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  • Evolution  (689)
  • Springer  (685)
  • Peter Lang International Academic Publishing Group  (4)
  • American Institute of Physics (AIP)
  • 101
    ISSN: 1432-1211
    Keywords: Key words Major histocompatibility complex (MHC) ; Sequence tagged sites (STS) ; Physical mapping ; Evolution ; HLA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  A yeast artificial chromosome (YAC) contig from the C57BL/6 (H2 b ) mouse was created from the major histocompatibility complex (Mhc, H2 in mouse) class Ib subregion, H2-M. It spans approximately 1.2 megabase (Mb) pairs and unites the previous 〉1.5-Mb YAC contigs (Jones et al. 1995) into a single contig, which includes 21 Mhc class I genes distal to H2-T1. A bacterial artificial chromosome (BAC) contig from the 129 (H2 bc ) mouse, spanning approximately 600 kilobases, was also built from Znf173 (Afp, a gene for acid finger protein), through Tctex5 (t-complex testis expressed-5) and Mog (myelin oligodendrocyte glycoprotein), to H2-M2. Twenty-four sequence-tagged site (STS) markers were newly developed, and 35 markers were mapped in the YAC/BAC contigs, which define the marker order as Cen –Znf173–Tctex5 – Mog–D17Tu42–D17Mit232–H2-M3–D17Leh525–H2-M2– Tel. The gene order of Znf173 – Tctex5 – Mog – D17Tu42 is conserved between mouse and human, showing that the middle H2-M region corresponds to the subregion of the human Mhc surrounding HLA-A.
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  • 102
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    Immunogenetics 47 (1998), S. 477-482 
    ISSN: 1432-1211
    Keywords: Key words Rat ; Major histocompatibility complex class I ; Mr1 ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  We isolated and analyzed a new rat gene which is homologous to the recently described human major histocompatibility complex class I-related gene MR1. The deduced amino acid sequence of the rat Mr1 gene shows conserved cysteine residues typical of class I genes as well as conserved β2-microglobulin and CD8 contact sites. Analysis of partial DNA sequences and restriction fragment length polymorphism patterns of several inbred rat strains indicate that Mr1 is not polymorphic. Mr1 is a single-copy gene, which could be mapped to rat chromosome 13 by co-segregation analysis of Mr1 and a microsatellite marker in the renin (Ren) gene in double-backcross hybrids. The recombination frequency between both genes was determined to be 14.7% (4.9–31.1, 95% confidence limits). Expression analysis revealed various Mr1 transcripts in each organ tested and occurrence of alternative splicing.
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  • 103
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    Immunogenetics 48 (1998), S. 82-86 
    ISSN: 1432-1211
    Keywords: Key words MHC ; H2 ; Kinases ; Alternative splicing ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
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  • 104
    ISSN: 1432-1211
    Keywords: Key words Major histocompatibility complex (Uhc) ; Retinoid receptor genes ; Evolution ; Linkage ; Zebrafish
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
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  • 105
    ISSN: 1432-1211
    Keywords: Key words β2-microglobulin ; Primates ; Evolution ; Diversity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Nucleotide sequences for the three exons of the β2-microglobulin (β2m) gene (B2m) were determined for 135 animals representing 37 species and all 16 genera of neotropical primates (Platyrrhini). Twenty-eight different nucleotide sequences, encoding for 26 different proteins, were obtained. In comparison with those of other primate species, the β2-microglobulins of the Platyrrhini form a distinct clade. Individual genera of neotropical primates have distinctive B2m sequences, but within a genera species can have either the same or different B2m sequences. B2m polymorphism was found within three of the species sampled: Callicebus personatus, Saguinus midas, and Aotus azarae. Of these only the polymorphism in A. azarae has an effect upon the mature, functional β2m protein: residue 4 being either alanine or threonine. The A. azarae B2m allele encoding alanine at position 4 is shared with another species of Aotus (A. infulatus). In pairwise comparison the mature β2m proteins of neotropical primates differ by 1–9 amino acid substitutions which can occur at 18 positions within the sequence. The substitutions are distributed throughout the primary structure but are more commonly found in loops rather than β strands of the tertiary structure. Of 17 residues of β2m which hydrogen-bond with the class I heavy chain in human MHC class I molecules, 13 are conserved in the neotropical primates. The overall pattern of sequence variation in the B2m genes of the Platyrrhini is consistent with an evolution by successive selectively neutral events.
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  • 106
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    International journal of game theory 27 (1998), S. 21-35 
    ISSN: 1432-1270
    Keywords: Evolution ; games ; multilevel ; group selection
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics , Economics
    Notes: Abstract In this paper, we analyze a generalization of the evolutionary model of Kandori, Mailath, & Rob (1993) where the population is partitioned into groups and evolution takes place “in parallel” at the following two levels: (i) within groups, at the lower level; among groups, at the higher one. Unlike in their context, efficiency considerations always overcome those of risk-dominance in the process of selecting the long-run equilibrium. This provides an explicitly dynamic basis for a conclusion reminiscent of those put forward in the biological literature by the so-called theories group selection. From a normative viewpoint, it suggests the potential importance of “decentralization”, here understood as local and independent interaction.
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  • 107
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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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  • 108
    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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  • 109
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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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  • 110
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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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  • 111
    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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  • 112
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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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  • 113
    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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  • 114
    ISSN: 1432-0762
    Keywords: Key words Bats ; Echolocation ; Foraging ; Evolution ; Piscivory
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    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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  • 115
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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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  • 116
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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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  • 117
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    Journal of human genetics 43 (1998), S. 185-186 
    ISSN: 1435-232X
    Keywords: Key words Chimpanzee ; Gorilla ; Orangutan ; Human Y-chromosome ; Amelogenin gene ; Telomeric sequences ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The Human Y-chromosome plays a central role in sex determination, and is composed of DNA sequences homologous to the Y-chromosome, families of Y-specific repetitive DNA sequences, and single copy sequences. We investigated the chromosomal location of Y-specific DNA sequences, in the chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), and orangutan (Pongo pygmaeus) by the fluorescence in situ hybridization (FISH) technique. The Yq subtelomeric DNA sequences (DYS427) have been observed to be intact at the presumed loci. Also, the amelogenin gene (AMELY, Yp11.2) revealed sequence homology and positional conservation in the higher primates, except in gorilla where positional divergence was observed.
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  • 118
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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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  • 119
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    Journal of comparative physiology 181 (1997), S. 367-382 
    ISSN: 1432-1351
    Keywords: Key words Stomatogastric ganglion ; Penaeus ; Pyloric circuit ; Neurotransmitter ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Pyloric pattern-generating neurons that control the pyloric region of the foregut were identified in the stomatogastric ganglion of the most primitive decapod genus Penaeus. Five types of motor neurons and one interneuron are involved in generation of pyloric motor pattern. One cell type of motor neurons innervates muscles of both the gastric mill and the pylorus like the gastric motor neurons in Cancer, but unlike those in Panulirus. These identified neurons are connected to each other either by electrical or inhibitory chemical synapses to construct the neural circuit. This pyloric circuit is similar to the homologous circuit of other crustacean species though some differences are seen in synaptic connections, supporting the hypothesis that the basic design of the neural circuit has been conserved during evolution of the Malacostraca, and that differences have occurred in the synaptic connectivity as the foregut structure has become complex. The motor neurons use either acetylcholine or glutamate as a neurotransmitter like in reptantians. The foregut structure, the number of the pyloric cells, muscle innervation, neurotransmitters, and circuitry are compared among malacostracan crustaceans to provide insight into how the neural circuits change and evolve to produce the motor patterns mediating behaviour.
