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An elevated differentiation occurred between broiler and layer birds of different populations, suggesting that adverse variants or haplotypes of WWP1 have probably been under parallel selection.
However, most of the GCNVs did not overlap with the divergent regions, which suggested that their copy numbers, but not sequences, would have been under parallel selection (Table 1).
The aforementioned gene cluster in the linkage group XIX overlapped with the divergent regions, suggesting that both nucleotide sequences and copy numbers of the genes in this region would have been under parallel selection during adaptation to the freshwater environment.
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Therefore, as with SNVs, GCNVs can also be under parallel selection through the evolution of sticklebacks.
The identification of GCNVs that were likely under parallel selection suggests that contribution of GCNVs should be considered in studies on adaptive evolution.
Genes that showed significant differences in the numbers of mapped reads between both groups were identified as GCNVs likely under parallel selection.
An important characteristic of the 24 GCNVs likely under parallel selection was that they frequently appeared at close locations on the genomes.
To confirm that the number of identified GCNVs under parallel selection was significantly larger than that expected by chance (i.e., by genetic drift), we calculated an empirical p value based on a permutation test.
To confirm whether the detected GCNVs under parallel selection were due to duplications or multiplications in the freshwater group, we counted the numbers of different allelic sequences within the regions of the GCNVs.
Among the 24 GCNVs likely under parallel selection, larger gene copy numbers were more frequently associated with the freshwater group (19 out of 24, Table 1).
To increase the sensitivity of detecting GCNVs under parallel selection, we devised a novel approach that was based on a statistical method.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com