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  • Articles  (207)
  • Evolution  (207)
  • Springer  (207)
  • 2020-2023
  • 1995-1999  (207)
  • 101
    ISSN: 1432-1017
    Keywords: Key words Sequence similarity ; Glyceraldehyde-3-phosphate dehydrogenase ; Phosphoglycerate kinase ; Pyruvate kinase ; Evolution ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Data are presented that suggest enzyme sequence similarities among species are not solely a function of their evolutionary relationship. It is demonstrated that sequence similarities of glyceraldehyde-3-phosphate dehydrogenases, phosphoglycerate kinases, and pyruvate kinases from yeast, bacteria, mammals and a bird possess a significant species optimal thriving temperature dependence that crosses through conventional phylogenetic divisions. It is therefore suggested that species which are distantly related evolutionarily may possess some degree of enzyme sequence similarity if they happen to thrive at near the same optimal temperature; conversely, organisms which are closely related evolutionarily but function at radically different temperatures will possess a sequence dissimilarity that may mask the close relatedness.
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  • 102
    ISSN: 1432-0983
    Keywords: Green algae ; Volvox ; Transcription signals ; Gene expression ; Intron ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The genome of the green alga Chlamydomonas reinhardtii contains approximately 15 gene clusters of the nucleosomal (or core) histone H2A, H2B, H3 and H4 genes and at least one histone H1 gene. Seven non-allelic histone gene loci were isolated from a genomic library, physically mapped, and the nucleotide sequences of three isotypes of each core histone gene species and one linked H1 gene determined. The core histone genes are organized in clusters of H2A–H2B and H3–H4 pairs, in which each gene pair shows outwardly divergent transcription from a short (300 bp) intercistronic region. These intercistronic regions contain typically conserved promoter elements, namely a TATA-box and the three motifs TGGCCAG-G(G/C)-CGAG, CGTTGACC and CGGTTG. Different from the genes of higher plants, but like those of animals and the related alga Volvox the 3′ untranslated regions contain no poly A signal, but a palindromic sequence (3′ palindrome) essential for mRNA processing is present. One single H1 gene was found in close linkage to a H2A–H2B pair. The H1 upstream region contains the octameric promoter element GGTTGA-CC (also found upstream of the core histone genes) and two specific sequence motifs that are shared only with the Volvox H1 promoters. This suggests differential transcription of the H1 and the core histone genes. The H1 gene is interrupted by two introns. Unlike Volvox H3 genes, the three sequenced H3 isoforms are intronfree. Primer-directed PCR of genomic DNA demonstrated, however, that at least 8 of the about 15 H3 genes do contain one intron at a conserved position. In synchronized C. reinhardtii cells, H4 mRNA levels (representative of all core histone mRNAs) peak during cell division, suggesting strict replication-dependent gene control. The derived peptide sequences place C. reinhardtii core histones closer to plants than to animals, except that the H2A histones are more animal-like. The peptide sequence of histone H1 is closely related to the V. carteri VH1-II (66% identity). Organization of the core histone gene in pairs, and non-polyadenylation of mRNAs are features shared with animals, whereas peptide sequences and enhancer elements are shared with higher plants, assigning the volvocalean histone genes a position intermediate between animals and plants.
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  • 103
    ISSN: 1432-0983
    Keywords: Key wordsKluyveromyces lactis ; Transketolase ; Evolution ; Carbohydrate metabolism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The role of the pentose-phosphate pathway in carbohydrate metabolism of the yeast Kluyveromyces lactis, and the evolutionary relationships between the encoding genes, was investigated. For this purpose, we isolated the gene encoding transketolase (KlTKL1) and determined its nucleotide sequence. Surprisingly, comparisons of the deduced amino-acid sequence with those from other organisms revealed that the yeast enzymes are more related to those from prokaryotic sources than to those from higher eukaryotes. Functional analyses showed that KlTKL1 also complemented a Saccharomyces cerevisiae tkl1 tkl2 double mutant for growth in the absence of aromatic amino acids and restored transketolase activity in this mutant. A band detected in these transformants by Western-blot analysis corresponded to a band detected in K. lactis both in a wild-type strain and in a multicopy transformant with elevated transketolase activity.
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  • 104
    ISSN: 1432-0983
    Keywords: Key words Mitochondrial genome ; Red algae ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The purpose of this review is to present an account of our current understanding of the structure, organization and evolution of mitochondrial genomes, and to discuss the origin and evolution of mitochondria from the perspective recently provided by the extensive sequenc-ing of various mitochondrial genomes. Mitochondrial-en-coded protein phylogenies are congruent with nuclear phylogenies and strongly support a monophyletic origin of mitochondria. The newly available data from red-algal mitochondrial genomes, in particular, show that the structural and functional diversity of mitochondrial genomes can be accounted for by paralogous evolution. We also discuss the influence of other constraints, such as uniparental inheritance, on the evolution of genome organization in mitochondria.
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  • 105
    ISSN: 1432-0983
    Keywords: Key words Mitochondria ; Introns ; Evolution ; Fungi
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The mitochondrial chromosome of 15 Podo-spora anserina and one Podospora comata wild-type strains have been extensively examined for the presence of optional elements and for sequence divergence. Among the P. anserina strains, nine optional sequences were found. By comparing P. anserina with the closely related and weakly interfertile P. comata species, six additional optional sequences were detected. These optional elements correspond to mitochondrial introns belonging to different groups and subgroups (11 cases), intronic open reading frames (two cases), a complex insert and an intergenic region. Although difficult to explain, the distribution of optional mitochondrial sequences among the 15 wild-type isolates of P. anserina is far from random.
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  • 106
    ISSN: 1432-0983
    Keywords: Key words Chloroplast ; Mitochondria ; Endosymbiosis ; Endosymbiotic gene transfer ; Calvin cycle ; Glycolysis ; Evolution ; Amitochondriate ; Metabolism ; Compartmentation ; Hydrogenosome ; Eukaryote ; Origin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The evolutionary histories of the 12 enzymes that catalyze the reactions of the Calvin cycle in higher-plant chloroplasts are summarized. They are shown to be encoded by a mixture of nuclear genes of cyanobacterial and proteobacterial origin. Moreover, where cytosolic isoforms of these enzymes are found they are almost invariably encoded by genes of clearly endosymbiont origin. We infer that endosymbiosis resulted in functional redundancy that was eliminated through differential gene loss, with intruding eubacterial genes repeatedly replacing pre-existing nuclear counterparts to which they were either functionally or structurally homologous. Our findings fail to support the `product-specificity corollary', which predicts re-targeting of nuclear-encoded gene products to the organelle from whose genome they originated. Rather it would appear that the enzymes of central carbohydrate metabolism have evolved novel targeting possibilities regardless of their origins. Our findings suggest a new hypothesis to explain organelle genome persistence, based on the testable idea that some organelle-encoded gene products might be toxic when present in the cytosol or other inappropriate cellular compartments.
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  • 107
    ISSN: 1432-0983
    Keywords: RNA editing ; Group-II intron ; Gene transfer ; Evolution ; tRNA genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A novel group II intron has been identified in the pea (Pisum sativum) mitochondrial genome. The gene harbouring this intron is identified as rps10 (encoding protein S10 of the small ribosomal subunit) by similarity to its known homologues in bacteria and in the mitochondrion of the liverwort Marchantia polymorpha. The rps10 gene is transcribed in pea, the intron is removed, and RNA editing in the rps10 reading frame increases similarity to its homologue in the M. polymorpha mitochondrion. Contrary to the situation in bacteria and Marchantia, rps10 is not part of a ribosomal-protein gene cluster in pea. It is flanked upstream by the genes trnF and trnP, encoding phenylalanine-and proline-accepting tRNAs, and downstream by cox1, encoding subunit 1 of the cytochrome-c-oxidase. Southern hybridization shows that sequences homologous to rps10 exist in potato mitochondria but not in mitochondria of Oenothera berteriana and Arabidopsis thaliana. The pea rps10 intron is homologous to introns in rrn26 and cox3 in the Marchantia mitochondrial genome, while the Marchantia rps10 gene lacks an intron.
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  • 108
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    Current genetics 28 (1995), S. 410-414 
    ISSN: 1432-0983
    Keywords: Mitochondrial DNA ; Multi-copy ; Pseudogene ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Four nuclear pseudogenes homologous to the 10031–10195-bp region of the human mitochondrial genome were detected by constant denaturant capillary electrophoresis. Among them, one pseudogene is present as at least five copies in each cell, in accordance with our previous observations of multi-copy mitochondrial DNA pseudogenes. The presence of multiple identical copies of pseudogenes suggests that the human genome underwent a series of genetic changes, including gene amplifications, very recently in evolutionary history, i.e., within the last 390000 years.
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  • 109
    ISSN: 1432-0983
    Keywords: Key wordsEuglena ; Mitochondria ; cox1 ; Evolution ; RNA editing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We present the nucleotide sequence of the cox 1 gene encoding subunit 1 of cytochrome c oxidase in Euglena gracilis, the first report on a mitochondrial gene from this protist. Its study reveals that the Euglena mitochondrial genome does not appear as a compact and homogeneous structure and that its A+T content is high (about 76%) whereas this value is less than 50% in nuclear DNA. The Euglena cox1 gene does not exhibit any intron, and an amino-acid alignment of Euglena COX1 with homologous proteins shows that the universal genetic code is used. Comparisons of the genomic and cDNA sequences of Euglena cox1 indicate that the transcript does not undergo RNA editing as found in trypanosomes and in higher plants. The phylogeny obtained with COX1 protein sequences is in agreement with that obtained with nuclear rRNA sequences and places Euglena and Trypanosoma far apart from other eukaryotes. This result strengthens the hypothesis that these protists represent the earliest mitochondrion-containing organisms.
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  • 110
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    Current genetics 28 (1995), S. 97-99 
    ISSN: 1432-0983
    Keywords: GIY-YIG ORF ; Endonuclease ; Plastid ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Group-I introns, containing open reading frames (ORFs) that code for homing endonucleases, are widely distributed amongst eukaryotic organellar genomes. However, endonucleases of the GIY-YIG subclass have a restricted distribution in mitochondria and bacteriophages, and have never been observed in plastids. We have found the GIY-YIG motif in an intronic ORF within the previously published psbA gene sequence from Chlamydomonas reinhardtii chloroplasts. Based on phylogenetic analysis and an evaluation of amino-acid substitutions, this ORF is not closely related to any of the other GIY-YIG ORFs. These results suggest that GIY-YIG ORFs have a longer evolutionary history than previously assumed.
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  • 111
    ISSN: 1432-1351
    Keywords: Key words Constraint ; Electroreception ; Evolution ; Sensory system ; Neural network
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Modification of an existing neural structure to support a second function will produce a trade-off between the two functions if they are in some way incompatible. The trade-off between two such sensory functions is modeled here in pyramidal neurons of the gymnotiform electric fish's medullar electrosensory lateral line lobe (ELL). These neurons detect two electric stimulus features produced when a nearby object interferes with the fish's autogenous electric field: (1) amplitude modulation across a cell's entire receptive field and (2) amplitude variation within a cell's receptive field produced by an object's edge. A model of sensory integration shows that detection of amplitude modulation and enhancement of spatial contrast involve an inherent mechanistic trade-off and that the severity of the trade-off depends on the particular algorithm of sensory integration. Electrophysiology data indicate that of the two algorithms for sensory integration modeled here for the gymnotiform fish Brachyhypopomus pinnicaudatus, the algorithm with the better trade-off function is used. Further, the intrinsic trade-off within single cells has been surmounted by the replication of ELL into multiple electrosensory map segments, each specialized to emphasize different sensory features.
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  • 112
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    Journal of comparative physiology 182 (1998), S. 737-746 
    ISSN: 1432-1351
    Keywords: Key words Auditory sensitivity ; Sound spectra ; ABR ; Evolution ; Communication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Several anabantoid species produce broad-band sounds with high-pitched dominant frequencies (0.8–2.5 kHz), which contrast with generally low-frequency hearing abilities in (perciform) fishes. Utilizing a recently developed auditory brainstem response recording-technique, auditory sensitivities of the gouramis Trichopsis vittata, T. pumila, Colisa lalia, Macropodus opercularis and Trichogaster trichopterus were investigated and compared with the sound characteristics of the respective species. All five species exhibited enhanced sound-detecting abilities and perceived tone bursts up to 5 kHz, which qualifies this group as hearing specialists. All fishes possessed a high-frequency sensitivity maximum between 800 Hz and 1500 Hz. Lowest hearing thresholds were found in T. trichopterus (76 dB re 1 μPa at 800 Hz). Dominant frequencies of sounds correspond with the best hearing bandwidth in T. vittata (1–2 kHz) and C. lalia (0.8–1 kHz). In the smallest species, T. pumila, dominant frequencies of acoustic signals (1.5–2.5 kHz) do not match lowest thresholds, which were below 1.5 kHz. However, of all species studied, T. pumila had best hearing sensitivity at frequencies above 2 kHz. The association between high-pitched sounds and hearing may be caused by the suprabranchial air-breathing chamber, which, lying close to the hearing and sonic organs, enhances both sound perception and emission at its resonant frequency.
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  • 113
    ISSN: 1432-1351
    Keywords: Key words Acetylcholine ; Evolution ; Histamine ; Homology ; Insect ; Vasopressin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The vasopressin-like immunoreactive (VPLI) neurons of grasshoppers have paired cell bodies in the suboesophageal ganglion and both anterior and posterior running axons. In non-oedipodine grasshopper species (e.g. Schistocerca gregaria), most of their arborisations are distributed in dorsal and lateral neuropil, while in oedipodine species (e.g. Locusta migratoria), the neurons have additional extensive axonal projections in both the optic lobes and proximal portions of the ganglionic peripheral nerves. This study demonstrates that these morphological differences correlate with their physiology. In L. migratoria, VPLI neuron activity is regulated primarily via a spontaneously active interneuron which descends from the brain. This descending interneuron is inhibited by a light-activated brain extraocular photoreceptor. Regulation of VPLI neuron activity by an extraocular photoreceptor is also seen in the other oedipodine grasshopper investigated. In the four non-oedipodines examined (from two subfamilies), we find no extraocular photoreceptor regulation of VPLI neuron activity. Despite this, VPLI neuron in S.␣gregaria does appear to be driven by a descending interneuron homologous to that in L. migratoria. The descending interneuron in both species receives similar mechanosensory input and excites the VPLI neuron via cholinergic synapses. Histamine injection into the medial protocerebrum of both species causes strong inhibition of the descending interneuron. The evolution of the neural circuitry, by which an extraocular photoreceptor comes to regulate the descending interneuron in oedipodine species, is discussed.
