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  • Articles  (137)
  • Evolution  (135)
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  • 1985-1989  (137)
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  • 1
    ISSN: 1432-0983
    Keywords: psbA ; Cyanelle ; Cyanophora paradoxa ; Evolution ; Sequence analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The psbA gene is part of the reaction center of photosystem II in cyanobacteria and the plastids of higher plants. Its primary sequence is highly conserved among all species investigated so far and its sequence shows homologies with the L and M subunits of the reaction center of photosynthetic bacteria. We have analyzed the psbA homolog from a eukaryotic alga, Cyanophora paradoxa, where the gene is encoded on cyanelle DNA. These cyanelles are surrounded by a murein sacculus and resemble cyanobacteria in many other characteristics, although they are genuine organelles that functionally replace plastids. Analysis of the gene revealed a psbA protein identical in length (360 codons) with the cyanobacterial counterpart. The overall sequence identity is, however, more pronounced between cyanelle psbA and the shorter (353 amino acids) psbA product found in higher plants. These data strongly support the postulated bridge position of cyanelles between chloroplasts and free-living cyanobacteria.
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  • 2
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    Current genetics 15 (1989), S. 99-106 
    ISSN: 1432-0983
    Keywords: Yeast ; Isoleucyl-tRNA synthetase ; Isoleucine ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The isoleucyl-tRNA synthetase gene (ILS1) from the yeast Saccharomyces cerevisiae was cloned and sequenced. This gene was initially cloned because it cross-hybridizated to what is now presumed to be the isoleucyl-tRNA synthetase gene (cupC) from the protozoan Tetrahymena hhermophila. The ILS1 gene was determined to be 1,072 amino acids in length. A comparison with a recently published sequence of ILS1 1 from another laboratory (Englisch et al. 1987) was made and differences noted. Two promoter elements were detected, one for general amino acid control and one for constitutive transcription. A heat shock protein (hsp70) gene (probably SSA3) was found 237 by upstream from the ILS1 translation start site. The ILS1 amino acid sequence was compared to isoleucyl-tRNA synthetases from other organisms, as well as to valyl-, leucyl- and methionyl-tRNA synthetases. Regions of conservation between these enzymes were found.
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  • 3
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    Current genetics 15 (1989), S. 221-229 
    ISSN: 1432-0983
    Keywords: Chloroplast DNA ; Chlorophyll a/c alga ; Evolution ; Ribosomal operon
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary There are almost no data describing chloroplast genome organization in chromophytic (chlorophyll a/c) plants. In this study chloroplast ribosomal operon placement and gene organization has been determined for the golden-brown alga Olisthodiscus luteus. Ribosomal RNA genes are located on the chloroplast DNA inverted repeat structure. Nucleotide sequence analysis, demonstrated that in contrast to the larger spacer regions in land plants, the 16S–23S rDNA spacer of O. luteus is only 265 by in length. This spacer contains tRNAIle and tRNAAla genes which lack introns and are separated by only 3 bp. The sequences of the tRNA genes and 16S and 23S rDNA termini flanking the spacer were examined to determine homology between O. luteus, chlorophytic plant chloroplast DNA, and prokaryotes.
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  • 4
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    Journal of molecular evolution 28 (1989), S. 175-184 
    ISSN: 1432-1432
    Keywords: Sheep ; Globin genes ; Evolution ; Gene duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Domestic sheep have two common alleles at the adult β-globin locus,β A andβ B. Here we report the structure of the β-globin locus of A-haplotype sheep. The locus consists of 12 genes, organized as a triplicated 4-gene set: 5′ ∈I-∈II-ΨβI-βC-∈III-∈IV-ΨβII-βA-∈V-∈VI-ΨβIII-βF 3′. This arrangement is identical to that of the closely related goat locus. Sheep with the B haplotype have a locus arrangement consisting of a duplicated four-gene set, lacking the βC gene as well as three other genes present in A sheep and goats. In order to understand the evolutionary history of the B sheep locus, we have sequenced the βB gene from these sheep, and the βB gene from A-haplotype sheep, and compared the sequences to those of the sheep βA, goat βC, and βA, and cow adult β genes. Our results indicate that the βB gene has diverged recently from the βA gene, and therefore the βB locus structure may have resulted from a recent deletion from a triplicated locus.
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  • 5
    ISSN: 1432-1432
    Keywords: Evolution ; Multiple sequence alignment ; NTP binding ; Phylogenetic analysis ; Positive-strand RNA viruses
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary NTP-motif, a consensus sequence previously shown to be characteristic of numerous NTP-utilizing enzymes, was identified in nonstructural proteins of several groups of positive-strand RNA viruses. These groups include picorna-, alpha-, and coronaviruses infecting animals and como-, poty-, tobamo-, tricorna-, hordei-, and furoviruses of plants, totalling 21 viruses. It has been demonstrated that the viral NTP-motif-containing proteins constitute three distinct families, the sequences within each family being similar to each other at a statistically highly significant level. A lower, but still valid similarity has also been revealed between the families. An overall alignment has been generated, which includes several highly conserved sequence stretches. The two most prominent of the latter contain the socalled “A” and “B” sites of the NTP-motif, with four of the five invariant amino acid residues observed within these sequences. These observations, taken together with the results of comparative analysis of the positions occupied by respective proteins (domains) in viral multidomain proteins, suggest that all the NTP-motif-containing proteins of positive-strand RNA viruses are homologous, constituting a highly diverged monophyletic group. In this group the “A” and “B” sites of the NTP-motif are the most conserved sequences and, by inference, should play the principal role in the functioning of the proteins. A hypothesis is proposed that all these proteins posses NTP-binding capacity and possibly NTPase activity, performing some NTP-dependent function in viral RNA replication. The importance of phylogenetic analysis for the assessment of the significance of the occurrence of the NTP-motif (and of sequence motifs of this sort in general) in proteins is emphasized.
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  • 6
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    Journal of molecular evolution 29 (1989), S. 28-39 
    ISSN: 1432-1432
    Keywords: Transposable elements ; Zea mays ; Evolution ; Inverted repeats
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The Robertson's Mutator stock of maize exhibits a high mutation rate due to the transposition of theMu family of transposable elements. All characterizedMu elements contain similar ≈200-bp terminal inverted repeats, yet the internal sequences of the elements may be completely unrelated. Non-Mutator stocks of maize have a 20–100-fold lower mutation rate relative to Mutator stocks, yet they contain multiple sequences that hybridize to theMu terminal inverted repeats. Most of these sequences do not cohybridize to internal regions of previously clonedMu elements. We have cloned two such sequences from the maize line B37, a non-Mutator inbred line. These sequences, termedMu4 andMu5, have an organization characteristic of transposable elements and possess ≈200-bpMu terminal inverted repeats that flank internal DNA, which is unrelated to other clonedMu elements.Mu4 andMu5 are both flanked by 9-bp direct repeats as has been observed for otherMu elements. However, we have no direct evidence that they have recently transposed because they have not been found in known genes. Although the internal regions ofMu4 andMu5 are not related by sequence similarity, both elements share an unusual structural feature: the terminal inverted repeats extend more than 100 bp internally fromMu-similar termini. The distribution of these elements in maize lines and related species suggests thatMu elements are an ancient component of the maize genome. Moreover, the structure of theMu termini and the fact thatMu termini are found flanking different internal sequences leads us to speculate thatMu termini once may have been capable of transposing as independent entities.
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  • 7
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    Journal of molecular evolution 29 (1989), S. 52-62 
    ISSN: 1432-1432
    Keywords: Genome organization ; Evolution ; Plant virus ; RNA recombination ; Sequence similarity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The relationships of genome organization among elongated (rod-shaped and filamentous) plant viruses have been analyzed. Sequences in coding and noncoding regions of barley stripe mosaic virus (BSMV) RNAs 1, 2, and 3 were compared with those of the monopartite RNA genomes of potato virus X (PVX), white clover mosaic virus (WClMV), and tobacco mosaic virus, the bipartite genome of tobacco rattle virus (TRV), the quadripartite genome of beet necrotic yellow vein virus (BNYVV), and icosahedral tricornaviruses. These plant viruses belong to a supergroup having 5′-capped genomic RNAs. The results suggest that the genomic elements in each BSMV RNA are phylogenetically related to those of different plant RNA viruses. RNA 1 resembles the corresponding RNA 1 of tricornaviruses. The putative proteins encoded in BSMV RNA 2 are related to the products of BNYVV RNA 2, PVX RNA, and WClMV RNA. Amino acid sequence comparisons suggest that BSMV RNA 3 resembles TRV RNA 1. Also, it can be proposed that in the case of monopartite genomes, as a rule, every gene or block of genes retains phylogenetic relationships that are independent of adjacent genomic elements of the same RNA. Such differential evolution of individual elements of one and the same viral genome implies a prominent role for gene reassortment in the formation of viral genetic systems.
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  • 8
    ISSN: 1432-1432
    Keywords: Carcinoembryonic antigen ; Evolution ; Gene family ; Human ; Rat ; Synonymous substitutions ; Silent molecular clock ; Evolutionary trees
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Various rodent and primate DNAs exhibit a stronger intra- than interspecies cross-hybridization with probes derived from the N-terminal domain exons of human and rat carcinoembryonic antigen (CEA)-like genes. Southern analyses also reveal that the human and rat CEA gene families are of similar complexity. We counted at least 10 different genes per human haploid genome. In the rat, approximately seven to nine different N-terminal domain exons that presumably represent different genes appear to be present. We were able to assign the corresponding genomic restriction endonuclease fragments to already isolated CEA gene family members of both human and rat. Highly similar subgroups, as found within the human CEA gene family, seem to be absent from the rat genome. Hybridization with an intron probe from the human nonspecific cross-reacting antigen (NCA) gene and analysis of DNA sequence data indicate the conservation of noncoding regions among CEA-like genes within primates, implicating that whole gene units may have been duplicated. With the help of a computer program and by calculating the rate of synonymous substitutions, evolutionary trees have been derived. From this, we propose that an independent parallel evolution, leading to different CEA gene families, must have taken place in, at least, the primate and rodent orders.
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  • 9
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    Journal of molecular evolution 29 (1989), S. 180-187 
    ISSN: 1432-1432
    Keywords: Divergence ; Mitochondrial DNA ; Molecular evolution ; Constraints ; Two-parameter model ; Evolutionary distance ; Evolution ; Mutation ; Neutral space ; Variable positions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Selective constraints on DNA sequence change were incorporated into a model of DNA divergence by restricting substitutions to a subset of nucleotide positions. A simple model showed that both mutation rate and the fraction of nucleotide positions free to vary are strong determinants of DNA divergence over time. When divergence between two species approaches the fraction of positions free to vary, standard methods that correct for multiple mutations yield severe underestimates of the number of substitutions per site. A modified method appropriate for use with DNA sequence, restriction site, or thermal renaturation data is derived taking this fraction into account. The model also showed that the ratio of divergence in two gene classes (e.g., nuclear and mitochondrial) may vary widely over time even if the ratio of mutation rates remains constant. DNA sequence divergence data are used increasingly to detect differences in rates of molecular evolution. Often, variation in divergence rate is assumed to represent variation in mutation rate. The present model suggests that differing divergence rates among comparisons (either among gene classes or taxa) should be interpreted cautiously. Differences in the fraction of nucleotide positions free to vary can serve as an important alternative hypothesis to explain differences in DNA divergence rates.
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  • 10
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    Journal of molecular evolution 29 (1989), S. 233-245 
    ISSN: 1432-1432
    Keywords: Mitochondrial DNA ; Salmonids ; Nucleotide sequence ; Transitions ; Transversions ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Sequence comparisons were made from 2214 bp of mitochondrial DNA cloned from six Pacific salmonid species. These sequences include the genes for ATPase subunit 6, cytochrome oxidase subunit 3, NADH dehydrogenase subunit 3, NADH dehydrogenase subunit 4L, tRNAGLY, and tRNAARG. Variation is found at 338 silent and 12 nonsilent positions of protein coding genes and 10 positions in the two tRNA sequences. A single 3-bp length difference was also detected. In all pairwise comparisons the sequence divergence observed in the fragment was higher than that previously predicted by restriction enzyme analysis of the entire molecule. The inferred evolutionary relationship of these species is consistent between methods. The distribution of silent variation shows a complex pattern with greatly reduced variation at the junctions of genes. The variation in the tRNA sequences is concentrated in the DHU loop. The close relationship of these species and extensive sequence analyzed allows for an analysis of the spectrum of substitutions that includes the frequencies of all 12 possible substitutions. The observed spectrum of substitutions is related to potential pathways of spontaneous substitution. The salmonid sequences show an extremely high ratio of silent to replacement substitutions. In addition the amino acid sequences of the four proteins coded in this fragment show a consistently high level of identity with theXenopus sequences. Taken together these data are consistent with a slower rate of amino acid substitution among the cold-blooded vertebrates when compared to mammals.
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  • 11
    ISSN: 1432-1432
    Keywords: α-Conotoxin ; α-Neurotoxin ; Erabutoxin b ; Evolution ; Venom
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary α-neurotoxins from elapid snake venoms andα-conotoxins from marine snails bind specifically and with high affinity to nicotinic cholinoceptors. Although both types of toxin are polypeptides, there is more than a fourfold difference in size between the two and no clear sequence homology is evident. A systematic computer search of the three-dimensional structure of erabutoxin b (anα-neurotoxin from the false sea snakeLaticauda semifasciata) was performed to identify the locality that most closely matched the amino acid compositions of the smallerα-conotoxins (from the marine snailsConus magus andConus geographus). The area of greatest similarity centered on residue position 25 of erabutoxin b, a locale that is conserved throughout the snakeα-neurotoxins and their homologues. Six Proteins unrelated to erabutoxin b were compared to theα-conotoxins to show that the extent of the erabutoxin b/α-conotoxin match was too high to be coincidental. Homologues of erabutoxin b, namelyα-cobratoxin fromNaja naja siamensis and cytotoxin VII4 fromNaja mossambica mossambica, were also analyzed. The extent of the matching with theα-conotoxins decreased in the series erabutoxin b〉α-cobratoxin〉cytotoxin VII4, and this also relates the order of similarity to the pharmacological properties of theα-conotoxins. Theα-conotoxin-like area of the snakeα-neurotoxins is peripheral to the site previously considered important for binding to the cholinoceptor, even though it seems to represent the focus of evolutionary convergence between the two types of neurotoxin. The area of resemblance does, however, have strong associations with the conformational behavior of the snake toxins. Hence, the outcome of this study has important consequences for the current ideas on snakeα-neurotoxin structure/activity relationships and the evolutionary origins of neurotoxicity.
