and Giardia lamblia exhibited two of the most divergent CDK-like sequences consistent with rRNA-phylogenetic inference of early divergence of these eukaryotic lineages. In the evolution from unicellular to multicellular organisms, a constellation of amino acid residues aligning with the human, CDK N-terminal β sheet may have undergone abrupt replacement.
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    Evolutionary relationships of the carbamoylphosphate synthetase genes (1995)
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    Journal of molecular evolution 41 (1995), S. 813-832 
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    ISSN: 1432-1432
    Keywords: Phylogeny ; Evolution ; Carbamoylphosphate synthetase ; Dihydroorotase ; Aspartate transcarbamoylase ; Intron ; Exon ; Arginine biosynthesis ; Pyrimidine biosynthesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Carbamoylphosphate is a common intermediate in the metabolic pathways leading to the biosynthesis of arginine and pyrimidines. The amino acid sequences of all available proteins that catalyze the formation of carbamoylphosphate were retrieved from Genbank and aligned to estimate their mutual phylogenetic relations. In gram-negative bacteria carbamoylphosphate is synthesized by a two-subunit enzyme with glutamiriase and carbamoylphosphate synthetase (CPS) activity, respectively. In gram-positive bacteria and lower eukaryotes this two-subunit CPS has become dedicated to arginine biosynthesis, while in higher eukaryotes the two subunits fused and subsequently lost the glutaminase activity. The CPS dedicated to pyrimidine synthesis is part of a multifunctional enzyme (CPS II), encoding in addition dihydroorotase and aspartate transcarbamoylase. Evidence is presented to strengthen the hypothesis that the two “kinas” subdomains of all CPS isozymes arose from a duplication of an ancestral gene in the progenote. A further duplication of the entire CPS gene occurred after the divergence of the plants and before the divergence of the fungi from the eukaryotec root, generating the two isoenzymes involved in either the synthesis of arginine or that of pyrimidines. The mutation rate was found to be five- to tenfold higher after the duplication than before, probably reflecting optimization of the enzymes for their newly acquired specialized function. We hypothesize that this duplication arose from a need for metabolic channeling for pyrimidine biosynthesis as it was accompanied by the tagging of the CPS gene with the genes for dihydroorotase and aspartate transcarbamoylase, and as the duplication occurred independently also in gram-positive bacteria. Analysis of the exon-intron organization of the two “kinase” subdomains in CPS I and II suggests that ancient exons may have comprised approx. 19 amino acids, in accordance with the prediction of the “intron-early” theory.
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    URL: http://dx.doi.org/10.1007/BF00173161
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    Molecular evolution of genes encoding ribonucleases in ruminant species (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 850-858 
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    ISSN: 1432-1432
    Keywords: Ribonuclease ; Gene duplication ; Evolution ; Ruminants
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Phylogenetic analysis, based on the primary structures of mammalian pancreatic-type ribonucleases, indicated that gene duplication events, which occurred during the evolution of ancestral ruminants, gave rise to the three paralogous enzymes present in the bovine species. Herein we report data that demonstrate the existence of the orthologues of the bovine pancreatic, seminal, and cerebral ribonucleases coding sequences in the genomes of giraffe and sheep. The “seminal” sequence is a pseudogene in both species. We also report an analysis of the transcriptional expression of ribonuclease genes in sheep tissues. The data presented support a model for positive selection acting on the molecular evolution of ruminant ribonuclease genes.
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    URL: http://dx.doi.org/10.1007/BF00173164
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    Procaryote phylogeny IV: Concerning the phylogenetic status of a photosynthetic bacterium (1975)
    Springer
    Journal of molecular evolution 5 (1975), S. 25-34 
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    ISSN: 1432-1432
    Keywords: Rhodopseudomonas spheroides ; 16S Ribosomal RNA ; T1 Ribonuclease Digest ; Phylogeny ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The 16S ribosomal RNA (30S subunit) ofRhodopseudomonas spheroides has been characterized in terms of T1 ribonuclease digestion products. This “fingerprint” ultimately permits the placement ofR. spheroides into a detailed procaryotic phylogenetic tree. Given the number of major procaryotic lines that have been characterized in these terms to date, one can tentatively place the Athiorhodaceae closer to the Vibrio-Enteric group than to the Bacillaceae or Cyanophyta.
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    URL: http://dx.doi.org/10.1007/BF01732011
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    The nucleotide sequence of the 5S ribosomal RNA from a photobacterium (1975)
    Springer
    Journal of molecular evolution 5 (1975), S. 35-46 
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    ISSN: 1432-1432
    Keywords: Photobacter Strain 8265 ; 5S Ribosomal RNA ; Primary Structure ; Comparative Characterization ; Evolution ; Energetically Constrained Helix
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Comparative sequencing studies provide powerful insights into molecular function and evolution. The sequence for 5S ribosomal RNA from Photobacter strain 8265 is eighteen base replacements removed from that ofEscherichia coli. Of these, the vast majority involve a G or C becoming an A or U. These variations also define unequivocally a hexanucleotide base paired region, which appears to be a universal feature of the 5S RNA molecule. The base composition of this helix seems to be under rather stringent, and so unusual, energetic constraints. The possible implications of this are discussed - in particular the prospect of a 5S RNA molecule that undergoes conformational transitions as a part of the overall state changes that constitute the function of the ribosome.
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    URL: http://dx.doi.org/10.1007/BF01732012
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    Sequence ofDrosophila 5S RNA synthesized by cultured cells and by the insect at different developmental stages (1977)
    Springer
    Journal of molecular evolution 9 (1977), S. 279-298 
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    ISSN: 1432-1432
    Keywords: 5S RNA ; Drosophila ; Evolution ; Secondary structure ; Development
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The nucleotide sequence ofDrosophila melanogaster 5S RNA has been determined and appears to be homogeneous both in the KC cell line and in the insect at different developmental stages. Experimental evidence on the conformation of this molecule is in agreement with a general class of 5S RNA models.
