Abstract
BackgroundGene and genome duplication events increase the amount of genetic material that might then contribute to an increase in the genomic and phenotypic complexity of organisms during evolution. Thus, it has been argued that there is a relationship between gene copy number and morphological complexity and/or species diversity. This hypothesis implies that duplicated genes have subdivided or evolved novel functions compared to their pre-duplication proto-orthologs. Such a functional divergence might be caused by an increase in evolutionary rates in one ortholog, by changes in expression, regulatory evolution, insertion of repetitive elements, or due to positive Darwinian selection in one copy. We studied a set of 2466 genes that were present in Danio rerio, Takifugu rubripes, Tetraodon nigroviridis and Oryzias latipes to test (i) for forces of positive Darwinian selection; (ii) how frequently duplicated genes are retained, and (iii) whether novel gene functions might have evolved.Results25% (610) of all investigated genes show significantly smaller or higher genetic distances in the genomes of particular fish species compared to their human ortholog than their orthologs in other fish according to relative rate tests. We identified 49 new paralogous pairs of duplicated genes in fish, in which one of the paralogs is under positive Darwinian selection and shows a significantly higher rate of molecular evolution in one of the four fish species, whereas the other copy apparently did not undergo adaptive changes since it retained the original rate of evolution. Among the genes under positive Darwinian selection, we found a surprisingly high number of ATP binding proteins and transcription factors.ConclusionThe significant rate difference suggests that the function of these rate-changed genes might be essential for the respective fish species. We demonstrate that the measurement of positive selection is a powerful tool to identify divergence rates of duplicated genes and that this method has the capacity to identify potentially interesting candidates for adaptive gene evolution.
Highlights
Gene and genome duplication events increase the amount of genetic material that might contribute to an increase in the genomic and phenotypic complexity of organisms during evolution
BLAST similarity searches of data sets of protein sequences of Tetraodon nigroviridis revealed a total of 12422 significant hits (e-value: 10-50) when compared to the human genome. 12176 hits were found when comparing Takifugu rubripes to the human genome, 9619 hits were found for Danio rerio and 4681 hits were obtained for Oryzias latipes
The majority of genes detected in Oryzias latipes and Danio rerio show smaller distances, whereas a higher amount of genes in both pufferfish species seem to have evolved faster (59%)
Summary
Gene and genome duplication events increase the amount of genetic material that might contribute to an increase in the genomic and phenotypic complexity of organisms during evolution. It has been argued that there is a relationship between gene copy number and morphological complexity and/or species diversity. This hypothesis implies that duplicated genes have subdivided or evolved novel functions compared to their pre-duplication proto-orthologs. Such a functional divergence might be caused by an increase in evolutionary rates in one ortholog, by changes in expression, regulatory evolution, insertion of repetitive elements, or due to positive Darwinian selection in one copy. Such a degree of evolutionary conservation has, for example, been a powerful guide in sorting functional from non-functional DNA [8,9,10,11] and to assign putative gene function
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