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  • 120
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    Journal of comparative physiology 181 (1997), S. 477-483 
    ISSN: 1432-1351
    Keywords: Key words Insects ; Bats ; Ears ; Evolution ; Neotropics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Assuming that bat-detection is the primary function of moth ears, the ears of moths that are no longer exposed to bats should be deaf to echolocation call frequencies. To test this, we compared the auditory threshold curves of 7 species of Venezuelan day-flying moths (Notodontidae: Dioptinae) to those of 12 sympatric species of nocturnal moths (Notodontidae: Dudusinae, Noctuidae and Arctiidae). Whereas 2 dioptines (Josia turgida, Zunacetha annulata) revealed normal ears, 2 (J. radians, J. gopala) had reduced hearing at bat-specific frequencies (20–80 kHz) and the remaining 3 (Thirmida discinota, Polypoetes circumfumata and Xenorma cytheris) revealed pronounced to complete levels of high-frequency deafness. Although the bat-deaf ears of dioptines could function in other purposes (e.g., social communication), the poor sensitivities of these species even at their best frequencies suggest that these moths represent a state of advanced auditory degeneration brought about by their diurnal life history. The phylogeny of the Notodontidae further suggests that this deafness is a derived (apomorphic) condition and not a retention of a primitive (pleisiomorphic), insensitive state.
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  • 121
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    Journal of comparative physiology 180 (1997), S. 245-255 
    ISSN: 1432-1351
    Keywords: Key words Mole-rat  ;  Vocalization  ;  Acoustic communication  ;  Subterranean mammal  ; Hearing  ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract In captive adult Zambian mole-rats 14 different sounds (13 true vocalizations) have been recorded during different behavioural contexts. The sound analysis revealed that all sounds occurred in a low and middle frequency range with main energy below 10 kHz. The majority of calls contained components of 1.6–2 kHz, 0.63–0.8 kHz, and/or 5–6.3 kHz. The vocalization range thus matched well the hearing range as established in other studies. The frequency content of courtship calls in two species of Zambian Cryptomys was compared with that in naked mole-rats (Heterocephalus glaber) and blind mole-rats (Spalax ehrenbergi) as described in the literature. The frequency range of maximum sound energy is negatively correlated with the body weight and coincides with the frequencies of best hearing in the respective species. In general, the vocalization range in subterranean mammals is shifted towards low frequencies which are best propagated in underground burrows.
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  • 122
    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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  • 123
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    Bulletin of volcanology 59 (1997), S. 161-170 
    ISSN: 1432-0819
    Keywords: Key words Structure ; Evolution ; Uplift ; Geodetic modeling ; Alban Hills
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences
    Notes: Abstract  The Alban Hills, a Quaternary volcanic center lying west of the central Apennines, 15–25 km southeast of Rome, last erupted 19 ka and has produced approximately 290 km3 of eruptive deposits since the inception of volcanism at 580 ka. Earthquakes of moderate intensity have been generated there at least since the Roman age. Modern observations show that intermittent periods of swarm activity originate primarily beneath the youngest features, the phreatomagmatic craters on the west side of the volcano. Results from seismic tomography allow identification of a low-velocity region, perhaps still hot or partially molten, more than 6 km beneath the youngest craters and a high-velocity region, probably a solidified magma body, beneath the older central volcanic construct. Thirty centimeters of uplift measured by releveling supports the contention that high levels of seismicity during the 1980s and 1990s resulted from accumulation of magma beneath these craters. The volume of magma accumulation and the amount of maximum uplift was probably at least 40×106 m3 and 40 cm, respectively. Comparison of newer levelings with those completed in 1891 and 1927 suggests earlier episodes of uplift. The magma chamber beneath the western Alban Hills is probably responsible for much of the past 200 ka of eruptive activity, is still receiving intermittent batches of magma, and is, therefore, continuing to generate modest levels of volcanic unrest. Bending of overburden is the most likely cause of the persistent earthquakes, which generally have hypocenters above the 6-km-deep top of the magma reservoir. In this view, the most recent uplift and seismicity are probably characteristic and not precursors of more intense activity.
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    Development genes and evolution 207 (1997), S. 264-281 
    ISSN: 1432-041X
    Keywords: Key words yolk protein genes ; Calliphora ; Musca ; Evolution ; doublesex
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  We have investigated the conservation of regulatory elements for sex- and tissue-specific gene expression in three dipteran species, Drosophila melanogaster, Musca domestica and Calliphora erythrocephala, using the yolk protein (yp) genes. Yolk proteins of the fruitfly, medfly, housefly and blowfly are very well conserved both in their sequence and their expression in ovarian follicle cells and in fat bodies of adult females. Furthermore, yp regulation by both hormonal and nutritional factors shows similar features in all four species. To study conservation of yp regulation in dipteran insects, we tested 5′ flanking regions from one Musca yp gene and one Calliphora yp gene for enhancer functions in D. melanogaster. Two fragments of 823 and 1046 bp isolated from Musca and Calliphora yp genes, respectively, are able to direct correct expression of a reporter gene in the ovarian follicle cells of transformed Drosophila at specific stages during oogenesis. Surprisingly, these enhancers do not confer sex-specific reporter gene expression in the fat body, as expression was found in both sexes of the transformed flies. None-the-less by in vitro DNA/protein interaction assays, a 284-bp DNA region from the Musca yp enhancer was able to bind the Drosophila DOUBLESEX (DSX) protein, which in D.melanogaster confers sex-specific expression of yp. We speculate that the sex-determining pathway is not directly involved in yp regulation in Musca or Calliphora adult females, but depends instead on hormonal controls to achieve sex-specific expression of yp genes in the adult.
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  • 125
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    Development genes and evolution 207 (1997), S. 287-295 
    ISSN: 1432-041X
    Keywords: Key words Sense organ embryology ; Ambystoma embryology ; Homeobox genes ; Vertebrate genetics ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Gene expression has been studied in considerable detail in the developing vertebrate brain, neural crest, and some placode-derived organs. As a further investigation of vertebrate head morphogenesis, expression patterns of several homeobox-containing genes were examined using whole-mount in situ hybridization in a sensory system primitive for the vertebrate subphylum: the axolotl lateral lines and the placodes from which they develop. Axolotl Msx-2 and Dlx-3 are expressed in all of the lateral line placodes. Both genes are expressed throughout development of the lateral line system and their expression continues in the fully developed neuromasts. Expression within support cells is highly polarized. In contrast to most other observations of Msx genes in vertebrate organogenesis, expression of Msx-2 in developing lateral line organs is exclusively epithelial and is not associated with epithelial-mesenchymal interactions. A Hox-complex gene, Hoxb-3, is shown to be expressed in the embryonic hindbrain and in a lateral line placode at the same rostrocaudal level, but not in other placodes nor in mature lateral line organs. A Hox gene of a separate paralog group, Hoxa-4, is expressed in a more posterior hindbrain domain in the embryo, but is not expressed in the lateral line placode at that rostrocaudal level. These data provide the first test of the hypothesis that the neurogenic placodes develop in two rostrocaudal series aligned with the rhombomeric segments and patterned by combinations of Hox genes in parallel with the central nervous system.