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  • 12
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    Archives of microbiology 151 (1989), S. 454-458 
    ISSN: 1432-072X
    Keywords: Photosynthesis ; Photosynthetic bacteria ; Evolution ; Bacteriochlorophyll ; Reaction centres ; Light harvesting
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract 1) A number of overlapping clones have been isolated from a Rhodobacter sphaeroides gene bank. Following conjugative gene transfer from Escherichia coli these clones restore a wild type phenotype to several mutants unable to synthesise bacteriochlorophyll. 2) The insert DNA was analysed by restriction mapping and together the clones form the basis of the first restriction map of the 45 kb photosynthetic gene cluster of Rb. sphaeroides. 3) This cluster is bounded on one side by puh A encoding the reaction centre H polypeptide and on the other by the puf operon encoding reaction centre L and M apoproteins and light harvesting LH1 and polypeptides. 4) DNA fragments from the 45 kb cluster were used to probe genomic DNA from other photosynthetic bacteria. Using heterologous hybridisation conditions, a significant degree of homology is shown between Rb. sphaeroides and these other bacteria, suggesting close evolutionary links with Rb. capsulatus in particular.
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  • 13
    ISSN: 1432-072X
    Keywords: Eubacteria ; Evolution ; Extreme thermophile ; Thermotoga
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Three new strains of eubacterial hyperthermophiles were isolated from continental solfataric springs at Lac Abbé (Djibouti, Africa). Due to their morphology, lipids, and RNA polymerases they belong to the genus Thermotoga. Strains LA4 and LA10 are closely related to Thermotoga neapolitana found up to now only in the marine environment. Strain LA 3 differs from Thermotoga maritima and Thermotoga neapolitana in significant physiological and molecular properties. It is described as the new species Thermotoga thermarum.
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  • 14
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    Theoretical and applied genetics 77 (1989), S. 634-640 
    ISSN: 1432-2242
    Keywords: Isoenzymes ; Evolution ; Domestication ; Biological structure ; Genetic distances
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The survey of enzyme polymorphism in West African pearl millet cultivars reported by Tostain et al. 1987 has been extended to include populations from other regions of Africa and from India. The eight enzyme systems studied included: alcohol dehydrogenase, β-esterase, catalase, phosphoglucoisomerase, phosphoglucomutase, 6-phosphogluconate dehydrogenase, glutamate oxaloacetate transaminase, and malate dehydrogenase. One-hundred-ninety-nine populations of millet were analyzed, including 74 populations studied earlier. No new enzyme diversity was observed. Intrapopulation diversity ranged from 70%–90% of the total diversity, depending on their regions of origin. Four principal groups were distinguished in the following decreasing order of diversity: early-maturing cultivars from West and East Africa, late — maturing cultivars from West and East Africa, cultivars from India, and cultivars from southern Africa. The early-maturing cultivars were distributed between two principal focal points from East Africa in the East to Mali in the West. In the center were found millets from Niger which were most diverse. Indian and southern African cultivars were distinct, with the former appearing relatively similar to those of Niger, and the latter somewhat similar to late-maturing cultivars from West Africa, a diverse group that included late-maturing cultivars from East Africa. Based on the results obtained, an evolutionary hypothesis proposed here includes: multiple domestications in the Sahel, creation of early-maturing cultivars and their migration eastwards to India plus a southwards migration to Sudanian zone, and creation of late-maturing cultivars and their migration simultaneously westwards, eastwards, and southwards to southern Africa.
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  • 15
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    Theoretical and applied genetics 77 (1989), S. 844-850 
    ISSN: 1432-2242
    Keywords: Evolution ; Restriction fragment length polymorphism ; Grasses ; Maize ; Sugarcane
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The structure and organization of the ribosomal DNA (rDNA) of sorghum (Sorghum bicolor) and several closely related grasses were determined by gel blot hybridization to cloned maize rDNA. Monocots of the genus Sorghum (sorghum, shattercane, Sudangrass, and Johnsongrass) and the genus Saccharum (sugarcane species) were observed to organize their rDNA as direct tandem repeats of several thousand rDNA monomer units. For the eight restriction enzymes and 14 cleavage sites examined, no variations were seen within all of the S. bicolor races and other Sorghum species investigated. Sorghum, maize, and sugarcane were observed to have very similar rDNA monomer sizes and restriction maps, befitting their close common ancestry. The restriction site variability seen between these three genera demonstrated that sorghum and sugarcane are more closely related to each other than either is to maize. Variation in rDNA monomer lengths were observed frequently within the Sorghum genus. These size variations were localized to the intergenic spacer region of the rDNA monomer. Unlike many maize inbreds, all inbred Sorghum diploids were found to contain only one rDNA monomer size in an individual plant. These results are discussed in light of the comparative timing, rates, and modes of evolutionary events in Sorghum and other grasses. Spacer size variation was found to provide a highly sensitive assay for the genetic contribution of different S. bicolor races and other Sorghum species to a Sorghum population.
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  • 16
    ISSN: 1432-2242
    Keywords: Wheat aneuploids ; Null forms ; Storage proteins ; Gliadins ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Electrophoretical analyses of the gliadin fraction extracted from seeds of the intervarietal substitution lines of T. aestivum ssp. spelta in the T. aestivum ssp. vulgare cv ‘Chinese Spring’ for the homoeologous groups 1 and 6 and substitution lines of 6D chromosome of ‘Chinese Spring’ in the durum wheat cv ‘Langdon’ allowed the identification of seeds without gliadin proteins controlled by genes on chromosome 6A and 6B. A gliadin component of ‘Chinese Spring’, not previously assigned to any specific chromosome, is controlled by chromosome 6D in the 6D (6A) and 6D (6B) disomic substitution lines of ‘Langdon’. Additional genes controlling the synthesis of this component may be present on other chromosomes, very likely 6A and 6B, since the analysis of the ‘Chinese Spring’ compensating nullisomic-tetrasomics involving the 6D chromosome does not show the loss of this component or any apparent change in staining intensity. Chromosomal location data and two-dimensional gliadin maps reveal close homologies between the two hexaploid wheats, ‘Chinese Spring’ (T. aestivum ssp. vulgare) and T. aestivum ssp. spelta, belonging to different subspecies in the hexaploid group of genomic formula AABBDD. The comparison of gliadin electrophoretic patterns aiding in the identification of evolutionary pathways in wheat is stressed.
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  • 17
    ISSN: 1432-2242
    Keywords: Lotus corniculatus ; Lotus tenuis ; 2n gametes ; Evolution ; Breeding
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Crosses between male sterile L. corniculatus (2n=4x=24) and L. tenuis (2n=2x=12) plants were performed in order to verify the presence of 2n gametes in L. tenuis. All but one of the plants from these crosses had 2n=4x=24 and the L. corniculatus phenotype; this plant had 2n=2x=12 and the L. tenuis phenotype. The plants also showed good quantity of pollen at tripping, good pollen fertility and good percentage of seed setting in the backcross to L. corniculatus. On the whole, both cytological and morphological observations, showing that all but one of the plants from L. corniculatus x L. tenuis were normal tetraploids, suggest the existence of diploandrous gametes in L. tenuis. On the other hand, haploid parthenogenesis probably gave origin to the dihaploid plant 2n=2x=12.
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  • 18
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    Theoretical and applied genetics 77 (1989), S. 689-700 
    ISSN: 1432-2242
    Keywords: Triticum ; Homoeoalleles ; Evolution ; Dough ; Gene library
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Two high-molecular-weight subunit (HMWS) glutenin genes from the A and B genomes of the hexaploid bread wheat Triticum aestivum L. cv Cheyenne have been isolated and sequenced. Both of these genes are of the high Mr class (x-type) of HMW glutenins, and have not been previously reported. The entire set of six HMW genes from cultivar Cheyenne have now been isolated and characterized. An analysis of the Ax and Bx sequences shows that the Ax sequence is similar to the homoeologous gene from the D genome, while the Bx repeat structure is significantly different. The repetitive region of these proteins can be modelled as a series of interspersed copies of repeat modifs of 6, 9, and 15 amino acid residues. The evolution of these genes includes single-base substitutions over the entire coding region, plus insertion/deletions of single or blocks of repeats in the central repetitive domain.
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  • 19
    ISSN: 1617-4623
    Keywords: Cyanobacteria ; Evolution ; Thylakoid ; Leader sequence ; Photosystem II
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A 9 kDa polypeptide which is loosely attached to the inner surface of the thylakoid membrane and is important for the oxygen-evolving activity of Photosystem II in the thermophilic cyanobacterium Phormidium laminosum has been purified, a partial amino acid sequence obtained and its gene cloned and sequenced. The derived amino acid sequence indicates that the 9 kDa polypeptide is initially synthesised with an N-terminal leader sequence of 44 amino acids to direct it across the thylakoid membrane. The leader sequence consists of a positively charged N-terminal region, a long hydrophobic region and a typical cleavage site. These features have analogous counterparts in the “thylakoid-transfer domain” of lumenal polypeptides from chloroplasts of higher plants. These findings support the view of the proposed function of this domain in the two-stage processing model for import of lumenal, nuclear-encoded polypeptides. In addition, there is striking primary sequence homology between the leader sequences of the 9 kDa polypeptide and those of alkaline phosphatase (from the periplasmic space of Escherichia coli) and, particularly in the region of the cleavage site, the 16 kDa polypeptide of the oxygen-evolving apparatus in the thylakoid lumen of spinach chloroplasts.
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  • 20
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    Molecular genetics and genomics 218 (1989), S. 323-329 
    ISSN: 1617-4623
    Keywords: Mutagenic DNA repair ; Evolution ; Murray collection ; impCAB
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Resistance transfer factors are natural conjugative plasmids encoding antibiotic resistance. Some also encode mutagenic DNA repair genes giving resistance to DNA damage and induced mutagenesis. It has been shown that antibiotic resistance has been acquired by recent transposition events; however, we show here that mutagenic repair genes existed much earlier on these types of plasmids. Conjugative plasmids from eight incompatibility groups from the Murray collection of ‘pre-antibiotic era’ enterobacteria were tested for complementation of mutagenic repair-deficient Escherichia coli umuC36. Although none of these plasmids carry transposon-encoded drug resistance genes, IncI1 and IncB plasmids were identified which restored ultraviolet resistance and induced mutability to umuC36 mutants. Furthermore they increased the UV resistance and induced mutability of wild-type E. coli, Klebsiella aerogenes and Citrobacter intermedius, thus showing that they could confer a general selective advantage to a variety of hosts. Like know mutagenic repair genes, complementation by these plasmid genes required the SOS response of the host cell. Nucleotide hybridisation showed that these plasmids harboured sequences similar to the impCAB locus, the mutagenic repair operon of modern-day IncI1 plasmids. The evolution of mutagenic repair genes is discussed.
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  • 21
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    Biology and philosophy 4 (1989), S. 255-273 
    ISSN: 1572-8404
    Keywords: Natural Selection ; Evolution ; Principle ; Probability ; Propensity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Philosophy
    Notes: Abstract The theory of natural selection is a rich systematization of biological knowledge without a first principle. When formulations of a proposed principle of natural selection are examined carefully, each is seen to be exhaustively analyzable into a proposition about sources of fitness and a proposition about consequences of fitness. But whenever the fitness of an organic variety is well defined in a given biological situation, its sources are local contingencies together with the background of laws from disciplines other than the theory of natural selection; and the consequences of fitness for the long range fate of organic varieties are essentially applications of probability theory. Hence there is no role and no need for a principle of the theory of natural selection, and any generalities that may hold in that theory are derivative rather than fundamental.
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  • 22
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    Biology and philosophy 4 (1989), S. 287-301 
    ISSN: 1572-8404
    Keywords: Evolution ; Incest Taboo ; Ethics ; Behavioral Development
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Philosophy
    Notes: Abstract Human propensities that are the products of Darwinian evolution may combine to generate a form of social behavior that is not itself a direct result of such pressure. This possibility may provide a satisfying explanation for the origin of socially transmitted rules such as the incest taboo. Similarly, the regulatory processes of development that generated adaptations to the environment in the circumstances in which they evolved can produce surprising and sometimes maladaptive consequences for the individual in modern conditions. These combinatorial aspects of social and developmental dynamics leave a subtle but not wholly uninteresting role for evolutionary biology in explaining the origins of human morality.
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  • 23
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    Biology and philosophy 4 (1989), S. 457-481 
    ISSN: 1572-8404
    Keywords: Evolution ; evolutionary biology ; fitness ; decision theory ; theory of choice ; rationality ; rational behavior ; reductionism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Philosophy
    Notes: Abstract A fundamental philosophical question that arises in connection with evolutionary theory is whether the fittest patterns of behavior are always the most rational. Are fitness and rationality fully compatible? When behavioral rationality is characterized formally as in classical decision theory, the question becomes mathematically meaningful and can be explored systematically by investigating whether the optimally fit behavior predicted by evolutionary process models is decision-theoretically coherent. Upon investigation, it appears that in nontrivial evolutionary models the expected behavior is not always in accord with the norms of the standard theory of decision as ordinarily applied. Many classically irrational acts, e.g. betting on the occurrence of one event in the knowledge that the probabilities favor another, can under certain circumstances constitute adaptive behavior. One interesting interpretation of this clash is that the criterion of rationality offered by classical decision theory is simply incorrect (or at least incomplete) as it stands, and that evolutionary theory should be called upon to provide a more generally applicable theory of rationality. Such a program, should it prove feasible, would amount to the logical reduction of the theory of rational choice to evolutionary theory.
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    Primates 30 (1989), S. 95-102 
    ISSN: 0032-8332
    Keywords: Macaques ; Hemoglobin ; Duplication hypothesis ; Evolution ; Isoelectric focusing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Blood samples were collected fromMacaca fascicularis andMacaca mulatta living in indoor breeding groups and investigated electrophoretically. Hemoglobin polymorphism was observed in both species. Isoelectric focusing was performed on urea denaturated samples to test the hypothesis of a site duplication at theα-chain locus inM. fascicularis (Barnicot et al., 1970). The results of our investigations do not support the above mentioned hypothesis. Only one locus coding theα-chain was detected, and this is under the control of two alleles. Evolutionary events at the molecular level are discussed, as well asWheatley's hypothesis (1980) that malaria was an important force behind divergence in both species. InM. fascicularis hemoglobin variants might be similarily connected with malaria resistance as in man. We suggest that this was not an important process behind speciation in macaques.
