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The dN/dS analysis was performed using the program Codeml in the PAML package 3.13 [ 23] to assess whether FOXE1 evolved under a differential selection in the avian lineage, relative to the rest of the phylogeny.
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We found no evidence for a differential selection bias with respect to social status.
These regions may therefore be subject to a differential selection pressure during tumor development.
Sliding window analysis of FST revealed high peaks of differentiation, potentially marking chromosome regions under differential selection in marine and freshwater.
If the support for the incorrect clade was connected to shifts in K a /K s in the two independent lineages, then the sites under differential selection should provide the strongest signal for the nectar-feeding clade.
Next we investigate how the infection polymorphism and unidirectional CI affect the genetic divergence at the locus under differential selection and interpret the results in terms of the concept of the effective migration rate [27], [41], [42].
The outlier analysis identified many genomic regions under differential selection between the ecotypes.
These coding repeats may be under differential selection pressure in the genome.
That is, codons under differential selection were overrepresented among both synapomorphies (support) and autapomorphies (rejection) of the nectar-feeding clade.
Sites indicated to be under differential selection in each clade-specific analysis are mostly different (Table 3).
Some of these outliers are likely to reflect variation in phenotypic traits that were not measured in this study, but are under differential selection between the ecotypes.
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