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    URL: http://dx.doi.org/10.1007/BF01796116
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    An ancient divergence among the bacteria (1977)
    Springer
    Journal of molecular evolution 9 (1977), S. 305-311 
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    ISSN: 1432-1432
    Keywords: Comparative cataloging ; Methanogenic bacteria ; Phylogeny ; 16S ribosomal RNA ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The 16S ribosomal RNAs from two species of methanogenic bacteria, the mesophileMethanobacterium ruminantium and the thermophileMethanobacterium thermoautotropbicum, have been characterized in terms of the oligonucleotides produced by digestion withT 1 ribonuclease. These two organisms are found to be sufficiently related that they can be considered members of the same genus or family. However, they bear only slight resemblance to “typical” Procaryotic genera; such asEschericbia, Bacillus andAnacystis. The divergence of the methanogeinc bacteria from other bacteria may be the most ancient phylogenetic event yet detected — antedating considerably the divergence of the blue green algal line for example, from the main bacterial line.
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    URL: http://dx.doi.org/10.1007/BF01796092
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    Chemical and physical microenvironments at the Viking landing sites (1979)
    Springer
    Journal of molecular evolution 14 (1979), S. 13-31 
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    ISSN: 1432-1432
    Keywords: Mars ; Evolution ; Planetary geochemistry ; Soil ; Ionizing radiation ; Exobiology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Physical and chemical considerations permit the division of the near-surface regolith on Mars into at least six zones of distinct microenvironments. The zones are euphotic, duricrust/peds, tempofrost, permafrost, endolithic, and interfacial/transitional. Microenvironments vary significantly in temperature extremes, mean temperature, salt content, relative pressure of water vapor, UV and visible light irradiance, and exposure to ionizing radiation events (100 Mrad) and oxidative molecular species. From what is known of the chemistry of the atmossphere and regolith fines (soil), limits upon the aqueous chemistry of soil pastesmay be estimated. Heat of wetting could reach 45 cal/g dry soil; initial pH is indeterminate between 1 and 10; ionic strength and salinity are predicted to be extremely high; freezing point depression is inadequate to provide quantities of liquid water except in special cases. The prospects for biotic survival are grim by terrestrial standards, but the extremes of biological resiliency are inaccessible to evaluation. Second-generation in situ experiments which will better define Martian microenvironments are clearly possible. Antarctic dry valleys are approximations to Martian conditions, but deviate significantly by at least half-a-dozen criteria.
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    On the cysteine and cystine content of proteins (1977)
    Springer
    Journal of molecular evolution 10 (1977), S. 155-160 
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    ISSN: 1432-1432
    Keywords: Cysteine ; Cystine ; Protein ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Analysis of published data on the cysteine and half-cystine content of proteins indicates that most intracellular proteins may be classified as sulfhydryl proteins (those containing cysteine but little or no half-cystine) and that such sulf-hydryl proteins have a low cysteine content. The mean cysteine content found for 32 intracellular mammalian proteins was 1.6 % and intracellular proteins of many bacteria have similar or lower values. Extracellular mammalian proteins are primarily disulfide proteins (those containing half-cystine but little or no cysteine) and have a high half-cystine content, the mean value found for some 34 extracellular mammalian proteins being 4.1 %. This is contrasted with many of the extracellular proteins from facultative bacteria which are cyst(e)ine-free proteins, being lacking in both cysteine and half-cystine. These and related observations are interpreted in terms of the evolution of life in a reducing atmosphere and the subsequent transition to an oxidizing environment. It is suggested that disulfide proteins evolved primarily after the accumulation of oxygen in the atmosphere.
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    Searching tRNA sequences for relatedness to aminoacyl-tRNA synthetase families (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 482-486 
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    ISSN: 1432-1432
    Keywords: Aminoacyl-tRNA synthetase ; Computer analysis ; Evolution ; Genetic code ; tRNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract tRNA sequences were analyzed for sequence features correlated with known classes of aminoacyl-tRNA synthetase enzymes. The tRNAs were searched for distinguishing nucleotides anywhere in their sequences. The analyses did not find nucleotides predictive of synthetase class membership. We conclude that such nucleotides never existed in tRNA sequences or that they existed and were lost from many of the tRNA sequences during evolution.
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    URL: http://dx.doi.org/10.1007/BF00166616
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    Divergence of glutamate and glutamine aminoacylation pathways: Providing the evolutionary rationale for mischarging (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 476-481 
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    ISSN: 1432-1432
    Keywords: Aminoacylation ; Aminoacyl-tRNA synthetases ; tRNA ; GluRS ; GlnRS ; Glutamate ; Glutamine ; Evolution ; Mischarging
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Aminoacyl-tRNA for protein synthesis is produced through the action of a family of enzymes called aminoacyl-tRNA synthetases. A general rule is that there is one aminoacyl-tRNA synthetase for each of the standard 20 amino acids found in all cells. This is not universal, however, as a majority of prokaryotic organisms and eukaryotic organelles lack the enzyme glutaminyl-tRNA synthetase, which is responsible for forming Gln-tRNAGln in eukaryotes and in Gram-negative eubacteria. Instead, in organisms lacking glutaminyl-tRNA synthetase, Gln-tRNAGln is provided by misacylation of tRNAGln with glutamate by glutamyl-tRNA synthetase, followed by the conversion of tRNA-bound glutamate to glutamine by the enzyme Glu-tRNAGln amidotransferase. The fact that two different pathways exist for charging glutamine tRNA indicates that ancestral prokaryotic and eukaryotic organisms evolved different cellular mechanisms for incorporating glutamine into proteins. Here, we explore the basis for diverging pathways for aminoacylation of glutamine tRNA. We propose that stable retention of glutaminyl-tRNA synthetase in prokaryotic organisms following a horizontal gene transfer event from eukaryotic organisms (Lamour et al. 1994) was dependent on the evolving pool of glutamate and glutamine tRNAs in the organisms that acquired glutaminyl-tRNA synthetase by this mechanism. This model also addresses several unusual aspects of aminoacylation by glutamyl- and glutaminyl-tRNA synthetases that have been observed.