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  • 114
    ISSN: 1432-072X
    Keywords: Magnetospirillum magnetotacticum ; Cytochrome c ; Amino acid sequence ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Cytochrome c-550 was purified from Magnetospirillum magnetotacticum to an electrophoretically homogeneous state, and some of its properties were determined. The cytochrome showed absorption peaks at 528 and 409 nm in the oxidized form, and at 550, 521, and 414 nm in the reduced form. Its midpoint redox potential at pH 7.0 was determined to be +289 mV. The primary structure of cytochrome c-550 was determined. Cytochrome c is composed of 97 amino acid residues, and its molecular weight was calculated to be 10,873, including heme c. Its primary structure is very similar to those of Rhodospirillum fulvum and Rhodospirillum molischianum cytochromes c 2, suggesting that M. magnetotacticum is phylogenetically related to photosynthetic bacteria.
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  • 115
    ISSN: 1432-072X
    Keywords: Glyceraldehyde-3-phosphate dehydrogenase ; Streptomyces arenae ; Antibiotic resistance ; Sequence comparison ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Streptomyces arenae produces the antibiotic pentalenolactone, a highly specific inhibitor of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). During the phase of pentalenolactone production,S. arenae expresses a pentalenolactone-insensitive GAPDH isoform; otherwise, a pentalenolactone-sensitive form is expressed. The gene of the pentalenolactone-insensitive GAPDH was cloned and sequenced. Regulatory elements typical for genes encoding antibiotic resistance and production are localized upstream and downstream of the open reading frame. No expression of pentalenolactone-insensitive GAPDH was detected inStreptomyces lividans transformed with the gene. InEscherichia coli, the gene was expressed from an inducedlac promoter. Amino-terminal sequencing of the heterologously expressed GAPDH proved its identity with pentalenolactone-insensitive GAPDH fromS. arenae. Sequence comparisons with GAPDH from other organisms showed a close relationship to GAPDH of plant chloroplasts, of other gram-positive bacteria, and of thermophilic gram-negative bacteria. Pentalenolactone-insensitive GAPDH differs from all closely related GAPDHs only in a few residues, none of which are directly involved in catalysis or substrate binding. The total amino acid composition is more similar to GAPDH of thermophilic species than to that of mesophilic species. The purified enzyme was moderately thermotolerant, which could be a side effect of the structural changes causing pentalenolactone-resistance.
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  • 116
    ISSN: 1432-072X
    Keywords: Key wordsMagnetospirillum magnetotacticum ; Cytochrome c ; Amino acid sequence ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Cytochrome c-550 was purified from Magnetospirillum magnetotacticum to an electrophoretically homogeneous state, and some of its properties were determined. The cytochrome showed absorption peaks at 528 and 409 nm in the oxidized form, and at 550, 521, and 414 nm in the reduced form. Its midpoint redox potential at pH 7.0 was determined to be +289 mV. The primary structure of cytochrome c-550 was determined. Cytochrome c is composed of 97 amino acid residues, and its molecular weight was calculated to be 10,873, including heme c. Its primary structure is very similar to those of Rhodospirillum fulvum and Rhodospirillum molischianum cytochromes c 2, suggesting that M. magnetotacticum is phylogenetically related to photosynthetic bacteria.
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  • 117
    ISSN: 1432-072X
    Keywords: Key words Glyceraldehyde-3-phosphate dehydrogenase ; Streptomyces arenae ; Antibiotic resistance ; Sequence comparison ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Streptomyces arenae produces the antibiotic pentalenolactone, a highly specific inhibitor of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). During the phase of pentalenolactone production, S. arenae expresses a pentalenolactone-insensitive GAPDH isoform; otherwise, a pentalenolactone-sensitive form is expressed. The gene of the pentalenolactone-insensitive GAPDH was cloned and sequenced. Regulatory elements typical for genes encoding antibiotic resistance and production are localized upstream and downstream of the open reading frame. No expression of pentalenolactone-insensitive GAPDH was detected in Streptomyces lividans transformed with the gene. In Escherichia coli, the gene was expressed from an induced lac promoter. Amino-terminal sequencing of the heterologously expressed GAPDH proved its identity with pentalenolactone-insensitive GAPDH from S. arenae. Sequence comparisons with GAPDH from other organisms showed a close relationship to GAPDH of plant chloroplasts, of other gram-positive bacteria, and of thermophilic gram-negative bacteria. Pentalenolactone-insensitive GAPDH differs from all closely related GAPDHs only in a few residues, none of which are directly involved in catalysis or substrate binding. The total amino acid composition is more similar to GAPDH of thermophilic species than to that of mesophilic species. The purified enzyme was moderately thermotolerant, which could be a side effect of the structural changes causing pentalenolactone-resistance.
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  • 118
    ISSN: 1432-1211
    Keywords: Key words KIR ; Natural killer cell ; Recombination ; Gene conversion ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
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  • 119
    ISSN: 1432-1327
    Keywords: Key words Iron-sulfur ; Nitrogen fixation ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  The [2Fe-2S] protein from Azotobacter vinelandii that was previously known as iron-sulfur protein I, or Shethna protein I, has been shown to be encoded by a gene belonging to the major nif gene cluster. Overexpression of this gene in Escherichia coli yielded a dimeric protein of which each subunit comprises 106 residues and contains one [2Fe-2S] cluster. The sequence of this protein is very similar to that of the [2Fe-2S] ferredoxin from Clostridium pasteurianum (2FeCpFd), and the four cysteine ligands of the [2Fe-2S] cluster occur in the same positions. The A. vinelandii protein differs from the C. pasteurianum one by the absence of the N-terminal methionine, the presence of a five-residue C-terminal extension, and a lesser number of acidic and polar residues. The UV-visible absorption and EPR spectra, as well as the redox potentials of the two proteins, are nearly identical. These data show that the A. vinelandii FeS protein I, which is therefore proposed to be designated 2FeAvFdI, is the counterpart of the [2Fe-2S] ferredoxin from C. pasteurianum. The occurrence of the 2FeAvFdI-encoding gene in the nif gene cluster, together with the previous demonstration of a specific interaction between the 2FeCpFd and the nitrogenase MoFe protein, suggest that both proteins might be involved in nitrogen fixation, with possibly similar roles.
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  • 120
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    Sexual plant reproduction 9 (1996), S. 357-361 
    ISSN: 1432-2145
    Keywords: Key words Self-incompatibility ; Evolution ; S-RNases ; Solanaceae ; Rosaceae ; Scrophulariaceae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  This review summarises current understanding of the evolution of self-incompatibility inferred from DNA sequence analysis. Self-incompatibility in many plant families is controlled by a single, highly polymorphic S-locus which, in the Solanaceae, encodes an allelic series of stylar ribonucleases known as the S-RNases. PCR approaches are a convenient way to examine the diversity of S-RNase sequences within and between wild populations of a self-incompatible species and provide a unique view into the species’ current and historic population structure. Similar molecular appoaches have also been used to show that S-RNases are involved in self-incompatibility in families other than the Solanaceae. A model for the evolution of ribonuclease-based self-incompatibility systems is discussed.
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  • 121
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    Astrophysics and space science 230 (1995), S. 169-176 
    ISSN: 1572-946X
    Keywords: Late-type Stars ; Evolution ; Carbon Stars ; RV Tauri Stars
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract The M, S and C stars may be placed in an evolutionary sequence on the basis of direct observation of the spectroscopic transitions on the AGB of rich intermediate-age clusters in the Magellanic Clouds, but some S and C stars cannot be accounted for in this way. The S stars inω Centauri owe their peculiarity to a primordial enrichment in s-process elements. The J-type (13C-rich) carbon stars originate in a different way to the ordinary cool N-type carbon stars. Some of them have silicate-rich circumstellar dust, contrary to expectation. Some of the carbon-rich RV Tauri stars also have silicate-rich dust and in both cases it may be organised in a disc. Observational evidence for gas and dust ejection by ordinary N-type carbon stars has been found and may be inferred for some RV Tauri stars.
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  • 122
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    Astrophysics and space science 224 (1995), S. 29-42 
    ISSN: 1572-946X
    Keywords: Protostars ; Evolution ; Infall ; Jets
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract The use of sensitive receivers on large ground-based radiotelescopes such as the JCMT, the IRAM 30 m MRT, and the VLA has recently yielded significant progress in our observational understanding of low-mass protostars. Submillimeter continuum observations suggest that the youngest stellar objects detected in the near-/mid-IR range -the so-called Class I sources or “infrared protostars” - have only residual amounts of circumstellar material and are thus relatively evolved. At the same time, a smaller number of colder and more obscured YSOs - designated “Class 0” - characterized by virtually no emission below 10µm but strong submillimeter emission have been identified. These Class 0 or “submillimeter protostars” have not yet assembled the bulk of their final stellar mass, and correspond to the youngest protostar stage known to date (probable age ≲ 104 yr). Direct evidence for gravitational infall has been found in some of these sources confirming their protostellar nature. However, most (if not all) Class 0 protostars already drive highly collimated CO outflows.
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  • 123
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    Journal of computer aided molecular design 9 (1995), S. 181-202 
    ISSN: 1573-4951
    Keywords: De novo drug design ; Evolution ; Automated structure generation ; 3D database ; Expert system
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A genetic algorithm has been designed which generates molecular structures within constraints. The constraints may be any useful function, for example an enzyme active site, a pharmacophore or molecular properties from pattern recognition or rule-induction analyses. The starting point may be random or may utilise known molecules. These are modified to ‘grow’ into families of structures which, using the evolutionary operators of selection, crossover and mutation evolve to better fit the constraints. The basis of the algorithm is described together with some applications in lead generation, 3D database construction and drug design. Genetic algorithms of this type may have wider applications in chemistry, for example in the design and optimisation of new polymers, materials (e.g. superconducting materials) or synthetic enzymes.
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  • 124
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    Journal of evolutionary economics 7 (1997), S. 339-353 
    ISSN: 1432-1386
    Keywords: Key words: Market organisation ; Network ; Communication ; Evolution ; Learning ; JEL-classification: C70; D23; D40; L11
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract. The purpose of this paper is to suggest a view of the economy as a network of links between the individuals involved. One approach is to consider the structure of links as fixed as is the case with spatial models in which agents are situated on a lattice, another is to regard all links as possible but stochastic. If the probability of any of the links existing is uniform we have the situation familiar from the “population games” of evolutionary game theory. The basic idea here is to allow the network to evolve and to make the probability of each of the links dependent on the experience of the agents involved. Such analysis can give rise to interesting behaviour on the aggregate level which is very different from that which might have been predicted by looking at the individuals in isolation.
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  • 125
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    Journal of evolutionary economics 9 (1999), S. 109-133 
    ISSN: 1432-1386
    Keywords: Key words: Discontinuity ; Evolution ; Logistic diffusion ; Non-linearity ; Non-stationarity ; Self-organisation ; Spectral methods ; JEL-classification: C4; C5; N1; N2
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract. This paper offers an econometric methodology for the detection of self-organisational change (defined in terms of the presence of time irreversibility, structural change and fundamental uncertainty) in economic processes that follow logistic diffusion growth paths in historical time. The approach we adopted is built upon recent developments in `moving window' spectral methods which are applied to the scaled residuals generated by estimated logistic diffusion models. We illustrate the use of such methods by examining the case of a financial instrument, namely, the Australian Building Society Deposit, which experienced logistic growth in its market share until bank deregulation was enacted in the 1980s. We show that there is clear evidence that self-organisational change is present over the historical period considered.
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  • 126
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    Journal of mathematical biology 34 (1996), S. 556-578 
    ISSN: 1432-1416
    Keywords: Key words: Dynamical systems ; Evolution ; Game theory ; Asymptotic stability ; Population dynamics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract.  Evolution takes place in an ecological setting that typically involves interactions with other organisms. To describe such evolution, a structure is needed which incorporates the simultaneous evolution of interacting species. Here a formal framework for this purpose is suggested, extending from the microscopic interactions between individuals – the immediate cause of natural selection, through the mesoscopic population dynamics responsible for driving the replacement of one mutant phenotype by another, to the macroscopic process of phenotypic evolution arising from many such substitutions. The process of coevolution that results from this is illustrated in the context of predator–prey systems. With no more than qualitative information about the evolutionary dynamics, some basic properties of predator–prey coevolution become evident. More detailed understanding requires specification of an evolutionary dynamic; two models for this purpose are outlined, one from our own research on a stochastic process of mutation and selection and the other from quantitative genetics. Much of the interest in coevolution has been to characterize the properties of fixed points at which there is no further phenotypic evolution. Stability analysis of the fixed points of evolutionary dynamical systems is reviewed and leads to conclusions about the asymptotic states of evolution rather different from those of game-theoretic methods. These differences become especially important when evolution involves more than one species.
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  • 127
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    Journal of mathematical biology 34 (1996), S. 556-578 
    ISSN: 1432-1416
    Keywords: Dynamical systems ; Evolution ; Game theory ; Asymptotic stability ; Population dynamics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract Evolution takes place in an ecological setting that typically involves interactions with other organisms. To describe such evolution, a structure is needed which incorporates the simultaneous evolution of interacting species. Here a formal framework for this purpose is suggested, extending from the microscopic interactions between individuals — the immediate cause of natural selection, through the mesoscopic population dynamics responsible for driving the replacement of one mutant phenotype by another, to the macroscopic process of phenotypic evolution arising from many such substitutions. The process of coevolution that results from this is illustrated in the context of predator-prey systems. With no more than qualitative information about the evolutionary dynamics, some basic properties of predator-prey coevolution become evident. More detailed understanding requires specification of an evolutionary dynamics; two models for this purpose are outlined, one from our own research on a stochastic process of mutation and selection and the other from quantitative genetics. Much of the interest in coevolution has been to characterize the properties of fixed points at which there is no further phenotypic evolution. Stability analysis of the fixed points of evolutionary dynamical systems is reviewed and leads to conclusions about the asymptotic states of evolution rather different from those of game-theoretic methods. These differences become especially important when evolution involves more than one species.
