Pattern of synonymous and nonsynonymous substitutions: An indicator of mechanisms of molecular evolution

1996 ◽  
Vol 75 (1) ◽  
pp. 91-115 ◽  
Author(s):  
Yasuo Ina
Keyword(s):  
Molecular Evolution ◽  
Nonsynonymous Substitutions ◽  
Synonymous And Nonsynonymous Substitutions

scholarly journals Nonneutral Evolution and Differential Mutation Rate of Gender-Associated Mitochondrial DNA Lineages in the Marine Mussel Mytilus

Genetics ◽  
1998 ◽  
Vol 149 (3) ◽  
pp. 1511-1526 ◽  
Author(s):  
Humberto Quesada ◽  
Mary Warren ◽  
David O F Skibinski
Keyword(s):  
Mitochondrial Dna ◽  
Molecular Evolution ◽  
Mutation Rate ◽  
Rare Variants ◽  
Purifying Selection ◽  
Nonsynonymous Substitutions ◽  
Replacement Substitution ◽  
Synonymous And Nonsynonymous Substitutions ◽  
M Genome ◽  
European Populations

Abstract Mussels have two types of mitochondrial DNA (mtDNA). The M type is transmitted paternally, and the F type is transmitted maternally. To test hypotheses of the molecular evolution of both mtDNA genomes, 50 nucleotide sequences were obtained for 396 bp of the COIII gene of European populations of Mytilus edulis and the Atlantic and Mediterranean forms of M. galloprovincialis. Analysis based on the proportion of synonymous and nonsynonymous substitutions indicate that mtDNA is evolving in a non-neutral and complex fashion. Previous studies on American mussels demonstrated that the F genome experiences a higher purifying selection and that the M genome evolves faster. Here we show that these patterns also hold in European populations. However, in contrast to American populations, where an excess of replacement substitution between F and M lineages has been reported, a significant excess of replacement polymorphism within mtDNA lineages is observed in European populations of M. galloprovincialis.European populations also show an excess of replacement polymorphism within the F but not within the M genome with respect to American M. trossulus, as well as a consistent pattern of excess of rare variants in both F and M genomes. These results are consistent with a nearly neutral model of molecular evolution and a recent relaxation of selective constraints on European mtDNA. Levels of diversity are significantly higher for the M than F genome, and the M genome also accumulates synonymous and nonsynonymous substitutions at a higher rate, in contrast with earlier reports where no difference for the synonymous rate was observed. It is suggested that a subtle balance between relaxed selection and a higher mutation rate explains the faster evolutionary rate of the M lineage.

scholarly journals Evaluation of Accumulation of Hepatitis C Virus Mutations in a Chronically Infected Chimpanzee: Comparison of the Core, E1, HVR1, and NS5b Regions

2001 ◽  
Vol 75 (6) ◽  
pp. 3004-3009 ◽  
Author(s):  
Ling Lu ◽  
Tatsunori Nakano ◽  
Etsuro Orito ◽  
Masashi Mizokami ◽  
Betty H. Robertson
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Virus Genome ◽  
Nucleotide Substitutions ◽  
Nonsynonymous Substitutions ◽  
The Core ◽  
Random Substitutions ◽  
Infected Chimpanzee ◽  
Synonymous And Nonsynonymous Substitutions ◽  
Over Time

ABSTRACT Four hepatitis C virus genome regions (the core, E1, HVR1, and NS5b) were amplified and sequenced from yearly samples obtained from a chronically infected chimpanzee over a 12-year span. Nucleotide substitutions were found to accumulate in the core, E1, and HVR1 regions during the course of chronic infection; substitutions within the NS5b region were not detected for the first 8 years and were found to be minimal during the last 4 years. The rate of accumulation of mutations in the core and E1 regions, based on a direct comparison between the first 1979 sequence and the last 1990 sequence, was 1.120 × 10−3, while phylogenetic ancestral comparison using the 12 yearly sequences showed a rate of 0.816 × 10−3bases per site per year. Temporal evaluation of the sequences revealed that there appeared to be periods in which substitutions accumulated and became fixed, followed by periods with relative stasis or random substitutions that did not persist. Synonymous and nonsynonymous substitutions within the core, E1, and HVR1 regions were also analyzed. In the core and E1 regions, synonymous substitutions predominated and gradually increased over time. However, within the HVR1 region, nonsynonymous substitutions predominated but gradually decreased over time.

scholarly journals Reevaluation of Amino Acid Variability of the Human Immunodeficiency Virus Type 1 gp120 Envelope Glycoprotein and Prediction of New Discontinuous Epitopes

2000 ◽  
Vol 74 (9) ◽  
pp. 4335-4350 ◽  
Author(s):  
Yumi Yamaguchi-Kabata ◽  
Takashi Gojobori
Keyword(s):  
Human Immunodeficiency Virus ◽  
Amino Acid ◽  
Envelope Glycoprotein ◽  
Nonsynonymous Substitutions ◽  
Gp120 Envelope ◽  
Immunodeficiency Virus ◽  
Α Helix ◽  
Synonymous And Nonsynonymous Substitutions ◽  
Discontinuous Epitopes