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  • 126
    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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  • 127
    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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  • 128
    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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  • 129
    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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  • 130
    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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    Theoretical and applied genetics 94 (1997), S. 452-457 
    ISSN: 1432-2242
    Keywords: Key words Lentil ; Evolution ; Domestication ; cpDNA ; Plastid inheritance
    Source: Springer Online Journal Archives 1860-2000
    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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  • 132
    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 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
    Topics: Biology
    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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    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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    Immunogenetics 47 (1997), S. 6-16 
    ISSN: 1432-1211
    Keywords: Key words TNF ; Microsatellites ; Haplotype ; Evolution ; Response
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  The human major histocompatibility complex (MHC) contains a variety of genes, many of which are highly polymorphic and of immunological importance. A database of MHC extended haplotypes was used to integrate experimental, cell line, and population data. Three alleles of the human TNF-beta (lymphotoxin-alpha) gene were identified, named TNFB *1SL, TNFB *2LL, and TNFB *1LS, each representing a different lineage in the evolution of TNF region haplotypes. Lower variability in the length of the associated microsatellite alleles indicates that *1SL characterizes the youngest of the three haplotype lineages. Microsatellite haplotypes in the two older lineages show evidence for a coevolution of alleles through concerted expansions. Genetic predispositions to high and low TNF-alpha (cachectin) responses seem to have evolved independently in more than one lineage. The literature data suggest different, or even opposite, associations concerning the regulation of TNF-alpha in macrophages and lymphoid cells. Microsatellite ud may be the most informative marker for studies of the associations of individual TNF region markers with secretion levels, immunity, and disease.
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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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    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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    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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    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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    Human evolution 12 (1997), S. 233-239 
    ISSN: 1824-310X
    Keywords: Y-chromosome ; Hominoids ; PCR ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Every species of non-human primates, especially those of hominoids, has a variety of reproductive structures and accompanying male traits, such as sexual dimorphism and relative size of testis to body weight, which may be at least partly triggered by DNA on the Y-chromosome. Recently, a panel of PCR (Polymerase Chain Reaction) primer sets were designed to amplify various DNA segments spread over the human Y-chromosome. We applied these primer sets for amplification of DNA segments on the Y-chromosome of hominoid species: chimpanzee, bonobo (Pygmy chimpanzee), gorilla, orangutan, whitehanded gibbon, agile gibbon, and Japanese monkey as an out group. The DNA segments including SRY, testis determining factor, and ZFX/ZFY could be amplified clearly in males of all species examined. These highly conserved genes may serve important biological functions. However, as the phylogenic distance from humans increased, some of the DNA segments could not be amplified. For example, DYZ1 (SY160) could be amplified only using human DNA as a template, and DYF60S1 (SY61), DYZ217 (SY126) and DYS233 (SY148) could be amplified only using human and African great ape DNA. It is interesting to note that locus DYS250 (SY17) could not be amplified in chimpanzee and bonobo but amplified in gorilla and orangutan. Locus DYS251 (SY18) was amplified in all species except the white-handed gibbon. These results indicate that a variety of evolutionary events including mutation, deletion, insertion, and rearrangement occurred in Y-chromosome DNA during primate evolution.
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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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    Sexual plant reproduction 9 (1996), S. 357-361 
    ISSN: 1432-2145
    Keywords: 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 polymorphicS-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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    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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    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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    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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    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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    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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  • 149
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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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  • 150
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    Journal of comparative physiology 179 (1996), S. 371-384 
    ISSN: 1432-1351
    Keywords: Visual pigment ; Stomatopoda ; Visual ecology ; Evolution ; Photoreceptor ; Retina
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract 1. Interspecific diversity in the visual pigments of stomatopod crustaceans was characterized using microspectrophotometry. We examined the 10 visual pigments in main rhabdoms in retinas of 3 species of each of two genera of stomatopod crustaceans of the superfamily Gonodactyloidea, Gonodactylus (G. oerstedii, G. aloha, and G. curacaoensis) and Odontodactylus (O. scyllarus, O. brevirostris, and O. “havanensis”). Species were selected to provide a matched diversity of habitats. 2. In each genus, visual pigments varied in λmax in several regions of the retina, as revealed by analysis of variance. The variation within closely related species of the same genus implies that visual pigments can evolve rapidly in stomatopods. 3. In photoreceptors of the peripheral retina, which are devoted to spatial vision, visual pigment λmax decreased as the depth range of the various species increased, a typical pattern for marine animals. In contrast, visual pigment λmax in photoreceptors of retinal regions devoted to polarization vision (midband Rows 5 and 6) is not obviously correlated with the spectral environment, implying that polarization information may be confined to particular spectral ranges. Visual pigments of the tiered rows of the midband, which are committed to spectral analysis, span a larger spectral range in shallow-water than deepwater species.
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  • 151
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    Journal of molecular evolution 42 (1996), S. 570-579 
    ISSN: 1432-1432
    Keywords: Evolution ; Catalase ; Phylogenetic tree,Zea mays L. ; Isozyme ; Antioxidant genes ; Gene Structure ; Oxidative stress
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have compared the nucleotide and protein sequences of the three maize catalase genes with other plant catalases to reconstruct the evolutionary relationship among these catalases. These sequences were also compared with other eukaryotic and prokaryotic catalases. Phylogenies based on distances and parsimony analysis show that all plant catalases derive from a common ancestral catalase gene and can be divided into three distinct groups. The first, and major, group includes maizeCatl, barleyCat1, riceCatB and most of the dicot catalases. The second group is an apparent dicot-specific catalase group encompassing the tobaccoCat2 and tomatoCat. The third is a monocot-specific catalase class including the maize Cat3, barley Cat2, and riceCatA. The maize Cat2 gene is loosely related to the first group. The distinctive features of monocot-specific catalases are their extreme high codon bias at the third position and low degree of sequence similarity to other plant catalases. Similarities in the intron positions for several plant catalase genes support the conclusion of derivation from a common ancestral gene. The similar intron position between bean catalases and human catalase implies that the animal and plant catalases might have derived from a common progenitor gene sequence.
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  • 152
    ISSN: 1432-1432
    Keywords: Metalloproteinase ; Disintegrin ; Evolution ; Venom ; Phylogeny ; Gene duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The evolution of the Metalloproteinase Disintegrin Cysteine-rich (MDC) gene family and that of the mammalian Matrix-degrading Metalloproteinases (MMPs) are compared. The alignment of snake venom and mammalian MDC and MMP precursor sequences generated a phylogenetic tree that grouped these proteins mainly according to their function. Based on this observation, a common ancestry is suggested for mammalian and snake venom MDCs; it is also possible that gene duplication of the already-assembled domain structure, followed by divergence of the copies, may have significantly contributed to the evolution of the functionally diverse MDC proteins. The data also suggest that the structural resemblance of the zinc-binding motif of venom MDCs and MMPs may best be explained by common ancestry and conservation of the proteolytic motifs during the divergence of the proteins rather than through convergent evolution.