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  • 128
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    Journal of evolutionary economics 6 (1996), S. 1-30 
    ISSN: 1432-1386
    Keywords: Innovation ; Technology ; Master equation ; Survival probability ; Evolution ; O3
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract Technological innovations have been investigated by means of substitution and diffusion as well as evolution models, each of them dealing with different aspects of the innovation problem. In this paper we follow the well known research traditions on self-organisation models of complex systems. For the first time in the literature we show the existence of a specific niche effect, which may occur in the first stage of establishment of a new technology. Using a stochastic Master equation approach, we obtain analytical expressions for the survival probabilities of a new technology in smaller or larger ensembles. As a main result we demonstrate how a hyperselection situation might be removed in a stochastic picture and thresholds against the prevailing of a new technology in a step-by-step process can be overcome.
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  • 129
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    Journal of evolutionary economics 6 (1996), S. 239-260 
    ISSN: 1432-1386
    Keywords: Synergetics ; Self-organisation ; Time-irreversibility ; Evolution ; Structural change ; O30 ; O31 ; C60 ; C63
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract This paper deals with synergetic methods, which have developed as a sub-field of the self-organisation approach in the natural sciences. Such methods have been used successfully to model structural transitions in physio-chemical contexts. The synergetic approach is explained in a non-technical way and the main elements of the synergetic methodology are introduced. The extent to which such methods can be applied in the presence of historical time series data, which are subject to underlying processes of evolutionary economic change, is assessed. Proposals, concerning more appropriate synergetic methods for evolutionary economic application, are considered.
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  • 130
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    Journal of evolutionary economics 8 (1998), S. 67-87 
    ISSN: 1432-1386
    Keywords: Key words: Bounded rationality ; Cognitive rationality ; Game equilibrium ; Evolution ; Learning ; JEL-classification: B 41; C 73; D 83; D 84
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract. In game theory, four dynamic processes converging towards an equilibrium are distinguished and ordered by way of agents' decreasing cognitive capacities. In the eductive process, each player has enough information to simulate perfectly the others' behavior and gets immediately to the equilibrium. In epistemic learning, each player updates his beliefs about others' future strategies, with regard to their sequentially observed actions. In behavioral learning, each player modifies his own strategies according to the observed payoffs obtained from his past actions. In the evolutionary process, each agent has a fixed strategy and reproduces in proportion to the utilities obtained through stochastic interactions. All along the spectrum, longer term dynamics makes up for weaker rationality, and physical relations substitute for mental interactions. Convergence, if any, is towards an always stronger equilibrium notion and selection of an equilibrium state becomes more sensitive to context and history. The processes can be mixed if associated to different periods, agents or mechanisms and deepened if obtained by formal reasoning principles.
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  • 131
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    Journal of evolutionary economics 9 (1999), S. 367-371 
    ISSN: 1432-1386
    Keywords: Key words: Bertrand ; Oligopoly ; Evolution ; Evolutionary stability ; JEL-classification: D43 ; L13 ; C72
    Source: Springer Online Journal Archives 1860-2000
    Topics: Economics
    Notes: Abstract. It is shown that the equilibrium notion of an evolutionary stable strategy (ESS) does have predictive power for standard models of Bertrand competition. This is in contrast to a recent claim by Qin and Stuart (1997). The claim is based on the observation that the solution concept ESS behaves discontinuously when finite (discrete) action games approach an infinite (continuous) action game in the limit. Furthermore, it is argued that from a model-theoretic point of view evolutionary stability in prices (i.e. in the Bertrand model) is quite different from evolutionary stability in quantities (i.e. in the Cournot model).
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  • 132
    ISSN: 1432-2242
    Keywords: 5S rDNA ; Evolution ; Protoplast fusion ; Somatic hybrids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The nucleotide sequences of the 5S rRNA genes (5S rDNA) of two Solanum tuberosum breeding lines (R1 and B15) and of the Mexican wild species S. pinnatisectum were determined and compared with each other and to the 5S rDNA of other Solanaceae species (Lycopersicon esculentum, Nicotiana rustica and Petunia hybrida). The 5S rDNA repeats of the Solanum species are 324–329 bp in length, and they exhibit 91–95% sequence identity. Sequence variability is mainly located in a short region of the spacer separating the 5S rRNA coding regions. A synthetic 28-mer oligonucleotide constructed according to this region can be used as a specific hybridization probe to distinguish symmetric somatic hybrids between S. tubersosum breeding line B15 and S. pinnatisectum produced by protoplast fusion. Interestingly, the two Solanum breeding lines R1 and B15 differ also in this spacer region.
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  • 133
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    Theoretical and applied genetics 92 (1996), S. 1108-1111 
    ISSN: 1432-2242
    Keywords: Evolution ; Tobacco ; Telomeres ; Ribosomal genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In order to investigate possible interactions between parental genomes in the composite genome of Nicotiana tabacum we have analyzed the organization of telomeric (TTTAGGG)n and ribosomal gene (rDNA) repeats in the progenitor genomes Nicotiana sylvestris and Nicotiana tomentosiformis or Nicotiana otophora. Telomeric arrays in the Nicotiana species tested are heterogeneous in length ranging from 20 to 200 kb in N. sylvestris, from 20 to 50 kb in N. tomentosiformis, from 15 to 100kb in N. otophora, and from 40 to 160kb in N. tabacum. The patterns of rDNA repeats (18S, 5.8S, 25S RNA) appeared to be highly homogeneous and speciesspecific; no parental rDNA units corresponding to N. sylvestris, N. tomentosiformis or N. otophora were found in the genome of N. tabacum by Southern hybridization. The results provide evidence for a species-specific evolution of telomeric and ribosomal repeats in the tobacco composite genome.
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  • 134
    ISSN: 1432-2242
    Keywords: Key words Glutenin loci ; Mapping ; Evolution ; Genome organization ; Wheat ; Aegilops umbellulata
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Eleven wheat-Ae. umbellulata recombinant lines involving chromosome 1U, including an important high-molecular-weight glutenin locus, were characterized by protein and RFLP markers. Four 1U-1A recombinants, one 1U-1B recombinant, two 1U deletions with either nullisomy for chromosome 1A or 1B and a 1U ditelosomic addition line were detected, while 3 recombinant lines involved 1U and non-homoeologous wheat chromosomes. Similar recombination events were found in independent lines, and no small segmental translocations of Ae. umbellulata chromatin were detected. Correlation of the markers with physical maps of the wheat-Ae. umbellulata breakpoints obtained using in situ hybridization enabled the marker order to be established on chromosomes 1A, 1B and 1U. The short arm of chromosome 1A probably differs from both 1U and 1B by one inversion. As now being found to be universal in the Triticeae, clustering of the genetical map in the distal physical regions of the group 1 chromosomes was found.
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    Theoretical and applied genetics 99 (1999), S. 203-209 
    ISSN: 1432-2242
    Keywords: Key words Homeobox gene ; KNOTTED1 ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Homeobox genes encode a family of DNA-binding regulatory proteins which are crucial for development. The first plant homeobox gene identified was knotted1 which plays a major role in leaf development. The knotted1 gene has a homeobox which encodes a homeodomain (HD) and HD proteins have been shown to function as transcription factors. A phylogenetic classification of the KNOTTED1 HD is presented. Here, we report six kn1 HDs from the cereals oat, barley, wheat, rye and rice. The KN1 class-I and -II genes can be divided into two distinct clades. Further, we hypothesize that KN1 and BELL1/MEIS HDs, (the closest non-KN1 class HDs) evolved from a common ancestor after divergence from the common precursor of all the homeobox genes. Our analysis clearly shows the presence of an ancestral KN1 HD from which all the known plant kn1 class of genes evolved.
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  • 136
    ISSN: 1432-2242
    Keywords: Pinus ; Allozymes ; Chloroplast DNA ; Genetic variation ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We studied allozyme and chloroplast (cp) DNA variation in natural populations of Pinus kesiya and P. merkusii from Thailand and Vietnam. The results showed striking differences between the two species in the amount and distribution of allozyme variation. P. kesiya harboured considerable allozyme variation and showed weak interpopulational differentiation. In contrast, P. merkmii had very low intrapopulational variability but a high level of interpopulational differentiation. The average Nei's genetic distance separating the two species was exceptionally high (0.701) taking into account their close taxonomic placement in the same subsection Sylvestres. The constructed phylogenetic trees revealed very early divergence of P. kesiya and P. merkusii. The present analysis of cpDNA variation also confirmed the dissimilar character of these two species and was compatible with other evidence indicating the outstanding position of P. merkusii as compared to other Asian members of the subsection Sylvestres. Analysis of cpDNA variation in sympatric populations of P. kesiya and P. merkusii revealed that they are pure representatives of the species in question. This result indicates that despite an overlapping distribution P. kesiya and P. merkusii do not hybridise in nature. We suggest that the distinctive character of P. merkusii is a result of an early separation from other Eurasian pines. Despite spatial proximity, P. kesiya and P. merkusii are kept apart by strong reproductive barriers. The low genetic variability of P. merkusii may be explained by previous bottlenecks, reduced gene flow among populations, and an inbreeding due to small population size and asynchronous flowering.
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    Theoretical and applied genetics 91 (1995), S. 189-194 
    ISSN: 1432-2242
    Keywords: Wheat ; HMW glutenin genes ; Polymerase chain reaction (PCR) ; Multigene families ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Specific amplification of the complete coding region of all six high-molecular-weight (HMW) glutenin genes present in hexaploid wheat was obtained by the polyerase chain reaction (PCR). Primers specific for the N-terminal region of the 1Dx gene and for the repetitive domain of the y-type HMW glutenin genes were also developed. Although the primers were constructed on the basis of the nucleotide sequences of HMW glutenin genes present in T. aestivum L. cv ‘Cheyenne’, they were very efficient in amplifying HMW glutenin genes of diploid and tetraploid wheat species. PCR analysis of HMW glutenin genes of T. urartu Tuman., T. longissimum (Schweinf. & Muschl.) Bowden and T. speltoides (Tausch) Gren. ex Richt, showed a high degree of length polymorphism, whereas a low degree of length variation was found in accessions of T. tauschii (Coss.) Schmal. Furthermore, using primers specific for the repetitive regions of HMW genes, we could demonstrate that the size variation observed was due to a different length of the central repetitive domain. The usefulness of the PCR-based approach to analyze the genetic polymorphism of HMW glutenin genes, to isolate new allelic variants, to estimate their molecular size and to verify the number of cysteine residues is discussed.
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    Theoretical and applied genetics 96 (1998), S. 904-911 
    ISSN: 1432-2242
    Keywords: Key words Musa ; Core collection ; Duplicates ; Evolution ; Variation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Proper classification and establishment of relationships between and within Musa taxonomic clusters will be important tools for the genetic improvement of plantain and banana. This paper assesses the value of a phenotypic diversity index, based on 16 quantitative descriptors, for germplasm clustering and for identification of duplicates among 92 triploid plantain and banana accessions. Data were recorded during the plant and ratoon crops at Onne, a humid forest location in southeastern Nigeria. The phenotypic distance matrix was developed by calculating the average difference between each pair of accessions for all quantitative descriptors. Significant differences were observed for this phenotypic distance index between Musa taxonomic clusters. The between-cluster variance was larger (0.001779) than the within-cluster variance (0.001380). Wright’s φFS, which measures the overall diversity, was 0.5663. This value suggested little gene flow among triploid taxonomic clusters via pollen, which explains the higher population differentiation exhibited by this vegetatively propagated crop with very low male fertility. The results also suggested that variation observed within each Musa taxonomic cluster arose from mutations accumulated throughout the history of cultivation of this crop. Some putative duplicates based on qualitative descriptors were not regarded as the same accession according to the phenotypic diversity index based on quantitative descriptors. Hence, gene-bank curators should assess quantitative descriptors for the identification of duplicate accessions in Musa.
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  • 139
    ISSN: 1432-2242
    Keywords: Endosperm development ; Evolution ; Imprinting ; Incompatibility ; Reciprocal crosses
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The Endosperm Balance Number (EBN) and the polar-nuclei activation (PNA) hypotheses have been developed to interpret, explain and predict interspecific and interploidy crossabilities in the Solanums and the Gramineae, respectively. Although these two hypotheses evolved independently, they share a number of common features. Assignment of EBNs and ‘activation/response values’ (AVs/RVs) depend on plumpness, size, and germinability of hybrid seeds. Also, both hypotheses emphasize the importance of a balanced parental genic contribution for the normal development of endosperm. However, in the EBN hypothesis a 2 maternal∶1 paternal EBN ratio is a prerequisite for successful interspecific crossability, while the PNA hypothesis is based on the stimulative strength of the male nuclei to initiate mitotic divisions in the primary endosperm nucleus and is idependent on a 2∶1 ratio between the RV of the polar nuclei and the AV of the male gamete. Differences and similarities betweeen the EBN and PNA hypotheses are summarized and contrasted. It is proposed that EBN and PNA be considered as the same concept.
