Journal ArticleDOI
Patterns of Nucleotide Substitution in Pseudogenes and Functional Genes
TLDR
The pattern obtained suggests that transition mutations occur somewhat more frequently than transversion mutations and that mutations result more often in A or T than in G or C.Abstract:
The pattern of point mutations is inferred from nucleotide substitutions in pseudogenes. The pattern obtained suggests that transition mutations occur somewhat more frequently than transversion mutations and that mutations result more often in A or T than in G or C. Our results are discussed with respect to the predictions from Topal and Fresco's model for the molecular basis of point (substitution) mutations (Nature 263:285–289, 1976). The pattern of nucleotide substitution at the first and second positions of codons in functional genes is quite similar to that in pseudogenes, but the relative frequency of the transition C→T in the sense strand is drastically reduced and those of the transversions C→G and G→C are doubled. The differences between the two patterns can be explained by the observation that in the protein evolution amino acid substitutions occur mainly between amino acids with similar biochemical properties (Grantham, Science 185:862–864, 1974). Our results for the patterns of nucleotide substitutions in pseudogenes and in functional genes lead to the prediction that both the coding and non-coding regions of protein coding genes should have high frequencies of A and T. Available data show that the non-coding regions are indeed high in A and T but the coding regions are low in T, though high in A.read more
Citations
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Journal ArticleDOI
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0
TL;DR: Version 4 of MEGA software expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses.
Journal ArticleDOI
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
Koichiro Tamura,Masatoshi Nei +1 more
TL;DR: In this paper, a new mathematical method for estimating the number of transitional and transversional substitutions per site, as well as the total number of nucleotide substitutions was proposed, taking into account excess transitions, unequal nucleotide frequencies, and variation of substitution rate among different sites.
Journal ArticleDOI
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
Masatoshi Nei,Takashi Gojobori +1 more
TL;DR: It is shown that all available methods tend to give an underestimate of the number of nonsynonymous substitutions when the number is large and computer simulation indicates that estimates of synonymous substitutions obtained by the two methods are quite accurate unless the numberof nucleotide substitutions per site is very large.
Journal ArticleDOI
Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae).
Paul Sunnucks,Dinah F. Hales +1 more
TL;DR: It is concluded that a proportion of the inferred change in the nonmitochondrial sequences occurred before transposition, and that Sitobion aphids (and other species exhibiting mtDNA transposition) may be important for studying the molecular evolution of mtDNA and pseudogenes.
Journal ArticleDOI
Estimating the pattern of nucleotide substitution.
TL;DR: It is concluded that the use of the REV model in phylogenetic analysis can be recommended, especially for large data sets or for sequences with extreme substitution patterns, while HKY85 may be expected to provide a good approximation.
References
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Journal ArticleDOI
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
TL;DR: Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
Journal ArticleDOI
Amino Acid Difference Formula to Help Explain Protein Evolution
TL;DR: A formula for diference between amino acids combines properties that correlate best with protein residue substitution frequencies: composition, polarity, and molecular volume.
Journal ArticleDOI
DNA methylation and gene function
Aharon Razin,Arthur D. Riggs +1 more
TL;DR: There is now reason to believe, from recent studies, that DNA methylation is a key element in the hierarchy of control mechanisms that govern vertebrate gene function and differentiation.
Journal ArticleDOI
Nucleotide sequence of cloned cDNA for bovine corticotropin-beta-lipotropin precursor.
Shigetada Nakanishi,Akira Inoue,Toru Kita,Masahiro Nakamura,Annie C. Y. Chang,Stanley N. Cohen,Shosaku Numa +6 more
TL;DR: The nucleotide sequence of a 1,091-base pair cloned cDNA insert encoding bovine corticotropin-β-lipotropin precursor mRNA indicates that the precursor protein consists of repetitive units and includes a third melanotropin sequence in its cryptic portion.
Book
Genetical implications of the structure of deoxyribonucleic acid
James D. Watson,Francis Crick +1 more
TL;DR: J. D. Watson, F. H. C. Crick: Genetical Implications of the Structure of Deoxyribonucleic Acid, 2nd Ed.
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