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    Molecular genetics and genomics 219 (1989), S. 199-203 
    ISSN: 1617-4623
    Keywords: Sequence rearrangement ; Gene localization ; Restriction analysis ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The chloroplast DNAs of Acetabularia mediterranea strains 5 and 17 differ significantly in their restriction patterns. Southern blotting analysis using gene probes derived from the coding regions of spinach genes showed that psbB and petB each map to unique restriction fragments which are shared in strains 5 and 17. On the other hand psaA, psbA and rbcL map to different restriction fragments in strains 5 and 17 probably as a result of restriction fragment length polymorphism. In addition to restriction fragment polymorphism there is evidence for much larger differences in the organization of the plastome. The most striking difference is the absence in strain 5 of a 10 kb repeated sequence which has previously been demonstrated in strain 17. However, both strains apparently share at least 8 kb of the 10 kb repeated sequence. Restriction analysis of independent clones of the 10 kb sequence revealed a family of non-identical repeats.
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  • 26
    ISSN: 1617-4623
    Keywords: Maltose transport ; malB region ; Positive regulation ; Palindromic units ; Evolution
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    Topics: Biology
    Notes: Summary The malE and malK genes from Salmonella typhimurium, and the MalEFG operon and a portion of malK from Enterobacter aerogenes were cloned and sequenced. Plasmid-borne malE genes from both species and the malF and malG genes from E. aerogenes were expressed normally in Escherichia coli, and their products function in maltose transport. This shows that the malB products from the three species are interchangeable, at least in the combinations tested. The general genetic organization of the malB region is conserved. Potential binding sites and distances between them are highly conserved in the regulatory intervals. An unexpected conserved region was detected, which we call the U box, and which could be another target for a regulatory protein. This hypothesis is supported by the presence of the U box in the regulatory, region of the pulA-malX operon in Klebsiella pneumoniae. The intergenic region between malE and malF from S. typhimurium and E. aerogenes, contains inverted repeats similar to the palindromic units (PU or REP) found at the same location in E. coli. The predicted amino acid sequence of the encoded proteins showed 90% or more identity in every pairwise comparison of species.
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    Environmental biology of fishes 24 (1989), S. 199-218 
    ISSN: 1573-5133
    Keywords: Blenniidae ; Chaenopsidae ; Evolution ; Generalization ; Labrisomidae ; Morphological series ; Oral jaw apparatus ; Specialization ; Tripterygiidae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Synopsis The ecomorphological relationships between the oral jaws and food spectra were highlighted in 34 species of Gulf of California blennioid fishes (5 Tripterygiidae, 13 Labrisomidae, 11 Chaenopsidae and 5 Blenniidae). Twenty-nine species are microcarnivorous, two are omnivorous browsers, two are algae grazers and one was an ‘ectoparasite’ feeder. The spectrum of oral (as opposed to pharyngeal) jaw (OJA) morphology ranges from plesiomorphic, suction-feeding (relatively large, protrusible jaws, with many coniform-caniniform teeth) to apomorphic, biting (relatively small, non protrusible jaws, with a single row of incisiform teeth). As species with similar morphology may widely differ in food, it is concluded, that morphology is not a reliable predictor for ecology in this case. With the exception of a few specialists, species with apomorphic, biting OJA utilize sessile items in addition to mobile categories and thus show a higher food diversity as compared to species with plesiomorphic OJA. Thus in the present case morphological differentiation goes along with ecological generalization. Only three blenniid species with the most apomorphic OJA may be considered as specialized also with regard to food resource utilization. Transformation of morphological characters and the ecological role of the OJA of blennioids may serve as a model to illustrate the steps required to achieve a biting-browsing and grazing feeding apparatus in many taxa of modern acanthopterygian reef fishes.
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    Journal of biological physics 17 (1989), S. 109-125 
    ISSN: 1573-0689
    Keywords: Evolution ; order ; complexity ; biological systems
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    Topics: Biology , Physics
    Notes: Abstract In this, Part III of a general theory, the large-scale features of evolution of structure, order, and complexity are considered as characteristic features of the biological state of matter. This starts with a rigorous formal definition of structure, classes of structural order, complexity, measures of complexity, and how these arise through evolution by a cumulative process of storing information in memory systems. Three such memory systems have evolved: the genetic memory, the immune memory, and the memories of the nervous system. The evolution, characteristic parameters and the limitations of these memory systems are explored. From these considerations emerge the large-scale features of the evolutionary pathways of biological structure, function, and complexity.
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  • 29
    ISSN: 1573-5133
    Keywords: Jaws ; Evolution ; Corals ; Teeth ; Cladistics ; Specialists
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    Topics: Biology
    Notes: Synopsis The jaw dentition of fifteen species of Pacific and Western Atlantic chaetodontid butterflyfishes was examined in light of their feeding habits and phylogenetic relationships. The ancestral tooth pattern is typical of many of the butterflyfishes, and variations on this basic pattern involve changes in the arrangement, length and number of teeth, and tooth shape to a lesser extent. Many of the more derived conditions can be explained by simple changes in relative jaw shape and size. Despite what appears to be adequate time for evolutionary changes to occur between the Pacific and Western Atlantic faunas, many species retain the generalized tooth arrangement permitting efficient exploitation in a very generalized manner. However, Pacific species as a whole show more specialized morphologies for hard coral feeding than do Western Atlantic species. Cases of parallel and divergent evolution are identified between and among the two faunas. Most morphological change associated with feeding in butterflyfishes is confined to the anterior region of the head, and particularly a few key elements. Suggestions for future morphological studies on the chaetodontids are outlined.
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    Journal of comparative physiology 159 (1989), S. 139-151 
    ISSN: 1432-136X
    Keywords: Calliphorin ; Hemocyanin ; Monoclonal antibodies ; Evolution ; Spiders
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    Topics: Biology , Medicine
    Notes: Summary Three murine hybridoma cell lines secreting IgG1 antibodies to 4×6 tarantula (Eurypelma californicum) hemocyanin were isolated, and the monoclonal antibodies Ec-7, Ec-8 and Ec-24 characterized by immunoblotting, immunoelectrophoresis and ELISA. WholeEurypelma hemocyanin, and the isolated subunitsa tog served as probes. For the subunits a novel, quick purification scheme on FPLC combined with immuno-affinity chromatography was established. Additionally, two cell lines secreting IgM antibodies were isolated. These antibodies showed irrelevant cross reactivities. Ec-7 strongly reacts with subunitd and weakly withb. Ec-8 and Ec-24 are specifically directed againstEurypelma subunitsa ande, respectively. The epitopes of Ec-7 and Ec-8 are sequence-dependent, whereas the Ec-24 epitope is conformation-dependent. Ec-8 and Ec-24 are specific forEurypelma hemocyanin. Ec-7 is not reactive to crustacean, centipede or gastropod hemocyanins, but binds to scorpion hemocyanin and to the immunological correlates of subunitsd andf in the hemocyanins of the spiderCupiennius salei and the xiphosuranLimulus polyphemus. In immunoblots with different polyclonal antisera,Eurypelma andAstacus hemocyanin cross-reacted with calliphorin, a larval serum protein from the blowflyCalliphora vicina. Calliphorin and chelicerate hemocyanins share the Ec-7 epitope. Sedimentation coefficients, pH stability regions, subunit size, and electron microscopical appearance of calliphorin are indiscernable from a typical 1×6 arthropod hemocyanin. This relationship is discussed in the context of hemocyanin evolution.
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    Human evolution 4 (1989), S. 63-71 
    ISSN: 1824-310X
    Keywords: Snub-nosed monkey ; Myology ; Evolution ; Functional anatomy
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    Topics: Biology
    Notes: Abstract Some differences between the muscular system of three species of golden monkeys were shown. The major features of the myology in these animals, besides that ofCercopithecoidea, are similar to the anthropoid apes and humans. Although most of the features between taxa of golden monkeys are largely homologous, there are also some differences. Our results differ slightly from thosePatterson (1942) obtained inR. roxellanae. Some conclusions reported by Patterson were obviously incorrect, since the specimen he used did not have a head. Many mylogical characters are similar to other species ofCercopithecoidea while some resemble those of apes. Many are similar to those of the leaf monkey, though some of them show much more development. The golden monkey is more advanced than any other species ofCercopithecoidea. We hypothesize that in terms of the myological characters the golden monkeys seem to occupy a position between the leaf monkeys and the apes.
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    Primates 30 (1989), S. 403-422 
    ISSN: 0032-8332
    Keywords: Evolution ; Polymorphism ; Phylogeny ; Genetic markers ; Cercopithecinae
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    Topics: Biology
    Notes: Abstract Serum proteins and RBC enzymes were surveyed in 16 species (183 animals) of African guenons (tribe Cercopithecini) in order to determine their genetic polymorphism and to establish dendrograms on the basis of their allele frequencies. The molecular data obtained were compared with those of mangabeys (16 animals tested) and discussed in the light of our results inPapio andMacaca. The species surveyed wereCercopithecus neglectus, C. hamlyni, C. l'hoesti (C. l'h. l'hoesti, C. l'h. preussi, andC. l'h. solatus), C. nictitans, C. mitis (C. m. kolbi, C. m. albotorquatus, C. m. stuhlmanni, andC. m. albogularis), C. cephus, C. ascanius, C. erythrotis, C. petaurista, C. mona, C. pogonias, C. wolfi, andC. aethiops, Miopithecus talapoin, Allenopithecus nigroviridis andErythrocebus patas, Lophocebus albigena, andCercocebus torquatus. Eleven loci (ten systems) were studied in red blood cell enzymes and the Gc, Gm, Km, and Bm systems in DBP and immunoglobulin serum proteins. Most of the loci were polymorphic. Similar and different polymorphisms occur in closely related species or subspecies, particularly inCercopithecus. Guenons have phenotypes clearly distinct from mangabeys.
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    Evolutionary ecology 3 (1989), S. 343-359 
    ISSN: 1573-8477
    Keywords: Evolution ; exploitation ; fisheries ; Gadus morhua ; life history ; optimization
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    Topics: Biology
    Notes: Summary Age-specific exploitation of a natural population acts as a selective force on genetic variation in life history traits. Evolution arising from this selection may bring about evolutionary changes in the total yield which the population is able to sustain. An analysis of this process is given for a harvested population with densitydependent recruitment, in which selection of life history traits by cropping is independent of density and frequency. Evolution of the total yield depends on an interplay between the yield from an individual over the course of its life and recruitment; whether the total yield increases or decreases depends on the properties of particular populations. Evolution brought about by harvesting does not, in general, lead to the maximization of the total yield. Nonetheless, by appropriate choice of an age-specific harvest pattern, it is possible in principle to select the life history which gives the maximum total yield following evolution; this harvest pattern is called the ‘evolutionarily stable optimal harvesting strategy’ (ESOHS). Results of the analysis are illustrated with data on the Arcto-Norwegian cod.
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  • 34
    ISSN: 1432-0983
    Keywords: Wheat chloroplast DNA ; Repeated sequences ; Ribosomal protein genes ; Evolution
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    Notes: Summary Some dispersed repeated sequences and their flanking regions from wheat and maize ctDNAs have been characterized. Two sets of wheat ctDNA repeats were found to be the chloroplast ribosomal protein genesrpl2 andrpl23, plus nonfunctional segments of them, designatedrpl2′ andrpl23′. Pairwise comparisons were made between the wheatrp123 andrpl23′, and the maizerp123′ sequences. The precise patterns of homology suggest that the divergence of the wheat and maize nonfunctional (rpl23′) sequences is being retarded by nonreciprocal recombination, biased by selection for individuals with functional (rpl23) sequences. The implied involvement of these sequences in mechanisms of homologous recombination, and therefore in the creation and spread of new ctDNA variants, is discussed.
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  • 35
    ISSN: 1432-0983
    Keywords: Physarum polycephalum ; rRNA ; Sequence ; Evolution
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    Topics: Biology
    Notes: Summary The nucleotide sequence of the Physarum polycephalum small subunit ribosomal RNA (SSU rRNA) gene has been determined. Sequence data indicate that the mature 19S SSU rRNA is 1,964 nucleotides long. A complete secondary structure model for P. polycephalum SSU rRNA has been constructed on the basis of the Escherichia coli 16S rRNA model and data from comparative analyses of 28 different eukaryotic sequences. A “four-helix” model is presented for the central domain variable region. This model can be applied both to vertebrate and most lower eukaryotic SSU rRNAs. The increased size of P. polycephalum SSU rRNA relative to the smaller SSU rRNAs from such other lower eukaryotes, as Dictyostelium, Tetrahymena or Saccharomyces is due mainly to three G+C-rich insertions found in two regions known to be of variable length in eukaryotes. In a phylogenetic tree constructed from pairwise comparisons of eukaryotic SSU rRNA sequences, the acellular myxomycete P. polycephalum is seen to diverge before the appearance of the cellular mycomycete Dictyostelium discoideum.
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  • 36
    ISSN: 1432-0983
    Keywords: Evolution ; Sequence comparison ; RUBISCO ; Transit peptide
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    Notes: Summary We have isolated and characterized a full-length cDNA clone encoding the precursor of the small subunit (pSU) of ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) from the green alga, Chlamydomonas moewusii. Comparison with the C. reinhardtii rbcS1 gene sequence reveals that both small subunit (SS) coding regions are 75% homologous and that their predicted mature polypeptide chains are each composed of 140 amino acids. In contrast, their transit peptides appear to be divergent. We also show that transcription of the C. moewusii rbcS gene(s) which generates a 1,230 and a 930 base mRNA species are light-stimulated/or accumulated during the light period of the cell cycle. Finally, the SS polypeptide sequences of fifteen different photosynthetic organisms are compared; this analysis reveals at least five well-conserved polypeptide domains.
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    Journal of molecular evolution 28 (1988), S. 98-112 
    ISSN: 1432-1432
    Keywords: rRNA ; Evolution ; Sequence comparison ; Parsimony ; Bootstrap
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    Topics: Biology
    Notes: Summary Sequences of small subunit (SSU) and large subunit (LSU) ribosomal RNA genes from archaebacteria, eubacteria, and the nucleus, chloroplasts, and mitochondria of eukaryotes have been compared in order to identify the most conservative positions. Aligned sets of these positions for both SSU and LSU rRNA have been used to generate tree diagrams relating the source organisms/organelles. Branching patterns were evaluated using the statistical bootstrapping technique. The resulting SSU and LSU trees are remarkably congruent and show a high degree of similarity with those based on alternative data sets and/or generated by different techniques. In addition to providing insights into the evolution of prokaryotic and eukaryotic (nuclear) lineages, the analysis reported here provides, for the first time, an extensive phylogeny of the mitochondrial lineage.
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  • 38
    ISSN: 1432-1432
    Keywords: Aspergillus nidulans ; 5S rRNA ; Pseudogenes ; Evolution
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    Topics: Biology
    Notes: Summary AllAspergillus nidulans 5S rRNA pseudogenes known so far are the result of integration of an approx. 0.2-kbp-long DNA sequence into the 5S rRNA genes. This sequence, called block C, is present in at least five copies in theA. nidulans genome and seems to be associated either with 5S rRNA genes or pseudogenes. In contrast to the 78% sequence conservation of the C-block in pseudogenes, the truncated 5′ halves of the pseudogenes are very highly conserved (96.9–100%). We postulate that the 5S rRNA pseudogenes are still a subject of concerted evolution. The C-block sequence shows similarity to the switch region of the mouse heavy chain immunoglobulin gene. A characteristic motif GGGTGAG is repeated several times in both sequences; the sequence conservation is 63%.
