The proliferation of sequenced genomes has permitted the evaluation of the role of natural selection at that level of organization. Studies have shown that some species, such as Drosophila melanogaster, show positive Darwinian selection in relatively large number of genes, whereas other species, such as Arabidopsis thaliana show very low levels of positive selection compared to purifying or negative selection. By comparison Homo sapiens show intermediate levels of positive selection.
Such studies have in common an evaluation of selection within a single lineage but generally do not address selection that may be occurring as new species arise, that is at splits in their respective phylogenetic trees. A few studies have targeted selection as species diverge, but most of them are restricted to evaluating SNPs scattered throughout the genome and not whole sequences of genes. Using this approach, one may infer whether selection is common or rare during speciation but not necessarily whether selection is associated with particular functional groups of genes, which in turn may inform hypotheses on the genetics of speciation.