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  • 1
    Electronic Resource
    Electronic Resource
    Ubiquitin genes as a paradigm of concerted evolution of tandem repeats (1987)
    Springer
    Journal of molecular evolution 25 (1987), S. 58-64 
    Details
    ISSN: 1432-1432
    Keywords: Molecular evolution ; Protein sequence conservation ; Synonymous substitution ; Unequal crossover ; Gene conversion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Ubiquitin is remarkable for its ubiquitous distribution and its extreme protein sequence conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences of several ubiquitin repeats from each of humans, chicken,Xenopus, Drosophila, barley, and yeast have recently been determined. By analysis of these data we show that ubiquitin is evolving more slowly than any other known protein, and that this (together with its gene organization) contributes to an ideal situation for the occurrence of concerted evolution of tandem repeats. By contrast, there is little evidence of between-cluster concerted evolution. We deduce that in ubiquitin genes, concerted evolution involves both unequal crossover and gene conversion, and that the average time since two repeated units within the polyubiquitin locus most recently shared a common ancestor is approximately 38 million years (Myr) in mammals, but perhaps only 11 Myr inDrosophila. The extreme conservatism of ubiquitin evolution also allows the inference that certain synonymous serine codons differing at the first two positions were probably mutated at single steps.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100041
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  • 2
    Electronic Resource
    Electronic Resource
    Determinants of DNA sequence divergence betweenEscherichia coli andSalmonella typhimurium: Codon usage, map position, and concerted evolution (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 23-33 
    Details
    ISSN: 1432-1432
    Keywords: Molecular clocks ; Enterobacteria ; Elongation factor Tu ; Genome evolution ; Synonymous codon usage
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The nature and extent of DNA sequence divergence between homologous proteincoding genes fromEscherichia coli andSalmonella typhimurium have been examined. The degree of divergence varies greatly among genes at both synonymous (silent) and nonsynonymous sites. Much of the variation in silent substitution rates can be explained by natural selection on synonymous codon usage, varying in intensity with gene expression level. Silent substitution rates also vary significantly with chromosomal location, with genes nearoriC having lower divergence. Certain genes have been examined in more detail. In particular, the duplicate genes encoding elongation factor Tu,tufA andtufB, fromS. typhimurium have been compared to theirE. coli homologues. As expected these very highly expressed genes have high codon usage bias and have diverged very little between the two species. Interestingly, these genes, which are widely spaced on the bacterial chromosome, also appear to be undergoing concerted evolution, i.e., there has been exchange between the loci subsequent to the divergence of the two species.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100192
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  • 3
    Electronic Resource
    Electronic Resource
    Mitochondrial DNA sequence divergence in theMelanogaster and oriental species subgroups ofDrosophila (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 156-162 
    Details
    ISSN: 1432-1432
    Keywords: Drosophila ; Mitochondrial DNA ; Nucleotide sequence ; Nonsynonymous substitutions ; Phylogeny ; A+T content
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The nucleotide sequence of a segment of the mitochondrial DNA from threeDrosophila species (D. erecta, D. eugracilis, andD. takahashii), belonging to different subgroups of themelanogaster group has been determined. The segment encompasses three complete tRNA genes (tRNAtrp, tRNAcys, and tRNAtyr) and portions of two protein-coding genes: the subunit 2 of the NADH dehydrogenase (ND2) and the subunit 1 of the cytochrome oxidase (COI). Comparisons also involve homologous sequences already known for four otherDrosophila species of themelanogaster group. Length differences were confined in the intergenic region where a long stretch of AT repeats was observed in one of the species analyzed. The three tRNA genes exhibit very different evolutionary rates, the most slowly evolving one, tRNAtyr, is adjacent to the 5′ end of COI; tRNAs in similar positions have been previously shown to evolve slowly because they are probably involved in transcript processing. Although the rate of synonymous substitutions was very similar between ND2 and COI genes there were strong discrepancies between them in terms of the number of nonsynonymous substitutions. Differences have also been found in G+C content of the genes, which are likely to be linked to different selective pressures. There is a reduction in G+C content in the region where selective constraints are reduced. This suggests the existence of different levels of constraints along the sequenced segment. An overall analysis of the types of substitutions showed a decrease in A+T content during the course of evolution of the species.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02193630
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  • 4
    Electronic Resource
    Electronic Resource