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  • 39
    ISSN: 1432-1432
    Keywords: Tropomyosin ; Differential splicing ; Evolution ; Isochore ; Codon usage ; Sequence convergence ; Functional constraints
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have cloned and determined the nucleotide sequence of a complementary DNA (cDNA) encoded by a newly isolated human tropomyosin gene and expressed in liver. Using the leastsquare method of Fitch and Margoliash, we investigated the nucleotide divergences of this sequence and those published in the literature, which allowed us to clarify the classification and evolution of the tropomyosin genes expressed in vertebrates. Tropomyosin undergoes alternative splicing on three of its nine exons. Analysis of the exons not involved in differential splicing showed that the four human tropomyosin genes resulted from a duplication that probably occurred early, at the time of the amphibian radiation. The study of the sequences obtained from rat and chicken allowed a classification of these genes as one of the types identified for humans. The divergence of exons 6 and 9 indicates that functional pressure was exerted on these sequences, probably by an interaction with proteins in skeletal muscle and perhaps also in smooth muscle; such a constraint was not detected in the sequences obtained from nonmuscle cells. These results have led us to postulate the existence of a protein in smooth muscle that may be the counterpart of skeletal muscle troponin. We show that different kinds of functional pressure were exerted on a single gene, resulting in different evolutionary rates and different convergences in some regions of the same molecule. Codon usage analysis indicates that there is no strict relationship between tissue types (and hence the tRNA precursor pool) and codon usage. G+C content is characteristic of a gene and does not change significantly during evolution. These results are in good agreement with an isochore composition of the genome, and thus suggest a similar chromosomal environment in chicken, rat, and human.
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    Journal of molecular evolution 27 (1988), S. 291-297 
    ISSN: 1432-1432
    Keywords: P1 P2 protamines ; Evolution ; Regulatory sequence ; Primordial sequence ; Similarity ; Alignment
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary With the recent availability of the primary structural data for the trout, bovine, and mouse protamine genes, a detailed comparison of their structures has been made. This has revealed extensive conservation of potentially biologically significant regions. An inverse correlation is apparent between gene copy number and the number of sequence-distinct protamines synthesized with the number of CP-box-like (CCYPCCC) putative transcription modulating sequences situated 5′ to these genes. A common nucleotide sequence 5′ to the CP-box-like putative transcription modulating sequence(s) at the end of a common region has been identified. It is postulated that this is the testis-specific protamine P1 transcription regulator sequence. Evidence based on sequence similarity is also provided for the existence of a primordial protamine gene and a scheme for the evolution of vertebrate protamine genes is proposed.
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    Journal of molecular evolution 27 (1988), S. 311-320 
    ISSN: 1432-1432
    Keywords: Genome composition ; Coding sequences ; Isochores ; Humans ; Murids
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    Topics: Biology
    Notes: Summary The compositional distributions of coding sequences and DNA molecules (in the 50-100-kb range) are remarkably narrower in murids (rat and mouse) compared to humans (as well as to all other mammals explored so far). In murids, both distributions begin at higher and end at lower GC values. A comparison of homologous coding sequences from murids and humans revealed that their different compositional distributions are due to differences in GC levels in all three codon positions, particularly of genes located at both ends of the distribution. In turn, these differences are responsible for differences in both codon usage and amino acids. When GC levels at first+second codon positions and third codon positions, respectively, of murid genes are plotted against corresponding GC levels of homologous human genes, linear relationships (with very high correlation coefficients and slopes of about 0.78 and 0.60, respectively) are found. This indicates a conservation of the order of GC levels in homologous genes from humans and murids. (The same comparison for mouse and rat genes indicates a conservation of GC levels of homologous genes.) A similar linear relationship was observed when plotting GC levels of corresponding DNA fractions (as obtained by density gradient centrifugation in the presence of a sequence-specific ligand) from mouse and human. These findings indicate that orderly compositional changes affecting not only coding sequences but also noncoding sequences took place since the divergence of murids. Such directional fixations of mutations point to the existence of selective pressures affecting the genome as a whole.
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    Journal of molecular evolution 27 (1988), S. 17-28 
    ISSN: 1432-1432
    Keywords: Actin genes ; Evolution ; 5′ and 3′ untranslated regions
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    Topics: Biology
    Notes: Summary We have sequenced the coding and leader regions, as well as part of the 3′ untranslated region, of aXenopus borealis type 1 cytoskeletal actin gene [defined according to the arrangement of acidic residues at the N-terminus; Vandekerckhove et al. (1981) J Mol Biol 152:413–426]. The encoded amino acid sequence is the same as the avian and mammalian β (type 1) cytoskeletal actins, except for an isoleucine at position 10 (as found in the mammalian γ cytoskeletal actins), and an extra amino acid, alanine, after the N-terminal methionine. Five introns were found, in the same positions as those of the rat and chicken β-actin genes. The 5′ and 3′ untranslated regions resemble those of the human γ (type 8) cytoskeletal actin gene more closely than the mammalian β genes. Primer extension showed that this type 1 gene is transcribed in ovary and tadpole. Sequencing of primer extension products demonstrated two additional mRNA species inX. borealis, encoding type 7 and 8 isoforms. This contrasts with the closely related speciesXenopus laevis, where type 4, 5, and 8 isoforms have been found. The type 7 isoform has not previously been found in any other species. The mRNAs of theX. borealis type 1 and 8 andX. laevis type 5 and 8 isoforms contain highly homologous leaders. TheX. borealis type 7 mRNA has no leader homology with the other mRNA species and, unlike them, has no extra N-terminal alanine codon. The evolutionary implications of these data are discussed.
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  • 43
    ISSN: 1432-1432
    Keywords: Histone genes ; Sea stars ; Echinoderms ; Evolution
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    Topics: Biology
    Notes: Summary The arrangement of core histone genes and their transcriptional polarity has been determined for three species of sea stars (Pisaster ochraceus, P. brevispinus, andDermasterias imbricata) representing two orders which diverged over 500 million years ago. Each species has approximately 500 core histone cluster repeats per haploid genome. The close phylogenetic relationship between thePisaster species is evident from the correspondence of restriction sites in the repeat element, identical arrangement of core histones, and high degree of sequence homology in both the coding and spacer regions of the H3 gene. TheDermasterias repeat has the same gene order and transcriptional polarity of core histones, but its restriction map is significantly different. Moreover, theDermasterias H3 gene has the same amino acid sequence, but in comparison toPisaster nucleotide sequences, shows a high level of silent substitutions. Analyses of the nucleotide sequence of the 5′ and 3′ regions surrounding the H3 gene from each species demonstrate the presence of appropriately spaced consensus and processing signal segments. The 3′ spacer segment of theDermasterias H4 gene contains an unusual, threefold tandemly repeated, 21-nucleotide, AT-rich sequence. No similar sequence is seen in theP. brevispinus H4 3′ region, but these two species show a striking regularity of distribution of five different homologous oligomers in the 3′ spacer.
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    Journal of molecular evolution 27 (1988), S. 102-108 
    ISSN: 1432-1432
    Keywords: Hemopexin ; Evolution ; Gene structure ; Recombination ; Sequence homology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The human hemopexin gene was isolated and its structure determined. The gene spans approximately 12 kb and is interrupted by nine introns. When the intron/exon pattern was examined with respect to the polypeptide segments they encode, a direct correspondence between exons and the 10 repeating units in the protein was observed. The introns are not randomly placed; they fall in the middle of the region of amino acid sequence homology in strikingly similar locations in 6 of the 10 units and in a symmetrical position in the two halves of the coding sequence. These features strongly support the hypothesis that the gene evolved through intron-mediated duplications of a primordial sequence to a five-exon cluster. A more recent gene duplication led to the present-day gene organization.
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    Archives of microbiology 150 (1988), S. 56-60 
    ISSN: 1432-072X
    Keywords: Fumarate reduction ; Quinones ; Rhodospirillaceae ; Phototrophic bacteria ; Evolution ; Taxonomy
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    Topics: Biology
    Notes: Abstract Nineteen established and one undesignated species of the Rhodospirillaceae were examined for fumarate reduction in connection with their quinone systems. The fumarate reductase activity with reduced methyl viologen (MVH) or FMNH2 as electron donor was found in membrane (chromatophore) preparations from phototrophically grown cells of all species containing menaquinone (MK) and/or rhodoquinone. The species having ubiquinone as the sole quinone contained no fumarate reductase activity, except some Rhodobacter species showing the FMNH2-dependent activity. The MVH-fumarate reductase activity of the MK-type species was not inhibited by Triton X-100 or acetone treatment, suggesting the presence of a fumarate reductase reacting directly with MVH, while such an enzyme was absent in the MK-lacking strains, with few exceptions. The FMNH2-fumarate reduction system was abolished by a detergent or acetone extraction in all bacteria but differed much among species with different quinone types as to the response to respiratory inhibitors. These differences in fumarate-reducing properties and quinone systems among the phototrophic bacteria are discussed from evolutionary and taxonomic viewpoints.
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  • 46
    ISSN: 1432-072X
    Keywords: Eubacteria ; Evolution ; Extreme thermophile ; Thermotoga
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    Topics: Biology
    Notes: Abstract A second species of the extremely thermophilic, eubacterial genus Thermotoga is described as clearly distinguished from the type species Thermotoga maritima by physiological and phylogenetic criteria. It is named Thermotoga neapolitana.
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    Journal of mathematical biology 26 (1988), S. 347-357 
    ISSN: 1432-1416
    Keywords: Transposable elements ; Evolution ; Branching processes ; Population genetics ; Mobile genetic elements
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    Topics: Biology , Mathematics
    Notes: Abstract A discrete-time multitype branching process model is presented for the evolution of transposable elements in haploid populations. An individual is classified as type i if it possesses i copies of the TE, i⩾0. The general model incorporates copy-dependent selection and transposition, and recursion relations are derived for the distribution of the number of individuals of the various types. The asymptotic relative proportions of individuals of the different types is studied in the neutral case. The behavior of this equilibrium distribution is examined for various patterns of regulated transposition and deletion.
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    Cell & tissue research 252 (1988), S. 349-358 
    ISSN: 1432-0878
    Keywords: Thyroglobulin ; Sulfation ; Thyroid gland ; Vertebrates ; Evolution ; Trout (Salmo gairdnerii) ; Clawed toad (Xenopus laevis) ; Chicken
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Mammalian thyroglobulin is released by thyroid follicle cells as a sulfated glycoprotein; the sulfate residues are mostly linked to tyrosine, but they are also attached to the high-mannose carbohydrate side-chains. To decide whether sulfation of thyroglobulin is confined to mammals, representatives of other vertebrate classes were analyzed for the presence of sulfated thyroglobulin: fish (trout), amphibians (clawed toad) and birds (chicken). Mini-organs were prepared from thyroid tissue and suspended in a 35SO 4 -- -containing culture medium. Light- and electron-microscope autoradiographs prepared from the mini-organs showed that thyroid follicle cells from all species examined incorporate 35SO 4 -- and synthesize a sulfated secretory product which accumulates in the follicle lumen. The Golgi complex was detected as the primary intracellular site of sulfate organification. The 35SO 4 -- -radiolabeled secretory product of all species was shown by polyacrylamide-gel-electrophoretic analyses to consist of thyroglobulin, identified by comparison with biosynthetically 125I-labeled thyroglobulin. The results indicate that the sulfation of thyroglobulin is a ubiquitous post-translational modification observed already in the thyroglobulin of lower vertebrates. Our observations suggest that sulfation of thyroglobulin was acquired in the early stages of thyroid evolution.
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    Molecular genetics and genomics 214 (1988), S. 439-450 
    ISSN: 1617-4623
    Keywords: trpA ; trpB ; Methanococcus voltae ; Archaebacteria ; Evolution
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    Topics: Biology
    Notes: Summary A cosmid bank of Methanococcus voltae DNA was obtained in Escherichia coli after ligation of partially HindIII-digested M. voltae DNA in the HindIII site of the transferable cosmid pVK100. The bank was used to perform complementation experiments with E. coli auxotrophic mutants. Five cosmids complementing trpA shared three adjacent HindIII fragments of 2.1, 2.3 and 14 kb. Two of these cosmids also complemented trpD and carried an additional 4.2 kb HindIII fragment. The trpA- and trpD-complementing regions were more precisely localized using Tn5 mutagenesis. A 1.7 kb PstI fragment, cloned into pUC9 in both orientations, was responsible for the trpA complementation. This fragment was sequenced and an open reading frame (ORF) of 852 nucleotides (ORFtrpA) encoding a 284 amino acid polypeptide of mol. wt. 31938 was found. The amino acid sequence was compared with that of the α subunit of tryptophan synthase (trpA gene product) from nine eubacterial species and to the N-terminal part of the tryptophan synthase of Saccharomyces cerevisiae (TRP5 gene product). Similarity varied from 24% (Brevibacterium lactofermentum) to 35% (S. cerevisiae). The nucleotide sequence of the region upstream from M. voltae ORFtrpA was determined and revealed the presence of an ORF of 1227 nucleotides (ORFtrpB) encoding a 409 amino acid polypeptide of mol. wt. 44634. The polypeptide sequence was similar to the β subunit of tryptophan synthase (trpB gene product) from six eubacterial species and to the C-terminal part of the tryptophan synthase of S. cerevisiae. Similarity varied from 49% (S. cerevisiae, B. lactofermentum) to 58% (Pseudomonas aeruginosa). This high conservation supports the hypothesis of a common ancestor for the trpA and trpB genes of archaebacteria, eubacteria and eucaryotes. M. voltae ORFtrpA and ORFtrpB, which are transcribed in the same direction, are separated by a 37 bp AT-rich region. Immediately upstream from ORFtrpB, the 3′ end of an ORF homologous to E. coli and Bacillus subtilis trpF was found. As the trpD-complementing region was located upstream from the trpFBA sequenced region, the organization of trp genes in the archaebacterium might thus be trpDFBA. Such an organization resembles that of enteric eubacteria, in which the trpEDCFBA genes are grouped in a single operon. However, M. voltae ORFtrpA and ORFtrpB do not overlap, in contrast with what is found in most eubacteria.