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    Structure, function and evolution of seryl-tRNA synthetases: Implications for the evolution of aminoacyl-tRNA synthetases and the genetic code (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 519-530 
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    ISSN: 1432-1432
    Keywords: Aminoacyl-tRNA synthetases ; tRNA ; Genetic code ; RNA world ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Two aspects of the evolution of aminoacyl-tRNA synthetases are discussed. Firstly, using recent crystal structure information on seryl-tRNA synthetase and its substrate complexes, the coevolution of the mode of recognition between seryl-tRNA synthetase and tRNAser in different organisms is reviewed. Secondly, using sequence alignments and phylogenetic trees, the early evolution of class 2 Amnoacyl-tRNA synthetases is traced. Arguments are presented to suggest that synthetases are not the oldest of protein enzymes, but survived as RNA enzymes during the early period of the evolution of protein catalysts. In this view, the relatedness of the current synthetases, as evidenced by the division into two classes with their associated subclasses, reflects the replacement of RNA synthetases by protein synthetases. This process would have been triggered by the acquisition of tRNA 3′ end charging activity by early proteins capable of activating small molecules (e.g., amino acids) with ATP. If these arguments are correct, the genetic code was essentially frozen before the protein synthetases that we know today came into existence. Correspondence to: S. Cusack
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    Differential homogenization and amplification of two satellite DNAs in the genus Cucurbita (Cucurbitaceae) (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 996-1005 
    Details
    ISSN: 1432-1432
    Keywords: Repetitive DNA ; Tandem repeats ; Sequence analysis ; Phylogenetic tree ; Silent repeats ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Two different satellite DNAs exist in the genus Cucurbita which are different with respect to repeat length (350 by and 170 bp), array size, and sequence homogenization. Whereas the 350-bp satellite DNA is prominent and very homogeneous in all species investigated except for C. maxima and C. lundelliana, the 170-bp satellite is rather evenly distributed in all species. In C. maxima and C. lundelliana the 350-bp satellite is present only in small amounts, but detectable by the sensitive PCR method. These repeats are also very homogeneous, reflecting a silent stage of satellite DNA. In contrast, the 170-bp satellite DNA is intra- and interspecifically heterogeneous. It is striking that the species with no detectable amount of 350-bp satellite contain 170-bp satellite DNA clusters with the highest degree of homogeneity. The evolution of satellite DNA repeats within cultivated and wild species in the genus Cucurbita is elucidated using the sequence data of both satellite DNAs from all species investigated. The value of satellite DNA for phylogenetic analysis between closely related species is discussed.
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    URL: http://dx.doi.org/10.1007/BF00173181
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    Simple repetitive DNA sequences from primates: Compilation and analysis (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 120-126 
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    ISSN: 1432-1432
    Keywords: Simple repetitive DNA ; Microsatellites ; Unstable triplets ; Database ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Simple repeats composed of tandemly repeated units 1–6 nucleotides (nt) long have been extracted from a selected set of primate genomic DNA sequences. Of the 501 theoretically possible, different types of repeats only 67 were present in the analyzed database in at least two different size ranges over 12 nt. They include all simple repeats known to be polymorphic in the primate genome. A list of moderately expanding and nonexpanding oligonucleotide patterns has also been included. Furthermore, we have compiled statistical data with emphasis on the overall variability of the most abundant 67 types of repeats. We have demonstrated that the expandability of at least some simple repeats may be affected by the overall base composition and by flanking sequences. In particular, the occurrence of tandemly repeated CAG and GCC triplets in exons positively correlates with their G+C content. We also noted that in the vicinity of Alu sequences tetrameric repeats are more abundant than in the total genomic DNA. This paper can be used as a comprehensive guide in identification of the most abundant and potentially polymorphic simple repeats. It is also of broader significance as a step toward understanding the contribution of flanking sequences and the overall sequence composition to variability of simple repeats.
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    URL: http://dx.doi.org/10.1007/BF00167107
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    Evolution of seed storage protein genes: Legumin genes of Ginkgo biloba (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 457-466 
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    ISSN: 1432-1432
    Keywords: Seed storage proteins ; Legumin ; Gene structure ; Evolution ; Gymnosperms ; Ginkgo biloba
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Legumin-like seed storage proteins have been intensively studied in crop plants. However, little is known about the molecular evolution of these proteins and their genes and it was assumed that they originated from an ancestral gene that already existed at the beginning of angiosperm evolution. We have evidence for the ubiquitous occurrence of homologous proteins in gymnosperms as well. We have characterized the major seed storage globulin from Ginkgo biloba by amino acid sequencing, which reveals clear homology to legumin-like proteins from angiosperms. The Ginkgo legumin is encoded by a gene family; we describe two of its members. The promoter regions contain sequence motifs which are known to function as regulatory elements involved in seed-specific expression of angiosperm legumins, although the tissues concerned are different in gymnosperms and angiosperms. The Ginkgo legumin gene structure is divergent from that of angiosperms and suggests that the evolution of legumin genes implicated loss of introns. From our data and from functional approaches recently described it becomes obvious that the posttranslational processing site of legumin precursors is less conserved than hitherto assumed. Finally, we present a phylogenetic analysis of legumin encoding sequences and discuss their utility as molecular markers for the reconstruction of seed plant evolution.
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    Polymorphism, monomorphism, and sequences in conserved microsatellites in primate species (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 492-497 
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    ISSN: 1432-1432
    Keywords: Primate ; Microsatellite ; Evolution ; Mutation process
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Dimeric short tandem repeats are a source of highly polymorphic markers in the mammalian genome. Genetic variation at these hypervariable loci is extensively used for linkage analysis, for the identification of individuals, and may be useful for interpopulation and interspecies studies. In this paper, we analyze the variability and the sequences of a segment including three microsatellites, first described in man, in several species of primates (chimpanzee, orangutan, gibbon, and macaque) using the heterologous primers (man primers). This region is located on the human chromosome 6p, near the tumor necrosis factor genes, in the major histocompatibility complex. The fact that these primers work in all species studied indicates that they are conserved throughout the different lineages of the two superfamilies, the Hominoidea and the Cercopithecidea, represented by the macaques. However, the intervening sequence displays intraspecific and interspecific variability. The sites of base substitutions and the insertion/ deletion events are not evenly distributed within this region. The data suggest that it is necessary to have a minimal number of repeats to increase the rate of mutation sufficiently to allow the development of polymorphism. In some species, the microsatellites present single base variations which reduce the number of contiguous repeats, thus apparently slowing the rate of additional slippage events. Species with such variations or a low number of repeats are monomorphic. These microsatellite sequences are informative in the comparison of closely related species and reflect the phylogeny of the Old World monkeys, apes, and man.