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  • 140
    ISSN: 1432-2242
    Keywords: Key words Common wild rice ; Cultivated rice ; Evolution ; Genetic analysis ; Molecular marker
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Domesticated rice differs from the wild progenitor in large arrays of morphological and physiological traits. The present study was conducted to identify the genetic factors controlling the differences between cultivated rice and its wild progenitor, with the intention to assess the genetic basis of the changes associated with the processes of rice domestication. A total of 19 traits, including seven qualitative and 12 quantitative traits, that are related to domestication were scored in an F2 population from a cross between a variety of the Asian cultivated rice (Oryza sativa) and an accession of the common wild rice (O. rufipogon). Loci controlling the inheritance of these traits were determined by making use of a molecular linkage map consisting of 348 molecular-marker loci (313 RFLPs, 12 SSRs and 23 AFLPs) based on this F2 population. All seven qualitative traits were each controlled by a single Mendelian locus. Analysis of the 12 quantitative traits resolved a total of 44 putative QTLs with an average of 3.7 QTLs per trait. The amount of variation explained by individual QTLs ranged from a low of 6.9% to a high of 59.8%, and many of the QTLs accounted for more than 20% of the variation. Thus, genes of both major and minor effect were involved in the differences between wild and cultivated rice. The results also showed that most of the genetic factors (qualitative or QTLs) controlling the domestication-related traits were concentrated in a few chromosomal blocks. Such a clustered distribution of the genes may provide explanations for the genetic basis of the “domestication syndrome” observed in evolutionary studies and also for the “linkage drag” that occurs in many breeding programs. The information on the genetic basis of some desirable traits possessed by the wild parent may also be useful for facilitating the utilization of these traits in rice-breeding programs.
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    Theoretical and applied genetics 98 (1999), S. 744-750 
    ISSN: 1432-2242
    Keywords: Key words Chromosome pairing ; Translocations ; T. timopheevii ; T. turgidum ; T. aestivum ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract.  Chromosome pairing at metaphase-I was analyzed in F1 hybrids among T. turgidum (AABB), T. aestivum (AABBDD), and T. timopheevii (AtAtGG) to study the chromosome structure of T. timopheevii relative to durum (T. turgidum) and bread (T. aestivum) wheats. Individual chromosomes and their arms were identified by means of C-banding. Homologous pairing between the A-genome chromosomes was similar in the three hybrid types AAtBG, AAtBGD, and AABBD. However, associations of B-G were less frequent than B-B. Homoeologous associations were also observed, especially in the AAtBGD hybrids. T. timopheevii chromosomes 1At, 2At, 5At, 7At, 2G, 3G, 5G, and 6G do not differ structurally from their counterpart in the A and B genomes. Thus, these three polyploid species inherited translocation 5AL/4AL from the diploid A-genome donor. Chromosome rearrangements that occurred at the tetraploid level were different in T. turgidum and T. timopheevii. Translocation 4AL/7BS and a pericentric inversion of chromosome 4A originated only in the T. turgidum lineage. The two lines of T. timophevii studied carry four different translocations, 6AtS/1GS, 1GS/4GS, 4GS/4AtL, and 4AtL/3AtL, which most likely arose in that sequence. These structural differences support a diphyletic origin of polyploid wheats.
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  • 142
    ISSN: 1432-2242
    Keywords: Key words Catalase ; Oryza ; Rice ; Evolution ; p-SINE1
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Intron-2 of the Oryza sativa CatA catalase gene is similar in nucleotide sequence to p-SINE1, a retroposon, and seems to have been added to the ancestral genome of rice. To examine when the p-SINE1-like intron was inserted into CatA during the evolutionary divergence of Oryza species, and to elucidate the evolutionary relationships among Oryza species using the sequence of the intron as a marker, we performed polymerase chain reaction (PCR) analyses of 32 accessions of 17 Oryza species with various genome types. Agarose-gel electrophoresis of the PCR products revealed that all the Oryza species with an AA genome have the CatA homolog with the intron, whereas other Oryza species have the CatA homolog without the intron. These results indicate that intron-2 of CatA is a good marker for distinguishing species with an AA genome among Oryza species. Sequencing of the PCR products showed that all the introns are similar to p-SINE1, though with slight variations in length. We also performed PCR analyses using four accessions of three species in genera related to Oryza, and found that there is an intron in the CatA homolog of Leersia perrieri. On the other hand, the CatA homolog of Porteresia coarctata has no intron. Sequence data showed that the L. perrieri homolog has a p-SINE1-like intron similar to that in Oryza species with an AA genome. These results suggest that the p-SINE1-like intron was already present in the common ancestor of Oryza and L. perrieri and was then lost in the ancestors of P. coarctata and of the Oryza species other than those with an AA genome. The phylogenetic tree of Oryza species with an AA genome based on the nucleotide sequences of the introns leads us to propose that Oryza species with an AA genome evolved from an ancestor of Oryza longistaminata.
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  • 143
    ISSN: 1432-2242
    Keywords: Key words Catalase ; Rice ; Gene structure ; Evolution ; Transposon
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In order to understand the molecular evolution of catalase genes in higher plants, we compared the exon-intron structures of 12 genomic sequences from six plant species. It was assumed that the putative single primordial catalase gene had seven introns, because only those catalase genes having this structure are found in the monocotyledonae and dicotyledonae classes. After the evolutionary divergence of monocots from dicots, consecutive duplication of the primordial gene followed by the differential loss of introns occurred in each class to form three (or possibly four in dicots) diverse isozyme genes. In monocots, three ancestral isozyme genes were formed before the divergence of ancestral rice and maize. One of the rice genes, CatA, has an entirely new short intron which was not found in any other plant catalase gene examined. We have investigated the existence of the intron in the CatA homolog in other rice species by polymerase chain reaction (PCR) analysis. One major PCR product was found with the genomic DNAs from O. sativa (indica and japonica types), O. rufipogon and O. glaberrima. DNAs from several accessions of O. longistaminata showed variation in both the number and size of the DNA fragments amplified. PCR analyses and sequencing of the PCR products revealed that there are several CatA homologs having different sequences in some accessions of O. longistaminata. We have extended our study to other species in the Poaceae. The results suggest that the gain of the intron, most likely by insertion of a retroposon, took place in the ancestral genome of rice after its evolutionary divergence from other ancestral cereals such as barley, wheat and oat.
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    Theoretical and applied genetics 90 (1995), S. 356-363 
    ISSN: 1432-2242
    Keywords: Domestication ; Potato ; Chloroplast DNA ; Solanum stenotomum ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Five chloroplast DNA (ctDNA) types (W, T, C, S, and A) have previously been identified in the Andean tetraploid cultivated potatoes (Solanum tuberosum ssp. andigena) and three types (C, S, and A) in diploid cultivated potatoes (S. stenotomum). In this study, ctDNA types were determined for an additional 35 accessions of S. stenotomum and 97 accessions of putative ancestral wild species (15 of S. brevicaule, 26 of S. bukasovii, 4 of S. candolleanum, 25 of S. canasense, 17 of S. leptophyes, and 10 of S. multidissectum). The first five ctDNA types were also identified in S. stenotomum. The wild species were also polymorphic for ctDNA types except for S. brevicaule, which had only W-type ctDNA. T-type ctDNA was not found in any of the wild species and could have originated from W-type ctDNA after S. stenotomum arose. The other types of ctDNA evolved in wild species. The geographical distribution of each ctDNA type indicated that A-type ctDNA arose in central Peru and T-type ctDNA in the Bolivia-Argentine boundary. It is implied that potatoes were successively domesticated and that, in parallel, several wild species were differentiated from time to time and place to place from the ‘ancestral species’ complex. Subsequent sexual polyploidization formed a wide ctDNA diversity among the Andean tetraploid potatoes, and selection from them formed the limited ctDNA diversity found in Chilean tetraploid potatoes (ssp. tuberosum).
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  • 145
    ISSN: 1432-2242
    Keywords: Key words  Pinus ; Allozymes ; Chloroplast DNA ; Genetic variation ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract   We studied allozyme and chloroplast (cp) DNA variation in natural populations of Pinus kesiya and P. merkusii from Thailand and Vietnam. The results showed striking differences between the two species in the amount and distribution of allozyme variation. P. kesiya harboured considerable allozyme variation and showed weak interpopulational differentiation. In contrast, P. merkusii had very low intrapopulational variability but a high level of interpopulational differentiation. The average Nei's genetic distance separating the two species was exceptionally high (0.701) taking into account their close taxonomic placement in the same subsection Sylvestres. The constructed phylogenetic trees revealed very early divergence of P. kesiya and P. merkusii. The present analysis of cpDNA variation also confirmed the dissimilar character of these two species and was compatible with other evidence indicating the outstanding position of P. merkusii as compared to other Asian members of the subsection Sylvestres. Analysis of cpDNA variation in sympatric populations of P. kesiya and P. merkusii revealed that they are pure representatives of the species in question. This result indicates that despite an overlapping distribution P. kesiya and P. merkusii do not hybridise in nature. We suggest that the distinctive character of P. merkusii is a result of an early separation from other Eurasian pines. Despite spatial proximity, P. kesiya and P. merkusii are kept apart by strong reproductive barriers. The low genetic variability of P. merkusii may be explained by previous bottlenecks, reduced gene flow among populations, and an inbreeding due to small population size and asynchronous flowering.
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    Theoretical and applied genetics 92 (1996), S. 1003-1008 
    ISSN: 1432-2242
    Keywords: Fraxinus ; Evolution ; rDNA ; IGS structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The 6.8-kb rDNA intergenic spacer region of F. excelsior was isolated from a CsCl/actinomycin-D gradient and cloned into pUC18 for further characterization. We observed the presence of subrepeats delimited by HaeIII enzyme sites. These subrepeats were sub-cloned and 11 clones were sequenced. These corresponded to subrepeated elements of either 32 bp or 41 bp that shared a 23-bp common sequence in the 5′ end. Within each family of subrepeats, the percentage of common nucleotides was 84.4% for the 5 32-bp subrepeats and 67.4% for the 640-bp subrepeats. Non-repeated HaeIII fragments of 450 bp and 650 bp were also sub-cloned. To compare homology at the IGS region between the rDNA spacers of F. excelsior and the three related species (F. oxyphylla, F. americana, F. ornus), we conducted Southern hybridization analyses using each member of the 32-bp and 40-bp subrepeat families and the unique 450-bp and 650-bp fragments as probes. These analyses indicated that (1) the American ash is more genetically distant from the other three species that the latter are from each other and (2) F. oxyphylla and F. excelsior are more closely related to each other than to F. ornus.
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    Theoretical and applied genetics 92 (1996), S. 1003-1008 
    ISSN: 1432-2242
    Keywords: Key words Fraxinus ; Evolution ; rDNA ; IGS structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The 6.8-kb rDNA intergenic spacer region of F. excelsior was isolated from a CsCl/actinomycin-D gradient and cloned into pUC18 for further characterization. We observed the presence of subrepeats delimited by HaeIII enzyme sites. These subrepeats were sub-cloned and 11 clones were sequenced. These corresponded to subrepeated elements of either 32 bp or 41 bp that shared a 23-bp common sequence in the 5′ end. Within each family of subrepeats, the percentage of common nucleotides was 84.4% for the 5 32-bp subrepeats and 67.4% for the 6 40-bp subrepeats. Non-repeated HaeIII fragments of 450 bp and 650 bp were also sub-cloned. To compare homology at the IGS region between the rDNA spacers of F. excelsior and the three related species (F. oxyphylla, F. americana, F. ornus), we conducted Southern hybridization analyses using each member of the 32-bp and 40-bp subrepeat families and the unique 450-bp and 650-bp fragments as probes. These analyses indicated that (1) the American ash is more genetically distant from the other three species that the latter are from each other and (2) F. oxyphylla and F. excelsior are more closely related to each other than to F. ornus.
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  • 148
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    Theoretical and applied genetics 98 (1999), S. 478-484 
    ISSN: 1432-2242
    Keywords: Key words Endosperm development ; Evolution ; 2n gametes ; Breeding ; Potato
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The Endosperm Balance Number (EBN) hypothesis was developed in the early ’80s to explain the basis for normal seed development after intra- and inter-specific crosses, first in the potato and then in several other crop species. According to this hypothesis, each species has a genome-specific effective ploidy, the EBN, which must be in a 2 : 1 maternal to paternal ratio in the hybrid endosperm for normal development of the endosperm itself. This paper reviews how the EBN may act as a powerful isolating mechanism in sexual reproduction, maintaining the genome integrity of the species and playing an important role in the speciation of polyploids from diploids. We also provide further evidence that EBN is more important than chromosome ploidy in determining the success or failure of interspecific crosses. In fact, results from inter-ploidy and inter-EBN crosses to infuse 1EBN Solanum commersonii into 4EBN S. tuberosum demonstrated that the knowledge and manipulation of EBN is a useful tool in designing breeding schemes and in predicting the offspring ploidy and EBN. In this paper we also discuss the exceptions to the 2 : 1 EBN ratio, and report the evidence for endomitosis in the polar nuclei to explain exceptions to the EBN model in the potato.
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  • 149
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    Theoretical and applied genetics 94 (1997), S. 452-457 
    ISSN: 1432-2242
    Keywords: Key words Lentil ; Evolution ; Domestication ; cpDNA ; Plastid inheritance
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    Topics: Biology
    Notes: Abstract  Chloroplast DNA (cpDNA) restriction site diversity was assessed by 21 enzyme/probe combinations in 30 accessions of six Lens species, including the recently recognized L. lamottei and L. tomentosus. A total of 118 fragments were scored and 26 restriction site mutations were identified. The cpDNA restriction pattern supports circumscribing L. lamottei and L. tomentosus as independent species. The value of the data for reconstructing phylogeny in the genus is discussed. The cpDNA of all 13 accessions of the lentil’s wild progenitor, L. culinaris subsp. orientalis, differed from that of the single lentil cultivars used in this study. This diversity indicates that other populations of this subspecies from Turkey and Syria examined by Mayer and Soltis (1994) are potentially the founder members of lentil. Examination of L. lamottei×L. nigricans hybrids between accessions having different restriction patterns showed paternal plastid inheritance in L. nigricans.
