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No vireos settled at two silent sites.
Molecular genetic studies have confirmed his prediction: silent sites evolve several times faster than replacement sites.
However, there is increasing evidence for selection pressure at silent sites due to constraints of RNA splicing.
LD and recombination were also estimated from silent sites.
Comparison of the number of singletons (η1) at silent sites among populations reveals a similar pattern.
Another discrepancy is the differences in the proportion of silent sites that are altered.
In fact, PPR genes as a group show interesting patterns of variation, exhibiting the four highest values of θπ at silent sites in Germany and the four highest range-wide values of FST for silent sites.
In both cases, the ratios of fixed to polymorphic sites were lower in NS sites than those in silent sites.
This suggests that codon usage is close to random indicating little or no selection at silent sites.
This study begins with a description of "major codon preference", a model of weak selection at silent sites.
Selection on synonymous sites is generally weak, and therefore silent sites are often used to approximate selectively neutral DNA[23].
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