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    Phylogenetic relationships of nonaxenic filamentous cyanobacterial strains based on 16S rRNA sequence analysis (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 194-200 
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    ISSN: 1432-1432
    Keywords: Evolution ; Ribosomal RNA ; Cyanobacteria ; Leptolyngbya ; Oscillatoria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In order to determine the nearly complete 16S rRNA gene sequences of cyanobacteria originating from nonaxenic cultures, a cyanobacterium-specific oligonucleotide probe was developed to distinguish polymerase chain reaction (PCR) products of the cyanobacterial rRNA operons from those resulting from amplification of contaminating bacteria. Using this screening method the 16S rRNA genes of four nonaxenic filamentous cyanobacterial strains belonging to the generaLeptolyngbya andOscillatoria were cloned and sequenced. For the genusLeptolyngbya, the 16S rRNA sequence of the axenic strain PCC 73110 was also determined. Phylogenetic trees were constructed based on complete and partial sequences. The results show that the strainsLeptolyngbya foveolarum Komárek 1964/112,Leptolyngbya sp. VRUC 135 Albertano 1985/1, andLeptolyngbya boryanum PCC 73110 belong to the same cluster. StrainOscillatoria cf.corallinae SAG 8.92, which contains the rare photosynthetic pigment CU-phycoerythrin, is not closely related to other CU-phycoerythrin-containing cyanobacteria.Oscillatoria agardhii CYA 18, which is a representative of planktonicOscillatoria species that form toxic blooms in Norwegian inland waters, has no close relatives in the tree.
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    Visual pigment diversity in two genera of mantis shrimps implies rapid evolution (Crustacea; Stomatopoda) (1996)
    Springer
    Journal of comparative physiology 179 (1996), S. 371-384 
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    ISSN: 1432-1351
    Keywords: Visual pigment ; Stomatopoda ; Visual ecology ; Evolution ; Photoreceptor ; Retina
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract 1. Interspecific diversity in the visual pigments of stomatopod crustaceans was characterized using microspectrophotometry. We examined the 10 visual pigments in main rhabdoms in retinas of 3 species of each of two genera of stomatopod crustaceans of the superfamily Gonodactyloidea, Gonodactylus (G. oerstedii, G. aloha, and G. curacaoensis) and Odontodactylus (O. scyllarus, O. brevirostris, and O. “havanensis”). Species were selected to provide a matched diversity of habitats. 2. In each genus, visual pigments varied in λmax in several regions of the retina, as revealed by analysis of variance. The variation within closely related species of the same genus implies that visual pigments can evolve rapidly in stomatopods. 3. In photoreceptors of the peripheral retina, which are devoted to spatial vision, visual pigment λmax decreased as the depth range of the various species increased, a typical pattern for marine animals. In contrast, visual pigment λmax in photoreceptors of retinal regions devoted to polarization vision (midband Rows 5 and 6) is not obviously correlated with the spectral environment, implying that polarization information may be confined to particular spectral ranges. Visual pigments of the tiered rows of the midband, which are committed to spectral analysis, span a larger spectral range in shallow-water than deepwater species.
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    Olfactory receptors in aquatic and terrestrial vertebrates (1998)
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    Journal of comparative physiology 183 (1998), S. 635-650 
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    ISSN: 1432-1351
    Keywords: Key words Olfactory receptors ; Multigene families ; Pseudogenes ; Vertebrate species ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract In species representing different levels of vertebrate evolution, olfactory receptor genes have been identified by molecular cloning techniques. Comparing the deduced amino-acid sequences revealed that the olfactory receptor gene family of Rana esculenta resembles that of Xenopus laevis, indicating that amphibians in general may comprise two classes of olfactory receptors. Whereas teleost fish, including the goldfish Carassius auratus, possess only class I receptors, the `living fossil' Latimeria chalumnae is endowed with both receptor classes; interestingly, most of the class II genes turned out to be pseudogenes. Exploring receptor genes in aquatic mammals led to the discovery of a large array of only class II receptor genes in the dolphin Stenella Coeruleoalba; however, all of these genes were found to be non-functional pseudogenes. These results support the notion that class I receptors may be specialized for detecting water-soluble odorants and class II receptors for recognizing volatile odorants. Comparing the structural features of both receptor classes from various species revealed that they differ mainly in their extracellular loop 3, which may contribute to ligand specificity. Comparing the number and diversity of olfactory receptor genes in different species provides insight into the origin and the evolution of this unique gene family.
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    Neural control of the pyloric region in the foregut of the shrimp Penaeus (Decapoda: Penaeidae) (1997)
    Springer
    Journal of comparative physiology 181 (1997), S. 367-382 
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    ISSN: 1432-1351
    Keywords: Key words Stomatogastric ganglion ; Penaeus ; Pyloric circuit ; Neurotransmitter ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Pyloric pattern-generating neurons that control the pyloric region of the foregut were identified in the stomatogastric ganglion of the most primitive decapod genus Penaeus. Five types of motor neurons and one interneuron are involved in generation of pyloric motor pattern. One cell type of motor neurons innervates muscles of both the gastric mill and the pylorus like the gastric motor neurons in Cancer, but unlike those in Panulirus. These identified neurons are connected to each other either by electrical or inhibitory chemical synapses to construct the neural circuit. This pyloric circuit is similar to the homologous circuit of other crustacean species though some differences are seen in synaptic connections, supporting the hypothesis that the basic design of the neural circuit has been conserved during evolution of the Malacostraca, and that differences have occurred in the synaptic connectivity as the foregut structure has become complex. The motor neurons use either acetylcholine or glutamate as a neurotransmitter like in reptantians. The foregut structure, the number of the pyloric cells, muscle innervation, neurotransmitters, and circuitry are compared among malacostracan crustaceans to provide insight into how the neural circuits change and evolve to produce the motor patterns mediating behaviour.
