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Volumn 287, Issue 5456, 2000, Pages 1283-1286

Evidence for a high frequency of simultaneous double-nucleotide substitutions

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CODON; GENE LOCUS; GENE MUTATION; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POINT MUTATION; PRIORITY JOURNAL;

EID: 0034681511     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.287.5456.1283     Document Type: Article
Times cited : (96)

References (42)
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    • note
    • We collected data sets of homologous proteins showing wide phylogenetic conservation (representing diverse eukaryotic and eubacterial lineages) and unambiguous relationships (excluding multigene families, cases of horizontal transfer, concerted evolution). For each data set, conserved protein sequences were obtained from the SWISS-PROT database (release 8/98) using BLAST (22). Protein sequences were aligned using CLUSTALW (23) and were searched for unambiguously aligned sites where serine is absolutely conserved (i.e., present in all available sequences). The corresponding codons were determined from the respective nucleotide sequences, obtained from the GenBank/EMBL (European Molecular Biology Laboratory) database. Changes in serine codon type were determined in the most parsimonious way on the basis of phytogenies (illustrated Fig. 1B), and rates of change were estimated as the number of inferred changes over the time sampled at each site (the sum of all branch lengths). Phylogenetic relationships and times of divergence svere based on published data for the respective species (20, 24) (Fig. 1A). Trees were also constructed from the protein sequences themselves [using the Neighbor-Joining method (25)], and sequences showing an inconsistent phylogenetic placement were eliminated. Because of difficulties in determining their times of divergence, eubacterial and eukaryotic sequences were treated separately and archaebacterial sequences were excluded. In estimating the rates of codon switches, we tried to be conservative, for example, by overestimating times of divergence in cases of uncertainty. The analysis was also carried out on the basis of alternative published phylogenies and the results were always robust (M. Averof et al., data not shown).
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    • 2L, where L is the total number of aligned nucleotides (sample size), ObsS and ObsD are the numbers of changes observed as single- and double-nucleotide substitutions, respectively, RealS and RealD are the numbers of changes that have occurred as single- and simultaneous double-nucleotide substitutions, respectively, and ExpD is the number of doublet substitutions (observed at adjacent nucleotides) that have occurred by coincidence of two separate single-nucleotide changes. The difference of ObsD and ExpD was evaluated by a chi-squared test. In mammalian genomes, CG dinucleotides are methylated, which renders them susceptible to mutation (by deamination), yielding TC and CA dinucleotides at relatively high frequencies [A. P. Bird, Nucleic Acids Res. 8, 1499 (1980)]. To prevent sequential CN→CG→TG and NG→CG→CA changes (or parallel CC→TG and CG→CA mutations in independent lineages) from being counted as doublet mutations, CN→TG and NG→CA substitutions were excluded from the analysis. We also examined the rates of substitution of each of the four nucleotides separately; the biases in these rates are not sufficient to affect our results.
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    • This work was initiated in the Genetics Department of Trinity College, University of Dublin, and was continued with the support of C. Delidakis at the IMBB, Crete. It was supported in part by the EPET II programme of the General Secretariat for Research and Technology, Greece, and a UK Biotechnology and Biological Sciences Research Council grant G04905
    • This work was initiated in the Genetics Department of Trinity College, University of Dublin, and was continued with the support of C. Delidakis at the IMBB, Crete. It was supported in part by the EPET II programme of the General Secretariat for Research and Technology, Greece, and a UK Biotechnology and Biological Sciences Research Council grant G04905.


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