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In the original version, we chose conserved receptor-binding residues as a control group for the antigenic sites because we wanted residues that we expected to be under strong constraint.
But as we have shown, sites that contribute to CTL escape may be under strong constraint, and so may only be able to change under certain circumstance (in this case when they co-occur with stabilizing mutations), even if a change might be beneficial.
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Highly expressed proteins are thought to be under stronger constraint to avoid spurious interactions that become more probable at increased concentration [ 9– 11].
To make analyses of these lineage-specific HCNSs easier, we extracted the top 1,000 largest HCNSs, as longer sequences were considered to be under stronger constraint.
To unify our observations with those of Noor, we need merely suppose that genes under strong constraint at the protein level are under strong constraint in the intronic and promoter regions as well.
When the acoustic signal design is under strong constraints as a result of dual functions and the available acoustic space is limited because of co-occurring species, species discrimination is mediated through improved sensory acuity in the receiver.
The resultant alignment was about 322 Mb, representing about one third of each genome, suggesting a large portion of the genome has been under strong constraints after different bird species diverged from their common ancestor.
This suggests that more ancestral CNSs are under stronger constraint than the recent ones.
Finally, we also found a significant correlation between temporal specificity of gene expression and evolutionary rate, supporting expectations that genes with ubiquitous expression are under stronger constraint.
This makes more sense with our discovery that more ancestral CNSs are under stronger constraint because of their indispensability and that newly gained sites have higher turnover rates.
Wolf et al. (2009) recently showed that the ratio of the rate of nonsynonymous to synonymous substitution (dN/ dS), decreases with gene age, indicating that older genes are under stronger constraint.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com