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    Plant systematics and evolution 159 (1988), S. 229-235 
    ISSN: 1615-6110
    Keywords: AngiospermsPoaceae ; Triticum ; Evolution ; in situ hybridization ; biotin labelling ; G genome chromosomes ; repeated DNA
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    Notes: Abstract The somatic chromosomes ofTriticum turgicum var.durum cv. Langdon andT. dicoccoides (AABB tetraploids),T. timopheevii, andT. araraticum (AAGG tetraploids) were assayed for distribution patterns of a highly repeated 120bp DNA sequence by in situ hybridization. The repeated sequence appears to be an ancient sequence shared withSecale andAegilops. The distribution patterns of the chromosomes were compared to the patterns of the A and B genome chromosomes ofT. aestivum cv. Chinese Spring (AABBDD hexaploid).T. turgidum andT. dicoccoides were observed to have identical in situ hybridization patterns. In both species, nine chromosomes with a total of 21 sites of hybridization were observed. The pattern, with few exceptions, was identical to that of Chinese Spring.T. araraticum andT. timopheevii were observed to have different patterns. InT. araraticum, six chromosomes with 21 total hybridization sites are present while inT. timopheevii nine chromosomes with 19 total sites exist. Major differences in hybridization patterns were observed between the B and G genomes. The divergence of the tetraploid wheats in this study appears to have resulted in changes in location, not in amount, of the ancient repeated sequence.
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    Biology and philosophy 3 (1988), S. 29-47 
    ISSN: 1572-8404
    Keywords: Louis Agassiz ; Empiricism ; Cladism ; Evolution
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    Topics: Biology , Philosophy
    Notes: Abstract The philosophy of “pattern cladism” has been variously explained by reference to the work of Louis Agassiz. The present study analyzes Agassiz's attempt to combine an empirical approach to the study of nature with an idealistic philosophy. From this emerges the problem of empiricism and of the isomorphy between the order of nature and human thinking. The analysis of the writings of Louis Agassiz serves as the basis for discussion of the “reality” of natural groups as postulated by pattern cladists.
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    Plant ecology 74 (1988), S. 107-112 
    ISSN: 1573-5052
    Keywords: Biogeography ; Desert ; Evolution ; Gradient ; Larrea
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    Topics: Biology
    Notes: Abstract In this paper the hypothesis is tested that the local distributions of perennial plants on a desert bajada are related to those at the regional/geographical level. Plant species reaching their highest density in the lower, mid-, or upper plant association on the bajada showed no difference in their latitudinal centers of distribution, or the latitudinal variation over the region. However, plants in the three associations did differ significally in the standardized distance of their regional distribution from the target bajada: i.e., plant species characteristic of the mid-bajada were significantly closer to their regional distribution centers than were plants in the lower or upper association. These results suggest that the local distribution of plants on desert bajadas are related to those at the regional level. Consideration of historical source-pools may provide a key to understanding both the ecological and biogeographic components of plant associations in North American desert regions.
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    Plant systematics and evolution 160 (1988), S. 123-142 
    ISSN: 1615-6110
    Keywords: Angiosperms ; Poaceae ; Triticeae ; Evolution ; isozymes
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    Topics: Biology
    Notes: Abstract An electrophoretic comparison of variation at 16 presumptive isozyme gene loci was performed for 17 species from the tribeTriticeae. Included in the analysis were annuals and perennials, and self- and cross-pollinating species, representing the H, I, P, N, R, V, S, E, J, J1J2, A, B, and D genomes. Perennial species were found to contain a significantly (marginally, at the 5% level) higher proportion of polymorphic loci and level of heterozygosity, than annual species. There were no significant differences between self- and crosspollinating species. Across all species, mean heterozygosity levels ranged from 0–0.225 and the % polymorphic loci from 6.3–56.3%. Genetic distance estimates varied from 0.08–0.39 for congeneric species. Relationships were deduced between the 17 species using phenetic and cladistic analyses and compared with relationships inferred from other parameters such as morphology and nucleotide sequence data. In general, the trees derived from the various relationships were concordant; the evolutionary basis for minor discrepancies between trees is also discussed.
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    Plant systematics and evolution 160 (1988), S. 29-37 
    ISSN: 1615-6110
    Keywords: Angiosperms ; Poaceae ; Evolution ; phylogenetic trees ; 18 S rRNA ; 26 S rRNA ; direct rRNA sequencing
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    Notes: Abstract We have isolated RNA from nine different grass species and fromPsilotum, a modern representative of a primitive land plant lineage. By direct RNA sequencing with reverse transcriptase, we have determined the nucleotide sequence for five regions of the 18 S rRNA molecule and three regions of the 26 S rRNA molecule. Over 1 600 positions have been elucidated for each plant species. These sequences were aligned by computer and the variable positions were identified by inspection. The data from the variable positions were input into phylogenetic inference computer programs to generate an evolutionary relationship among the grass species. This evolutionary tree based on nucleotide sequence data was compared to a recent classification of thePoaceae based on morphological data.
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    Plant systematics and evolution 160 (1988), S. 39-59 
    ISSN: 1615-6110
    Keywords: Angiosperms ; Poaceae ; Triticeae ; Evolution ; dispersed repeated sequences
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    Notes: Abstract Four representatives of a family of dispersed repetitive sequences which were prominent and dispersed in the E genome ofThinopyrum elongatum but poorly represented in wheat, were studied in detail. The 1.4kb sequences were present both as part of tandem and more complex arrays and appeared to have resulted from repeated amplification of the sequence and their dispersion throughout the genome. Subcloning of sections of the 1.4 kb sequences resulted in probes which improved the resolution of the E genome from the genomes in wheat and enabled identification of single E genome chromosomes introduced into wheat. The generality of these types of sequences in the tribeTriticeae was confirmed by isolating analogous sequences from the R (rye,Secale cereale), V (Dasypyrum villosum), and N (Psathyrostachys juncea) genomes. — The cloned repetitive sequences from the R, V, and N genomes each showed characteristic fluctuations in amount within the grasses examined in addition to being virtually absent from wheat. It is thus possible that these sequences may provide useful taxonomic indicators for establishing relationships within theTriticeae, as well as valuable probes for tracing alien chromatin introduced into wheat.
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  • 56
    ISSN: 1617-4623
    Keywords: Erythromycin ; Kasugamycin ; Adenosine dimethylation ; Ribosomal RNA ; Evolution
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    Notes: Summary An inducible erythromycin resistance gene (erm) of Streptococcus pyogenes was introduced into Escherichia coli by transformation with a plasmid. The recipient E. coli cells were either kasugamycin sensitive (wildtype) or kasugamycin resistant (ksgA). The MIC values of erythromycin increased from 150 μg/ml to〉3000 μg/ml for E. coli. An extract of transformed cells, particularly a high-salt ribosomal wash, contained an enzyme that was able to methylate 23S rRNA from untransformed cells in vitro; however, 23S rRNA from transformed cells was not a substrate for methylation by such an extract. 165 rRNA and 30S ribosomal subunits of either the wild type or a kasugamycin resistant (ksgA) mutant were not methylated in vitro. Transformation of E. coli by the erm-containing plasmid led to a reduction of the MIC values for kasugamycin. This happened in wild-type as well as in ksgA cells. However, in vitro experiments with purified ksgA encoded methylase demonstrated that also in erm transformed E. coli, the ksgA encoded enzyme was active in wild-type, but not in ksgA cells. It was also shown by in vitro experiments that ribosomes from erm ksgA cells have become sensitive to kasugamycin. Our experiments show that in vivo methylation of 23S rRNA, presumably of the adenosine at position 2058, leads to enhanced resistance to erythromycin and to reduced resistance to kasugamycin. This, together with previous data, argues for a close proximity of the two sites on the ribosome that are substrates for adenosine dimenthylation.
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  • 57
    ISSN: 1573-5133
    Keywords: Comoro Islands ; Grand Comoro ; Anjouan ; History ; Living fossil ; Evolution ; Phylogenetic relationships ; Morphology ; Demography ; Reproduction ; Locomotion ; Habitat ; Predators and prey ; Gombessa ; Trade ; Endangered species ; Artisanal fishing ; Coelacanth Conservation Council
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    Notes: Synopsis It all started about 400 million years ago, when representatives of a group of fish-like fleshy-finned creatures appeared in the fossil record (or was it through a childhood dream shared by all of us that we would one day study the coelacanth?). Many of the coelacanth's characters placed them close to the ancestry of terrestrial vertebrates. About 70 million years ago they disappeared from the fossil record. The discovery in 1938 of the first living coelacanth, in 1952 of the second and until now over 200 specimens parallels in excitement an encounter with a live dinosaur on a weekend walk, and in significance even more than that. For this year's 50th anniversary of the famous discovery of the first living coelacanth, we retraced the routes and visited the main actors of this zoological drama. New insights into coelacanth natural history were facilitated by novel interpretation of earlier data and our expeditions to the Comoro Islands, retracing the route of the second specimen, measuring unrecorded specimens, interviewing fishermen and describing their fishing crafts, and taking part in recent events on land and water near the only known habitat of the living coelacanth. Entry into this habitat and observations from the research submersible GEO opened up a new era in coelacanth research. Past studies of preserved specimens, which were caught as an incidental bycatch, were supplemented for the first time by studies of free-living coelacanths in their natural habitat. The first film footage taken from the submersible revealed the entirely unfishlike movements of this creature. Its mode of locomotion is a combination of flying and gliding, interspersed with head stands and belly-up drifts which appear to defy gravity. The narrow range of habitat in which the coelacanth has been encountered has led us to realize how vulnerable this ancient relict is. The members of our expeditions therefore cooperated in establishing an international organisation to coordinate efforts to conserve the coelacanth.
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    Environmental biology of fishes 23 (1988), S. 283-297 
    ISSN: 1573-5133
    Keywords: H-Y antigen ; Gene structure ; Size advantage model ; Evolution
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    Topics: Biology
    Notes: Synopsis The interpretation of experiments, designed to reveal whether sex change is induced behaviorally, can influence the type of physiological mechanism we propose to underlie sex change. Mechanisms involving stimulation differ from mechanisms of disinhibition and each is inferred from different ways of conceptualizing behavioral experiments. Both types of mechanism are likely to involve CNS, hypothalamus, pituitary, and gonad. Recent work, however, also implicates H-Y antigen and Bkm satellite DNA in the sex-change process. These studies raise the exciting possibility that the changes in behavioral relationships between the sexes that induce sex change also produce changes in certain aspects of DNA. The nature of the proximate causes of sex change plays a surprisingly important role in influencing evolutionary models of sex change. Such models can be evaluated by first examining their applicability to real populations and, if they are applicable, then testing their validity by comparing their predictions with observed data. The size advantage model, in spite of its proven ability to stimulate and direct research, does not fare well in either of these stages of evaluation. The basic weakness of the model is its failure to incorporate individual adaptability into the life history of sex-changing fishes.
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    Primates 29 (1988), S. 535-547 
    ISSN: 0032-8332
    Keywords: Homo ; Australopithecus ; Model ; Dentition ; Evolution
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    Notes: Abstract The complete dentition of the common ancestor ofAustralopithecus andHomo, intermediate between that of a pongid and a hominid, is virtually unknown. The maxillary dentition (P3-M2) ofRamapithecus brevirostris Lewis, 1934, a pongid from the Early Pliocene, and that of hominids from the Late Pliocene and Plio/Pleistocene is known. SinceR. brevirostris is probably ancestral to the hominids, a model of intermediate maxillary dentition (P3-M2) is extrapolated and described. The model represents a hypothetical protohominid dentition. It does not conform with the teeth ofAustralopithecus, but shows greater morphological affinity to hominine dentition and to 5 myo hominids. TheHomo lineage, therefore, may go back to the Middle Pliocene. According to the normal sequence of evolution, it is most unlikely thatAustralopithecus gave rise toHomo, but much more probable that a very early, generalizedHomo evolved into an advanced, specializedAustralopithecus.
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    Cellular and molecular life sciences 43 (1987), S. 202-205 
    ISSN: 1420-9071
    Keywords: Evolution ; substrate specificity ; serological homologies ; flavone biosynthesis ; Silene ; glycosyltransferases
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    Topics: Biology , Medicine
    Notes: Summary The variation in flavone glycosylation patterns inSilene is the result of the expression of six genetic loci, which control either the presence of allozymes differing in substrate specificity or isozymes regulated differently during development. Serological studies showed that at least three of these six loci are evolutionarily related. The genetic mechanisms leading to these complicated variation patterns and the role of this polymorphism for the plant in its interaction with the environment are discussed.
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  • 61
    ISSN: 1432-0983
    Keywords: Comparative restriction site mapping ; Gene mapping ; Deletions and additions ; Chloroplast genome ; Evolution
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    Notes: Summary The chloroplast genomes from the interfertile green algae Chlamydomonas eugametos and C. moewusii have been compared in their overall sequence organization. Physical mapping of Aval, BstEII and EcoRI restriction sites on the C. moewusii chloroplast genome revealed that this 292 kilobase-pair (kbp) genome is 49 kbp larger than the C. eugametos genome. Heterologous fragment hybridizations indicated the same order of common sequence elements on the two algal genomes. Almost all of the 49 kbp size difference is accounted for by the presence of two large extra sequences in C. moewusii: a 21 kbp sequence in the inverted repeat and a 5.8 kbp sequence in the single copy-region bordering the 16S ribosomal RNA (rRNA) genes. In addition to these two major deletion/addition differences, 42 restriction site and fragment length differences (ranging from 100 to 500 base pairs) were mapped on the two algal genomes. Surprisingly, the greatest density of these differences was found to be confined within the inverted repeat, one of the most conserved regions of land plant chloroplast genomes.
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    Journal of molecular evolution 25 (1987), S. 141-150 
    ISSN: 1432-1432
    Keywords: 20S particle ; Prosome ; Evolution ; Small cytoplasmic RNAs ; Heat shock proteins
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    Notes: Summary We have purified and characterized a particle sedimenting at 20S from the postribosomal fraction of yeast, wheat germ,Drosophila melanogaster tissue culture cells, chicken embryo fibroblasts, rabbit reticulocyte lysate, and HeLa cells. Most of the protein constituents of the 20S particle have molecular weights of 20–35 kd and differ between species; however, some do have similar molecular weights and isoelectric points, suggesting they are related. Several low-molecular-weight RNAs, distinct from tRNAs, co-purify with the particle isolated from all these species and show increasingly more complex patterns ascending the arbitrary order from yeast to human (yeast, plant, insect, bird, and mammals). InDrosophila, we present evidence that these small RNAs are tightly associated with this 20S structure.
