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Evaluation of whether accelerated protein evolution in chordates has occurred before, after, or simultaneously with gene duplication

Johnston, Catriona R., O'Dushlaine, Colm, Fitzpatrick, David A., Edwards, Richard J. and Shields, Denis C. (2006) Evaluation of whether accelerated protein evolution in chordates has occurred before, after, or simultaneously with gene duplication Molecular Biology and Evolution, 24, (1), pp. 315-323. (doi:10.1093/molbev/msl162).

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Gene duplication and loss are predicted to be at least of the order of the substitution rate and are key contributors to the development of novel gene function and overall genome evolution. Although it has been established that proteins evolve more rapidly after gene duplication, we were interested in testing to what extent this reflects causation or association. Therefore, we investigated the rate of evolution prior to gene duplication in chordates. Two patterns emerged; firstly, branches, which are both preceded by a duplication and followed by a duplication, display an elevated rate of amino acid replacement. This is reflected in the ratio of nonsynonymous to synonymous substitution (mean nonsynonymous to synonymous nucleotide substitution rate ratio [Ka:Ks]) of 0.44 compared with branches preceded by and followed by a speciation (mean Ka:Ks of 0.23). The observed patterns suggest that there can be simultaneous alteration in the selection pressures on both gene duplication and amino acid replacement, which may be consistent with cooccurring increases in positive selection, or alternatively with concurrent relaxation of purifying selection. The pattern is largely, but perhaps not completely, explained by the existence of certain families that have elevated rates of both gene duplication and amino acid replacement. Secondly, we observed accelerated amino acid replacement prior to duplication (mean Ka:Ks for postspeciation preduplication branches was 0.27). In some cases, this could reflect adaptive changes in protein function precipitating a gene duplication event. In conclusion, the circumstances surrounding the birth of new proteins may frequently involve a simultaneous change in selection pressures on both gene-copy number and amino acid replacement. More precise modeling of the relative importance of preduplication, postduplication, and simultaneous amino acid replacement will require larger and denser genomic data sets from multiple species, allowing simultaneous estimation of lineage-specific fluctuations in mutation rates and adaptive constraints.

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Published date: 25 October 2006
Keywords: genome evolution, gene duplication, positive selection


Local EPrints ID: 143465
PURE UUID: be4ee63e-cfea-4294-bcff-a3ab7410158d

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Date deposited: 22 Jun 2010 08:33
Last modified: 18 Jul 2017 23:09

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Author: Catriona R. Johnston
Author: Colm O'Dushlaine
Author: David A. Fitzpatrick
Author: Richard J. Edwards
Author: Denis C. Shields

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