Ever since King and Wilson compared protein sequence between chimpanzee and human and concluded that there was insufficient coding divergence to explain phenotypic differences (King and Wilson 1975), biologists have highlighted regulatory change in gene expression as a source for adaptive evolution (Wray 2007; Carroll 2008).
Statistical assessments could be skewed by inclusion of observations that are not independent, such as several closely related genomes (e.g. different strains of the same species or closely related species), which are likely to feature similar levels of representations of various sequence patterns simply as a result of insufficient evolutionary divergence.
Aside from the sympatric species, the lack of resolution may be caused by the insufficient time for divergence between lineages.
Interestingly, the sequences from the non-producing Microcystis strains did not diverged from the rest, suggesting insufficient time for any divergence or that the selective constraints still are the same.
Common criticisms are that bidirectional CI (the mode that most obviously can promote reciprocal reductions in gene flow) will be uncommon in nature, that levels of CI are insufficient to allow genetic divergence, and that CI is not effective in promoting the evolution of premating isolation.
The phylogeographic and population genetic results are consistent with the monopolization hypothesis where gene flow is insufficient to prevent population divergence [ 2, 3].
However, one of the major caveats of footprinting is the need to select the appropriate phylogenetic range between compared genomes: if the species are too close, divergence is insufficient to be conclusive, whereas if they are too far, alignment could be difficult, and moreover, some elements could have undergone major turnover (Hare et al. 2008).
In theory, when PST ≠ FST, drift alone would be insufficient to explain observed phenotypic divergence, and divergent (PST > FST) or convergent (PST < FST) selection on the trait of interest may be invoked (Leinonen et al. 2008).
HSEs have thus neither appeared nor disappeared in the individual species of the melanogaster subgroup or the two species of the obscura group (Figures 2 9) presumably because the time since their divergence has been insufficient.
However, vicariance is insufficient to completely explain the divergence between these taxa and other isolating mechanisms are appropriate to explore in this system.