    Recombination in AIDS viruses (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 249-259 
    Details
    ISSN: 1432-1432
    Keywords: AIDS ; Human immunodeficiency virus ; Simian immunodeficiency virus ; Phylogenetics ; Recombination ; Superinfection
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Recombination contributes to the generation of genetic diversity in human immunodeficiency viruses (HIV) but can only occur between viruses replicating within the same cell. Since individuals have not been found to be simultaneously coinfected with multiple divergent strains of HIV-1 or HIV-2, recombination events have been thought to be restricted to the rather closely related members of the quasispecies that evolves during the course of HIV infection. Here we describe examples of both HIV-1 and HIV-2 genomes that appear to be hybrids of genetically quite divergent viruses. Phylogenetic analyses were used to examine the evolutionary relationships among multiple HIV strains. Evolutionary trees derived from different genomic regions were consistent with respect to most of the viruses investigated. However, some strains of HIV-1 and HIV-2 exhibited significantly discordant branching orders indicative of genetic exchanges during their evolutionary histories. The crossover points of these putative recombination events were mapped by examining the distribution of phylogenetically informative sites supporting alternative tree topologies. A similar example of a recombinant simian immunodeficiency virus identified in West African green monkeys has also been described recently. These results indicate that coinfection with highly divergent viral strains can occur in HIV-infected humans and SIV-infected primates and could lead to the generation of hybrid genomes with significantly altered biological properties. Thus, future characterization of primate lentiviruses should include careful phylogenetic investigation of possible genomic mosaicism.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00163230
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  • 5
    Electronic Resource
    Electronic Resource
    Selection pressures on codon usage in the complete genome of bacteriophage T7 (1985)
    Springer
    Journal of molecular evolution 21 (1985), S. 150-160 
    Details
    ISSN: 1432-1432
    Keywords: Bacteriophage T7 ; DNA sequence analysis ; Codon usage ; Molecular evolution ; Synonymous codons ; RNY codons ; Restriction sites ; tRNA ; Pretermination codons
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We searched the complete 39,936 base DNA sequence of bacteriophage T7 for nonrandomness that might be attributed to natural selection. Codon usage in the 50 genes of T7 is nonrandom, both over the whole code and among groups of synonymous codons. There is a great excess of purineany base-pyrimidine (RNY) codons. Codon usage varies between genes, but from the pooled data for the whole genome (12,145 codons) certain putative selective constraints can be identified. Codon usage appears to be influenced by host tRNA abundance (particularly in highly expressed genes), tRNA-mRNA interactions (one such interaction being perhaps responsible for maintaining the excess of RNY codons) and a lack of short palindromes. This last constraint is probably due to selection against host restriction enzyme recognition sites; this is the first report of an effect of this kind on codon usage. Selection against susceptibility to mutational damage does not appear to have been involved.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100089
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  • 6
    Electronic Resource
    Electronic Resource
    Rates of synonymous substitution in plant nuclear genes (1989)
    Springer
    Journal of molecular evolution 29 (1989), S. 208-211 
    Details
    ISSN: 1432-1432
    Keywords: Plant molecular evolution ; Molecular clock ; Chloroplast DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The rate of synonymous nucleotide substitution in nuclear genes of higher plants has been estimated. The rate varies among genes by a factor of up to two, in a manner that is not immediately explicable in terms of base composition or codon usage bias. The average rate, in both monocots and dicots, is about four times higher than that in chloroplast genes. This leads to an estimated absolute silent substitution rate of 6 × 10−9 substitutions per site per year that falls within the range of average rates (2−8 × 10−9) seen in different mammalian nuclear genomes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100204
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  • 7
    Electronic Resource
    Electronic Resource
    Mammalian gene evolution: Nucleotide sequence divergence between mouse and rat (1993)
    Springer
    Journal of molecular evolution 37 (1993), S. 441-456 
    Details
    ISSN: 1432-1432
    Keywords: Molecular clocks ; Rodents ; Genome evolution ; G + C content ; Codon usage ; Dinucleotide mutation effects