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  • 150
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    Theoretical and applied genetics 94 (1997), S. 1038-1046 
    ISSN: 1432-2242
    Keywords: Key words Lolium ; Festuca ; Phylogeny ; Chloroplast DNA ; ITS sequence ; Genetic distance ; Evolution
    Source: Springer Online Journal Archives 1860-2000
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    Notes: Abstract  Molecular markers were used to investigate phylogenetic relationships among the eight species of ryegrass (Lolium) and 11 species of fescue (Festuca). RAPD and RFLP analyses were carried out on total bulked DNA from each population. Factorial analysis of a phenetic distance matrix yielded three major groups: (1) fine-leaved fescues, (2) broad-leaved fescues and (3) ryegrasses. Six non-coding regions of chloroplastic DNA were PCR-amplified, then digested by 20 restriction enzymes. Nuclear rDNA sequences, including internal transcribed spacers (ITSs) were used to estimate the average proportion of nucleotide substitutions. The correlation between substitution rate estimated from ITS sequences and that estimated from organelle DNA restriction sites was very high (0.94), and the corresponding UPGMA trees were very similar, with a slightly better resolution of the ITS tree in the Lolium genus. The time-scale inferred from substitution rates indicated that the period since divergence of the broad-leaved fescues from the fine-leaved fescues was four times as long as that since divergence of the genus Lolium from the former. Among the broad-leaved fescues, meadow fescue was closer to the Lolium group, while F. glaucescens and tall fescue were very closely related. North-African fescues were clustered together and giant fescue was the most differentiated species in this group. Our dataset was merged with ITS sequences recovered from the EMBL database, and the neighbor-joining method was used to draw a phylogenetic tree. In this tree, the tribe Poeae was clearly monophyletic, and more closely related to the Aveneae than to the Triticeae or Bromoideae. The genus Festuca appeared somewhat artificial, since Vulpia myuros and Dactylis glomerata were placed between fine-leaved and broad-leaved fescues.
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    Theoretical and applied genetics 94 (1997), S. 1065-1071 
    ISSN: 1432-2242
    Keywords: Key words Trees ; Chloroplast DNA ; PCR-RFLP ; Genetic variation ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  This paper reports on a PCR-RFLP analysis in a chloroplast DNA region consisting of coding and intergenic spacer sequences of trnS and the adjacent psbC gene. This region was PCR-amplified in 62 woody plant species, predominantly tree species, that represent a broad systematic range in both gymnosperms and dicotyledonous angiosperms. The amplification products were digested by the restriction endonuclease HaeIII (GG↓CC). Fourteen different restriction patterns occurred, 5 of which characterised representatives of the gymnosperms, and 9 angiosperm representatives. A single restriction site polymorphism revealed most of the species to share restriction patterns. Groups formed which showed relationships to plant systematic units. This phenomenon is discussed with regard to the psbC gene and the GGCC motif for tracing species’ relationships on a high taxonomic level of gymnosperms and angiosperms.
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  • 152
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    Theoretical and applied genetics 97 (1998), S. 657-670 
    ISSN: 1432-2242
    Keywords: Key words Triticum aestivum ; Phylogeny ; Genetic distance ; Genome ; Introgression ; Allopolyploidy ; RFLP ; Glutenin ; rRNA ; Non-transcribed spacers ; Evolution
    Source: Springer Online Journal Archives 1860-2000
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    Notes: Abstract  Polymorphism in the lengths of restriction fragments at 53 single-copy loci, the rRNA locus Nor3, and the high-molecular-weight glutenin locus Glu1 was investigated in the D genome of hexaploid Triticum aestivum and that of Aegilops tauschii, the source of the T. aestivum D genome. The distribution of genetic variation in Ae. tauschii suggests gene flow between Ae. tauschii ssp. strangulata and ssp. tauschii in Iran but less in Transcaucasia. The “strangulata” genepool is wider than it appears on the basis of morphology and includes ssp. strangulata in Transcaucasia and southeastern (SE) Caspian Iran and ssp. tauschii in north-central Iran and southwestern (SW) Caspian Iran. In the latter region, Ae. tauschii morphological varieties ‘meyeri’ and ‘typica’ are equidistant to ssp. strangulata in Transcaucasia, and both belong to the “strangulata” genepool. A model of the evolution of Ae. tauschii is presented. On the geographic region basis, the D genomes of all investigated forms of T. aestivum are most closely related to the “strangulata” genepool in Transcaucasia, Armenia in particular, and SW Caspian Iran. It is suggested that the principal area of the origin of T. aestivum is Armenia, but the SW coastal area of the Caspian Sea and a corridor between the two areas may have played a role as well. Little genetic differentiation was found among the D genomes of all investigated free-threshing and hulled forms of T. aestivum, and all appear to share a single D-genome genepool, in spite of the fact that several Ae. tauschii parents were involved in the evolution of T. aestivum.
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    Behavioral ecology and sociobiology 39 (1996), S. 189-194 
    ISSN: 1432-0762
    Keywords: Key words Sex ratio ; Evolution ; Heterogeneity ; Orthoptera ; Motility
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    Notes: Abstract Offspring sex ratio at hatching was examined in the bushcricket Poecilimon veluchianus. Offspring sex ratios varied significantly between females (Fig. 1). Low mortality prior to sex determination established that this heterogeneity was already present in the primary offspring sex ratio. Sperm age and female age had no influence on offspring sex ratio (Fig. 2). Male age at copulation, however, correlated significantly with offspring sex ratio (Fig. 3). There were two types of males: one type produced predominantly daughters when young and an increasing proportion of sons with age. The other type produced, independent of age, 1:1 offspring sex ratios (Fig. 4). The two types of males seem to occur in approximately equal numbers. Sex ratio variation (1) may adaptively compensate for local sex ratio biases caused by sex-specific motility, or (2) it may be adaptive if there is a sex-differential effect of laying date on offspring fitness.
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  • 154
    ISSN: 1432-0762
    Keywords: Key words Bats ; Echolocation ; Foraging ; Evolution ; Piscivory
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    Notes: Abstract We studied variability in foraging behavior of Noctilio albiventris (Chiroptera: Noctilionidae) in Costa Rica and Panamá and related it to properties of its echolocation behavior. N. albiventris searches for prey in high (〉20 cm) or low (〈20 cm) search flight, mostly over water. It captures insects in mid-air (aerial captures) and from the water surface (pointed dip). We once observed an individual dragging its feet through the water (directed random rake). In search flight, N. albiventris emits groups of echolocation signals (duration 10–11 ms) containing mixed signals with constant-frequency (CF) and frequency-modulated (FM) components, or pure CF signals. Sometimes, mostly over land, it produces long FM signals (duration 15–21 ms). When N. albiventris approaches prey in a pointed dip or in aerial captures, pulse duration and pulse interval are reduced, the CF component is eliminated, and a terminal phase with short FM signals (duration 2 ms) at high repetition rates (150–170 Hz) is emitted. Except for the last pulses in the terminal phase N. albiventris avoids overlap between emitted signals and echoes returning from prey. During rakes, echolocation behavior is similar to that in high search flight. We compare N. albiventris with its larger congener, N. leporinus, and discuss behavioral and morphological specializations that can be interpreted as preadaptations favoring the evolution of piscivory as seen in N. leporinus. Prominent among these specializations are the CF components of the echolocation signals which allow detection and evaluation of fluttering prey amidst clutter-echoes, high variability in foraging strategy and the associated echolocation behavior, as well as morphological specializations such as enlarged feet for capturing prey from the water surface.
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    Behavioral ecology and sociobiology 45 (1999), S. 269-275 
    ISSN: 1432-0762
    Keywords: Key words Polyandry ; Evolution ; Social insects ; Apis mellifera ; Task allocation ; Division of labor
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    Notes: Abstract A number of hypotheses have been proposed to explain the evolution of multiple mating in the honeybee queen. In particular, the consequences of reduced intracolonial relatedness provide plausible explanations for multiple mating with up to ten drones, but fail to account for the much higher mating frequencies observed in nature. In this paper, we propose an alternative mechanism which builds on non-linear relationships between intracolonial frequencies in genotypic worker specialization and colony fitness. If genes for any worker specialization confer an advantage on colony fitness only when they are rare, this would require a stable mix of sperm from a few drones which contribute that trait, and many which do not. To ensure both specific, low within-colony proportions of “rare specialist” genes, and to reduce random variation of these proportions would require mating with high numbers of drones. The quantitative implementation shows that moderate to very high numbers of matings are required to exploit colony advantages from genotypic allocation of workers to rare tasks. Extreme polyandry thus could result from colony selection dependent on the intracolonial frequency of rare genetic specialists.
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    Cell & tissue research 296 (1999), S. 19-25 
    ISSN: 1432-0878
    Keywords: Key wordsHoxA ; HoxD ; Limb ; Development ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Homeobox genes located in the 5’ part of the HoxA and HoxD complexes are required for proliferation of skeletal progenitor cells of the vertebrate limb. Specific combinations of gene products determine the length of the upper arm (genes belonging to groups 9 and 10), the lower arm (groups 10, 11 and 12) and the digits (groups 11, 12 and 13). In these different domains, individual gene products quantitatively contribute to an overall protein dose, with predominant roles for groups 11 and 13. Quantitative reduction in the gene dose in each set results in truncations of the corresponding anatomical regions. The physical order of the genes in the HoxA and HoxD complexes, as well as a unidirectional sequence in gene activation, allow for completion of the process in a precise order, which in turn makes possible the sequential outgrowth of the respective primordia. While the skeletal patterns of upper and lower limb are relatively stable throughout the tetrapods, more variation is seen in the digits. Molecular analysis of the underlying regulatory processes promises further exciting insights into the genetic control of development, pathology and the course of evolution.
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  • 157
    ISSN: 1432-0878
    Keywords: Key words Metabotropic glutamate/GABA-like receptor ; Evolution ; Geodia cydonium (Porifera)
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    Topics: Biology , Medicine
    Notes: Abstract To date, no conclusive evidence has been presented for the existence of neuronal-like elements in Porifera (sponges). In the present study, isolated cells from the marine sponge Geodia cydonium are shown to react to the excitatory amino acid glutamate with an increase in the concentration of intracellular calcium[Ca2+]i. This effect can also be observed when the compounds L-quisqualic acid (L-QA) or L-(+)-2-amino-4-phosphonobutyric acid (L-AP-4) are used. The effect of L-QA and L-AP-4, both agonists for metabotropic glutamate receptors (mGluRs), can be abolished by the antagonist of group I mGluRs, (RS)-α-methyl-4-carboxyphenylglycine. These data suggest that sponge cells contain an mGluR-like protein. A cDNA encoding rat mGluR subtype 1 has been used to identify the complete nucleotide sequence of G. cydonium cDNA coding for a 528-amino-acid-long protein (59 kDa) that displays marked overall similarity to mGluRs and to γ-amino-butyric acid B receptors. The deduced sponge polypeptide, termed putative mGlu/GABA-like receptor, displays the highest similarity to the two families of metabotropic receptors within the transmembrane segment. The N-terminal part of the sponge sequence shows similarity to mGluR4 and mGluR5. These findings suggest that the earliest evolutionary metazoan phylum, the Porifera, possesses a sophisticated intercellular communication and signaling system, as seen in the neuronal network of higher Metazoa.
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  • 158
    ISSN: 1617-4623
    Keywords: Chlamydomonas reinhardtii ; Chloroplast aldolase ; Evolution ; Intron/exon structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Genomic clones encoding the plastidic fructose- 1,6-bisphosphate aldolase ofChlamydomonas reinhardtii were isolated and sequenced. The gene contains three introns which are located within the coding sequence for the mature protein. No introns are located within or near the sequence encoding the transit-peptide, in contrast to the genes for plastidic aldolases of higher plants. Neither the number nor the positions of the three introns of theC. reinhardtii aldolase gene are conserved in the plastidic or cytosolic aldolase genes of higher plants and animals. The 5′ border sequences of introns in the aldolase gene ofC. reinhardtii exhibit the conserved plant consensus sequence. The 3′ acceptor splice sites for introns 1 and 3 show much less similarity to the eukaryotic consensus sequences than do those of intron 2. The plastidic aldolase gene has two tandemly repeated CAAT box motifs in the promoter region. Genomic Southern blots indicate that the gene is encoded by a single locus in theC. reinhardtii genome.
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    Molecular genetics and genomics 249 (1995), S. 265-273 
    ISSN: 1617-4623
    Keywords: Agrobacterium rhizogenes ; Horizontal gene transfer ; Evolution ; Ri plasmid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A tobacco homologue (trolC) of the rolC gene of the Agrobacterium rhizogenes Ri-plasmid was cloned and sequenced from Nicotiana tabacum L. cv. Havana 425. The coding region of trolC is similar in sequence (69–87% for DNA and 5489% for the deduced amino acid sequence) to rolC genes of the agropine, mannopine, and mikimopine strains of Ri-plasmids and the N. glauca rolC homologue. Southern analyses showed that trolC is encoded by a small gene family derived from the tomentosiformis ancestor of tobacco. This suggests that trolC resulted from an ancient transfer of DNA between A. rhizogenes and a progenitor of modern tobacco. Transcripts of trolC were detected in three morphologically distinct cultivars of tobacco. trolC mRNA accumulated in young leaves and shoot tips, but not in lower leaves and roots of mature plants. Accumulation of trolC mRNA in cultured leaf tissues was strongly down-regulated by auxin and induced by cytokinin. These results are of particular interest because they suggest that a gene of bacterial origin introduced during evolution can have a function in a modern plant.
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    Molecular genetics and genomics 250 (1996), S. 635-646 
    ISSN: 1617-4623
    Keywords: Drosophila ; Acid phosphatase ; Lysosomes ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract InDrosophila, unlike humans, the lysosomal acid phosphatase (Acph-1) is a non-essential enzyme. It is also one of the most rapidly evolving gene-enzyme systems in the genus. In order to determine which parts of the enzyme are conserved and which parts are apparently under little functional constraint, we cloned the gene fromDrosophila melanogaster via a chromosomal walk. Fragments from the gene were used to recover an apparently full-length cDNA. The cDNA was subcloned into aDrosophila transformation vector where it was under the control of the 5′ promoter sequence of thehsp-70 gene. Three independent transformants were obtained; in each, Acph-1 expression from the cDNA was constitutive and not dependent on heat shock, as determined by densitometric analyses of the allozymic forms of the enzyme. The pattern of expression indicates thehsp-70 and endogenousAcph-1 promoters act together in some, but not all, tissues. The sequence of the cDNA was determined using deletions made with exonuclease III, and primers deduced from the cDNA sequence were used to sequence the genomic clone. Five introns were found, and putative 5′ up-stream regulatory sequences were identified. Amino acid sequence comparisons have revealed several highly conserved motifs betweenDrosophila Acph-1 and vertebrate lysosomal and prostatic acid phosphatases.