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    Journal of molecular evolution 25 (1987), S. 248-254 
    ISSN: 1432-1432
    Keywords: Intervening sequence ; Evolution ; Archaebacteria
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    Notes: Summary Nucleotide sequences of four tRNA genes from the archaebacteriumSulfolobus solfataricus have been determined. Based upon DNA sequence analysis, three of the four genes contain presumptive intervening sequences (introns) in their anticodon loops. The three introns can form similar, but not identical, secondary structures. The cleavage site at the 3′ end of all three introns occurs in a three-base bulge loop. All four genes lack an encoded 3′ CCA terminus and are flanked by A+T-rich DNA sequences. Two of the genes are located on antiparallel DNA strands, with their 3′ termini separated by 414 bp of sequence. Including two previously published sequences, a total of five introns have now been detected among sixS. solfataricus tRNA genes. Occurrence of introns at corresponding locations in both archaebacterial and eukaryotic tRNA genes suggests that the intron/exon form of gene structure predates the evolutionary divergence of the archaebacteria and the eukaryotes.
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    Journal of molecular evolution 25 (1987), S. 261-269 
    ISSN: 1432-1432
    Keywords: Fimbriae ; Pili ; Protein structure ; Microbial phylogeny ; Evolution
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    Notes: Summary We have analyzed and compared the amino acid sequences of the type 4 fimbrial subunits fromPseudomonas aeruginosa, Moraxella bovis, M. nonliquefaciens, Bacteroides nodosus, Neisseria gonorrhoeae, andN. meningitidis. We propose a consensus sequence for the highly conserved aminoterminal regions of these proteins. In the variable regions, a domain corresponding to an epitope common toN. gonorrhoeae andN. meningitidis fimbriae is conserved, both in sequence and in environment, in fimbrial subunits fromB. nodosus. The subunits fromM. bovis andP. aeruginosa do not show any homologies to this sequence. In all of the subunits, the carboxy-terminal half of the molecule consists of a series of fairly hydrophobic domains. The last three domains, two of which include the cysteines of the disulfide bridge inN. gonorrhoeae, P. aeruginosa, andM. bovis, are more or less conserved in sequence in all of the proteins including that ofB. nodosus. We propose that these conserved hydrophobic regions, which have the potential to form a series of beta-sheets, form a structural framework around which more variable hydrophilic sequences determining immunological profile are arranged. The evolutionary relationships of the contemporary proteins and the distribution of type 4 fimbriae are also discussed.
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    Journal of molecular evolution 26 (1987), S. 274-283 
    ISSN: 1432-1432
    Keywords: Cardiotoxin ; Circular dichroism ; Cytotoxin ; Evolution ; Protein
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    Notes: Summary In order to analyze the evolutionary behavior of the cobra venom cytotoxins, their probable tertiary structure was predicted using computer graphics. The 41 amino acid sequences known show that the major evolutionary changes have taken place in two particularly exposed areas of the molecular surface. In each area, neighboring residue positions seem to have evolved interdependently, but there is no obvious interdependence between the two areas. Indeed, the relative evolution of these two areas prompts a subdivision of the sequence set into four groups. According to the known cytotoxin circular dichroism spectra, one of these four groups could be characterized by a difference in molecular secondary structure. Sine the two variable areas have functional associations, it is suggested that their evolution may be governed by a target with several similar binding sites.
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    Journal of molecular evolution 26 (1987), S. 341-346 
    ISSN: 1432-1432
    Keywords: Evolution ; tRNA ; Recognition sites ; Statistics
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    Notes: Summary A compilation of known tRNA, and tRNA gene sequences from archaebacteria, eubacteria, and eukaryotes permits the construction of tRNA cloverleafs which show conserved structural elements for each tRNA family. Positions conserved across the three kingdoms are thought to represent archetypical features of tRNAs which preceded the divergence of these kingdoms.
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    Journal of molecular evolution 24 (1987), S. 228-235 
    ISSN: 1432-1432
    Keywords: 5S RNA ; Correspondence analysis ; Multivariate statistics ; Evolution ; Phylogeny
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    Notes: Summary Correspondence analysis (a form of multivariate statistics) applied to 74 5S ribosomal RNA sequences indicates that the sequences are interrelated in a systematic, nonrandom fashion. Aligned sequences are represented as vectors in a 5N-dimensional space, where N is the number of base positions in the 5S RNA molecule. Mutually orthogonal directions (called factor axes) along which intersequence variance is greatest are defined in this hyperspace. Projection of the sequences onto planes defined by these factorial directions reveals clustering of species that is suggestive of phylogenetic relationships. For each factorial direction, correspondence analysis points to regions of “importance”, i.e., those base positions at which the systematic changes occur that define that particular direction. In effect, the technique provides a rapid determination of group-specific signatures. In several instances, similarities between sequences are indicated that have only recently been inferred from visual base-to-base comparisons. These results suggest that correspondence analysis may provide a valuable starting point from which to uncover the patterns of change underlying the evolution of a macromolecule, such as 5S RNA.
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    Journal of molecular evolution 24 (1987), S. 236-251 
    ISSN: 1432-1432
    Keywords: 28S rRNA ; RNA secondary structure ; Evolution ; Ribosome ; Translation
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    Notes: Summary We have determined the secondary structure of the human 28S rRNA molecule based on comparative analysis of available eukaryotic cytoplasmic and prokaryotic large-rRNA gene sequences. Examination of large-rRNA sequences of both distantly and closely related species has enabled us to derive a structure that accounts both for highly conserved sequence tracts and for previously unanalyzed variable-sequence tracts that account for the evolutionary differences in size among the large rRNAs. Human 28S rRNA is composed of two different types of sequence tracts: conserved and variable. They differ in composition, degree of conservation, and evolution. The conserved regions demonstrate a striking constancy of size and sequence. We have confirmed that the conserved regions of large-rRNA molecules are capable of forming structures that are superimposable on one another. The variable regions contain the sequences responsible for the 83% increase in size of the human large-rRNA molecule over that ofEscherichia coli. Their locations in the gene are maintained during evolution. They are G+C rich and largely nonhomologous, contain simple repetitive sequences, appear to evolve by frequent recombinational events, and are capable of forming large, stable hairpins. The secondary-structure model presented here is in close agreement with existing prokaryotic 23S rRNA secondary-structure models. The introduction of this model helps resolve differences between previously proposed prokaryotic and eukaryotic large-rRNA secondary-structure models.
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    Journal of molecular evolution 25 (1987), S. 15-19 
    ISSN: 1432-1432
    Keywords: β-Turns ; Secondary structures ; Chirality ; Genetic code ; Biosynthetic pathways ; Evolution
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    Topics: Biology
    Notes: Summary The physicochemical properties of β-turns suggest their biological importance prior to the formation of the genetic code. These properties include ones potentially affecting the preference for eitherl- ord-amino acids. The abundance of certain amino acids in β-turns is correlated with their assignment to a small, well-defined part of the genetic code and with their role as metabolic precursors for other amino acids. It is proposed that in the prebiotic environment, β-turns became objects of selection that influenced the evolution of the genetic code and biosynthetic pathways for amino acids.
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    ISSN: 1432-1432
    Keywords: Balbiani rings ; Evolution ; Immunological detection ; Nucleotide sequence ; 3′ End
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    Notes: Summary Two cDNA clones representing the 3′-end regions of BR1 and BR2 75S mRNA were obtained fromChironomus pallidivittatus. The regular structure characterizing the core of these genes, consisting of tandemly arranged repeat units, changes into a more irregular structure toward the 3′ end. Distal to a standard type of repeat unit with a characteristic excess of positive charges, a new type of repeat with a high, negative charge density is interspersed among parts of the standard unit. The last 111 amino acids before the stop codon represent a unique region distinctly different in amino acid composition from upstream regions, and include two partially homologous hydrophobic regions. Sequence comparison of 3′-end regions from clones representing BR1 and BR2 genes indicates striking sequence conservation in the unique part of the region. Analysis of the level of silent site divergence shows that the homology increases in the 3′ direction up to the polyadenylation site. That the unique region is retained as a part of the secreted protein is shown by Western blotting.
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  • 71
    ISSN: 1432-1432
    Keywords: Histone genes ; Echinoderms ; Maternal mRNA ; Development ; Evolution
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    Topics: Biology
    Notes: Summary The organization and maternal expression of histone genes differ greatly between the two echinoderm classes represented by the sea stars and sea urchins. We have isolated and characterized a 5.3-kb genomic DNA fragment encoding core histone genes in the sea starPisaster ochraceus. The majority of histone genes are organized as tandem repeats of the 5.3-kb fragment, which is present in as many as 700 copies per haploid genome. The identity, precise location, and transcriptional polarity of individual core histone genes within the repeat were determined by DNA sequence analyses. The gene order in the sea star (H2B, H2A, H4, H3) is different from that in sea urchins (H2B, H3, H2A, H4). What is remarkable is the low level of maternal histone mRNA inP. ochraceus eggs relative to that in sea urchins. This observation supports a recent suggestion that major changes in mode of gene expression, rather than in gene organization or copy number, can be correlated with major events in echinoderm evolution.
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  • 72
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    Journal of molecular evolution 25 (1987), S. 81-88 
    ISSN: 1432-1432
    Keywords: Glutathione ; Evolution ; Phototrophic microorganisms ; Oxygen toxicity
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    Topics: Biology
    Notes: Summary Of the many roles ascribed to glutathione (GSH) the one most clearly established is its role in the protection of higher eucaryotes against oxygen toxicity through destruction of thiol-reactive oxygen byproducts. If this is the primary function of GSH then GSH metabolism should have evolved during or after the evolution of oxygenic photosynthesis. That many bacteria do not produce GSH is consistent with this view. In the present study we have examined the low-molecular-weight thiol composition of a variety of phototrophic microorganisms to ascertain how evolution of GSH production is related to evolution of oxygenic photosynthesis. Cells were extracted in the presence of monobromobimane (mBBr) to convert thiols to fluorescent derivatives, which were analyzed by highpressure liquid chromatography. Significant levels of GSH were not found in the green bacteria (Chlorobium thiosulfatophilum andChloroflexus aurantiacus). Substantial levels of GSH were present in the purple bacteria (Chromatium vinosum, Rhodospirillum rubrum, Rhodobacter sphaeroides, andRhodocyclus gelatinosa), the cyanobacteria [Anacystis nidulans, Microcoleus chthonoplastes S.G., Nostoc muscorum, Oscillatoria amphigranulata, Oscillatoria limnetica, Oscillatoria sp. (Stinky Spring, Utah),Oscillatoria terebriformis, Plectonema boryanum, andSynechococcus lividus], and eucaryotic algae (Chlorella pyrenoidsa, Chlorella vulgaris, Euglena gracilis, Scenedesmus obliquus, andChlamydomonas reinhardtii). Other thiols measured included cysteine, γ-glutamylcysteine, thiosulfate, coenzyme A, and sulfide; several unidentified thiols were also detected. Many of the organisms examined also exhibited a marked ability to reduce mBBr to syn-(methyl,methyl)bimane, an ability that was quenched by treatment with 2-pyridyl disulfide or 5,5′-bisdithio-(2-nitrobenzoic acid) prior to reaction with mBBR. These observations indicate the presence of a reducing system capable of electron transfer to mBBr and reduction of reactive disulfides. The distribution of GSH in phototrophic eubacteria indicates that GSH synthesis evolved at or around the time that oxygenic photosynthesis evolved.
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    Oecologia 72 (1987), S. 69-76 
    ISSN: 1432-1939
    Keywords: Cabbage butterfly ; Pieris rapae ; Evolution ; Adaptation ; Colonisation
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    Topics: Biology
    Notes: Summary Australian and U.K. Pieris rapae differ markedly in their oviposition behaviour; U.K. females produce a more aggregated egg distribution, and lay their eggs more quickly, than do Australian females. The adaptive reason for this divergence probably lies in the relative costs of increased flight time (more costly in the U.K.) and increased local crowding (more costly in Australia). There is also a strong relationship between juvenile developmental rate (at constant temperature) and oviposition behaviour, but the form of this relationship differed between the two populations. The adaptive reasons for the link between developmental rate and behaviour is not clear. It may be that this link represents the tip of the iceberg; i.e. that physiological, developmental, and behabioral characters all co-vary in ways and for reasons that we do not yet understand.
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  • 74
    ISSN: 1432-0983
    Keywords: ATP synthase β ; Selective constraint ; mtDNA ; Evolution
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    Notes: Abstract We have cloned and sequenced human and bovine cDNAs for the β subunit of the ATP synthase (ATP-synß), a nuclear DNA (nDNA) encoded oxidative phosphorylation (OXPHOS) gene. The two cDNAs were found to share 99% amino acid homology and 94% nucleotide homology. The evolutionary rate of ATPsynß was then compared with that of two mitochondrial DNA (mtDNA) ATP synthase genes (ATPase 6 and 8), seven other mtDNA OXPHOS genes, and a number of nuclear genes. The synonymous substitution rate for ATPsynß proved to be 1.9 × 10−9 substitutions per site per year (substitutions × site−1 × year−1) (SSY). This is less than 1/2 that of the average nDNA gene, 1/12 the rate of ATPase 6 and 8, and 1/17 the rate of the average mtDNA gene. The synonymous and replacement substitution rates were used to calculate a new parameter, the “selective constraint ratio”. This revealed that even the most variable mtDNA protein was more constrained than the average nDNA protein. Thus, the high substitution mutation rate and strong selective constraints of mammalian mtDNA proteins suggest that mtDNA mutations may result in a disproportionately large number of human hereditary diseases of OXPHOS.
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    Ecological research 2 (1987), S. 175-183 
    ISSN: 1440-1703
    Keywords: Egg size ; Evolution ; Hesperiidae ; Host specificity ; Leaf toughness
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    Notes: Abstract The adaptive significance of egg size of skippers (Lepidoptera; Hesperiidae) in Japan was evaluated in relation to the leaf toughness of their major host grasses. The hesperids that fed on tougher grasses laid larger eggs. Hesperids that laid larger eggs were larger in body size, but lower in fecundity. They also had a wider host range. Thus, despite the lower fecundity, hesperids may benefit from large eggs by having a wider host range of larvae. Grass feeders had wider range of host plants than broadleaf feeders.
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    Journal of mathematical biology 25 (1987), S. 393-409 
    ISSN: 1432-1416
    Keywords: Evolution ; Evolutionary stable states ; Games theory ; Linear programming ; Convex polyhedra ; Linear complementarity
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    Topics: Biology , Mathematics
    Notes: Abstract The problem of finding an Evolutionary Stable Strategy (ESS) for an animal species is defined. It is shown how such strategies are a subset of the equilibrium solutions for a particular non-zero sum game. These equilibrium solutions are then shown to arise from the vertices of a particular convex polyhedron. A method of finding these equilibrium solutions through the vertices and then the ESS solutions is given. This is illustrated by a number of numerical examples taken from the literature. Finally an alternative approach based on solving a Linear Complementarity Problem is discussed.