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    A nose that looks like a hand and acts like an eye: the unusual mechanosensory system of the star-nosed mole (1999)
    Springer
    Journal of comparative physiology 185 (1999), S. 367-372 
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    ISSN: 1432-1351
    Keywords: Key words Cortical magnification ; Somatosensory cortex ; Development ; Evolution ; Behavior
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The star-nosed mole (Condylura cristata) has a snout surrounded by 22 fleshy and mobile appendages. This unusual structure is not an olfactory organ, as might be assumed from its location, nor is it used to manipulate objects as might be guessed from its appearance. Rather, the star is devoted to the sense of touch, and for this purpose the appendages are covered with thousands of small mechanoreceptive Eimer's organs. Recent behavioral studies find that the star acts much like a tactile eye, having a small behavioral focus, or “fovea” at the center – used for detailed explorations of objects of interest. The peripheral and central nervous systems of the mole reflect these behavioral specializations, such that the small behavioral focus on the nose is more densely innervated in the periphery, and has a greatly enlarged representation in the somatosensory cortex. This somatosensory representation of the tactile fovea is not correlated with anatomical parameters (innervation density) as found in other species, but rather is highly correlated with patterns of behavior. The many surprising parallels between the somatosensory system of the mole, and the visual systems of other mammals, suggest a convergent and perhaps common organization for highly developed sensory systems.
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    URL: http://dx.doi.org/10.1007/s003590050396
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    Peripheral frequency mis-match in the primitive ensiferan Cyphoderris monstrosa (Orthoptera: Haglidae) (1999)
    Springer
    Journal of comparative physiology 184 (1999), S. 543-551 
    Details
    ISSN: 1432-1351
    Keywords: Key words Auditory physiology ; Insect ; Frequency discrimination ; Evolution ; Song recognition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Peripheral auditory frequency tuning in the ensiferan insect Cyphoderris monstrosa (Orthoptera: Haglidae) was examined by comparing tympanal vibrations and primary auditory receptor responses. In this species there is a mis-match between the frequency of maximal auditory sensitivity and the frequency content of the species' acoustic signals. The mis-match is not a function of the mechanical properties of the tympanum, but is evident at the level of primary receptors. There are two classes of primary receptors: low-tuned and broadly tuned. Differences in the absolute sensitivity of the two receptor types at the male song frequency would allow the auditory system to discriminate intraspecific signals from sounds containing lower frequencies. Comparisons of tympanal and receptor tuning indicated that the sensitivity of the broadly tuned receptors did not differ from that of the tympanum, while low-tuned receptors had significantly narrower frequency tuning. The results suggest that the limited specialization for the encoding of intraspecific signals in the auditory system of C. monstrosa is a primitive rather than a degenerate condition. The limited specialization of C. monstrosa may reflect the evolutionary origin of communication-related hearing from a generalized precursor through the addition of peripheral adaptations (tympana, additional receptors) to enhance frequency sensitivity and discrimination.
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    URL: http://dx.doi.org/10.1007/s003590050354
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    Comparison of morphology and physiology of two plurisegmental sound-activated interneurones in a bushcricket (1999)
    Springer
    Journal of comparative physiology 185 (1999), S. 199-205 
    Details
    ISSN: 1432-1351
    Keywords: Key words Hearing ; Orthoptera ; Phaneropteridae ; Cercal system ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The unusual morphology of a sound-activated plurisegmental ascending interneurone (AN5-AG7) in an insect (Ancistrura nigrovittata, Ensifera, Phaneropteridae) is described. This neurone's soma is located in the penultimate abdominal ganglion. The most prominent arborisations with smooth endings are found in the prothoracic ganglion. The neurone terminates with numerous beaded endings in the brain (protocerebrum). All abdominal ganglia including the penultimate contain only tiny side branches of beaded appearance. The neurone's morphology is compared to the morphology of a `typical' sound-activated plurisegmental neurone of bushcrickets with its soma in the prothorax. In the prothoracic ganglion and in the brain the arborisations of the two cells are very similar. Graded potentials and action potentials are generated in the prothoracic portion of both neurones. Both receive excitation mainly by ultrasound, and inhibition by soma-ipsilateral stimuli. Neither wind, substrate vibration nor touch of the abdomen evoke responses in AN5-AG7. It is assumed that early in evolution this neurone had its dendrites in the ganglion which houses the cell body (like cercal interneurones of this neuromere). Profound evolutionary changes probably have taken place to bring about this neuron's modern morphology.
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    URL: http://dx.doi.org/10.1007/s003590050378
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    Bat-deafness in day-flying moths (Lepidoptera, Notodontidae, Dioptinae) (1997)
    Springer
    Journal of comparative physiology 181 (1997), S. 477-483 
    Details
    ISSN: 1432-1351
    Keywords: Key words Insects ; Bats ; Ears ; Evolution ; Neotropics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Assuming that bat-detection is the primary function of moth ears, the ears of moths that are no longer exposed to bats should be deaf to echolocation call frequencies. To test this, we compared the auditory threshold curves of 7 species of Venezuelan day-flying moths (Notodontidae: Dioptinae) to those of 12 sympatric species of nocturnal moths (Notodontidae: Dudusinae, Noctuidae and Arctiidae). Whereas 2 dioptines (Josia turgida, Zunacetha annulata) revealed normal ears, 2 (J. radians, J. gopala) had reduced hearing at bat-specific frequencies (20–80 kHz) and the remaining 3 (Thirmida discinota, Polypoetes circumfumata and Xenorma cytheris) revealed pronounced to complete levels of high-frequency deafness. Although the bat-deaf ears of dioptines could function in other purposes (e.g., social communication), the poor sensitivities of these species even at their best frequencies suggest that these moths represent a state of advanced auditory degeneration brought about by their diurnal life history. The phylogeny of the Notodontidae further suggests that this deafness is a derived (apomorphic) condition and not a retention of a primitive (pleisiomorphic), insensitive state.
