over, regions of divergence hitchhiking are dynamic. They increase in size as the evolution of specialization reduces the effective migration between diverging races, and regions of divergence hitchhiking around loosely linked QTL may overlap and merge. Perhaps most importantly, however, regions of divergence hitchhiking leave no permanent signature because they do not involve physical alterations to chromosomes. These regions of reduced interrace recombination can only be detected while divergence elsewhere in the genome is low. They will not be seen in retrospective analyses of good species, because as speciation progresses they become assimilated into the overall genomewide pattern of genetic divergence and by the time speciation is complete, they have disappeared.

Hawthorne and Via (2001) found that QTL for different traits under divergent selection in the pea aphid host races tended to colocalize on the linkage map. Colocalization of QTL increases selection experienced by that genomic region, thereby increasing the size of the region of divergence hitchhiking, and facilitating both QTL detection and the accumulation of additional QTL. In addition, any given QTL may actually be a cluster of several genes. Thus, it seems likely that most regions of divergence hitchhiking will contain multiple genes that affect 1 or more traits under divergent selection.

Determining the size of a given region of divergence hitchhiking is not entirely straightforward. There are 2 contrasting views:

Via and West (2008) proposed that a cluster of outliers defines a single region of divergence hitchhiking, which may include 1 or more QTL. They suggested that the boundaries of a given region of divergence hitchhiking be estimated by curve fitting in a genome scan of F_st values at various map distances around individual QTL under divergent selection (Fig. 1.5A). In this view, markers with low F_st values that lie within hitchhiking regions are interpreted as polymorphisms that predate divergence at the QTL. They are thus uninformative about population divergence and should not be used to mark the boundaries of divergence hitchhiking.