ABSTRACT To elucidate the evolutionary mechanisms of the human immunodeficiency virus type 1 gp120 envelope glycoprotein at the single-site level, the degree of amino acid variation and the numbers of synonymous and nonsynonymous substitutions were examined in 186 nucleotide sequences for gp120 (subtype B). Analyses of amino acid variabilities showed that the level of variability was very different from site to site in both conserved (C1 to C5) and variable (V1 to V5) regions previously assigned. To examine the relative importance of positive and negative selection for each amino acid position, the numbers of synonymous and nonsynonymous substitutions that occurred at each codon position were estimated by taking phylogenetic relationships into account. Among the 414 codon positions examined, we identified 33 positions where nonsynonymous substitutions were significantly predominant. These positions where positive selection may be operating, which we call putative positive selection (PS) sites, were found not only in the variable loops but also in the conserved regions (C1 to C4). In particular, we found seven PS sites at the surface positions of the α-helix (positions 335 to 347 in the C3 region) in the opposite face for CD4 binding. Furthermore, two PS sites in the C2 region and four PS sites in the C4 region were detected in the same face of the protein. The PS sites found in the C2, C3, and C4 regions were separated in the amino acid sequence but close together in the three-dimensional structure. This observation suggests the existence of discontinuous epitopes in the protein's surface including this α-helix, although the antigenicity of this area has not been reported yet.

scholarly journals Molecular Evolution of the dotA Gene in Legionella pneumophila

2003 ◽  
Vol 185 (21) ◽  
pp. 6269-6277 ◽  
Author(s):  
Kwan Soo Ko ◽  
Seong Karp Hong ◽  
Hae Kyung Lee ◽  
Mi-Yeoun Park ◽  
Yoon-Hoh Kook
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Legionella Pneumophila ◽  
Decomposition Analysis ◽  
Amino Acid Sequences ◽  
Intragenic Recombination ◽  
Heterogeneous Structure ◽  
Gene Encoding ◽  
Synonymous And Nonsynonymous Substitutions ◽  
Different Sources

ABSTRACT The molecular evolution of dotA, which is related to the virulence of Legionella pneumophila, was investigated by comparing the sequences of 15 reference strains (serogroups 1 to 15). It was found that dotA has a complex mosaic structure. The whole dotA gene of Legionella pneumophila subsp. pneumophila serogroups 2, 6, and 12 has been transferred from Legionella pneumophila subsp. fraseri. A discrepancy was found between the trees inferred from the nucleotide and deduced amino acid sequences of dotA, which suggests that multiple hits, resulting in synonymous substitutions, have occurred. Gene phylogenies inferred from three different segments (the 5′-end region, the central, large periplasmic domain, and the 3′-end region) showed impressively dissimilar topologies. This was concordant with the sequence polymorphisms, indicating that each region has experienced an independent evolutionary history, and was evident even within the same domain of each strain. For example, the PP2 domain was found to have a heterogeneous structure, which led us hypothesize that the dotA gene of L. pneumophila may have originated from two or more different sources. Comparisons of synonymous and nonsynonymous substitutions demonstrated that the PP2 domain has been under strong selective pressure with respect to amino acid change. Split decomposition analysis also supported the intragenic recombination of dotA. Multiple recombinational exchange within the dotA gene, encoding an integral cytoplasmic membrane protein that is secreted, probably provided increased fitness in certain environmental niches, such as within a particular biofilm community or species of amoebae.

scholarly journals Molecular Evolution of the Avian CHD1 Genes on the Z and W Sex Chromosomes

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 1903-1912 ◽  
Author(s):  
Anna-Karin Fridolfsson ◽  
Hans Ellegren
Keyword(s):  
Molecular Evolution ◽  
Sex Chromosomes ◽  
Sequence Data ◽  
Neutral Evolution ◽  
Z Chromosome ◽  
W Chromosome ◽  
Effective Population ◽  
Synonymous Substitutions ◽  
Nonsynonymous Substitutions ◽  
Female Specific

Abstract Genes shared between the nonrecombining parts of the two types of sex chromosomes offer a potential means to study the molecular evolution of the same gene exposed to different genomic environments. We have analyzed the molecular evolution of the coding sequence of the first pair of genes found to be shared by the avian Z (present in both sexes) and W (female-specific) sex chromosomes, CHD1Z and CHD1W. We show here that these two genes evolve independently but are highly conserved at nucleotide as well as amino acid levels, thus not indicating a female-specific role of the CHD1W gene. From comparisons of sequence data from three avian lineages, the frequency of nonsynonymous substitutions (Ka) was found to be higher for CHD1W (1.55 per 100 sites) than for CHD1Z (0.81), while the opposite was found for synonymous substitutions (Ks, 13.5 vs. 22.7). We argue that the lower effective population size and the absence of recombination on the W chromosome will generally imply that nonsynonymous substitutions accumulate faster on this chromosome than on the Z chromosome. The same should be true for the Y chromosome relative to the X chromosome in XY systems. Our data are compatible with a male-biased mutation rate, manifested by the faster rate of neutral evolution (synonymous substitutions) on the Z chromosome than on the female-specific W chromosome.

Synonymous and Nonsynonymous Substitutions in Genes from Gramineae: Intragenic Correlations

1999 ◽  
Vol 49 (3) ◽  
pp. 330-342 ◽  
Author(s):  
Fernando Alvarez-Valin ◽  
Kamel Jabbari ◽  
Nicolas Carels ◽  
Giorgio Bernardi
Keyword(s):  
Nonsynonymous Substitutions ◽  
Synonymous And Nonsynonymous Substitutions
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