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    URL: http://dx.doi.org/10.1007/s003590050131
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    Acoustic communication underground: vocalization characteristics in subterranean social mole-rats (Cryptomys sp., Bathyergidae) (1997)
    Springer
    Journal of comparative physiology 180 (1997), S. 245-255 
    Details
    ISSN: 1432-1351
    Keywords: Key words Mole-rat  ;  Vocalization  ;  Acoustic communication  ;  Subterranean mammal  ; Hearing  ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract In captive adult Zambian mole-rats 14 different sounds (13 true vocalizations) have been recorded during different behavioural contexts. The sound analysis revealed that all sounds occurred in a low and middle frequency range with main energy below 10 kHz. The majority of calls contained components of 1.6–2 kHz, 0.63–0.8 kHz, and/or 5–6.3 kHz. The vocalization range thus matched well the hearing range as established in other studies. The frequency content of courtship calls in two species of Zambian Cryptomys was compared with that in naked mole-rats (Heterocephalus glaber) and blind mole-rats (Spalax ehrenbergi) as described in the literature. The frequency range of maximum sound energy is negatively correlated with the body weight and coincides with the frequencies of best hearing in the respective species. In general, the vocalization range in subterranean mammals is shifted towards low frequencies which are best propagated in underground burrows.
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    URL: http://dx.doi.org/10.1007/s003590050045
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    Spatial discrimination of pheromones and behavioural antagonists by the tortricid moths Cydia pomonella and Adoxophyes orana (1999)
    Springer
    Journal of comparative physiology 185 (1999), S. 419-425 
    Details
    ISSN: 1432-1351
    Keywords: Key wordsCydia pomonella ; Adoxophyes orana ; Sex pheromone ; Interspecific interruption ; Evolution ; AbbreviationsZ9-14:Ac (Z9)-tetradecenylacetate Z11-14:Ac (Z11)-tetradecenylacetate ; E8, E10-12:OH (E8, E10)-dodecadienol
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Male moths responding to their species-specific sex pheromone, may cease their upwind flight when pheromone components of sympatric species are added to the mixture. The interspecific interaction between the pheromone response of the tortricid moths Cydia pomonella and Adoxophyes orana was investigated in field-trapping and wind-tunnel studies. Addition of the A. orana pheromone [(Z9)-tetradecenylacetate and (Z11)-tetradecenylacetate] to a source containing the C. pomonella pheromone [(E8, E10)-dodecadienol] resulted in a significant inhibition of attraction by male C. pomonella. It is demonstrated that this behavioural antagonist for C. pomonella must be emitted from the same point source to induce this inhibitory effect. A spatial separation of the two interspecific pheromones (at 14 cm, 5 cm and 0.5 cm crosswind) restored the attraction of the conspecific pheromone for male C. pomonella. In contrast to C. pomonella, male A. orana were not inhibited by point sources releasing both the C. pomonella and A. orana pheromone. We suggest that the discrepancy in the interspecific pheromone interaction between these two tortricids can be explained if we consider the evolutionary ecology of interspecific pheromone communication in C. pomonella and A. orana.
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    URL: http://dx.doi.org/10.1007/s003590050402
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    The concept of cellular evolution (1977)
    Springer
    Journal of molecular evolution 10 (1977), S. 1-6 
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    ISSN: 1432-1432
    Keywords: Evolution ; Ribosomes ; Genotype-Phenotype ; Cytoplasm ; Endosymbiosis ; Procaryote ; Eucaryote ; Progenote
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A central evolutionary question is whether the eucaryotic cytoplasm represents a line of descent that is separate from the typical bacterial line. It is argued on the basis of differences between their respective translation mechanisms that the two lines do represent separate phylogenetic trees in the sense that each line of descent independently evolved to a level of organization that could be called procaryotic. The two lines of descent, nevertheless shared a common ancestor, that was far simpler than the procaryote. This primitive entity is called a progenote, to recognize the possibility that it had not yet completed evolving the link between genotype and phenotype. This concept changes considerably the view one takes toward cellular evolution.
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    URL: http://dx.doi.org/10.1007/BF01796132
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    Structural data concerning reptilian (tortoise) egg lysozyme (1977)
    Springer
    Journal of molecular evolution 10 (1977), S. 261-264 
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    ISSN: 1432-1432
    Keywords: Lysozyme ; Tortoise ; Evolution ; Reptile
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A first series of structural studies allowed a reptilian egg-white lysozyme isolated fromTrionyx gangeticus to be classified among the c (chicken) type lysozymes
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    URL: http://dx.doi.org/10.1007/BF01764601
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    Are extreme halophiles actually “bacteria”? (1978)
    Springer
    Journal of molecular evolution 11 (1978), S. 1-8 
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    ISSN: 1432-1432
    Keywords: Halobacteria ; Archaebacteria ; Phylogeny ; 16S rRNA catalog ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Comparative cataloging of the 16S rRNA ofHalobacterium halobium indicates that the organism did not arise, as a halophilic adaptation, from some typical bacterium. Rather,H. halobium is a member of the Archaebacteria, an ancient group of organisms that are no more related to typical bacteria than they are to eucaryotes.
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    URL: http://dx.doi.org/10.1007/BF01768019
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    Relationship between gene function and gene location inEscherichia coli (1978)
    Springer
    Journal of molecular evolution 11 (1978), S. 47-56 
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    ISSN: 1432-1432
    Keywords: Genome duplication ; Genome topography ; Evolution ; Gene expression
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Genes ofEscherichia coli were grouped according to the “biochemical relatedness” of the enzymes they specifiy, using two schemes to determine relatedness: similarity of reaction or similarity of reactants. The tendency of biochemically related genes as so defined to lie approximately 90° or 180° from one another on the circular genetic map was analyzed statistically. Of the classes analyzed, only the genes for the enzymes of glucose catabolism showed a significant departure from random distribution in this respect. The glucose catabolism genes showed a pronounced tendency to lie either 90° or 180° from one another (P = ca. 10−9), and, furthermore, most of these genes were found to lie in only four gene clusters on theE. coli genome. The significance of this observation is discussed in relation to evolutionary mechanisms and to mechanisms of gene expression.