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  • 161
    ISSN: 1617-4623
    Keywords: Key words Phytoene synthase ; Lycopene cyclase ; Complementation ; Astaxanthin ; Evolution
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    Topics: Biology
    Notes: Abstract The red heterobasidiomycetous yeast Xanthophyllomyces dendrorhous (perfect state of Phaffia rhodozyma) contains a novel type of carotenoid biosynthetic enzyme. Its structural gene, designated crtYB, was isolated by functional complementation in a genetically modified, carotenogenic Escherichia coli strain. Expression studies in different carotenogenic E. coli strains demonstrated that the crtYB gene encodes a bifunctional protein involved both in synthesis of phytoene from geranylgeranyl diphosphate and in cyclisation of lycopene to β-carotene. By sequence comparison with other phytoene synthases and complementation studies in E. coli with various deletion derivatives of the crtYB gene, the regions responsible for phytoene synthesis and lycopene cyclisation were localised within the protein.
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    Journal of plant research 108 (1995), S. 517-526 
    ISSN: 1618-0860
    Keywords: Cactaceae ; Evolution ; Water stress ; Wood ; Xeric adaptation ; Xylem
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Wide-band tracheids are a specialized tracheid type in which an annular or helical secondary wall projects deeply into the cell lumen. They are short, wide and spindle-shaped, and their bandlike secondary walls cover little of the primary wall, leaving most of it available for water diffusion. Wide-band tracheids appear to store and conduct water while preventing the spread of embolisms. They may be the most abundant tracheary element in the xylem, but they are always accompanied by at least a few vessels. Typically, fibers are absent wherever wide-band tracheids are present. Wide-band tracheids occur in the primary and secondary xylem of succulent stems, leaves and roots in genera of all three subfamilies of Cactaceae but were not found in the relictual genusPereskia, which lacks succulent tissues. In the large subfamily Cactoideae, wide-band tracheids occur only in derived members, and wide-band tracheids of North American Cactoideae are narrower and are aligned in a more orderly radial pattern than those of South American Cactoideae. Wide-band tracheids probably arose at least three times in Cactaceae.
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    Molecular genetics and genomics 251 (1996), S. 99-107 
    ISSN: 1617-4623
    Keywords: Key words Ribosomal genes ; Agrobacterium ; Evolution ; 23S rRNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  One of the four ribosomal RNA operons (rrnA) from the Agrobacterium vitis vitopine strain S4 was sequenced. rrnA is most closely related to the rrn operons of Bradyrhizobium japonicum and Rhodobacter sphaeroides and carries an fMet-tRNA gene downstream of its 5S gene, as in the case of R. sphaeroides. The 16S rRNA sequence of S4 differs from the A. vitis K309 type strain sequence by only one nucleotide, in spite of the fact that S4 and K309 have very different Ti plasmids. The predicted secondary structure of the S4 23S rRNA shows several features that are specific for the alpha proteobacteria, and an unusual branched structure in the universal B8 stem. The 3′ ends of the three other rrn copies of S4 were also cloned and sequenced. Sequence comparison delimits the 3′ ends of the four repeats and defines two groups: rrnA/rrnB and rrnC/rrnD.
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  • 164
    ISSN: 1617-4623
    Keywords: Key words Stigma glycoprotein ; Orychophragmus violaceus ; Cheiranthus cheiri ; Iberis amara ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The S-locus glycoprotein gene, SLG, which participates in the pollen-stigma interaction of self-incompatibility, and its unlinked homologue, SLR1, were analyzed in Raphanus sativus and three self-incompatible ornamental plants in the Brassicaceae. Among twenty-nine inbred lines of R. sativus, eighteen S haplotypes were identified on the basis of DNA polymorphisms detected by genomic Southern analysis using Brassica SLG probes. DNA fragments of SLG alleles specifically amplified from eight S haplotypes by PCR with class I SLG-specific primers showed different profiles following polyacrylamide gel electrophoresis, after digestion with a restriction endonuclease. The nucleotide sequences of the DNA fragments of these eight R. sativus SLG alleles were determined. Degrees of similarity of the nucleotide sequences to a Brassica SLG (S  6 SLG) ranged from 85.6% to 91.9%. Amino acid sequences deduced from these had the twelve conserved cysteine residues and the three hypervariable regions characteristic of Brassica SLGs. Phylogenetic analysis of the SLG sequences from Raphanus and Brassica revealed that the Raphanus SLGs did not form an independent cluster, but were dispersed in the tree, clustering together with Brassica SLGs. These results suggest that diversification of the SLG alleles of Raphanus and Brassica occurred before differentiation of these genera. Although SLR1 sequences from Orychophragmus violaceus were shown to be relatively closely related to Brassica and Raphanus SLR1 sequences, DNA fragments that are highly homologous to the Brassica SLG were not detected in this species. Two other ornamental plants in the Brassicaceae, which are related more distantly to Brassica than Orychophragmus, also lacked sequences highly homologous to Brassica SLG genes. The evolution of self-incompatibility in the Brassicaceae is discussed.
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    Plant systematics and evolution 210 (1998), S. 113-139 
    ISSN: 1615-6110
    Keywords: Solanaceae ; Solanum ; Evolution ; male sterility ; breeding system ; dioecy ; inaperturate pollen ; pollen development ; palynology ; plant reproduction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Dioecy has evolved independently several times in the large, mostly tropical genusSolanum. In all cases of dioecy inSolanum functionally male flowers have normal anthers, normal pollen and reduced stigmas while functionally female flowers have stigmas and anthers that appear normal but contain non-functional, usually inaperturate pollen. The inaperturate pollen has living cytoplasm, but apparently never germinates and it has been hypothesised that the pollen in these functionally female flowers is retained as a pollinator reward. Pollen morphology is compared in twelve of the thirteen known dioecious species ofSolanum, and some stages in the the development of inaperturate pollen in the anthers of functionally female flowers ofSolanum confertiseriatum of Western Ecuador are examined. Observations on the development and morphology of inaperturate pollen in functionally female flowers ofSolanum are related to hypotheses about the evolution of dioecy in the genus.
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    Plant systematics and evolution 219 (1999), S. 55-64 
    ISSN: 1615-6110
    Keywords: Evolution ; Encyclia cochleata ; inbreeding depression ; isozymes ; Orchidaceae ; outcrossing ; phenotype ; population genetics ; selfing
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    Topics: Biology
    Notes: Abstract To determine whether inbreeding depression accounts for the maintenance of outcrossing in populations of the self-compatible orchidEncyclia cochleata, the estimated selective advantage of selfing was compared to a measure of inbreeding depression. Individuals from three populations ofE. cochleata and some of their progeny were phenotyped using isozyme analysis. The electrophoretic data were used to estimate the outcrossing rate and the theoretical cost of outcrossing. Inbreeding depression was estimated by comparing the fitness of the progeny resulting from both types of pollinations. The seeds from outcrossed and selfed hand-pollinations and naturally pollinated seeds from a population of the triandrous form ofE. cochleata were grown aseptically on culture media, and their development over the next three years recorded. Inbreeding was common, particularly in one population (outcrossing rate 40%). However, the level of inbreeding depression was only 1–2%, considerably less inbreeding depression than expected.
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    Artificial life and robotics 1 (1997), S. 21-26 
    ISSN: 1614-7456
    Keywords: Evolution ; Software ; Artificial life ; Natural selection ; Artificial selection ; Evolvability ; Ecology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science
    Notes: Abstract A review of efforts to implement the process of evolution in a computational medium. The review will cover prominent examples, and discuss the major classes of implementations, their successes, and the obstacles they face.
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    Artificial life and robotics 2 (1998), S. 179-183 
    ISSN: 1614-7456
    Keywords: Evolution ; Vision system ; Genetic algorithm ; Neural network ; Artificial life
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science
    Notes: Abstract This paper proposes a framework for a genetic algorithm applied to determine and construct an organ, especially the neural network of a virtual creature. The vision system of the creature is a result of genetic evolution, and we are trying to realize this on the computer. We examine how the visual organ of the animal is evolved under a special environment (e.g., the specialized visual organ of an animal to catch a moving insect), and how many variations of neural networks exist. We also think it is possible to generalize the method to an automatic generation of various kinds of visual recognition system by adding various kinds of evolution any directions.
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    Artificial life and robotics 3 (1999), S. 127-132 
    ISSN: 1614-7456
    Keywords: Evolution ; Cooperative behavior ; Communication ; Species fitness ; Reciprocative
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science
    Notes: Abstract This paper considers the evolution of cooperative behaviors as the interaction among agents using a genetic algorithm to improve the performance of the task in a group (group performance). Previous research often usedthe group fitness method, which evaluates group performance for the evolution of multiple groups in parallel. However, this entails large simulation costs and the evolution speed is slow.The individual fitness method that evaluates theindividual performance of the task entails a smaller simulation cost. However, it can not improve the group performance since each agent behaves selfishly. To optimize the group performance, it is important to include bothcompetition andsharing. Therefore, this paper presentsthe species fitness method, which shares the individual performances of agents belonging to the same species in a group that all have the same chromosomes. We show comparative experiments on these three methods on the evolutionary simulation of a foraging task in a group. To test the interaction among the agents, four kinds of species are evolved which show their communication ability by demonstrating whether the agent can send or receive the signal for food. Experimental results show that evaluating the species variance fitness leads the agents into reciprocative actions.
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    Artificial life and robotics 3 (1999), S. 133-138 
    ISSN: 1614-7456
    Keywords: Bipedal walking ; Evolution ; Neuro-musculoskeletal model ; Genetic algorithms
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science
    Notes: Abstract The acquisition process of bipedal walking in humans was simulated using a neuro-musculo-skeletal model and genetic algorithms, based on the assumption that the shape of the body has been adapted for locomotion. The model was constructed as 10 two-dimensional rigid links with 26 muscles and 18 neural oscillators. Bipedal walking was generated as a mutual entrainment between neural oscillations and the pendulous movement of body dynamics. Evolutionary strategies incorporated, for example, as fitness in the genetic algorithms were assumed to decrease energy consumption, muscular fatigue, and load on the skeletal system. An initial population of 50 individuals was created, and an evolutionary simulation of 5000 steps was conducted. As a result, the shape of the body changed from that of a chimpanzee to that of a modern human, and the body size nearly reached the size of a modern human. These simulation results show that improving locomotive efficiency and reducing the load on the musculo-skeletal system are important factors affecting the evolution of the human body shape and bipedal walking. Such computer simulations help us to understand the process of evolution and adaptation for locomotion in humans.
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    International journal of anthropology 10 (1995), S. 177-181 
    ISSN: 1824-3096
    Keywords: Single cell gel electrophoresis assay ; Comet assay ; DNA damage ; DNA repair ; Human biology ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The estimation of genetic instability by direct extent of DNA damage and repair is an important aspect of studies on mutagenesis, carcinogenesis, aging and evolution. Different methods have been introduced from time to time in an effort to meet this need. Single cell gel electrophoresis (SCGE) assay is a new, simple and sensitive method of evaluating DNA damage and repair at individual cell level. This assay can be performed on extremely small number of cells and results can be obtained within a relatively short time. The SCGE assay has the potential to play an important role not only in the understanding of some of the fundamental aspects of human biology but also can be helpful in many practical ways.
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    Biology and philosophy 10 (1995), S. 129-180 
    ISSN: 1572-8404
    Keywords: Evolution ; explanation ; morality ; rationality ; normative communication ; fact/value distinction ; utilitarianism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Philosophy
    Notes: Abstract Gibbard's theory of rationality is “evolutionary” in terms of its result as well as its underpinning argument. The result is that judgments about what is “rational” are analyzed as being similar to judgments of morality — in view of what Darwin suggests concerning the latter. According to the Darwinian theory, moral judgments are based on sentiments which evolve to promote the survival and welfare of human societies. On Gibbard's theory, rationality judgments should be similarly regarded as expressing emotional attachments to behavioral norms which originate and function to coordinate social interaction. Consequently, Gibbard's theory of rationality might be used to illuminate Darwin's theory of morality, and vice versa. Additionally, as argued in the present essay, both can be further elaborated, and defended, by developing related themes in philosophical ethics: viz., connected with Hume and 20th-century emotivists. The main problem is that this general Darwinian approach faces widespread opposition nowadays, not only in ethics but in philosophy of science. The purpose of this essay is to analyze Gibbard's theory, critically and constructively, with emphasis on the pertinent commonalities in Darwin, Hume and the emotivists, while also critically addressing their common enemies. The pervasive methodological orientation is to relate this analysis to (philosophy of) science in general, and biological science in particular.
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    Biology and philosophy 10 (1995), S. 255-285 
    ISSN: 1572-8404
    Keywords: Animal ; Biology ; Consciousness ; Economics ; Evolution ; Natural Selection ; Suffering ; Welfare
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Philosophy
    Notes: Abstract Welfare biology is the study of living things and their environment with respect to their welfare (defined as net happiness, or enjoyment minus suffering). Despite difficulties of ascertaining and measuring welfare and relevancy to normative issues, welfare biology is a positive science. Evolutionary economics and population dynamics are used to help answer basic questions in welfare biology: Which species are affective sentients capable of welfare? Do they enjoy positive or negative welfare? Can their welfare be dramatically increased? Under plausible axioms, all conscious species are plastic and all plastic species are conscious (and, with a stronger axiom, capable of welfare). More complex niches favour the evolution of more rational species. Evolutionary economics also supports the common-sense view that individual sentients failing to survive to mate suffer negative welfare. A kind of God-made (or evolution-created) fairness between species is also unexpectedly found. The contrast between growth maximization (as may be favoured by natural selection), average welfare, and total welfare maximization is discussed. It is shown that welfare could be increased without even sacrificing numbers (at equilibrium). Since the long-term reduction in animal suffering depends on scientific advances, strict restrictions on animal experimentation may be counter-productive to animal welfare.