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    Theoretical and applied genetics 73 (1987), S. 883-892 
    ISSN: 1432-2242
    Keywords: Lens ; Isozymes ; Translocation break-point ; Linkage ; Evolution
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    Notes: Summary Segregation of 18 marker genes was monitored in selfed progeny of a Lens culinaris × L. ervoides hybrid; five linkage groups were mapped, one of which contained a reciprocal translocation break-point that differentiates between the parents. Four markers were found to be linked to the translocation break-point: Aco-1 and Pgm-2 on one side and Gs and Got-2 on the other. The gene pairs on both sides of the translocation are not linked in L. culinaris or in L. orientalis. The L. ervoides gene order was also found in L. odemensis but with significantly reduced map distances. Analysis of monogenic segregations in a number of Lens inter-specific crosses revealed some consistent patterns of deviations from the expected Mendelian ratios. The factors responsible for these unequal segregations, genotypic effects on recombination frequencies, negative interference, and the possible ancient origin of the translocation are discussed.
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    Theoretical and applied genetics 73 (1987), S. 675-682 
    ISSN: 1432-2242
    Keywords: Isozyme ; Genetic variability ; Evolution ; Rice ; Africa
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    Notes: Summary Eight hundred and thirtyone traditional varieties of rice, Oryza sativa L., were collected in Africa and analysed for their isozymic variability on 15 enzymatic systems, representing 37 presumed loci. There appears to be a correlation between the type of rice growing and the two groups Indica and Japonica. The degree of genetic diversity is nearly equal in African rice and the Asian one. Alleles due to introgression or mutational events were identified. The results suggest that the evolution of O. sativa is continuous in Africa by means of inter-subspecific or inter-specific crosses.
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    Theoretical and applied genetics 74 (1987), S. 188-193 
    ISSN: 1432-2242
    Keywords: Isoenzymes ; Evolution ; Domestication ; Biological structure ; Genetic distances
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    Notes: Summary Polymorphism in twelve genes coding for eight enzymes in pearl millet (Pennisetum glaucum (L.) R. Br.): alcohol dehydrogenases (ADH), catalases (CAT), β-esterases (EST), glutamate oxaloacetate transaminases (GOT), malate dehydrogenases (MDH), 6-Phosphogluconate dehydrogenases (PGD), phosphoglucoisomerases (PGI) and phosphoglucomutases (PGM), was observed by electrophoresis on 74 cultivated samples and 8 wild samples from West Africa. Six genes: Est A, Adh A, Pgm A, Cat A, Pgi A, Pgd A contain 95% of the total variation. Principal component analyses and discriminant analyses of the 82 samples described by 46 allelic frequencies showed an almost complete separation into 3 groups: wilds, early maturing cultivars and late maturing cultivars. The early group has the highest enzyme diversity, with cultivated millets from Niger showing the most diversity. The high diversity of the early group and its extensive divergence from West-African wild millets suggest, firstly, the existence, elsewhere in Africa of other enzymatically different sources of wild millet, and secondly, the occurrence, prehistorically, of several different domestications. The late group of cultivars has the lowest variability and a relatively low coefficient of differentiation. This relatively homogeneous enzyme structure does not seem to be associated to ecology. A hypothesis is advanced suggesting that West African late-cultivars were derived from a common cultivated early complex. This complex must have been distributed across the Sudanian zone and must have been later sumitted to modifications by limited gene flow with local early maturing cultivars.
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    Theoretical and applied genetics 75 (1987), S. 138-143 
    ISSN: 1432-2242
    Keywords: Wheat ; Ribosomal RNA genes ; Synthetic tetraploids ; Evolution ; Nucleolar activity
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    Notes: Summary The ribosomal RNA genes in the A genome of tetraploid (AABB) wheats are either absent or present at low levels. In four synthetic AABB tetraploids tested by in situ hybridization with a radioactive probe, the level of radioactive label at A and B NOR's corresponded to those of the parent species. There was no reduction after ten generations. In addition, the A chromosome rDNA is transcriptively active, the numbers of nucleoli being governed by the number of rRNA gene repeats in the smaller of the two A-genome NOR's. Since the wild tetraploid Triticum dicoccoides, as well as its domesticated derivatives, lack A-genome NOR's, their deletion is likely to have occurred prior to domestication, i.e. more than 10,000 years ago.
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    Molecular genetics and genomics 209 (1987), S. 203-205 
    ISSN: 1617-4623
    Keywords: Polymorphisms ; Genome structure ; Evolution
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    Notes: Summary Many cloned regions of the Drosophila genome show minimal variation between strains in overall sequence arrangement. While restriction site polymorphisms occur and the location of transposable elements may vary from one strain to another, such changes appear to be relatively minor variations, superimposed on overall genome stability. In contrast to this general situation, we describe here a segment of the X chromosome that is highly polymorphic in four strains of D. melanogaster and in D. simulans. The strains differ in the presence and extent of a short duplication and the presence of repetitive DNA. These results suggest that different regions of the genome may be subject to different evolutionary constraints, with some regions being particularly prone to extensive changes, even within a single species.
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  • 82
    ISSN: 1617-4623
    Keywords: Antibiotics ; Archaebacteria ; Ribosomes ; Evolution ; Thermoplasma
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    Notes: Summary The susceptibility of Thermoplasma acidophilum (an extremely acidophilic, moderately thermophilic, wall-less sulphur-oxidizing archaebacterium) to 50 ribosome-specific inhibitors of polypeptide elongation was surveyed using efficient poly(U)-and poly(UG)-directed cell-free systems and comparable reference systems derived from eubacterial (Bacillus stearothermophilus, Escherichia coli) and eukaryotic (Saccharomyces cerevisiae) species. Under optimum temperature (58° C) and ionic conditions for polypeptide synthesis Thermoplasma ribosomes are only sensitive to the 70 S/80 S ribosome-directed aminoglycoside neomycin, and to five 80 S ribosome-directed inhibitors all of which (α-sarcin, mitogillin, restrictocin, dianthin and gelonin) impair the functioning of the large (60 S) ribosomal subunit. Sensitivity of the three structurally related compounds α-sarcin, mitogillin and restrictocin and susceptibility to neomycin place Thermoplasma ribosomes between those of Sulfolobus solfataricus (only sensitive to α-sarcin) and Methanococcus vannielli (sensitive to α-sarcin, mitogillin, restrictocin and neomycin but also affected by a variety of 70 S ribosome-directed drugs). The phylogenetic significance of the greatly diversified antibiotic sensitivity spectra displayed by archaebacteria in general, as opposed to the uniform ones exhibited by eubacteria and eukaryotes, is discussed.
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  • 83
    ISSN: 1617-4623
    Keywords: TOL plasmid ; NAH plasmid ; Pseudomonas putida ; Catechol 2,3-dioxygenase ; Evolution
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    Notes: Summary TOL plasmid pWW0 and plasmid NAH7 encode catabolic enzymes required for oxidative degradation of toluene and naphthalene, respectively. The gene order of the catabolic operon of NAH7 for salicylate oxidation was determined to be: promoter-nahG (the structural gene for salicylate hydroxylase)-nahH (catechol 2,3-dioxygenase)-nahI (hydroxymuconic semialdehyde dehydrogenase)-nahN (hydroxymuconic semialdehyde hydrolase)-nahL (2-oxopent-4-enoate hydratase). This order is identical to that of the isofunctional genes of TOL plasmid pWW0. The complete nucleotide sequence of nahH was determined and compared with that of xylE, the isofunctional gene of TOL plasmid pWW0. There were 20% and 16% differences in their nucleotide and amino acid sequences, respectively. The homology between the NAH7 and TOL pWW0 plasmids ends upstream of the Shine-Dalgarno sequences of nahH and xylE, but the homology continues downstream of these genes. This observation suggested that genes for the catechol oxidative enzymes of NAH7 and TOL pWW0 were derived from a common ancestral sequence which was transferred as a discrete segment of DNA between plasmids.
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    Molecular genetics and genomics 209 (1987), S. 374-381 
    ISSN: 1617-4623
    Keywords: Alcohol dehydrogenase ; Saccharomyces cerevisiae ; Zymomonas mobilis ; Evolution
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    Topics: Biology
    Notes: Summary Insertion of the transposable element Ty at the ADH4 locus results in increased levels of a new alcohol dehydrogenase (ADH) activity in Saccharomyces cerevisiae. The DNA sequence of this locus has been determined. It contains a long open reading frame which is not homologous to the other ADH isozymes that have been characterized in S. cerevisiae nor does it show obvious homology to Drosophila ADH. The hypothetical ADH does, however, show strong homology to the sequence of an iron-activated ADH from the bacterium Zymomonas mobilis. Thus ADH4 appears to encode an ADH structural gene which, along with the Zymomonas enzyme, may define a new family of alcohol dehydrogenases.
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  • 85
    ISSN: 1615-6110
    Keywords: Angiosperms ; Asteraceae ; Ligularia calthifolia ; Araceae ; Acorus calamus ; Evolution ; phylogenetic trees ; 4.5 S rRNA ; 5 S rRNA ; chloroplasts
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    Topics: Biology
    Notes: Abstract Chloroplast 4.5 S rRNAs of the monocotAcorus calamus and the dicotLigularia calthifolia have been sequenced. Phylogenetic trees for the chloroplast 4.5 S and 5 S rRNAs and also for cytosol 5 S rRNAs have been constructed by several methods. They are compared with previous studies. Evidently, it is necessary to consider the inequality of nucleotide substitution rates in different lines for adequate phylogenetic reconstructions. Some relevant conclusions are presented. The possibilities and prospects for using data on low-molecular-weight rRNAs from cytosol and organelles for deducing phylogenetic relationships in plants are discussed.
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    Plant systematics and evolution 156 (1987), S. 151-157 
    ISSN: 1615-6110
    Keywords: Angiosperms ; Lythraceae ; Lythrum salicaria ; Evolution ; heterostyly ; pollen ; gender specialization
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    Topics: Biology
    Notes: Abstract Some of the factors governing seed-set in three populations ofLythrum salicaria are examined during two seasons. Plants spatially segregated from legitimate neighbours by distances exceeding 1m set few seeds. Plants with small inflorescences set fewer seeds than those with medium or large inflorescences. Flowers having self pollen applied to the stigma before legitimate pollination set fewer seed per flower than those pollinated with legitimate pollen only. Seeds of the mid-style morph germinated more effectively than those of the long style morph and seeds of the short-style morph showed very low levels of germination.
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    Plant ecology 68 (1987), S. 131-138 
    ISSN: 1573-5052
    Keywords: History of phytocoenology ; Paradigm ; Organismic concept ; Continuum concept ; Classification ; Evolution ; Succession
    Source: Springer Online Journal Archives 1860-2000
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    Notes: Abstract Paradigm change (organismic-continuum) in Soviet phytocoenology occurred in the 1960s, though the idea of a continuum is well known in the Soviet Union since L. G. Ramensky's works, written at the beginning of our century. This change has been influenced by American continuum-ecologists from the Schools of J. T. Curtis and R. H. Whittaker. The organismic approach in Soviet phytocoenology has never had an extreme character, and for this reason paradigm change appeared gradually. The impact of vegetation classification on the paradigm succession is emphasized: whether an investigator admits ‘real’, discontinuous communities or considers them part of a continuum, in either case he must reduce continuity to discontinuity to achieve a classification. Nevertheless, the dominant classification systems typical of the organismic period in Soviet phytocoenology were mostly of an organismic character, because they were based on the idea of the organizing role of edificators-dominants in the community, rather than on environmental conditions. The classification system based on the Braun-Blanquet approach which is widely spreading now in the USSR corresponds better to the idea of a continuum, because the floristic-sociological classification criteria reflect habitat conditions, rather than coenotic interrelations. Organismic and continuum paradigms are compared according to ten principal aspects, the most important of which are: the nature of the plant community, estimation of population differences within a community, synmorphology, syndynamics and relation to the classification problem.
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    Plant ecology 70 (1987), S. 135-147 
    ISSN: 1573-5052
    Keywords: Biogeography ; Climate dynamics ; Community pattern ; Evolution ; Western North America
    Source: Springer Online Journal Archives 1860-2000
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    Notes: Abstract New methods of weather analysis accompanied by microhabitat ‘bioassays’ have been applied in several case studies to demonstrate effects of atmospheric processes on patterns of community composition and structure and potential species evolution. Average spatial and seasonal airmass dynamics which determine regional and elevational patterns of relative microhabitat favorability, were found to vary between a recent global warming trend (ca 1900 to 1940) and the subsequent global cooling trend (ca 1940 to 1970). These apparently systematic spatial and temporal shifts in weather were related to plant establishment patterns and community composition and structure. The proposed causal mechanisms function, in part, through regional shifts in microhabitat size. These effects are similar to larger scale, longer term shifts deduced from the late Quaternary fossil record. By modifying the spatial approach, month-to-month and year-to-year variability of weather has been examined for the last 130 years at individual points in southwestern North America. Three climatic regimes (the end of the Little Ice Age, the recent warming trend and the recent cooling trend) exhibited distinct year-to-year patterns of weather that can be related to the establishment of different kinds of plants (e.g., C4 grasses versus C3 shrubs). Oscillations between different temporal climatic regimes appear to promote the episodic establishment of different life forms, but not necessarily their local extinction. The two methods of weather analysis have been combined in a regional assessment of climatic controls of different biomes in space and time with a primary focus on the Chihuahuan desert. Natural ecotones between the Chihuahuan desert and neighboring biomes are clearly related to large scale airmass dynamics associated with seasonal oscillations in jetstream position. The weather patterns controlling ecotonal positions result from seasonal topographic influences on the general circulation of the atmosphere. The apparent stability of these patterns allows causal hypotheses of biogeographic dynamics and the evolution of physiological traits and life history characteristics.
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    Molecular genetics and genomics 209 (1987), S. 489-493 
    ISSN: 1617-4623
    Keywords: Endonuclease ; Immunity ; Lysis ; Signal peptide ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The primary structures of the immunity (Imm) and lysis (Lys) proteins, and the C-terminal 205 amino acid residues of colicin E8 were deduced from nucleotide sequencing of the 1,265 bp ClaI-PvuI DNA fragment of plasmid ColE8-J. The gene order is col-imm-lys confirming previous genetic data. A comparison of the colicin E8 peptide sequence with the available colicin E2-P9 sequence shows an identical receptor-binding domain but 20 amino acid replacements and a clustering of synonymous codon usage in the nuclease-active region. Sequence homology of the two colicins indicates that they are descended from a common ancestral gene and that colicin E8, like colicin E2, may also function as a DNA endonuclease. The native ColE8 imm (resident copy) is 258 bp long and is predicted to encode an acidic protein of 9,604 mol. wt. The six amino acid replacements between the resident imm and the previously reported non-resident copy of the ColE8 imm ([E8 imm]) found in the ribonuclease-producing ColE3-CA38 plasmid offer an explanation for the incomplete protection conferred by [E8 Imm] to exogenously added colicin E8. Except for one nucleotide and amino acid change in the putative signal peptide sequence, the ColE8 lys structure is identical to that present in ColE2-P9 and ColE3-CA38.