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  • 153
    ISSN: 1432-1432
    Keywords: Krebs cycle ; Evolution ; Metabolism ; Citric acid cycle ; Chemical design
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The evolutionary origin of the Krebs citric acid cycle has been for a long time a model case in the understanding of the origin and evolution of metabolic pathways: How can the emergence of such a complex pathway be explained? A number of speculative studies have been carried out that have reached the conclusion that the Krebs cycle evolved from pathways for amino acid biosynthesis, but many important questions remain open: Why and how did the full pathway emerge from there? Are other alternative routes for the same purpose possible? Are they better or worse? Have they had any opportunity to be developed in cellular metabolism evolution? We have analyzed the Krebs cycle as a problem of chemical design to oxidize acetate yielding reduction equivalents to the respiratory chain to make ATP. Our analysis demonstrates that although there are several different chemical solutions to this problem, the design of this metabolic pathway as it occurs in living cells is the best chemical solution: It has the least possible number of steps and it also has the greatest ATP yielding. Study of the evolutionary possibilities of each one-taking the available material to build new pathways-demonstrates that the emergence of the Krebs cycle has been a typical case of opportunism in molecular evolution. Our analysis proves, therefore, that the role of opportunism in evolution has converted a problem of several possible chemical solutions into asingle-solution problem, with the actual Krebs cycle demonstrated to be the best possible chemical design. Our results also allow us to derive the rules under which metabolic pathways emerged during the origin of life.
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  • 154
    ISSN: 1432-1432
    Keywords: Alleles ; Evolution ; Gene conversion ; Introns ; Nematode
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Globin genes from theCaenorhabditis speciesbriggsae andremanei were identified and compared with a previously describedC. elegans globin gene. The encoded globins share between 86% and 93% amino acid identity, with most of the changes in or just before the putative B helix.C. remanei was found to have two globin alleles,Crg1-1 andCrgl-2. The coding sequence for each is interrupted by a single intron in the same position. The exons of the two genes are only 1 % divergent at the nucleotide level and encode identical polypeptides. In contrast, intron sequence divergence is 16% and numerous insertions and deletions have significantly altered the size and content of both introns. Genetic crosses show thatCrg1-1 andCrgl-2 segregate as alleles. Homozygous lines for each allele were constructed and northern analysis confirmed the expression of both alleles. These data reveal an unusual situation wherein two alleles encoding identical proteins have diverged much more rapidly in their introns than the silent sites of their coding sequences, suggesting multiple gene conversion events.
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  • 155
    ISSN: 1432-1432
    Keywords: Histone H1° ; 3′ untranslated region ; Slippage ; Sequence simplicity ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The H1° gene has a long 3′ untranslated region (3′UTR) of 1,125 nucleotides in the rat and 1,310 in humans. Analysis of the sequences shows that they have features of simple DNA that suggest involvement of replication slippage in their evolution. These features include the length imbalance between the rat and human sequences; the abundance of single-base repeats, two-base runs and other simple motifs clustered along the sequence; and the presence of single-base repeat length polymorphisms in the rat and mouse sequences. Pairwise comparisons show numerous short insertions/deletions, often flanked by direct repeats. In addition, a proportion of short insertions/deletions results from length differences in conserved single-base repeats. Quantification of the sequence simplicity shows that simple sequences have been more actively incorporated in the human lineage than in the rodent lineage. The combination of insertions/deletions and nucleotide substitutions along the sequence gives rise to three main regions of homology: a highly variable central region flanked by more conserved regions nearest the coding region and the polyA addition site.
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  • 156
    ISSN: 1432-1432
    Keywords: Evolution ; Multigene family ; Recombination ; Trypanosome ; Variant surface glycoprotein
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The surface of the parasitic protozoanTrypanosoma brucei spp. is covered with a dense coat consisting of a single type of glycoprotein molecule, the variant surface glycoprotein (VSG). There may be as many as 1,000 genes for VSG within the genome ofT. brucei, and the switch of expression from one to another is the phenomenon of antigenic variation. As an approach to understanding the evolution of VSG genes we have determined the genomic DNA sequences of the eight genes encoding the variant surface glycoprotein 117 (VSG) family. From these data we have observed a number of features concerning the relationships between these genes: (1) there is a region of high variability confined to the N-terminus of the coding sequence, and comparison of the sequences with the available X-ray diffraction crystal structures suggests that two of the most variable stretches within the N-terminal domain are present on surface-exposed loops, indicating a role for epitope selection in evolution of these genes; (2) the 29 nucleotides surrounding the splice acceptor site are absolutely conserved in all eight 117 VSG genes; (3) numerous insertion/deletion mutations are located within or immediately downstream of the C-terminal protein-coding sequences: (4) within 500 by downstream of the insertion/deletion mutations are one or two copies of a repeat motif highly homologous to the recombinogenic 76-bp repeat sequences present upstream of many VSG basic copy genes and the expression-linked copy.
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  • 157
    ISSN: 1432-1432
    Keywords: Transposable elements ; Evolution ; Horizontal transfers and alternative hypotheses
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The integrase domain of RNA-mediated elements (class I) and the transposase domain of DNA-mediated transposable elements (class II) were compared. A number of elements contain the DDE signature, which plays an important role in their integration. The possible relationships betweenmariner-Tc1 andIS elements, retrotransposons, and retroviruses were analyzed from an alignment of this region. Themariner-Tc1 superfamily, and LTR retrotransposons and retroviruses were found to be monophyletic groups. However, theIS elements of bacteria were found in several groups. These results were used to propose an evolutionary history that suggests a common ancestor for some integrases and transposases.
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  • 158
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    Journal of molecular evolution 42 (1996), S. 79-84 
    ISSN: 1432-1432
    Keywords: LacY ; Lactose permease ; Evolution ; Reduced synonymous polymorphism ; Positive selection ; E. coli
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have determined the nucleotide sequences of sevenlacY alleles isolated from natural isolates ofEscherichia coli. Nucleotide heterozygosity estimates for this locus were compared to those obtained from previous studies of intraspecific variation at chromosomal loci, revealing thatlacY has unusually low synonymous site variation. The average pairwise heterozygosity of synonymous sites (Ks=0.0112+/-0.0100) is the second lowest reported and the lowest for loci that have an equivalent level of nonsynonymous variation. We consider several hypotheses to explain how different forces in evolution could act to create the observed pattern of polymorphism, including selection for translational efficiency and positive selection. Our analysis most strongly supports the hypothesis that positive selection has acted on thelacY locus inE. coli.
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  • 159
    ISSN: 1432-1432
    Keywords: Evolution ; Ribosomal RNA ; Cyanobacteria ; Leptolyngbya ; Oscillatoria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In order to determine the nearly complete 16S rRNA gene sequences of cyanobacteria originating from nonaxenic cultures, a cyanobacterium-specific oligonucleotide probe was developed to distinguish polymerase chain reaction (PCR) products of the cyanobacterial rRNA operons from those resulting from amplification of contaminating bacteria. Using this screening method the 16S rRNA genes of four nonaxenic filamentous cyanobacterial strains belonging to the generaLeptolyngbya andOscillatoria were cloned and sequenced. For the genusLeptolyngbya, the 16S rRNA sequence of the axenic strain PCC 73110 was also determined. Phylogenetic trees were constructed based on complete and partial sequences. The results show that the strainsLeptolyngbya foveolarum Komárek 1964/112,Leptolyngbya sp. VRUC 135 Albertano 1985/1, andLeptolyngbya boryanum PCC 73110 belong to the same cluster. StrainOscillatoria cf.corallinae SAG 8.92, which contains the rare photosynthetic pigment CU-phycoerythrin, is not closely related to other CU-phycoerythrin-containing cyanobacteria.Oscillatoria agardhii CYA 18, which is a representative of planktonicOscillatoria species that form toxic blooms in Norwegian inland waters, has no close relatives in the tree.
