tions (Fig. 3.6). Absence of geographic structure in high-armor Eda alleles is associated with a low overall level of sequence heterogeneity, suggesting that the marine populations of the Pacific are well mixed compared with freshwater populations (Fig. 3.6). Such mixing would also be expected to eliminate any geographic pattern in the sequences of low Eda alleles present as standing variation in the sea. The presence of geographic structure in freshwater implies that standing variation for low-armor alleles in the sea was also structured biogeographically at the time of colonization. The most likely cause of such structure in an otherwise well-mixed sea would have been continuous replenishment from nearby freshwater sources as proposed in the transporter hypothesis.
This transporter hypothesis helps to explain the parallel evolution of premating reproductive isolation in widely distant freshwater populations (McKinnon et al., 2004). Further tests are warranted aimed at distinguishing this hypothesis from the alternative hypothesis that speciation is the result of new mutations that occurred in freshwater populations after colonization (or in the sea immediately before colonization). Both hypotheses make the same prediction regarding expected phylogenetic histories of neutral markers, namely that the alleles present in freshwater populations should be descended from alleles present in nearby marine populations (e.g., Fig. 3.4A). If selected genes arose by new mutation after (or immediately before) freshwater colonization, then they should show a similar history to that of neutral markers. However, under the transporter process, genes underlying reproductive isolation in freshwater populations were positively selected from standing variation maintained in the sea, in which case the genes should be most closely related to gene copies found in other freshwater populations nearby. Further tests await the discovery of genes underlying reproductive isolation.
Ecological speciation differs conspicuously from the mutation-order speciation by the pattern of selection on genes. Under ecological speciation, alleles at diverging loci are favored in the environment of one population but not that of the other. In contrast, under the mutation-order process the same alleles are favored in both populations, at least initially; yet by chance each allele arises and fixes in just one of them. An immediate consequence is that ecologically based prezygotic and postzygotic isolation should evolve only under ecological speciation. In contrast, the buildup of intrinsic postzygotic isolation by incompatible side-effects of selected loci can occur under either mechanism (Barton, 2001). Under the right conditions both mechanisms would leave a signature of positive selection at the molecular level, and it is difficult to think of an easy way