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This result also raises the question of why blue eyes would be under selection.
If that is the case then only males would be under selection for improving their insemination rates.
The basic premise in such cases is that functionally relevant nucleotides like TFBS would be under selection, and would hence be distinguishable from surrounding sequence on the basis of evolutionary parameters.
It may also explain a negative correlation of the GC-content with expression level (Table 2): first, selection on thermodynamic stability may vary with expression, and secondly, higher expressed genes will be shorter, and if the absolute stability would be under selection, their GC-content may be higher.
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While population genetics theory predicts that genes with dN/dS > 1 would be under positive selection, in reality positive selection is likely to be acting only on a limited number of sites in a gene.
Male plants, in contrast, could deploy greater growth and faster leaf turnover rates, sould have greater capacity to compensate for tissue loss to herbivory, and would be under lesser selection for allocation to defenses.
At this evolutionary stage interpretive molecular behaviour would be advantageous and would be under positive selection.
Such genes may provide a target for genome alterations, such as gene decay, that would be under no selection.
As the evolutionary reconstruction reveals episodes of repeat array rearrangement and diversification, we wondered whether repeats in closely related species would be under positive selection (higher nonsynonymous vs. synonymous substitution rate).
The high degree of sequence conservation that we observed in short introns between spruce and pine may also depend on the recombination rate within genes, where small introns would be under stronger selection because of efficiency in transcription and splicing, and long introns in regions of low recombination diverge because of reduced selection pressure.
The figures obtained for C. intestinalis indicate that a large fraction (between 50% and 78%) of amino acid changes would be under positive selection, a figure that is even larger than that observed in other species like Drosophila (Smith and Eyre-Walker 2002).
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