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  • 160
    ISSN: 1432-1432
    Keywords: Sperm nuclear basic proteins (SNBPs) ; Histone H1 ; Cnidaria ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have analyzed the chromosomal protein composition of the sperm from several species belonging to three different classes (Hydrozoa, Scyphozoa, Anthozoa) of the phylum Cnidaria. In every instance, the sperm nuclear basic proteins (SNBPs) were found to consist of one to two major protein fractions that belong to the histone H1 family, as can be deduced from their amino acid composition and solubility in dilute perchloric acid, and the presence of a trypsin-resistant core. In those species where mature spawned sperm could be obtained, we were able to show that these proteins completely replace the somatic histones from the stem cells that are present at the onset of spermatogenesis. The presence of a highly specialized histone H1 molecule in the sperm of this phylum provides support for the idea that the protamine-like proteins (PL) from higher groups in the phylogenetic tree (and possibly protamines as well) may all have evolved from a primitive histone H1 ancestor.
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  • 161
    ISSN: 1432-1432
    Keywords: Soybean ; Ferritin ; Plant-animal ; Monocotyledons ; Dicotyledons ; Plastid ; Gene organization ; Evolution ; Intron
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Ferritin, a protein widespread in nature, concentrates iron −1011−1012-fold above the solubility within a spherical shell of 24 subunits; it derives in plants and animals from a common ancestor (based on sequence) but displays a cytoplasmic location in animals compared to the plastid in contemporary plants. Ferritin gene regulation in plants and animals is altered by development, hormones, and excess iron; iron signals target DNA in plants but mRNA in animals. Evolution has thus conserved the two end points of ferritin gene expression, the physiological signals and the protein structure, while allowing some divergence of the genetic mechanisms. Comparison of ferritin gene organization in plants and animals, made possible by the cloning of a dicot (soy-bean) ferritin gene presented here and the recent cloning of two monocot (maize) ferritin genes, shows evolutionary divergence in ferritin gene organization between plants and animals but conservation among plants or among animals; divergence in the genetic mechanism for iron regulation is reflected by the absence in all three plant genes of the IRE, a highly conserved, noncoding sequence in vertebrate animal ferritin mRNA. In plant ferritin genes, the number of introns (n = 7) is higher than in animals (n = 3). Second, no intron positions are conserved when ferritin genes of plants and animals are compared, although all ferritin gene introns are in the coding region; within kingdoms, the intron positions in ferritin genes are conserved. Finally, secondary protein structure has no apparent relationship to intron/exon boundaries in plant ferritin genes, whereas in animal ferritin genes the correspondence is high. The structural differences in introns/exons among phylogenetically related ferritin coding sequences and the high conservation of the gene structure within plant or animal kingdoms suggest that kingdom-specific functional constraints may exist to maintain a particular intron/exon pattern within ferritin genes. In the case of plants, where ferritin gene intron placement is unrelated to triplet codons or protein structure, and where ferritin is targeted to the plastid, the selection pressure on gene organization may relate to RNA function and plastid/nuclear signaling.
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  • 162
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    Journal of molecular evolution 43 (1996), S. 399-404 
    ISSN: 1432-1432
    Keywords: Asarum ; Dioscorea ; Angiosperms ; Evolution ; Legumins ; Seed proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Analysis of legumin-encoding cDNAs fromDioscorea caucasica Lipsky (Dioscoreaceae) and fromAsarum europaeum L. (Aristolochiaceae) shows that there is an especially methionine-rich legumin subfamily present in the lower angiosperm clades including the Monocotyledoneae. It is characterized by a methionine content of 3–4 mol% which is roughly triple the methionine proportion of most other legumins. These “MetR” legumins, if present, still have to be detected in the higher angiosperms including the important seed crops. Evolutionary analysis suggests that the MetR legumins are the result of a gene duplication allowing the differentiation of legumin genes according to their sulfur content. The duplication event must have taken place before the split into mono- and dicotyledonous plants but probably after the separation of angiosperms and gymnosperms.
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  • 163
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    Journal of molecular evolution 43 (1996), S. 685-689 
    ISSN: 1432-1432
    Keywords: Retroposons ; Integration targets ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Genomic DNA fragments generated by the reverse transcription of cellular RNA are called retroposons. Because they are flanked by short repeats, mammalian retroposons are believed to integrate at staggered chromosomal breaks. Recently, a significant sequence pattern associated with the integration of Alu and ID repeats was identified (Jurka 1996). It is represented by the 5′ TTAAAA consensus sequence around the 5′ ends of flanking repeats of Alu, ID, as well as, of B1 and B2 retroposed elements as shown in this paper. This consensus is a potential target for enzymatic nicking which probably occurs in the complementary strand between 3′ AA and the following 3′ TTTT bases. The first four bases of the flanking repeats corresponding to the 3′ TTTT consensus sequence show some sequence variations that may be affected by complementary base pairing between the A-rich RNA tails and the DNA target sequences prior to nicking and reverse transcription. We discuss potential evidence for such base pairing based on correlated variations in nucleotide composition of different tail and target regions.
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  • 164
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    Development genes and evolution 206 (1996), S. 136-146 
    ISSN: 1432-041X
    Keywords: Key words Compound eye development ; Equator ; Evolution ; Homology ; Tribolium (Insecta ; Coleoptera)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Using electron microscopy, the first stages of ommatidial development in the flour beetle Tribolium castaneum were analysed in relation to the cellular architecture of the adult compound eye and were compared to the corresponding patterning process in the fruit fly Drosophila melanogaster. The ommatidia of the slightly horse-shoe shaped beetle compound eye contain six peripheral and two central retinula cells. The rhabdomere of the posteriorly located central photoreceptor cell is restricted to the distal half of the rhabdom whilst that of the anterior one is restricted to its proximal half. The development of the compound eye takes place in an external eye imaginal disc. Most stages of ommatidial development, as known from Drosophila, i.e. arc-like cell groups, five-cell clusters, immature eight-cell clusters and symmetrical eight-cell clusters, are very precisely conserved between the two species. Two major differences exist: 1. In Tribolium, the cone cell precursor cells synchronously join to the immature eight-cell cluster. As a consequence, the symmetrical eight-cell cluster immediately transforms into a four-cone-cell cluster. 2. The maturing ommatidia do not undergo rotation in Tribolium. Overall, no morphological indiation for an equator in the adult Tribolium compound eye could be found. Considering the strong evolutionary conservation of early ommatidial development, homology of photoreceptor cells of distantly related insects is proposed to be inferred from their ontogenetic origin.