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    Environmental biology of fishes 19 (1987), S. 3-26 
    ISSN: 1573-5133
    Keywords: Captive propagation ; Extinction ; Genetic variability ; Evolution ; Speciation ; Lates niloticus ; Nile perch ; Haplochromines ; Tilapia ; Clupeids ; Oil pollution ; Productivity
    Source: Springer Online Journal Archives 1860-2000
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    Notes: Synopsis Man has been associated with a variety of lakes throughout his evolutionary history in Africa. Lakeside dwellers have a close association with and understanding of these lakes. In the past four decades, however, overexploitation, introductions of alien fishes and the possibility of oil pollution present frightening prospects of irreversible losses and massive extinction. The development of scientific understanding of the life support processes, the ecosystems and the rich communities of these lakes has been so outpaced by exploitation and manipulations that accurate predictions regarding the future are impossible. Shallow lakes are more sensitive to physico-chemical changes caused by climatic as well as agricultural and industrial development than deep lakes, but their biotae are endowed with a resilience which facilitates recovery from major depletions to population size. In contrast, the speciose endemic cichlid faunae of deep lakes are sensitive to fishing pressure, are awkward to manage and should be regarded as representing a much smaller resource than initially imagined. The clupeids of Lake Tanganyika can sustain intensive fishing, but their introduction into other natural lakes is not recommended. Enormous changes to native faunae followed the introduction of Lates niloticus to lakes Kyoga and Victoria with dramatic consequences for the fisheries, for the socio-economic status of the region and for the maintenance of biotic diversity. Extinction of almost 300 fish species is a possible further consequence of L. niloticus predation. Intensive selective fishing for L. niloticus is being initiated, but is unlikely to resolve the problem. In the time necessary to substantially reduce L. niloticus, numerous endemic fishes may suffer extinction. A viable alternative to extinction of these species is captive propagation. Conservation of fishes by captive propagation is not a common or well documented practice. To encourage the acceptance of this conservation option a theoretical scenario in which the concepts and protocols are applied to the fishes of Lake Victoria is given. The possibility of returning rescued populations to the lake at a later date, assuming L. niloticus populations have been reduced, is also discussed. It is recommended that captive propagation should be practised to conserve species and to retain the option of returning rescued taxa. Scientists are urged to seek the funding to study tropical ecosystems so that conservation and rational development may acquire a sound foundation.
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    Human evolution 2 (1987), S. 445-457 
    ISSN: 1824-310X
    Keywords: Primates ; Chromosomes ; Fluorochromes ; Evolution ; Phylogeny ; Heterochromatin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Recently, in addition to quinacrine staining, fluorochrome techniques have been developed which brilliantly stain other heterochromatic regions. Two of these staining techniques are Distamycin/DAPI (DA/DAPI) and D287/170. We stained the chromosomes of all species of great apes and 14 species of primates (48 individuals) using these three fluorochrome techniques. Only african apes and man show brilliant quinacrine staining while, man and all the great apes show brilliant DA/DAPI staining and only species belonging to the hominoidea (including the siamang) showed bright D287/170 staining. In the lower primates a medium level of DA/DAPI fluorescence was found in some species with large amount of pericentromeric heterochromatin. Brilliant DA/DAPI staining could represent a derived trait linking all great apes and humans, while D287/170 may link all hominoidea. Fluorochrome staining is believed to be correlated with some satellite DNA sequences. However, data available on the chromosome location of satellite DNAs in non-human primates were derived from buoyant density fractions resulting in cross hybridization and now are not considered reliable. Before making any correlation between fluorochrome staining and satellite DNAs in non human primates there is need of data onin situ hybridization with cloned DNA sequences on primate chromosomes. These data would help clarify the evolution and relationship of satellite DNAs and heterochromatin in primates.
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    Human evolution 2 (1987), S. 121-133 
    ISSN: 1824-310X
    Keywords: Apes ; Date Choice ; Evolution ; Foresight ; Plan ; Sense of Time ; Time Flow ; Time Projection
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract It is shown that in the evolution of man's «sense of time» the conceptDATE played an important role. Inthe first part of the paper, time concepts, such as present, period, duration, change and date, are related to each other in a conceptualstructure, which is represented bothgraphically and by means ofpropositions. That conceptual structure also illustrates the relationship of the concepts of time to theflow of time in theevolution of the cosmos and of life on earth. This flow of time is measured by means of the date concept. In thesecond part, the limited «sense of time» of apes is analyzed. The ability of apes to project their experiences intoforesights of the future is illustrated graphically in a conceptual structure. In thethird part, it is shown that man has the additional ability tochoose from such foresights aplan for the future. Plans are made by assigning a specificdate to future time. The relationship between foresights, plans and dates is also illustrated in a conceptual structure. Finally, thefourth part discusses how man's ability to assign dates to the flow of time evolved simultaneously with his hunting activities and with his faculty to communicate by means of language.
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  • 93
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    Human evolution 2 (1987), S. 517-537 
    ISSN: 1824-310X
    Keywords: Hominoid locomotion ; Evolution ; Locomotor patterns ; Ontogeny ; Monkeys ; Apes ; Miocene hominoids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Evolution of hominoid locomotion is a traditional topic in primate evolution. Views have changed during the last decade because a number of crucial differences between early and advanced hominoid morphologies have been demonstrated. Increasing evidence on primate behaviour and ecology show that any direct analogies between living and fossil hominoids must be made extremely carefully. The necessity of synthesizing data on primate behaviour, locomotion, morphology and ecology and simultaneously defining the framework in which the data should be interpreted are explained. Results of our studies of ontogeny of locomotor and behavioural patterns (LBP) are presented that could help identify the main features of early hominoid locomotor patterns (LP) and the mechanisms of their changes. The early hominoid LP was different from those of pronograde monkeys and specialized antipronograde living apes. Some similar features could be expected between early hominoid LP and the LP of ceboid monkeys. Analogous mechanisms of change of LBP exist in all groups of living higher primates. Crucial early mechanisms of change are the ontogenetic shifts in LBP connected with ethoecological changes. Analysis of fossil evidence has shown that Miocene hominoids differ morphologically from any group of living primates. Certain features present in Miocene hominoids could be found in Atelinae and living Asian apes but they are limited to some functional regions of the postcrania only. Consequently the early hominoid general LP can not be strictly analogous either to that of any monkey group or to the LP of apes. We suppose that certain pronograde adaptations, such as climbing, bipedality, limited suspensory activity and sitting constituted the main part of their LP.
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  • 94
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    Acta biotheoretica 35 (1986), S. 77-106 
    ISSN: 1572-8358
    Keywords: Evolution ; nonequilibrium thermodynamics ; boundary conditions models ; initial conditions models
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Proponents of two axioms of biological evolutionary theory have attempted to find justification by reference to nonequilibrium thermodynamics. One states that biological systems and their evolutionary diversification are physically improbable states and transitions, resulting from a selective process; the other asserts that there is an historically constrained inherent directionality in evolutionary dynamics, independent of natural selection, which exerts a self-organizing influence. The first, the Axiom of Improbability, is shown to be nonhistorical and thus, for a theory of change through time, acausal. Its perception of the improbability of living states is at least partially an artifact of closed system thinking. The second, the Axiom of Historically Determined Inherent Directionality, is supported evidentially and has an explicit historical component. Historically constrained dynamic populations are inherently nonequilibrium systems. It is argued that living, evolving systems, when considered to be historically constrained nonequilibrium systems, do not appear improbable at all. Thus, the two axioms are not compatible. Instead, the Axiom of Improbability is considered to result from an unjustified attempt to extend the contingent proximal actions of natural selection into the area of historical, causal explanations. It is thus denied axiomatic status, and the effects of natural selection are subsumed as an additional level of constraint in an evolutionary theory derived from the Axiom of Historically Determined Inherent Directionality.
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  • 95
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    Current genetics 10 (1986), S. 931-941 
    ISSN: 1432-0983
    Keywords: T. aestivum ; Chloroplast DNA ; Repeat DNA ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Low-stringency hybridisation between recombinant plasmids representing the complete T. aestivum chloroplast genome has revealed small repeated DNA segments dispersed through the molecule. Thirty-two repeated DNA segments were detected, and they could be divided into 12 unrelated sets; no repeat was detected as multiple copies. The longest of the small repeats mapped just within the large inverted repeat in spinach and mung-bean ctDNAs. It was found to have been duplicated after the divergence of a cereal progenitor to generate a third, dispensible copy, 0.2 kbp downstream of rbcL. In maize at least, this copy has also become integrated, with rbcL, in the mitochondrial genome. Another of the repeats is thought to have mediated a chloroplast DNA inversion (Howe 1985). Thus the diverse collection of small repeats probably represents some consequences and causes of past recombination events as well as a mechanism for further intramolecular ctDNA recombination. Their possible significance in the restructuring and evolution of chloroplast genomes is discussed.
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  • 96
    ISSN: 1432-1432
    Keywords: Xenopus tropicalis ; Xenopus borealis ; Globin cDNAs ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Globin mRNAs ofXenopus borealis andXenopus tropicalis have been cloned and sequenced. The nucleotide and derived amino acid sequences were compared with each other and with already available data fromXenopus laevis. This analysis rendered clear evidence that the common ancestor ofX. laevis andX. borealis, but not ofX. tropicalis, had lost one amino acid of the β-globins prior to a genome duplication event that preceded the segregation of the former two species. Replacement-site substitutions were used to calculate a rough time scale of genome duplication and species segregation. The results suggest an ancient separation between theX. laevis and theX. tropicalis groups occurring approximately 110–120 million years ago. Analysis of the amino acid chains demonstrated various alterations. However, some functional domains, like heme-binding sites andα1β2 contact sites, were subject to a high degree of conservation, indicating the existence of functional constraints on them also in the genusXenopus.
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  • 97
    ISSN: 1432-1432
    Keywords: Actin-coding regions ; Sequence divergence ; Conversion ; Codon usage ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have determined the sequences of three recombinant cDNAs complementary to different mouse actin mRNAs that contain more than 90% of the coding sequences and complete or partial 3′ untranslated regions (3′UTRs): pAM 91, complementary to the actin mRNA expressed in adult skeletal muscle (αsk actin); pAF 81, complementary to an actin mRNA that is accumulated in fetal skeletal muscle and is the major transcript in adult cardiac muscle (αc actin); and pAL 41, identified as complementary to a β nonmuscle actin mRNA on the basis of its 3′UTR sequence. As in other species, the protein sequences of these isoforms are highly (〉93%) conserved, but the three mRNAs show significant divergence (13.8–16.5%) at silent nucleotide positions in their coding regions. A nucleotide region located toward the 5′ end shows significantly less divergence (5.6–8.7%) among the three mouse actin mRNAs; a second region, near the 3′ end, also shows less divergence (6.9%), in this case between the mouse β and αsk actin mRNAs. We propose that recombinational events between actin sequences may have homogenized these regions. Such events distort the calculated evolutionary distances between sequences within a species. Codon usage in the three actin mRNAs is clearly different, and indicates that there is no strict relation between the tissue type, and hence the tRNA precursor pool, and codon usage in these and other muscle mRNAs examined. Analysis of codon usage in these coding sequences in different vertebrate species indicates two tendencies: increases in bias toward the use of G and C in the third codon position in paralogous comparisons (in the order αc), and in orthologous comparisons (in the order chicken 〈 rodent 〈 man). Comparison of actin-coding sequences between species was carried out using the Perler method of analysis. As one moves backward in time, changes at silent sites first accumulate rapidly, then begin to saturate after −(30–40) million years (MY), and actually decrease between −400 and −500 MY. Replacements or silent substitutions therefore cannot be used as evolutionary clocks for these sequences over long periods. Other phenomena, such as gene conversion or isochore compartmentalization, probably distort the estimated divergence time.
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  • 98
    ISSN: 1432-1432
    Keywords: Evolution ; 5S Ribosomal RNA sequences ; Arthropoda ; Secondary structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary 5S Ribosomal RNA sequences have proven to be useful tools in the study of evolutionary relationships among species. However, in reviewing previously published trees constructed from alignments of metazoan 5S RNAs, we noticed several discrepancies with classical evolutionary views. One such discrepancy concerned the phylum Arthropoda, where a crustacean,Artemia salina, seemed to be evolutionarily very remote from four insects. The cause of this phenomenon was studied by determining the 5S RNA sequences of additional arthropods, viz.Limulus polyphemus, Eurypelma californica, Lasiodora erythrocythara, Areneus diadematus, Daphnia magna, Ligia oceanica, Homarus gammarus, Cancer pagurus, Spirobolus sp.,Locusta migratoria, andTenebrio molitor. A tree was then constructed from a dissimilarity matrix by a clustering method known as weighted pair grouping. Application of a correction for unequal evolutionary rates improved the apparent evolutionary position of the arthropods and of some other metazoan species. However, neither the uncorrected nor the corrected tree permitted a completely acceptable reconstruction of metazoan evolution. We presume that this phenomenon is due to random deviations in the evolutionary rate of 5S RNA.
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  • 99
    ISSN: 1432-1432
    Keywords: Glycoprotein ; Evolution ; Ribonuclease
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The glycosylation characteristics of the digestive enzyme ribonuclease are summarized. The evolutionary role of this posttranslational modification is discussed and evidence is presented that selection has much influence on the presence or absence of carbohydrate in glycoproteins and on the positions of the carbohydrate attachment sites.
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  • 100
    ISSN: 1432-1432
    Keywords: Ribosomal RNAs ; Cross-hybridization ; Hybridization yield ; Fractional hybridization ; Hybridization homology ; Phylogenetic tree ; Phylogeny ; Evolution ; Archaebacteria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Ribosomal RNAs of 17 species of archaebacteria were hybridized to corresponding and non-corresponding nitrocellulose bound DNAs. The temperature stability of these hybrids and the amount of bound rRNA were determined. A formula was derived to correct the hybridization yields for the different genome lengths and numbers of rRNA operons per genome. This correction made it possible to determine hybridization homologies, as functions of velocity constants, which could then be used in a similar way as sequence homologies. The results were consistent with those from 16S rRNA total sequence data. No correlation was found between the hybridization homologies and the temperature stabilities of the hybrids. This new method is faster and simpler than the method based on total 16S rRNA sequence determination although it provides less total information. Its application to archaebacterial phylogeny has shown theThermococcales to represent a third branch of the kingdom beside the branch of the methanogens + halophiles, and that of theThermoproteales + Sulfolobales. The method has also provided a detailed description of the phylogeny of theSulfolobales showing their origin within theThermoproteales.
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