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract As a paradigm of mammalian gene evolution, the nature and extent of DNA sequence divergence between homologous protein-coding genes from mouse and rat have been investigated. The data set examined includes 363 genes totalling 411 kilobases, making this by far the largest comparison conducted between a single pair of species. Mouse and rat genes are on average 93.4% identical in nucleotide sequence and 93.9% identical in amino acid sequence. Individual genes vary substantially in the extent of nonsynonymous nucleotide substitution, as expected from protein evolution studies; here the variation is characterized. The extent of synonymous (or silent) substitution also varies considerably among genes, though the coefficient of variation is about four times smaller than for nonsynonymous substitutions. A small number of genes mapped to the X-chromosome have a slower rate of molecular evolution than average, as predicted if molecular evolution is “male-driven.” Base composition at silent sites varies from 33% to 95% G + C in different genes; mouse and rat homologues differ on average by only 1.7% in silent-site G + C, but it is shown that this is not necessarily due to any selective constraint on their base composition. Synonymous substitution rates and silent site base composition appear to be related (genes at intermediate G + C have on average higher rates), but the relationship is not as strong as in our earlier analyses. Rates of synonymous and nonsynonymous substitution are correlated, apparently because of an excess of substitutions involving adjacent pairs of nucleotides. Several factors suggest that synonymous codon usage in rodent genes is not subject to selection.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00178874
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  • 8
    Electronic Resource
    Electronic Resource
    Codon usage and base composition inRickettsia prowazekii (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 525-536 
    Details
    ISSN: 1432-1432
    Keywords: Codon usage ; Mutation bias ; Rickettsia prowazekii
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Codon usage and base composition in sequences from the A + T-rich genome ofRickettsia prowazekii, a member of the alpha Proteobacteria, have been investigated. Synonymous codon usage patterns are roughly similar among genes, even though the data set includes genes expected to be expressed at very different levels, indicating that translational selection has been ineffective in this species. However, multivariate statistical analysis differentiates genes according to their G + C contents at the first two codon positions. To study this variation, we have compared the amino acid composition patterns of 21R. prowazekii proteins with that of a homologous set of proteins fromEscherichia coli. The analysis shows that individual genes have been affected by biased mutation rates to very different extents: genes encoding proteins highly conserved among other species being the least affected. Overall, protein coding and intergenic spacer regions have G + C content values of 32.5% and 21.4%, respectively. Extrapolation from these values suggests thatR. prowazekii has around 800 genes and that 60–70% of the genome may be coding.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02352282
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  • 9
    Electronic Resource
    Electronic Resource
    An evolutionary perspective on synonymous codon usage in unicellular organisms (1986)
    Springer
    Journal of molecular evolution 24 (1986), S. 28-38 
    Details
    ISSN: 1432-1432
    Keywords: Codon usage ; Synonymous substitution rate ; Codon Adaptation Index ; Enterobacterial genes ; G+C content ; Theoretical models
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Observed patterns of synonymous codon usage are explained in terms of the joint effects of mutation, selection, and random drift. Examination of the codon usage in 165Escherichia coli genes reveals a consistent trend of increasing bias with increasing gene expression level. Selection on codon usage appears to be unidirectional, so that the pattern seen in lowly expressed genes is best explained in terms of an absence of strong selection. A measure of directional synonymous-codon usage bias, the Codon Adaptation Index, has been developed. In enterobacteria, rates of synonymous substitution are seen to vary greatly among genes, and genes with a high codon bias evolve more slowly. A theoretical study shows that the patterns of extreme codon bias observed for someE. coli (and yeast) genes can be generated by rather small selective differences. The relative plausibilities of various theoretical models for explaining nonrandom codon usage are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02099948
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  • 10
    Electronic Resource
    Electronic Resource
    Evolution of the recA gene and the molecular phylogeny of bacteria (1993)
    Springer
    Journal of molecular evolution 37 (1993), S. 399-407 
    Details
    ISSN: 1432-1432
    Keywords: Enterobacteria ; Proteobacteria ; Molecular phylogenetics ; recA gene ; RecA protein ; G + C content ; Codon usage
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The DNA sequences of the recA gene from 25 strains of bacteria are known. The evolution of these recA gene sequences, and of the derived RecA protein sequences, is examined, with special reference to the effect of variations in genomic G + C content. From the aligned RecA protein sequences, phylogenetic trees have been drawn using both distance matrix and maximum parsimony methods. There is a broad concordance between these trees and those derived from other data (largely 16S ribosomal RNA sequences). There is a fair degree of certainty in the relationships among the “Purple” or Proteobacteria, but the branching pattern between higher taxa within the eubacteria cannot be reliably resolved with these data.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00178869
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