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    Biology and philosophy 11 (1996), S. 445-491 
    ISSN: 1572-8404
    Keywords: Th. Dobzhansky ; J.C. Greene ; Evolution ; Progress ; Christianity ; Teilhard de Chardin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Philosophy
    Notes: Abstract This is the correspondence (1959–1969), on the nature of the evolutionary process, between the biologist Theodosius Dobzhansky and the historian John C. Greene.
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    Perspectives in drug discovery and design 2 (1995), S. 437-444 
    ISSN: 1573-9023
    Keywords: Cysteine protease ; Parasite ; Helminths ; Protozoa ; Evolution ; Drug design
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Papain family cysteine proteases function primarily intracellularly in higher eukaryotes, but are often extracellular proteases in protozoan helminths. The utility of this class of enzymes is reflected in the diversity of functions they perform in both parasite life cycles and the pathogenesis of parasitic diseases. Examples include secretion of proteases into the gut of parasitic worms for hemoglobin degradation, release from the surface of nematodes to degrade cuticular proteins during molting, and facilitating excystment of protozoa.
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  • 176
    ISSN: 0032-8332
    Keywords: Reproductive behavior ; Sexual hormones ; Evolution ; Clawed New World monkeys ; Callimico goeldii
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    Topics: Biology
    Notes: Abstract The fate of most nonhuman primate species is intimately related to man. The increasing encroachment on the natural habitat has resulted in the decimation and even near extinction of some species. Along with this development, the basic concept in many modern zoos has changed from one of merely display to self-perpetuating units. Primate research facilities are orienting their research programs towards reproductive physiology and behavior in an effort to provide basic knowledge of reproduction in these species. This increased emphasis in the area of reproductive biology and the various efforts to improve breeding of these mostly endangered primates in captivity has stimulated the author to write this review. It represents an attempt to provide the reader with basic background information relating to the endocrinology and behavior of reproduction in the clawed New World monkeys as it exists at the time of publication. The intermediate evolutionary position ofCallimico goeldii between the clawed New World monkeys and the ‘true New World monkeys’ and our relatively poor knowledge about reproduction and behavior in this particular species fully justifies the focus on Goeldi’s monkey in this essay. This review is an attempt to provide a brief history of previous studies but also the basis for research in the future. The current status of knowledge of the small-bodied clawed monkeys is also discussed in an evolutionary context, with an emphasis on the different reproductive strategies in this dynamic group of primates. The outcome, not surprisingly, confirms the unique position ofCallimico goeldii in its social, ecological, and evolutionary environment.
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    Geologische Rundschau 85 (1996), S. 58-64 
    ISSN: 0016-7835
    Keywords: Key words Aperiodicity ; Buckling ; Evolution ; Modelling ; Spatial chaos
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    Topics: Geosciences
    Notes: Abstract  Naturally occurring fold systems are typically irregular. Although such systems may sometimes be approximated by a periodic geometry, in reality they are commonly aperiodic. Ord (1994) has proposed that naturally occurring fold systems may display spatial chaos in their geometry. Previous work has indicated that linear theories for the formation of fold systems, such as those developed by Biot (1965), result in strictly periodic geometries. In this paper the development of spatially chaotic geometries is explored for a thin compressed elastic layer embedded in a viscoelastic medium which shows elastic softening. In particular, it is shown that spatially localized forms of buckling can develop and the evolution of these systems in the time domain is presented. A nonlinear partial differential equation, fourth order in a spatial variable and first order in time, is found to govern the evolution. A related nonlinear fourth-order ordinary differential equation governs an initial elastic phase of folding. The latter equation belongs to a class with spatially chaotic solutions. The paper reviews the implications of localization in the geological framework, and draws some tentative conclusions about the development of spatial chaos. Crudely arrived-at, yet plausible, evolutionary time plots under the constraint of constant applied end displacement are presented. Emphasis throughout is on phenomenology, rather than underlying mathematics or numerics.
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    Molecular genetics and genomics 251 (1996), S. 99-107 
    ISSN: 1617-4623
    Keywords: Ribosomal genes ; Agrobacterium ; Evolution ; 23S rRNA
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    Topics: Biology
    Notes: Abstract One of the four ribosomal RNA operons (rrnA) from theAgrobacterium vitis vitopine strain S4 was sequenced.rrnA is most closely related to therrn operons ofBradyrhizobium japonicum andRhodobacter sphaeroides and carries an fMet-tRNA gene downstream of its 5S gene, as in the case ofR. sphaeroides. The 16S rRNA sequence of S4 differs from theA. vitis K309 type strain sequence by only one nucleotide, in spite of the fact that S4 and K309 have very different Ti plasmids. The predicted secondary structure of the S4 23S rRNA shows several features that are specific for the alpha proteobacteria, and an unusual branched structure in the universal B8 stem. The 3′ ends of the three otherrrn copies of S4 were also cloned and sequenced. Sequence comparison delimits the 3′ ends of the four repeats and defines two groups:rrnA/rrnB andrrnC/rrnD.
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    Plant systematics and evolution 197 (1995), S. 19-32 
    ISSN: 1615-6110
    Keywords: Juglandaceae ; Juglans ; Evolution ; nuclear DNA ; phylogeny ; restriction fragment length polymorphism ; RFLPs ; walnuts
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract RFLPs were studied in 13Juglans species to determine phylogenetic relationships inJuglans. Allele frequency data were used to generate genetic distance matrices and fragment data were used to generate genetic distances based upon shared-fragments and to perform parsimony analysis. Although similar cluster analyses result from analysing allelic and shared-fragment distance, the two types of distance values displayed variable correspondence with each other. Parsimony analysis produced a tree similar to distance data trees, but with additional phylogenetic resolution agreeing with previous systematic studies. All analyses indicate an ancient origin ofJ. regia, previously considered a recently derived species.
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    Molecular genetics and genomics 256 (1997), S. 277-281 
    ISSN: 1617-4623
    Keywords: Key words Starvation ; Catabolite repression ; DNA repair ; SOS response ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Bacteria live in unstructured and structured environments, experiencing feast and famine lifestyles. Bacterial colonies can be viewed as model structured environments. SOS induction and mutagenesis have been observed in aging Escherichia coli colonies, in the absence of exogenous sources of DNA damage. This cAMP-dependent mutagenesis occurring in Resting Organisms in a Structured Environment (ROSE) is unaffected by a umuC mutation and therefore differs from both targeted UV mutagenesis and recA730 (SOS constitutive) untargeted mutagenesis. As a recB mutation has only a minor effect on ROSE mutagenesis it also differs from both adaptive reversion of the lacI33 allele and from iSDR (inducible Stable DNA Replication) mutagenesis. Besides its recA and lexA dependence, ROSE mutagenesis is also uvrB and polA dependent. These genetic requirements are reminiscent of the untargeted mutagenesis in λ phage observed when unirradiated λ infects UV-irradiated E. coli. These mutations, which are not observed in aging liquid cultures, accumulate linearly with the age of the colonies. ROSE mutagenesis might offer a good model for bacterial mutagenesis in structured environments such as biofilms and for mutagenesis of quiescent eukaryotic cells.
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  • 181
    ISSN: 1617-4623
    Keywords: Key wordsTc1-mariner ; Filamentous fungi ; Fusarium oxysporum ; Transposase ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The transposable element impala is a member of the widespread superfamily of Tc1-mariner transposons, identified in the genome of the plant pathogenic fungus Fusarium oxysporum. This element is present in a low copy number and is actively transposed in the F.␣oxysporum strain F24 that is pathogenic for melons. The structure of the impala family was investigated by cloning and sequencing all the genomic copies. The analysis revealed that this family is composed of full-length and truncated copies. Four copies contained a long open reading frame that could potentially encode a transposase of 340 amino acids. The presence of conserved functional domains (a nuclear localisation signal, a catalytic DDE domain and a DNA-binding domain) suggests that these four copies may be autonomous elements. Sequence comparisons and phylogenetic analysis of the impala copies defined three subfamilies, which differ by a high level of nucleotide polymorphism (around 20%). The coexistence of these divergent subfamilies in the same genome may indicate that the impala family is of ancient origin and/or that it arose by successive horizontal transmission events.
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  • 182
    ISSN: 1617-4623
    Keywords: Key words Catalase ; Oryza ; Rice ; Evolution ; Tourist
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Tourist-OsaCatA, a transposable element, was found in the 5′-flanking region of the rice gene CatA. The characteristics of this element are similar to those of the other Tourist elements so far found in Oryza sativa. PCR and sequence analyses of 37 accessions of 18 species revealed that all the Oryza species examined, except for one accession, have either a full-length or a partial Tourist element at this locus. Unlike the Tourist elements previously reported, this Tourist element is found in all four Oryza species complexes in the Oryzeae tribe. All AA genome Oryza species, except O. longistaminata, contain the full-length Tourist element. O. longistaminata and the species of the O. officinalis, O. meyeriana and O. ridleyi complexes contain the partial element. A phylogenetic tree of Oryza species based on the nucleotide sequences of these Tourist elements was constructed. The O. longistaminata accessions were placed near the neighboring cluster of the officinalis complex. We propose that the ancestor of O. longistaminata and that of other species with the AA genome diverged, and the ancestor(s) of the O. officinalis, O. ridleyi and O. meyeriana complexes then diverged from the ancestor of O. longistaminata in the course of the evolution of the Oryza species. The Tourist elements associated with CatA and its orthologs thus provide useful tools for examining evolutionary relationships among Oryza species.
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    Molecular genetics and genomics 257 (1998), S. 264-270 
    ISSN: 1617-4623
    Keywords: Key words Fibroin ; Glycosylation ; DNA sequence ; Evolution ; Silkworm
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The water-insoluble core of lepidopteran silk is composed of four major proteins, but only three genes have been identified. This study demonstrates that the 29- and 30-kDa components of Galleria mellonella silk are derived from a single gene designated P25. The gene is expressed exclusively in the posterior section of the silk glands as a 2-kb mRNA, which accumulates in the feeding larvae and declines at molting. The mRNA encodes a peptide of 24 864 Da that exhibits 51% identity with the putative product of the P25 gene of Bombyx. The conservation of several amino acid stretches, including the relative positions of all 8 cysteines in the mature polypeptide, implies that the P25 proteins play similar, and apparently significant roles in silk formation in the two species. A Galleria P25 cDNA yields a peptide of about 25 kDa when translated in vitro; the 29- and 30-kDa forms present in the silk are derived from this primary translation product by differential glycosylation.
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    Molecular genetics and genomics 255 (1997), S. 201-208 
    ISSN: 1617-4623
    Keywords: Key words Cell differentiation ; Evolution ; Gene expression ; Protein phosphorylation ; Stochastic processes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In this theory, cell differentiation is a two-step mechanism at each stage of development. In the first step, gene expression is unstable. It occurs stochastically and produces different cell types. In the second step gene expression is stabilized by means of cellular interactions. However, this stabilization cannot occur until the combination of cell phenotypes corresponding to the developmental stage is expressed. This selection mechanism prevents disorganizing consequences of stochasticity in gene expression and directs the embryo towards the adult stage. Instability and stochasticity in gene expression are caused by random displacement of regulators along DNA, whereas phosphorylation and/or dephosphorylation of transcriptional regulators triggered by signal transduction between cells are responsible for the stabilization of stochastic gene expression. The origin of cellular differentiation is explained as an adaptation of cells to metabolic gradients created by substrate diffusion inside growing cell populations. This mechanism provides cells with complementary metabolism, increasing their ability to use food resources. Because the metabolic gradients are dependent on external substrate concentrations, cellular differentiation can also be viewed as an extension of natural selection inside organisms.
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    Journal of plant research 109 (1996), S. 353-361 
    ISSN: 1618-0860
    Keywords: Chlorophyta ; Cladistic analysis ; Evolution ; Molecular phylogeny-morphology ; Sexual reproduction ; Volvocaceae ; Volvocales
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Morphological features of sexual reproduction in the Volvocaceae are reviewed, focusing particularly on gametic union and zygote gemination. Both of the two conjugating gametes of the isogamous generaPandorina, Volvulina andYamagishiella bear a tubular mating structure (mating papilla), and plasmogamy is initiated by union of the papillae tips. On zygote germination, a single biflagellate gone cell is released from the zygote wall. Although all the anisogamous and oogamous genera of the Volvocaceae produce “sperm packets” during gametogenesis and a single gone cell at zygote germination, some difference can be recognized in the male gametes. The male gametes ofEudorina bear a tubular cytoplasmic protuberance (putative mating papllla) near the base of the flagella, whereas such a structure recognized at the light microscopic level is not evident inPleodorina andVolvox. Evolution of the sexual reproduction characteristics of volvocacean algae is discussed on the basis of recent cladistic analysis of morphological data as well as of the ribosomal (r) RNA phylogeny and large subunit of the ribulose-1, 5-biphosphate carboxylase/oxygenase(rbcL) gene trees.
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    Molecular genetics and genomics 257 (1997), S. 45-54 
    ISSN: 1617-4623
    Keywords: Key wordsEuglena ; Chloroplast ; Group II intron ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract 82 of the 155 chloroplast introns in Euglena gracilis have been categorized as group II introns. Because they are shorter and more divergent than group II introns from other organisms, the assignment of these Euglena introns to the group II class has been questioned. In the current study, two homologs of E. gracilispetB intron 1 and four homologs of psbC intron 2 have been isolated from related species and characterized. Based on a comparative sequence analysis of intron homologs, the intron core and four of the six helical domains present in the canonical group II intron structural model are conserved in E. gracilispetB intron 1 and psbC intron 2 and all of their homologs. Distal portions of domain I, which are involved in most of the tertiary interactions, are less well conserved than the central core.