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    URL: http://dx.doi.org/10.1007/BF01768024
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    The asymmetry of life (1978)
    Springer
    Journal of molecular evolution 11 (1978), S. 313-332 
    Details
    ISSN: 1432-1432
    Keywords: Evolution ; Optical activity ; Photolysis ; Circularly ; polarized radiation ; Selection
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Stereoselective physical phenomena and their possible importance for the prevalence of D-sugars and L-aminoacids in living matter are reviewed. A classification is presented according to which a selective force provides a microscopic or macroscopic selection depending on its generality when taken over a macrosystem (a ‘unitary biosphere’ such as the Earth). The microscopic ‘selections’ are not genuine selections because the final sense of asymmetry is here determined by chance, in other words the initial choice is ‘random’, while it is ‘directed’ in the macroscopic selection. Two macroscopic selections appear possible: 1. selection due to an intrinsic energy difference between enantiomorph configurations, 2. selection accomplished by elliptically polarised radiation.
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    A new estimate of sequence divergence of mitochondrial DNA using restriction endonuclease mappings (1979)
    Springer
    Journal of molecular evolution 13 (1979), S. 295-304 
    Details
    ISSN: 1432-1432
    Keywords: Evolution ; Restriction endonuclease mappings and mitochondrial DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A new estimate of the sequence divergence of mitochondrial DNA in related species using restriction enzyme maps is constructed. The estimate is derived assuming a simple Posisson-like model for the evolutionary process and is chosen to maximize an expression which is a reasonable approximation to the true likelihood of the restriction map data. Using this estimate, four sets of mitochondrial DNA data are analyzed and discussed.
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    URL: http://dx.doi.org/10.1007/BF01731370
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    Analysis of GC-rich repetitive nucleotide sequences in great apes (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 405-412 
    Details
    ISSN: 1432-1432
    Keywords: Primate ; Evolution ; Heterochromatin ; Repetitive sequences ; β Satellite sequences ; L1 transposon ; Polymerase chain reaction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The genomes of four primate species, belonging to the families Pongidae (chimpanzee, gorilla, and orangutan) and Hylobatidae (gibbons), have been analyzed for the presence and organization of two human GC-rich heterochromatic repetitive sequences: βSatellite (βSat) and LongSau (LSau) repeats. By Southern blot hybridization and PCR, both families of repeats were detected in all the analyzed species, thus indicating their origin in an ape ancestor. In the chimpanzee and gorilla, as in man, βSat sequences showed a 68-bp Sau3A periodicity and were preferentially organized in large clusters, whereas in the orangutan, they were organized in DNA fragments of 550 bp, which did not seem to be characterized by a tandem organization. On the contrary, in each of the analyzed species, the bulk of LSau sequences showed a longer Sau3A periodicity than that observed in man (450–550 bp). Furthermore, only in the chimpanzee genome some of LSau repeats seemed to be interspersed within blocks of βSat sequences. This sequence organization, which also characterizes the human genome, is probably absent in the gorilla. In fact, the analysis of a gorilla genomic library suggested that LSau repeats are not preferentially in linkage with βSat sequences. Moreover, LSau sequences were found in a genomic sector characterized by the simultaneous presence of L1 and (CA) repeats, as well as of anonymous sequences and known genes. In spite of the different sequence organization, the nucleotide differences between complete human and gorilla LSau repeats were very few, whereas one gorilla LSau repeat, interrupted by a probably-truncated L1 transposon, showed a higher degree of divergence. Besides the gorilla, this unusual sequence organization was detected in man, and, to a lesser extent, in the chimpanzee.
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    URL: http://dx.doi.org/10.1007/BF00164027
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    Partial sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase and the phylogeny of Prochloron and Prochlorococcus (Prochlorales) (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 671-677 
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    ISSN: 1432-1432
    Keywords: Chloroplasts ; Evolution ; Rubisco ; Picoplankton ; Prochloron ; Prochlorothrix ; Prochlorococcus ; Prochlorales
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The prochlorophytes, oxygenic photosynthetic prokaryotes having no phycobiliprotein but possessing chlorophylls a and b, have been proposed to have a common ancestry with green chloroplasts, yet this is still controversal. We report here that partial sequence comparisons of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, including sequence data from two prochlorophytes, Prochlorococcus and Prochloron, indicate that Prochlorococcus is more closely related to a photosynthetic bacterium, Chromatium vinosum (γ-purple bacteria), than to cyanobacteria, while Prochloron is closely related to the prochlorophyte Prochlorothrix and to cyanobacteria. The molecular phylogenetic tree indicates that a common ancestor of Prochlorococcus and γ-purple bacteria branched off from the land plant lineage earlier than Prochloron, Prochlorothrix, and cyanobacteria.
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    URL: http://dx.doi.org/10.1007/BF00160516
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    Caenorhabditis elegans contains genes encoding two new members of the Zn-containing alcohol dehydrogenase family (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 46-53 
    Details
    ISSN: 1432-1432
    Keywords: Alcohol dehydrogenase ; Caenorhabditis elegans ; Evolution ; Gene families
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have characterized two cDNA clones from the nematode Caenorhabditis elegans that display similarity to the alcohol dehydrogenase (ADH) gene family. The nucleotide sequences of these cDNAs predict that they encode Zn-containing long-chain ADH enzymes. Phylogenetic analysis suggests that one is most similar to dimeric class III ADHs found in diverse taxa; the other is most similar to the tetrameric forms of ADH previously described only in fungi.
