Genes with unusually strong differentiation between populations, for example, Phr1 for grain discoloration in rice [2], are often suggested to be under population-specific selection [18].
Among the traits with potential sexually antagonistic effects proposed by Day & Bonduriansky [ 33] is growth because size dimorphism observed in many species suggests that loci modulating growth may be under sex-specific selection.
When a trait is under sex-specific selection, it is constrained to evolve to its sex-specific optima, because the sexes share the same genome.
Because of this fundamental sex difference in parental investment, males and females are under sex-specific selection pressures, and so are driven to develop phenotypic sex differences [ 27].
As a rare member of the community, these new populations may be under selection for specific traits, including being highly competitive or aggressive against other species.
Genes with dN/dS lower than 1 can in fact be under positive selection at specific sites [ 3] and dN/dS measured over the whole gene length is thus considered too conservative to identify genes or groups of genes putatively under positive selection.
Sites indicated to be under differential selection in each clade-specific analysis are mostly different (Table 3).
By contrast, the regulation model predicts that the NMD-specific exons should be under purifying selection and that the NMD regulation of orthologous genes be conserved in relatively distant species.
Based on the hypothesis that lineage-specific genes are often involved in adaptation [ 4], such as invasion of hosts or evasion of the immune responses, lineage-specific genes may be under positive selection and have a faster rate of sequence divergence.
In addition to identifying specific genes likely to be under positive selection during the evolutionary history of Drosophila, this analysis can address whether, on average, different cuticular protein families evolve at similar or different rates.
