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. 2006 Feb 8:7:20.
doi: 10.1186/1471-2164-7-20.

Many genes in fish have species-specific asymmetric rates of molecular evolution

Dirk Steinke  1 , Walter Salzburger, Ingo Braasch, Axel Meyer
Affiliations

Many genes in fish have species-specific asymmetric rates of molecular evolution

Dirk Steinke et al. BMC Genomics. .

Abstract

Background: Gene 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.

Results: 25% (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.

Conclusion: The 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.

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Figures

Figure 1
Figure 1
Flowchart of the analysis routine used in this study.
Figure 2
Figure 2
Example of a ternary representation of distances of fish species to human orthologs (Danio rerio, Oryzias latipes, Tetraodon nigroviridis). The red circle represents Lysyl-oxidase-like-1 (LOXL-1), a gene with significantly lower distance from Tetraodon nigroviridis to the human ortholog than to other fish species. The blue circle represents the ankyrin repeat domain 10, a gene with significantly higher distance from Danio rerio to the human ortholog than to other fish species.
Figure 3
Figure 3
Phylogeny of the studied fish species. The proportion of genes with significantly lower (red) or higher (blue) distance to the human ortholog than to other fish species, are mapped onto the phylogeny as proportional triangles. Numbers within the triangle represent the total abundance of those genes. The percentages represent the corresponding proportion of transcription factors.
Figure 4
Figure 4
Abundances of gene functions (according to GO) of all fish protein genes with significantly lower or higher distance to the human ortholog than to other fish species (blue) compared to total abundances of gene functions (violet). The percentages represent the rates of the chosen genes compared to the total number of proteins of a given gene function. Significant differences between total and divergent gene abundances according to a χ2-Test are given at the 5% level with one asterisk and at the 1% level with two asterisks.
Figure 5
Figure 5
Abundances of gene functions (according to GO) of all fish protein genes under positive Darwinian selection with significantly lower or higher distance to the human ortholog than to other fish species.
Figure 6
Figure 6
Comparison of rates of gene functions (according to GO) of all fish protein genes with significantly lower distance to the human ortholog than other fish species.
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