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    Analyses of ribosomal RNA sequences from glaucocystophyte cyanelles provide new insights into the evolutionary relationships of plastids (1995)
    Springer
    Journal of molecular evolution 41 (1995), S. 203-210 
    Details
    ISSN: 1432-1432
    Keywords: Cyanelles ; Cyanophora paradoxa ; Endosymbiosis ; Evolution ; Glaucocystophyta ; Glaucophyta ; Phylogeny ; Plastid ; 16S ribosomal RNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Glaucocystophyte algae (sensu Kies, Berl. Deutsch. Bot. Ges. 92, 1979) contain plastids (cyanelles) that retain the peptidoglycan wall of the putative cyanobacterial endosymbiont; this and other ultrastructural characters (e.g., unstacked thylakoids, phycobilisomes) have suggested that cyanelles are “primitive” plastids that may represent undeveloped associations between heterotrophic “host” cells (i.e., glaucocystophytes) and cyanobacteria. To test the monophyly of glaucocystophyte cyanelles and to determine their evolutionary relationship to other plastids, complete 16S ribosomal RNA sequences were determined for Cyanophora paradoxa, Glaucocystis nostochinearum, Glaucosphaera vacuolata, and Gloeochaete wittrockiana. Plastid rRNAs were analyzed with the maximum-likelihood, maximumparsimony, and neighbor joining methods. The phylogenetic analyses show that the cyanelles of C. paradoxa, G. nostochinearum, and G. wittrockiana form a distinct evolutionary lineage; these cyanelles presumably share a monophyletic origin. The rDNA sequence of G. vacuolata was positioned within the nongreen plastid lineage. This result is consistent with analyses of nuclear-encoded rRNAs that identify G. vacuolata as a rhodophyte and support its removal from the Glaucocystophyta. Results of a global search with the maximumlikelihood method suggest that cyanelles are the first divergence among all plastids; this result is consistent with a single loss of the peptidoglycan wall in plastids after the divergence of the cyanelles. User-defined tree analyses with the maximum-likelihood method indicate, however, that the position of the cyanelles is not stable within the rRNA phylogenies. Both maximumparsimony and neighbor-joining analyses showed a close evolutionary relationship between cyanelles and nongreen plastids; these phylogenetic methods were sensitive to inclusion/exclusion of the G. wittrockiana cyanelle sequence. Base compositional bias within the G. wittrockiana 16S rRNA may explain this result. Taken together the phylogenetic analyses are interpreted as supporting a near-simultaneous radiation of cyanelles and green and nongreen plastids; these organelles are all rooted within the cyanobacteria.
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    Molecular evolution of maize catalases and their relationship to other eukaryotic and prokaryotic catalases (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 570-579 
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    ISSN: 1432-1432
    Keywords: Evolution ; Catalase ; Phylogenetic tree,Zea mays L. ; Isozyme ; Antioxidant genes ; Gene Structure ; Oxidative stress
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have compared the nucleotide and protein sequences of the three maize catalase genes with other plant catalases to reconstruct the evolutionary relationship among these catalases. These sequences were also compared with other eukaryotic and prokaryotic catalases. Phylogenies based on distances and parsimony analysis show that all plant catalases derive from a common ancestral catalase gene and can be divided into three distinct groups. The first, and major, group includes maizeCatl, barleyCat1, riceCatB and most of the dicot catalases. The second group is an apparent dicot-specific catalase group encompassing the tobaccoCat2 and tomatoCat. The third is a monocot-specific catalase class including the maize Cat3, barley Cat2, and riceCatA. The maize Cat2 gene is loosely related to the first group. The distinctive features of monocot-specific catalases are their extreme high codon bias at the third position and low degree of sequence similarity to other plant catalases. Similarities in the intron positions for several plant catalase genes support the conclusion of derivation from a common ancestral gene. The similar intron position between bean catalases and human catalase implies that the animal and plant catalases might have derived from a common progenitor gene sequence.
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    Low synonymous site variation at thelacY locus inEscherichia coli suggests the action of positive selection (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 79-84 
    Details
    ISSN: 1432-1432
    Keywords: LacY ; Lactose permease ; Evolution ; Reduced synonymous polymorphism ; Positive selection ; E. coli
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have determined the nucleotide sequences of sevenlacY alleles isolated from natural isolates ofEscherichia coli. Nucleotide heterozygosity estimates for this locus were compared to those obtained from previous studies of intraspecific variation at chromosomal loci, revealing thatlacY has unusually low synonymous site variation. The average pairwise heterozygosity of synonymous sites (Ks=0.0112+/-0.0100) is the second lowest reported and the lowest for loci that have an equivalent level of nonsynonymous variation. We consider several hypotheses to explain how different forces in evolution could act to create the observed pattern of polymorphism, including selection for translational efficiency and positive selection. Our analysis most strongly supports the hypothesis that positive selection has acted on thelacY locus inE. coli.
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    URL: http://dx.doi.org/10.1007/BF02198831
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    Replacement of nucleosomal histones by histone H1-like proteins during spermiogenesis in Cnidaria: Evolutionary implications (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 240-246 
    Details
    ISSN: 1432-1432
    Keywords: Sperm nuclear basic proteins (SNBPs) ; Histone H1 ; Cnidaria ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have analyzed the chromosomal protein composition of the sperm from several species belonging to three different classes (Hydrozoa, Scyphozoa, Anthozoa) of the phylum Cnidaria. In every instance, the sperm nuclear basic proteins (SNBPs) were found to consist of one to two major protein fractions that belong to the histone H1 family, as can be deduced from their amino acid composition and solubility in dilute perchloric acid, and the presence of a trypsin-resistant core. In those species where mature spawned sperm could be obtained, we were able to show that these proteins completely replace the somatic histones from the stem cells that are present at the onset of spermatogenesis. The presence of a highly specialized histone H1 molecule in the sperm of this phylum provides support for the idea that the protamine-like proteins (PL) from higher groups in the phylogenetic tree (and possibly protamines as well) may all have evolved from a primitive histone H1 ancestor.
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    Relationships between transposable elements based upon the integrase-transposase domains: Is there a common ancestor? (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 359-368 
    Details
    ISSN: 1432-1432
    Keywords: Transposable elements ; Evolution ; Horizontal transfers and alternative hypotheses
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The integrase domain of RNA-mediated elements (class I) and the transposase domain of DNA-mediated transposable elements (class II) were compared. A number of elements contain the DDE signature, which plays an important role in their integration. The possible relationships betweenmariner-Tc1 andIS elements, retrotransposons, and retroviruses were analyzed from an alignment of this region. Themariner-Tc1 superfamily, and LTR retrotransposons and retroviruses were found to be monophyletic groups. However, theIS elements of bacteria were found in several groups. These results were used to propose an evolutionary history that suggests a common ancestor for some integrases and transposases.
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    URL: http://dx.doi.org/10.1007/BF02337546
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