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  • 165
    ISSN: 1432-041X
    Keywords: Key words Hydra ; Insulin ; Development ; Receptor ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  A gene encoding a receptor protein-tyrosine kinase closely related to the vertebrate insulin receptor has been identified in the Cnidarian Hydra vulgaris. The gene is expressed in both epithelial layers of the adult polyp. A particularly high level of expression is seen in the ectoderm of the proximal portions of the tentacles and in a ring of ectodermal cells at the border between the foot basal disk and body column. The expression pattern of the gene in asexual buds is dynamic; expression is high throughout the newly emerging bud but the area of high expression becomes restricted to the apex as the bud lengthens. When the bud begins hypostome and tentacle formation, a high level of expression appears at the bases of the emerging tentacles. Finally, a ring of high expression appears just above the foot of the bud, completing the pattern seen in the adult polyp. The presence of this receptor and its pattern of expression suggested that an endogenous molecule related to insulin plays a role in regulating cell division in the body column and in differentiation of the tentacle and foot cells in Hydra, with the switch between the two being determined by the level of the receptor. Treatment of Hydra polyps with mammalian insulin caused an increase in the number of ectodermal and endodermal cells undergoing DNA synthesis.
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  • 166
    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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  • 167
    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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  • 168
    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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  • 169
    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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    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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  • 171
    ISSN: 1572-8358
    Keywords: Animal cognition ; Evolution ; Representation ; Computation ; Significance ; Phenomenology ; Autonomy
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    Topics: Biology
    Notes: Abstract A distinction is made between two definitions of animal cognition: the one most frequently employed in cognitive sciences considers cognition as extracting and processing information; a more phenomenologically inspired model considers it as attributing to a form of the outside world a significance, linked to the state of the animal. The respective fields of validity of these two models are discussed along with the limitations they entail, and the questions they pose to evolutionary biologists are emphasized. This is followed by a presentation of a general overview of what might be the study of the evolution of knowledge in animals.
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    Geologische Rundschau 85 (1996), S. 58-64 
    ISSN: 0016-7835
    Keywords: Key words Aperiodicity ; Buckling ; Evolution ; Modelling ; Spatial chaos
    Source: Springer Online Journal Archives 1860-2000
    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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  • 173
    ISSN: 0032-8332
    Keywords: Reproductive behavior ; Sexual hormones ; Evolution ; Clawed New World monkeys ; Callimico goeldii
    Source: Springer Online Journal Archives 1860-2000
    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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    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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    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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    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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    Molecular genetics and genomics 250 (1996), S. 635-646 
    ISSN: 1617-4623
    Keywords: Key words Drosophila ; Acid phosphatase ; Lysosomes ; Evolution
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    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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    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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    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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    Environmental biology of fishes 45 (1996), S. 109-131 
    ISSN: 1573-5133
    Keywords: Evolution ; Diversity ; Behaviour ; Superspecialisation ; Sibling species ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis Evolution in great lakes has often been both quantitative (many endemic species of distantly related taxa often being present) and qualitative (outstanding levels of adaptive radiation having sometimes been achieved). These situations pose many questions, such as why there are so many endemics and so many superspecialists (and at the same time often many sibling species), as well as presenting problems relating to such matters as convergent evolution in different lakes, the possible role of key innovations, the nature of isolating mechanisms, competition and co-existence in complex communities, the roles of diverse mutualistic associations, and many others. These rich faunas also provide particularly favourable opportunities for studying patterns of speciation, while attempts to elucidate phylogenies in groups such as African cichlid fishes, that have radiated in several lakes, can be pursued on both a broad scale and at the intralacustrine level using both recently developed techniques and time-honoured methods. Rates of evolution, which differ widely between ecologically equivalent taxa in different lakes, have sometimes been extremely rapid, as attested by both molecular data and evidence from field studies. Notwithstanding their evolutionary exuberance, these rich faunas are fragile as demonstrated dramatically by the appalling tragedy that has befallen the haplochromine cichlid flock of Lake Victoria.
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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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    Environmental biology of fishes 46 (1996), S. 1-5 
    ISSN: 1573-5133
    Keywords: Hosts ; Origins ; Evolution ; Aquatic ecosystems ; Heteroxeny ; Paratenesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis Although they are the oldest and most diverse members of the subphylum, the fishes have relatively few nematode parasites in comparison with other vertebrate classes. It is hypothesized that this paucity of parasite species has occurred because nematode parasites first evolved in terrestrial hosts and only a few lines of these parasites were able to transfer to fish after the appearance of heteroxeny (use of intermediate hosts) and paratenesis (use of transport hosts). The inability of nematodes to initiate parasitism in aquatic ecosystems restricted fish parasites mainly to forms first adapted to terrestrial vertebrates and at the same time deprived large groups of aquatic invertebrates such as the crustaceans, annelids and molluscs of a nematode parasite fauna.
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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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    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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    Behavioral ecology and sociobiology 39 (1996), S. 189-194 
    ISSN: 1432-0762
    Keywords: Key words Sex ratio ; Evolution ; Heterogeneity ; Orthoptera ; Motility
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    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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    International journal of earth sciences 85 (1996), S. 58-64 
    ISSN: 1437-3262
    Keywords: Aperiodicity ; Buckling ; Evolution ; Modelling ; Spatial chaos
    Source: Springer Online Journal Archives 1860-2000
    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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  • 187
    ISSN: 1432-2242
    Keywords: Endosperm development ; Evolution ; Imprinting ; Incompatibility ; Reciprocal crosses
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    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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    Journal of molecular evolution 40 (1995), S. 570-577 
    ISSN: 1432-1432
    Keywords: Alternate reading frames ; Evolution ; Overlapping frames ; Homology search ; Primary sequence analysis ; Polycistronic genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Hypothetical Products from Noncoding Frames (i.e., HyPNoFs) are hypothetical, not-coded proteins, translated from alternate reading frames (i.e., coding+1 and coding+2) of cDNAs. HyPNoFs of CD4, PKC, oncostatin, bcl-2 proto-oncogene, tumor suppressor p53, cystic fibrosis transmembrane regulator (CFTR), and tumor necrosis factors a and β were searched as query sequences vs the SWISS-PROT data bank. Homology searches carried out revealed that hypothetical products (i.e., HyPNoFs) may share high similarity with real protein products actually coded. Sequence similarity of hypothetical products to real proteins is sometimes very high, suggesting common conformational features, according to the Sander and Schneider cutoff value. This finding supports the hypothesis that eukaryotic DNA, currently considered to be monocistronic, might occasionally have polycistronic regions, carrying different protein messages on overlapping frames. As yet, polycistronic genes have been observed in viral genomes only. The presence of polycistronic regions in eukaryotic genes is likely reminiscent of an ancient strategy, rather than a present feature of the genome in eukaryotes. These data suggest that thorough investigation of HyPNoFs is likely to improve our ability to trace genes' evolution and to investigate structure-function relationships of protein and DNA sequences.
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    ISSN: 1432-1432
    Keywords: Alcohol dehydrogenase ; Caenorhabditis elegans ; Evolution ; Gene families
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    Topics: Biology
    Notes: Abstract We have characterized two cDNA clones from the nematode Caenorhabditis elegans that display similarity to the alcohol dehydrogenase (ADH) gene family. The nucleotide sequences of these cDNAs predict that they encode Zn-containing long-chain ADH enzymes. Phylogenetic analysis suggests that one is most similar to dimeric class III ADHs found in diverse taxa; the other is most similar to the tetrameric forms of ADH previously described only in fungi.
