regions are large enough that they capture 5% of randomly chosen markers (Via and West, 2008), or that so many genes are under divergent selection that 5 of them can be found with only 100 markers (Wood et al., 2008). If the latter were true, we would expect that in an average-sized genome of ≈25,000 genes, ≈1,250 of them (5%) would be involved in ecotypic differentiation and early speciation. This seems unlikely, given the prevailing view that speciation with gene flow typically involves just a handful of traits, each influenced by just a few major genes (Rice and Hostert, 1993). Second, even with very strong phenotypic selection during population divergence, the selection coefficients on each of 1,250 genes would be far too small to generate either a detectable QTL or an Fst outlier.
Consideration of the mosaic nature of the genome during early ecological speciation with gene flow suggests that genetic change in this form of speciation occurs in 2 distinct stages:
During the first stage of ecological speciation with gene flow, genomic regions containing major QTL for key traits quickly diverge under selection and become resistant to gene exchange. This establishes the commonly observed pattern of genomic heterogeneity in divergence between incipient species, which we call the genetic mosaic.
As divergent selection proceeds, ecologically based reproductive isolation increases because of resource-based selection against migrants and hybrids and the evolution of habitat choice. These factors limit “effective migration,” i.e., the joint probability that a migrant will choose the alternate resource, survive to mate with a resident, and then that a subsequent F1 will produce a recombinant gamete. This reduction in migration increases the size of hitchhiking regions genomewide and tips the migration-selection balance, which permits QTL of smaller effect to diverge between the populations. By the end of stage 1, ecologically based reproductive isolation may be nearly complete between the new lineages, and genetic divergence is expected to be concentrated in just a handful of genomic regions.
Although this first stage of divergence may involve relatively few traits and a small fraction of the genome, the divergence of QTL for key phenotypic traits under selection defines the branching pattern with which other loci will eventually become phylogenetically concordant. The phenotypic traits that diverge under selection are those that are likely