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Phylogenetic footprinting is a powerful technique for the identification of regions that, being functionally relevant, have been maintained under selective constraint during evolution [ 53].
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As revealed by the lower number of SNPs and indels in human, adaptive selection in the chimp/human ancestral branch (with a much larger Ne) might increase the fitness of PIPSL to an extent such that it could be maintained in the current population under selective constraint.
We removed first introns and short (less than 250 bps) introns from further analyses, since these may be under selective constraint to preserve regulatory signals.
Andolfatto (2005) has concluded that non-coding regions of Drosophila are under selective constraint and also subject to bouts of adaptive selection.
If the dN/dS rate ratio is <1, there is evidence for purifying (negative) selection, and the duplicated genes are thought to be under selective constraint.
Thus the promoter region of sphinx seems to be under selective constraint.
The presence of conserved non-coding nucleotide stretches implies that a region is under selective constraint and therefore is likely to perform an important function.
The underlying assumption is that an accurate prediction algorithm should identify functionally important sites that are likely to be under selective constraint.
Regions of high conservation harbor biological function and therefore are likely to be under selective constraint.
A substantial fraction of non-coding DNA sequences of multicellular eukaryotes is under selective constraint.
Loci under selective constraint are expected to show reduced nucleotide diversity and divergence.
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