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    Journal of molecular evolution 41 (1995), S. 293-298 
    ISSN: 1432-1432
    Keywords: β-tubulin ; Evolution ; Gene cluster ; Gene dispersion ; Drosophila montium subgroup
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The β1-, β2-, and β3-tubulin genes have been mapped by in situ hybridization on the polytene chromosomes of 11 selected species (15 strains) belonging to theDrosophila montium subgroup. Although the hybridization pattern among the strains of the same species does not differ, this pattern is significantly different among the species. The β-tubulin genes in themontium subgroup seem to be organized in a cluster, or in a semi-cluster, or are completely dispersed. The clustered arrangement is found in the North-Oriental sibling speciesD. auraria, D. triauraria, andD. quadraria. The semi-clustered arrangement, wherein the β1 and β2 genes are located at the same locus while β3 is at a different one, appears in the South-Oriental speciesD. bicomuta, D. serrata, andD. birchii, as well as in the Afrotropical speciesD. diplacantha andD. seguyi. The complete separation of the genes is observed in the Indian speciesD. kikkawai andD. jambulina and in the Afrotropical speciesD. vulcana. Based on the above results, a possible mode of evolution of the β-tubulin genes in the montium subgroup is attempted. In addition, phylogenetic relationships among themontium species are discussed.
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    Journal of molecular evolution 41 (1995), S. 293-298 
    ISSN: 1432-1432
    Keywords: β-tubulin ; Evolution ; Gene cluster ; Gene dispersion ; Drosophila montium subgroup
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The β1-, β2-, and β3-tubulin genes have been mapped by in situ hybridization on the polytene chromosomes of 11 selected species (15 strains) belonging to the Drosophila montium subgroup. Although the hybridization pattern among the strains of the same species does not differ, this pattern is significantly different among the species. The β-tubulin genes in the montium subgroup seem to be organized in a cluster, or in a semi-cluster, or are completely dispersed. The clustered arrangement is found in the North-Oriental sibling species D. auraria, D. triauraria, and D. quadraria. The semi-clustered arrangement, wherein the β1 and β2 genes are located at the same locus while β3 is at a different one, appears in the South-Oriental species D. bicomuta, D. serrata, and D. birchii, as well as in the Afrotropical species D. diplacantha and D. seguyi. The complete separation of the genes is observed in the Indian species D. kikkawai and D. jambulina and in the Afrotropical species D. vulcana. Based on the above results, a possible mode of evolution of the β-tubulin genes in the montium subgroup is attempted. In addition, phylogenetic relationships among the montium species are discussed.
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  • 192
    ISSN: 1432-1432
    Keywords: Giardia ; Trichomonas ; CDK ; CDC ; Unicellular ; Metazoa ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Cyclin-dependent kinase (CDK) and cell division control (CDC2) sequences are strongly conserved among eukaryotes and may complement the use of other sequence families in eukaryotic phylogenetic inference. We synthesized degenerate PCR primers to amplify the catalytic region of CDK homologs in representatives of the earliest available lineages of eukaryotes. CDK family sequence-based, maximum-likelihood distance measurements with neighbor joining, and Fitch-Margoliash least-squares analyses produced unrooted dendrograms that included protists, yeasts, and higher eukaryotes. Bootstrap confidence estimates supported CDK-based phylogenetic groupings among the protists, fungi, and vertebrates although resolution within these groups was often insignificant. However, Trichomonas vaginalis and Giardia lamblia exhibited two of the most divergent CDK-like sequences consistent with rRNA-phylogenetic inference of early divergence of these eukaryotic lineages. In the evolution from unicellular to multicellular organisms, a constellation of amino acid residues aligning with the human, CDK N-terminal β sheet may have undergone abrupt replacement.
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    Journal of molecular evolution 41 (1995), S. 813-832 
    ISSN: 1432-1432
    Keywords: Phylogeny ; Evolution ; Carbamoylphosphate synthetase ; Dihydroorotase ; Aspartate transcarbamoylase ; Intron ; Exon ; Arginine biosynthesis ; Pyrimidine biosynthesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Carbamoylphosphate is a common intermediate in the metabolic pathways leading to the biosynthesis of arginine and pyrimidines. The amino acid sequences of all available proteins that catalyze the formation of carbamoylphosphate were retrieved from Genbank and aligned to estimate their mutual phylogenetic relations. In gram-negative bacteria carbamoylphosphate is synthesized by a two-subunit enzyme with glutamiriase and carbamoylphosphate synthetase (CPS) activity, respectively. In gram-positive bacteria and lower eukaryotes this two-subunit CPS has become dedicated to arginine biosynthesis, while in higher eukaryotes the two subunits fused and subsequently lost the glutaminase activity. The CPS dedicated to pyrimidine synthesis is part of a multifunctional enzyme (CPS II), encoding in addition dihydroorotase and aspartate transcarbamoylase. Evidence is presented to strengthen the hypothesis that the two “kinas” subdomains of all CPS isozymes arose from a duplication of an ancestral gene in the progenote. A further duplication of the entire CPS gene occurred after the divergence of the plants and before the divergence of the fungi from the eukaryotec root, generating the two isoenzymes involved in either the synthesis of arginine or that of pyrimidines. The mutation rate was found to be five- to tenfold higher after the duplication than before, probably reflecting optimization of the enzymes for their newly acquired specialized function. We hypothesize that this duplication arose from a need for metabolic channeling for pyrimidine biosynthesis as it was accompanied by the tagging of the CPS gene with the genes for dihydroorotase and aspartate transcarbamoylase, and as the duplication occurred independently also in gram-positive bacteria. Analysis of the exon-intron organization of the two “kinase” subdomains in CPS I and II suggests that ancient exons may have comprised approx. 19 amino acids, in accordance with the prediction of the “intron-early” theory.
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  • 194
    ISSN: 1432-1432
    Keywords: Ribonuclease ; Gene duplication ; Evolution ; Ruminants
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Phylogenetic analysis, based on the primary structures of mammalian pancreatic-type ribonucleases, indicated that gene duplication events, which occurred during the evolution of ancestral ruminants, gave rise to the three paralogous enzymes present in the bovine species. Herein we report data that demonstrate the existence of the orthologues of the bovine pancreatic, seminal, and cerebral ribonucleases coding sequences in the genomes of giraffe and sheep. The “seminal” sequence is a pseudogene in both species. We also report an analysis of the transcriptional expression of ribonuclease genes in sheep tissues. The data presented support a model for positive selection acting on the molecular evolution of ruminant ribonuclease genes.
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  • 195
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    Journal of molecular evolution 40 (1995), S. 482-486 
    ISSN: 1432-1432
    Keywords: Aminoacyl-tRNA synthetase ; Computer analysis ; Evolution ; Genetic code ; tRNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract tRNA sequences were analyzed for sequence features correlated with known classes of aminoacyl-tRNA synthetase enzymes. The tRNAs were searched for distinguishing nucleotides anywhere in their sequences. The analyses did not find nucleotides predictive of synthetase class membership. We conclude that such nucleotides never existed in tRNA sequences or that they existed and were lost from many of the tRNA sequences during evolution.
