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The present simulations were conducted without regard to the fact that the base population for any real GS will have been under phenotypic selection for some time.
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The high level of intraspecific polymorphism observed is characteristic of balancing selection on this locus, as expected if the gene engrailed is under phenotypic selection for the maintenance of multiple mimetic morphs.
The opposite effect would be expected under phenotypic selection: as genetic variance is depleted and heritability declines, PS accuracy would decline and selection would become random.
Altogether, these analyses aimed at localizing the genomic regions that have been under divergent selection and responsible for the phenotypic differences between cider and dessert apples.
However, isolated populations of Atlantic salmon do exist in Norway, and show clear evidence of substantial phenotypic differences from production fish that have been under artificial selection for several generations.
Understanding the genetic mechanisms leading to phenotypic differentiation requires identification of the genomic regions that have been under artificial selection in cattle breeds.
The selection of all genes was done in one generation, which could not be achieved through phenotypic selection.
To date molecular markers have improved efficiency of selection largely for traits under simple genetic control and in specific conditions where marker selection is easier/cheaper than phenotypic selection [44] [50].
To date there are very few phenotypic selection studies of ecotypes showing that contemporary selection maintains phenotypic differences between populations.
A second hypothesis is that there may be a pleiotropic effect where genes associated with nitrogen uptake are also linked with other phenotypic traits that are under stronger selection and thus sub-optimal uptake is maintained because of selection on other traits.
Of those that were under positive selection, no clear pattern of phenotypic enrichment was observed.
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