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    Molecular genetics and genomics 250 (1996), S. 635-646 
    ISSN: 1617-4623
    Keywords: Key words Drosophila ; Acid phosphatase ; Lysosomes ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  In Drosophila, unlike humans, the lysosomal acid phosphatase (Acph-1) is a non-essential enzyme. It is also one of the most rapidly evolving gene-enzyme systems in the genus. In order to determine which parts of the enzyme are conserved and which parts are apparently under little functional constraint, we cloned the gene from Drosophila melanogaster via a chromosomal walk. Fragments from the gene were used to recover an apparently full-length cDNA. The cDNA was subcloned into a Drosophila transformation vector where it was under the control of the 5′ promoter sequence of the hsp-70 gene. Three independent transformants were obtained; in each, Acph-1 expression from the cDNA was constitutive and not dependent on heat shock, as determined by densitometric analyses of the allozymic forms of the enzyme. The pattern of expression indicates the hsp-70 and endogenous Acph-1 promoters act together in some, but not all, tissues. The sequence of the cDNA was determined using deletions made with exonuclease III, and primers deduced from the cDNA sequence were used to sequence the genomic clone. Five introns were found, and putative 5′ upstream regulatory sequences were identified. Amino acid sequence comparisons have revealed several highly conserved motifs between Drosophila Acph-1 and vertebrate lysosomal and prostatic acid phosphatases.
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  • 188
    ISSN: 1617-4623
    Keywords: Key words Chitinase ; Tobacco ; Transposition ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Various chitinases have been identified in plants and categorized into several groups based on the analysis of their sequences and domains. We have isolated a tobacco gene that encodes a predicted polypeptide consisting of a 20-amino acid N-terminal signal peptide, followed by a 245-amino acid chitinolytic domain. Although the predicted mature protein is basic and shows greater sequence identity to basic class I chitinases (75%) than to acidic class II chitinases (67%), it lacks the N-terminal cysteine-rich domain and the C-terminal vacuolar targeting signal that is diagnostic for class I chitinases. Therefore, this gene appears to encode a novel, basic, class II chitinase, which we have designated NtChia2;B1. Accumulation of Chia2;B1 mRNA was induced in leaves in association with the local-lesion response to tobacco mosaic virus (TMV) infection, and in response to treatment with salicylic acid, but was only slightly induced by treatment with ethephon. Little or no Chia2;B1 mRNA was detected in roots, flowers, and cell-suspension cultures, in which class I chitinase mRNAs accumulate to high concentrations. Sequence comparisons of Chia2;B1 with known tobacco class I and class II chitinase genes suggest that Chia2;B1 might encode an ancestral prototype of the present-day class I and class II isoforms. Possible mechanisms for chitinase gene evolution are discussed.
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    Molecular genetics and genomics 262 (1999), S. 189-198 
    ISSN: 1617-4623
    Keywords: Key wordsBordetella spp. ; Evolution ; Lipopolysaccharide biosynthesis ; Pulsed-field gel electrophoresis ; Representational difference analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Bordetella pertussis and B. bronchiseptica are genetically very closely related but differ significantly in their virulence properties. Using Representational Difference Analysis (RDA), 11 DNA fragments specific for B. pertussis Tohama I or B. bronchiseptica BB7865 were identified. All B. bronchiseptica BB7865-derived fragments also hybridized with chromosomal DNA from B. parapertussis but not from the B. pertussis strains Tohama I and W28, underlining the close phylogenetic relationship between B. bronchiseptica and B. parapertussis. The B. pertussis type strain BP18323 is a special case, as it contains DNA sequences characteristic for both B. pertussis and B. bronchiseptica. As demonstrated by pulsed-field gel electrophoresis, several of the BB7865-derived fragments are present on a single 30-kb XbaI fragment. Based on the sequences of putative coding regions, four of these fragments may code for proteins involved in carbohydrate metabolism or transport. In agreement with this notion, a mutant for one of these loci synthesizes a significantly altered lipopolysaccharide that lacks the O-specific side chains. The analysis of the corresponding genomic region in various Bordetella species showed that this locus is present in B. bronchiseptica and B. parapertussis but not in B. pertussis. This confirms that the RDA approach has identified a novel strain-specific LPS biosynthesis locus which accounts for the differences between the LPS structures elaborated by different Bordetella species.
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    Journal of plant research 108 (1995), S. 257-268 
    ISSN: 1618-0860
    Keywords: Aspleniaceae ; Evolution ; Hymenasplenium ; Molecular phylogeny ; Species ; Systematics ; Taxonomy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In Aspleniaceae,Hymenasplenium is a well-defined group with dorsiventral creeping rhizomes. Members ofHymenasplenium are widely distributed in the tropic zones of the world and have great variation in morphology and ecolgy, making it a good model group for plant systematics and evolutionary biology. I have worked on this group using techniques such as comparative morphology, ecology, cytology (for examining chromosomes and reproductive modes), phytochemistry and molecular biology. I considered the evolution of various phenetic characters based on a molecular phylogenetic tree which I recently obtained from sequence comparisons ofrbcL. In this paper, I will summarize the results.
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    Journal of plant research 108 (1995), S. 429-442 
    ISSN: 1618-0860
    Keywords: Aconitum SubgenusAconitum ; Chloroplast DNA ; Evolution ; Molecular phylogeny ; Plant geography ; Taxonomy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Classification of the genusAconitum (Ranunculaceae) has long been considered quite difficult because its species show high levels of morphological and ecological variability. The molecular phylogeny of Asian aconites,Aconitum subgenusAconitum was, therefore, studied based on RFLP and sequences of the intergenic spacer between thetrnL (UAA) 3′ exon andtrnF (GAA), and of thetrnL intron, of the chloroplast DNA. UsingAconitum subgenusLycoctonum as an outgroup, we obtained a statistically reliable molecular tree composed of six clades branched radiatively at the very base. There are three clades of Japanese aconites, a single clade of the species of Yunnan and Himalayas, and two clades of Siberian plants. All the tetraploid taxa of Japan we studied did not show any difference based on the molecular characters analyzed, though they have been classified into many taxa. Evolution and phytogeography of the Asian aconites as well as the phylogeny are discussed.
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  • 192
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    Protoplasma 203 (1998), S. 65-74 
    ISSN: 1615-6102
    Keywords: Cell plate ; Chara zeylanica ; Cytokinesis ; Evolution ; Meristem ; Plasmodesmata
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Cell plate formation inChara zeylanica was compared with recent models of cytokinesis in higher plants in order to gain insight into the evolutionary origin of plant cytokinetic processes. Transmission electron microscopy (TEM) reveals that while cytokinesis inC. zeylanica bears many features in common with that in higher plants, there are significant differences. Unlike that in higher plants, cytokinesis inC. zeylanica begins with a congregation of smooth membrane tubules that are closely associated with endoplasmic reticulum (ER) and Golgi membranes. Mitochondria and other organelles excluded by the phragmoplast in higher plants are present as well. Unlike in higher plants, phragmoplast microtubules persist throughout cytokinesis inC. zeylanica, and the cell plate generally forms across the whole cell at once, though development is patchy, due to small regions developing at different rates; the ends of the plate form last. By identifying aspects of cytokinesis that are different inC. zeylanica and plants, our study indicates which cytokinetic features are more likely to be derived, and which are more likely to be ancestral. In addition, we demonstrated that all nodal cells ofC. zeylanica are interconnected via plasmodesmata, lending support to the idea that, whileChara spp. are generally considered to be filamentous organisms, nodal regions may be thought of as meristemlike tissues.
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    Environmental biology of fishes 45 (1996), S. 219-235 
    ISSN: 1573-5133
    Keywords: Ecology ; Behaviour ; Evolution ; Cichlids ; Fisheries ; Conservation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis Ecological conditions in tropical lacustrine systems are considered by focusing on the evolution, maintenance, exploitation and vulnerability of fish communities in the African Great Lakes. The exceptionally high biodiversities in the littoral/sublittoral zones of the very ancient, deep, clear, permanently stratified rift lakes Tanganyika and Malawi, are contrasted with the simpler systems in their pelagic zones, also with biodiversity in the much younger, shallower Victoria, the world's largest tropical lake.
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  • 194
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    Theory and decision 42 (1997), S. 147-175 
    ISSN: 1573-7187
    Keywords: Evolution ; fairness ; dominance ; bargaining ; mutation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Sociology , Economics
    Notes: Abstract Empirical research has discovered that experimental subjects in ultimatum bargaining situations generally fail to play the decision-theoretic optimum strategy, and instead play something between that strategy and a fair split. In evolutionary dynamics, fair division and nearly fair division strategies often go to fixation and weakly dominated strategies can do quite well. Computer simulations were done using three different ultimatum bargaining games as determinates of fitness. (1) No tendency toward the elimination of weakly dominated strategies was observed, with or without mutation. (2) Strategies making fair demands had sizable basins of attraction. (3) In a system where five different demands can be made, demands closest to (approximately) 91% had the largest basins of attraction. (4) If the strategies have thresholds for acceptable demands, rather than individuated responses to each demand, the apparent optimum demand may be quite low: 64% for one set of trials.
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  • 195
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    World journal of microbiology and biotechnology 14 (1998), S. 607-610 
    ISSN: 1573-0972
    Keywords: Evolution ; life ; microorganisms ; molecular ; origin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract The origin of prokaryotic life is discussed with an emphasis on the self-assembly of early life in a microscale environment where ordered cellular structures and integrated functions evolved from disorder. Early molecular evolution may have been due to both molecular chaos and evolving molecular order.
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    Journal of chemical ecology 21 (1995), S. 911-923 
    ISSN: 1573-1561
    Keywords: Evolution ; ecology ; learning ; memory ; foraging ; habitat ; spotted owl
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Three kinds of memory help herbivores track changes in the environment. The first is the collective memory of the species with genetic instructions that have been shaped by the environment through millennia. This includes skin and gut defense systems. Auditory and visual stimuli and sensations of pain impinge upon the skin defense system that evolved in response to predation. The taste of food and the sensations of nausea and satiety are an integral part of the gut defense system that evolved in response to toxins and nutrients in plants. The second kind of memory in social mammals is represented by the mother, a source of transgenerational knowledge, who increases efficiency and reduces risk of learning about foods and environments. The third kind of memory is acquired by individual experience. Postingestive feedback from nutrients and toxins enables individuals to experience the consequences of food ingestion and to adjust food preference and selection commensurate with a food's utility. The three memories interact, each linking the past to the present, and collectively shape the present and future of every individual. Thus, the dynamics of foraging involves appreciating the uniqueness of individuals and subgroups of animals, each with their own genetic and behavioral history, and recognizing that foraging behaviors may not be stable, optimal, or even predictable in the conventional sense.
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    Earth, moon and planets 72 (1996), S. 31-34 
    ISSN: 1573-0794
    Keywords: Oort Cloud ; Evolution ; Close Encounters
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract The probability of variation of the integrals of the orbit as a result of an encounter was found for a two dimensional system. A method of solution of the Kolmogorov-Feller's equation is obtained using this probability function as a kernel, and it allows us to obtain the distribution of the integrals of the orbit as a function of time. The method is applied to the investigation of the evolution of orbits in the outer cometary cloud under the action of galactic stars. We consider the variations of orbits as a purely discontinuous random process, so we take into account not only distant but also close interactions.
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    Space science reviews 74 (1995), S. 363-367 
    ISSN: 1572-9672
    Keywords: Stars ; Abundances ; Evolution ; Rotation ; Mixing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract One of the most powerful tests of the stellar evolution theory is analysis of stars' atmospheric chemical composition. It has shown that some non-standard mixing different from ordinary convection, semiconvection and convective overshooting seems to occur in stellar interiors. In the present study Zahn's rotationally induced turbulent diffusion is assumed to be responsible for such kind of mixing. We compare results of our evolutionary calculations with available observational data for massive main-sequence stars and red giants in globular clusters.
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    Journal of statistical physics 87 (1997), S. 519-544 
    ISSN: 1572-9613
    Keywords: Evolution ; birth/death processes ; mean-field ; population dynamics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract We study in detail a recently proposed simple discrete model for evolution on smooth landscapes. An asymptotic solution of this model for long times is constructed. We find that the dynamics of the population is governed by correlation functions that although being formally down by powers ofN (the population size), nonetheless control the evolution process after a very short transient. The long-time behavior can be found analytically since only one of these higher order correlators (the two-point function) is relevant. We compare and contrast the exact findings derived herein with a previously proposed phenomenological treatment employing mean-field theory supplemented with a cutoff at small population density. Finally, we relate our results to the recently studied case of mutation on a totally flat landscape.
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    Experimental and applied acarology 22 (1998), S. 81-100 
    ISSN: 1572-9702
    Keywords: Evolution ; phytophagy ; trombidiform mites ; gnathosoma ; dispersal ; sex determination
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract This paper reviews the evolutionary aspects of obligate phytophagy (excluding mycophagy and phycophagy) in the mite suborder Trombidiformes. Phytophagy in the other acariform suborder, Sarcoptiformes, is limited to just a few species, amidst otherwise saprophagous or fungivorous taxa, that attack the living tissues of higher plants. The phylogenetic relationships of lineages that contain taxa of plant-feeding mites are reviewed briefly, to facilitate hypotheses about the number of times that phytophagy has arisen within the Trombidiformes. The relationship between the two most important plant-feeding taxa, the Tetranychoidea and Eriophyoidea, is so distant that their obligate phytophagy represents independent events. Outgroup comparisons allow an estimate of the relative ages when phytophagy arose. This background facilitates analyses of the evolutionary patterns of attributes relevant to phytophagy as a way of life. Styliform modifications of chelate chelicerae for predation or fungivory were fundamental pre-adaptations for effective phytophagy. Dispersal among the major lineages of phytophagous mites seems generally passive, with little evidence of phoretic behaviour. Continued individual mobility seems to be needed during ontogeny and adulthood, such that no scale-like or sac-like instars have arisen. Trends towards physogastric reproduction and ovoviviparity are not evident. Arrhenotokous sex determination predominates among lineages of phytophagous mites. The primary sex ratios are not usually highly female biased. Direct sperm transfer does not seem to have been advantageous or disadvantageous to adaptive radiations of plant-feeding lineages. Adaptive trends towards thelytoky are scattered and do not seem to have played major roles in speciation, diversification or trends towards increasing host specificity in lineages. Alternate asexual and sexual generations and life cycles on different species of hosts, as occur among families of aphid and scale insects, are not known. Among unrelated lineages of trombidiform mites, there appears to have been convergent evolution of attributes, such as those noted above, in response to similar selective pressures for a phytophagous way of life. The patterns of attributes discussed need experimental analysis and detailed documentation to test their accuracy and generality and to understand the selective pressures that have formed them.
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