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  • 196
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    Journal of molecular evolution 40 (1995), S. 476-481 
    ISSN: 1432-1432
    Keywords: Aminoacylation ; Aminoacyl-tRNA synthetases ; tRNA ; GluRS ; GlnRS ; Glutamate ; Glutamine ; Evolution ; Mischarging
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Aminoacyl-tRNA for protein synthesis is produced through the action of a family of enzymes called aminoacyl-tRNA synthetases. A general rule is that there is one aminoacyl-tRNA synthetase for each of the standard 20 amino acids found in all cells. This is not universal, however, as a majority of prokaryotic organisms and eukaryotic organelles lack the enzyme glutaminyl-tRNA synthetase, which is responsible for forming Gln-tRNAGln in eukaryotes and in Gram-negative eubacteria. Instead, in organisms lacking glutaminyl-tRNA synthetase, Gln-tRNAGln is provided by misacylation of tRNAGln with glutamate by glutamyl-tRNA synthetase, followed by the conversion of tRNA-bound glutamate to glutamine by the enzyme Glu-tRNAGln amidotransferase. The fact that two different pathways exist for charging glutamine tRNA indicates that ancestral prokaryotic and eukaryotic organisms evolved different cellular mechanisms for incorporating glutamine into proteins. Here, we explore the basis for diverging pathways for aminoacylation of glutamine tRNA. We propose that stable retention of glutaminyl-tRNA synthetase in prokaryotic organisms following a horizontal gene transfer event from eukaryotic organisms (Lamour et al. 1994) was dependent on the evolving pool of glutamate and glutamine tRNAs in the organisms that acquired glutaminyl-tRNA synthetase by this mechanism. This model also addresses several unusual aspects of aminoacylation by glutamyl- and glutaminyl-tRNA synthetases that have been observed.
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  • 197
    ISSN: 1432-1432
    Keywords: Aminoacyl-tRNA synthetases ; tRNA ; Genetic code ; RNA world ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Two aspects of the evolution of aminoacyl-tRNA synthetases are discussed. Firstly, using recent crystal structure information on seryl-tRNA synthetase and its substrate complexes, the coevolution of the mode of recognition between seryl-tRNA synthetase and tRNAser in different organisms is reviewed. Secondly, using sequence alignments and phylogenetic trees, the early evolution of class 2 Amnoacyl-tRNA synthetases is traced. Arguments are presented to suggest that synthetases are not the oldest of protein enzymes, but survived as RNA enzymes during the early period of the evolution of protein catalysts. In this view, the relatedness of the current synthetases, as evidenced by the division into two classes with their associated subclasses, reflects the replacement of RNA synthetases by protein synthetases. This process would have been triggered by the acquisition of tRNA 3′ end charging activity by early proteins capable of activating small molecules (e.g., amino acids) with ATP. If these arguments are correct, the genetic code was essentially frozen before the protein synthetases that we know today came into existence. Correspondence to: S. Cusack
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  • 198
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    Journal of molecular evolution 40 (1995), S. 601-607 
    ISSN: 1432-1432
    Keywords: Prolamine ; Sperm proteins ; Evolution ; Mammals
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Prolamine P1 genes have been sequenced following PCR amplification from 11 mammals representing five major mammalian orders: Rodentia (rat and guinea pig), Carnivora (cat and bear), Proboscidea (elephant), Perissodactyla (horse), and Artiodactyla (camel, deer, elk, moose, and gazelle). The predicted amino acid sequence for these genes together with previously reported sequences results in a data set of 25 different P1 genes and 30 different P1 amino acid sequences. The alignment of all these sequences reveals that prolamines are amongst the most rapidly diverging proteins studied. In spite of the large number of differences there are conserved motifs that are also common to birds such as the N-terminal ARYR followed by the triple alternating SRSRSR phosphorylation site. The central region contains 3 arginine clusters consisting of 5–6 arginines each. The C-terminus appears to be the most variable region of the protamines. Overall the molecular evolution of P1 genes is in agreement with the expected species evolution supporting that these genes have evolved vertically.
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  • 199
    ISSN: 1432-1432
    Keywords: Snake venom ; Bothrops ; Phospholipase ; Myotoxin ; Evolution ; cDNA ; Gene duplication ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The sequence coding for a snake venom phospholipase A2 (PLA2), BJUPLA2, has been cloned from a Bothrops jararacussu venom gland cDNA library. The cDNA sequence predicts a precursor containing a 16-residue signal peptide followed by a molecule of 122 amino acid residues with a strong sequence similarity to group II snake venom PLA2's. A striking feature of the cDNA is the high sequence conservation of the 5′ and 3′ untranslated regions in cDNAs coding for PLA2's from a number of viper species. The greatest sequence variation was observed between the regions coding for the mature proteins, with most substitutions occurring in nonsynonymous sites. The phylogenetic tree constructed by alignment of the amino acid sequence of BJUPLA2 with group II PLA2's in general groups them according to current taxonomical divisions and/or functional activity. It also suggests that gene duplications may have occurred at a number of different points during the evolution of snake venom group II PLA2's.
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  • 200
    ISSN: 1432-1432
    Keywords: Cyanelles ; Cyanophora paradoxa ; Endosymbiosis ; Evolution ; Glaucocystophyta ; Glaucophyta ; Phylogeny ; Plastid ; 16S ribosomal RNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Glaucocystophyte algae (sensu Kies, Berl. Deutsch. Bot. Ges. 92, 1979) contain plastids (cyanelles) that retain the peptidoglycan wall of the putative cyanobacterial endosymbiont; this and other ultrastructural characters (e.g., unstacked thylakoids, phycobilisomes) have suggested that cyanelles are “primitive” plastids that may represent undeveloped associations between heterotrophic “host” cells (i.e., glaucocystophytes) and cyanobacteria. To test the monophyly of glaucocystophyte cyanelles and to determine their evolutionary relationship to other plastids, complete 16S ribosomal RNA sequences were determined for Cyanophora paradoxa, Glaucocystis nostochinearum, Glaucosphaera vacuolata, and Gloeochaete wittrockiana. Plastid rRNAs were analyzed with the maximum-likelihood, maximumparsimony, and neighbor joining methods. The phylogenetic analyses show that the cyanelles of C. paradoxa, G. nostochinearum, and G. wittrockiana form a distinct evolutionary lineage; these cyanelles presumably share a monophyletic origin. The rDNA sequence of G. vacuolata was positioned within the nongreen plastid lineage. This result is consistent with analyses of nuclear-encoded rRNAs that identify G. vacuolata as a rhodophyte and support its removal from the Glaucocystophyta. Results of a global search with the maximumlikelihood method suggest that cyanelles are the first divergence among all plastids; this result is consistent with a single loss of the peptidoglycan wall in plastids after the divergence of the cyanelles. User-defined tree analyses with the maximum-likelihood method indicate, however, that the position of the cyanelles is not stable within the rRNA phylogenies. Both maximumparsimony and neighbor-joining analyses showed a close evolutionary relationship between cyanelles and nongreen plastids; these phylogenetic methods were sensitive to inclusion/exclusion of the G. wittrockiana cyanelle sequence. Base compositional bias within the G. wittrockiana 16S rRNA may explain this result. Taken together the phylogenetic analyses are interpreted as supporting a near-simultaneous radiation of cyanelles and green and nongreen plastids; these organelles are all rooted within the cyanobacteria.
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